Influence of Acidity on Uranyl Nitrate Association in Aqueous Solutions: A Molecular Dynamics Simulation Study

International Nuclear Information System (INIS)

de Almeida, Valmor F.; Cui, Shengting; Khomami, Bamin; Ye, Xianggui; Smith, Rodney Bryan

2010-01-01

Uranyl ion complexation with water and nitrate is a key aspect of the uranium/plutonium extraction process. We have carried out a molecular dynamics simulation study to investigate this complexation process, including the molecular composition of the various complex species, the corresponding structure, and the equilibrium distribution of the complexes. The observed structures of the complexes suggest that in aqueous solution, uranyls are generally hydrated by 5 water molecules in the equatorial plane. When associating with nitrate ions, a water molecule is replaced by a nitrate ion, preserving the five-fold coordination and planar symmetry. Analysis of the pair correlation function between uranyl and nitrate suggests that nitrates bind to uranyl in aqueous solution mainly in a monodentate mode, although a small portion of bidentates occur. Dynamic association and dissociation between uranyls and nitrates take place in aqueous solution with a substantial amount of fluctuation in the number of various uranyl nitrate species. The average number of the uranyl mononitrate complexes shows a dependence on acid concentration consistent with equilibrium-constant analysis, namely, the concentration of [UO2NO3]+ increases with nitric acid concentration.

Molecular Dynamics and Neutron Scattering Studies of Mixed Solutions of Caffeine and Pyridine in Water.

Science.gov (United States)

Tavagnacco, Letizia; Mason, Philip E; Neilson, George W; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W

2018-05-31

Insight into the molecular interactions of homotactic and heterotactic association of caffeine and pyridine in aqueous solution is given on the basis of both experimental and simulation studies. Caffeine is about 5 times more soluble in a 3 m aqueous pyridine solution than it is in pure water (an increase from ∼0.1 m to 0.5 m). At this elevated concentration the system becomes suitable for neutron scattering study. Caffeine-pyridine interactions were studied by neutron scattering and molecular dynamics simulations, allowing a detailed characterization of the spatial and orientational structure of the solution. It was found that while pyridine-caffeine interactions are not as strong as caffeine-caffeine interactions, the pyridine-caffeine interactions still significantly disrupted caffeine-caffeine stacking. The alteration of the caffeine-caffeine stacking, occasioned by the presence of pyridine molecules in solution and the consequent formation of heterotactic interactions, leads to the experimentally detected increase in caffeine solubility.

Hydration of the chloride ion in concentrated aqueous solutions using neutron scattering and molecular dynamics

Czech Academy of Sciences Publication Activity Database

Pluhařová, Eva; Fischer, H. E.; Mason, Philip E.; Jungwirth, Pavel

2014-01-01

Roč. 112, 9/10 (2014), s. 1230-1240 ISSN 0026-8976 R&D Projects: GA ČR GBP208/12/G016; GA MŠk LH12001 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : lithium * solution * molecular dynamics * chloride * neutron scattering Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.720, year: 2014

Simple electrolyte solutions: Comparison of DRISM and molecular dynamics results for alkali halide solutions

Science.gov (United States)

Joung, In Suk; Luchko, Tyler; Case, David A.

2013-01-01

Using the dielectrically consistent reference interaction site model (DRISM) of molecular solvation, we have calculated structural and thermodynamic information of alkali-halide salts in aqueous solution, as a function of salt concentration. The impact of varying the closure relation used with DRISM is investigated using the partial series expansion of order-n (PSE-n) family of closures, which includes the commonly used hypernetted-chain equation (HNC) and Kovalenko-Hirata closures. Results are compared to explicit molecular dynamics (MD) simulations, using the same force fields, and to experiment. The mean activity coefficients of ions predicted by DRISM agree well with experimental values at concentrations below 0.5 m, especially when using the HNC closure. As individual ion activities (and the corresponding solvation free energies) are not known from experiment, only DRISM and MD results are directly compared and found to have reasonably good agreement. The activity of water directly estimated from DRISM is nearly consistent with values derived from the DRISM ion activities and the Gibbs-Duhem equation, but the changes in the computed pressure as a function of salt concentration dominate these comparisons. Good agreement with experiment is obtained if these pressure changes are ignored. Radial distribution functions of NaCl solution at three concentrations were compared between DRISM and MD simulations. DRISM shows comparable water distribution around the cation, but water structures around the anion deviate from the MD results; this may also be related to the high pressure of the system. Despite some problems, DRISM-PSE-n is an effective tool for investigating thermodynamic properties of simple electrolytes. PMID:23387564

Modeling the liquid-liquid interface and the transfer of a solute by molecular dynamics simulation

International Nuclear Information System (INIS)

Hayoun, Marc

1990-11-01

Molecular Dynamics method and Lennard-Jones potential functions have been employed to model Liquid-Liquid Interfaces. The variation of the miscibilities between the two liquids is obtained by changing the interaction between the two atomic species. The resulting interfaces have a thickness of about three atomic diameters and are stable on the time scale of the simulation. They have been characterized by the density and pressure profiles. The interfacial tension has also been computed and is of the order of magnitude of experimental values. The diffusion process is anisotropic in the interfacial region: the transverse diffusion coefficient (parallelly to the interface) is higher than the normal one. A qualitative explanation of this behaviour is suggested by considering the pressure tensor. The second part of this work, performed by Molecular Dynamics in the canonical ensemble, is devoted to the kinetic study of the transfer of a solute through the interface. A model of a symmetric interface with an atomic solute has been used. The interaction potential between the solute and the solvents has been built in order to obtain an activation barrier to the transfer. We have computed the mean force exerted by the solvent on the solute as a function of its distance to the interface. The resulting mean force potential corresponds to a free energy difference. The height of the energy barrier involved is about 4 kT. The potential energy and entropy profiles have also been calculated and discussed. The diffusion coefficient of the solute has been computed by equilibrium and non-equilibrium methods. We deduced the friction coefficient of the solvent, which is essential to determine the Kramers transmission coefficient. This coefficient is compared to the one obtained by simulation. Finally, the solute transfer rate constant has been calculated. (author) [fr

Molecular-dynamics simulations of urea nucleation from aqueous solution

Science.gov (United States)

Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele

2015-01-01

Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete. PMID:25492932

Molecular-dynamics simulations of urea nucleation from aqueous solution.

Science.gov (United States)

Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele

2015-01-06

Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

Energy Technology Data Exchange (ETDEWEB)

Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Fujimoto, K. [Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga 525-8577 (Japan); Nakagawa, A. [Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871 (Japan); Nomoto, A. [Institute of Microbial Chemistry, Kamiosaki, Shinagawa-ku, Tokyo 141-0021 (Japan)

2014-10-28

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

International Nuclear Information System (INIS)

Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.

2014-01-01

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10 6 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

Science.gov (United States)

Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

2014-10-01

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

Structure and dynamics of solutions

CERN Document Server

Ohtaki, H

2013-01-01

Recent advances in the study of structural and dynamic properties of solutions have provided a molecular picture of solute-solvent interactions. Although the study of thermodynamic as well as electronic properties of solutions have played a role in the development of research on the rate and mechanism of chemical reactions, such macroscopic and microscopic properties are insufficient for a deeper understanding of fast chemical and biological reactions. In order to fill the gap between the two extremes, it is necessary to know how molecules are arranged in solution and how they change their pos

Study of lanthanide tri-cations in aqueous solution by molecular dynamic

International Nuclear Information System (INIS)

Duvail, M.

2007-11-01

This is essentially a lanthanide tri-cation hydration study by means of classical molecular dynamics (CLMD) simulations using explicit polarization. Explicit polarization is calculated with a Car-Parrinello type of dynamics on induced dipoles, which decreases the CPU time as compared to the self-consistent resolution. Several pair interaction potentials are parametrized from ab initio calculations (MP2) and tested for the La 3+ -OH 2 interaction. The best results are obtained with an exponential-6 Buckingham potential. Next, the La 3+ -OH 2 interaction potential parameters are extrapolated to the other Ln 3+ -OH 2 interactions, only by using the ionic radii. The CLMD results reproduce the reliable experimental data (EXAFS distances), and the sigmoidal variation of the coordination number (with S shape), from 9 for La 3+ to 8 for Lu 3+ . This variation is explained by the linear variation of DrG0 (9,298) vs. atomic number. Insights are also given on the Co 2+ hydration, CPMD simulations, reconstruction of EXAFS signal from MD simulations, and OH - complexation of La 3+ in aqueous solution. (author)

[Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

Science.gov (United States)

Abaturov, L V; Nosova, N G

2013-01-01

The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the

Aggregation work at polydisperse micellization: ideal solution and "dressed micelle" models comparing to molecular dynamics simulations.

Science.gov (United States)

Burov, S V; Shchekin, A K

2010-12-28

General thermodynamic relations for the work of polydisperse micelle formation in the model of ideal solution of molecular aggregates in nonionic surfactant solution and the model of "dressed micelles" in ionic solution have been considered. In particular, the dependence of the aggregation work on the total concentration of nonionic surfactant has been analyzed. The analogous dependence for the work of formation of ionic aggregates has been examined with regard to existence of two variables of a state of an ionic aggregate, the aggregation numbers of surface active ions and counterions. To verify the thermodynamic models, the molecular dynamics simulations of micellization in nonionic and ionic surfactant solutions at two total surfactant concentrations have been performed. It was shown that for nonionic surfactants, even at relatively high total surfactant concentrations, the shape and behavior of the work of polydisperse micelle formation found within the model of the ideal solution at different total surfactant concentrations agrees fairly well with the numerical experiment. For ionic surfactant solutions, the numerical results indicate a strong screening of ionic aggregates by the bound counterions. This fact as well as independence of the coefficient in the law of mass action for ionic aggregates on total surfactant concentration and predictable behavior of the "waterfall" lines of surfaces of the aggregation work upholds the model of "dressed" ionic aggregates.

Dynamics of solutions and fluid mixtures by NMR

International Nuclear Information System (INIS)

Delpuech, J.J.

1994-01-01

After a short introduction to NMR spectroscopy, with a special emphasis on dynamical aspects, an overview on two fundamental aspects of molecular dynamics, NMR relaxation and its relationship with molecular reorientation, and magnetization transfer phenomena induced by molecular rate processes (dynamic NMR) is presented, followed by specific mechanisms of relaxation encountered in paramagnetic systems or with quadrupolar nuclei. Application fields are then reviewed: solvent exchange on metal ions with a variable pressure NMR approach, applications of field gradients in NMR, aggregation phenomena and micro-heterogeneity in surfactant solutions, polymers and biopolymers in the liquid state, liquid-like molecules in rigid matrices and in soft matter (swollen polymers and gels, fluids in and on inorganic materials, food)

Factors responsible for the aggregation behavior of hydrophobic polyelectrolyte PEA in aqueous solution studied by molecular dynamics simulations.

Science.gov (United States)

Sappidi, Praveenkumar; Natarajan, Upendra

2017-08-01

Self-association (i.e. interchain aggregation) behavior of atactic poly(ethacrylic acid) PEA in dilute aqueous solution as function of degree-of-neutralization by Na + counter-ions (i.e. charge fraction f) was investigated by molecular dynamics simulations. Aggregation is found to occur in the range 0≤f≤0.7 in agreement with experimental results compared at specified polymer concentration C p =0.36mol/l in dilute solution. The macromolecular solution was characterized and analysed for radius-of-gyration, torsion angle distribution, inter and intra-molecular hydrogen bonds, radial distribution functions of intermolecular and inter-atomic pairs, inter-chain contacts and solvation enthalpy. The PEA chains form aggregate through attractive inter-chain interaction via hydrogen bonding, in the range fenthalpy. The PEA solvation enthalpy becomes increasingly favorable with increase in f. The transition enthalpy change, in going from uncharged (acid) state to fully charged state (f=1) is unfavorable towards aggregate formation. Copyright © 2017 Elsevier Inc. All rights reserved.

Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

Science.gov (United States)

Rosa, Marta; Micciarelli, Marco; Laio, Alessandro; Baroni, Stefano

2016-09-13

We introduce a method to evaluate the relative populations of different conformers of molecular species in solution, aiming at quantum mechanical accuracy, while keeping the computational cost at a nearly molecular-mechanics level. This goal is achieved by combining long classical molecular-dynamics simulations to sample the free-energy landscape of the system, advanced clustering techniques to identify the most relevant conformers, and thermodynamic perturbation theory to correct the resulting populations, using quantum-mechanical energies from density functional theory. A quantitative criterion for assessing the accuracy thus achieved is proposed. The resulting methodology is demonstrated in the specific case of cyanin (cyanidin-3-glucoside) in water solution.

Concentrated Aqueous Sodium Chloride Solution in Clays at Thermodynamic Conditions of Hydraulic Fracturing: Insight from Molecular Dynamics Simulations.

Czech Academy of Sciences Publication Activity Database

Svoboda, Martin; Lísal, Martin

2018-01-01

Roč. 148, č. 22 (2018), č. článku 222806. ISSN 0021-9606 R&D Projects: GA ČR GA17-25100S EU Projects: European Commission(XE) 640979 - ShaleXenvironmenT Institutional support: RVO:67985858 Keywords : aqueous NaCl solutions * hydrogen bond networks * molecular dynamics simulations Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 2.965, year: 2016

Effect of molecular topology on the transport properties of dendrimers in dilute solution at Θ temperature: A Brownian dynamics study

Science.gov (United States)

Bosko, Jaroslaw T.; Ravi Prakash, J.

2008-01-01

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Θ conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.

Molecular Dynamics Investigation of the Effects of Concentration on Hydrogen Bonding in Aqueous Solutions of Methanol, Ethylene Glycol and Glycerol

International Nuclear Information System (INIS)

Zhang, Ning; Li, Weizhong; Chen, Cong; Zuo, Jianguo; Weng, Lindong

2013-01-01

Hydrogen bonding interaction between alcohols and water molecules is an important characteristic in the aqueous solutions of alcohols. In this paper, a series of molecular dynamics simulations have been performed to investigate the aqueous solutions of low molecular weight alcohols (methanol, ethylene glycol and glycerol) at the concentrations covering a broad range from 1 to 90 mol %. The work focuses on studying the effect of the alcohols molecules on the hydrogen bonding of water molecules in binary mixtures. By analyzing the hydrogen bonding ability of the hydroxyl (-OH) groups for the three alcohols, it is found that the hydroxyl group of methanol prefers to form more hydrogen bonds than that of ethylene glycol and glycerol due to the intra-and intermolecular effects. It is also shown that concentration has significant effect on the ability of alcohol molecule to hydrogen bond water molecules. Understanding the hydrogen bonding characteristics of the aqueous solutions is helpful to reveal the cryoprotective mechanisms of methanol, ethylene glycol and glycerol in aqueous solutions

Advances in molecular vibrations and collision dynamics molecular clusters

CERN Document Server

Bacic, Zatko

1998-01-01

This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...

Molecular dynamics study of salt–solution interface: Solubility and surface charge of salt in water

International Nuclear Information System (INIS)

Kobayashi, Kazuya; Liang, Yunfeng; Matsuoka, Toshifumi; Sakka, Tetsuo

2014-01-01

The NaCl salt–solution interface often serves as an example of an uncharged surface. However, recent laser-Doppler electrophoresis has shown some evidence that the NaCl crystal is positively charged in its saturated solution. Using molecular dynamics (MD) simulations, we have investigated the NaCl salt–solution interface system, and calculated the solubility of the salt using the direct method and free energy calculations, which are kinetic and thermodynamic approaches, respectively. The direct method calculation uses a salt–solution combined system. When the system is equilibrated, the concentration in the solution area is the solubility. In the free energy calculation, we separately calculate the chemical potential of NaCl in two systems, the solid and the solution, using thermodynamic integration with MD simulations. When the chemical potential of NaCl in the solution phase is equal to the chemical potential of the solid phase, the concentration of the solution system is the solubility. The advantage of using two different methods is that the computational methods can be mutually verified. We found that a relatively good estimate of the solubility of the system can be obtained through comparison of the two methods. Furthermore, we found using microsecond time-scale MD simulations that the positively charged NaCl surface was induced by a combination of a sodium-rich surface and the orientation of the interfacial water molecules

Extended Lagrangian Excited State Molecular Dynamics.

Science.gov (United States)

Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

2018-02-13

An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

Next generation extended Lagrangian first principles molecular dynamics.

Science.gov (United States)

Niklasson, Anders M N

2017-08-07

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

Nonpolar solvation dynamics for a nonpolar solute in room ...

Indian Academy of Sciences (India)

Sandipa Indra

2018-01-30

Jan 30, 2018 ... Keywords. Solvation dynamics; nonpolar solvation; ionic liquid; molecular dynamics; linear response theory. 1. ... J. Chem. Sci. (2018) 130:3 spectrum of the excited probe molecule for imida- .... Therefore, the solute and the RTIL ions interact only ... interval of 30 ps from a long equilibrium trajectory of dura-.

Rheology via nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Hoover, W.G.

1982-10-01

The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference

Ultrafast dynamics of hydrogen bond exchange in aqueous ionic solutions.

Science.gov (United States)

Park, Sungnam; Odelius, Michael; Gaffney, Kelly J

2009-06-04

The structural and dynamical properties of aqueous ionic solutions influence a wide range of natural and biological processes. In these solutions, water has the opportunity to form hydrogen bonds with other water molecules and anions. Knowing the time scale with which these configurations interconvert represents a key factor to understanding the influence of molecular scale heterogeneity on chemical events in aqueous ionic solutions. We have used ultrafast IR spectroscopy and Car-Parrinello molecular dynamics (CPMD) simulations to investigate the hydrogen bond (H-bond) structural dynamics in aqueous 6 M sodium perchlorate (NaClO4) solution. We have measured the H-bond exchange dynamics between spectrally distinct water-water and water-anion H-bond configurations with 2DIR spectroscopy and the orientational relaxation dynamics of water molecules in different H-bond configurations with polarization-selective IR pump-probe experiments. The experimental H-bond exchange time correlates strongly with the experimental orientational relaxation time of water molecules. This agrees with prior observations in water and aqueous halide solutions, and has been interpreted within the context of an orientational jump model for the H-bond exchange. The CPMD simulations performed on aqueous 6 M NaClO4 solution clearly demonstrate that water molecules organize into two radially and angularly distinct structural subshells within the first solvation shell of the perchlorate anion, with one subshell possessing the majority of the water molecules that donate H-bonds to perchlorate anions and the other subshell possessing predominantly water molecules that donate two H-bonds to other water molecules. Due to the high ionic concentration used in the simulations, essentially all water molecules reside in the first ionic solvation shells. The CPMD simulations also demonstrate that the molecular exchange between these two structurally distinct subshells proceeds more slowly than the H

Molecular dynamics simulations of the calcite/solution interface as a means to explore surface modifications induced by nitrate

Energy Technology Data Exchange (ETDEWEB)

Hofmann, Sascha; Schmidt, Moritz [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Div. Surface Processes; Spijker, P. [Aalto Univ., Helsinki (Finland). Dept. of Applied Physics; Voitchovsky, K. [Durham Univ. (United Kingdom). Physics Dept.

2016-07-01

The reactivity of calcite, one of the most abundant minerals in the earth's crust, is determined by the molecular details of its interface with the contacting solution. Recently, it has been found that trace concentrations of NaNO{sub 3} severely affect calcite's (104) surface and its reactivity. Molecular dynamics (MD) simulations reveal density profiles of different ions near calcite's surface, with NO{sub 3}{sup -} able to reach closer to the surface than CO{sub 3}{sup 2-} and in higher concentrations. Additionally, incorporation of NO{sub 3}{sup -} into the surface significantly disturbs the water structure at the interface.

Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

Science.gov (United States)

Jakobtorweihen, S.; Zuniga, A. Chaides; Ingram, T.; Gerlach, T.; Keil, F. J.; Smirnova, I.

2014-07-01

Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations.

Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

International Nuclear Information System (INIS)

Jakobtorweihen, S.; Ingram, T.; Gerlach, T.; Smirnova, I.; Zuniga, A. Chaides; Keil, F. J.

2014-01-01

Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations

Molecular dinamics of tetrahedral clelate compounds of Cd(2) in solutions

International Nuclear Information System (INIS)

Nivorozhkin, L.E.; Minkin, V.I.; Borisenko, N.I.; Konstantinovskij, L.E.; Korobov, M.S.; Olekhnovich, R.Ya.

1981-01-01

Interconversion kinetics of enantiomers of tetrahedral intracomplex compounds of metals (ICM) on the base of unsymmetric ligands in solu-- tions is studied for several series of compounds according to the temperature dependence of the shape of line of prochiral substituents using the methods of the dynamic NMR (DNMR). The use of tetracoordinated ICM in the solutions of synthesized compounds of Cd(2) with the inclusion of magnetic isotope 111 Cd(S=1/2) to study molecular dynamics and the application of the corresponding methods of calculation of the DNMR signal forms permitted to clearly separate the mechanisms of digonal twist and degenerated ligand exchange. In ICM solutions the low-barrier transformations, connected with intramolecular digonal twist, take place as well as high-barrier processes of degenerated ligand exchange. The technique suggested can be applied to the studies of ICM molecular dynamics with other magnetic isotopes of metals ( 207 Pb, 199 Hg, etc.) and rapid non-degenerated ligand exchanges [ru

Thermodynamic Models from Fluctuation Solution Theory Analysis of Molecular Simulations

DEFF Research Database (Denmark)

Christensen, Steen; Peters, Günther H.j.; Hansen, Flemming Yssing

2007-01-01

Fluctuation solution theory (FST) is employed to analyze results of molecular dynamics (MD) simulations of liquid mixtures. The objective is to generate parameters for macroscopic GE-models, here the modified Margules model. We present a strategy for choosing the number of parameters included...

Making Molecular Balloons in Laser-Induced Explosive Boiling of Polymer Solutions

International Nuclear Information System (INIS)

Leveugle, Elodie; Sellinger, Aaron; Fitz-Gerald, James M.; Zhigilei, Leonid V.

2007-01-01

The effect of the dynamic molecular rearrangements leading to compositional segregation is revealed in coarse-grained molecular dynamics simulations of short pulse laser interaction with a polymer solution in a volatile matrix. An internal release of matrix vapor at the onset of the explosive boiling of the overheated liquid is capable of pushing polymer molecules to the outskirts of a transient bubble, forming a polymer-rich surface layer enclosing the volatile matrix material. The results explain unexpected 'deflated balloon' structures observed in films deposited by the matrix-assisted pulsed laser evaporation technique

Classical and quantum molecular dynamics in NMR spectra

CERN Document Server

Szymański, Sławomir

2018-01-01

The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

Protocol for classical molecular dynamics simulations of nano-junctions in solution

KAUST Repository

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

KAUST Repository

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.

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...

Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

Science.gov (United States)

Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

1997-01-01

Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

Orientational order and dynamics of water in bulk and in aqueous solutions of uranyl ions

International Nuclear Information System (INIS)

Chopra, Manish; Choudhury, Niharendu

2014-01-01

Molecular dynamics simulations in canonical ensemble of aqueous solutions of uranyl nitrate and bulk water at ambient condition have been carried out to investigate orientational order and dynamics of water. The orientational distributions of water around a central water molecule in bulk water and around a uranyl ion in an aqueous uranyl solution have been calculated. Orientational dynamics of water in bulk and in aqueous uranyl nitrate solution have also been analysed. (author)

Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

International Nuclear Information System (INIS)

Ko, Soon Heum; Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel; Jha, Shantenu

2014-01-01

Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.

Dislocation glide in Ni-Al solid solutions from the atomic scale up: a molecular dynamics study

International Nuclear Information System (INIS)

Rodary, E.

2003-01-01

The glide of an edge dislocation in solid solutions is studied by molecular dynamics, at fixed temperature and imposed external stress. We have optimized an EAM potential for Ni(1 a 8% A1): it well reproduces the lattice expansion, local atomic order, stacking fault energy as a function of composition, as well as the elastic properties of the γ' phase with L1 2 structure. On increasing the stress, the dislocation is first immobile, then glides with a velocity proportional to the stress and the velocity saturates on reaching the transverse sound velocity. However, only beyond a static threshold stress, σ s , does the dislocation glide a distance large enough to allow macroscopic shear; the linear part of the velocity-stress curve extrapolates to zero at a dynamical threshold stress, σ d , The friction coefficient, and the threshold stresses (σ s and σ d ), increase with the A1 concentration and decrease with temperature (300 and 500 K). Close to the critical shear stress, σ s , the dislocation glide is analysed with a 'stop and go' model. The latter yields the flight velocity between obstacles, the mean obstacle density and the distribution of the waiting time on each obstacle as a function of stress, composition and temperature. The obstacle to the glide is proposed to be the strong repulsion between Al atoms brought into nearest neighbour position by the glide process, and not the dislocation-solute interaction. The microscopic parameters so defined are introduced into a micro-mechanical model, which well reproduces the known behaviour of nickel base solid solutions. (author)

Molecular dynamics study of the coordination sphere of trivalent lanthanum in a highly concentrated LiCl aqueous solution: A combined classical and ab initio approach

International Nuclear Information System (INIS)

Vuilleumier, R.; Petit, L.; Maldivi, P.; Adamo, C.

2008-01-01

The first coordination sphere of trivalent lanthanum in a highly concentrated (14 M) lithium chloride solution is studied with a combination of classical molecular dynamics and density functional theory based first principle molecular dynamics. This method enables us to obtain a solvation shell of La 3+ containing 2 chloride ions and 6 water molecules. After refinement using first principle molecular dynamics, the resulting cation-water and cation-anion distances are in very good agreement with experiment. The 2 Cl - and the 6 water molecules arrange in a square anti-prism around La 3+ . Exchange of water molecules was also observed in the first-principle simulation, with an intermediate structure comprising 7 water molecules stable for 2.5 ps. Finally, evaluation of dipole moments using maximally localized Wannier functions shows a substantial polarization of the chloride anions and the water molecules in the first solvation shell of trivalent lanthanum. (authors)

Structure and dynamics of the uranyl tricarbonate complex in aqueous solution: insights from quantum mechanical charge field molecular dynamics.

Science.gov (United States)

Tirler, Andreas O; Hofer, Thomas S

2014-11-13

This investigation presents the characterization of structural and dynamical properties of uranyl tricarbonate in aqueous solution employing an extended hybrid quantum mechanical/molecular mechanical (QM/MM) approach. It is shown that the inclusion of explicit solvent molecules in the quantum chemical treatment is essential to mimic the complex interaction occurring in an aqueous environment. Thus, in contrast to gas phase cluster calculations on a quantum chemical level proposing a 6-fold coordination of the three carbonates, the QMCF MD simulation proposes a 5-fold coordination. An extensive comparison of the simulation results to structural and dynamical data available in the literature was found to be in excellent agreement. Furthermore, this work is the first theoretical study on a quantum chemical level of theory able to observe the conversion of carbonate (CO₃²⁻) to bicarbonate (HCO₃⁻) in the equatorial coordination sphere of the uranyl ion. From a comparison of the free energy ΔG values for the unprotonated educt [UO₂(CO₃)₃]⁴⁻ and the protonated [UO₂(CO₃)₂(HCO₃)]³⁻, it could be concluded that the reaction equilibrium is strongly shifted toward the product state confirming the benignity for the observed protonation reaction. Structural properties and the three-dimensional arrangement of carbonate ligands were analyzed via pair-, three-body, and angular distributions, the dynamical properties were evaluated by hydrogen-bond correlation functions and vibrational power spectra.

