Molecular potentials and relaxation dynamics
Karo, A.M.
1981-03-27
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. As an example, recent calculations of the chi/sup 1/..sigma../sup +/ and a/sup 3/..sigma../sup +/ states of LiH, NaH, KH, RbH, and CsH and the chi/sup 2/..sigma../sup +/ 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, highly-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/sup -1/ over most of the potential curves) with the difference curves being considerably more accurate.
Molecular Dynamics Simulations of Solutions at Constant Chemical Potential
Perego, Claudio; Parrinello, Michele
2015-01-01
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, that range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, that influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Grand-Canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work we propose the C$\\mu$MD method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C$\\mu$MD method to the paradigmatic case of urea crystall...
Ladd, A.J.C.
1988-08-01
The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.
Southern California, University of
with molecular dynamics simulation based on an effective interatomic potentials consisting of two- and three-body of their properties in extreme condition of temperature and pressure is very important for a systematic understanding to the structural arrangement of the oxygen atoms: structures with fcc oxygen symmetries include , cubic
How accurate is Born-Oppenheimer molecular dynamics for crossings of potential surfaces ?
Hakon Hoel; Ashraful Kadir; Petr Plechac; Mattias Sandberg; Anders Szepessy
2014-06-13
The difference of the value of observables for the time-independent Schr\\"odinger equation, with matrix valued potentials, and the values of observables for ab initio Born-Oppenheimer molecular dynamics, of the ground state, depends on the probability to be in excited states and the electron/nuclei mass ratio. The paper first proves an error estimate (depending on the electron/nuclei mass ratio and the probability to be in excited states) for this difference of observables, assuming that molecular dynamics space-time averages converge, with a rate related to the maximal Lyapunov exponent. The analysis does not assume a uniform lower bound on the spectral gap and consequently the probability to be in excited states can be large. A numerical method to determine the probability to be in excited states is then presented, based on Ehrenfest molecular dynamics and stability analysis of a perturbed eigenvalue problem.
Gereben, Orsolya; Pusztai, László
2013-10-28
The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ?11 A? and a very small third one at ?16 A? can be found as well, without preference for any axis or plane orientation. PMID:24182051
The chemical potential of water: molecular dynamics computer simulation of the CF and SPC models
NASA Astrophysics Data System (ADS)
Quintana, Jacqueline; Haymet, A. D. J.
1992-02-01
The excess Helmholtz free energy ? A of two models of water, the revised central force model and the simple point charge model, has been calculated by molecular dynamics computer simulation. The method of "thermodynamic integration" has been used to calculate the free energy difference between the (model) water and an ideal gas of molecules at the same temperature and volume. For this particular thermodynamic property, Ewald sums and truncated potentials yield the same results.
Pseudoatom molecular dynamics.
Starrett, C E; Daligault, J; Saumon, D
2015-01-01
An approach to simulating warm and hot dense matter that combines density-functional-theory-based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The method, which we call pseudoatom molecular dynamics, can be applied to single-component or multicomponent plasmas. It gives equation of state and self-diffusion coefficients with an accuracy comparable to orbital-free molecular dynamics simulations but is computationally much more efficient. PMID:25679720
NASA Astrophysics Data System (ADS)
Starrett, C. E.; Daligault, J.; Saumon, D.
2015-01-01
An approach to simulating warm and hot dense matter that combines density-functional-theory-based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The method, which we call pseudoatom molecular dynamics, can be applied to single-component or multicomponent plasmas. It gives equation of state and self-diffusion coefficients with an accuracy comparable to orbital-free molecular dynamics simulations but is computationally much more efficient.
Kreck, Cara A; Mancera, Ricardo L
2014-02-20
Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials. PMID:24467489
NASA Astrophysics Data System (ADS)
Tejada, I. G.; Brochard, L.; Stoltz, G.; Legoll, F.; Lelièvre, T.; Cancès, E.
2015-01-01
Molecular dynamics is a simulation technique that can be used to study failure in solids, provided the inter-atomic potential energy is able to account for the complex mechanisms at failure. Reactive potentials fitted on ab initio results or on experimental values have the ability to adapt to any complex atomic arrangement and, therefore, are suited to simulate failure. But the complexity of these potentials, together with the size of the systems considered, make simulations computationally expensive. In order to improve the efficiency of numerical simulations, simpler harmonic potentials can be used instead of complex reactive potentials in the regions where the system is close to its ground state and a harmonic approximation reasonably fits the actual reactive potential. However the validity and precision of such an approach has not been investigated in detail yet. We present here a methodology for constructing a reduced potential and combining it with the reactive one. We also report some important features of crack propagation that may be affected by the coupling of reactive and reduced potentials. As an illustrative case, we model a crystalline two-dimensional material (graphene) with a reactive empirical bond-order potential (REBO) or with harmonic potentials made of bond and angle springs that are designed to reproduce the second order approximation of REBO in the ground state. We analyze the consistency of this approximation by comparing the mechanical behavior and the phonon spectra of systems modeled with these potentials. These tests reveal when the anharmonicity effects appear. As anharmonic effects originate from strain, stress or temperature, the latter quantities are the basis for establishing coupling criteria for on the fly substitution in large simulations.
NASA Astrophysics Data System (ADS)
Carré, A.; Horbach, J.; Ispas, S.; Kob, W.
2008-04-01
A fitting scheme is proposed to obtain effective potentials from Car-Parrinello molecular-dynamics (CPMD) simulations. It is used to parameterize a new pair potential for silica. MD simulations with this new potential are done to determine structural and dynamic properties and to compare these properties to those obtained from CPMD and a MD simulation using the so-called BKS potential. The new potential reproduces accurately the liquid structure generated by the CPMD trajectories, the experimental activation energies for the self-diffusion constants and the experimental density of amorphous silica. Also lattice parameters and elastic constants of ?-quartz are well reproduced, showing the transferability of the new potential.
Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner
2014-09-01
The intergranular fracture behavior of UO2 was studied using molecular dynamics simulations with a bicrystal model. The anisotropic fracture behavior due to the different grain boundary characters was investigated with the View the MathML source symmetrical tilt S5 and the View the MathML source symmetrical tilt S3 ({1 1 1} twin) grain boundaries. Nine interatomic potentials, seven rigid-ion plus two core–shell ones, were utilized to elucidate possible potential dependence. Initiating from a notch, crack propagation along grain boundaries was observed for most potentials. The S3 boundary was found to be more prone to fracture than the S5 one, indicated by a lower energy release rate associated with the former. However, some potential dependence was identified on the existence of transient plastic deformation at crack tips, and the results were discussed regarding the relevant material properties including the excess energies of metastable phases and the critical energy release rate for intergranular fracture. In general, local plasticity at crack tips was observed in fracture simulations with potentials that predict low excess energies for metastable phases and high critical energy release rates for intergranular fracture.
NASA Astrophysics Data System (ADS)
Yamashita, Takefumi
Accurate modeling of potential functions is critical for realistic molecular dynamics (MD) simulations. In this study, improvement in potential functions is discussed by revisiting the multistate empirical valence bond (MS-EVB) method and the FUJI force field. The MS-EVB method enables simulation of dynamic chemical reactions in various situations. In this study, excess protons in water under shear were investigated by combining the MS-EVB method with the non-equilibrium MD technique. It was found that the orientation of the hydronium-like moiety is considerably more anisotropic under shear than that of the water molecule. Separately, the FUJI force field includes main-chain torsional parameters carefully derived on the basis of high-level ab initio calculations. To further demonstrate that the use of the FUJI force field improves the accuracy of MD results beyond previously reported examples, the conformational distribution of the Ala dipeptide was investigated. The results obtained using the FUJI force field agreed more closely with the experimental results than those obtained using other standard force fields. Interestingly, the MD trajectories with the FUJI force field undergo the Y conformation more frequently than those with other popular force fields. Furthermore, it was found that the choice of force field affects the structures of an antigen-antibody complex obtained using MD simulations. These improvements in the force fields essentially extend the range of applications for the MD simulation method.
Redox potentials and acidity constants from density functional theory based molecular dynamics.
Cheng, Jun; Liu, Xiandong; VandeVondele, Joost; Sulpizi, Marialore; Sprik, Michiel
2014-12-16
CONSPECTUS: All-atom methods treat solute and solvent at the same level of electronic structure theory and statistical mechanics. All-atom computation of acidity constants (pKa) and redox potentials is still a challenge. In this Account, we review such a method combining density functional theory based molecular dynamics (DFTMD) and free energy perturbation (FEP) methods. The key computational tool is a FEP based method for reversible insertion of a proton or electron in a periodic DFTMD model system. The free energy of insertion (work function) is computed by thermodynamic integration of vertical energy gaps obtained from total energy differences. The problem of the loss of a physical reference for ionization energies under periodic boundary conditions is solved by comparing with the proton work function computed for the same supercell. The scheme acts as a computational hydrogen electrode, and the DFTMD redox energies can be directly compared with experimental redox potentials. Consistent with the closed shell nature of acid dissociation, pKa estimates computed using the proton insertion/removal scheme are found to be significantly more accurate than the redox potential calculations. This enables us to separate the DFT error from other sources of uncertainty such as finite system size and sampling errors. Drawing an analogy with charged defects in solids, we trace the error in redox potentials back to underestimation of the energy gap of the extended states of the solvent. Accordingly the improvement in the redox potential as calculated by hybrid functionals is explained as a consequence of the opening up of the bandgap by the Hartree-Fock exchange component in hybrids. Test calculations for a number of small inorganic and organic molecules show that the hybrid functional implementation of our method can reproduce acidity constants with an uncertainty of 1-2 pKa units (0.1 eV). The error for redox potentials is in the order of 0.2 V. PMID:25365148
Hua Y. Geng
2014-12-19
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of $r_{s}=0.912$.
NASA Astrophysics Data System (ADS)
Shvab, I.; Sadus, Richard J.
2012-05-01
The temperature and density dependence of the structure and polarization properties of bulk water were systematically investigated using the ab initio MCYna potential [Li , J. Chem. Phys.JCPSA60021-960610.1063/1.2786449 127, 154509 (2007)], which includes nonadditive contributions to intermolecular interactions. Molecular dynamics simulations were conducted for isochores of 1, 0.8, and 0.6 g/cm3 and temperatures from 278 to 750 K. Special attention was paid to the structural change of water in the range from the normal boiling point to supercritical temperatures. At temperatures below the normal boiling temperature, water exhibits a tetrahedral structure along the 0.8 and 0.6 g/cm3 isochores. A significant collapse of the hydrogen bonding network was observed at temperatures of 450, 550, and 650 K. The MCYna potential was able to successfully reproduce the experimental dielectric constant. The dielectric constant and average dipole moments decrease with increasing temperature and decreasing density due to weakened polarization. A comparison is also made with SPC-based models.
Redox potentials and pKa for benzoquinone from density functional theory based molecular dynamics.
Cheng, Jun; Sulpizi, Marialore; Sprik, Michiel
2009-10-21
The density functional theory based molecular dynamics (DFTMD) method for the computation of redox free energies presented in previous publications and the more recent modification for computation of acidity constants are reviewed. The method uses a half reaction scheme based on reversible insertion/removal of electrons and protons. The proton insertion is assisted by restraining potentials acting as chaperones. The procedure for relating the calculated deprotonation free energies to Brønsted acidities (pK(a)) and the oxidation free energies to electrode potentials with respect to the normal hydrogen electrode is discussed in some detail. The method is validated in an application to the reduction of aqueous 1,4-benzoquinone. The conversion of hydroquinone to quinone can take place via a number of alternative pathways consisting of combinations of acid dissociations, oxidations, or dehydrogenations. The free energy changes of all elementary steps (ten in total) are computed. The accuracy of the calculations is assessed by comparing the energies of different pathways for the same reaction (Hess's law) and by comparison to experiment. This two-sided test enables us to separate the errors related with the restrictions on length and time scales accessible to DFTMD from the errors introduced by the DFT approximation. It is found that the DFT approximation is the main source of error for oxidation free energies. PMID:20568869
Implementing molecular dynamics on hybrid high performance computers—Three-body potentials
NASA Astrophysics Data System (ADS)
Brown, W. Michael; Yamada, Masako
2013-12-01
The use of coprocessors or accelerators such as graphics processing units (GPUs) has 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, defined as machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. Although there has been extensive research into methods to use accelerators efficiently to improve the performance of molecular dynamics (MD) codes employing pairwise potential energy models, little is reported in the literature for models that include many-body effects. 3-body terms are required for many popular potentials such as MEAM, Tersoff, REBO, AIREBO, Stillinger-Weber, Bond-Order Potentials, and others. Because the per-atom simulation times are much higher for models incorporating 3-body terms, there is a clear need for efficient algorithms usable on hybrid high performance computers. Here, we report a shared-memory force-decomposition for 3-body potentials that avoids memory conflicts to allow for a deterministic code with substantial performance improvements on hybrid machines. We describe modifications necessary for use in distributed memory MD codes and show results for the simulation of water with Stillinger-Weber on the hybrid Titan supercomputer. We compare performance of the 3-body model to the SPC/E water model when using accelerators. Finally, we demonstrate that our approach can attain a speedup of 5.1 with acceleration on Titan for production simulations to study water droplet freezing on a surface.
Kim, Junghan; Iype, Eldhose; Frijns, Arjan J.H.; Nedea, Silvia V.; Steenhoven, Anton A. van
2014-07-01
Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid–solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water–silicon and water–silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon–water contact angle of 129°, a quartz–water contact angle of 0°, and a cristobalite–water contact angle of 40°, which are in reasonable agreement with experimental values.
NASA Astrophysics Data System (ADS)
Wu, Xiaojie; Li, Xiantao
2015-01-01
Results from molecular dynamics simulations often need to be further processed to understand the physics on a larger scale. This paper considers the definitions of momentum and energy fluxes obtained from a control-volume approach. To assess the validity of these defined quantities, two consistency criteria are proposed. As examples, the embedded atom potential and the Tersoff potential are considered. The consistency is verified using analytical and numerical methods.
Molecular dynamics study-based mechanism of nefiracetam-induced NMDA receptor potentiation.
Omotuyi, Olaposi I; Ueda, Hiroshi
2015-04-01
Plastic changes in the brain required for memory formation and long-term learning are dependent on N-methyl-d-aspartic acid (NMDA) receptor signaling. Nefiracetam reportedly boosts NMDA receptor functions as a basis for its nootropic properties. Previous studies suggest that nefiracetam potentiates the NMDA receptor activation, as a more potent co-agonist for glycine binding site than glycine, though the underlying mechanisms remain elusive. Here, using BSP-SLIM method, a novel binding site within the core of spiral ?-strands-1-5 of LBD-GLUN1 has been predicted in glycine-bound GLUN1 conformation in addition to the glycine pocket in Apo-GLUN1. Within the core of spiral ?-strands-1-5 of LBD-GLUN1 pocket, all-atom molecular dynamics simulation revealed that nefiracetam disrupts Arg523-glycine-Asp732 interaction resulting in open GLUN1 conformation and ultimate diffusion of glycine out of the clamshell cleft. Open GLUN1 conformation coerces other intra-chain domains and proximal inter-chain domains to sample inactivate conformations resulting in closure of the transmembrane gate via a novel gauche trap on threonine 647 (chi-1 dihedral (?1)=-45° instead of +45°). Docking of nefiracetam into the glycine pocket reversed the gauche trap and meditates partial opening of the TMD gate within a time-scale of 100ns as observed in glycine-only state. All these results suggest that nefiracetam can favorably complete with glycine for GLUN1-LBD in a two-step process, first by binding to a novel site of GLUN1-LBD-NMDA receptor followed by disruption of glycine-binding dynamics then replacing glycine in the GLUN1-LBD cleft. PMID:25659913
Performance Models on QCDOC for Molecular Dynamics with Coulomb Potentials1
New York at Stoney Brook, State University of
as memory management) is required of the programmer. A related machine, Blue Gene/L, is under development method as a function of the required accuracy, the size of the molecular dynamics cell, and the hardware of memory located on the each chip. For this reason it has been named QCDOC for quantum chromodynamics
Introduction to Accelerated Molecular Dynamics
Perez, Danny [Los Alamos National Laboratory
2012-07-10
Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.