Magnetic effects on the solvent properties investigated by molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Moosavi, Fatemeh, E-mail: moosavibaigi@um.ac.ir; Gholizadeh, Mostafa

2014-03-15

This paper investigates how an external constant magnetic field in the Z-direction affects the performance of a solvent. The molecular dynamics simulation comprised common inorganic and organic solvents including water, acetone, acetonitrile, toluene, and n-hexane at the ambient temperature and pressure. A static magnetic field applied in the simulation process is able to reduce the solvent mobility in the solution in order to enhance the solvent–solute reaction. Simulation results show that the diffusivity decreases because of increasing the effective interactions. Besides, magnetic field reduces the volume of the solvent and increases the strength of the hydrogen bonds by maximizing attractive electrostatic and vdW interactions caused by changes in the radial distribution function of the solvents. Hydrogen-bonding characteristics of solvents investigated by molecular dynamics simulations were evidence for the hydrogen bonding strength of O···H that is a more efficient intermolecular hydrogen-bonding in comparison with N···H. - Highlights: • Molecular dynamics simulation technique investigates the effect of magnetic field on transport dynamics inside the solvent bulk. • External constant magnetic field influences on intermolecular interactions, thermophysics, and transport properties of the solvents. • Applying magnetic field strengthened hydrogen bond maximizes attractive electrostatic interactions, charge distribution becomes stronger, and the molecule mobility is demoted. • The low diffusivity of the solvents in the solutions increases the performance of the interactions and promotes the interactions. • On introducing a magnetic field of flux density parallel to the Z-direction, solvent acts as an obstacle to diffusion of solutes.

Stochastic entangled chain dynamics of dense polymer solutions.

Science.gov (United States)

Kivotides, Demosthenes; Wilkin, S Louise; Theofanous, Theo G

2010-10-14

We propose an adjustable-parameter-free, entangled chain dynamics model of dense polymer solutions. The model includes the self-consistent dynamics of molecular chains and solvent by describing the former via coarse-grained polymer dynamics that incorporate hydrodynamic interaction effects, and the latter via the forced Stokes equation. Real chain elasticity is modeled via the inclusion of a Pincus regime in the polymer's force-extension curve. Excluded volume effects are taken into account via the combined action of coarse-grained intermolecular potentials and explicit geometric tracking of chain entanglements. We demonstrate that entanglements are responsible for a new (compared to phantom chain dynamics), slow relaxation mode whose characteristic time scale agrees very well with experiment. Similarly good agreement between theory and experiment is also obtained for the equilibrium chain size. We develop methods for the solution of the model in periodic flow domains and apply them to the computation of entangled polymer solutions in equilibrium. We show that the number of entanglements Π agrees well with the number of entanglements expected on the basis of tube theory, satisfactorily reproducing the latter's scaling of Π with the polymer volume fraction φ. Our model predicts diminishing chain size with concentration, thus vindicating Flory's suggestion of excluded volume effects screening in dense solutions. The predicted scaling of chain size with φ is consistent with the heuristic, Flory theory based value.

Dynamical interactions between solute and solvent studied by nonlinear infrared spectroscopy

International Nuclear Information System (INIS)

Ohta, K.; Tominaga, K.

2006-01-01

Interactions between solute and solvent play an important role in chemical reaction dynamics and in many relaxation processes in condensed phases. Recently third-order nonlinear infrared (IR) spectroscopy has shown to be useful to investigate solute-solvent interaction and dynamics of the vibrational transition. These studies provide detailed information on the energy relaxation of the vibrationally excited state, and the time scale and the magnitude of the time correlation functions of the vibrational frequency fluctuations. In this work we have studied vibrational energy relaxation (VER) of solutions and molecular complexes by nonlinear IR spectroscopy, especially IR pump-probe method, to understand the microscopic interactions in liquids. (authors)

Hydration and Ion Pairing in Aqueous Mg2+ and Zn2+ Solutions: Force-Field Description Aided by Neutron Scattering Experiments and Ab Initio Molecular Dynamics Simulations.

Science.gov (United States)

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.

Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data.

Science.gov (United States)

Allison, Jane R; Hertig, Samuel; Missimer, John H; Smith, Lorna J; Steinmetz, Michel O; Dolenc, Jožica

2012-10-09

NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.

A concurrent multiscale micromorphic molecular dynamics

International Nuclear Information System (INIS)

Li, Shaofan; Tong, Qi

2015-01-01

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation

Efficient "on-the-fly" calculation of Raman spectra from ab-initio molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water.

Science.gov (United States)

Partovi-Azar, Pouya; Kühne, Thomas D

2015-11-05

We present a novel computational method to accurately calculate Raman spectra from first principles. Together with an extension of the second-generation Car-Parrinello method of Kühne et al. (Phys. Rev. Lett. 2007, 98, 066401) to propagate maximally localized Wannier functions together with the nuclei, a speed-up of one order of magnitude can be observed. This scheme thus allows to routinely calculate finite-temperature Raman spectra "on-the-fly" by means of ab-initio molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra. © 2015 Wiley Periodicals, Inc.

Solvation of magnesium dication: molecular dynamics simulation and vibrational spectroscopic study of magnesium chloride in aqueous solutions.

Science.gov (United States)

Callahan, Karen M; Casillas-Ituarte, Nadia N; Roeselová, Martina; Allen, Heather C; Tobias, Douglas J

2010-04-22

Magnesium dication plays many significant roles in biochemistry. While it is available to the environment from both ocean waters and mineral salts on land, its roles in environmental and atmospheric chemistry are still relatively unknown. Several pieces of experimental evidence suggest that contact ion pairing may not exist at ambient conditions in solutions of magnesium chloride up to saturation concentrations. This is not typical of most ions. There has been disagreement in the molecular dynamics literature concerning the existence of ion pairing in magnesium chloride solutions. Using a force field developed during this study, we show that contact ion pairing is not energetically favorable. Additionally, we present a concentration-dependent Raman spectroscopic study of the Mg-O(water) hexaaquo stretch that clearly supports the absence of ion pairing in MgCl(2) solutions, although a transition occurring in the spectrum between 0.06x and 0.09x suggests a change in solution structure. Finally, we compare experimental and calculated observables to validate our force field as well as two other commonly used magnesium force fields, and in the process show that ion pairing of magnesium clearly is not observed at higher concentrations in aqueous solutions of magnesium chloride, independent of the choice of magnesium force field, although some force fields give better agreement to experimental results than others.

NMR and molecular dynamics of small solutes in liquid crystals

International Nuclear Information System (INIS)

Luyten, P.R.

1984-01-01

NMR relaxation measurements, using a wide variety of modern pulse techniques, can yield valuable information about molecular motions. In this thesis the applicability of theories developed to describe spin relaxation phenomena in partially ordered media is studied for small solutes in liquid crystals. 1 H, 2 H, 13 C and 14 N relaxation measurements are interpreted by means of a model, in which fast anisotropic re-orientational motion in an orienting potential combined with contributions from cooperative fluctuations in the surrounding liquid crystal molecules, induce the observed frequency dependent relaxation behavior. (orig.)

Study of lanthanide tri-cations in aqueous solution by molecular dynamic; Etude des trications lanthanide en solution aqueuse par dynamique moleculaire

Energy Technology Data Exchange (ETDEWEB)

Duvail, M

2007-11-15

This is essentially a lanthanide tri-cation hydration study by means of classical molecular dynamics (CLMD) simulations using explicit polarization. Explicit polarization is calculated with a Car-Parrinello type of dynamics on induced dipoles, which decreases the CPU time as compared to the self-consistent resolution. Several pair interaction potentials are parametrized from ab initio calculations (MP2) and tested for the La{sup 3+}-OH{sub 2} interaction. The best results are obtained with an exponential-6 Buckingham potential. Next, the La{sup 3+}-OH{sub 2} interaction potential parameters are extrapolated to the other Ln{sup 3+}-OH{sub 2} interactions, only by using the ionic radii. The CLMD results reproduce the reliable experimental data (EXAFS distances), and the sigmoidal variation of the coordination number (with S shape), from 9 for La{sup 3+} to 8 for Lu{sup 3+}. This variation is explained by the linear variation of DrG0 (9,298) vs. atomic number. Insights are also given on the Co{sup 2+} hydration, CPMD simulations, reconstruction of EXAFS signal from MD simulations, and OH{sup -} complexation of La{sup 3+} in aqueous solution. (author)

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

International Nuclear Information System (INIS)

Lehtivarjo, Juuso; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino; Peräkylä, Mikael

2012-01-01

While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1 H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6–17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for 1 Hα, 1 HN, 13 Cα, 13 Cβ, 13 CO and backbone 15 N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

Energy Technology Data Exchange (ETDEWEB)

Lehtivarjo, Juuso, E-mail: juuso.lehtivarjo@uef.fi; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino [University of Eastern Finland, School of Pharmacy (Finland); Peraekylae, Mikael [University of Eastern Finland, Institute of Biomedicine (Finland)

2012-03-15

While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein {sup 1}H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6-17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for {sup 1}H{alpha}, {sup 1}HN, {sup 13}C{alpha}, {sup 13}C{beta}, {sup 13}CO and backbone {sup 15}N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

DEFF Research Database (Denmark)

Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

2007-01-01

The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...

Free-solution, label-free molecular interactions studied by back-scattering interferometry

DEFF Research Database (Denmark)

Bornhop, D.J.; Latham, J.C.; Kussrow, A.

2007-01-01

Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules...... and protein, were determined with high dynamic range dissociation constants (K-d spanning six decades) and unmatched sensitivity (picomolar K-d's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G...

Preferential solvation, ion pairing, and dynamics of concentrated aqueous solutions of divalent metal nitrate salts

Science.gov (United States)

Yadav, Sushma; Chandra, Amalendu

2017-12-01

We have investigated the characteristics of preferential solvation of ions, structure of solvation shells, ion pairing, and dynamics of aqueous solutions of divalent alkaline-earth metal nitrate salts at varying concentration by means of molecular dynamics simulations. Hydration shell structures and the extent of preferential solvation of the metal and nitrate ions in the solutions are investigated through calculations of radial distribution functions, tetrahedral ordering, and also spatial distribution functions. The Mg2+ ions are found to form solvent separated ion-pairs while the Ca2+ and Sr2+ ions form contact ion pairs with the nitrate ions. These findings are further corroborated by excess coordination numbers calculated through Kirkwood-Buff G factors for different ion-ion and ion-water pairs. The ion-pairing propensity is found to be in the order of Mg(NO3) 2 lead to the presence of substantial dynamical heterogeneity in these solutions of strongly interacting ions. The current study helps us to understand the molecular details of hydration structure, ion pairing, and dynamics of water in the solvation shells and also of ion diffusion in aqueous solutions of divalent metal nitrate salts.

Dynamical quenching of tunneling in molecular magnets

International Nuclear Information System (INIS)

José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.

2015-01-01

It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation

Dynamical quenching of tunneling in molecular magnets

Energy Technology Data Exchange (ETDEWEB)

José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)

2015-12-15

It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.

CONDENSED MATTER: STRUCTURE, MECHANICAL AND THERMAL PROPERTIES: Molecular Dynamics Study of Stability of Solid Solutions and Amorphous Phase in the Cu-Al System

Science.gov (United States)

Yang, Bin; Lai, Wen-Sheng

2009-06-01

The relative stability of fcc and bcc solid solutions and amorphous phase with different compositions in the Cu-Al system is studied by molecular dynamics simulations with n-body potentials. For Cu1-xAlx alloys, the calculations show that the fcc solid solution has the lowest energies in the composition region with x 0.72, while the bee solid solution has the lowest energies in the central composition range, in agreement with the ball-milling experiments that a single bcc solid solution with 0.30 < x < 0.70 is obtained. The evolution of structures in solid solutions and amorphous phase is studied by the coordination number (CN) and bond-length analysis so as to unveil the underlying physics. It is found that the energy sequence among three phases is determined by the competition in energy change originating from the bond length and CNs (or the number of bonds).

Molecular dynamics study of structure and vibrational spectra at zwitterionoic lipid/aqueous KCl, NaCl, and CaCl2 solution interfaces

Science.gov (United States)

Ishiyama, Tatsuya; Shirai, Shinnosuke; Okumura, Tomoaki; Morita, Akihiro

2018-06-01

Molecular dynamics (MD) simulations of KCl, NaCl, and CaCl2 solution/dipalmytoylphosphatidylcholine lipid interfaces were performed to analyze heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectra in relation to the interfacial water structure. The present MD simulation well reproduces the experimental spectra and elucidates a specific cation effect on the interfacial structure. The K+, Na+, and Ca2+ cation species penetrate in the lipid layer more than the anions in this order, due to the electrostatic interaction with negative polar groups of lipid, and the electric double layer between the cations and anions cancels the intrinsic orientation of water at the water/lipid interface. These mechanisms explain the HD-VSFG spectrum of the water/lipid interface and its spectral perturbation by adding the ions. The lipid monolayer reverses the order of surface preference of the cations at the solution/lipid interface from that at the solution/air interface.

The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

International Nuclear Information System (INIS)

Bianchi, L.

2000-05-01

obtained from the X-rays. Nevertheless, comparisons between the MD and ND results for the C-H and H-H pdfs show significant discrepancies, which highlight the need to further refine the existing force field models. Neutron diffraction (ND) measurements were also performed on benzene-methanol liquid mixture (molar ratio 1:2) under ambient conditions. The H/D isotopic substitution technique on the hydrogens of both the hydroxyl group of methanol (Ho) and benzene (HB) was used to extract the solvent-solvent, solute-solute and solute-solvent correlations. The ND structural results of the mixture are interpreted with the help of the experimental results of its pure components. The results reveal that the self-association of methanol due to hydrogen bonding is hardly disrupted by the addition of benzene. Investigations of the solute-solvent and solute-solute correlations show that although a weak association exists between benzene and methanol molecules, there is no evidence to suggest the formation of a π-hydrogen bond between them in the liquid state. The benzene molecules thus, play the role of an inert solute in the mixture. The experimental structural results for the benzene-methanol liquid mixture are compared with those obtained from molecular dynamics (MD) simulations performed with an inter-molecular potential model built from the two force field models used in simulating the behaviour of the two pure components. The simulated structural results of the mixture are interpreted with the help of the simulated results of the pure components. Although an overall agreement is obtained between the simulated and experimental inter-molecular rdfs, a comparison of the partial distribution functions reveals that model potentials for the mixture need to be refined. (author)

Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

Science.gov (United States)

Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

2017-08-22

A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

International Nuclear Information System (INIS)

Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

1992-09-01

Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

Cyclic trimer of human cystatin C, an amyloidogenic protein - molecular dynamics and experimental studies

Science.gov (United States)

Chrabåszczewska, Magdalena; Maszota-Zieleniak, Martyna; Pietralik, Zuzanna; Taube, Michał; Rodziewicz-Motowidło, Sylwia; Szymańska, Aneta; Szutkowski, Kosma; Clemens, Daniel; Grubb, Anders; Kozak, Maciej

2018-05-01

Human cystatin C (HCC) is a cysteine protease inhibitor that takes a series of oligomeric forms in solution (e.g., dimers, trimers, tetramers, decamers, dodecamers, and other higher oligomers). The best-known form of cystatin C is the dimer, which arises as a result of a domain swapping mechanism. The formation of the HCC oligomeric forms, which is most likely due to this domain swapping mechanism, is associated with the aggregation of HCC into amyloid fibrils and deposits. To investigate the structure of a specific HCC oligomer, we developed a covalently stabilized trimer of HCC. An atomic model of this HCC trimer was proposed on the basis of molecular docking and molecular dynamics simulations. The most stable model of the HCC trimer obtained from the molecular dynamics simulations is characterized by a well-preserved secondary structure. The molecular size and structural parameters of the HCC trimer in solution were also confirmed by Small Angle Neutron Scattering and Nuclear Magnetic Resonance Diffusometry.

Comparison of molecular dynamics and kinetic modeling of gas-surface interactions

NARCIS (Netherlands)

Frezzotti, A.; Gaastra - Nedea, S.V.; Markvoort, A.J.; Spijker, P.; Gibelli, L.

2008-01-01

The interaction of a dilute monatomic gas with a solid surface is studied byMolecular Dynamics (MD) simulations and by numerical solutions of a recently proposed kinetic model. Following previous investigations, the heat transport between parallel walls and Couette flow have been adopted as test

Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation

NARCIS (Netherlands)

Mangoni, R; Roccatano, D; Di Nola, A

1999-01-01

In this paper, a method of simulating the docking of small flexible ligands to flexible receptors in water is reported. The method is based on molecular dynamics simulations and is an extension of an algorithm previously reported by Di Nola et al, (Di Nola et al,, Proteins 1994;19:174-182), The

Structural elucidation of dendritic host-guest complexes by X-ray crystallography and molecular dynamics simulations

NARCIS (Netherlands)

Chang, T.; Pieterse, K.; Broeren, M.A.C.; Kooijman, H.; Spek, A.L.; Hilbers, P.A.J.; Meijer, E.W.

2007-01-01

The multiple monovalent binding of adamantyl-urea poly(propyleneimine) dendrimers with carboxylic acid-urea guests was investigated using molecular dynamics simulations and X-ray crystallography to better understand the structure and behavior of the dynamic multivalent complex in solution. The

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

Science.gov (United States)

Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting

2017-07-01

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project

Exploring Nuclear Photorelaxation of Pyranine in Aqueous Solution: an Integrated Ab-Initio Molecular Dynamics and Time Resolved Vibrational Analysis Approach.

Science.gov (United States)

Chiariello, Maria Gabriella; Rega, Nadia

2018-03-22

Advances in time-resolved vibrational spectroscopy techniques provided a new stimulus for understanding the transient molecular dynamics triggered by the electronic excitation. The detailed interpretation of such time-dependent spectroscopic signals is a challenging task from both experimental and theoretical points of view. We simulated and analyzed the transient photorelaxation of the pyranine photoacid in aqueous solution, with special focus on structural parameters and low frequency skeleton modes that are possibly preparatory for the photoreaction occurring at later time, as suggested by experimental spectroscopic studies. To this aim, we adopted an accurate computational protocol that combines excited state ab initio molecular dynamics within an hybrid quantum mechanical/molecular mechanics framework and a time-resolved vibrational analysis based on the Wavelet transform. According to our results, the main nuclear relaxation on the excited potential energy surface is completed in about 500 fs, in agreement with experimental data. The rearrangement of C-C bonds occurs according to a complex vibrational dynamics, showing oscillatory patterns that are out of phase and modulated by modes below 200 cm -1 . We also analyzed in both the ground and the excited state the evolution of some structural parameters involved in excited state proton transfer reaction, namely, those involving the pyranine and the water molecule hydrogen bonded to the phenolic O-H group. Both the hydrogen bond distance and the intermolecular orientation are optimized in the excited state, resulting in a tighter proton donor-acceptor couple. Indeed, we found evidence that collective low frequency skeleton modes, such as the out of plane wagging at 108 cm -1 and the deformation at 280 cm -1 , are photoactivated by the ultrafast part of the relaxation and modulate the pyranine-water molecule rearrangement, favoring the preparatory step for the photoreactivity.

Comparison of nanoparticle diffusion using fluorescence correlation spectroscopy and differential dynamic microscopy within concentrated polymer solutions

Science.gov (United States)

Shokeen, Namita; Issa, Christopher; Mukhopadhyay, Ashis

2017-12-01

We studied the diffusion of nanoparticles (NPs) within aqueous entangled solutions of polyethylene oxide (PEO) by using two different optical techniques. Fluorescence correlation spectroscopy, a method widely used to investigate nanoparticle dynamics in polymer solution, was used to measure the long-time diffusion coefficient (D) of 25 nm radius particles within high molecular weight, Mw = 600 kg/mol PEO in water solutions. Differential dynamic microscopy (DDM) was used to determine the wave-vector dependent dynamics of NPs within the same polymer solutions. Our results showed good agreement between the two methods, including demonstration of normal diffusion and almost identical diffusion coefficients obtained by both techniques. The research extends the scope of DDM to study the dynamics and rheological properties of soft matter at a nanoscale. The measured diffusion coefficients followed a scaling theory, which can be explained by the coupling between polymer dynamics and NP motion.

Molecular Structure of Salt Solutions: A New View of the Interface with Implications for Heterogeneous Atmospheric Chemistry

Czech Academy of Sciences Publication Activity Database

Jungwirth, Pavel; Tobias, D. J.

2001-01-01

Roč. 105, č. 43 (2001), s. 10468-10472 ISSN 1089-5647 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : air-solution interface * salt solutions * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.379, year: 2001

Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal.

Science.gov (United States)

Neale, Chris; Madill, Chris; Rauscher, Sarah; Pomès, Régis

2013-08-13

All molecular dynamics simulations are susceptible to sampling errors, which degrade the accuracy and precision of observed values. The statistical convergence of simulations containing atomistic lipid bilayers is limited by the slow relaxation of the lipid phase, which can exceed hundreds of nanoseconds. These long conformational autocorrelation times are exacerbated in the presence of charged solutes, which can induce significant distortions of the bilayer structure. Such long relaxation times represent hidden barriers that induce systematic sampling errors in simulations of solute insertion. To identify optimal methods for enhancing sampling efficiency, we quantitatively evaluate convergence rates using generalized ensemble sampling algorithms in calculations of the potential of mean force for the insertion of the ionic side chain analog of arginine in a lipid bilayer. Umbrella sampling (US) is used to restrain solute insertion depth along the bilayer normal, the order parameter commonly used in simulations of molecular solutes in lipid bilayers. When US simulations are modified to conduct random walks along the bilayer normal using a Hamiltonian exchange algorithm, systematic sampling errors are eliminated more rapidly and the rate of statistical convergence of the standard free energy of binding of the solute to the lipid bilayer is increased 3-fold. We compute the ratio of the replica flux transmitted across a defined region of the order parameter to the replica flux that entered that region in Hamiltonian exchange simulations. We show that this quantity, the transmission factor, identifies sampling barriers in degrees of freedom orthogonal to the order parameter. The transmission factor is used to estimate the depth-dependent conformational autocorrelation times of the simulation system, some of which exceed the simulation time, and thereby identify solute insertion depths that are prone to systematic sampling errors and estimate the lower bound of the

Concentrated aqueous sodium chloride solution in clays at thermodynamic conditions of hydraulic fracturing: Insight from molecular dynamics simulations

Science.gov (United States)

Svoboda, Martin; Lísal, Martin

2018-06-01

To address a high salinity of flow-back water during hydraulic fracturing, we use molecular dynamics (MD) simulations and study the thermodynamics, structure, and diffusion of concentrated aqueous salt solution in clay nanopores. The concentrated solution results from the dissolution of a cubic NaCl nanocrystal, immersed in an aqueous NaCl solution of varying salt concentration and confined in clay pores of a width comparable to the crystal size. The size of the nanocrystal equals to about 18 Å which is above a critical nucleus size. We consider a typical shale gas reservoir condition of 365 K and 275 bar, and we represent the clay pores as pyrophyllite and Na-montmorillonite (Na-MMT) slits. We employ the Extended Simple Point Charge (SPC/E) model for water, Joung-Cheatham model for ions, and CLAYFF for the slit walls. We impose the pressure in the normal direction and the resulting slit width varies from about 20 to 25 Å when the salt concentration in the surrounding solution increased from zero to an oversaturated value. By varying the salt concentration, we observe two scenarios. First, the crystal dissolves and its dissolution time increases with increasing salt concentration. We describe the dissolution process in terms of the number of ions in the crystal, and the crystal size and shape. Second, when the salt concentration reaches a system solubility limit, the crystal grows and attains a new equilibrium size; the crystal comes into equilibrium with the surrounding saturated solution. After crystal dissolution, we carry out canonical MD simulations for the concentrated solution. We evaluate the hydration energy, density profiles, orientation distributions, hydrogen-bond network, radial distribution functions, and in-plane diffusion of water and ions to provide insight into the microscopic behaviour of the concentrated aqueous sodium chloride solution in interlayer galleries of the slightly hydrophobic pyrophyllite and hydrophilic Na-MMT pores.

Structure and dynamics of aqueous solution of uranyl ions

International Nuclear Information System (INIS)

Chopra, Manish; Choudhury, Niharendu

2014-01-01

The present work describes a molecular dynamics simulation study of structure and dynamics of aqueous solution of uranyl ions in water. Structural properties of the system in terms of radial distribution functions and dynamical characteristics as obtained through velocity autocorrelation function and mean square displacements have been analyzed. The results for radial distribution functions show the oxygen of water to form the first solvation shell at 2.4 Å around the uranium atom, whereas the hydrogen atoms of water are distributed around the uranium atom with the major peak at around 3.0 Å. Analyses of transport behaviors of ions and water through MSD indicates that the diffusion of the uranyl ion is much less as compared to that of the water molecules. It is also observed that the dynamical behavior of water molecules gets modified due to the presence of uranyl ion. The effect of increase in concentration of uranyl ions on the structure and dynamics of water molecules is also studied

Computing UV/vis spectra using a combined molecular dynamics and quantum chemistry approach: bis-triazin-pyridine (BTP) ligands studied in solution.

Science.gov (United States)

Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J

2016-03-21

We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution.

Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration

Energy Technology Data Exchange (ETDEWEB)

Varanasi, S. R., E-mail: s.raovaranasi@uq.edu.au, E-mail: guskova@ipfdd.de; John, A. [Institut Theorie der Polymere, Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden D-01069 (Germany); Guskova, O. A., E-mail: s.raovaranasi@uq.edu.au, E-mail: guskova@ipfdd.de [Institut Theorie der Polymere, Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden D-01069 (Germany); Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, Dresden D-01069 (Germany); Sommer, J.-U. [Institut Theorie der Polymere, Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden D-01069 (Germany); Dresden Center for Computational Materials Science (DCMS), Technische Universität Dresden, Dresden D-01069 (Germany); Institut für Theoretische Physik, Technische Universität Dresden, Zellescher Weg 17, Dresden D-01069 (Germany)

2015-06-14

Fullerene C{sub 60} sub-colloidal particle with diameter ∼1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C{sub 60} fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientational correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent molecules—water retardation—in the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the “dangling” –OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some “dry” regions of C{sub 60} are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique.

Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration

International Nuclear Information System (INIS)

Varanasi, S. R.; John, A.; Guskova, O. A.; Sommer, J.-U.

2015-01-01

Fullerene C 60 sub-colloidal particle with diameter ∼1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C 60 fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientational correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent molecules—water retardation—in the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the “dangling” –OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some “dry” regions of C 60 are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique

Atomic and Molecular Dynamics on and in Superfluid Helium Nanodroplets

Science.gov (United States)

Lehmann, Kevin K.

2003-03-01

Studies of intramolecular and intermolecular dynamics is at the core of Molecular Spectroscopic research several decades. Gas phase, particularly molecular beam, studies have greatly illuminated these processes in isolated molecules, bimolecular collisions, or small covalent and van der Waals complexes. Parallel to this effort have been studies in condensed phases, but there has unfortunately been little intellectual contact between these. The recent development of Helium Nanodropet Isolation Spectroscopy is providing an intellectual bridge between gas phase and condensed phase spectroscopy. While droplets of 10,000 He atoms are effectively a condensed phase, their low temperature ( 0.4 K) and ultralow heat capacities combined with their superfluid state make them an almost ideal matrix in which to study both molecular dynamics, including solute induced relaxations. The nsec times scales for many of the relaxation events, orders of magnitude slower than in classical liquids, results in spectra with unprecedented resolution for the liquid state. In this talk, studies of the Princeton group will be highlighted, with particular emphasis on those for which a combination of theory and experiment have combined to reveal dynamics in this unique Quantum Fluid.

Communication: Relationship between solute localization and diffusion in a dynamically constrained polymer system

Energy Technology Data Exchange (ETDEWEB)

Saylor, David M.; Jawahery, Sudi; Silverstein, Joshua S.; Forrey, Christopher [Center for Devices and Radiological Health, FDA, Silver Spring, Maryland 20993 (United States)

2016-07-21

We investigate the link between dynamic localization, characterized by the Debye–Waller factor, 〈u{sup 2}〉, and solute self-diffusivity, D, in a polymer system using atomistic molecular dynamics simulations and vapor sorption experiments. We find a linear relationship between lnD and 1/〈u{sup 2}〉 over more than four decades of D, encompassing most of the glass formation regime. The observed linearity is consistent with the Langevin dynamics in a periodically varying potential field and may offer a means to rapidly assess diffusion based on the characterization of dynamic localization.

Color molecular dynamics for dense matter

International Nuclear Information System (INIS)

Maruyama, Toshiki; Hatsuda, Tetsuo

2000-01-01

We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)

Lattice dynamics and molecular dynamics simulation of complex materials

International Nuclear Information System (INIS)

Chaplot, S.L.

1997-01-01

In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

Molecular dynamics study on the structural and dynamic properties of xanthan gum in a dilute solution under the effect of temperature

Science.gov (United States)

Ong, Ernest E. S.; O'Byrne, Sean; Liow, Jong-Leng

2018-04-01

Xanthan gum (XG) is considered one of the most industrially important polysaccharides, with applications ranging from food products such as ice creams and salad dressings to pharmaceuticals and oil well drilling fluids. The wide application of XG is due to its favourable rheological properties and its capability to resist degradation under a high shear or high temperature environment. It is generally accepted that both inter- and intramolecular interactions, including hydrogen bonding (HB), are responsible for its unique properties. To date, there is still a lack of comprehensive examination on the HB mechanism in polysaccharides. Therefore, the study proposed here was conducted using molecular dynamics (MD) simulations that are able to provide insights with an unparalleled temporal and spatial resolution. Since XG is used over a broad range of temperatures, the implications of thermal effect on the structure and molecular interactions of XG in an aqueous solution are discussed in this paper. MD simulations were run at an isobaric-isothermal condition with 1 atm target pressure and five temperatures ranging between 283K and 353K. From the simulation results, an increasingly extended conformation of XG is observed as the temperature rises, and this finding matches qualitatively with the results published in the literature. The radius of gyration, radial pair distribution functions and intramolecular HB of XG were also discussed. The outcomes of the present study may serve as a stepping stone for the future studies on polysaccharides using MD simulations.

Molecular dynamics for irradiation driven chemistry

DEFF Research Database (Denmark)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-01-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

Science.gov (United States)

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.

Nanojets, Electrospray, and Ion Field Evaporation: Molecular Dynamics Simulations and Laboratory Experiments

Science.gov (United States)

2008-07-22

Eft (d) (otherwise Coulomb fission occurs), and the solute residue diameter is less than the critical diameter at which E\\ = ER(</); i.e., in the...12 / tap " Figure 10. Atomic configurations taken from a molecular dynamics simulation of a 10 nm formamide droplet prior to and after the

Substructured multibody molecular dynamics.

Energy Technology Data Exchange (ETDEWEB)

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

2006-11-01

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

Energy Technology Data Exchange (ETDEWEB)

Hsu, Po Jen; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw [Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320, Taiwan and Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan (China); Rapallo, Arnaldo [Istituto per lo Studio delle Macromolecole (ISMAC) Consiglio Nazionale delle Ricerche (CNR), via E. Bassini 15, C.A.P 20133 Milano (Italy)

2014-03-14

Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

International Nuclear Information System (INIS)

Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo

2014-01-01

Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

Electron-nuclear corellations for photoinduced dynamics in molecular dimers

Science.gov (United States)

Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

2003-03-01

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

Phenomenology of polymer solution dynamics

National Research Council Canada - National Science Library

Phillies, George D. J

2011-01-01

... solutions, not dilute solutions or polymer melts. From centrifugation and solvent dynamics to viscosity and diffusion, experimental measurements and their quantitative representations are the core of the discussion...

Analyzing the Molecular Kinetics of Water Spreading on Hydrophobic Surfaces via Molecular Dynamics Simulation.

Science.gov (United States)

Zhao, Lei; Cheng, Jiangtao

2017-09-07

In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

Science.gov (United States)

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

Local hydrated structure of an Fe2+/Fe3+ aqueous solution: an investigation using a combination of molecular dynamics and X-ray absorption fine structure methods

International Nuclear Information System (INIS)

Ye Qing; Zhou Jing; Zhao Haifeng; Chen Xing; Chu Wangsheng; Zheng Xusheng; Marcelli, Augusto; Wu Ziyu

2013-01-01

The hydrated shell of both Fe 2+ and Fe 3+ aqueous solutions are investigated by using the molecular dynamics (MD) and X-ray absorption structure (XAS) methods. The MD simulations show that the first hydrated shells of both Fe 2+ and Fe 3+ are characterized by a regular octahedron with an Fe-O distance of 2.08Å for Fe 2+ and 1.96Å for Fe 3+ , and rule out the occurrence of a Jahn-Teller distortion in the hydrated shell of an Fe 2+ aqueous solution. The corresponding X-ray absorption near edge fine structure (XANES) calculation successfully reproduces all features in the XANES spectra in Fe 2+ and Fe 3+ aqueous solution. A feature that is located at energy 1 eV higher than the white line (WL) in an Fe 3+ aqueous solution may be assigned to the contribution of the charge transfer. (authors)

Fluctuation Solution Theory Properties from Molecular Simulation

DEFF Research Database (Denmark)

Abildskov, Jens; Wedberg, R.; O’Connell, John P.

2013-01-01

The thermodynamic properties obtained in the Fluctuation Solution Theory are based on spatial integrals of molecular TCFs between component pairs in the mixture. Molecular simulation, via either MD or MC calculations, can yield these correlation functions for model inter- and intramolecular...

Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-01

In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-06

In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

Polymer friction Molecular Dynamics

DEFF Research Database (Denmark)

Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

On the microstructure of organic solutions of mono-carboxylic acids: Combined study by infrared spectroscopy, small-angle neutron scattering and molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Eremin, Roman A., E-mail: era@jinr.ru [Joint Institute for Nuclear Research, Dubna 141980 (Russian Federation); Kholmurodov, Kholmirzo T. [Joint Institute for Nuclear Research, Dubna 141980 (Russian Federation); International University “Dubna”, Dubna 141980 (Russian Federation); Petrenko, Viktor I. [Joint Institute for Nuclear Research, Dubna 141980 (Russian Federation); Taras Shevchenko National University of Kyiv, Kyiv 03022 (Ukraine); Rosta, László [Wigner Research Centre for Physics, Hungarian Academy of Sciences, Budapest H-1525 (Hungary); Grigoryeva, Natalia A. [Faculty of Physics, Saint-Petersburg State University, 198504 Saint-Petersburg (Russian Federation); Avdeev, Mikhail V. [Joint Institute for Nuclear Research, Dubna 141980 (Russian Federation)

2015-11-05

Highlights: • The model of the scattering particle for a reliable SANS analysis is proposed. • The structural parameters of saturated mono-carboxylic acids in solutions are obtained. • The differences in nematic transitions correlate to solvation peculiarities. - Abstract: The data of infrared spectroscopy (IR), molecular dynamics (MD) simulations and small-angle neutron scattering (SANS) have been combined to conclude about the nanoscale structural organization of organic non-polar solutions of saturated mono-carboxylic acids with different alkyl chain lengths for diluted solutions of saturated myristic (C14) and stearic (C18) acids in benzene and decalin. In particular, the degree of dimerization was found from the IR spectra. The structural anisotropy of the acids and their dimers was used in the treatment of the data of MD simulations to describe the solute–solvent interface in a cylindrical approximation and show its rather strong influence on SANS. The corresponding scattering length density profiles were used to fit the experimental SANS data comprising the information about the acid molecule isomerization. The SANS data from concentrated solutions showed a partial self-assembling of the acids within the nematic transition is different for two solvents due to lyophobic peculiarities.

Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

Directory of Open Access Journals (Sweden)

Lin Lin

2013-12-01

Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

A Molecular Dynamics Study of Lunasin | Singh | South African ...

African Journals Online (AJOL)

A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

Fissile solution dynamics: Student research

Energy Technology Data Exchange (ETDEWEB)

Hetrick, D.L.

1994-09-01

There are two research projects in criticality safety at the University of Arizona: one in dynamic simulation of hypothetical criticality accidents in fissile solutions, and one in criticality benchmarks using transport theory. We have used the data from nuclear excursions in KEWB, CRAC, and SILENE to help in building models for solution excursions. An equation of state for liquids containing gas bubbles has been developed and coupled to point-reactor dynamics in an attempt to predict fission rate, yield, pressure, and kinetic energy. It appears that radiolytic gas is unimportant until after the first peak, but that it does strongly affect the shape of the subsequent power decrease and also the dynamic pressure.

Molecular Dynamics Simulation of Binary Fluid in a Nanochannel

International Nuclear Information System (INIS)

Mullick, Shanta; Ahluwalia, P. K.; Pathania, Y.

2011-01-01

This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12σ, 14σ and 16σ and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.

Density Fluctuation in Aqueous Solutions and Molecular Origin of Salting-Out Effect for CO2

International Nuclear Information System (INIS)

Ho, Tuan Anh; Ilgen, Anastasia

2017-01-01

Using molecular dynamics simulation, we studied the density fluctuations and cavity formation probabilities in aqueous solutions and their effect on the hydration of CO 2 . With increasing salt concentration, we report an increased probability of observing a larger than the average number of species in the probe volume. Our energetic analyses indicate that the van der Waals and electrostatic interactions between CO 2 and aqueous solutions become more favorable with increasing salt concentration, favoring the solubility of CO 2 (salting in). However, due to the decreasing number of cavities forming when salt concentration is increased, the solubility of CO 2 decreases. The formation of cavities was found to be the primary control on the dissolution of gas, and is responsible for the observed CO 2 salting-out effect. Finally, our results provide the fundamental understanding of the density fluctuation in aqueous solutions and the molecular origin of the salting-out effect for real gas.

Molecular dynamics study of interstitial-solute interactions in irradiated alloys

International Nuclear Information System (INIS)

Lam, N.Q.; Doan, N.V.; Adda, Y.

1980-01-01

The molecular dynamics technique has been used, in conjunction with the interionic potentials of Dagens et al, to study the stability, configuration, binding, and induced migration of mixed dumbbells in an irradiated Al-Zn alloy. For the purpose of comparisons, self-interstitials in pure Al were also investigated. The Al-Al and Al-Zn interactions were described by pair potentials which extended to ninth-neighbour distances. Both the self-interstitial dumbbell and the mixed dumbbell were found to be stable in the configuration. The formation energy of the self-interstitial is 2.89 eV and the mixed-dumbbell binding energy is 0.38 eV. As a result of this strong binding, the threshold energy required to induce the migration of the mixed dumbbell is about 1.2 eV, which is significantly larger than the minimum energy of about 0.15 eV transferred to a self-interstitial to induce its jumps in pure Al. Caging motions of the mixed dumbbell were observed. The present computer-simulation results are compared with experimental measurements. (author)

State conditions transferability of vapor-liquid equilibria via fluctuation solution theory with correlation function integrals from molecular dynamics simulations

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...

Molecular dynamics simulations of the adsorption of DNA segments onto graphene oxide

International Nuclear Information System (INIS)

Chen, Junlang; Chen, Shude; Chen, Liang; Wang, Yu

2014-01-01

Molecular dynamics simulations were performed to investigate the dynamic process of DNA segments’ adsorption on graphene oxide (GO) in aqueous solution. We find that DNA segments finally ‘stand on’ GO’s surface. Due to energy penalty and electrostatic repulsion, DNA segments cannot lie on the surface of GO with their helical axes parallel to GO’s surface. Both π–π stacking and electrostatic interactions contribute to their binding affinity between the contacting basepair and GO. The results are of great importance to understand the interactions between DNA segments and GO. (paper)

Solvation and Aggregation of Meta-Aminobenzoic Acid in Water: Density Functional Theory and Molecular Dynamics Study

Directory of Open Access Journals (Sweden)

Etienne Gaines

2018-01-01

Full Text Available Meta-aminobenzoic acid, an important model system in the study of polymorphism and crystallization of active pharmaceutical ingredients, exist in water in both the nonionic (mABA and zwitterionic (mABA± forms. However, the constituent molecules of the polymorph that crystallizes from aqueous solutions are zwitterionic. This study reports atomistic simulations of the events surrounding the early stage of crystal nucleation of meta-aminobenzoic acid from aqueous solutions. Ab initio molecular dynamics was used to simulate the hydration of mABA± and mABA and to quantify the interaction of these molecules with the surrounding water molecules. Density functional theory calculations were conducted to determine the low-lying energy conformers of meta-aminobenzoic acid dimers and to compute the Gibbs free energies in water of nonionic, (mABA2, zwitterionic, (mABA±2, and nonionic-zwitterionic, (mABA(mABA±, species. Classical molecular dynamics simulations of mixed mABA–mABA± aqueous solutions were carried out to examine the aggregation of meta-aminobenzoic acid. According to these simulations, the selective crystallization of the polymorphs whose constituent molecules are zwitterionic is driven by the formation of zwitterionic dimers in solution, which are thermodynamically more stable than (mABA2 and (mABA(mABA± pairs. This work represents a paradigm of the role of molecular processes during the early stages of crystal nucleation in affecting polymorph selection during crystallization from solution.

Dynamic viscosity of polymer solutions

Energy Technology Data Exchange (ETDEWEB)

Peterlin, A

1982-03-01

The dynamic viscosity investigation of solutions of long chain polymers in very viscous solvents has definitely shown the existence of the low and high frequency plateau with the gradual transition between them. In both extreme cases the extrapolation of the measured Newtonian viscosities of the plateaus to the infinite dilution yields the limiting intrinsic viscosities. Such a behavior is expected from the dynamic intrinsic viscosity of the necklace model of the linear polymer with finite internal viscosity. The plateau at low frequency shows up in any model of polymer solution. This work shows the constant dynamic intrinsic viscosity in both extreme cases is well reproducible by the necklace model with the internal viscosity acting only between the beads on the same link. 20 references.

Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

Energy Technology Data Exchange (ETDEWEB)

Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

2014-10-15

The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

Algebraic dynamics solutions and algebraic dynamics algorithm for nonlinear partial differential evolution equations of dynamical systems

Institute of Scientific and Technical Information of China (English)

2008-01-01

Using functional derivative technique in quantum field theory, the algebraic dy-namics approach for solution of ordinary differential evolution equations was gen-eralized to treat partial differential evolution equations. The partial differential evo-lution equations were lifted to the corresponding functional partial differential equations in functional space by introducing the time translation operator. The functional partial differential evolution equations were solved by algebraic dynam-ics. The algebraic dynamics solutions are analytical in Taylor series in terms of both initial functions and time. Based on the exact analytical solutions, a new nu-merical algorithm—algebraic dynamics algorithm was proposed for partial differ-ential evolution equations. The difficulty of and the way out for the algorithm were discussed. The application of the approach to and computer numerical experi-ments on the nonlinear Burgers equation and meteorological advection equation indicate that the algebraic dynamics approach and algebraic dynamics algorithm are effective to the solution of nonlinear partial differential evolution equations both analytically and numerically.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

Science.gov (United States)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

Molecular dynamics simulation of siderite-hematite-quartz flotation with sodium oleate

Science.gov (United States)

Li, Lixia; Hao, Haiqing; Yuan, Zhitao; Liu, Jiongtian

2017-10-01

Models of sodium oleate adsorption on siderite, hematite and quartz were investigated by molecular dynamic simulation, respectively. Surface energy was calculated to confirm the cleavage plan of hematite and quartz. Both natural cleavage plane of siderite and calculated plane were used to investigate the flotation of the three minerals. Based on the molecular simulation in solution with water as medium, adsorption quantity and interaction capability of oleate ions on the three minerals indicated that siderite could be collected efficiently by sodium oleate at neutral pH. Results of flotation experiments were further demonstrated by analysis of relative concentration of carbon atoms and oxygen atoms.

High-Order Ca(II)-Chloro Complexes in Mixed CaCl2-LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations.

Science.gov (United States)

Wang, Yu-Lin; Wang, Ying; Yi, Hai-Bo

2016-07-21

In this study, the structural characteristics of high-coordinated Ca-Cl complexes present in mixed CaCl2-LiCl aqueous solution were investigated using density functional theory (DFT) and molecular dynamics (MD) simulations. The DFT results show that [CaClx](2-x) (x = 4-6) clusters are quite unstable in the gas phase, but these clusters become metastable when hydration is considered. The MD simulations show that high-coordinated Ca-chloro complexes are possible transient species that exist for up to nanoseconds in concentrated (11.10 mol·kg(-1)) Cl(-) solution at 273 and 298 K. As the temperature increases to 423 K, these high-coordinated structures tend to disassociate and convert into smaller clusters and single free ions. The presence of high-order Ca-Cl species in concentrated LiCl solution can be attributed to their enhanced hydration shell and the inadequate hydration of ions. The probability of the [CaClx](2-x)aq (x = 4-6) species being present in concentrated LiCl solution decreases greatly with increasing temperature, which also indicates that the formation of the high-coordinated Ca-Cl structure is related to its hydration characteristics.

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States); Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States)

2016-01-28

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

Science.gov (United States)

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).

First-principles molecular dynamics simulation study on electrolytes for use in redox flow battery

Science.gov (United States)

Choe, Yoong-Kee; Tsuchida, Eiji; Tokuda, Kazuya; Ootsuka, Jun; Saito, Yoshihiro; Masuno, Atsunobu; Inoue, Hiroyuki

2017-11-01

Results of first-principles molecular dynamics simulations carried out to investigate structural aspects of electrolytes for use in a redox flow battery are reported. The electrolytes studied here are aqueous sulfuric acid solutions where its property is of importance for dissolving redox couples in redox flow battery. The simulation results indicate that structural features of the acid solutions depend on the concentration of sulfuric acid. Such dependency arises from increase of proton dissociation from sulfuric acid.

Thermally driven molecular linear motors - A molecular dynamics study

DEFF Research Database (Denmark)

Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

2009-01-01

We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...

An efficient finite element solution for gear dynamics

International Nuclear Information System (INIS)

Cooley, C G; Parker, R G; Vijayakar, S M

2010-01-01

A finite element formulation for the dynamic response of gear pairs is proposed. Following an established approach in lumped parameter gear dynamic models, the static solution is used as the excitation in a frequency domain solution of the finite element vibration model. The nonlinear finite element/contact mechanics formulation provides accurate calculation of the static solution and average mesh stiffness that are used in the dynamic simulation. The frequency domain finite element calculation of dynamic response compares well with numerically integrated (time domain) finite element dynamic results and previously published experimental results. Simulation time with the proposed formulation is two orders of magnitude lower than numerically integrated dynamic results. This formulation admits system level dynamic gearbox response, which may include multiple gear meshes, flexible shafts, rolling element bearings, housing structures, and other deformable components.

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

Science.gov (United States)

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

Molecular dynamics simulations of interfacial interactions between small nanoparticles during diffusion-limited aggregation

International Nuclear Information System (INIS)

Lu, Jing; Liu, Dongmei; Yang, Xiaonan; Zhao, Ying; Liu, Haixing; Tang, Huan; Cui, Fuyi

2015-01-01

Graphical abstract: - Highlights: • Diffusion-limited aggregation is analyzed using molecular dynamic simulations. • The aggregation processand aggregate structure vary with particle size. • Particle-particle interaction and surface diffusion result in direct bonding. • Water-mediated interaction is responsible for the separation betweennanoparticles. - Abstract: Due to the limitations of experimental methods at the atomic level, research on the aggregation of small nanoparticles (D < 5 nm) in aqueous solutions is quite rare. The aggregation of small nanoparticles in aqueous solutions is very different than that of normal sized nanoparticles. The interfacial interactions play a dominant role in the aggregation of small nanoparticles. In this paper, molecular dynamics simulations, which can explore the microscopic behavior of nanoparticles during the diffusion-limited aggregation at an atomic level, were employed to reveal the aggregation mechanism of small nanoparticles in aqueous solutions. First, the aggregation processes and aggregate structure were depicted. Second, the particle–particle interaction and surface diffusion of nanoparticles during aggregation were investigated. Third, the water-mediated interactions during aggregation were ascertained. The results indicate that the aggregation of nanoparticle in aqueous solutions is affected by particle size. The strong particle–particle interaction and high surface diffusion result in the formation of particle–particle bonds of 2 nm TiO 2 nanoparticles, and the water-mediated interaction plays an important role in the aggregation process of 3 and 4 nm TiO 2 nanoparticles.

Introduction to Molecular Dynamics and Accelerated Molecular Dynamics

International Nuclear Information System (INIS)

Perez, Danny

2012-01-01

We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

Haptization of molecular dynamics simulation with thermal display

International Nuclear Information System (INIS)

Tamura, Yuichi; Fujiwara, Susumu; Nakamura, Hiroaki

2010-01-01

Thermal display, which is a type of haptic display, is effective in providing intuitive information of temperature. However, in many studies, the user has assumed a sitting position during the use of these devices. In contrast, the user generally watches 3D objects while standing and walking around in large-scale virtual reality system, In addition, in scientific visualization, the response time is very important for observing physical phenomena, especially for dynamic numerical simulation. One solution is to provide two types of thermal information: information about the rate of thermal change and information about the actual temperature. We propose a thermal display with two Peltier elements which can show above two pairs of information and the result (for example energy and temperature, as thermal information) of numerical simulation. Finally, we represent an example of visualizing and haptizing the result of molecular dynamics simulation. (author)

Single molecule dynamics at a mechanically controllable break junction in solution at room temperature.

Science.gov (United States)

Konishi, Tatsuya; Kiguchi, Manabu; Takase, Mai; Nagasawa, Fumika; Nabika, Hideki; Ikeda, Katsuyoshi; Uosaki, Kohei; Ueno, Kosei; Misawa, Hiroaki; Murakoshi, Kei

2013-01-23

The in situ observation of geometrical and electronic structural dynamics of a single molecule junction is critically important in order to further progress in molecular electronics. Observations of single molecular junctions are difficult, however, because of sensitivity limits. Here, we report surface-enhanced Raman scattering (SERS) of a single 4,4'-bipyridine molecule under conditions of in situ current flow in a nanogap, by using nano-fabricated, mechanically controllable break junction (MCBJ) electrodes. When adsorbed at room temperature on metal nanoelectrodes in solution to form a single molecule junction, statistical analysis showed that nontotally symmetric b(1) and b(2) modes of 4,4'-bipyridine were strongly enhanced relative to observations of the same modes in solid or aqueous solutions. Significant changes in SERS intensity, energy (wavenumber), and selectivity of Raman vibrational bands that are coincident with current fluctuations provide information on distinct states of electronic and geometrical structure of the single molecule junction, even under large thermal fluctuations occurring at room temperature. We observed the dynamics of 4,4'-bipyridine motion between vertical and tilting configurations in the Au nanogap via b(1) and b(2) mode switching. A slight increase in the tilting angle of the molecule was also observed by noting the increase in the energies of Raman modes and the decrease in conductance of the molecular junction.

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

International Nuclear Information System (INIS)

Clore, G.M.; Gronenborn, A.M.; Nilges, M.; Ryan, C.A.

1987-01-01

The solution conformation of potato carboxypeptidase inhibitor (CPI) has been investigated by 1 H NMR spectroscopy. The spectrum is assigned in a sequential manner by using two-dimensional NMR techniques to identify through-bond and through-space (<5 A) connectivities. A set of 309 approximate interproton distance restraints is derived from the two-dimensional nuclear Overhauser enhancement spectra and used as the basis of a three-dimensional structure determination by a combination of metric matrix distance geometry and restrained molecular dynamics calculations. A total of 11 converged distance geometry structures were computed and refined by using restrained molecular dynamics. The average atomic root mean square (rms) difference between the final 11 structures and the mean structure obtained by averaging their coordinates is 1.4 +/- 0.3 A for residues 2-39 and 0.9 +/- 0.2 A for residues 5-37. The corresponding values for all atoms are 1.9 +/- 0.3 and 1.4 +/- 0.2 A, respectively. The computed structures are very close to the X-ray structure of CPI in its complex with carboxypeptidase, and the backbone atomic rms difference between the mean of the computed structures and the X-ray structure is only 1.2 A. Nevertheless, there are some real differences present which are evidenced by significant deviations between the experimental upper interproton distance limits and the corresponding interproton distances derived from the X-ray structure. These principally occur in two regions, residues 18-20 and residues 28-30, the latter comprising part of the region of secondary contact between CPI and carboxypeptidase in the X-ray structure

On the influence of molecular structure on the conductivity of electrolyte solutions - sodium nitrate in water

Directory of Open Access Journals (Sweden)

H. Krienke

2013-01-01

Full Text Available Theoretical calculations of the conductivity of sodium nitrate in water are presented and compared with experimental measurements. The method of direct correlation force in the framework of the interionic theory is used for the calculation of transport properties in connection with the associative mean spherical approximation (AMSA. The effective interactions between ions in solutions are derived with the help of Monte Carlo and Molecular Dynamics calculations on the Born-Oppenheimer level. This work is based on earlier theoretical and experimental studies of the structure of concentrated aqueous sodium nitrate solutions.

Current-driven dynamics in molecular-scale devices

International Nuclear Information System (INIS)

Seideman, Tamar

2003-01-01

We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)

Exploring Ion-Ion Interactions in Aqueous Solutions by a Combination of Molecular Dynamics and Neutron Scattering

Czech Academy of Sciences Publication Activity Database

Kohagen, Miriam; Pluhařová, E.; Mason, Philip E.; Jungwirth, Pavel

2015-01-01

Roč. 6, č. 9 (2015), s. 1563-1567 ISSN 1948-7185 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : ion pairing * molecular dynamics * neutron scattering Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 8.539, year: 2015 http://pubs.acs.org/doi/pdf/10.1021/acs.jpclett.5b00060

Molecular Dynamics Studies of Nanofluidic Devices

DEFF Research Database (Denmark)

Zambrano Rodriguez, Harvey Alexander

of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

Energy Technology Data Exchange (ETDEWEB)

Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)

1994-12-31

Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

International Nuclear Information System (INIS)

Wei Gu; Garcia, A.E.; Schoenborn, B.P.

1994-01-01

Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies

Unusual concentration-dependent microscopic dynamics of dendrimers in aqueous solution

International Nuclear Information System (INIS)

Wong, Kaikin; Wu, Chin Ming; Lam, Hak Fai; Chathoth, Suresh M.