Ohta, H.; Iwakawa, A.; Eriguchi, K.; Ono, K. [Department of Aeronautics and Astronautics, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501 (Japan)
2008-10-01
An interatomic potential model for Si-Br systems has been developed for performing classical molecular dynamics (MD) simulations. This model enables us to simulate atomic-scale reaction dynamics during Si etching processes by Br{sup +}-containing plasmas such as HBr and Br{sub 2} plasmas, which are frequently utilized in state-of-the-art techniques for the fabrication of semiconductor devices. Our potential form is based on the well-known Stillinger-Weber potential function, and the model parameters were systematically determined from a database of potential energies obtained from ab initio quantum-chemical calculations using GAUSSIAN03. For parameter fitting, we propose an improved linear scheme that does not require any complicated nonlinear fitting as that in previous studies [H. Ohta and S. Hamaguchi, J. Chem. Phys. 115, 6679 (2001)]. In this paper, we present the potential derivation and simulation results of bombardment of a Si(100) surface using a monoenergetic Br{sup +} beam.
Guarini, E.; Barocchi, F. [Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Sampoli, M. [Dipartimento di Energetica, Universita di Firenze, via S. Marta 3, I-50139 Firenze (Italy); CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Venturi, G. [CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Bafile, U. [Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del Piano 10, I-50019 Sesto Fiorentino (Italy)
2007-10-19
Anisotropic interactions of liquid CD{sub 4} are studied in detail by comparison of inelastic neutron Brillouin scattering data with molecular dynamics simulations using up to four different models of the methane site-site potential. We demonstrate that the experimental dynamic structure factor S(Q,{omega}) acts as a highly discriminating quantity for possible interaction schemes. In particular, the Q evolution of the spectra enables a selective probing of the short- and medium-range features of the anisotropic potentials. We show that the preferential configuration of methane dimers at liquid densities can thus be discerned by analyzing the orientation-dependent model potential curves, in light of the experimental and simulation results.
NASA Astrophysics Data System (ADS)
Zheng, Zhijun; Bai, Yilong
2010-05-01
The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.
NASA Astrophysics Data System (ADS)
Lin, Xubo; Bai, Tingting; Zuo, Yi Y.; Gu, Ning
2014-02-01
Nanoparticles (NPs) show great promises in biomedical applications as the respiratory drug carrier system. Once reaching the alveolar region, NPs first interact with the pulmonary surfactant (PS) film, which serves as the first biological barrier and plays an important role in maintaining the normal respiratory mechanics. Therefore, understanding the interactions between NPs and PS can help promote the NP-based respiratory drug carrier systems. Using coarse-grained molecular dynamics simulations, we studied the effect of rigid spherical NPs with different hydrophobicity and sizes on a dipalmitoylphosphatidylcholine (DPPC) monolayer at the air-water interface. Four different NPs were considered, including hydrophilic and hydrophobic NPs, each with two diameters of 3 nm and 5 nm (the sizes are comparable to that of generation 3 and 5 PAMAM dendrimers, which have been widely used for nanoscale drug carrier systems). Our simulations showed that hydrophilic NPs can readily penetrate into the aqueous phase with little or no disturbance on the DPPC monolayer. However, hydrophobic NPs tend to induce large structural disruptions, thus inhibiting the normal phase transition of the DPPC monolayer upon film compression. Our simulations also showed that this inhibitory effect of hydrophobic NPs can be mitigated through PEGylation. Our results provide useful guidelines for molecular design of NPs as carrier systems for pulmonary drug delivery.Nanoparticles (NPs) show great promises in biomedical applications as the respiratory drug carrier system. Once reaching the alveolar region, NPs first interact with the pulmonary surfactant (PS) film, which serves as the first biological barrier and plays an important role in maintaining the normal respiratory mechanics. Therefore, understanding the interactions between NPs and PS can help promote the NP-based respiratory drug carrier systems. Using coarse-grained molecular dynamics simulations, we studied the effect of rigid spherical NPs with different hydrophobicity and sizes on a dipalmitoylphosphatidylcholine (DPPC) monolayer at the air-water interface. Four different NPs were considered, including hydrophilic and hydrophobic NPs, each with two diameters of 3 nm and 5 nm (the sizes are comparable to that of generation 3 and 5 PAMAM dendrimers, which have been widely used for nanoscale drug carrier systems). Our simulations showed that hydrophilic NPs can readily penetrate into the aqueous phase with little or no disturbance on the DPPC monolayer. However, hydrophobic NPs tend to induce large structural disruptions, thus inhibiting the normal phase transition of the DPPC monolayer upon film compression. Our simulations also showed that this inhibitory effect of hydrophobic NPs can be mitigated through PEGylation. Our results provide useful guidelines for molecular design of NPs as carrier systems for pulmonary drug delivery. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr04163h
Bauchy, M., E-mail: bauchy@mit.edu [Concrete Sustainability Hub, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA and Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095 (United States)
2014-07-14
We study a calcium aluminosilicate glass of composition (SiO{sub 2}){sub 0.60}(Al{sub 2}O{sub 3}){sub 0.10}(CaO){sub 0.30} by means of molecular dynamics. To this end, we conduct parallel simulations, following a consistent methodology, but using three different potentials. Structural and elastic properties are analyzed and compared to available experimental data. This allows assessing the respective abilities of the potentials to produce a realistic glass. We report that, although all these potentials offer a reasonable glass structure, featuring tricluster oxygen atoms, their respective vibrational and elastic predictions differ. This allows us to draw some general conclusions about the crucial role, or otherwise, of the interaction potential in silicate systems.
Guillaume Galliéro; Christian Boned; Antoine Baylaucq; François Montel
2006-01-01
In this work, using molecular dynamics simulation, the viscosity (dynamic property) and the pressure (static property) of spherical fluid particles interacting through Lennard-Jones alpha -6 and exponential alpha -6 potentials are computed. Simulations are performed for alpha going from 10 to 20 for the Lennard-Jones potential and from 12 to 22 for the exponential one. Six different thermodynamic states are
NASA Astrophysics Data System (ADS)
Jover, J.; Haslam, A. J.; Galindo, A.; Jackson, G.; Müller, E. A.
2012-10-01
We present a continuous pseudo-hard-sphere potential based on a cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). Using this potential one can mimic the volumetric, structural, and dynamic properties of the discontinuous hard-sphere potential over the whole fluid range. The continuous pseudo potential has the advantage that it may be incorporated directly into off-the-shelf molecular-dynamics code, allowing the user to capitalise on existing hardware and software advances. Simulation results for the compressibility factor of the fluid and solid phases of our pseudo hard spheres are presented and compared both to the Carnahan-Starling equation of state of the fluid and published data, the differences being indistinguishable within simulation uncertainty. The specific form of the potential is employed to simulate flexible chains formed from these pseudo hard spheres at contact (pearl-necklace model) for mc = 4, 5, 7, 8, 16, 20, 100, 201, and 500 monomer segments. The compressibility factor of the chains per unit of monomer, mc, approaches a limiting value at reasonably small values, mc < 50, as predicted by Wertheim's first order thermodynamic perturbation theory. Simulation results are also presented for highly asymmetric mixtures of pseudo hard spheres, with diameter ratios of 3:1, 5:1, 20:1 over the whole composition range.
NASA Astrophysics Data System (ADS)
Ma, Qian; Dai, Jiayu; Kang, Dongdong; Zhao, Zengxiu; Yuan, Jianmin; Zhao, Xueqing
2014-12-01
Molecular dynamics (MD) simulations are performed to investigate the temperature relaxation between electrons and ions in a fully ionized, dense hydrogen plasma. We used HM (J. P. Hansen and I. R. McDonald) potential and introduced a truncated Coulomb interaction, which can avoid Coulomb catastrophe by choosing an appropriate cutting radius. The calculated results are compared with those from theoretical models (LS, GMS, BPS), whose applicability is also discussed. The effect of the interaction between ions and electrons on the temperature relaxation process is also investigated in the strong collision region. Finally, we discuss the effect of exchange interaction of electrons to the temperature relaxation.
Accelerated molecular dynamics methods
Perez, Danny [Los Alamos National Laboratory
2011-01-04
The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.
NASA Astrophysics Data System (ADS)
Patel, Sandeep A.; Brooks, Charles L.
2006-05-01
We present results addressing properties of a polarizable force field for hexane based on the fluctuating charge (FQ) formalism and developed in conjunction with the Chemistry at Harvard Molecular Mechanics (CHARMM) potential function. Properties of bulk neat hexane, its liquid-vapor interface, and its interface with a polarizable water model (TIP4P-FQ) are discussed. The FQ model is compared to a recently modified alkane model, C27r, also based on the CHARMM potential energy function. With respect to bulk properties, both models predict bulk density within 1%; the FQ model predicts the liquid vaporization enthalpy within 2%, while the C27r force field underestimates the property by roughly 20% (and in this sense reflects the quality of the C27r force field across the spectrum of linear and branched alkanes). The FQ hexane model realistically captures the dielectric properties of the bulk in terms of a dielectric constant of 1.94, in excellent agreement with experimental values in the range of 1.9-2.02. This behavior is also in conformity with a recent polarizable alkane model based on Drude oscillators. Furthermore, the bulk dielectric is essentially captured in the infinite frequency, or optical, dielectric contribution. The FQ model is in this respect a more realistic force field for modeling lipid bilayer interiors for which most current state-of-the-art force fields do not accurately capture the dielectric environment. The molecular polarizability of the FQ model is 11.79Å3, in good agreement with the range of experimental and ab initio values. In contrast to FQ models of polar solvents such as alcohols and water, there was no need to scale gas-phase polarizabilities in order to avoid polarization catastrophes in the pure bulk. In terms of the liquid-vapor and liquid-liquid interfaces, the FQ model displays a rich orientational structure of alkane and water in the respective interfacial systems, in general conforming with earlier simulation studies of such interfaces. The FQ force field shows a marked deviation in the interfacial dipole potentials computed from the charge densities averaged over simulation trajectories. At the liquid-vapor interface, the FQ model predicts a potential drop of -178.71mV in contrast to the C27r estimate of -433.80mV. For the hexane-water interface, the FQ force field predicts a dipole potential drop of -379.40mV in contrast to the C27r value of -105.42mV. Although the surface dipole potential predicted by the FQ model is roughly 3.5 times that predicted by the C27r potential, it is consistent with reported experimental potentials across solvated lipid bilayers in the range of 400-600mV.
Molecular dynamics simulations.
Lindahl, Erik
2015-01-01
Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform ?s-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation. PMID:25330956
NASA Astrophysics Data System (ADS)
Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li; Allen, Roland E.
2015-02-01
It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900–1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100–2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860–2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C=C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Perhaps remarkably, but apparently because of electrostatic repulsion, the direction of rotation is the same for both reactions.
Fan, Zheyong; Wang, Hui-Qiong; Zheng, Jin-Cheng; Donadio, Davide; Harju, Ari
2015-01-01
We derive expressions of interatomic force and heat current for many-body potentials such as the Tersoff, the Brenner, and the Stillinger-Weber potential used extensively in molecular dynamics simulations of covalently bonded materials. Although these potentials have a many-body nature, a pairwise force expression that follows Newton's third law can be found without referring to any partition of the potential. Based on this force formula, a stress applicable for periodic systems can be unambiguously defined. The force formula can then be used to derive the heat current formulas using a natural potential partitioning. Our heat current formulation is found to be equivalent to most of the seemingly different heat current formulas used in the literature, but to deviate from the stress-based formula derived from two-body potential. We validate our formulation numerically on various systems descried by the Tersoff potential, namely three-dimensional silicon and diamond, two-dimensional graphene, and quasi-one-dimen...
NASA Astrophysics Data System (ADS)
Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping
2012-04-01
Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.
Ping, Tan Ai; Hoe, Yeak Su [Department of Mathematical Sciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor Bahru, Johor Darul Takzim (Malaysia)
2014-07-10
Typically, short range potential only depends on neighbouring atoms and its parameters function can be categorized into bond stretching, angle bending and bond rotation potential. In this paper, we present our work called Angle Bending (AB) potential, whereas AB potential is the extension of our previous work namely Bond Stretching (BS) potential. Basically, potential will tend to zero after truncated region, potential in specific region can be represented by different piecewise polynomial. We proposed the AB piecewise potential which is possible to solve a system involving three atoms. AB potential able to handle the potential of covalent bonds for three atoms as well as two atoms cases due to its degeneracy properties. Continuity for the piecewise polynomial has been enforced by coupling with penalty methods. There are still plenty of improvement spaces for this AB potential. The improvement for three atoms AB potential will be studied and further modified into torsional potential which are the ongoing current research.
NASA Astrophysics Data System (ADS)
Ping, Tan Ai; Hoe, Yeak Su
2014-07-01
Typically, short range potential only depends on neighbouring atoms and its parameters function can be categorized into bond stretching, angle bending and bond rotation potential. In this paper, we present our work called Angle Bending (AB) potential, whereas AB potential is the extension of our previous work namely Bond Stretching (BS) potential. Basically, potential will tend to zero after truncated region, potential in specific region can be represented by different piecewise polynomial. We proposed the AB piecewise potential which is possible to solve a system involving three atoms. AB potential able to handle the potential of covalent bonds for three atoms as well as two atoms cases due to its degeneracy properties. Continuity for the piecewise polynomial has been enforced by coupling with penalty methods. There are still plenty of improvement spaces for this AB potential. The improvement for three atoms AB potential will be studied and further modified into torsional potential which are the ongoing current research.
NASA Astrophysics Data System (ADS)
Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro; Rino, José Pedro; CollaboratoryAdvanced Computing; Simulations
2011-02-01
An effective interatomic interaction potential for AlN is proposed. The potential consists of two-body and three-body covalent interactions. The two-body potential includes steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between atoms, charge-induced dipole-interactions due to the electronic polarizability of ions, and induced dipole-dipole (van der Waals) interactions. The covalent characters of the Al-N-Al and N-Al-N bonds are described by the three-body potential. The proposed three-body interaction potential is a modification of the Stillinger-Weber form proposed to describe Si. Using the molecular dynamics method, the interaction potential is used to study structural, elastic, and dynamical properties of crystalline and amorphous states of AlN for several densities and temperatures. The structural energy for wurtzite (2H) structure has the lowest energy, followed zinc-blende and rock-salt (RS) structures. The pressure for the structural transformation from wurtzite-to-RS from the common tangent is found to be 24 GPa. For AlN in the wurtzite phase, our computed elastic constants (C11, C12, C13, C33, C44, and C66), melting temperature, vibrational density-of-states, and specific heat agree well with the experiments. Predictions are made for the elastic constant as a function of density for the crystalline and amorphous phase. Structural correlations, such as pair distribution function and neutron and x-ray static structure factors are calculated for the amorphous and liquid state.