2016-01-01

Dendrimers are novel three-dimensional, hyperbranched globular nanopolymeric macromolecules. The nanoscopic size, narrow polydispersity index, excellent control over molecular structure, availability of multiple functional groups at the periphery, and cavities in the interior made them very attractive candidate for drug delivery. In this communication, we have studied the microscopic dynamics of tetra-acid and pentaerythritol glycidyl ether dendrimers dissolved in aqueous solution with different concentrations. The effects of concentration and temperature to their long-range diffusion process are investigated by dynamic light scattering. Experimental results show a huge variation in the translational diffusion coefficient for the two dendrimers samples. Besides, the dependence of diffusion coefficients on concentration is unusually different in these dendrimer samples. Although the diffusion process follows Arrhenius relation with the temperature in both systems, the activation energy for the diffusion process has a distinct concentration dependence.

Unusual concentration-dependent microscopic dynamics of dendrimers in aqueous solution

Science.gov (United States)

Wong, Kaikin; Wu, Chin Ming; Lam, Hak Fai; Chathoth, Suresh M.

2016-05-01

Dendrimers are novel three-dimensional, hyperbranched globular nanopolymeric macromolecules. The nanoscopic size, narrow polydispersity index, excellent control over molecular structure, availability of multiple functional groups at the periphery, and cavities in the interior made them very attractive candidate for drug delivery. In this communication, we have studied the microscopic dynamics of tetra-acid and pentaerythritol glycidyl ether dendrimers dissolved in aqueous solution with different concentrations. The effects of concentration and temperature to their long-range diffusion process are investigated by dynamic light scattering. Experimental results show a huge variation in the translational diffusion coefficient for the two dendrimers samples. Besides, the dependence of diffusion coefficients on concentration is unusually different in these dendrimer samples. Although the diffusion process follows Arrhenius relation with the temperature in both systems, the activation energy for the diffusion process has a distinct concentration dependence.

Unusual concentration-dependent microscopic dynamics of dendrimers in aqueous solution

Energy Technology Data Exchange (ETDEWEB)

Wong, Kaikin; Wu, Chin Ming; Lam, Hak Fai; Chathoth, Suresh M., E-mail: smavilac@cityu.edu.hk [City University of Hong Kong, Department of Physics and Materials Science (Hong Kong, People’s Republic of China) (China)

2016-05-15

Dendrimers are novel three-dimensional, hyperbranched globular nanopolymeric macromolecules. The nanoscopic size, narrow polydispersity index, excellent control over molecular structure, availability of multiple functional groups at the periphery, and cavities in the interior made them very attractive candidate for drug delivery. In this communication, we have studied the microscopic dynamics of tetra-acid and pentaerythritol glycidyl ether dendrimers dissolved in aqueous solution with different concentrations. The effects of concentration and temperature to their long-range diffusion process are investigated by dynamic light scattering. Experimental results show a huge variation in the translational diffusion coefficient for the two dendrimers samples. Besides, the dependence of diffusion coefficients on concentration is unusually different in these dendrimer samples. Although the diffusion process follows Arrhenius relation with the temperature in both systems, the activation energy for the diffusion process has a distinct concentration dependence.

Molecular dynamics investigation of tracer diffusion in a simple liquid

International Nuclear Information System (INIS)

Ould-Kaddour, F.; Barrat, J.L.

1991-05-01

Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs

Aggregation in concentrated protein solutions: Insights from rheology, neutron scattering and molecular simulations

Science.gov (United States)

Castellanos, Maria Monica

-angle neutron scattering experiments were used to characterize the antibody aggregates responsible for this non-Newtonian response. From the neutron scattering data, a weak barrier leading to reversible aggregation is identified. Therefore, proteins aggregate weakly after colliding hydrodynamically, unless they find a favorable contact with high binding energy. Two types of antibody aggregates were identified: oligomers with average radius of gyration of ˜10 nm, and fractal aggregates larger than ˜ 0.1 microm formed by a reaction-limited aggregation process. A characteristic upturn in the scattered intensity at low wavevector and a low shear viscosity increase are observed in aggregated protein solutions. These features are removed by filtering with a 0.2 microm filter, which also eliminates the submicron fractal aggregates. Biophysical characterization supports the conclusions from the rheology and neutron scattering experiments. Finally, molecular dynamics simulations were used to understand the effects of disulfide bonds on the conformational stability of serum albumin. Changes in disulfide bonds in the native structure could lead to partial unfolding, and the formation of aggregates through inter-molecular disulfide bonds. Therefore, it is important to understand the role of each disulfide bond on the structure and dynamics of the protein. After removing disulfide bonds, changes occur in the dynamic correlations between different residues, and the secondary and tertiary structure of albumin. However, not all disulfide bonds affect the conformation of the protein, suggesting that other interactions are more relevant to keep the stability in certain regions. Removal of all disulfide bonds using molecular dynamics is proposed as a practical prescreening tool to identify disulfide bonds that are important for the conformational stability. As a result, some disulfide bonds can be mutated without affecting the conformation of the protein.

Theoretical Concepts in Molecular Photodissociation Dynamics

DEFF Research Database (Denmark)

Henriksen, Niels Engholm

1995-01-01

This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

Lattice dynamics of a crystal with a molecular impurity

International Nuclear Information System (INIS)

Sahoo, D.; Venkataraman, G.

1975-01-01

The dynamics of a crystal containing a molecular impurity is discussed with allowance for the effects of internal vibrations of the molecule. Cartesian coordinates are used to describe internal vibrations, angular oscillations and centre of mass translations of the impurity, and the displacement of atoms of the host lattice. Next the Hamiltonian is set up and the equations of motion derived. In this process, use is made of Dirac brackets when dealing with vibrational coordinates (of the molecule) which have redundancy and constraints. A method of solution of the normal modes of the system is indicated by using the defect space matrixpartitioning technique. The special case of a rigid molecular impurity is then discussed along with the relevance of the present formalism in the interpretation of a recent neutron scattering experiment. It is also shown how the results of crystal-field approximation model and those of the molecular model approximation are obtained as further special cases of the present formalism. A comparison of the present work with those of others has been made. (author)

First principles molecular dynamics without self-consistent field optimization

International Nuclear Information System (INIS)

Souvatzis, Petros; Niklasson, Anders M. N.

2014-01-01

We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations

Structure and dynamics of biomembranes in room-temperature ionic liquid water solutions studied by neutron scattering and by molecular dynamics simulations

Science.gov (United States)

Benedetto, Antonio; Ballone, Pietro

2018-05-01

Increasing attention is being devoted to the interaction of a new class of organic ionic liquids known as room-temperature ionic liquids (RTILs) with biomolecules, partly because of health and environment concerns, and, even more, for the prospect of exciting new applications in biomedicine, sensing and energy technologies. Here we focus on the interaction between RTILs and phospholipid bilayers that are well-accepted models for bio-membranes. We discuss how neutron scattering has been used to probe both the structure and the dynamics of these systems, and how its integration with molecular dynamics simulation has allowed the determination of the microscopic details of their interaction.

Molecular dynamics and diffusion a compilation

CERN Document Server

Fisher, David

2013-01-01

The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...

Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution.

Science.gov (United States)

Usui, Kota; Hunger, Johannes; Sulpizi, Marialore; Ohto, Tatsuhiko; Bonn, Mischa; Nagata, Yuki

2015-08-20

Ab initio molecular dynamics (AIMD) simulations in trimethylamine N-oxide (TMAO)-D2O solution are employed to elucidate the effects of TMAO on the reorientational dynamics of D2O molecules. By decomposing the O-D groups of the D2O molecules into specific subensembles, we reveal that water reorientational dynamics are retarded considerably in the vicinity of the hydrophilic TMAO oxygen (O(TMAO)) atom, due to the O-D···O(TMAO) hydrogen-bond. We find that this reorientational motion is governed by two distinct mechanisms: The O-D group rotates (1) after breaking the O-D···O(TMAO) hydrogen-bond, or (2) together with the TMAO molecule while keeping this hydrogen-bond intact. While the orientational slow-down is prominent in the AIMD simulation, simulations based on force field models exhibit much faster dynamics. The simulated angle-resolved radial distribution functions illustrate that the O-D···O(TMAO) hydrogen-bond has a strong directionality through the sp(3) orbital configuration in the AIMD simulation, and this directionality is not properly accounted for in the force field simulation. These results imply that care must be taken when modeling negatively charged oxygen atoms as single point charges; force field models may not adequately describe the hydration configuration and dynamics.

Parsing partial molar volumes of small molecules: a molecular dynamics study.

Science.gov (United States)

Patel, Nisha; Dubins, David N; Pomès, Régis; Chalikian, Tigran V

2011-04-28

We used molecular dynamics (MD) simulations in conjunction with the Kirkwood-Buff theory to compute the partial molar volumes for a number of small solutes of various chemical natures. We repeated our computations using modified pair potentials, first, in the absence of the Coulombic term and, second, in the absence of the Coulombic and the attractive Lennard-Jones terms. Comparison of our results with experimental data and the volumetric results of Monte Carlo simulation with hard sphere potentials and scaled particle theory-based computations led us to conclude that, for small solutes, the partial molar volume computed with the Lennard-Jones potential in the absence of the Coulombic term nearly coincides with the cavity volume. On the other hand, MD simulations carried out with the pair interaction potentials containing only the repulsive Lennard-Jones term produce unrealistically large partial molar volumes of solutes that are close to their excluded volumes. Our simulation results are in good agreement with the reported schemes for parsing partial molar volume data on small solutes. In particular, our determined interaction volumes() and the thickness of the thermal volume for individual compounds are in good agreement with empirical estimates. This work is the first computational study that supports and lends credence to the practical algorithms of parsing partial molar volume data that are currently in use for molecular interpretations of volumetric data.

Molecular-dynamics Simulation-based Cohesive Zone Representation of Intergranular Fracture Processes in Aluminum

Science.gov (United States)

Yamakov, Vesselin I.; Saether, Erik; Phillips, Dawn R.; Glaessgen, Edward H.

2006-01-01

A traction-displacement relationship that may be embedded into a cohesive zone model for microscale problems of intergranular fracture is extracted from atomistic molecular-dynamics simulations. A molecular-dynamics model for crack propagation under steady-state conditions is developed to analyze intergranular fracture along a flat 99 [1 1 0] symmetric tilt grain boundary in aluminum. Under hydrostatic tensile load, the simulation reveals asymmetric crack propagation in the two opposite directions along the grain boundary. In one direction, the crack propagates in a brittle manner by cleavage with very little or no dislocation emission, and in the other direction, the propagation is ductile through the mechanism of deformation twinning. This behavior is consistent with the Rice criterion for cleavage vs. dislocation blunting transition at the crack tip. The preference for twinning to dislocation slip is in agreement with the predictions of the Tadmor and Hai criterion. A comparison with finite element calculations shows that while the stress field around the brittle crack tip follows the expected elastic solution for the given boundary conditions of the model, the stress field around the twinning crack tip has a strong plastic contribution. Through the definition of a Cohesive-Zone-Volume-Element an atomistic analog to a continuum cohesive zone model element - the results from the molecular-dynamics simulation are recast to obtain an average continuum traction-displacement relationship to represent cohesive zone interaction along a characteristic length of the grain boundary interface for the cases of ductile and brittle decohesion. Keywords: Crack-tip plasticity; Cohesive zone model; Grain boundary decohesion; Intergranular fracture; Molecular-dynamics simulation

Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

Czech Academy of Sciences Publication Activity Database

Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel

2016-01-01

Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

Clay-enhanced DNA separation in low-molecular-weight poly(N,N-dimethylacrylamide) solution by capillary electrophoresis.

Science.gov (United States)

Liang, D; Song, L; Chen, Z; Chu, B

2001-06-01

The effect of the separation medium in capillary electrophoresis consisting of a low-molecular-mass poly(N,N-dimethylacrylamide) (PDMA) solution on the DNA separation by adding a small amount of montmorillonite clay into the polymer matrix is presented. On the separation of the pBR322/HaeIII digest, both the resolution and the efficiency were increased by adding 2.5-5.0 x 10(-5) g/mL clay into the 5% w/v PDMA with a molecular mass of only 100 K. Moreover, there was no increase in the migration time of DNA fragments. Similar results were observed by using a C-terminated pGEM-3Zf(+) sequencing DNA sample in a sequencing buffer. Experimental data also showed that the addition of clay increased the viscosity of the polymer solution. We attribute this effect to the structural change of the polymer matrix caused by the exfoliated clay sheets, whereby the thin clay sheets function like a "dynamic cross-linking plate" for the PDMA chains and effectively increase the apparent molecular mass of PDMA.

Visualizing Energy on Target: Molecular Dynamics Simulations

Science.gov (United States)

2017-12-01

ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

Science.gov (United States)

Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K.

2017-01-01

Abstract In the canonical DNA double helix, Watson–Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02–0.4%) and short-lived (lifetimes ∼0.2–2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. PMID:28369571

Dielectric dispersion, relaxation dynamics and thermodynamic studies of Beta-Alanine in aqueous solutions using picoseconds time domain reflectometry

Science.gov (United States)

Vinoth, K.; Ganesh, T.; Senthilkumar, P.; Sylvester, M. Maria; Karunakaran, D. J. S. Anand; Hudge, Praveen; Kumbharkhane, A. C.

2017-09-01

The aqueous solution of beta-alanine characterised and studied by their dispersive dielectric properties and relaxation process in the frequency domain of 10×106 Hz to 30×109 Hz with varying concentration in mole fractions and temperatures. The molecular interaction and dielectric parameters are discussed in terms of counter-ion concentration theory. The static permittivity (ε0), high frequency dielectric permittivity (ε∞) and excess dielectric parameters are accomplished by frequency depended physical properties and relaxation time (τ). Molecular orientation, ordering and correlation factors are reported as confirmation of intermolecular interactions. Ionic conductivity and thermo dynamical properties are concluded with the behaviour of the mixture constituents. Solute-solvent, solute-solute interaction, structure making and breaking abilities of the solute in aqueous medium are interpreted. Fourier Transform Infrared (FTIR) spectra of beta- alanine single crystal and liquid state have been studied. The 13C Nuclear Magnetic Resonance (NMR) spectral studies give the signature for resonating frequencies and chemical shifts of beta-alanine.

Nonadiabatic electron wavepacket dynamics behind molecular autoionization

Science.gov (United States)

Matsuoka, Takahide; Takatsuka, Kazuo

2018-01-01

A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

Ultrafast molecular dynamics illuminated with synchrotron radiation

International Nuclear Information System (INIS)

Bozek, John D.; Miron, Catalin

2015-01-01

Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

Experimental evidence of the role of viscosity in the molecular kinetic theory of dynamic wetting.

Science.gov (United States)

Duvivier, D; Seveno, D; Rioboo, R; Blake, T D; De Coninck, J

2011-11-01

We report an experimental study of the dynamics of spontaneous spreading of aqueous glycerol drops on glass. For a range of glycerol concentrations, we follow the evolution of the radius and contact angle over several decades of time and investigate the influence of solution viscosity. The application of the molecular kinetic theory to the resulting data allows us to extract the coefficient of contact-line friction ζ, the molecular jump frequency κ(0), and the jump length λ for each solution. Our results show that the modified theory, which explicitly accounts for the effect of viscosity, can successfully be applied to droplet spreading. The viscosity affects the jump frequency but not the jump length. In combining these data, we confirm that the contact-line friction of the solution/air interface against the glass is proportional to the viscosity and exponentially dependent on the work of adhesion.

First-principles molecular dynamics for metals

International Nuclear Information System (INIS)

Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.

1989-01-01

A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases

Molecular hydrodynamic approach to dynamical correlations in quantum liquids

International Nuclear Information System (INIS)

Rabani, Eran; Reichman, David R.

2002-01-01

A quantum molecular hydrodynamic formalism is developed for the study of dynamics in quantum liquids. The method combines exact static input, generated by path-integral Monte Carlo, and an approximate form of the quantum memory function for the solution of the exact quantum generalized Langevin equation under consideration. This methodology is applied to the study of the spectrum of density fluctuations in liquid para-H 2 . Using a physically motivated approximation for the memory function, semiquantitative agreement is obtained for S(k,ω) in comparison to the recent experiments of Bermejo et al. [Phys. Rev. Lett. 84, 5359 (2000)]. Improvement of the methodology and future applications are discussed

A Coarse-Grained Molecular Dynamics Study of DLPC, DMPC, DPPC, and DSPC Mixtures in Aqueous Solution

Directory of Open Access Journals (Sweden)

Roghayeh Abedi Karjiban

2013-01-01

Full Text Available The structural and dynamics properties of the bilayer comprising 128 molecules of dipalmitoylphosphatidylcholine (DPPC, dilauroylphosphatidylcholine (DLPC, dimyristoylphosphatidylcholine (DMPC, and distearoylphosphatidylcholine (DSPC in water were investigated using a coarse-grained molecular dynamics (CG-MD simulation technique. The model mixture system was simulated at 298 K under semi-isotropic pressure conditions. The aggregation was initiated from the random configurations followed by the formation of a bilayer over a period of 500 ns. The calculated values of the area per lipid, thickness, and lateral diffusion for the mixed model were different from when a single lipid was used. Our results confirmed that the chain length of the lipid molecules strongly affects the phospholipid bilayer’s physical properties.

Variations in calcite growth kinetics with surface topography: molecular dynamics simulations and process-based growth kinetics modelling

NARCIS (Netherlands)

Wolthers, M.; Di Tommaso, D.; Du, Zhimei; de Leeuw, Nora H.

2013-01-01

It is generally accepted that cation dehydration is the rate-limiting step to crystal growth from aqueous solution. Here we employ classical molecular dynamics simulations to show that the water exchange frequency at structurally distinct calcium sites in the calcite surface varies by about two

How Dynamic Visualization Technology Can Support Molecular Reasoning

Science.gov (United States)

Levy, Dalit

2013-01-01

This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

Hydration dynamics in water clusters via quantum molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)

2014-05-28

We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of

Molecular thermodynamics using fluctuation solution theory

DEFF Research Database (Denmark)

Ellegaard, Martin Dela

. The framework relates thermodynamic variables to molecular pair correlation functions of liquid mixtures. In this thesis, application of the framework is illustrated using two approaches: 1. Solubilities of solid solutes in mixed solvent systems are determined from fluctuation solution theory application......Properties of chemicals and their mutual phase equilibria are critical variables in process design. Reliable estimates of relevant equilibrium properties, from thermodynamic models, can form the basis of good decision making in the development phase of a process design, especially when access...... to relevant experimental data is limited. This thesis addresses the issue of generating and using simple thermodynamic models within a rigorous statistical mechanical framework, the so-called fluctuation solution theory, from which relations connecting properties and phase equilibria can be obtained...

Physical adsorption and molecular dynamics

International Nuclear Information System (INIS)

Cohan, N.V.

1981-01-01

Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt

Thomas-Fermi molecular dynamics

International Nuclear Information System (INIS)

Clerouin, J.; Pollock, E.L.; Zerah, G.

1992-01-01

A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated

Molecular dynamics for dense matter

International Nuclear Information System (INIS)

Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro

2012-01-01

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear “pasta”, i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)

Molecular dynamics for dense matter

Science.gov (United States)

Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

2012-08-01

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

Parallel computations of molecular dynamics trajectories using the stochastic path approach

Science.gov (United States)

Zaloj, Veaceslav; Elber, Ron

2000-06-01

A novel protocol to parallelize molecular dynamics trajectories is discussed and tested on a cluster of PCs running the NT operating system. The new technique does not propagate the solution in small time steps, but uses instead a global optimization of a functional of the whole trajectory. The new approach is especially attractive for parallel and distributed computing and its advantages (and disadvantages) are presented. Two numerical examples are discussed: (a) A conformational transition in a solvated dipeptide, and (b) The R→T conformational transition in solvated hemoglobin.

Molecular dynamics test of the Brownian description of Na+ motion in water

International Nuclear Information System (INIS)

Wilson, M.A.; Pohorille, A.; Pratt, L.R.

1985-01-01

The autocorrelation function of the velocity of an infinitely dilute Na + ion in aqueous solution, and the autocorrelation function of the force exerted on a stationary Na + under the same conditions are evaluated by molecular dynamics calculations. The results are used to test the accuracy of Brownian motion assumptions which are basic to hydrodynamic models of ion dynamics in solution. The self-diffusion coefficient of the Na + ion predicted by Brownian motion theory is (0.65 +- 0.1) x 10 -5 cm 2 /s. This value is about 60% greater than the one obtained for the proper dynamics of the finite mass ion, (0.4 +- 0.1) x 10 -5 cm 2 /s. The numerically correct velocity autocorrelation function is nonexponential, and the autocorrelation of the force on the stationary ion does not decay faster than the ion velocity autocorrelation function. Motivated by previous hydrodynamic modeling of friction kernels, we examine the approximation in which the memory function for the velocity autocorrelation function is identified with the autocorrelation function of the force on the stationary ion. The overall agreement between this approximation for the velocity autocorrelation function and the numerically correct answer is quite good

Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

Science.gov (United States)

2014-01-01

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

Hydrogen bonding analysis of hydroxyl groups in glucose aqueous solutions by a molecular dynamics simulation study

International Nuclear Information System (INIS)

Chen, Cong; Li, Wei Zhong; Song, Yong Chen; Weng, Lin Dong; Zhang, Ning

2012-01-01

Molecular dynamics simulations have been performed to investigate hydrogen bonding characteristics of hydroxyl groups in glucose aqueous solutions with different concentrations. The hydrogen bonding abilities and strength of different O and H atom types have been calculated and compared. The acceptor/donor efficiencies have been predicted and it has been found that: (1) O2-HO2 and O3-HO3 are more efficient intramolecular hydrogen bonding acceptors than donors; (2) O1-HO1, O4-HO4 and O6-HO6 are more efficient intramolecular hydrogen bonding donors than acceptors; (5) O1-HO1 and O6-HO6 are more efficient intermolecular hydrogen bonding acceptors than donors while hydroxyl groups O2-HO2 and O4-HO4 are more efficient intermolecular hydrogen bonding donors than acceptors. The hydrogen bonding abilities of hydroxyl groups revealed that: (1) the hydrogen bonding ability of OH2-H w is larger than that of hydroxyl groups in glucose; (2) among the hydroxyl groups in glucose, the hydrogen bonding ability of O6-HO6 is the largest and the hydrogen bonding ability of O4-HO4 is the smallest; (3) the intermolecular hydrogen bonding ability of O6-HO6 is the largest; (4) the order for intramolecular hydrogen bonding abilities (from large to small) is O2-HO2, O1-HO1, O3-HO3, O6-HO6 and O4-HO4

Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

International Nuclear Information System (INIS)

Carnevale, V.; Raugei, S.

2009-01-01

Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

Rabi dynamics of coupled atomic and molecular Bose-Einstein condensates

International Nuclear Information System (INIS)

Ishkhanyan, Artur; Chernikov, G.P.; Nakamura, Hiroki

2004-01-01

The dynamics of coherent Rabi oscillations in coupled atomic and molecular Bose-Einstein condensates is considered taking into account the atom-atom, atom-molecule, and molecule-molecule elastic interactions. The exact solution for the molecule formation probability is derived in terms of the elliptic functions. The two-dimensional space of the involved parameters intensity and detuning is analyzed and divided into two regions where the Rabi oscillations show different characteristics. A resonance curve is found, on which the molecular formation probability monotonically increases as a function of time. The maximum value of the final transition probability on this curve is 1/2 (i.e., total transition to the molecular state) and it is achieved at high field intensities starting from a minimal threshold defined by the interspecies interaction scattering lights. The explicit form of the resonance curve is determined, and it is shown that the resonance frequency position reveals a nonlinear dependence on the Rabi frequency of the applied field. A singular point is found on the resonance curve, where a power-law time evolution of the system is observed

Evaluation of Kirkwood-Buff integrals via finite size scaling: a large scale molecular dynamics study

Science.gov (United States)

Dednam, W.; Botha, A. E.

2015-01-01

Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution

Evaluation of Kirkwood-Buff integrals via finite size scaling: a large scale molecular dynamics study

International Nuclear Information System (INIS)

Dednam, W; Botha, A E

2015-01-01

Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution

Bicanonical ab Initio Molecular Dynamics for Open Systems.

Science.gov (United States)

Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2017-08-08

Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

International Nuclear Information System (INIS)

Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao

2009-01-01

A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.

Science.gov (United States)

Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K; Al-Hashimi, Hashim M

2017-05-19

In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multiscale molecular dynamics using the matched interface and boundary method

International Nuclear Information System (INIS)

Geng Weihua; Wei, G.W.

2011-01-01

The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.

Semiclassical Monte Carlo: A first principles approach to non-adiabatic molecular dynamics

International Nuclear Information System (INIS)

White, Alexander J.; Gorshkov, Vyacheslav N.; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry

2014-01-01

Modeling the dynamics of photophysical and (photo)chemical reactions in extended molecular systems is a new frontier for quantum chemistry. Many dynamical phenomena, such as intersystem crossing, non-radiative relaxation, and charge and energy transfer, require a non-adiabatic description which incorporate transitions between electronic states. Additionally, these dynamics are often highly sensitive to quantum coherences and interference effects. Several methods exist to simulate non-adiabatic dynamics; however, they are typically either too expensive to be applied to large molecular systems (10's-100's of atoms), or they are based on ad hoc schemes which may include severe approximations due to inconsistencies in classical and quantum mechanics. We present, in detail, an algorithm based on Monte Carlo sampling of the semiclassical time-dependent wavefunction that involves running simple surface hopping dynamics, followed by a post-processing step which adds little cost. The method requires only a few quantities from quantum chemistry calculations, can systematically be improved, and provides excellent agreement with exact quantum mechanical results. Here we show excellent agreement with exact solutions for scattering results of standard test problems. Additionally, we find that convergence of the wavefunction is controlled by complex valued phase factors, the size of the non-adiabatic coupling region, and the choice of sampling function. These results help in determining the range of applicability of the method, and provide a starting point for further improvement

Molecular dynamics with deterministic and stochastic numerical methods

CERN Document Server

Leimkuhler, Ben

2015-01-01

This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications.  Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...

Atmospheric-pressure solution-cathode glow discharge: A versatile ion source for atomic and molecular mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

Schwartz, Andrew J. [Department of Chemistry, Indiana University, Bloomington, IN, 47405 (United States); Williams, Kelsey L. [Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242 (United States); Hieftje, Gary M. [Department of Chemistry, Indiana University, Bloomington, IN, 47405 (United States); Shelley, Jacob T., E-mail: shellj@rpi.edu [Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242 (United States); Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180 (United States)

2017-01-15

An atmospheric-pressure solution-cathode glow discharge (SCGD) has been evaluated as an ion source for atomic, molecular, and ambient desorption/ionization mass spectrometry. The SCGD consists of a direct-current plasma, supported in the ambient air in the absence of gas flows, and sustained upon the surface of a flowing liquid cathode. Analytes introduced in the flowing liquid, as an ambient gas, or as a solid held near the plasma are vaporized and ionized by interactions within or near the discharge. Introduction of acidic solutions containing metal salts produced bare elemental ions as well as H{sub 2}O, OH{sup −} and NO{sub 3}{sup −} adducts. Detection limits for these elemental species ranged from 0.1 to 4 ppb, working curves spanned more than 4 orders of linear dynamic range, and precision varied between 5 and 16% relative standard deviation. Small organic molecules were also efficiently ionized from solution, and both the intact molecular ion and fragments were observed in the resulting SCGD mass spectra. Fragmentation of molecular species was found to be tunable; high discharge currents led to harder ionization, while low discharge currents produced stronger molecular-ion signals. Ambient gases and solids, desorbed by the plasma from a glass probe, were also readily ionized by the SCGD. Indeed, strong analyte signals were obtained from solid samples placed at least 2 cm from the plasma. These findings indicate that the SCGD might be useful also for ambient desorption/ionization mass spectrometry. Combined with earlier results that showed the SCGD is useful for ionization of labile biomolecules, the results here indicate that the SCGD is a highly versatile ion source capable of providing both elemental and molecular mass-spectral information. - Highlights: • Solution-cathode glow discharge used as an ionization source for mass spectrometry. • SCGD-MS can provide atomic as well as intact molecular mass spectra. • Atomic limits of detection range

Molecular ions, Rydberg spectroscopy and dynamics

International Nuclear Information System (INIS)

Jungen, Ch.

2015-01-01

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

Molecular ions, Rydberg spectroscopy and dynamics

Energy Technology Data Exchange (ETDEWEB)

Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

2015-01-22

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

Directory of Open Access Journals (Sweden)

Renata De Paris

2015-01-01

Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

Molecular dynamics simulations of the electrical double layer on smectite surfaces contacting concentrated mixed electrolyte (NaCl-CaCl2) solutions.

Science.gov (United States)

Bourg, Ian C; Sposito, Garrison

2011-08-15

We report new molecular dynamics results elucidating the structure of the electrical double layer (EDL) on smectite surfaces contacting mixed NaCl-CaCl(2) electrolyte solutions in the range of concentrations relevant to pore waters in geologic repositories for CO(2) or high-level radioactive waste (0.34-1.83 mol(c) dm(-3)). Our results confirm the existence of three distinct ion adsorption planes (0-, β-, and d-planes), often assumed in EDL models, but with two important qualifications: (1) the location of the β- and d-planes are independent of ionic strength or ion type and (2) "indifferent electrolyte" ions can occupy all three planes. Charge inversion occurred in the diffuse ion swarm because of the affinity of the clay surface for CaCl(+) ion pairs. Therefore, at concentrations ≥0.34 mol(c) dm(-3), properties arising from long-range electrostatics at interfaces (electrophoresis, electro-osmosis, co-ion exclusion, colloidal aggregation) will not be correctly predicted by most EDL models. Co-ion exclusion, typically neglected by surface speciation models, balanced a large part of the clay mineral structural charge in the more concentrated solutions. Water molecules and ions diffused relatively rapidly even in the first statistical water monolayer, contradicting reports of rigid "ice-like" structures for water on clay mineral surfaces. Published by Elsevier Inc.

Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

Science.gov (United States)

Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

2012-07-15

The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.

Dislocation glide in Ni-Al solid solutions from the atomic scale up: a molecular dynamics study; Etude du glissement des dislocations dans la solution solide Ni-Al par simulation a l'echelle atomique

Energy Technology Data Exchange (ETDEWEB)

Rodary, E

2003-01-01

The glide of an edge dislocation in solid solutions is studied by molecular dynamics, at fixed temperature and imposed external stress. We have optimized an EAM potential for Ni(1 a 8% A1): it well reproduces the lattice expansion, local atomic order, stacking fault energy as a function of composition, as well as the elastic properties of the {gamma}' phase with L1{sub 2} structure. On increasing the stress, the dislocation is first immobile, then glides with a velocity proportional to the stress and the velocity saturates on reaching the transverse sound velocity. However, only beyond a static threshold stress, {sigma}{sub s}, does the dislocation glide a distance large enough to allow macroscopic shear; the linear part of the velocity-stress curve extrapolates to zero at a dynamical threshold stress, {sigma}{sub d}, The friction coefficient, and the threshold stresses ({sigma}{sub s} and {sigma}{sub d}), increase with the A1 concentration and decrease with temperature (300 and 500 K). Close to the critical shear stress, {sigma}{sub s}, the dislocation glide is analysed with a 'stop and go' model. The latter yields the flight velocity between obstacles, the mean obstacle density and the distribution of the waiting time on each obstacle as a function of stress, composition and temperature. The obstacle to the glide is proposed to be the strong repulsion between Al atoms brought into nearest neighbour position by the glide process, and not the dislocation-solute interaction. The microscopic parameters so defined are introduced into a micro-mechanical model, which well reproduces the known behaviour of nickel base solid solutions. (author)

Lane-Emden equation with inertial force and general polytropic dynamic model for molecular cloud cores

Science.gov (United States)

Li, DaLei; Lou, Yu-Qing; Esimbek, Jarken

2018-01-01

We study self-similar hydrodynamics of spherical symmetry using a general polytropic (GP) equation of state and derive the GP dynamic Lane-Emden equation (LEE) with a radial inertial force. In reference to Lou & Cao, we solve the GP dynamic LEE for both polytropic index γ = 1 + 1/n and the isothermal case n → +∞; our formalism is more general than the conventional polytropic model with n = 3 or γ = 4/3 of Goldreich & Weber. For proper boundary conditions, we obtain an exact constant solution for arbitrary n and analytic variable solutions for n = 0 and n = 1, respectively. Series expansion solutions are derived near the origin with the explicit recursion formulae for the series coefficients for both the GP and isothermal cases. By extensive numerical explorations, we find that there is no zero density at a finite radius for n ≥ 5. For 0 ≤ n 0 for monotonically decreasing density from the origin and vanishing at a finite radius for c being less than a critical value Ccr. As astrophysical applications, we invoke our solutions of the GP dynamic LEE with central finite boundary conditions to fit the molecular cloud core Barnard 68 in contrast to the static isothermal Bonnor-Ebert sphere by Alves et al. Our GP dynamic model fits appear to be sensibly consistent with several more observations and diagnostics for density, temperature and gas pressure profiles.

Crystal Nucleation of Tolbutamide in Solution: Relationship to Solvent, Solute Conformation, and Solution Structure.

Science.gov (United States)

Zeglinski, Jacek; Kuhs, Manuel; Khamar, Dikshitkumar; Hegarty, Avril C; Devi, Renuka K; Rasmuson, Åke C

2018-04-03

The influence of the solvent in nucleation of tolbutamide, a medium-sized, flexible and polymorphic organic molecule, has been explored by measuring nucleation induction times, estimating solvent-solute interaction enthalpies using molecular modelling and calorimetric data, probing interactions and clustering with spectroscopy, and modelling solvent-dependence of molecular conformation in solution. The nucleation driving force required to reach the same induction time is strongly solvent-dependent, increasing in the order: acetonitrilenucleation difficulty is a function of the strength of solvent-solute interaction, with emphasis on the interaction with specific H-bonding polar sites of importance in the crystal structure. A clear exception from this rule is the most difficult nucleation in toluene despite the weakest solvent-solute interactions. However molecular dynamics modelling predicts that tolbutamide assumes an intramolecularly H-bonded conformation in toluene, substantially different from and more stable than the conformation in the crystal structure, and thus presenting an additional barrier to nucleation. This explains why nucleation in toluene is the most difficult and why the relatively higher propensity for aggregation of tolbutamide molecules in toluene solution, as observed with FTIR spectroscopy, does not translate into easier nucleation. Thus, our combined experimental and molecular modelling study suggests that the solvent can influence on the nucleation not only via differences in the desolvation but also through the influence on molecular conformation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

How to combine binary collision approximation and multi-body potential for molecular dynamics

International Nuclear Information System (INIS)

Saito, Seiki; Nakamura, Hiroaki; Takayama, Arimichi; Ito, Atsushi M.; Kenmotsu, Takahiro

2010-01-01

Our group has been developing a hybrid simulation of the molecular dynamics (MD) and the binary collision approximation (BCA) simulation. One of the main problems of this hybridization model is that the multi-body potential suddenly appears at the moment when the simulation method switches from the BCA to the MD. This instantaneously emerged multi-body potential causes the acceleration or deceleration of atoms of the system. To solve this problem, the kinetic energy of atoms should be corrected to conserve the total energy in the system. This paper gives the solution. The hybrid simulation for hydrogen atom injection into a graphite material is executed in order to demonstrate the solution. (author)

A fermionic molecular dynamics technique to model nuclear matter

International Nuclear Information System (INIS)

Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

2009-01-01

Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

Molecular dynamics study of the solvation of calcium carbonate in water.

Science.gov (United States)

Bruneval, Fabien; Donadio, Davide; Parrinello, Michele

2007-10-25

We performed molecular dynamics simulations of diluted solutions of calcium carbonate in water. To this end, we combined and tested previous polarizable models. The carbonate anion forms long-living hydrogen bonds with water and shows an amphiphilic character, in which the water molecules are expelled in a region close to its C(3) symmetry axis. The calcium cation forms a strongly bound ion pair with the carbonate. The first hydration shell around the CaCO(3) pair is found to be very similar to the location of the water molecules surrounding CaCO(3) in ikaite, the hydrated mineral.

Dynamical photo-induced electronic properties of molecular junctions

Science.gov (United States)

Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

2018-03-01

Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

Dynamical processes in atomic and molecular physics

CERN Document Server

Ogurtsov, Gennadi

2012-01-01

Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

Theory and application of quantum molecular dynamics

CERN Document Server

Zeng Hui Zhang, John

1999-01-01

This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli

Dynamics and Thermodynamics of Molecular Machines

DEFF Research Database (Denmark)

Golubeva, Natalia

2014-01-01

to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

Constant-pH molecular dynamics using stochastic titration

Science.gov (United States)

Baptista, António M.; Teixeira, Vitor H.; Soares, Cláudio M.

2002-09-01

A new method is proposed for performing constant-pH molecular dynamics (MD) simulations, that is, MD simulations where pH is one of the external thermodynamic parameters, like the temperature or the pressure. The protonation state of each titrable site in the solute is allowed to change during a molecular mechanics (MM) MD simulation, the new states being obtained from a combination of continuum electrostatics (CE) calculations and Monte Carlo (MC) simulation of protonation equilibrium. The coupling between the MM/MD and CE/MC algorithms is done in a way that ensures a proper Markov chain, sampling from the intended semigrand canonical distribution. This stochastic titration method is applied to succinic acid, aimed at illustrating the method and examining the choice of its adjustable parameters. The complete titration of succinic acid, using constant-pH MD simulations at different pH values, gives a clear picture of the coupling between the trans/gauche isomerization and the protonation process, making it possible to reconcile some apparently contradictory results of previous studies. The present constant-pH MD method is shown to require a moderate increase of computational cost when compared to the usual MD method.

Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

International Nuclear Information System (INIS)

Mori, Yukie; Masuda, Yuichi

2015-01-01

Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl 4 , acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the 17 O and 1

Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

Energy Technology Data Exchange (ETDEWEB)

Mori, Yukie, E-mail: mori.yukie@ocha.ac.jp; Masuda, Yuichi

2015-09-08

Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl{sub 4}, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the {sup 17

Multiple time step integrators in ab initio molecular dynamics

International Nuclear Information System (INIS)

Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

2014-01-01

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics.

Science.gov (United States)

van den Broek, Karina; Kuhn, Hubert; Zielesny, Achim

2018-05-21

Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The new kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated "all-in-one" simulation systems.

Dynamic signature of molecular association in methanol

International Nuclear Information System (INIS)

Bertrand, C. E.; Copley, J. R. D.; Faraone, A.; Self, J. L.

2016-01-01

Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.

Molecular dynamics for fermions

International Nuclear Information System (INIS)

Feldmeier, H.; Schnack, J.

2000-02-01

The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)

Pattern recognition in molecular dynamics. [FORTRAN

Energy Technology Data Exchange (ETDEWEB)

Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)

1977-07-01

An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.

Synergetics of molecular systems

CERN Document Server

Lupichev, Lev N; Kadantsev, Vasiliy N

2014-01-01

Synergetics is the quantitative study of multicomponent systems that exhibit nonlinear dynamics and cooperativity. This book specifically considers basic models of the nonlinear dynamics of molecular systems and discusses relevant applications in biological physics and the polymer sciences.Emphasis is placed on specific solutions to the dynamical equations that correspond to the coherent formation of spatial-temporal structures, such as solitons, kinks and breathers, in particular. The emergence of these patterns in molecular structures provides a variety of information on their structural pro

On the existence of the H3 tautomer of adenine in aqueous solution. Rationalizations based on hybrid quantum mechanics/molecular mechanics predictions

DEFF Research Database (Denmark)

Aidas, Kestutis; Mikkelsen, Kurt V; Kongsted, Jacob

2010-01-01

The (15)N NMR spectrum of adenine in aqueous solution has been modeled using high-level combined density functional theory/molecular mechanics techniques coupled to a dynamical averaging scheme. The explicit consideration of the three lowest-energy tautomers of adenine-H9, H7 and H3-allows...

Determination of the activity of a molecular solute in saturated solution

International Nuclear Information System (INIS)

Nordstroem, Fredrik L.; Rasmuson, Ake C.

2008-01-01

Prediction of the solubility of a solid molecular compound in a solvent, as well as, estimation of the solution activity coefficient from experimental solubility data both require estimation of the activity of the solute in the saturated solution. The activity of the solute in the saturated solution is often defined using the pure melt at the same temperature as the thermodynamic reference. In chemical engineering literature also the activity of the solid is usually defined on the same reference state. However, far below the melting temperature, the properties of this reference state cannot be determined experimentally, and different simplifications and approximations are normally adopted. In the present work, a novel method is presented to determine the activity of the solute in the saturated solution (=ideal solubility) and the heat capacity difference between the pure supercooled melt and solid. The approach is based on rigorous thermodynamics, using standard experimental thermodynamic data at the melting temperature of the pure compound and solubility measurements in different solvents at various temperatures. The method is illustrated using data for ortho-, meta-, and para-hydroxybenzoic acid, salicylamide and paracetamol. The results show that complete neglect of the heat capacity terms may lead to estimations of the activity that are incorrect by a factor of 12. Other commonly used simplifications may lead to estimations that are only one-third of the correct value

Determination of the activity of a molecular solute in saturated solution

Energy Technology Data Exchange (ETDEWEB)

Nordstroem, Fredrik L. [Department of Chemical Engineering and Technology, Royal Institute of Technology, 100 44 Stockholm (Sweden); Rasmuson, Ake C. [Department of Chemical Engineering and Technology, Royal Institute of Technology, 100 44 Stockholm (Sweden)], E-mail: rasmuson@ket.kth.se

2008-12-15

Prediction of the solubility of a solid molecular compound in a solvent, as well as, estimation of the solution activity coefficient from experimental solubility data both require estimation of the activity of the solute in the saturated solution. The activity of the solute in the saturated solution is often defined using the pure melt at the same temperature as the thermodynamic reference. In chemical engineering literature also the activity of the solid is usually defined on the same reference state. However, far below the melting temperature, the properties of this reference state cannot be determined experimentally, and different simplifications and approximations are normally adopted. In the present work, a novel method is presented to determine the activity of the solute in the saturated solution (=ideal solubility) and the heat capacity difference between the pure supercooled melt and solid. The approach is based on rigorous thermodynamics, using standard experimental thermodynamic data at the melting temperature of the pure compound and solubility measurements in different solvents at various temperatures. The method is illustrated using data for ortho-, meta-, and para-hydroxybenzoic acid, salicylamide and paracetamol. The results show that complete neglect of the heat capacity terms may lead to estimations of the activity that are incorrect by a factor of 12. Other commonly used simplifications may lead to estimations that are only one-third of the correct value.

Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

Institute of Scientific and Technical Information of China (English)

Chengzhen Sun; Bofeng Bai

2017-01-01

Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

Acidity constants from DFT-based molecular dynamics simulations

International Nuclear Information System (INIS)

Sulpizi, Marialore; Sprik, Michiel

2010-01-01

In this contribution we review our recently developed method for the calculation of acidity constants from density functional theory based molecular dynamics simulations. The method is based on a half reaction scheme in which protons are formally transferred from solution to the gas phase. The corresponding deprotonation free energies are computed from the vertical energy gaps for insertion or removal of protons. Combined to full proton transfer reactions, the deprotonation energies can be used to estimate relative acidity constants and also the Broensted pK a when the deprotonation free energy of a hydronium ion is used as a reference. We verified the method by investigating a series of organic and inorganic acids and bases spanning a wide range of pK a values (20 units). The thermochemical corrections for the biasing potentials assisting and directing the insertion are discussed in some detail.

Multiscale equation-free algorithms for molecular dynamics

Science.gov (United States)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

Scalable Molecular Dynamics for Large Biomolecular Systems

Directory of Open Access Journals (Sweden)

Robert K. Brunner

2000-01-01

Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

Molecular Level Structure and Dynamics of Electrolytes Using 17O Nuclear Magnetic Resonance Spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Murugesan, Vijayakumar; Han, Kee Sung; Hu, Jianzhi; Mueller, Karl T.

2017-03-19

Electrolytes help harness the energy from electrochemical processes by serving as solvents and transport media for redox-active ions. Molecular-level interactions between ionic solutes and solvent molecules – commonly referred to as solvation phenomena – give rise to many functional properties of electrolytes such as ionic conductivity, viscosity, and stability. It is critical to understand the evolution of solvation phenomena as a function of competing counterions and solvent mixtures to predict and design the optimal electrolyte for a target application. Probing oxygen environments is of great interest as oxygens are located at strategic molecular sites in battery solvents and are directly involved in inter- and intramolecular solvation interactions. NMR signals from 17O nuclei in battery electrolytes offer nondestructive bulk measurements of isotropic shielding, electric field gradient tensors, and transverse and longitudinal relaxation rates, which are excellent means for probing structure, bonding, and dynamics of both solute and solvent molecules. This article describes the use of 17O NMR spectroscopy in probing the solvation structures of various electrolyte systems ranging from transition metal ions in aqueous solution to lithium cations in organic solvent mixtures.

Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

Science.gov (United States)

Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

2015-05-01

Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon–Mann–Whitney Test

Directory of Open Access Journals (Sweden)

Alexander Marx

2016-02-01

Full Text Available In many research disciplines, hypothesis tests are applied to evaluate whether findings are statistically significant or could be explained by chance. The Wilcoxon–Mann–Whitney (WMW test is among the most popular hypothesis tests in medicine and life science to analyze if two groups of samples are equally distributed. This nonparametric statistical homogeneity test is commonly applied in molecular diagnosis. Generally, the solution of the WMW test takes a high combinatorial effort for large sample cohorts containing a significant number of ties. Hence, P value is frequently approximated by a normal distribution. We developed EDISON-WMW, a new approach to calculate the exact permutation of the two-tailed unpaired WMW test without any corrections required and allowing for ties. The method relies on dynamic programing to solve the combinatorial problem of the WMW test efficiently. Beyond a straightforward implementation of the algorithm, we presented different optimization strategies and developed a parallel solution. Using our program, the exact P value for large cohorts containing more than 1000 samples with ties can be calculated within minutes. We demonstrate the performance of this novel approach on randomly-generated data, benchmark it against 13 other commonly-applied approaches and moreover evaluate molecular biomarkers for lung carcinoma and chronic obstructive pulmonary disease (COPD. We found that approximated P values were generally higher than the exact solution provided by EDISON-WMW. Importantly, the algorithm can also be applied to high-throughput omics datasets, where hundreds or thousands of features are included. To provide easy access to the multi-threaded version of EDISON-WMW, a web-based solution of our algorithm is freely available at http://www.ccb.uni-saarland.de/software/wtest/.

Algebraic dynamics solutions and algebraic dynamics algorithm for nonlinear ordinary differential equations

Institute of Scientific and Technical Information of China (English)

WANG; Shunjin; ZHANG; Hua

2006-01-01

The problem of preserving fidelity in numerical computation of nonlinear ordinary differential equations is studied in terms of preserving local differential structure and approximating global integration structure of the dynamical system.The ordinary differential equations are lifted to the corresponding partial differential equations in the framework of algebraic dynamics,and a new algorithm-algebraic dynamics algorithm is proposed based on the exact analytical solutions of the ordinary differential equations by the algebraic dynamics method.In the new algorithm,the time evolution of the ordinary differential system is described locally by the time translation operator and globally by the time evolution operator.The exact analytical piece-like solution of the ordinary differential equations is expressd in terms of Taylor series with a local convergent radius,and its finite order truncation leads to the new numerical algorithm with a controllable precision better than Runge Kutta Algorithm and Symplectic Geometric Algorithm.

Molecular quantum dynamics. From theory to applications

International Nuclear Information System (INIS)

Gatti, Fabien

2014-01-01

An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the

Molecular quantum dynamics. From theory to applications

Energy Technology Data Exchange (ETDEWEB)

Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253

2014-09-01

An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible

Time-dependent theoretical treatments of the dynamics of electrons and nuclei in molecular systems

International Nuclear Information System (INIS)

Deumens, E.; Diz, A.; Longo, R.; Oehrn, Y.

1994-01-01

An overview is presented of methods for time-dependent treatments of molecules as systems of electrons and nuclei. The theoretical details of these methods are reviewed and contrasted in the light of a recently developed time-dependent method called electron-nuclear dynamics. Electron-nuclear dynamics (END) is a formulation of the complete dynamics of electrons and nuclei of a molecular system that eliminates the necessity of constructing potential-energy surfaces. Because of its general formulation, it encompasses many aspects found in other formulations and can serve as a didactic device for clarifying many of the principles and approximations relevant in time-dependent treatments of molecular systems. The END equations are derived from the time-dependent variational principle applied to a chosen family of efficiently parametrized approximate state vectors. A detailed analysis of the END equations is given for the case of a single-determinantal state for the electrons and a classical treatment of the nuclei. The approach leads to a simple formulation of the fully nonlinear time-dependent Hartree-Fock theory including nuclear dynamics. The nonlinear END equations with the ab initio Coulomb Hamiltonian have been implemented at this level of theory in a computer program, ENDyne, and have been shown feasible for the study of small molecular systems. Implementation of the Austin Model 1 semiempirical Hamiltonian is discussed as a route to large molecular systems. The linearized END equations at this level of theory are shown to lead to the random-phase approximation for the coupled system of electrons and nuclei. The qualitative features of the general nonlinear solution are analyzed using the results of the linearized equations as a first approximation. Some specific applications of END are presented, and the comparison with experiment and other theoretical approaches is discussed

Implementing Molecular Dynamics for Hybrid High Performance Computers - 1. Short Range Forces

International Nuclear Information System (INIS)

Brown, W. Michael; Wang, Peng; Plimpton, Steven J.; Tharrington, Arnold N.

2011-01-01

The use of accelerators such as general-purpose graphics processing units (GPGPUs) have become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high performance computers, machines with more than one type of floating-point processor, are now becoming more prevalent due to these advantages. In this work, we discuss several important issues in porting a large molecular dynamics code for use on parallel hybrid machines - (1) choosing a hybrid parallel decomposition that works on central processing units (CPUs) with distributed memory and accelerator cores with shared memory, (2) minimizing the amount of code that must be ported for efficient acceleration, (3) utilizing the available processing power from both many-core CPUs and accelerators, and (4) choosing a programming model for acceleration. We present our solution to each of these issues for short-range force calculation in the molecular dynamics package LAMMPS. We describe algorithms for efficient short range force calculation on hybrid high performance machines. We describe a new approach for dynamic load balancing of work between CPU and accelerator cores. We describe the Geryon library that allows a single code to compile with both CUDA and OpenCL for use on a variety of accelerators. Finally, we present results on a parallel test cluster containing 32 Fermi GPGPUs and 180 CPU cores.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

Science.gov (United States)

Wallace, Jason A; Shen, Jana K

2012-11-14

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

Excited-state molecular photoionization dynamics

International Nuclear Information System (INIS)

Pratt, S.T.

1995-01-01

This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)

Symmetry of quantum molecular dynamics

International Nuclear Information System (INIS)

Burenin, A.V.

2002-01-01

The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru

Molecular dynamics modeling of polymer flammability

International Nuclear Information System (INIS)

Nyden, M.R.; Brown, J.E.; Lomakin, S.M.

1992-01-01

Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)

Electron-nuclear dynamics of molecular systems

International Nuclear Information System (INIS)

Diz, A.; Oehrn, Y.

1994-01-01

The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

Science.gov (United States)

Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

2015-04-21

Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

Recognition of RNA by amide modified backbone nucleic acids: molecular dynamics simulations of DNA-RNA hybrids in aqueous solution.

Science.gov (United States)

Nina, Mafalda; Fonné-Pfister, Raymonde; Beaudegnies, Renaud; Chekatt, Habiba; Jung, Pierre M J; Murphy-Kessabi, Fiona; De Mesmaeker, Alain; Wendeborn, Sebastian

2005-04-27

Thermodynamic and structural properties of a chemically modified DNA-RNA hybrid in which a phosphodiester linkage is replaced by a neutral amide-3 linkage (3'-CH(2)-CONH-5') were investigated using UV melting experiments, molecular dynamics simulations in explicit water, and continuum solvent models. van't Hoff analysis of the experimental UV melting curves suggests that the significant increase of the thermodynamic stability of a 15-mer DNA-RNA with seven alternated amide-3 modifications (+11 degrees C) is mainly due to an increased binding enthalpy. To further evaluate the origin in the observed affinities differences, the electrostatic contribution to the binding free energy was calculated by solving the Poisson-Boltzmann equation numerically. The nonelectrostatic contribution was estimated as the product of a hydrophobic surface tension coefficient and the surface area that is buried upon double strand formation. Structures were taken from 10 ns molecular dynamics simulations computed in a consistent fashion using explicit solvent, counterions, and the particle-mesh Ewald procedure. The present preliminary thermodynamic study suggests that the favorable binding free energy of the amide-3 DNA single strand to the complementary RNA is equally driven by electrostatic and nonpolar contributions to the binding compared to their natural analogues. In addition, molecular dynamics simulations in explicit water were performed on an amide-3 DNA single strand and the corresponding natural DNA. Results from the conformations cluster analysis of the simulated amide-3 DNA single strand ensembles suggest that the 25% of the population sampled within 10 ns has a pre-organized conformation where the sugar C3' endo pucker is favored at the 3'-flanking nucleotides. These structural and thermodynamic features contribute to the understanding of the observed increased affinities of the amide-3 DNA-RNA hybrids at the microscopic level.

Dynamics of molecular superrotors in an external magnetic field

Science.gov (United States)

Korobenko, Aleksey; Milner, Valery

2015-08-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

Well-posed two-temperature constitutive equations for stable dense fluid shock waves using molecular dynamics and generalizations of Navier-Stokes-Fourier continuum mechanics.

Science.gov (United States)

Hoover, Wm G; Hoover, Carol G

2010-04-01

Guided by molecular dynamics simulations, we generalize the Navier-Stokes-Fourier constitutive equations and the continuum motion equations to include both transverse and longitudinal temperatures. To do so we partition the contributions of the heat transfer, the work done, and the heat flux vector between the longitudinal and transverse temperatures. With shockwave boundary conditions time-dependent solutions of these equations converge to give stationary shockwave profiles. The profiles include anisotropic temperature and can be fitted to molecular dynamics results, demonstrating the utility and simplicity of a two-temperature description of far-from-equilibrium states.

Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations.