Introduction to Molecular Dynamics
Ralf Schneider; Amit Raj Sharma; Abha Rai
2008-01-01
Molecular dynamics is the science of simulating the time dependent behavior of a system of particles. The time evolution of the set of interacting atoms is followed by integrating their equation of motion with boundary conditions appropriate for the geometry or symmetry of the system. Molecular dynamics generate information at the microscopic level, which are: atomic positions, velocities. In order
Efimov, Yuri Ya; Naberukhin, Yuri I
2011-02-01
Potential of hydrogen bond is the function which relates its energy to geometrical parameters of hydrogen bridge: its length R(O…O) and angles between direction O…O and OH group [? (H-O…O)] and/or lone pair of proton accepting oxygen atom [?(-O…O)]. Previously we have suggested an approach to design such potentials based on the approximate numerical solution of a reverse problem of the spectrum band shape in the frames of the fluctuation theory of hydrogen bonding. In the given work this method is applied to construction of the two-parameter potentials that depend on parameters {R(O…O), ? (H-O…O} or {? (H-O…O), ? (-O…O)}. Using them, the spectra of OH vibrations of HOD molecules in a liquid phase are calculated theoretically in good agreement with experiment in the temperature range up to 200 °C. Distributions of angles P(?, T), P(?, T), and energies P(E) are calculated also. The same distributions and spectra are independently calculated on the basis of the geometrical parameters of the hydrogen bridges obtained from molecular dynamics models of water. The shapes of the spectral contours and their temperature evolution calculated for computer models turned out to be similar to experimental ones only for the potential that includes the length of H-bond R(O…O). PMID:21190891
High-precision molecular dynamics simulation of UO 2-PuO 2: Pair potentials comparison in UO 2
NASA Astrophysics Data System (ADS)
Potashnikov, S. I.; Boyarchenkov, A. S.; Nekrasov, K. A.; Kupryazhkin, A. Ya.
2011-12-01
Our series of articles is devoted to high-precision molecular dynamics simulation of mixed actinide-oxide (MOX) fuel in the approximation of rigid ions and pair interactions (RIPI) using high-performance graphics processors (GPU). In this first article ten most recent and widely used interatomic sets of pair potentials (SPP) are assessed by reproduction of solid phase properties of uranium dioxide (UO 2) - temperature dependences of the lattice constant, bulk modulus, enthalpy and heat capacity. Measurements were performed with 1 K accuracy in a wide temperature range from 300 K up to melting points. The best results are demonstrated by two recent SPPs MOX-07 and Yakub-09, which both had been fitted to the recommended thermal expansion in the range of temperatures 300-3100 K. They reproduce the experimental data better than the widely used SPPs Basak-03 and Morelon-03 at temperatures above 2500 K.
Fu, Yao; Song, Jeong-Hoon
2014-08-01
Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems. PMID:25106571
NASA Astrophysics Data System (ADS)
Fu, Yao; Song, Jeong-Hoon
2014-08-01
Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.
NASA Astrophysics Data System (ADS)
Uline, Mark J.; Corti, David S.
2008-07-01
Based on the approach of Gruhn and Monson [Phys. Rev. E 63, 061106 (2001)], we present a new method for deriving the collisions dynamics for particles that interact via discontinuous potentials. By invoking the conservation of the extended Hamiltonian, we generate molecular dynamics (MD) algorithms for simulating the hard-sphere and square-well fluids within the isothermal-isobaric (NpT) ensemble. Consistent with the recent rigorous reformulation of the NpT ensemble partition function, the equations of motion impose a constant external pressure via the introduction of a shell particle of known mass [M. J. Uline and D. S. Corti, J. Chem. Phys. 123, 164101 (2005); 123, 164102 (2005)], which serves to define uniquely the volume of the system. The particles are also connected to a temperature reservoir through the use of a chain of Nosé-Hoover thermostats, the properties of which are not affected by a hard-sphere or square-well collision. By using the Liouville operator formalism and the Trotter expansion theorem to integrate the equations of motion, the update of the thermostat variables can be decoupled from the update of the positions of the particles and the momentum changes upon a collision. Hence, once the appropriate collision dynamics for the isobaric-isenthalpic (NpH ) equations of motion is known, the adaptation of the algorithm to the NpT ensemble is straightforward. Results of MD simulations for the pure component square-well fluid are presented and serve to validate our algorithm. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the influence of the shell particle algorithm on the dynamics of the square-well fluid.
Pradeepkiran, Jangampalli Adi; Kumar, Konidala Kranthi; Kumar, Yellapu Nanda; Bhaskar, Matcha
2015-01-01
The zoonotic disease brucellosis, a chronic condition in humans affecting renal and cardiac systems and causing osteoarthritis, is caused by Brucella, a genus of Gram-negative, facultative, intracellular pathogens. The mode of transmission and the virulence of the pathogens are still enigmatic. Transcription regulatory elements, such as rho proteins, play an important role in the termination of transcription and/or the selection of genes in Brucella. Adverse effects of the transcription inhibitors play a key role in the non-successive transcription challenges faced by the pathogens. In the investigation presented here, we computationally predicted the transcription termination factor rho (TtFRho) inhibitors against Brucella melitensis 16M via a structure-based method. In view the unknown nature of its crystal structure, we constructed a robust three-dimensional homology model of TtFRho’s structure by comparative modeling with the crystal structure of the Escherichia coli TtFRho (Protein Data Bank ID: 1PVO) as a template in MODELLER (v 9.10). The modeled structure was optimized by applying a molecular dynamics simulation for 2 ns with the CHARMM (Chemistry at HARvard Macromolecular Mechanics) 27 force field in NAMD (NAnoscale Molecular Dynamics program; v 2.9) and then evaluated by calculating the stereochemical quality of the protein. The flexible docking for the interaction phenomenon of the template consists of ligand-related inhibitor molecules from the ZINC (ZINC Is Not Commercial) database using a structure-based virtual screening strategy against minimized TtFRho. Docking simulations revealed two inhibitors compounds – ZINC24934545 and ZINC72319544 – that showed high binding affinity among 2,829 drug analogs that bind with key active-site residues; these residues are considered for protein-ligand binding and unbinding pathways via steered molecular dynamics simulations. Arg215 in the model plays an important role in the stability of the protein-ligand complex via a hydrogen bonding interaction by aromatic-? contacts, and the ADMET (absorption, distribution, metabolism, and excretion) analysis of best leads indicate nontoxic in nature with good potential for drug development.
NASA Astrophysics Data System (ADS)
Hou, Qing; Li, Min; Zhou, Yulu; Cui, Jiechao; Cui, Zhenguo; Wang, Jun
2013-09-01
Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of MD usually run in a one-host-process-one-GPU (OHPOG) scheme. This scheme may pose a limitation on the system size that an implementation can handle due to the small device memory relative to the host memory. In this paper, we present a one-host-process-multiple-GPU (OHPMG) implementation of MD with embedded-atom-model or semi-empirical tight-binding many-body potentials. Because more device memory is available in an OHPMG process, the system size that can be handled is increased to a few million or more atoms. In comparison with the serial CPU implementation, in which Newton's third law is applied to improve the computational efficiency, our OHPMG implementation has achieved a 28.9x-86.0x speedup in double precision, depending on the system size, the cut-off ranges and the number of GPUs. The implementation can also handle a group of small simulation boxes in one run by combining the small boxes into a large box. This approach greatly improves the GPU computing efficiency when a large number of MD simulations for small boxes are needed for statistical purposes.
NASA Astrophysics Data System (ADS)
Gamallo, P.; Rutigliano, M.; Orlandini, S.; Cacciatore, M.; Sayós, R.
2012-11-01
A new analytical potential energy surface (PES) based on new density functional theory data is constructed for the interaction of atomic hydrogen with both a clean and an H-preadsorbed ?-cristobalite (001) surface. For the atomic interaction, six adsorption sites have been considered, the Si site (T1') being the most stable one. The PES was developed as a sum of pairwise atom-atom interactions between the gas-phase hydrogen atoms and the Si and O atoms of the ?-cristobalite surface. A preliminary molecular dynamics semiclassical study of the different heterogeneous processes (e.g., H2 formation via Eley-Rideal reaction, H adsorption) that occur when H collides with an H-preadsorbed ?-cristobalite (001) surface was carried out. The calculations were performed for collisional energy in the range (0.06 ? Ekin ? 3.0 eV), normal incidence and a surface temperature Tsurf = 1000 K. The recombination probability reaches its maximum value of approximately 0.1 for collisional energies in the range 0.3 ? Ekin ? 0.8 eV. The H2 molecules are formed in medium-lying vibrational levels, while the energy exchanged with the surface in the recombination process is very low.
Molecular electrostatic potentials by systematic molecular fragmentation
Reid, David M.; Collins, Michael A. [Research School of Chemistry, Australian National University, Canberra, ACT 0200 (Australia)] [Research School of Chemistry, Australian National University, Canberra, ACT 0200 (Australia)
2013-11-14
A simple method is presented for estimating the molecular electrostatic potential in and around molecules using systematic molecular fragmentation. This approach estimates the potential directly from the electron density. The accuracy of the method is established for a set of organic molecules and ions. The utility of the approach is demonstrated by estimating the binding energy of a water molecule in an internal cavity in the protein ubiquitin.
Substructured multibody molecular dynamics.
Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.
2006-11-01
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
Yuan, Fang; Wang, Shihu; Larson, Ronald G
2015-02-01
We calculate potentials of mean force (PMFs) and mean first passage times for a surfactant to escape a micelle, for both ionic sodium dodecyl sulfate (SDS) and nonionic ethoxylated alcohol (C12E5) micelles using both atomistic and coarse-grained molecular dynamics (MD) simulations. The PMFs are obtained by umbrella sampling and used in a Smoluchowski first-passage-time theory to obtain the times for a surfactant to escape a micelle. The calculated mean first passage time for an SDS molecule to break away from a micelle (with an aggregation number of 60) is around 2 ?s, which is consistent with previous experimental measurements of the "fast relaxation time" for exchange of surfactants between the micellar phase and the bulk solvent. The corresponding escape time calculated for a nonionic ethoxylated alcohol C12E5, with the same tail length as SDS, is 60 ?s, which is significantly longer than for SDS primarily because the PMF for surfactant desorption is about 3kT smaller than for C12E5. We also show that two coarse-grained (CG) force fields, MARTINI and SDK, give predictions similar to the atomistic CHARMM force field for the nonionic C12E5 surfactant, but for the ionic SDS surfactant, the CG simulations give a PMF similar to that obtained with CHARMM only if long-range electrostatic interactions are included in the CG simulations, rather than using a shifted truncated electrostatic interaction. We also calculate that the mean first passage time for an SDS and a C12E5 to escape from a latex binder surface is of the order of milliseconds, which is more than 100 times longer than the time for escape from the micelle, indicating that in latex waterborne coatings, SDS and C12E5 surfactants likely bind preferentially to the latex polymer interface rather than form micelles, at least at low surfactant concentrations. PMID:25560633
Scalable molecular dynamics with NAMD
James C. Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D. Skeel; Laxmikant V. Kalé; Klaus Schulten
2005-01-01
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomo- lecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed
Molecular dynamics simulations: insight into molecular phenomena at interfaces.
Razavi, Sepideh; Koplik, Joel; Kretzschmar, Ilona
2014-09-30
Molecular dynamics simulations, when aptly devised, can enhance our fundamental understanding of a system, set up a platform for testing theoretical predictions, and provide insight and a framework for further experimental studies. This feature article highlights the importance of molecular dynamics simulations in understanding interfacial phenomena using three case studies involving liquid-liquid and solid-liquid interfaces. After briefly reviewing molecular dynamics methods, we discuss velocity slip at a liquid-liquid interface, the coalescence of liquid drops in suspension and in free space, and the behavior of colloidal nanoparticles at a liquid-liquid interface. We emphasize the utility of simple intermolecular potentials and generic liquids. The case studies exemplify the significant insight gained through the molecular modeling approach regarding the interfacial phenomena studied. We conclude the highlight with a brief discussion illustrating potential shortcomings and pitfalls of molecular dynamics simulations. PMID:24684531
Pahari, Swagata; Choudhury, Chandan Kumar; Pandey, Prithvi Raj; More, Minal; Venkatnathan, Arun; Roy, Sudip
2012-06-21
Phosphoric acid doped polybenzimidazole is promising electrolyte membranes for high temperature (100 °C and above) fuel cells. Proton conduction is governed by the amount of phosphoric acid content in the polymer membrane. In this present work, we perform molecular dynamics simulations on phosphoric acid doped 2-phenyl-1H,1'H-5,5'-bibenzo[d]imidazole (monomer unit of polybenzimidazole) to characterize the structural and dynamical properties at varying phosphoric acid content and temperature. From the structural analysis, we have predicted the arrangement of the phosphoric acids, formation of H-bonds in the system, and the contribution of different atoms toward H-bonding. We have also examined the stacking of 2-phenyl-1H,1'H-5,5'-bibenzo[d]imidazole molecules and how their arrangement changes with the increasing amount of PA in the system with the help of cluster analysis. From the molecular dynamics simulation conducted at different temperatures and phosphoric acid doping level, we have predicted the diffusion of phosphoric acid and monomer. As a dynamic quantity, we have also calculated ring flipping of the imidazole ring of the monomer. PMID:22651825
Toby W. Allen; Olaf S. Andersen; Benoit Roux
2006-01-01
We investigate methods for extracting the potential of mean force (PMF) governing ion permeation from molecular dynamics simulations (MD) using gramicidin A as a prototypical narrow ion channel. It is possible to obtain well-converged meaningful PMFs using all-atom MD, which predict experimental observables within order-of-magnitude agreement with experimental results. This was possible by careful attention to issues of statistical convergence
Sakiyama, Yukinori; Takagi, Shu; Matsumoto, Yoichiro
2005-06-15
We demonstrate a validation of the intermolecular pair potential model of SiH(4), which is constructed from ab initio molecular-orbital calculations and expressed as the sum of the exponential and the London dispersion terms. The saturated liquid densities of SiH(4) are calculated for temperatures from 100 to 225 K by molecular-dynamics (MD) simulation. The average deviation between the experiment and the MD simulation using the present potential model is 3.9%, while the deviations exceed 10% for other well-known potential models such as the five-center Lennard-Jones (LJ) model. Subsequently, the shear viscosity, the thermal conductivity, and the self-diffusion coefficient of liquid SiH(4) are calculated by an equilibrium MD simulation with the Green-Kubo formula from 100 to 225 K. The average deviations from experiment are 11.8% and 13.7% for the shear viscosity and the thermal conductivity, respectively. Comparing the present model with an empirical one-center LJ model, it turns out that the rotational energy transfer through the intermolecular potential energy, which comes from the anisotropic potential energy, plays an important role in the thermal conductivity of liquid SiH(4). These results indicate that the present intermolecular potential model has an ability to give realistic pictures for liquid SiH(4) through molecular simulations. PMID:16008456
NASA Astrophysics Data System (ADS)
Warrier, M.; Pahari, P.; Chaturvedi, S.
2012-07-01
The parameter sets of the ReaxFF potential distributed with the open source, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code, is validated for simulating crystal RDX. These parameters are used to model crystal RDX and obtain its unit cell size and bulk modulus. It is seen that the parameters supplied with LAMMPS (5-April, 2011 release) do not reproduce the unit cell size and bulk modulus of crystal RDX as reported by experiments and by other simulations using the ReaxFF potential. The simulation method and relevant parts of the LAMMPS code implementing the method has been earlier validated for Cu. We conclude that either the parameter sets provided with the LAMMPS distribution or its implementation of the ReaxFF potential are not suitable for modeling crystal RDX.