Science.gov (United States)

Ohto, Tatsuhiko; Hunger, Johannes; Backus, Ellen H G; Mizukami, Wataru; Bonn, Mischa; Nagata, Yuki

2017-03-08

The osmolyte molecule trimethylamine-N-oxide (TMAO) stabilizes the structure of proteins. As functional proteins are generally found in aqueous solutions, an important aspect of this stabilization is the interaction of TMAO with water. Here, we review, using vibrational spectroscopy and molecular dynamics simulations, recent studies on the structure and dynamics of TMAO with its surrounding water molecules. This article ends with an outlook on the open questions on TMAO-protein and TMAO-urea interactions in aqueous environments.

Molecular Dynamics Simulation of Solidification of Pd-Ni Clusters with Different Nickel Content

Directory of Open Access Journals (Sweden)

Chen Gang

2014-01-01

Full Text Available Molecular dynamics simulation has been performed for investigating the glass transition of Pd-Ni alloy nanoparticles in the solidification process. The results showed that the Pd-Ni nanoparticles with composition far from pure metal should form amorphous structure more easily, which is in accordance with the results of the thermodynamic calculation. There are some regular and distorted fivefold symmetry in the amorphous Pd-Ni alloy nanoparticles. The nanoclusters with bigger difference value between formation enthalpies of solutions and glasses will transform to glass more easily than the other Pd-Ni alloy nanoclusters.

An Event-Driven Hybrid Molecular Dynamics and Direct Simulation Monte Carlo Algorithm

Energy Technology Data Exchange (ETDEWEB)

Donev, A; Garcia, A L; Alder, B J

2007-07-30

A novel algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with the solvent particles with hard core potentials. The algorithm uses event-driven molecular dynamics (MD) for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in event-driven algorithms, rather, the momentum and energy exchange in the solvent is determined stochastically using the Direct Simulation Monte Carlo (DSMC) method. The coupling between the solvent and the solute is consistently represented at the particle level, however, unlike full MD simulations of both the solvent and the solute, the spatial structure of the solvent is ignored. The algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard wall subjected to uniform shear. The algorithm closely reproduces full MD simulations with two orders of magnitude greater efficiency. Results do not confirm the existence of periodic (cycling) motion of the polymer chain.

Femtochemistry and femtobiology ultrafast dynamics in molecular science

CERN Document Server

Douhal, Abderrazzak

2002-01-01

This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

Science.gov (United States)

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of

Molecular dynamics simulation of ribosome jam

KAUST Repository

Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

2011-01-01

We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

DEFF Research Database (Denmark)

Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

2010-01-01

We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...

Structure and dynamics of solvated Ba(II) in dilute aqueous solution - an ab initio QM/MM MD approach

International Nuclear Information System (INIS)

Hofer, Thomas S.; Rode, Bernd M.; Randolf, Bernhard R.

2005-01-01

Structural properties of the hydrated Ba(II) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at double zeta HF quantum mechanical level. The first shell coordination number was found to be 9.3, and several other structural parameters such as angular distribution functions, radial distribution functions and tilt- and θ-angle distributions allowed the full characterization of the hydration structure of the Ba(II) ion in dilute aqueous solution. Velocity autocorrelation functions were used to calculate librational and vibrational motions, ion-ligand motions as well as reorientation times. Different dynamical parameters such as water reorientation, mean ligand residence time, the number of ligand exchange processes and rate constants were also analyzed and the ligand exchange rate constant for the first shell was determined as k = 5.3 x 10 10 s -1

Charge-dependent conformations and dynamics of pamam dendrimers revealed by neutron scattering and molecular dynamics

Science.gov (United States)

Wu, Bin

Neutron scattering and fully atomistic molecular dynamics (MD) are employed to investigate the structural and dynamical properties of polyamidoamine (PAMAM) dendrimers with ethylenediamine (EDA) core under various charge conditions. Regarding to the conformational characteristics, we focus on scrutinizing density profile evolution of PAMAM dendrimers as the molecular charge of dendrimer increases from neutral state to highly charged condition. It should be noted that within the context of small angle neutron scattering (SANS), the dendrimers are composed of hydrocarbon component (dry part) and the penetrating water molecules. Though there have been SANS experiments that studied the charge-dependent structural change of PAMAM dendrimers, their results were limited to the collective behavior of the aforementioned two parts. This study is devoted to deepen the understanding towards the structural responsiveness of intra-molecular polymeric and hydration parts separately through advanced contrast variation SANS data analysis scheme available recently and unravel the governing principles through coupling with MD simulations. Two kinds of acids, namely hydrochloric and sulfuric acids, are utilized to tune the pH condition and hence the molecular charge. As far as the dynamical properties, we target at understanding the underlying mechanism that leads to segmental dynamic enhancement observed from quasielstic neutron scattering (QENS) experiment previously. PAMAM dendrimers have a wealth of potential applications, such as drug delivery agency, energy harvesting medium, and light emitting diodes. More importantly, it is regarded as an ideal system to test many theoretical predictions since dendrimers conjugate both colloid-like globular shape and polymer-like flexible chains. This Ph.D. research addresses two main challenges in studying PAMAM dendrimers. Even though neutron scattering is an ideal tool to study this PAMAM dendrimer solution due to its matching temporal and

Dynamics of molecular superrotors in an external magnetic field

International Nuclear Information System (INIS)

Korobenko, Aleksey; Milner, Valery

2015-01-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

Science.gov (United States)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Kinetics from Replica Exchange Molecular Dynamics Simulations.

Science.gov (United States)

Stelzl, Lukas S; Hummer, Gerhard

2017-08-08

Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

DEFF Research Database (Denmark)

Papaleo, Elena

2015-01-01

that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

AceCloud: Molecular Dynamics Simulations in the Cloud.

Science.gov (United States)

Harvey, M J; De Fabritiis, G

2015-05-26

We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

Molecular dynamics studies of the conformation of sorbitol

Science.gov (United States)

Lerbret, A.; Mason, P.E.; Venable, R.M.; Cesàro, A.; Saboungi, M.-L.; Pastor, R.W.; Brady, J.W.

2009-01-01

Molecular dynamics simulations of a 3 m aqueous solution of D-sorbitol (also called D-glucitol) have been performed at 300 K, as well as at two elevated temperatures to promote conformational transitions. In principle, sorbitol is more flexible than glucose since it does not contain a constraining ring. However, a conformational analysis revealed that the sorbitol chain remains extended in solution, in contrast to the bent conformation found experimentally in the crystalline form. While there are 243 staggered conformations of the backbone possible for this open-chain polyol, only a very limited number were found to be stable in the simulations. Although many conformers were briefly sampled, only eight were significantly populated in the simulation. The carbon backbones of all but two of these eight conformers were completely extended, unlike the bent crystal conformation. These extended conformers were stabilized by a quite persistent intramolecular hydrogen bond between the hydroxyl groups of carbon C-2 and C-4. The conformational populations were found to be in good agreement with the limited available NMR data except for the C-2–C-3 torsion (spanned by the O-2–O-4 hydrogen bond), where the NMR data supports a more bent structure. PMID:19744646

Analytic solution of integral equations for molecular fluids

International Nuclear Information System (INIS)

Cummings, P.T.

1984-01-01

We review some recent progress in the analytic solution of integral equations for molecular fluids. The site-site Ornstein-Zernike (SSOZ) equation with approximate closures appropriate to homonuclear diatomic fluids both with and without attractive dispersion-like interactions has recently been solved in closed form analytically. In this paper, the close relationship between the SSOZ equation for homonuclear dumbells and the usual Ornstein-Zernike (OZ) equation for atomic fluids is carefully elucidated. This relationship is a key motivation for the analytic solutions of the SSOZ equation that have been obtained to date. (author)

Efficient parallel implementations of QM/MM-REMD (quantum mechanical/molecular mechanics-replica-exchange MD) and umbrella sampling: isomerization of H2O2 in aqueous solution.

Science.gov (United States)

Fedorov, Dmitri G; Sugita, Yuji; Choi, Cheol Ho

2013-07-03

An efficient parallel implementation of QM/MM-based replica-exchange molecular dynamics (REMD) as well as umbrella samplings techniques was proposed by adopting the generalized distributed data interface (GDDI). Parallelization speed-up of 40.5 on 48 cores was achieved, making our QM/MM-MD engine a robust tool for studying complex chemical dynamics in solution. They were comparatively used to study the torsional isomerization of hydrogen peroxide in aqueous solution. All results by QM/MM-REMD and QM/MM umbrella sampling techniques yielded nearly identical potentials of mean force (PMFs) regardless of the particular QM theories for solute, showing that the overall dynamics are mainly determined by solvation. Although the entropic penalty of solvent rearrangements exists in cisoid conformers, it was found that both strong intermolecular hydrogen bonding and dipole-dipole interactions preferentially stabilize them in solution, reducing the torsional free-energy barrier at 0° by about 3 kcal/mol as compared to that in gas phase.

Structure and dynamics of hydrated Fe(II) and Fe(III) ions. Quantum mechanical and molecular mechanical simulations

International Nuclear Information System (INIS)

Remsungnen, T.

2002-11-01

Classical molecular dynamics (MD) and combined em ab initio quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations have been performed to investigate structural, dynamical and energetical properties of Fe(II), and Fe(III) transition metal ions in aqueous solution. In the QM/MM-MD simulations the ion and its first hydration sphere were treated at the Hartree-Fock ab initio quantum mechanical level, while ab initio generated pair plus three-body potentials were employed for the remaining system. For the classical MD simulation the pair plus three-body potential were employed for all ion-water interactions. The coordination number of the first hydration shell is 100 % of 6 in both cases. The number of waters in the second hydration shell obtained from classical simulations are 13.4 and 15.1 for Fe(II) and Fe(III), respectively, while QM/MM-MD gives the values of 12.4 and 13.4 for Fe(II) and Fe(III). The energies of hydration obtained from MD and QM/MM-MD for Fe(II) are 520 and 500 kcal/mol, and for Fe(III) 1160 and 1100 kcal/mol respectively. The mean residence times of water in the second shell obtained from QM/MM-MD are 24 and 48 ps for Fe(II) and Fe(III), respectively. In contrast to the data obtained from classical MD simulation, the QM/MM-MD values are all in good agreement with the experimental data available. These investigations and results clearly indicate that many-body effects are essential for the proper description of all properties of the aqueous solution of both Fe(II) and Fe(III) ions. (author)

Molecular dynamics simulations of RNA motifs

Czech Academy of Sciences Publication Activity Database

Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

2002-01-01

Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

Monte Carlo-molecular dynamics simulations for two-dimensional magnets

International Nuclear Information System (INIS)

Kawabata, C.; takeuchi, M.; Bishop, A.R.

1985-01-01

A combined Monte Carlo-molecular dynamics simulation technique is used to study the dynamic structure factor on a square lattice for isotropic Heisenberg and planar classical ferromagnetic spin Hamiltonians

A molecular-thermodynamic model for polyelectrolyte solutions

Energy Technology Data Exchange (ETDEWEB)

Jiang, J.; Liu, H.; Hu, Y. [Thermodynamics Research Laboratory, East China University of Science and Technology, Shanghai 200237 (China); Prausnitz, J.M. [Department of Chemical Engineering, University of California, Berkeley, and Chemical Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)

1998-01-01

Polyelectrolyte solutions are modeled as freely tangent-jointed, charged hard-sphere chains and corresponding counterions in a continuum medium with permitivity {var_epsilon}. By adopting the sticky-point model, the Helmholtz function for polyelectrolyte solutions is derived through the r-particle cavity-correlation function (CCF) for chains of sticky, charged hard spheres. The r-CCF is approximated by a product of effective nearest-neighbor two-particle CCFs; these are determined from the hypernetted-chain and mean-spherical closures (HNC/MSA) inside and outside the hard core, respectively, for the integral equation theory for electrolytes. The colligative properties are given as explicit functions of a scaling parameter {Gamma} that can be estimated by a simple iteration procedure. Osmotic pressures, osmotic coefficients, and activity coefficients are calculated for model solutions with various chain lengths. They are in good agreement with molecular simulation and experimental results. {copyright} {ital 1998 American Institute of Physics.}

High hydrostatic pressure specifically affects molecular dynamics and shape of low-density lipoprotein particles

Science.gov (United States)

Golub, M.; Lehofer, B.; Martinez, N.; Ollivier, J.; Kohlbrecher, J.; Prassl, R.; Peters, J.

2017-04-01

Lipid composition of human low-density lipoprotein (LDL) and its physicochemical characteristics are relevant for proper functioning of lipid transport in the blood circulation. To explore dynamical and structural features of LDL particles with either a normal or a triglyceride-rich lipid composition we combined coherent and incoherent neutron scattering methods. The investigations were carried out under high hydrostatic pressure (HHP), which is a versatile tool to study the physicochemical behavior of biomolecules in solution at a molecular level. Within both neutron techniques we applied HHP to probe the shape and degree of freedom of the possible motions (within the time windows of 15 and 100 ps) and consequently the flexibility of LDL particles. We found that HHP does not change the types of motion in LDL, but influences the portion of motions participating. Contrary to our assumption that lipoprotein particles, like membranes, are highly sensitive to pressure we determined that LDL copes surprisingly well with high pressure conditions, although the lipid composition, particularly the triglyceride content of the particles, impacts the molecular dynamics and shape arrangement of LDL under pressure.

Molecular dynamics and Monte Carlo calculations in statistical mechanics

International Nuclear Information System (INIS)

Wood, W.W.; Erpenbeck, J.J.

1976-01-01

Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references

Hard sphere-like glass transition in eye lens α-crystallin solutions.

Science.gov (United States)

Foffi, Giuseppe; Savin, Gabriela; Bucciarelli, Saskia; Dorsaz, Nicolas; Thurston, George M; Stradner, Anna; Schurtenberger, Peter

2014-11-25

We study the equilibrium liquid structure and dynamics of dilute and concentrated bovine eye lens α-crystallin solutions, using small-angle X-ray scattering, static and dynamic light scattering, viscometry, molecular dynamics simulations, and mode-coupling theory. We find that a polydisperse Percus-Yevick hard-sphere liquid-structure model accurately reproduces both static light scattering data and small-angle X-ray scattering liquid structure data from α-crystallin solutions over an extended range of protein concentrations up to 290 mg/mL or 49% vol fraction and up to ca. 330 mg/mL for static light scattering. The measured dynamic light scattering and viscosity properties are also consistent with those of hard-sphere colloids and show power laws characteristic of an approach toward a glass transition at α-crystallin volume fractions near 58%. Dynamic light scattering at a volume fraction beyond the glass transition indicates formation of an arrested state. We further perform event-driven molecular dynamics simulations of polydisperse hard-sphere systems and use mode-coupling theory to compare the measured dynamic power laws with those of hard-sphere models. The static and dynamic data, simulations, and analysis show that aqueous eye lens α-crystallin solutions exhibit a glass transition at high concentrations that is similar to those found in hard-sphere colloidal systems. The α-crystallin glass transition could have implications for the molecular basis of presbyopia and the kinetics of molecular change during cataractogenesis.

Molecular Twister: A Game for Exploring Solution Chemistry †

OpenAIRE

Masonjones, Sawyer R.; Masonjones, Heather D.; Malone, Megan C.; Williams, Ann H.; Beemer, Margaret M.; Waggett, Rebecca J.

2014-01-01

pH is an essential biological concept with critical importance at various scales, from the molecular level, dealing with blood buffers, homeostasis, and proton gradients, all the way up to the ecosystem level, with soil chemistry and acid rain. However, pH is also a concept that spawns student misconceptions and misunderstanding in terms of what is happening in a solution on the atomic level. The Molecular Twister game, created for a Florida Department of Education funded professional develop...

Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties

Czech Academy of Sciences Publication Activity Database

Fojtíková, J.; Kalvoda, L.; Sedlák, Petr

2015-01-01

Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf

Nanotribology investigations with classical molecular dynamics

NARCIS (Netherlands)

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:

Hydration of amino acids: FTIR spectra and molecular dynamics studies.

Science.gov (United States)

Panuszko, Aneta; Adamczak, Beata; Czub, Jacek; Gojło, Emilia; Stangret, Janusz

2015-11-01

The hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results, molecular dynamics simulations of amino acids were performed. The structural-energetic characteristic of these solute-affected water molecules shows that, on average, water affected by amino acids forms stronger and shorter H-bonds than those in pure water. Differences in the influence of amino acids on water structure have been noticed. The effect of the hydrophobic side chain of an amino acid on the solvent interactions seems to be enhanced because of the specific cooperative coupling of water strong H-bond chain, connecting the carboxyl and amino groups, with the clathrate-like H-bond network surrounding the hydrocarbon side chain. The parameter derived from the spectral data, which corresponds to the contributions of the population of weak hydrogen bonds of water molecules which have been substituted by the stronger ones in the hydration sphere of amino acids, correlated well with the amino acid hydrophobicity indexes.

Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu, H.G.; Muckerman, J.T.

2010-06-01

The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

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.

Dynamics of polymers in a good solvent - a molecular dynamics study using the Connection Machine

International Nuclear Information System (INIS)

Shannon, S.R.; Choy, T.C.

1996-01-01

In recent times the use of molecular dynamics simulations has become an important tool in modelling and understanding the dynamics of interacting many-body systems. With recent advances in computing power it is now feasible to perform modelling of systems which contain a large number of interacting particles, and thus to simulate the behaviour of real systems reasonably. Our earlier discoveries of anomalous corrections to scaling behaviour of the Edward's polymer were applied to study the dynamical behaviour of two dimensional polymer systems - either a single chain immersed in a fluid, a pure polymer melt, or with any concentration of polymers in the fluid. By choosing a suitable interaction potential between the fluid particles and the monomers, we are able to study the experimentally observable time dependent structure factor of polymers in a good solvent. Simulations were performed using the Connection Machine CM5 supercomputer at the Australian National University which due to its fast multi- processor nearest neighbour communications facility, enables us to easily model large systems of at least 3000 fluid plus monomer particles. Our study is based on a finite difference solution of Newton's equations of motion i.e. the Verlet algorithm, and the results are used to test current theories of polymer dynamics, which were based primarily on the earlier models proposed by Rouse (1953) and Zimm (1956). In particular dynamical scaling predictions is scrutinised to examine the effects due to the anomalous corrections-to-scaling behaviour found in an earlier work using finite-size scaling analysis of Monte-Carlo data and now understood via a new perturbation concept

The role of molecular conformation and polarizable embedding for one- and two-photon absorption of disperse orange 3 in solution.

Science.gov (United States)

Silva, Daniel L; Murugan, N Arul; Kongsted, Jacob; Rinkevicius, Zilvinas; Canuto, Sylvio; Ågren, Hans

2012-07-19

Solvent effects on the one- and two-photon absorption (1PA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

Science.gov (United States)

Cawkwell, M J; Niklasson, Anders M N

2012-10-07

Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

An adaptive quantum mechanics/molecular mechanics method for the infrared spectrum of water: incorporation of the quantum effect between solute and solvent.

Science.gov (United States)

Watanabe, Hiroshi C; Banno, Misa; Sakurai, Minoru

2016-03-14

Quantum effects in solute-solvent interactions, such as the many-body effect and the dipole-induced dipole, are known to be critical factors influencing the infrared spectra of species in the liquid phase. For accurate spectrum evaluation, the surrounding solvent molecules, in addition to the solute of interest, should be treated using a quantum mechanical method. However, conventional quantum mechanics/molecular mechanics (QM/MM) methods cannot handle free QM solvent molecules during molecular dynamics (MD) simulation because of the diffusion problem. To deal with this problem, we have previously proposed an adaptive QM/MM "size-consistent multipartitioning (SCMP) method". In the present study, as the first application of the SCMP method, we demonstrate the reproduction of the infrared spectrum of liquid-phase water, and evaluate the quantum effect in comparison with conventional QM/MM simulations.

Molecular dispersion energy parameters for alkali and halide ions in aqueous solution

International Nuclear Information System (INIS)

Reiser, S.; Deublein, S.; Hasse, H.; Vrabec, J.

2014-01-01

Thermodynamic properties of aqueous solutions containing alkali and halide ions are determined by molecular simulation. The following ions are studied: Li + , Na + , K + , Rb + , Cs + , F − , Cl − , Br − , and I − . The employed ion force fields consist of one Lennard-Jones (LJ) site and one concentric point charge with a magnitude of ±1 e. The SPC/E model is used for water. The LJ size parameter of the ion models is taken from Deublein et al. [J. Chem. Phys. 136, 084501 (2012)], while the LJ energy parameter is determined in the present study based on experimental self-diffusion coefficient data of the alkali cations and the halide anions in aqueous solutions as well as the position of the first maximum of the radial distribution function of water around the ions. On the basis of these force field parameters, the electric conductivity, the hydration dynamics of water molecules around the ions, and the enthalpy of hydration is predicted. Considering a wide range of salinity, this study is conducted at temperatures of 293.15 and 298.15 K and a pressure of 1 bar

Modeling ramp compression experiments using large-scale molecular dynamics simulation.

Energy Technology Data Exchange (ETDEWEB)

Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

2011-10-01

Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

KAUST Repository

Neumann, Philipp; Tchipev, Nikola

2012-01-01

We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm

The MOLDY short-range molecular dynamics package

Science.gov (United States)

Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.

2011-12-01

measuring thermodynamic properities, diffusion, radiation damage, fracture, twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces. Solution method: Molecular dynamics involves integrating Newton's equations of motion. MOLDY uses verlet (for good energy conservation) or predictor-corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello-Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals. Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order- N scaling will fail. Different interatomic potential forms require recompilation of the code. Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects. Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop.

Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

KAUST Repository

Yoon, Seyoon; Monteiro, Paulo J.M.

2013-01-01

The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current

Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

DEFF Research Database (Denmark)

Toxvaerd, Søren

2001-01-01

Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

Thermal- and urea-induced unfolding processes of glutathione S-transferase by molecular dynamics simulation.

Science.gov (United States)

Li, Jiahuang; Chen, Yuan; Yang, Jie; Hua, Zichun

2015-05-01

The Schistosoma juponicum 26 kDa glutathione S-transferase (sj26GST) consists of the N-terminal domain (N-domain), containing three alpha-helices (named H1-H3) and four anti-parallel beta-strands (S1-S4), and the C-terminal domain (C-domain), comprising five alpha-helices (named H4-H8). In present work, molecular dynamics simulations and fluorescence spectroscopic were used to gain insights into the unfolding process of sj26GST. The molecular dynamics simulations on sj26GST subunit both in water and in 8 M urea were carried out at 300 K, 400 K and 500 K, respectively. Spectroscopic measurements were employed to monitor structural changes. Molecular dynamics simulations of sj26GST subunit induced by urea and temperature showed that the initial unfolding step of sj26GST both in water and urea occurred on N-domain, involving the disruption of helices H2, H3 and strands S3 and S4, whereas H6 was the last region exposed to solution and was the last helix to unfold. Moreover, simulations analyses combining with fluorescence and circular dichroism spectra indicated that N-domain could not fold independent, suggesting that correct folding of N-domain depended on its interactions with C-domain. We further proposed that the folding of GSTs could begin with the hydrophobic collapse of C-domain whose H4, H5, H6 and H7 could move close to each other and form a hydrophobic core, especially H6 wrapped in the hydrophobic center and beginning spontaneous formation of the helix. S3, S4, H3, and H2 could form in the wake of the interaction between C-domain and N-domain. The paper can offer insights into the molecular mechanism of GSTs unfolding. © 2014 Wiley Periodicals, Inc.

Knotted solutions for linear and nonlinear theories: Electromagnetism and fluid dynamics

Directory of Open Access Journals (Sweden)

Daniel W.F. Alves

2017-10-01

Full Text Available We examine knotted solutions, the most simple of which is the “Hopfion”, from the point of view of relations between electromagnetism and ideal fluid dynamics. A map between fluid dynamics and electromagnetism works for initial conditions or for linear perturbations, allowing us to find new knotted fluid solutions. Knotted solutions are also found to be solutions of nonlinear generalizations of electromagnetism, and of quantum-corrected actions for electromagnetism coupled to other modes. For null configurations, electromagnetism can be described as a null pressureless fluid, for which we can find solutions from the knotted solutions of electromagnetism. We also map them to solutions of Euler's equations, obtained from a type of nonrelativistic reduction of the relativistic fluid equations.

molecular dynamics simulations and quantum chemical calculations

African Journals Online (AJOL)

ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.

Invariant molecular-dynamics approach to structural phase transitions

International Nuclear Information System (INIS)

Wentzcovitch, R.M.

1991-01-01

Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

International Nuclear Information System (INIS)

Aradi, Balint; Frauenheim, Thomas

2015-01-01

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology

Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

Science.gov (United States)

Dizkirici, Ayten; Tekpinar, Mustafa

2015-03-01

GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

Science.gov (United States)

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

NMR investigations of molecular dynamics

Science.gov (United States)

Palmer, Arthur

2011-03-01

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

Hydration dynamics near a model protein surface

International Nuclear Information System (INIS)

Russo, Daniela; Hura, Greg; Head-Gordon, Teresa

2003-01-01

The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering and molecular dynamics simulation for both the completely deuterated and completely hydrogenated leucine monomer. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational water dynamics are analyzed in a first approximation with a jump diffusion model. At the highest solute concentrations, the hydration water dynamics is significantly suppressed and characterized by a long residential time and a slow diffusion coefficient. The analysis of the more dilute concentration solutions takes into account the results of the 2.0M solution as a model of the first hydration shell. Subtracting the first hydration layer based on the 2.0M spectra, the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis shows spatially heterogeneous dynamics at high concentration that becomes homogeneous at more dilute concentrations. We discuss the hydration dynamics results of this model protein system in the context of glassy systems, protein function, and protein-protein interfaces

Jacobian elliptic wave solutions in an anharmonic molecular crystal model

International Nuclear Information System (INIS)

Teh, C.G.R.; Lee, B.S.; Koo, W.K.

1997-07-01

Explicit Jacobian elliptic wave solutions are found in the anharmonic molecular crystal model for both the continuum limit and discrete modes. This class of wave solutions include the famous pulse-like and kink-like solitary modes. We would also like to report on the existence of some highly discrete staggered solitary wave modes not found in the continuum limit. (author). 9 refs, 1 fig

Proteins in solution: Fractal surfaces in solutions

Directory of Open Access Journals (Sweden)

R. Tscheliessnig

2016-02-01

Full Text Available The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly. Molecular dynamics simulation, as an appropriate computational tool for studying the hydration shell of proteins, is also discussed. The concept of protein surfaces with fractal dimensions is elaborated. We finish by exposing an experimental (using small angle X-ray scattering and a computer simulation case study, which are meant as demonstrations of the possibilities we have at hand for investigating the delicate interfaces that connect (and divide protein molecules and the neighboring electrolyte solution.

Excitation dynamics and relaxation in a molecular heterodimer

International Nuclear Information System (INIS)

Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.

2012-01-01

Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.

The nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Hoover, W.G.

1992-03-01

MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments

Understanding flocculation mechanism of graphene oxide for organic dyes from water: Experimental and molecular dynamics simulation

Directory of Open Access Journals (Sweden)

Jun Liu

2015-11-01

Full Text Available Flocculation treatment processes play an important role in water and wastewater pretreatment. Here we investigate experimentally and theoretically the possibility of using graphene oxide (GO as a flocculant to remove methylene blue (MB from water. Experimental results show that GO can remove almost all MB from aqueous solutions at its optimal dosages and molecular dynamics simulations indicate that MB cations quickly congregate around GO in water. Furthermore, PIXEL energy contribution analysis reveals that most of the strong interactions between GO and MB are of a van der Waals (London dispersion character. These results offer new insights for shedding light on the molecular mechanism of interaction between GO and organic pollutants.

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum-classical approximation. II. Proton transfer reaction in non-polar solvent

Science.gov (United States)

Kojima, H.; Yamada, A.; Okazaki, S.

2015-05-01

The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum-classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates is reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute-solvent interactions.

Reaction dynamics of molecular hydrogen on silicon surfaces

DEFF Research Database (Denmark)

Bratu, P.; Brenig, W.; Gross, A.

1996-01-01

of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...

A Long-Range Electric Field Solver for Molecular Dynamics Based on Atomistic-to-Continuum Modeling.

Science.gov (United States)

Templeton, Jeremy A; Jones, Reese E; Lee, Jonathan W; Zimmerman, Jonathan A; Wong, Bryan M

2011-06-14

Understanding charge transport processes at a molecular level is currently hindered by a lack of appropriate models for incorporating nonperiodic, anisotropic electric fields in molecular dynamics (MD) simulations. In this work, we develop a model for including electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and the algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. Our model represents the electric potential on a FE mesh satisfying a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagate to each atom through modified forces. The method is verified using simulations where analytical solutions are known or comparisons can be made to existing techniques. In addition, a calculation of a salt water solution in a silicon nanochannel is performed to demonstrate the method in a target scientific application in which ions are attracted to charged surfaces in the presence of electric fields and interfering media.

State-to-state dynamics of molecular energy transfer

Energy Technology Data Exchange (ETDEWEB)

Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

1993-12-01

The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

Line-shape theory and molecular dynamics in collision-induced light scattering

International Nuclear Information System (INIS)

Balucani, U.; Tognetti, V.; Vallauri, R.

1979-01-01

Molecular-dynamics studies in argon at 148 amagats are presented for gaining information on the dynamical properties responsible for the depolarized light scattering from simple fluids. The total and pair-correlation functions are computed within the simple dipole--induced-dipole model of polarizability anisotropy. The pair spectral shape is derived. These results are compared with a theoretical analysis based on a continued-fraction approach. The necessary frequency moments are calculated both in the low-density limit and taking into account first-order density corrections, and compared with the molecular-dynamics data. The agreement between the theoretical spectra and molecular-dynamics data shows the validity of the memory-function approach. The comparison with the real experimental results allows one to test the relevant physical contributions to the polarizability anisotropy

Dynamic characterization of hydrophobic and hydrophilic solutes in oleic-acid enhanced transdermal delivery using two-photon fluorescence microscopy

Energy Technology Data Exchange (ETDEWEB)

Tseng, Te-Yu; Yang, Chiu-Sheng; Chen, Yang-Fang [Department of Physics, National Taiwan University, Taipei, Taiwan (China); Tsai, Tsung-Hua [Department of Dermatology, Far Eastern Memorial Hospital, New Taipei City, Taiwan (China); Dong, Chen-Yuan, E-mail: cydong@phys.ntu.edu.tw [Department of Physics, National Taiwan University, Taipei, Taiwan (China); Center for Quantum Science and Engineering, National Taiwan University, Taipei, Taiwan (China); Center for Optoelectronic Biomedicine, National Taiwan University, Taipei, Taiwan (China)

2014-10-20

In this letter, we propose an efficient methodology of investigating dynamic properties of sulforhodamine B and rhodamine B hexyl ester molecules transporting across ex-vivo human stratum corneum with and without oleic acid enhancement. Three-dimensional, time-lapse fluorescence images of the stratum corneum can be obtained using two-photon fluorescence microscopy. Furthermore, temporal quantifications of transport enhancements in diffusion parameters can be achieved with the use of Fick's second law. Dynamic characterization of solutes transporting across the stratum corneum is an effective method for understanding transient phenomena in transdermal delivery of probe molecules, leading to improved delivery strategies of molecular species for therapeutic purposes.

Coulomb interactions via local dynamics: a molecular-dynamics algorithm

International Nuclear Information System (INIS)

Pasichnyk, Igor; Duenweg, Burkhard

2004-01-01

We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

DEFF Research Database (Denmark)

Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

2012-01-01

In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

High-Performance First-Principles Molecular Dynamics for Predictive Theory and Modeling

Energy Technology Data Exchange (ETDEWEB)

Gygi, Francois [Univ. of California, Davis, CA (United States). Dept. of Computer Science; Galli, Giulia [Univ. of Chicago, IL (United States); Schwegler, Eric [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2017-12-03

This project focused on developing high-performance software tools for First-Principles Molecular Dynamics (FPMD) simulations, and applying them in investigations of materials relevant to energy conversion processes. FPMD is an atomistic simulation method that combines a quantum-mechanical description of electronic structure with the statistical description provided by molecular dynamics (MD) simulations. This reliance on fundamental principles allows FPMD simulations to provide a consistent description of structural, dynamical and electronic properties of a material. This is particularly useful in systems for which reliable empirical models are lacking. FPMD simulations are increasingly used as a predictive tool for applications such as batteries, solar energy conversion, light-emitting devices, electro-chemical energy conversion devices and other materials. During the course of the project, several new features were developed and added to the open-source Qbox FPMD code. The code was further optimized for scalable operation of large-scale, Leadership-Class DOE computers. When combined with Many-Body Perturbation Theory (MBPT) calculations, this infrastructure was used to investigate structural and electronic properties of liquid water, ice, aqueous solutions, nanoparticles and solid-liquid interfaces. Computing both ionic trajectories and electronic structure in a consistent manner enabled the simulation of several spectroscopic properties, such as Raman spectra, infrared spectra, and sum-frequency generation spectra. The accuracy of the approximations used allowed for direct comparisons of results with experimental data such as optical spectra, X-ray and neutron diffraction spectra. The software infrastructure developed in this project, as applied to various investigations of solids, liquids and interfaces, demonstrates that FPMD simulations can provide a detailed, atomic-scale picture of structural, vibrational and electronic properties of complex systems

A model of lipid-free apolipoprotein A-I revealed by iterative molecular dynamics simulation.

Directory of Open Access Journals (Sweden)

Xing Zhang

Full Text Available Apolipoprotein A-I (apo A-I, the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS. Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore, by integrating various experimental results, we proposed a new structural model for lipid-free apo A-I, which contains a bundled four-helix N-terminal domain (1-192 that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193-243. This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.

Nuclear spin dynamics in soap solutions and related systems

International Nuclear Information System (INIS)

Bloom, M.

1973-01-01

Soap molecules consist of a hydrophilic head and a hydrophobic lipid tail. For example, potassium laureate, the soap molecule on which the most complete study of nuclear spin dynamics has been made has the chemical formula KCOO(CH 2 ) 10 CH 3 . High concentration (greater than or approximately equal to 20% soap molecules by weight) soap solutions in water form ordered, liquid crystal structures in which the polar heads are arranged on regular surfaces which define a lattice having long range order. The soap molecules diffuse very rapidly parallel to the surfaces and undergo rapid conformational changes. Studies of T 1 , Tsub(1p) and Tsub(D) have indicated a wide spectrum of correlation times associated with these changes. Because of the orientational order of the soap molecules, the dipolar interactions between nuclear spins on a single molecule are not averaged to zero by the molecular motions. Thus, it is possible to use NMR techniques normally applied to solids (i.e. transfer of Zeeman into dipolar order, etc.) to study their static and dynamical properties. These systems are unusual in that they are basically one-dimensional systems in which the effective, time-averaged, dipolar coupling constants become progressively stronger for protons closer to the polar heads ot the molecules. A review will be presented of the experimental and theoretical NMR work performed on such systems to date. (author)

[UO2(NH3)5]Br2·NH3: synthesis, crystal structure, and speciation in liquid ammonia solution by first-principles molecular dynamics simulations.

Science.gov (United States)

Woidy, Patrick; Bühl, Michael; Kraus, Florian

2015-04-28

Pentaammine dioxido uranium(VI) dibromide ammonia (1/1), [UO2(NH3)5]Br2·NH3, was synthesized in the form of yellow crystals by the reaction of uranyl bromide, UO2Br2, with dry liquid ammonia. The compound crystallizes orthorhombic in space group Cmcm and is isotypic to [UO2(NH3)5]Cl2·NH3 with a = 13.2499(2), b = 10.5536(1), c = 8.9126(1) Å, V = 1246.29(3) Å(3) and Z = 4 at 123 K. The UO2(2+) cation is coordinated by five ammine ligands and the coordination polyhedron can be best described as pentagonal bipyramid. Car-Parrinello molecular dynamics simulations are reported for [UO2(NH3)5](2+) in the gas phase and in liquid NH3 solution (using the BLYP density functional). According to free-energy simulations, solvation by ammonia has only a small effect on the uranyl-NH3 bond strength.

Molecular computation: RNA solutions to chess problems.

Science.gov (United States)

Faulhammer, D; Cukras, A R; Lipton, R J; Landweber, L F

2000-02-15

We have expanded the field of "DNA computers" to RNA and present a general approach for the solution of satisfiability problems. As an example, we consider a variant of the "Knight problem," which asks generally what configurations of knights can one place on an n x n chess board such that no knight is attacking any other knight on the board. Using specific ribonuclease digestion to manipulate strands of a 10-bit binary RNA library, we developed a molecular algorithm and applied it to a 3 x 3 chessboard as a 9-bit instance of this problem. Here, the nine spaces on the board correspond to nine "bits" or placeholders in a combinatorial RNA library. We recovered a set of "winning" molecules that describe solutions to this problem.

Association of radionuclides with different molecular size fractions in soil solution: implications for plant uptake

International Nuclear Information System (INIS)

Nisbet, A.F.; Shaw, S.; Salbu, B.

1993-01-01

The feasibility of using hollow fibre ultrafiltration to determine the molecular size distribution of radionuclides in soil solution was investigated. The physical and chemical composition of soil plays a vital role in determining radionuclide uptake by plant roots. Soil solution samples were extracted from loam, peat and sand soils that had been artificially contaminated with 137 Cs, 90 Sr, 239 Pu and 241 Am six years previously as part of a five-year lysimeter study on radionuclide uptake to crops. Ultrafiltration of soil solution was performed using hollow fibre cartridges with a nominal molecular weight cut off of 3 and 10 kD. The association of 137 Cs, 90 Sr, 239 Pu and 241 Am with different molecular size fractions of the soil solution is discussed in terms of radionuclide bioavailability to cabbage grown in the same three soils. 137 Cs and 90 Sr were present in low molecular weight forms and as such were mobile in soil and potentially available for uptake by the cabbage. In contrast, a large proportion (61-87%) of the 239 Pu and 241 Am were associated with colloidal and high molecular weight material and therefore less available for uptake by plant roots. The contribution from low molecular weight species of 239 Pu and 241 Am to the total activity in soil solution decreased in the order loam ≥ peat ≥ sand. Association of radionuclides with low molecular weight species of less than 3 kD did not, however, automatically imply availability to plants. (author)

Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

Science.gov (United States)

Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

2016-05-12

An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data.

A domain specific language for performance portable molecular dynamics algorithms

Science.gov (United States)

Saunders, William Robert; Grant, James; Müller, Eike Hermann

2018-03-01

Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

Ab initio molecular dynamics in a finite homogeneous electric field.

Science.gov (United States)

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

MOLECULAR DESCRIPTION OF ELECTROLYTE SOLUTION IN A CARBON AEROGEL ELECTRODE

Directory of Open Access Journals (Sweden)

A.Kovalenko

2003-01-01

Full Text Available We develop a molecular theory of aqueous electrolyte solution sorbed in a nanoporous carbon aerogel electrode, based on the replica reference interaction site model (replica RISM for realistic molecular quenched-annealed systems. We also briefly review applications of carbon aerogels for supercapacitor and electrochemical separation devices, as well as theoretical and computer modelling of disordered porous materials. The replica RISM integral equation theory yields the microscopic properties of the electrochemical double layer formed at the surface of carbon aerogel nanopores, with due account of chemical specificities of both sorbed electrolyte and carbon aerogel material. The theory allows for spatial disorder of aerogel pores in the range from micro- to macroscopic size scale. We considered ambient aqueous solution of 1 M sodium chloride sorbed in two model nanoporous carbon aerogels with carbon nanoparticles either arranged into branched chains or randomly distributed. The long-range correlations of the carbon aerogel nanostructure substantially affect the properties of the electrochemical double layer formed by the solution sorbed in nanopores.

Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Bresme, F.; Armstrong, J.

2014-01-01

We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation

Crossover to entangled dynamics in polymer solutions and melts

International Nuclear Information System (INIS)

Schweizer, K.S.; Szamel, G.

1995-01-01

A statistical dynamical theory of the crossover from unentangled Rouse dynamics to entangled behavior is constructed for chain polymer solutions and melts. Both time and spatial crossovers in long chain fluids, and the degree of polymerization crossover for short polymers, are treated. The analysis is based on a microscopic theory of the perturbative dynamical corrections to Rouse theory arising from chain connectivity and intermolecular excluded volume forces. The dependence of crossover properties such as the plateau shear modulus and entanglement time and length scale on solution density, solvent quality, and chain statistical segment length are derived by combining the dynamical theory with equilibrium liquid state integral equation methods. Scaling relations are obtained which appear to be in general accord with most experiments on both solutions and melts. The physical origin of the predicted scaling behaviors is the fractional power law temporal decay of the entanglement friction memory function on intermediate time scales, and power law reduced density dependence of the equilibrium force correlations. The theory is also applied to compute the dependence of the chain normal mode relaxation times on polymer density and chain length. Favorable qualitative comparisons with recent neutron spin echo experiments are made. copyright 1995 American Institute of Physics

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

Science.gov (United States)

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Fermionic molecular dynamics for colliding and decaying nuclei

International Nuclear Information System (INIS)

Feldmeier, H.; Schnack, J.

1993-11-01

Fermionic Molecular Dynamics models a system of fermions by means of a trial many-body state composed of an antisymmetrized product of single-particle states which are localized gaussians in coordinate and momentum space. The parameters specifying them are the analogue to the variables in classical molecular dynamics. The time-dependent variational principle yields the equations of motion which are solved for collisions of 12 C+ 12 C and deexcitations of 12 C. The collisions show a great variety of phenomena including explosion, sequential fragmentation and multifragmentation. The deexcitation for nuclei with E * /A ∼ 5MeV is dominated by particle evaporation on time scales of the order of 10 -20 s or longer. (orig.)

Optical spectra and lattice dynamics of molecular crystals

CERN Document Server

Zhizhin, GN

1995-01-01

The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

Full Dynamic Analysis of Mooring Solution Candidates - First Iteration

DEFF Research Database (Denmark)

Thomsen, Jonas Bjerg; Ferri, Francesco

This report covers an initial full dynamic analysis of the mooring solutions for the four wave energy converters in the project “Mooring Solutions for Large Wave Energy Converters”. The analysis tends to provide the first understanding of the layouts and provide discussion on what parameters that...

Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids

International Nuclear Information System (INIS)

De Leeuw, S.W.; Brakkee, M.J.D.

1990-01-01

Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations.

Science.gov (United States)

Sosso, Gabriele C; Chen, Ji; Cox, Stephen J; Fitzner, Martin; Pedevilla, Philipp; Zen, Andrea; Michaelides, Angelos

2016-06-22

The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments.

Partition Coefficients of Organic Molecules in Squalane and Water/Ethanol Mixtures by Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Lundsgaard, Rasmus; Kontogeorgis, Georgios; Economou, Ioannis G.

2011-01-01

coefficient can be estimated for both a small hydrophilic and a hydrophobic organic molecules between squalane (used here to mimic low density poly ethylene) and water/ethanol solutes using thermodynamic integration to calculate the free energy of solvation. Molecular dynamics simulations are performed, using...... the GROMACS software, by slowly decoupling of firstly the electrostatic and then the Lennard–Jones interactions between molecules in the simulation box. These calculations depend very much on the choice of force field. Two force fields have been tested in this work, the TraPPE-UA (united-atom) and the OPLS...

Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

Energy Technology Data Exchange (ETDEWEB)

Lambert, F

2007-08-15

The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

Science.gov (United States)

Cooke, Ben; Schmidler, Scott C

2008-10-28

We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.

Non-linear dynamics and alternating 'flip' solutions in ferrofluidic Taylor-Couette flow

Science.gov (United States)

Altmeyer, Sebastian

2018-04-01

This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow - flow confined between two concentric independently rotating cylinders. We detected alternating 'flip' solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion.

Orthonormal Wavelet Bases for Quantum Molecular Dynamics

International Nuclear Information System (INIS)

Tymczak, C.; Wang, X.

1997-01-01

We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society

Non-Adiabatic Molecular Dynamics Methods for Materials Discovery

Energy Technology Data Exchange (ETDEWEB)

Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)

2017-04-04

The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations of vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.

Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes

NARCIS (Netherlands)

Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes

2007-01-01

This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the

Molecular dynamics for reactions of heterogeneous catalysis

NARCIS (Netherlands)

Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

1991-01-01

An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

Static and dynamic light scattering studies on dilute polyrotaxane solutions

International Nuclear Information System (INIS)

Kume, Tetsuya; Sakai, Yasuhiro; Mayumi, Koichi; Kidowaki, Masatoshi; Yokoyama, Hideaki; Ito, Kohzo; Araki, Jun

2009-01-01

Static and dynamic light scattering measurements were performed for dilute polyrotaxane solutions in different types of solvent systems, i.e. dimethylacetamide (DMAc) or dimethylformamide (DMF) containing 1-6 wt% lithium chloride (LiCl), 1 M aqueous sodium hydroxide (NaOH) and dimethylsulfoxide (DMSO). No aggregation of the polyrotaxane in DMF/LiCl was confirmed in the present study. Radius of gyration of the dissolved polyrotaxane was largest in NaOHaq., followed by values in amide solvents/LiCl and that in DMSO, and was probably dominated not by Coulombic repulsion but by the mutual affinity between solvent and polyrotaxane. Ratio of radius of gyration to hydrodynamic radius suggested the flexible random-coiled conformation in DMSO and relatively more extended, semi-flexible ones in amide solvents/LiCl and NaOHaq. The obtained values of second virial coefficient and weight average molecular weight seemed to be affected by a potential change in differential refractive index increments, caused by selective macrocationization or ionization.

Static and dynamic light scattering studies on dilute polyrotaxane solutions

Science.gov (United States)

Kume, Tetsuya; Araki, Jun; Sakai, Yasuhiro; Mayumi, Koichi; Kidowaki, Masatoshi; Yokoyama, Hideaki; Ito, Kohzo

2009-08-01

Static and dynamic light scattering measurements were performed for dilute polyrotaxane solutions in different types of solvent systems, i.e. dimethylacetamide (DMAc) or dimethylformamide (DMF) containing 1-6 wt% lithium chloride (LiCl), 1 M aqueous sodium hydroxide (NaOH) and dimethylsulfoxide (DMSO). No aggregation of the polyrotaxane in DMF/LiCl was confirmed in the present study. Radius of gyration of the dissolved polyrotaxane was largest in NaOHaq., followed by values in amide solvents/LiCl and that in DMSO, and was probably dominated not by Coulombic repulsion but by the mutual affinity between solvent and polyrotaxane. Ratio of radius of gyration to hydrodynamic radius suggested the flexible random-coiled conformation in DMSO and relatively more extended, semi-flexible ones in amide solvents/LiCl and NaOHaq. The obtained values of second virial coefficient and weight average molecular weight seemed to be affected by a potential change in differential refractive index increments, caused by selective macrocationization or ionization.

Dynamic Beam Solutions for Real-Time Simulation and Control Development of Flexible Rockets

Science.gov (United States)

Su, Weihua; King, Cecilia K.; Clark, Scott R.; Griffin, Edwin D.; Suhey, Jeffrey D.; Wolf, Michael G.

2016-01-01

In this study, flexible rockets are structurally represented by linear beams. Both direct and indirect solutions of beam dynamic equations are sought to facilitate real-time simulation and control development for flexible rockets. The direct solution is completed by numerically integrate the beam structural dynamic equation using an explicit Newmark-based scheme, which allows for stable and fast transient solutions to the dynamics of flexile rockets. Furthermore, in the real-time operation, the bending strain of the beam is measured by fiber optical sensors (FOS) at intermittent locations along the span, while both angular velocity and translational acceleration are measured at a single point by the inertial measurement unit (IMU). Another study in this paper is to find the analytical and numerical solutions of the beam dynamics based on the limited measurement data to facilitate the real-time control development. Numerical studies demonstrate the accuracy of these real-time solutions to the beam dynamics. Such analytical and numerical solutions, when integrated with data processing and control algorithms and mechanisms, have the potential to increase launch availability by processing flight data into the flexible launch vehicle's control system.

Molecular dynamics simulations on PGLa using NMR orientational constraints

Energy Technology Data Exchange (ETDEWEB)

Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

2015-11-15

NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

Chemical structure and dynamics: Annual report 1993

Energy Technology Data Exchange (ETDEWEB)

Colson, S.D.

1994-07-01

The Chemical Structure and Dynamics program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally-important interfaces. The research program is built around the established relationship between structure, thermodynamics, and kinetics. This research effort continues to evolve into a program of rigorous studies of fundamental molecular processes in model systems (e.g., well-characterized surfaces, single-component solutions, clusters, and biological molecules), and studies of complex systems found in the environment. Experimental studies of molecular and supramolecular structures and thermodynamics are key to understanding the nature of matter, and lead to direct comparison with computational results. Kinetic and mechanistic measurements, combined with real-time dynamics measurements of atomic and molecular motions during chemical reactions, provide for a molecular-level description of chemical reactions. The anticipated results of this work are the achievement of a quantitative understanding of chemical processes at complex interfaces, the development of new techniques for the detection and measurement of species at such interfaces, and the interpretation and extrapolation of the observations in terms of models of interfacial chemistry. The Chemical Structure and Dynamics research program includes five areas described in detail in this report: Reaction mechanisms at solid interfaces; Solution and solution interfaces; Structure and dynamics of biological systems; Analytical methods development; and atmospheric chemistry. Extended abstracts are presented for 23 studies.

Molecular dynamics simulations

International Nuclear Information System (INIS)

Alder, B.J.

1985-07-01

The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs

A new algorithm for extended nonequilibrium molecular dynamics simulations of mixed flow

NARCIS (Netherlands)

Hunt, T.A.; Hunt, Thomas A.; Bernardi, Stefano; Todd, B.D.

2010-01-01

In this work, we develop a new algorithm for nonequilibrium molecular dynamics of fluids under planar mixed flow, a linear combination of planar elongational flow and planar Couette flow. To date, the only way of simulating mixed flow using nonequilibrium molecular dynamics techniques was to impose

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

NARCIS (Netherlands)

van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J

2012-01-01

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations

NARCIS (Netherlands)

van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.

2012-01-01

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

Molecular sieves as dehydrating agent of nonaqueous solutions of rare earths

International Nuclear Information System (INIS)

Kuya, M.K.; Mello Filho, A.E.C. de; Oliveira, D. de

1982-01-01

Systematic studies on drying solutions of hydrated lanthanide perchlorate salts in acetonitrile and ethanol, with 3A molecular sieves, are performed. Most of water is removed in the first hours period (about 70% in 2hs). Ion exchange process is negligible in ethanol but appreciable in acetonitrile solutions. This drying process may be important during the synthesis of lanthanide coordination compounds, since the success of preparation depends often, on the elimination or reduction of water present in the starting lanthanide solutions. (Author) [pt

Reaction dynamics in polyatomic molecular systems

Energy Technology Data Exchange (ETDEWEB)

Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01

The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

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...

Implementation of surface hopping molecular dynamics using semiempirical methods

International Nuclear Information System (INIS)

Fabiano, E.; Keal, T.W.; Thiel, W.

2008-01-01

A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained

Ab Initio molecular dynamics with excited electrons

NARCIS (Netherlands)

Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

1994-01-01

A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

Molecular dynamics coupled with a virtual system for effective conformational sampling.

Science.gov (United States)

Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

2018-07-15

An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

International Nuclear Information System (INIS)

Mendez, Derek; Watkins, Herschel; Qiao, Shenglan; Raines, Kevin S.; Lane, Thomas J.

2016-01-01

During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlined for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. Finally, it is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.

Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

Science.gov (United States)

Shekhar, Adarsh

Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

Molecular dynamics as a method to gain understanding in questions concerning montmorillonite

International Nuclear Information System (INIS)

Seppaelae, A.; Vaari, J.; Puhakka, E.; Tanhua-Tyrkkoe, M.; Olin, M.; Kasa, S.

2012-01-01

Document available in extended abstract form only. Bentonite is one of the main material components to be used in the KBS-3 concept for safe disposal of spent nuclear fuel. The functional material in bentonite giving its beneficial properties is montmorillonite mineral. Montmorillonite consists of two completely different components: one nano-metre thick and approximately 200-400 nano-metres wide mineral layers carrying constant charge and charge compensating cations very near the mineral surfaces. The first component is more of a passive component while the second can absorb water molecules and change the cationic composition. In addition to montmorillonite bentonite usually contains some salts dissolved into water and accessory minerals. Any bulk bentonite is formed from these components via many scales of which structure is not yet fully known to science. Therefore the beneficial macroscopic properties of bentonite are assumed to follow from the nano-level structure and reactions. In safety studies of spent fuel disposal the time span to be considered extends beyond a hundred thousand years making any straightforward experimenting impossible. However, by modelling it is possible to study even very long periods of time. Unfortunately the model data and reactions are at least implicitly based on our short term experiments and may therefore be biased in some way. One possible solution to this may be the application of molecular chemistry or dynamics to construct the basis for our modelling studies. We have applied molecular chemistry on surface properties of kaolinite clay and biotite mineral but molecular dynamics is a new type of modelling for us. We believe that (during the coming ten years) molecular dynamics could make it easier to understand for example the following topics: How do charge compensating (exchanged) and aqueous cations interact? Why does water expand montmorillonite during wetting? Exact mechanism? How does water leave montmorillonite during

Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu H. G.; Muckerman, J.T.

2012-05-29

The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

The quantum Rabi model: solution and dynamics

International Nuclear Information System (INIS)

Xie, Qiongtao; Zhong, Honghua; Lee, Chaohong; Batchelor, Murray T

2017-01-01

This article presents a review of recent developments on various aspects of the quantum Rabi model. Particular emphasis is given on the exact analytic solution obtained in terms of confluent Heun functions. The analytic solutions for various generalisations of the quantum Rabi model are also discussed. Results are also reviewed on the level statistics and the dynamics of the quantum Rabi model. The article concludes with an introductory overview of several experimental realisations of the quantum Rabi model. An outlook towards future developments is also given. (topical review)

Molecular dynamics simulation of self-diffusion coefficients for liquid metals

International Nuclear Information System (INIS)

Ju Yuan-Yuan; Zhang Qing-Ming; Gong Zi-Zheng; Ji Guang-Fu

2013-01-01

The temperature-dependent coefficients of self-diffusion for liquid metals are simulated by molecular dynamics methods based on the embedded-atom-method (EAM) potential function. The simulated results show that a good inverse linear relation exists between the natural logarithm of self-diffusion coefficients and temperature, though the results in the literature vary somewhat, due to the employment of different potential functions. The estimated activation energy of liquid metals obtained by fitting the Arrhenius formula is close to the experimental data. The temperature-dependent shear-viscosities obtained from the Stokes—Einstein relation in conjunction with the results of molecular dynamics simulation are generally consistent with other values in the literature. (atomic and molecular physics)

A Comparative Study of [CaEDTA](2-) and [MgEDTA](2-): Structural and Dynamical Insights from Quantum Mechanical Charge Field Molecular Dynamics.