Multiscale reactive molecular dynamics
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-01-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062
Interactive molecular dynamics
NASA Astrophysics Data System (ADS)
Schroeder, Daniel V.
2015-03-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.
Interactive molecular dynamics
Schroeder, Daniel V
2015-01-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
NASA Astrophysics Data System (ADS)
Koleske, D. D.; Sibener, S. J.
The surface phonon dispersion curves have been calculated for fcc (100), (110), and (111) surfaces using molecular dynamics (MD) simulations and Lennard-Jones pair potentials. In the low-temperature limit these MD simulations have been compared to the results from slab-technique lattice dynamics calculations of the type pioneered by Allen, Alldredge and de Wette. We compare the dispersion results between these two methods as a prelude to MD studies of the dispersion curves at elevated temperatures. At temperatures where the dynamical behavior is well described within the harmonic approximation, the two techniques should provide equal descriptions of surface phonon spectral densities and phonon frequencies. In this paper we demonstrate this agreement.
Torres, Rodrigo; Swift, Robert V.; Chim, Nicholas; Wheatley, Nicole; Lan, Benson; Atwood, Brian R.; Pujol, Céline; Sankaran, Banu; Bliska, James B.; Amaro, Rommie E.; Goulding, Celia W.
2011-01-01
Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway. PMID:21966419
Molecular Dynamics Calculations
NASA Technical Reports Server (NTRS)
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two winning videos in a competition held at the meeting of the American Physical Society's Division of Fluid Dynamics, held in Atlanta, Georgia, in November 1994. Of great interest was the result that in every shock there were a few high-speed precursor particles racing ahead of the shock, carrying information about its impending arrival. Most recently, Dr. Woo has been applying molecular dynamics techniques to the problem of determining the drag produced by the space station truss structure as it flies through the thin residual atmosphere of low-Earth orbit. This problem is made difficult by the complex structure of the truss and by the extreme supersonic nature of the flow. A fully filled section of the truss has already been examined, and drag predictions have been made. Molecular dynamics techniques promise to make realistic drag calculations possible even for very complex partially filled truss segments flying at arbitrary angles.
Scalable Molecular Dynamics with NAMD
Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kalé, Laxmikant; Schulten, Klaus
2008-01-01
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This paper, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. PMID:16222654
Thompson, M.A. [Pacific Northwest Lab., Richland, WA (United States)
1995-11-15
We present a hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) molecular dynamics study of the free energy profile for the association of K{sup +} with dimethyl ether (DME) in H{sub 2}O. We calculate a potential of mean force and find a weak solvent separated ion-dipole pair (SSIDP) at 5.4 A separation and a contact ion-dipole (CIDP) free energy minimum at 2.7 A separation of the K{sup +} with the oxygen of DME. The latter distance agrees well with the gas-phase optimized K{sup +}/DME structure. This study demonstrates the nonadditive interactions of a solvated cation with a simple monodentate organic ligand. These results are useful for interpreting K{sup +} complexation by multidentate ligands, such as the crown ethers. 36 refs., 4 figs., 1 tab.
VMD: visual molecular dynamics.
Humphrey, W; Dalke, A; Schulten, K
1996-02-01
VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web. PMID:8744570
Agrawal, Paras M; Raff, Lionel M; Hagan, Martin T; Komanduri, Ranga
2006-04-01
The neural network (NN) procedure to interpolate ab initio data for the purpose of molecular dynamics (MD) simulations has been tested on the SiO(2) system. Unlike other similar NN studies, here, we studied the dissociation of SiO(2) without the initial use of any empirical potential. During the dissociation of SiO(2) into Si+O or Si+O(2), the spin multiplicity of the system changes from singlet to triplet in the first reaction and from singlet to pentet in the second. This paper employs four potential surfaces. The first is a NN fit [NN(STP)] to a database comprising the lowest of the singlet, triplet, and pentet energies obtained from density functional calculations in 6673 nuclear configurations. The other three potential surfaces are obtained from NN fits to the singlet, triplet, and pentet-state energies. The dissociation dynamics on the singlet-state and NN(STP) surfaces are reported. The results obtained using the singlet surface correspond to those expected if the reaction were to occur adiabatically. The dynamics on the NN(STP) surface represent those expected if the reaction follows a minimum-energy pathway. This study on a small system demonstrates the application of NNs for MD studies using ab initio data when the spin multiplicity of the system changes during the dissociation process. PMID:16613454
Sarman, Sten; Laaksonen, Aatto
2015-02-01
Molecular dynamics simulations of planar elongational flow in a nematic liquid crystal model system based on the Gay-Berne fluid were undertaken by applying the SLLOD equations of motion with an elongational velocity field or strain rate. In order to facilitate the simulation, Kraynik-Reinelt periodic boundary conditions allowing arbitrarily long simulations were used. A Lagrangian constraint algorithm was utilized to fix the director at different angles relative to the elongation direction, so that the various pressure tensor elements could be calculated as a function of this angle. This made it possible to obtain accurate values of the shear viscosities which were found to agree with results previously obtained by shear flow simulations. The torque needed to fix the director at various angles relative to the elongation direction was evaluated in order to determine the stable orientation of the director, where this torque is equal to zero. This orientation was found to be parallel to the elongation direction. It was also noted that the irreversible entropy production was minimal when the director attained this orientation. Since the simulated system was rather large and fairly long simulation runs were undertaken it was also possible to study the cross coupling between the strain rate and the order tensor. It turned out to be very weak at low strain rates but at higher strain rates it could lead to break down of the liquid crystalline order. PMID:25523414
Floating orbital molecular dynamics simulations.
Perlt, Eva; Brüssel, Marc; Kirchner, Barbara
2014-04-21
We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated. PMID:24600690
Molecular Dynamics (MD) Gas Module
NSDL National Science Digital Library
Iacovella, Christopher R.
2007-12-10
This simulation consists of a single-component system of particles that interact as either ideal gas particles with no intermolecular potential or as Lennard-Jones Particles . The system runs NVT Molecular Dynamics utilizing the Berendsen Thermostat. The number of particles, volume and temperature are all user-modifiable variables. Additionally, one can select between non-interacting ideal gas particles or particles that interact via the Lennard-Jones Potential. The system can be changed between Argon and Krypton based on reduced unit variables. The average temperature and pressure are displayed on the screen. Additional information is also provided such simulation model/method description, detailed instructions for running the simulation, tutorials, sample questions, literature examples, and links to other relevant data.
Molecular dynamics with quantum fluctuations
NASA Astrophysics Data System (ADS)
Georgescu, Ionu?; Mandelshtam, Vladimir A.
2010-09-01
A quantum dynamics approach, called Gaussian molecular dynamics, is introduced. As in the centroid molecular dynamics, the N -body quantum system is mapped to an N -body classical system with an effective Hamiltonian arising within the variational Gaussian wave-packet approximation. The approach is exact for the harmonic oscillator and for the high-temperature limit, accurate in the short-time limit and is computationally very efficient.
Vitaliy Kapko; Dmitry V. Matyushov; C. Austen Angell
2011-06-07
The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and/or crystal growth) becoming small- thus a matter of kinetics. However there is evidence, dating back to the empirics of coal briquetting for maximum trucking efficiency, that ellipsoids pack efficiently when disordered. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids or spherocylinders (diatomics excepted) into the world of molecules with attractive forces, we have made a molecular dynamics MD study of crystal melting and glass formation on the Gay- Berne (G-B) model of ellipsoidal objects across the aspect ratio range of the hard ellipsoid studies. Here we report that, in the aspect ratio range of maximum ellipsoid packing efficiency, various G-B crystalline states, that cannot be obtained directly from the liquid, disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Without claiming to have proved the existence of single component examples, we use the present observations, together with our knowledge of non-ideal mixing effects, to discuss the probable existence of "ideal glassformers" - single or multicomponent liquids that vitrify before ever becoming metastable with respect to crystals. The existence of crystal-free routes to the glassy state removes any precrystalline fluctuation perspective from the "glass problem". Unexpectedly we find that liquids with aspect ratios in the "crystallophobic" range also behave in an unusual (non-hysteritic) way during temperature cycling through the glass transition. We link this to the highly volume fraction-sensitive ("fragile") behavior observed in recent hard dumbbell studies at similar length/diameter ratios.
Sheldon Goldstein; Ward Struyve
2014-11-05
Non-relativistic de Broglie-Bohm theory describes particles moving under the guidance of the wave function. In de Broglie's original formulation, the particle dynamics is given by a first-order differential equation. In Bohm's reformulation, it is given by Newton's law of motion with an extra potential that depends on the wave function--the quantum potential--together with a constraint on the possible velocities. It was recently argued, mainly by numerical simulations, that relaxing this velocity constraint leads to a physically untenable theory. We provide further evidence for this by showing that for various wave functions the particles tend to escape the wave packet. In particular, we show that for a central classical potential and bound energy eigenstates the particle motion is often unbounded. This work seems particularly relevant for ways of simulating wave function evolution based on Bohm's formulation of the de Broglie-Bohm theory. Namely, the simulations may become unstable due to deviations from the velocity constraint.
NASA Astrophysics Data System (ADS)
Goldstein, Sheldon; Struyve, Ward
2015-01-01
Non-relativistic de Broglie–Bohm theory describes particles moving under the guidance of the wave function. In de Broglie?s original formulation, the particle dynamics is given by a first-order differential equation. In Bohm?s reformulation, it is given by Newton?s law of motion with an extra potential that depends on the wave function—the quantum potential—together with a constraint on the possible velocities. It was recently argued, mainly by numerical simulations, that relaxing this velocity constraint leads to a physically untenable theory. We provide further evidence for this by showing that for various wave functions the particles tend to escape the wave packet. In particular, we show that for a central classical potential and bound energy eigenstates the particle motion is often unbounded. This work seems particularly relevant for ways of simulating wave function evolution based on Bohm?s formulation of the de Broglie–Bohm theory. Namely, the simulations may become unstable due to deviations from the velocity constraint.
Liu, Jianling; Liu, Mengmeng; Yao, Yao; Wang, Jinan; Li, Yan; Li, Guohui; Wang, Yonghua
2012-01-01
Chitinolytic ?-N-acetyl-d-hexosaminidases, as a class of chitin hydrolysis enzyme in insects, are a potential species-specific target for developing environmentally-friendly pesticides. Until now, pesticides targeting chitinolytic ?-N-acetyl-d-hexosaminidase have not been developed. This study demonstrates a combination of different theoretical methods for investigating the key structural features of this enzyme responsible for pesticide inhibition, thus allowing for the discovery of novel small molecule inhibitors. Firstly, based on the currently reported crystal structure of this protein (OfHex1.pdb), we conducted a pre-screening of a drug-like compound database with 8 × 10(6) compounds by using the expanded pesticide-likeness criteria, followed by docking-based screening, obtaining 5 top-ranked compounds with favorable docking conformation into OfHex1. Secondly, molecular docking and molecular dynamics simulations are performed for the five complexes and demonstrate that one main hydrophobic pocket formed by residues Trp424, Trp448 and Trp524, which is significant for stabilization of the ligand-receptor complex, and key residues Asp477 and Trp490, are respectively responsible for forming hydrogen-bonding and ?-? stacking interactions with the ligands. Finally, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis indicates that van der Waals interactions are the main driving force for the inhibitor binding that agrees with the fact that the binding pocket of OfHex1 is mainly composed of hydrophobic residues. These results suggest that screening the ZINC database can maximize the identification of potential OfHex1 inhibitors and the computational protocol will be valuable for screening potential inhibitors of the binding mode, which is useful for the future rational design of novel, potent OfHex1-specific pesticides. PMID:22605995
Uncertainty quantification in molecular dynamics
NASA Astrophysics Data System (ADS)
Rizzi, Francesco
This dissertation focuses on uncertainty quantification (UQ) in molecular dynamics (MD) simulations. The application of UQ to molecular dynamics is motivated by the broad uncertainty characterizing MD potential functions and by the complexity of the MD setting, where even small uncertainties can be amplified to yield large uncertainties in the model predictions. Two fundamental, distinct sources of uncertainty are investigated in this work, namely parametric uncertainty and intrinsic noise. Intrinsic noise is inherently present in the MD setting, due to fluctuations originating from thermal effects. Averaging methods can be exploited to reduce the fluctuations, but due to finite sampling, this effect cannot be completely filtered, thus yielding a residual uncertainty in the MD predictions. Parametric uncertainty, on the contrary, is introduced in the form of uncertain potential parameters, geometry, and/or boundary conditions. We address the UQ problem in both its main components, namely the forward propagation, which aims at characterizing how uncertainty in model parameters affects selected observables, and the inverse problem, which involves the estimation of target model parameters based on a set of observations. The dissertation highlights the challenges arising when parametric uncertainty and intrinsic noise combine to yield non-deterministic, noisy MD predictions of target macroscale observables. Two key probabilistic UQ methods, namely Polynomial Chaos (PC) expansions and Bayesian inference, are exploited to develop a framework that enables one to isolate the impact of parametric uncertainty on the MD predictions and, at the same time, properly quantify the effect of the intrinsic noise. Systematic applications to a suite of problems of increasing complexity lead to the observation that an uncertain PC representation built via Bayesian regression is the most suitable model for the representation of uncertain MD predictions of target observables in the presence of intrinsic noise and parametric uncertainty. The dissertation is organized in successive, self-contained problems of increasing complexity aimed at investigating the target UQ challenge in a progressive fashion.
NASA Astrophysics Data System (ADS)
Zhang, Yan; Lin, Hai
2009-05-01
Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6?-hydrogen abstraction and the 6?-d1-testosterone 6?-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.
Silicene nanoribbons: Molecular-dynamics simulations
Alper Ince; Sakir Erkoc
2011-01-01
Structural properties of silicene nanoribbons have been investigated by performing classical molecular-dynamics simulations using atomistic many-body potential energy functions at low and room temperatures with finite and infinite lengths. It has been found that finite length models are more likely to form tubular structures at room temperature.
VMD: Visual molecular dynamics
William Humphrey; Andrew Dalke; Klaus Schulten
1996-01-01
VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more “representations,” in which each representation embodies a particular rendering method and
Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G; Gao, Jiali
2009-02-17
A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å(3), and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from -0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible. PMID:20490369
Moonsamy, Suri; Dash, Radha Charan; Soliman, Mahmoud E S
2014-01-01
Using integrated in-silico computational techniques, including homology modeling, structure-based and pharmacophore-based virtual screening, molecular dynamic simulations, per-residue energy decomposition analysis and atom-based 3D-QSAR analysis, we proposed ten novel compounds as potential CCR5-dependent HIV-1 entry inhibitors. Via validated docking calculations, binding free energies revealed that novel leads demonstrated better binding affinities with CCR5 compared to maraviroc, an FDA-approved HIV-1 entry inhibitor and in clinical use. Per-residue interaction energy decomposition analysis on the averaged MD structure showed that hydrophobic active residues Trp86, Tyr89 and Tyr108 contributed the most to inhibitor binding. The validated 3D-QSAR model showed a high cross-validated rcv2 value of 0.84 using three principal components and non-cross-validated r2 value of 0.941. It was also revealed that almost all compounds in the test set and training set yielded a good predicted value. Information gained from this study could shed light on the activity of a new series of lead compounds as potential HIV entry inhibitors and serve as a powerful tool in the drug design and development machinery. PMID:24762964
Soliton dynamics in complex potentials
NASA Astrophysics Data System (ADS)
Kominis, Yannis
2015-01-01
Soliton propagation dynamics under the presence of a complex potential are investigated. Cases of both symmetric and non-symmetric potentials are studied in terms of their effect on soliton dynamics. The existence of an invariant of soliton propagation under specific symmetry conditions for the real and the imaginary part of the potential is shown. The rich set of dynamical features of soliton propagation include dynamical trapping, periodic and nonperiodic soliton mass variation and non-reciprocal dynamics. These features are systematically investigated with the utilization of an effective particle phase space approach which is shown in remarkable agreement with direct numerical simulations. The generality of the results enables the consideration of potential applications where the inhomogeneity of the gain and loss is appropriately engineered in order to provide desirable soliton dynamics.