Science.gov (United States)

Tirler, Andreas O; Hofer, Thomas S

2015-07-09

Structure and dynamics of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution have been investigated via quantum mechanical/molecular mechanical (QM/MM) simulations. While for the first a 6-fold octahedral complex has been observed, the presence of an additional coordinating water ligand has been observed in the latter case. Because of rapidly exchanging water molecules, this 7-fold coordination complex was found to form pentagonal bipyramidal as well as capped trigonal prismatic configurations along the simulation interchanging on the picosecond time scale. Also in the case of [MgEDTA](2-) a trigonal prismatic configuration has been observed for a very short time period of approximately 1 ps. This work reports for the first time the presence of trigonal prismatic structures observed in the coordination sphere of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution. In addition to the detailed characterization of structure and dynamics of the systems, the prediction of the associated infrared spectra indicates that the ion-water vibrational mode found at approximately 250 cm(-1) provides a distinctive measure to experimentally detect the presence of the coordinating water molecule via low-frequency IR setups.

Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Federica Chiappori

Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.

Catalysis and communication in dynamic molecular networks

NARCIS (Netherlands)

Fanlo Virgos, Hugo

2015-01-01

The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity

Molecular dynamics study of atomic displacements in disordered solid alloys

Science.gov (United States)

Puzyrev, Yevgeniy S.

The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

Science.gov (United States)

Chen, Wei; Shen, Jana K

2014-10-15

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma. Copyright © 2014 Wiley Periodicals, Inc.

Elucidation of the structure of organic solutions in solvent extraction by combining molecular dynamics and X-ray scattering

International Nuclear Information System (INIS)

Ferru, G.; Gomes Rodrigues, D.; Berthon, L.; Guilbaud, P.; Diat, O.; Bauduin, P.

2014-01-01

Knowledge of the supramolecular structure of the organic phase containing amphiphilic ligand molecules is mandatory for full comprehension of ionic separation during solvent extraction. Existing structural models are based on simple geometric aggregates, but no consensus exists on the interaction potentials. Herein, we show that molecular dynamics crossed with scattering techniques offers key insight into the complex fluid involving weak interactions without any long range ordering. Two systems containing mono- or diamide extractants in heptane and contacted with an aqueous phase were selected as examples to demonstrate the advantages of coupling the two approaches for furthering fundamental studies on solvent extraction. (authors)

Bridging the gap between molecular dynamics simulations and phase-field modelling: dynamics of a [NixZr1-x]liquid-Zrcrystal solidification front

International Nuclear Information System (INIS)

Danilov, Denis; Nestler, Britta; Guerdane, Mohammed; Teichler, Helmar

2009-01-01

Results are presented from phase-field modelling and molecular dynamics simulations concerning the relaxation dynamics in a finite-temperature two-phase crystal-liquid sample subjected to an abrupt temperature drop. Relaxation takes place by propagation of the solidification front under formation of a spatially varying concentration profile in the melt. The molecular dynamics simulations are carried out with an interatomic model appropriate for the NiZr alloy system and provide the thermophysical data required for setting up the phase-field simulations. Regarding the concentration profile and velocity of the solidification front, best agreement between the phase-field model and molecular dynamics simulation is obtained when increasing the apparent diffusion coefficients in the phase-field treatment by a factor of four against their molecular dynamics estimates.

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Science.gov (United States)

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

DNA strand exchange catalyzed by molecular crowding in PEG solutions

KAUST Repository

Feng, Bobo; Frykholm, Karolin; Nordé n, Bengt; Westerlund, Fredrik

2010-01-01

DNA strand exchange is catalyzed by molecular crowding and hydrophobic interactions in concentrated aqueous solutions of polyethylene glycol, a discovery of relevance for understanding the function of recombination enzymes and with potential applications to DNA nanotechnology. © 2010 The Royal Society of Chemistry.

Laser Controlled Molecular Orientation Dynamics

International Nuclear Information System (INIS)

Atabek, O.

2004-01-01

Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation

Interaction of the model alkyltrimethylammonium ions with alkali halide salts: an explicit water molecular dynamics study

Directory of Open Access Journals (Sweden)

M. Druchok

2013-01-01

Full Text Available We present an explicit water molecular dynamics simulation of dilute solutions of model alkyltrimethylammonium surfactant ions (number of methylene groups in the tail is 3, 5, 8, 10, and 12 in mixture with NaF, NaCl, NaBr, and NaI salts, respectively. The SPC/E model is used to describe water molecules. Results of the simulation at 298 K are presented in form of the radial distribution functions between nitrogen and carbon atoms of CH2 groups on the alkyltrimethylammonium ion, and the counterion species in the solution. The running coordination numbers between carbon atoms of surfactants and counterions are also calculated. We show that I- counterion exhibits the highest, and F- the lowest affinity to "bind" to the model surfactants. The results are discussed in view of the available experimental and simulation data for this and similar solutions.

Molecular potentials and relaxation dynamics

International Nuclear Information System (INIS)

Karo, A.M.

1981-01-01

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

Propensities of oxalic, citric, succinic, and maleic acids for the aqueous solution/vapour interface: Surface tension measurements and molecular dynamics simulations

Czech Academy of Sciences Publication Activity Database

Mahiuddin, S.; Minofar, Babak; Borah, J. M.; Das, M. R.; Jungwirth, Pavel

2008-01-01

Roč. 462, 4/6 (2008), s. 217-221 ISSN 0009-2614 R&D Projects: GA MŠk LC512; GA ČR(CZ) GD203/05/H001 Grant - others:NSF(US) CHE0431312 Institutional research plan: CEZ:AV0Z40550506 Keywords : carboxylic acids * molecular dynamics * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.169, year: 2008

The 2011 Dynamics of Molecular Collisions Conference

Energy Technology Data Exchange (ETDEWEB)

Nesbitt, David J. [JILA, NIST

2011-07-11

The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

Science.gov (United States)

Löytynoja, T; Niskanen, J; Jänkälä, K; Vahtras, O; Rinkevicius, Z; Ågren, H

2014-11-20

Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

Towards the molecular bases of polymerase dynamics

International Nuclear Information System (INIS)

Chela Flores, J.

1991-03-01

One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs

A stochastic phase-field model determined from molecular dynamics

KAUST Repository

von Schwerin, Erik

2010-03-17

The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

A stochastic phase-field model determined from molecular dynamics

KAUST Repository

von Schwerin, Erik; Szepessy, Anders

2010-01-01

The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

Effect of acetone accumulation on structure and dynamics of lipid membranes studied by molecular dynamics simulations.

Science.gov (United States)

Posokhov, Yevgen O; Kyrychenko, Alexander

2013-10-01

The modulation of the properties and function of cell membranes by small volatile substances is important for many biomedical applications. Despite available experimental results, molecular mechanisms of action of inhalants and organic solvents, such as acetone, on lipid membranes remain not well understood. To gain a better understanding of how acetone interacts with membranes, we have performed a series of molecular dynamics (MD) simulations of a POPC bilayer in aqueous solution in the presence of acetone, whose concentration was varied from 2.8 to 11.2 mol%. The MD simulations of passive distribution of acetone between a bulk water phase and a lipid bilayer show that acetone favors partitioning into the water-free region of the bilayer, located near the carbonyl groups of the phospholipids and at the beginning of the hydrocarbon core of the lipid membrane. Using MD umbrella sampling, we found that the permeability barrier of ~0.5 kcal/mol exists for acetone partitioning into the membrane. In addition, a Gibbs free energy profile of the acetone penetration across a bilayer demonstrates a favorable potential energy well of -3.6 kcal/mol, located at 15-16Å from the bilayer center. The analysis of the structural and dynamics properties of the model membrane revealed that the POPC bilayer can tolerate the presence of acetone in the concentration range of 2.8-5.6 mol%. The accumulation of the higher acetone concentration of 11.2 mol% results, however, in drastic disordering of phospholipid packing and the increase in the membrane fluidity. The acetone molecules push the lipid heads apart and, hence, act as spacers in the headgroup region. This effect leads to the increase in the average headgroup area per molecule. In addition, the acyl tail region of the membrane also becomes less dense. We suggest, therefore, that the molecular mechanism of acetone action on the phospholipid bilayer has many common features with the effects of short chain alcohols, DMSO, and

Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

Science.gov (United States)

Tsukanov, A. A.; Psakhie, S. G.

2017-12-01

The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.

Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics

International Nuclear Information System (INIS)

Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.

2004-01-01

Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the 'Wannier gauge'. An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches

Comparison of single-ion molecular dynamics in common solvents

Science.gov (United States)

Muralidharan, A.; Pratt, L. R.; Chaudhari, M. I.; Rempe, S. B.

2018-06-01

Laying a basis for molecularly specific theory for the mobilities of ions in solutions of practical interest, we report a broad survey of velocity autocorrelation functions (VACFs) of Li+ and PF6- ions in water, ethylene carbonate, propylene carbonate, and acetonitrile solutions. We extract the memory function, γ(t), which characterizes the random forces governing the mobilities of ions. We provide comparisons controlling for the effects of electrolyte concentration and ion-pairing, van der Waals attractive interactions, and solvent molecular characteristics. For the heavier ion (PF6-), velocity relaxations are all similar: negative tail relaxations for the VACF and a clear second relaxation for γ (t ), observed previously also for other molecular ions and with n-pentanol as the solvent. For the light Li+ ion, short time-scale oscillatory behavior masks simple, longer time-scale relaxation of γ (t ). But the corresponding analysis of the solventberg Li+(H2O)4 does conform to the standard picture set by all the PF6- results.

The use of molecular dynamics for the thermodynamic properties of simple and transition metals

International Nuclear Information System (INIS)

Straub, G.K.

1987-04-01

The technique of computer simulation of the molecular dynamics in metallic systems to calculate thermodynamic properties is discussed. The nature of a metal as determined by its electronic structure is used to determine the total adiabatic potential. The effective screened ion-ion interaction can then be used in a molecular dynamics simulation. The method for the construction of a molecular dynamics ensemble, its relation to the canonical ensemble, and the definition of thermodynamic functions from the Helmholtz free energy is given. The method for the analysis of the molecular dynamics results from quasiharmonic lattice dynamics and the decomposition in terms of harmonic and anharmonic contributions is given for solids. For fluid phase metals, procedures for calculating the thermodynamics and determining the constant of entropy are presented. The solid-fluid phase boundary as a function of pressure and temperature is determined using the results of molecular dynamics. Throughout, examples and results for metallic sodium are used. The treatment of the transition metal electronic d-states in terms of an effective pair-wise interaction is also discussed and the phonon dispersion curves of Al, Ni, and Cu are calculated

Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene

Energy Technology Data Exchange (ETDEWEB)

Cawkwell, M. J., E-mail: cawkwell@lanl.gov; Niklasson, Anders M. N. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Dattelbaum, Dana M. [Weapons Experiments Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2015-02-14

The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene.

Science.gov (United States)

Cawkwell, M J; Niklasson, Anders M N; Dattelbaum, Dana M

2015-02-14

The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS

NARCIS (Netherlands)

AHLSTROM, P; BERENDSEN, HJC

1993-01-01

Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)

Correlations and symmetry of interactions influence collective dynamics of molecular motors

International Nuclear Information System (INIS)

Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B

2015-01-01

Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)

Molecular dynamics simulation of impact test

International Nuclear Information System (INIS)

Akahoshi, Y.; Schmauder, S.; Ludwig, M.

1998-01-01

This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

Molecular dynamics simulation of impact test

Energy Technology Data Exchange (ETDEWEB)

Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

1998-11-01

This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

A QM/MM study of the absorption spectrum of harmane in water solution and interacting with DNA: the crucial role of dynamic effects.

Science.gov (United States)

Etienne, Thibaud; Very, Thibaut; Perpète, Eric A; Monari, Antonio; Assfeld, Xavier

2013-05-02

We present a time-dependent density functional theory computation of the absorption spectra of one β-carboline system: the harmane molecule in its neutral and cationic forms. The spectra are computed in aqueous solution. The interaction of cationic harmane with DNA is also studied. In particular, the use of hybrid quantum mechanics/molecular mechanics methods is discussed, together with its coupling to a molecular dynamics strategy to take into account dynamic effects of the environment and the vibrational degrees of freedom of the chromophore. Different levels of treatment of the environment are addressed starting from purely mechanical embedding to electrostatic and polarizable embedding. We show that a static description of the spectrum based on equilibrium geometry only is unable to give a correct agreement with experimental results, and dynamic effects need to be taken into account. The presence of two stable noncovalent interaction modes between harmane and DNA is also presented, as well as the associated absorption spectrum of harmane cation.

Molecular Basis of Clay Mineral Structure and Dynamics in Subsurface Engineering Applications

Science.gov (United States)

Cygan, R. T.

2015-12-01

Clay minerals and their interfaces play an essential role in many geochemical, environmental, and subsurface engineering applications. Adsorption, dissolution, precipitation, nucleation, and growth mechanisms, in particular, are controlled by the interplay of structure, thermodynamics, kinetics, and transport at clay mineral-water interfaces. Molecular details of these processes are typically beyond the sensitivity of experimental and analytical methods, and therefore require accurate models and simulations. Also, basal surfaces and interlayers of clay minerals provide constrained interfacial environments to facilitate the evaluation of these complex processes. We have developed and used classical molecular and quantum methods to examine the complex behavior of clay mineral-water interfaces and dynamics of interlayer species. Bulk structures, swelling behavior, diffusion, and adsorption processes are evaluated and compared to experimental and spectroscopic findings. Analysis of adsorption mechanisms of radionuclides on clay minerals provides a scientific basis for predicting the suitability of engineered barriers associated with nuclear waste repositories and the fate of contaminants in the environment. Similarly, the injection of supercritical carbon dioxide into geological reservoirs—to mitigate the impact of climate change—is evaluated by molecular models of multi-fluid interactions with clay minerals. Molecular dynamics simulations provide insights into the wettability of different fluids—water, electrolyte solutions, and supercritical carbon dioxide—on clay surfaces, and which ultimately affects capillary fluid flow and the integrity of shale caprocks. This work is supported as part of Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science and by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Geosciences Research Program

PHP Solutions Dynamic Web Design Made Easy

CERN Document Server

Powers, David

2010-01-01

This is the second edition of David Power's highly-respected PHP Solutions: Dynamic Web Design Made Easy. This new edition has been updated by David to incorporate changes to PHP since the first edition and to offer the latest techniques - a classic guide modernized for 21st century PHP techniques, innovations, and best practices. You want to make your websites more dynamic by adding a feedback form, creating a private area where members can upload images that are automatically resized, or perhaps storing all your content in a database. The problem is, you're not a programmer and the thought o

Molecular Dynamics Simulations of a Linear Nanomotor Driven by Thermophoretic Forces

DEFF Research Database (Denmark)

Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

Molecular Dynamics of a Linear Nanomotor Driven by Thermophoresis Harvey A. Zambrano1, Jens H. Walther1,2 and Richard L. Jaffe3 1Department of Mechanical Engineering, Fluid Mechanics, Technical University of Denmark, DK-2800 Lyngby, Denmark; 2Computational Science and Engineering Laboratory, ETH...... future molecular machines a complete understanding of the friction forces involved on the transport process at the molecular level have to be addressed.18 In this work we perform Molecular Dynamics (MD) simulations using the MD package FASTTUBE19 to study a molecular linear motor consisting of coaxial...... the valence forces within the CNT using Morse, harmonic angle and torsion potentials.19We include a nonbonded carbon-carbon Lennard-Jones potential to describe the vdW interaction between the carbon atoms within the double wall portion of the system. We equilibrate the system at 300K for 0.1 ns, by coupling...

Dynamic surface properties of poly(methylalkyldiallylammonium chloride) solutions

Czech Academy of Sciences Publication Activity Database

Novikova, A. A.; Vlasov, P. S.; Lin, S.-Y.; Sedláková, Zdeňka; Noskov, B. A.

2017-01-01

Roč. 80, November (2017), s. 122-127 ISSN 1876-1070 Institutional support: RVO:61389013 Keywords : polymer solutions * dynamic surface tension * dilational surface rheology Subject RIV: CD - Macromolecular Chemistry OBOR OECD: Polymer science Impact factor: 4.217, year: 2016

Molecular dynamics simulation of a phospholipid membrane

NARCIS (Netherlands)

Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.

We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

2013-12-21

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

International Nuclear Information System (INIS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-01-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

Science.gov (United States)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Dynamic rheology behavior of electron beam-irradiated cellulose pulp/NMMO solution

International Nuclear Information System (INIS)

Zhou Ruimin; Deng Bangjun; Hao Xufeng; Zhou Fei; Wu Xinfeng; Chen Yongkang

2008-01-01

The rheological behavior of irradiated cellulose pulp solution by electron beam was investigated. Storage modulus G', loss modulus G'', the dependence of complex viscosity η* and frequency ω of cellulose solutions were measured by DSR-200 Rheometer (Rheometrics co., USA). The molecular weight of irradiated cellulose was measured via the intrinsic viscosity measurement using an Ubbelohde capillary viscometer. The crystalline structure was studied by FTIR Spectroscopy. The results congruously showed that the molecular weight of pulp cellulose decrease and the molecular weight distribution of cellulose become narrow with increase in the irradiation dose. Moreover, the crystalline structure of the cellulose was destroyed, the force of the snarl between the cellulose molecules weakens and the accessibility of pulp spinning is improved. The study supplies some useful data for spinnability of irradiated cellulose and technical data to the filature industry

Shapiro like steps reveals molecular nanomagnets’ spin dynamics

International Nuclear Information System (INIS)

Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid

2015-01-01

We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields

Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

DEFF Research Database (Denmark)

Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.

-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science...... of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational...... practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational...

Extended Lagrangian formulation of charge-constrained tight-binding molecular dynamics.

Science.gov (United States)

Cawkwell, M J; Coe, J D; Yadav, S K; Liu, X-Y; Niklasson, A M N

2015-06-09

The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [Niklasson, Phys. Rev. Lett., 2008, 100, 123004] has been applied to a tight-binding model under the constraint of local charge neutrality to yield microcanonical trajectories with both precise, long-term energy conservation and a reduced number of self-consistent field optimizations at each time step. The extended Lagrangian molecular dynamics formalism restores time reversal symmetry in the propagation of the electronic degrees of freedom, and it enables the efficient and accurate self-consistent optimization of the chemical potential and atomwise potential energy shifts in the on-site elements of the tight-binding Hamiltonian that are required when enforcing local charge neutrality. These capabilities are illustrated with microcanonical molecular dynamics simulations of a small metallic cluster using an sd-valent tight-binding model for titanium. The effects of weak dissipation on the propagation of the auxiliary degrees of freedom for the chemical potential and on-site Hamiltonian matrix elements that is used to counteract the accumulation of numerical noise during trajectories was also investigated.

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

Science.gov (United States)

Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Kunaseth, Manaschai; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Ohmura, Satoshi; Rajak, Pankaj; Shimamura, Kohei; Vashishta, Priya

2014-05-01

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 106-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

International Nuclear Information System (INIS)

Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya; Kunaseth, Manaschai; Ohmura, Satoshi; Shimamura, Kohei

2014-01-01

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10 6 -atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of

Vectorization, parallelization and implementation of Quantum molecular dynamics codes (QQQF, MONTEV)

Energy Technology Data Exchange (ETDEWEB)

Kato, Kaori [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan); Kunugi, Tomoaki; Kotake, Susumu; Shibahara, Masahiko

1998-03-01

This report describes parallelization, vectorization and implementation for two simulation codes, Quantum molecular dynamics simulation code QQQF and Photon montecalro molecular dynamics simulation code MONTEV, that have been developed for the analysis of the thermalization of photon energies in the molecule or materials. QQQF has been vectorized and parallelized on Fujitsu VPP and has been implemented from VPP to Intel Paragon XP/S and parallelized. MONTEV has been implemented from VPP to Paragon and parallelized. (author)

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

Science.gov (United States)

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

NARCIS (Netherlands)

JUFFER, AH; BERENDSEN, HJC

1993-01-01

A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics †

Science.gov (United States)

Chen, Wei; Shen, Jana K.

2014-01-01

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma. PMID:25142416

Molecular dynamics simulations and quantum chemical calculations ...

African Journals Online (AJOL)

Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

NARCIS (Netherlands)

Periole, Xavier; Vendruscolo, Michele; Mark, Alan E.

2007-01-01

A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which

Droplet spreading driven by van der Waals force: a molecular dynamics study

KAUST Repository

Wu, Congmin

2010-07-07

The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t) ∼ √t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid. © 2010 IOP Publishing Ltd.

Molecular dynamics simulations of melting behavior of alkane as phase change materials slurry

International Nuclear Information System (INIS)

Rao Zhonghao; Wang Shuangfeng; Wu Maochun; Zhang Yanlai; Li Fuhuo

2012-01-01

Highlights: ► The melting behavior of phase change materials slurry was investigated by molecular dynamics simulation method. ► Four different PCM slurry systems including pure water and water/n-nonadecane composite were constructed. ► Amorphous structure and periodic boundary conditions were used in the molecular dynamics simulations. ► The simulated melting temperatures are very close to the published experimental values. - Abstract: The alkane based phase change materials slurry, with high latent heat storage capacity, is effective to enhance the heat transfer rate of traditional fluid. In this paper, the melting behavior of composite phase change materials slurry which consists of n-nonadecane and water was investigated by using molecular dynamics simulation. Four different systems including pure water and water/n-nonadecane composite were constructed with amorphous structure and periodic boundary conditions. The results showed that the simulated density and melting temperature were very close to the published experimental values. Mixing the n-nonadecane into water decreased the mobility but increased the energy storage capacity of composite systems. To describe the melting behavior of alkane based phase change materials slurry on molecular or atomic scale, molecular dynamics simulation is an effective method.

Magnetic nanoparticles in fluid environment: combining molecular dynamics and Lattice-Boltzmann

Energy Technology Data Exchange (ETDEWEB)

Melenev, Petr, E-mail: melenev@icmm.ru [Ural Federal University, 4, Turgeneva str., 620000 Ekaterinburg (Russian Federation); Institute of Continuous Media Mechanics, 1, Koroleva str., 614013 Perm (Russian Federation)

2017-06-01

Hydrodynamic interactions between magnetic nanoparticles suspended in the Newtonian liquid are accounted for using a combination of the lattice Boltzmann method and molecular dynamics simulations. Nanoparticle is modelled by the system of molecular dynamics material points (which form structure resembles raspberry) coupled to the lattice Boltzmann fluid. The hydrodynamic coupling between the colloids is studied by simulations of the thermo-induced rotational diffusion of two raspberry objects. It was found that for the considered range of model parameters the approaching of the raspberries leads to slight retard of the relaxation process. The presence of the weak magnetic dipolar interaction between the objects leads to modest decrease of the relaxation time and the extent of the acceleration of the diffusion is intensified along with magnetic forces. - Highlights: • The combination of molecular dynamics and lattice Boltzmann method is utilized for the reveal of the role of hydrodynamic interaction in rotational dynamics of colloid particles. • The verification of the model parameters is done based on the comparison with the results of Langevin dynamics. • For the task of free rotational diffusion of the pair of colloid particles the influence of the hydrodynamic interactions on the relaxation time is examined in the case of nonmagnetic particles and at the presence of weak dipolar interaction.

Microsecond atomic-scale molecular dynamics simulations of polyimides

NARCIS (Netherlands)

Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.

2013-01-01

We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long

Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

Directory of Open Access Journals (Sweden)

Dirk-Sören Lühmann

2015-08-01

Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.

Moving contact lines: linking molecular dynamics and continuum-scale modelling.

Science.gov (United States)

Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

2018-05-04

Despite decades of research, the modelling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily-life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide the link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which govern the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modelling, and highlight the opportunities for future developments in this area.

Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

Science.gov (United States)

Li, Jianwei; Nowak, Piotr; Otto, Sijbren

2013-06-26

Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

Scorpion toxins prefer salt solutions

Czech Academy of Sciences Publication Activity Database

Nikouee, A.; Khabiri, Morteza; Cwiklik, Lukasz

2015-01-01

Roč. 21, č. 11 (2015), 287/1-287/14 ISSN 1610-2940 R&D Projects: GA ČR GA13-06181S Institutional support: RVO:61388963 ; RVO:61388955 Keywords : ionic solutions * molecular dynamics * nonaqueous media * secondary structure Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.438, year: 2015

Estimation of flow stress of radiation induced F/M steels using molecular dynamics and discrete dislocation dynamics approach

International Nuclear Information System (INIS)

More, Ameya; Dutta, B.K.; Durgaprasad, P.V.; Arya, A.K.

2012-01-01

Fe-Cr based Ferritic/Martensitic (F/M) steels are the candidate structural materials for future fusion reactors. In this work, a multi-scale approach comprising atomistic Molecular Dynamics (MD) simulations and Discrete Dislocation Dynamics (DDD) simulations are used to model the effect of irradiation dose on the flow stress of F/M steels. At the atomic scale, molecular dynamics simulations are used to study the dislocation interaction with irradiation induced defects, i.e. voids and He bubbles. Whereas, the DDD simulations are used to estimate the change in flow stress of the material as a result of irradiation hardening. (author)

Molecular dynamics studies of superionic conductors

International Nuclear Information System (INIS)

Rahman, A.; Vashishta, P.

1983-01-01

Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables

Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces

International Nuclear Information System (INIS)

Kirkpatrick, R. James; Kalinichev, Andrey G.

2008-01-01

Research supported by this grant focuses on molecular scale understanding of central issues related to the structure and dynamics of geochemically important fluids, fluid-mineral interfaces, and confined fluids using computational modeling and experimental methods. Molecular scale knowledge about fluid structure and dynamics, how these are affected by mineral surfaces and molecular-scale (nano-) confinement, and how water molecules and dissolved species interact with surfaces is essential to understanding the fundamental chemistry of a wide range of low-temperature geochemical processes, including sorption and geochemical transport. Our principal efforts are devoted to continued development of relevant computational approaches, application of these approaches to important geochemical questions, relevant NMR and other experimental studies, and application of computational modeling methods to understanding the experimental results. The combination of computational modeling and experimental approaches is proving highly effective in addressing otherwise intractable problems. In 2006-2007 we have significantly advanced in new, highly promising research directions along with completion of on-going projects and final publication of work completed in previous years. New computational directions are focusing on modeling proton exchange reactions in aqueous solutions using ab initio molecular dynamics (AIMD), metadynamics (MTD), and empirical valence bond (EVB) approaches. Proton exchange is critical to understanding the structure, dynamics, and reactivity at mineral-water interfaces and for oxy-ions in solution, but has traditionally been difficult to model with molecular dynamics (MD). Our ultimate objective is to develop this capability, because MD is much less computationally demanding than quantum-chemical approaches. We have also extended our previous MD simulations of metal binding to natural organic matter (NOM) to a much longer time scale (up to 10 ns) for