Kapko, Vitaliy; Angell, C Austen
2010-01-01
The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and/or crystal growth) becoming small [1] - thus a matter of kinetics. However there is evidence, dating back to the empirics of coal briquetting for maximum trucking efficiency [2] that some object shapes find little advantage in self- assembly to ordered structures - meaning random packings prevail. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids [3,4] or spherocylinders [5] into the world of molecules with attractive forces, we have carried out potential tuning MD studies on the behavior of the Gay-Berne (G-B) model [6] at aspect ratios in the range of the hard ellipsoid studies. Here we report that, in the aspect ratio range of maximum ellipsoid packing efficiency, some G-B crystalline states disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Cooling of the liquids in this range...
Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.
1999-05-21
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule.
Molecular Dynamics with Quantum Fluctuations
NASA Astrophysics Data System (ADS)
Georgescu, Ionut; Deckman, Jason; Mandelshtam, Vladimir
2011-03-01
A new Quantum Dynamics approach, called Gaussian Molecular Dynamics (GMD), is introduced. As in the Centroid Molecular Dynamics (CMD), the N-body quantum system is mapped to an N-body classical system with an effective Hamiltonian arising within the Variational Gaussian Wave-packet approximation. The approach is exact for the harmonic oscillator and for the high-temperature limit, accurate in the short time limit and is computationally very efficient. GMD is furthermore used to estimate the diffusion constant and the spectrum of the velocity auto-correlation function of low pressure para-hydrogen at 14K and respectively 25K. The results are consistent with known experimental and theoretical results, such as CMD and RPMD.
Simon, Aude; Iftner, Christophe; Mascetti, Joëlle; Spiegelman, Fernand
2015-03-19
The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1-6). The potential energy surface is obtained from a hybrid self-consistent charge density functional-based tight binding/force-field approach (SCC-DFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ?340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion-rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the bending modes. This is in agreement with experimental data. Furthermore, in the case of the water monomer and dimer, the magnitudes of the computed shifts are in fair agreement with the experimental values. The complex case of the water hexamer, which presents several low-energy isomers, is discussed. PMID:25650885
Molecular dynamics studies of silica wafer bonding
NASA Astrophysics Data System (ADS)
Timpel, Dirk; Schaible, Max; Scheerschmidt, Kurt
1999-03-01
Molecular dynamics simulations are performed to investigate the atomic processes initiated by the adhesion of two silica surfaces, which are covered with adsorbates of oxygen, hydrogen or water molecules. The calculations describe the mechanism of hydrophilic silicon wafer bonding in terms of empirical potentials assumed. The challenge of the macroscopically relevant computations is to understand and to predict the formation of covalent bonds as a function of initial silica structures, external forces, adsorbates, and annealing temperatures applied.
Grand canonical Molecular Dynamics Simulations
Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K
2011-01-01
For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.
Molecular dynamics investigation of nanoscale cavitation dynamics.
Sasikumar, Kiran; Keblinski, Pawel
2014-12-21
We use molecular dynamics simulations to investigate the cavitation dynamics around intensely heated solid nanoparticles immersed in a model Lennard-Jones fluid. Specifically, we study the temporal evolution of vapor nanobubbles that form around the solid nanoparticles heated over ps time scale and provide a detail description of the following vapor formation and collapse. For 8 nm diameter nanoparticles we observe the formation of vapor bubbles when the liquid temperature 0.5-1 nm away from the nanoparticle surface reaches ?90% of the critical temperature, which is consistent with the onset of spinodal decomposition. The peak heat flux from the hot solid to the surrounding liquid at the bubble formation threshold is ?20 times higher than the corresponding steady state critical heat flux. Detailed analysis of the bubble dynamics indicates adiabatic formation followed by an isothermal final stage of growth and isothermal collapse. PMID:25527949
Molecular dynamics investigation of nanoscale cavitation dynamics
NASA Astrophysics Data System (ADS)
Sasikumar, Kiran; Keblinski, Pawel
2014-12-01
We use molecular dynamics simulations to investigate the cavitation dynamics around intensely heated solid nanoparticles immersed in a model Lennard-Jones fluid. Specifically, we study the temporal evolution of vapor nanobubbles that form around the solid nanoparticles heated over ps time scale and provide a detail description of the following vapor formation and collapse. For 8 nm diameter nanoparticles we observe the formation of vapor bubbles when the liquid temperature 0.5-1 nm away from the nanoparticle surface reaches ˜90% of the critical temperature, which is consistent with the onset of spinodal decomposition. The peak heat flux from the hot solid to the surrounding liquid at the bubble formation threshold is ˜20 times higher than the corresponding steady state critical heat flux. Detailed analysis of the bubble dynamics indicates adiabatic formation followed by an isothermal final stage of growth and isothermal collapse.
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics
Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.
2012-01-01
It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924
From Molecular Dynamics to Brownian Dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.
From molecular dynamics to Brownian dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane. PMID:25002825
Molecular Heterogeneity in Glioblastoma: Potential Clinical Implications
Parker, Nicole Renee; Khong, Peter; Parkinson, Jonathon Fergus; Howell, Viive Maarika; Wheeler, Helen Ruth
2015-01-01
Glioblastomas, (grade 4 astrocytomas), are aggressive primary brain tumors characterized by histopathological heterogeneity. High-resolution sequencing technologies have shown that these tumors also feature significant inter-tumoral molecular heterogeneity. Molecular subtyping of these tumors has revealed several predictive and prognostic biomarkers. However, intra-tumoral heterogeneity may undermine the use of single biopsy analysis for determining tumor genotype and has implications for potential targeted therapies. The clinical relevance and theories of tumoral molecular heterogeneity in glioblastoma are discussed. PMID:25785247
Potential formulation of sleep dynamics
NASA Astrophysics Data System (ADS)
Phillips, A. J. K.; Robinson, P. A.
2009-02-01
A physiologically based model of the mechanisms that control the human sleep-wake cycle is formulated in terms of an equivalent nonconservative mechanical potential. The potential is analytically simplified and reduced to a quartic two-well potential, matching the bifurcation structure of the original model. This yields a dynamics-based model that is analytically simpler and has fewer parameters than the original model, allowing easier fitting to experimental data. This model is first demonstrated to semiquantitatively match the dynamics of the physiologically based model from which it is derived, and is then fitted directly to a set of experimentally derived criteria. These criteria place rigorous constraints on the parameter values, and within these constraints the model is shown to reproduce normal sleep-wake dynamics and recovery from sleep deprivation. Furthermore, this approach enables insights into the dynamics by direct analogies to phenomena in well studied mechanical systems. These include the relation between friction in the mechanical system and the timecourse of neurotransmitter action, and the possible relation between stochastic resonance and napping behavior. The model derived here also serves as a platform for future investigations of sleep-wake phenomena from a dynamical perspective.
Better, Cheaper, Faster Molecular Dynamics
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
NASA Astrophysics Data System (ADS)
Neri, Marilisa; Anselmi, Claudio; Carnevale, Vincenzo; Vargiu, Attilio V.; Carloni, Paolo
2006-04-01
Outer-membrane proteases T (OmpT) are membrane enzymes used for defense by Gram-negative bacteria. Here we use hybrid molecular mechanics/coarse-grained simulations to investigate the role of large-scale motions of OmpT from Escherichia coli for its function. In this approach, the enzyme active site is treated at the all-atom level, whilst the rest of the protein is described at the coarse-grained level. Our calculations agree well with previously reported all-atom molecular dynamics simulations, suggesting that this approach is well suitable to investigate membrane proteins. In addition, our findings suggest that OmpT large-scale conformational fluctuations might play a role for its biological function, as found for another protease class, the aspartyl proteases.
Molecular Dynamics Simulations of Crystal Copper: Bulk Modulus and Shocks
NASA Astrophysics Data System (ADS)
Warrier, M.; Rawat, S.; Chaturvedi, S.
2011-07-01
Molecular dynamics is used to study the response of single crystal copper target to impacts by single crystal copper at velocities in the range 1 km/s to 3 km/s. The Embedded Atom Method (EAM) potential by Foiles et al. for Cu [1] was used in the simulation. The potential and its implementation in the open source, Large-scale Atomic Molecular Massively Parallel Simulator (LAMMPS) [2] was verified by reproducing the experimental values of bulk modulus of Cu. The shock velocity (us) as a function of particle velocity (up) matches published experimental and molecular dynamic simulations results.
Radiation in molecular dynamic simulations
Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M
2008-10-13
Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.
Ab initio molecular dynamics for liquid metals
G. Kresse; J. Hafner
1993-01-01
We present ab initio quantum-mechanical molecular-dynamics calculations based on the calculation of the electronic ground state and of the Hellmann-Feynman forces in the local-density approximation at each molecular-dynamics step. This is possible using conjugate-gradient techniques for energy minimization, and predicting the wave functions for new ionic positions using subspace alignment. This approach avoids the instabilities inherent in quantum-mechanical molecular-dynamics calculations
Unified approach for molecular dynamics and density-functional theory
R. Car; M. Parrinello
1985-01-01
We present a unified scheme that, by combining molecular dynamics and density-functional theory, profoundly extends the range of both concepts. Our approach extends molecular dynamics beyond the usual pair-potential approximation, thereby making possible the simulation of both covalently bonded and metallic systems. In addition it permits the application of density-functional theory to much larger systems than previously feasible. The new
Application of optimal prediction to molecular dynamics
Barber IV, John Letherman
2004-12-01
Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is {delta}-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.
Molecular dynamics simulations of nanostructures
NASA Astrophysics Data System (ADS)
Yuan, Zaoshi
This dissertation is focused on multimillion-atom molecular dynamics (MD) simulations of nanoscale materials. In the past decade, nanoscale materials have made significant commercial impacts, which will potentially lead to the next industrial revolution. The interest lies in the novel and promising features nanoscale materials exhibit due to their confined sizes. However, not all novel behaviors are understood or controllable. Many uncontrollable parameters, e.g. defects and dangling bonds, are known to hinder the performance of nanodevices. Solutions to these problems rely on our understanding of fundamental elements in nanoscience: isolated individual nanostructures and their assemblies. In this dissertation, we will address atomistic foundations of several problems of technological importance in nanoscience. Specifically, three basic problems are discussed: (1) embrittlement of nanocrystalline metal; (2) novel thermo-mechanical behaviors of nanowires (NWs); and (3) planar defect generation in NWs. With a scalable algorithm implemented on massively parallel computing platforms and various data mining methods, MD simulations can provide valuable insights into these problems. An essential role of sulfur segregation-induced amorphization of crystalline nickel was recently discovered experimentally, but the atomistic mechanism of the amorphization remains unexplained. Our MD simulations reveal that the large steric size of sulfur impurity causes strong sulfur-sulfur interaction mediated by lattice distortion, which leads to amorphization near the percolation threshold at the sulfur-sulfur network in nickel crystal. The generality of the mechanism due to the percolation of an impurity network is further confirmed by a model binary system. In our study of novel behaviors of semiconductor NWs, MD simulations construct a rich size-temperature `phase diagram' for the mechanical response of a zinc-oxide NW under tension. For smaller diameters and higher temperatures, novel transitions are found from brittle cleavage to structural transformation-mediated brittle cleavage to ductile failure. Atomistic mechanisms of the unique nano-thermo-mechanical behavior are elucidated as a consequence of surface-structural relaxation, which in particular predicts spontaneous formation of a core/shell structure under tension. The phase diagram resolves controversies between previous experiments and theory, and the predicted `intrinsic' core/shell structure may find novel device applications. Generation of stacking faults (SFs) during the growth of NWs is a major concern for the efficiency of NW-based devices such as solar cells. MD simulation of a [111]-oriented gallium arsenide NW reveals an atomistic mechanism of SF generation. Spatial distribution of the adatom energy on the (111)B top surface exhibits a novel core/shell structure due to the contraction of atomic bonds at the sidewall surfaces, where SFs are preferentially nucleated in the shell. A nucleation growth model incorporating the core/shell mechanism suggests a size and growth-condition controlled approach for SF-free growth of NWs.
Fragment recognition in molecular dynamics
Strachan, A.; Dorso, C.O. [Departamento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellon I, Ciudad Universitaria, Nunez (1428), Buenos Aires (Argentina)] [Departamento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellon I, Ciudad Universitaria, Nunez (1428), Buenos Aires (Argentina)
1997-08-01
We investigate the properties of three methods of fragment recognition in microscopic simulations of molecular dynamics. They are (a) the early cluster recognition algorithm (ECRA) which looks for the most bound partitions in phase space, (b) the minimum spanning tree in two particle energy space (MSTE) which looks for those simply connected partitions in which each particle is bound to, at least, one other member of the cluster to which it belongs, and (c) the standard minimum spanning tree (MST) in configuration space. It is found that, if the objective of a given calculation is to study the time evolution of properties related to the fragment distribution, the MST should be discarded, MSTE results will be valid for not too short times, and ECRA results will give the most complete description of such properties. {copyright} {ital 1997} {ital The American Physical Society}
Emergent Phenomena via Molecular Dynamics
NASA Astrophysics Data System (ADS)
Rapaport, D. C.
Emergent phenomena are unusual because they are not obvious consequences of the design of the systems in which they appear, a feature no less relevant when they are being simulated. Several systems that exhibit surprisingly rich emergent behavior, each studied by molecular dynamics (MD) simulation, are described: (i) Modeling self-assembly processes associated with virus growth reveals the ability to achieve error-free assembly, where paradoxically, near-maximum yields are due to reversible bond formation. (ii) In fluids studied at the atomistic level, complex hydrodynamic phenomena in rotating and convecting fluids - the Taylor- Couette and Rayleigh-Bénard instabilities - can be reproduced, despite the limited length and time scales accessible by MD. (iii) Segregation studies of granular mixtures in a rotating drum reproduce the expected, but counterintuitive, axial and radial segregation, while for the case of a vertically vibrated layer a novel form of horizontal segregation is revealed.
Molecular dynamics simulation of liquid trimethylphosphine
Luciano T. Costa; Thaciana Malaspina; Eudes E. Fileti; Mauro C. C. Ribeiro
2011-01-01
Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH3)3P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual
Kabiri, Mona; Amiri-Tehranizadeh, Zeinab; Baratian, Ali; Saberi, Mohammad Reza; Chamani, Jamshidkhan
2012-01-01
For the first time, the binding of ropinirole hydrochloride (ROP) and aspirin (ASA) to human holo-transferrin (hTf) has been investigated by spectroscopic approaches (fluorescence quenching, synchronous fluorescence, time-resolved fluorescence, three-dimensional fluorescence, UV-vis absorption, circular dichroism, resonance light scattering), as well as zeta potential and molecular modeling techniques, under simulated physiological conditions. Fluorescence analysis was used to estimate the effect of the ROP and ASA drugs on the fluorescence of hTf as well as to define the binding and quenching properties of binary and ternary complexes. The synchronized fluorescence and three-dimensional fluorescence spectra demonstrated some micro-environmental and conformational changes around the Trp and Tyr residues with a faint red shift. Thermodynamic analysis displayed the van der Waals forces and hydrogen bonds interactions are the major acting forces in stabilizing the complexes. Steady-state and time-resolved fluorescence data revealed that the fluorescence quenching of complexes are static mechanism. The effect of the drugs aggregating on the hTf resulted in an enhancement of the resonance light scattering (RLS) intensity. The average binding distance between were computed according to the forster non-radiation energy transfer theory. The circular dichroism (CD) spectral examinations indicated that the binding of the drugs induced a conformational change of hTf. Measurements of the zeta potential indicated that the combination of electrostatic and hydrophobic interactions between ROP, ASA and hTf formed micelle-like clusters. The molecular modeling confirmed the experimental results. This study is expected to provide important insight into the interaction of hTf with ROP and ASA to use in various toxicological and therapeutic processes. PMID:22410420
Molecular dynamics in amorphous ergocalciferol
NASA Astrophysics Data System (ADS)
Mohamed, Sahra; Thayyil, M. Shahin; Capaccioli, S.
2014-04-01
While developing new pharmaceutical products based on drug substances in their amorphous form, the molecular mobility of amorphous active ingredients have to be characterized in detail. The molecular mobility in the supercooled liquid and glassy states of ergocalciferol is studied using broadband dielectric spectroscopy over wide frequency and temperature ranges. Dielectric studies revealed a number of relaxation process of different molecular origin.
Hydration dynamics in water clusters via quantum molecular dynamics simulations
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 the non-cavity type model. Relaxation associated with cavity collapse presents, however, unique dynamical signatures.
First principles molecular dynamics without self-consistent field optimization
Souvatzis, Petros, E-mail: petros.souvatsiz@fysik.uu.se [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120 Uppsala (Sweden)] [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120 Uppsala (Sweden); Niklasson, Anders M. N., E-mail: amn@lanl.gov [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)
2014-01-28
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.
Molecular-dynamics simulations of lead clusters
NASA Astrophysics Data System (ADS)
Hendy, S. C.; Hall, B. D.
2001-08-01
Molecular-dynamics simulations of nanometer-sized lead clusters have been performed using the Lim-Ong-Ercolessi glue potential [Surf. Sci. 269/270, 1109 (1992)]. The binding energies of clusters forming crystalline (fcc), decahedron and icosahedron structures are compared, showing that fcc cuboctahedra are the most energetically favored of these polyhedral model structures. However, simulations of the freezing of liquid droplets produced a characteristic form of surface-reconstructed ``shaved'' icosahedron, in which atoms are absent at the edges and apexes of the polyhedron. This arrangement is energetically favored for 600-4000 atom clusters. Larger clusters favor crystalline structures. Indeed, simulated freezing of a 6525-atom liquid droplet produced an imperfect fcc Wulff particle, containing a number of parallel stacking faults. The effects of temperature on the preferred structure of crystalline clusters below the melting point have been considered. The implications of these results for the interpretation of experimental data is discussed.
Thermal transpiration: A molecular dynamics study
NASA Astrophysics Data System (ADS)
T, Joe Francis; Sathian, Sarith P.
2014-12-01
Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.
Molecular dynamics simulations of sonoluminescence
NASA Astrophysics Data System (ADS)
Bass, Alexander
Molecular Dynamics (MD) techniques are uniquely suited for simulating sonoluminescing bubbles, thanks to the bubbles' small size. Unlike hydrodynamic methods, MD does not assume local thermodynamic equilibrium, neither does it require knowledge of equation of state and transport properties at high pressures and temperatures. Full-scale MD simulations of experimentally observable bubbles, however, are still too expensive computationally. A symmetry reduction technique that makes use of the bubble's spherical symmetry is proposed. This technique is shown to be capable of manifold reduction of the machine time required to simulate a bubble collapse, while the few artifacts introduced by it are carefully analyzed. The model developed is then applied to a variety of experimentally observed bubbles, in particular to a class of "extreme" bubbles with collapse ratios of around 25:1. It is shown that different noble gases exhibit vastly different behaviors under such conditions, largely explained by the difference in the speed of sound at a given temperature. Heavier gases generate strong shock waves and reach much higher temperatures than lighter gases. However if a small amount of lighter gas is added to the heavier gas, the two gases will segregate, often completely, during the final stage of the collapse, resulting in the lighter gas being trapped in the center of the bubble and heating up to temperatures by several orders of magnitude exceeding those attained with the lighter gas alone. While the simulations presented in this work constitute an approach to a well defined mathematical problem they have been carried out with goal of gaining insight into a real phenomenon: light emission from a rapidly collapsing bubble of gas. In this process---sonoluminescence---acoustic energy density concentrates by at least 12 orders of magnitude to generate picosecond flashes of ultraviolet light. The simulations in this dissertation are aimed at explaining and predicting the experimental parameters which could lead to even greater levels of energy focusing in these bubbly systems.
Molecular dynamics simulations of supramolecular polymer rheology.
Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E
2010-11-14
Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate ? and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation. PMID:21073229
Molecular dynamics simulations of supramolecular polymer rheology
NASA Astrophysics Data System (ADS)
Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.
2010-11-01
Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate ? and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.
Sobolewski, Emil; O?dziej, Stanis?aw; Wi?niewska, Marta; Liwo, Adam; Makowski, Mariusz
2012-01-01
By means of molecular dynamics simulations of 15 pairs of molecules selected to model the interactions of nonpolar, nonpolar and polar, nonpolar and charged, polar, and polar and charged side chains in water, we determined the potentials of mean force (PMFs) of pairs of interacting molecules in water as functions of distance between the interacting particles or their distance and orientations at three temperatures: 283 K, 323 K and 373 K, respectively. The systems were found to fall into the following four categories as far as the temperature dependence of the potential of mean force is concerned: (i) pairs, for which association is entropy-driven (ii) pairs, for which association is energy-driven, (iii), pairs of positively-charged solute molecules, for which association is energy-driven with unfavorable entropy change, and (iv) the remaining systems for which temperature dependence is weak. For each pair of PMFs entropic and energetic contributions have been discussed. PMID:22475198
Modeling the Hydrogen Bond within Molecular Dynamics
ERIC Educational Resources Information Center
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Molecular Dynamics Simulations of Simple Liquids
ERIC Educational Resources Information Center
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Multiple time step integrators in ab initio molecular dynamics
Luehr, Nathan; Martínez, Todd J. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States) [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); The PULSE Institute, Stanford University, Stanford, California 94305 (United States); SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Markland, Thomas E. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)] [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)
2014-02-28
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.
Molecular Dynamics of Methanol Monocation (CH3OH+ ) in Strong
Schlegel, H. Bernhard
Molecular Dynamics of Methanol Monocation (CH3OH+ ) in Strong Laser Fields Bishnu Thapa and H surfaces of methanol neutral, monocation, and singlet and triplet dication were explored using the CBS in the presence of a 2.9 Ã? 1014 W/cm2 800 nm laser field for methanol monocation on the ground state potential
MOLECULAR DYNAMICS SIMULATIONS OF HEAT TRANSFER OF CARBON NANOTUBES
Maruyama, Shigeo
MOLECULAR DYNAMICS SIMULATIONS OF HEAT TRANSFER OF CARBON NANOTUBES J. Shiomi, Y. Igarashi, Y-ku, Tokyo 113-8656, JAPAN Several heat transfer problems related to single-walled carbon nanotubes (SWNTs] is employed as the potential function between carbon and carbon within a nanotube. MD simulations of thermal
Confinement of conjugated polymers into soft nanoparticles: molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Wijesinghe, Sidath; Perahia, Dvora; Grest, Gary S.
2013-03-01
The structure and dynamics of conjugated polymers confined into soft nanoparticles (SNPs) have been studies by molecular dynamic simulations. This new class of tunable luminescent SNPs exhibits an immense potential as bio-markers as well as targeted drug delivery agents where tethering specific groups to the surface particles offers a means to target specific applications. Of particular interest are SNPs that consist of non- crosslinked polymers, decorated with polar groups. These SNPs are potentially tunable through the dynamics of the polymer chains, whereas the polar entity serves as internal stabilizer and surface encore. Confinement of a polymer whose inherent conformation is extended impacts not only their dynamics and as a result their optical properties. Here we will present insight into the structure and dynamics of dialkyl poly para phenylene ethynylene (PPE), decorated by a carboxylate groups, confined into a soft particle. The conformation and dynamics of polymer within SNP will be discussed and compared with that of the linear chain in solution.
A Molecular Based Dynamic Model for Viscoelastic
2 #12; A Molecular Based Dynamic Model for Viscoelastic Responses of Rubber in Tensile Deformations; Abstract Dynamic equations are developed for rubber viscoelasticity based upon a stickslip continuum density functions constitutes one basis to model viscoelastic effects in rubber deformations. #12; 1
Osmosis : a molecular dynamics computer simulation study
NASA Astrophysics Data System (ADS)
Lion, Thomas
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..
Trillion-atom molecular dynamics becomes a reality
Kadau, Kai [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory
2008-01-01
By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD{_}render.
NASA Astrophysics Data System (ADS)
Kapko, Vitaliy; Zhao, Zuofeng; Matyushov, Dmitry V.; Austen Angell, C.
2013-03-01
The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and/or crystal growth) becoming small [D. R. Uhlmann, J. Non-Cryst. Solids 7, 337 (1972), 10.1016/0022-3093(72)90269-4] - and thus a matter of kinetics. However, there is evidence dating back to the empirics of coal briquetting for maximum trucking efficiency [D. Frenkel, Physics 3, 37 (2010), 10.1103/Physics.3.37] that some object shapes find little advantage in self-assembly to ordered structures - meaning random packings prevail. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids [A. Donev, F. H. Stillinger, P. M. Chaikin, and S. Torquato, Phys. Rev. Lett. 92, 255506 (2004), 10.1103/PhysRevLett.92.255506; A. Donev, I. Cisse, D. Sachs, E. A. Variano, F. H. Stillinger, R. Connelly, S. Torquato, and P. M. Chaikin, Science 303, 990 (2004), 10.1126/science.1093010] or spherocylinders [S. R. Williams and A. P. Philipse, Phys. Rev. E 67, 051301 (2003), 10.1103/PhysRevE.67.051301] (diatomics excepted [S.-H. Chong, A. J. Moreno, F. Sciortino, and W. Kob, Phys. Rev. Lett. 94, 215701 (2005), 10.1103/PhysRevLett.94.215701] into the world of molecules with attractive forces, we have made a molecular dynamics study of crystal melting and glass formation on the Gay-Berne (G-B) model of ellipsoidal objects [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981), 10.1063/1.441483] across the aspect ratio range of the hard ellipsoid studies. Here, we report that in the aspect ratio range of maximum ellipsoid packing efficiency, various G-B crystalline states that cannot be obtained directly from the liquid, disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Without claiming to have proved the existence of single component examples, we use the present observations, together with our knowledge of non-ideal mixing effects, to discuss the probable existence of "ideal glassformers" - single or multicomponent liquids that vitrify before ever becoming metastable with respect to crystals. We find evidence that "ideal glassformer" systems might also be highly fragile systems, approaching the "ideal glass" condition. We link this to the high "volume fragility" behavior observed in recent hard dumbbell studies at similar length/diameter ratios [R. Zhang and K. S. Schweitzer, J. Chem. Phys. 133, 104902 (2010), 10.1063/1.3483601]. The discussion suggests some unusual systems for laboratory study. Using differential scanning calorimetry detection of fusion points Tm, liquidus temperatures Tl, and glass transition temperatures Tg, we describe a system that would seem incapable of crystallizing before glass transition, i.e., an "ideal glassformer." The existence of crystal-free routes to the glassy state will eliminate precrystalline fluctuations as a source of the dynamic heterogeneities that are generally considered important in the discussion of the "glassy state problem [P. W. Anderson, Science 267, 1615 (1995), 10.1126/science.267.5204.1615-e]."
Kapko, Vitaliy; Zhao, Zuofeng; Matyushov, Dmitry V; Austen Angell, C
2013-03-28
The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and?or crystal growth) becoming small [D. R. Uhlmann, J. Non-Cryst. Solids 7, 337 (1972)]--and thus a matter of kinetics. However, there is evidence dating back to the empirics of coal briquetting for maximum trucking efficiency [D. Frenkel, Physics 3, 37 (2010)] that some object shapes find little advantage in self-assembly to ordered structures--meaning random packings prevail. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids [A. Donev, F. H. Stillinger, P. M. Chaikin, and S. Torquato, Phys. Rev. Lett. 92, 255506 (2004); A. Donev, I. Cisse, D. Sachs, E. A. Variano, F. H. Stillinger, R. Connelly, S. Torquato, and P. M. Chaikin, Science 303, 990 (2004)] or spherocylinders [S. R. Williams and A. P. Philipse, Phys. Rev. E 67, 051301 (2003)] (diatomics excepted [S.-H. Chong, A. J. Moreno, F. Sciortino, and W. Kob, Phys. Rev. Lett. 94, 215701 (2005)] into the world of molecules with attractive forces, we have made a molecular dynamics study of crystal melting and glass formation on the Gay-Berne (G-B) model of ellipsoidal objects [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)] across the aspect ratio range of the hard ellipsoid studies. Here, we report that in the aspect ratio range of maximum ellipsoid packing efficiency, various G-B crystalline states that cannot be obtained directly from the liquid, disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Without claiming to have proved the existence of single component examples, we use the present observations, together with our knowledge of non-ideal mixing effects, to discuss the probable existence of "ideal glassformers"--single or multicomponent liquids that vitrify before ever becoming metastable with respect to crystals. We find evidence that "ideal glassformer" systems might also be highly fragile systems, approaching the "ideal glass" condition. We link this to the high "volume fragility" behavior observed in recent hard dumbbell studies at similar length?diameter ratios [R. Zhang and K. S. Schweitzer, J. Chem. Phys. 133, 104902 (2010)]. The discussion suggests some unusual systems for laboratory study. Using differential scanning calorimetry detection of fusion points T(m), liquidus temperatures T(l), and glass transition temperatures T(g), we describe a system that would seem incapable of crystallizing before glass transition, i.e., an "ideal glassformer." The existence of crystal-free routes to the glassy state will eliminate precrystalline fluctuations as a source of the dynamic heterogeneities that are generally considered important in the discussion of the "glassy state problem [P. W. Anderson, Science 267, 1615 (1995)]." PMID:23556800
Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code
NASA Astrophysics Data System (ADS)
Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín
2010-12-01
Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summaryProgram title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.
NVU dynamics. III. Simulating molecules at constant potential energy
NASA Astrophysics Data System (ADS)
Ingebrigtsen, Trond S.; Dyre, Jeppe C.
2012-12-01
This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 135, 104101 (2011), 10.1063/1.3623585; T. S. Ingebrigtsen, S. Toxvaerd, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 135, 104102 (2011), 10.1063/1.3623586], a numerical algorithm for simulating geodesic motion of atomic systems was developed and tested against standard algorithms. The conclusion was that the NVU algorithm has the same desirable properties as the Verlet algorithm for Newtonian NVE dynamics, i.e., it is time-reversible and symplectic. Additionally, it was concluded that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit. In this paper, the NVU algorithm for atomic systems is extended to be able to simulate the geodesic motion of molecules at constant potential energy. We derive an algorithm for simulating rigid bonds and test this algorithm on three different systems: an asymmetric dumbbell model, Lewis-Wahnström o-terphenyl (OTP) and rigid SPC/E water. The rigid bonds introduce additional constraints beyond that of constant potential energy for atomic systems. The rigid-bond NVU algorithm conserves potential energy, bond lengths, and step length for indefinitely long runs. The quantities probed in simulations give results identical to those of Nosé-Hoover NVT dynamics. Since Nosé-Hoover NVT dynamics is known to give results equivalent to those of NVE dynamics, the latter results show that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit also for molecular systems.
NVU dynamics. III. Simulating molecules at constant potential energy.
Ingebrigtsen, Trond S; Dyre, Jeppe C
2012-12-28
This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 135, 104101 (2011); T. S. Ingebrigtsen, S. Toxvaerd, T. B. Schrøder, and J. C. Dyre, ibid. 135, 104102 (2011)], a numerical algorithm for simulating geodesic motion of atomic systems was developed and tested against standard algorithms. The conclusion was that the NVU algorithm has the same desirable properties as the Verlet algorithm for Newtonian NVE dynamics, i.e., it is time-reversible and symplectic. Additionally, it was concluded that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit. In this paper, the NVU algorithm for atomic systems is extended to be able to simulate the geodesic motion of molecules at constant potential energy. We derive an algorithm for simulating rigid bonds and test this algorithm on three different systems: an asymmetric dumbbell model, Lewis-Wahnström o-terphenyl (OTP) and rigid SPC/E water. The rigid bonds introduce additional constraints beyond that of constant potential energy for atomic systems. The rigid-bond NVU algorithm conserves potential energy, bond lengths, and step length for indefinitely long runs. The quantities probed in simulations give results identical to those of Nosé-Hoover NVT dynamics. Since Nose?-Hoover NVT dynamics is known to give results equivalent to those of NVE dynamics, the latter results show that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit also for molecular systems. PMID:23277922
González-Romero, Rodrigo; Rivera-Casas, Ciro; Frehlick, Lindsay J.; Méndez, Josefina; Ausió, Juan; Eirín-López, José M.
2012-01-01
Histone variants are used by the cell to build specialized nucleosomes, replacing canonical histones and generating functionally specialized chromatin domains. Among many other processes, the specialization imparted by histone H2A (H2A.X and H2A.Z) variants to the nucleosome core particle constitutes the earliest response to DNA damage in the cell. Consequently, chromatin-based genotoxicity tests have been developed in those cases where enough information pertaining chromatin structure and dynamics is available (i.e., human and mouse). However, detailed chromatin knowledge is almost absent in most organisms, specially protostome animals. Molluscs (which represent sentinel organisms for the study of pollution) are not an exception to this lack of knowledge. In the present work we first identified the existence of functionally differentiated histone H2A.X and H2A.Z variants in the mussel Mytilus galloprovincialis (MgH2A.X and MgH2A.Z), a marine organism widely used in biomonitoring programs. Our results support the functional specialization of these variants based on: a) their active expression in different tissues, as revealed by the isolation of native MgH2A.X and MgH2A.Z proteins in gonad and hepatopancreas; b) the evolutionary conservation of different residues encompassing functional relevance; and c) their ability to confer specialization to nucleosomes, as revealed by nucleosome reconstitution experiments using recombinant MgH2A.X and MgH2A.Z histones. Given the seminal role of these variants in maintaining genomic integrity and regulating gene expression, their preliminary characterization opens up new potential applications for the future development of chromatin-based genotoxicity tests in pollution biomonitoring programs. PMID:22253857
Theoretical analysis of dynamic processes for interacting molecular motors
NASA Astrophysics Data System (ADS)
Teimouri, Hamid; Kolomeisky, Anatoly B.; Mehrabiani, Kareem
2015-02-01
Biological transport is supported by the collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.
Molecular dynamics simulation of polycrystalline copper
NASA Astrophysics Data System (ADS)
Bolesta, A. V.; Fomin, V. M.
2014-09-01
An approach for molecular dynamics simulation of the formation of polycrystalline materials from a melt during its cooling is proposed. Atomic configurations of copper corresponding to polycrystals with the mean grain size from 2 to 16 nm are obtained. Isothermal uniaxial tension and compression of these polycrystals is studied by the molecular dynamics method. For the mean grain size of polycrystalline copper being smaller than 10 nm, it is shown that Young's modulus and yield stress decrease as the grain size decreases. Shock adiabats for polycrystalline copper are constructed. For a material with the grain size approximately equal to 2 nm, the temperature behind the shock wave front is demonstrated to be 10% higher than that in a polycrystal with the grain size greater than 10 nm. Molecular dynamics calculations predict the presence of copper with a body-centered cubic lattice behind the shock wave front at pressures ranging from 100 to 200 GPa.
Molecular dynamics simulations of displacement cascades in metallic systems
NASA Astrophysics Data System (ADS)
Doan, N. V.; Tietze, H.
1995-08-01
We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature.
Molecular dynamic simulations of ocular tablet dissolution.
Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire
2013-11-25
Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies. PMID:24073784
Understanding Modularity in Molecular Networks Requires Dynamics
NSDL National Science Digital Library
Roger P. Alexander (Yale University; Program in Computational Biology and Bioinformatics REV)
2009-07-28
The era of genome sequencing has produced long lists of the molecular parts from which cellular machines are constructed. A fundamental goal in systems biology is to understand how cellular behavior emerges from the interaction in time and space of genetically encoded molecular parts, as well as nongenetically encoded small molecules. Networks provide a natural framework for the organization and quantitative representation of all the available data about molecular interactions. The structural and dynamic properties of molecular networks have been the subject of intense research. Despite major advances, bridging network structure to dynamics—and therefore to behavior—remains challenging. A key concept of modern engineering that recurs in the functional analysis of biological networks is modularity. Most approaches to molecular network analysis rely to some extent on the assumption that molecular networks are modular—that is, they are separable and can be studied to some degree in isolation. We describe recent advances in the analysis of modularity in biological networks, focusing on the increasing realization that a dynamic perspective is essential to grouping molecules into modules and determining their collective function.
Molecular Scale Dynamics of Large Ring Polymers
NASA Astrophysics Data System (ADS)
Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.
2014-10-01
We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.
Molecular rotovibrational dynamics excited in optical filamentation.
Calegari, F; Vozzi, C; De Silvestri, S; Stagira, S
2008-12-15
The rotovibrational dynamics excited by optical filamentation in molecular gases is studied in the temporal domain. Two time-delayed replicas of the same laser pulse have been used to generate a first filament, for the rotovibrational excitation of the sample, and a second collinear filament probing the Raman dynamics. The Fermi doublet structure in CO(2) as well as the very fast stretching mode of H(2) were clearly resolved. PMID:19079493
A molecular-dynamics study of thermal and physical properties of platinum nanoclusters
Hamed Akbarzadeh; Gholam Abbas Parsafar
2009-01-01
Metallic nanoclusters are interesting because of their utility in catalysis and sensors. The thermal and physical characteristics of metallic Pt nanoclusters with different sizes were investigated via molecular-dynamics simulations using Quantum Sutton-Chen (QSC) potential. This force field accurately predicts solid and liquid states properties as well as melting of the bulk platinum. Molecular dynamic simulations of Pt nanoclusters with 256,
Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes
Maruyama, Shigeo
Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes Shigeo MARUYAMA #12;The hydrogen storage mechanism of SWNTs was studied through molecular dynamics simulations,12) Fig. 6 Hydrogen storage inside each SWNT #12;Table 1 Potential parameters between SWNTs Tube d0 [Ã?
Fundamental frequency from classical molecular dynamics.
Yamada, Tomonori; Aida, Misako
2015-02-01
We give a theoretical validation for calculating fundamental frequencies of a molecule from classical molecular dynamics (MD) when its anharmonicity is small enough to be treated by perturbation theory. We specifically give concrete answers to the following questions: (1) What is the appropriate initial condition of classical MD to calculate the fundamental frequency? (2) From that condition, how accurately can we extract fundamental frequencies of a molecule? (3) What is the benefit of using ab initio MD for frequency calculations? Our analytical approaches to those questions are classical and quantum normal form theories. As numerical examples we perform two types of MD to calculate fundamental frequencies of H2O with MP2/aug-cc-pVTZ: one is based on the quartic force field and the other one is direct ab initio MD, where the potential energies and the gradients are calculated on the fly. From those calculations, we show comparisons of the frequencies from MD with the post vibrational self-consistent field calculations, second- and fourth-order perturbation theories, and experiments. We also apply direct ab initio MD to frequency calculations of C-H vibrational modes of tetracene and naphthalene. We conclude that MD can give the same accuracy in fundamental frequency calculation as second-order perturbation theory but the computational cost is lower for large molecules. PMID:25519091
Structural and dynamic properties of calcium aluminosilicate melts: A molecular dynamics study
NASA Astrophysics Data System (ADS)
Bouhadja, M.; Jakse, N.; Pasturel, A.
2013-06-01
The structural and dynamic properties of calcium aluminosilicate (CaO-Al2O3)1-x(SiO2)x melts with low silica content, namely, along the concentration ratio R = 1 are studied by classical molecular dynamics. An empirical potential has been developed here on the basis of our previous ab initio molecular dynamics. The new potential gives a description of the structural as well as the dynamics with a good accuracy. The self-intermediate scattering function and associated ?-relaxation times are analyzed within the mode-coupling theory. Our results indicate a decrease of the fragility whose structural origin is a reduction of the number of fivefold coordinated Al atoms and non-bridging oxygen.
Dynamics and Molecular Evolution of Influenza
Goldschmidt, Christina
Dynamics and Molecular Evolution of Influenza Gunnar Sigurðsson Hlynur Sigurgíslason Jón Ingi Sveinbjörnsson #12;The Orthomyxoviridae family Influenza is in the Orthomyxoviridae family. The family contains Influenza A,B,C and the following viruses: Isavirus Infectious salmon anemia virus Atlantic salmon
Mathematical Modeling and Analysis Molecular Dynamics
Kurien, Susan
Mathematical Modeling and Analysis Molecular Dynamics Simulations of Peptide Nucleic Acid in Lipid- tant bio-molecule is peptide nucleic acids (PNA). PNA is a lab-created analogue of DNA, in which water-insoluble or nonpo- lar compounds of biological origin. The simplest lipids are linear fatty acids
Reaction dynamics in polyatomic molecular systems
Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
Structure and dynamics of nonaqueous mixtures of dipolar liquids. II. Molecular dynamics simulations
2000 Molecular dynamics simulations have been used to study mixtures of acetone/methanol, acetonitrile/ methanol, and acetone/acetonitrile over their entire composition range. Using the effective pair potentials for the single dipole moment as well as the translational and rotational velocities of each component
Numerical methods for molecular dynamics
Skeel, R.D.
1991-01-01
This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.
Molecular Dynamics and Electron Density Studies of Siderophores and Peptides.
NASA Astrophysics Data System (ADS)
Fidelis, Krzysztof Andrzej
1990-08-01
The dissertation comprises three separate studies of siderophores and peptides. In the first of these studies the relative potential energies for a series of diastereomers of a siderophore neocoprogen I are evaluated with molecular mechanics force field methods. Charges on the hydroxamate moiety are determined with a synthetic model siderophore compound using valence population refinements, and alternatively, with the theoretical ab initio/ESP calculations. The single diastereomer found in the crystal structure is among four characterized by the low potential energy, while prevalence of Delta vs. Lambda configuration about the iron is found to be a property of the entire series. In the second study the crystal structure of a ferrichrome siderophore ferrirhodin is reported. The crystal structure conformation of the molecular backbone as well as the iron coordination geometry compare well with other ferrichrome structures. The differences between the acyl groups of ferrirubin and ferrirhodin are explored using the methods of molecular mechanics. The third study a 300 ps, 300 K, in vacuo molecular dynamics simulation of didemnin A and B yields distinct molecular conformers, which are different from the one found in the crystal structure or modeled in solution, using the Nuclear Overhauser Effect data. Evaluations of the relative potential energy are performed with short 10 ps simulations in solution. Didemnins are natural depsipeptides isolated from a Caribbean tunicate and characterized by particularly potent antiproliferative and immunomodulatory activity. Conformationally rigid and flexible regions of the molecule are described. A short review of the molecular mechanics methodology is given in the introduction.
Warm dense matter through classical molecular dynamics
NASA Astrophysics Data System (ADS)
Calisti, A.; Ferri, S.; Marciante, M.; Talin, B.
2014-12-01
A classical Molecular Dynamics code has been developed to simulate dense plasmas i.e. neutral systems of interacting ions and electrons. Our goal is to design a tool that relies on a reduced set of microscopic mechanisms in order to obtain solutions of complex time dependent N-body problems and to allow an efficient description of the plasma states between classical high temperature systems to strongly coupled plasmas. Our present objective is an attempt to explore the behavior of such a classical approach for typical conditions of warm dense matter. We calculate the dynamic structure factor in warm dense beryllium by means of our molecular dynamics simulations. The results are then compared with those obtained within the framework of the random phase approximation (RPA).
Anomalous molecular dynamics in the vicinity of conical intersections
Jonas Larson; Elham Nour Ghassemi; Asa Larson
2013-10-29
Conical intersections between molecular electronic potential surfaces greatly affect various properties of the molecule. Molecular gauge theory is capable of explaining many of these often unexpected phenomena deriving from the physics of the conical intersection. Here we give an example of anomalous dynamics in the paradigm of the Exe Jahn-Teller model, which does not allow a simple explenation in terms of standard molecular gauge theory. By introducing a dual gauge theory, we unwind this surprising behavior by identifying it with an intrinsic spin Hall effect. Thus, this work link knowledge of condensed matter theories with molecular vibrations. Furthermore, via ab initio calculations the findings are as well demonstrated to appear in realistic systems such as the Li3 molecule.
A random rotor molecule: Vibrational analysis and molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Li, Yu; Zhang, Rui-Qin; Shi, Xing-Qiang; Lin, Zijing; Van Hove, Michel A.
2012-12-01
Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4',4??-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2':6',2?-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation.
Molecular dynamics simulator for optimal control of molecular motion
NASA Astrophysics Data System (ADS)
Rabitz, Herschel
1990-12-01
In recognition of recent interest in developing optimal control techniques for manipulating molecular motion, this paper introduces a computer-driven electro-mechanical analog of this process. The resultant Molecular Dynamic Simulator (MDS) is centered around a linear air track for which the atoms of the controlled molecule are simulated as nearly frictionless carts on the track. Bonds in the simulated molecule are described by precision springs, and the interaction with an external optical field is simulated through a computer-based linear driver. When the MDS is operated in the harmonic regime, it can be used as an exact analog of molecular scale quantum systems through Ehrenfest's Theorem, or equivalently as a classical set of coupled oscillators. The tools of optimal control theory currently being applied at the molecular scale are used to design the forcing function for the MDS. Optical encoders are used to measure bond distances for graphic representation of the MDS behavior. Bond breaking can also be simulated by bond-length sensitive trigger-release mechanisms. The MDS is especially useful as a modelling tool to bridge theoretical studies and eventual laboratory experiments at the true molecular scale.
Molecular-dynamics simulator for optimal control of molecular motion
NASA Astrophysics Data System (ADS)
Husman, M.; Schwieters, C.; Littman, M.; Rabitz, H.
1991-11-01
In recognition of recent interest in developing optimal control techniques for manipulating molecular motion, this paper introduces a computer-driven electromechanical analog of this process. The resultant molecular-dynamics simulator (MDS) is centered around a linear air track for which the atoms of the controlled molecule are simulated as nearly frictionless carts on the track. Bonds in the simulated molecule are described by precision springs, and the interaction with an external optical field is simulated through a computer-based linear driver. When the MDS is operated in the harmonic regime, it can be used as an exact analog of molecular-scale quantum systems through Ehrenfest's theorem or, equivalently, as a classical set of coupled oscillators. The tools of optimal control theory currently being applied at the molecular scale are used to design the forcing function for the MDS. Optical encoders are used to measure bond distances for graphic representation of the MDS behavior. Bond breaking can also be simulated by bond-length-sensitive trigger-release mechanisms. The MDS is especially useful as a modeling tool to bridge theoretical studies and eventual laboratory experiments at the true molecular scale.
DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations
Filip Lankaš; Ji?í Šponer; Jörg Langowski; Thomas E. Cheatham III
2003-01-01
The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers: d(GCCTATAAACGCCTATAA) and d(CTAGGTGGATGACTCATT). From an analysis of the structural fluctuations, the harmonic potential energy functions for all 10 unique steps with respect to the six step parameters have been evaluated. In the case of roll, three distinct
Potential molecular targets for Ewing's sarcoma therapy
Jully, Babu; Rajkumar, Thangarajan
2012-01-01
Ewing's sarcoma (ES) is a highly malignant tumor of children and young adults. Modern therapy for Ewing's sarcoma combines high-dose chemotherapy for systemic control of disease, with advanced surgical and/or radiation therapeutic approaches for local control. Despite optimal management, the cure rate for localized disease is only approximately 70%, whereas the cure rate for metastatic disease at presentation is less than 30%. Patients who experience long-term disease-free survival are at risk for significant side-effects of therapy, including infertility, limb dysfunction and an increased risk for second malignancies. The identification of new targets for innovative therapeutic approaches is, therefore, strongly needed for its treatment. Many new pharmaceutical agents have been tested in early phases of clinical trials in ES patients who have recurrent disease. While some agents led to partial response or stable disease, the percentages of drugs eliciting responses or causing an overall effect have been minimal. Furthermore, of the new pharmaceuticals being introduced to clinical practice, the most effective agents also have dose-limiting toxicities. Novel approaches are needed to minimize non-specific toxicity, both for patients with recurrence and at diagnosis. This report presents an overview of the potential molecular targets in ES and highlights the possibility that they may serve as therapeutic targets for the disease. Although additional investigations are required before most of these approaches can be assessed in the clinic, they provide a great deal of hope for patients with Ewing's sarcoma. PMID:23580819
The Dynamic Potential of Firms
Baba Prasad
2001-01-01
If I were to wish for anything, I should not wish for wealth and power, but for the passionate sense of the potential, for the eye which, ever young and ardent, sees the possible. Pleasure disappoints, possibility never. And what wine is so sparkling, what so fragrant, what so intoxicating, as possibility! Soren Kierkegaard. “Diapsalmata, ” vol. 1, Either/Or (1843) 1.
Combined molecular dynamics-spin dynamics simulations of bcc iron
NASA Astrophysics Data System (ADS)
Perera, Dilina; Landau, David P.; Nicholson, Don M.; Stocks, G. Malcolm; Eisenbach, Markus; Yin, Junqi; Brown, Gregory
2014-03-01
Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.
Combined molecular dynamics-spin dynamics simulations of bcc iron
Perera, Meewanage Dilina N [ORNL] [ORNL; Yin, Junqi [ORNL] [ORNL; Landau, David P [University of Georgia, Athens, GA] [University of Georgia, Athens, GA; Nicholson, Don M [ORNL] [ORNL; Stocks, George Malcolm [ORNL] [ORNL; Eisenbach, Markus [ORNL] [ORNL; Brown, Greg [ORNL] [ORNL
2014-01-01
Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.
Potential energy surfaces and reaction dynamics of polyatomic molecules
Chang, Yan-Tyng.
1991-11-01
A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.
Polar solvation dynamics of lysozyme from molecular dynamics studies
NASA Astrophysics Data System (ADS)
Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
2012-05-01
The solvation dynamics of a protein are believed to be sensitive to its secondary structures. We have explored such sensitivity in this article by performing room temperature molecular dynamics simulation of an aqueous solution of lysozyme. Nonuniform long-time relaxation patterns of the solvation time correlation function for different segments of the protein have been observed. It is found that relatively slower long-time solvation components of the ?-helices and ?-sheets of the protein are correlated with lower exposure of their polar probe residues to bulk solvent and hence stronger interactions with the dynamically restricted surface water molecules. These findings can be verified by appropriate experimental studies.
Sanville, Edward J [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, William M [Los Alamos National Laboratory; Cawkwell, Marc J [Los Alamos National Laboratory; Niklasson, Anders M N [Los Alamos National Laboratory; Dattelbaum, Dana M [Los Alamos National Laboratory; Sheffield, Stephen [Los Alamos National Laboratory; Sewell, Thomas D [UNIV OF MISSOURI
2010-01-01
A set of interatomic potentials for hydrocarbons that are based upon the self-consistent charge transfer tight-binding approximation to density functional theory have been developed and implemented into the quantum molecular dynamics code ''LATTE''. The interatomic potentials exhibit an outstanding level of transferability and have been applied in molecular dynamics simulations of tert-butylacetylene under thermodynamic conditions that correspond to its single-shock Hugoniot. We have achieved precise conservation of the total energy during microcanonical molecular dynamics trajectories under incomplete convergence via the extended Lagrangian Born-Oppenheimer molecular dynamics formalism. In good agreement with the results of a series of flyer-plate impact experiments, our SCC-TB molecular dynamics simulations show that tert-butylactylene molecules polymerize at shock pressures around 6.1 GPa.
Molecular understanding of mutagenicity using potential energy methods
Broyde, S.; Shapiro, R.
1992-07-01
Our objective, has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by 2-aminofluorene and its N-acetyl derivative, 2-acetylaminofluorene (AAF). The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence, for example by the formation of hairpin loops in appropriate sequences, but it may be enhanced greatly after covalent modification by a mutagenic substance. We use computational methods and have been able to incorporate the first data from NMR studies in our calculations. Computational approaches are important because x-ray and spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations, with full solvent and salt, of the important static structures are carried out with the program AMBER; this yields mobile views in a medium that mimics the natural aqueous environment of the cell as well as can be done with current available computing resources.
A molecular dynamics study on surface properties of supercooled water
NASA Astrophysics Data System (ADS)
Lü, Yongjun; Wei, Bingbo
2006-10-01
Molecular dynamics simulations were performed to study the surface properties of water in a temperature range from 228 to 293 K by using the extended simple point charge (SPC/E) and four-site TIP4P potentials. The calculated surface tension increases with the decrease of temperature, and moreover the slopes of the surface tension-temperature curves show a weak rise below 273 K, whereas no obvious anomalies appear near 228 K, which accords with the previous experiments. Compared with the measured values, the SPC/E potential shows a good agreement, and the TIP4P potential underestimates the surface tension. The main reason for that may be the reasonable description of the surface structure of supercooled water for the SPC/E. When simulating the orientational distributions of water molecules near the surface, the SPC/E potential produces higher ordering and larger surface potentials than the TIP4P potential.
New Developments in Tight-Binding Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Ho, Kai-Ming
1996-03-01
In recent years, tight-binding molecular-dynamics has emerged as a useful method for studying the structural, dynamical and electronic properties of covalent systems. In this talk, we will present some recent results on the implementation of linear-scaling algorithms and the development of new transferable tight-binding potentials for metallic environments. Work done in collaboration with C. Z. Wang, J. R. Morris, D. Turner, J. Corkill, M. S. Tang, B. Pan, H. Haas, D. Deaven, S. Y. Qiu and C. T. Chan
Molecular dynamics simulation in RNA interference.
Wang, Xia; Wang, Yonghua; Zheng, Lei; Chen, Jianxin
2014-06-01
RNA interference (RNAi) is a mechanism that utilizes small RNA molecules to silence gene expression after the gene has been transcribed. To understand the mechanisms of small RNA biogenesis, target nucleic acid recognition and cleavage, and how they are influenced by other regulators, one needs to know the structures and dynamics of the proteins or/and nucleic acids in these processes. Molecular dynamics (MD) simulation is a powerful tool for understanding motions and dynamics of macro-biomolecules at an atomic-scale via theoretical and empirical principles in physical chemistry. With its application to RNAi, an excellent overview of structural and dynamical mechanistic of RNAi processes has already emerged. In this review, we summarize the recent advances in MD simulations in the study of functional modules and their assemblies and target recognition and cleavage in RNAi processes. Additionally, we also present some perspectives on this technique. PMID:24350843
Thermal conductivities of molecular liquids by reverse nonequilibrium molecular dynamics.
Zhang, Meimei; Lussetti, Enrico; de Souza, Luís E S; Müller-Plathe, Florian
2005-08-11
The reverse nonequilibrium molecular dynamics method for thermal conductivities is adapted to the investigation of molecular fluids. The method generates a heat flux through the system by suitably exchanging velocities of particles located in different regions. From the resulting temperature gradient, the thermal conductivity is then calculated. Different variants of the algorithm and their combinations with other system parameters are tested: exchange of atomic velocities versus exchange of molecular center-of-mass velocities, different exchange frequencies, molecular models with bond constraints versus models with flexible bonds, united-atom versus all-atom models, and presence versus absence of a thermostat. To help establish the range of applicability, the algorithm is tested on different models of benzene, cyclohexane, water, and n-hexane. We find that the algorithm is robust and that the calculated thermal conductivities are insensitive to variations in its control parameters. The force field, in contrast, has a major influence on the value of the thermal conductivity. While calculated and experimental thermal conductivities fall into the same order of magnitude, in most cases the calculated values are systematically larger. United-atom force fields seem to do better than all-atom force fields, possibly because they remove high-frequency degrees of freedom from the simulation, which, in nature, are quantum-mechanical oscillators in their ground state and do not contribute to heat conduction. PMID:16852906
Molecular dynamics simulation of layered double hydroxides
KALINICHEV,ANDREY G.; WANG,JIANWEI; KIRKPATRICK,R. JAMES; CYGAN,RANDALL T.
2000-05-19
The interlayer structure and the dynamics of Cl{sup {minus}} ions and H{sub 2}O molecules in the interlayer space of two typical LDH [Layered Double Hydroxide] phases were investigated by molecular dynamics computer simulations. The simulations of hydrocalumite, [Ca{sub 2}Al(OH){sub 6}]Cl{center_dot}2H{sub 2}O reveal significant dynamic disorder in the orientations of interlayer water molecules. The hydration energy of hydrotalcite, [Mg{sub 2}Al(0H){sub 6}]Cl{center_dot}nH{sub 2}O, is found to have a minimum at approximately n = 2, in good agreement with experiment. The calculated diffusion coefficient of Cl{sup {minus}} as an outer-sphere surface complex is almost three times that of inner-sphere Cl{sup {minus}}, but is still about an order of magnitude less than that of Cl{sup {minus}} in bulk solution. The simulations demonstrate unique capabilities of combined NMR and molecular dynamics studies to understand the structure and dynamics of surface and interlayer species in mineral/water systems.
Molecular dynamics of a model dimerizing fluid.
Bertrand, C E; Liu, Y
2015-01-28
A model dimer forming fluid has been investigated by continuous molecular dynamics simulations. This study emphasizes the volume fraction and temperature dependence of the dynamic properties of the system, including the self and collective diffusion coefficients and the forward and reverse rate constants. The self and collective diffusion coefficients are found to be well described by a monomer fraction controlled interpolation formula. The forward rate constant (dimer formation) is found to be weakly temperature dependent and strongly volume fraction dependent. The opposite holds for the reverse rate constant. The dimer and monomer decay rates are not found to affect the intermediate scattering functions at the conditions studied. PMID:25637991
Molecular dynamics study on entrainment phenomenon in model molecular systems
NASA Astrophysics Data System (ADS)
Nagao, Hidemi; Kawamoto, Shuhei; Rusmerryani, Micke; Purqon, Acep; Kawaguchi, Kazutomo; Saito, Hiroaki
2013-02-01
The usual molecular dynamics (MD) simulation adopts a non-liner term (friction force) in the equation of motion to control the system temperature. Since such equation of motion is similar to the van der Pol equation, the synchronization motion could be induced by the particle interactions in some cases. In this study, we carried out the MD simulations of the model diatomic molecules in the gas and solution systems to investigate a possible synchronization phenomenon of molecules. The synchronization of vibrational motions of two diatomic molecules was observed in the gas system when the system temperature was controlled by thermostat. In the case of solution system, the synchronization of two molecules was found to depend on the density of solvent particles. These findings indicate that the synchronization of vibrational motion should be induced by the thermostat and the molecular interaction with surrounding solvent and solute molecules.
DENSITY-FUNCTIONAL MOLECULAR DYNAMICS SIMULATIONS OF SHOCKED MOLECULAR LIQUIDS
Kress, J. D. (Joel D.); Mazevet, S. (Stephane); Collins, L. A. (Lee A.)
2001-01-01
Molecular dynamics (MD) simulations have been performed for highly compressed fluid deuterium, nitrogen, and oxygen, in the density and temperature regime of shock-compression experiments, using density functional (DF) electronic structure techniques to describe the interatomic forces. The Hugoniots derived from the calculated equation-of-state for deuterium does not exhibit the large compression predicted by the recently reported laser-driven experiments. However, the Hugoniot derived for nitrogen and oxygen agree well with explosively-driven and gas-gun experiments. The nature of the fluid along the Hugoniot, as calculated with DF-MD, has been analyzed. All three species (D2, N2, amd 02) undergo a continuous transition from a molecular to a partially dissociated fluid containing a mixture of atoms and molecules.
Molecular dynamics studies of polyurethane nanocomposite hydrogels
NASA Astrophysics Data System (ADS)
Strankowska, J.; Piszczyk, ?.; Strankowski, M.; Danowska, M.; Szutkowski, K.; Jurga, S.; Kwela, J.
2013-10-01
Polyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite® 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means of NMR spectroscopy, DMA and DSC analysis. The mechanical properties and thermal stability of the systems were improved by incorporation of clay and controlled by varying the clay content in polymeric matrix. Molecular dynamics of polymer chains depends on interaction of Cloisite® 30B nanoparticles with soft segments of polyurethanes. The characteristic nanosize effect is observed.
NASA Astrophysics Data System (ADS)
Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.
2013-03-01
The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.
Calculation of molecular free energies in classical potentials
Farhi, Asaf
2015-01-01
Free energy calculations in molecular simulations are used to predict the strength of molecular processes such as binding and solvation. We present an accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms that depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non interacting systems, the free energy associated with these atoms is analytically or numerically calculated. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations.
Exploring Transmembrane Diffusion Pathways with Molecular Dynamics
Wang, Yi; Shaikh, Saher A.; Tajkhorshid, Emad
2013-01-01
Transmembrane exchange of materials is a fundamental process in biology. Molecular dynamics provides a powerful method to investigate in great detail various aspects of the phenomenon, particularly the permeation of small uncharged molecules, which continues to pose a challenge to experimental studies. We will discuss some of the recent simulation studies investigating the role of lipid-mediated and protein-mediated mechanisms in permeation of water and gas molecules across the membrane. PMID:20551228
New faster CHARMM molecular dynamics engine
Hynninen, Antti-Pekka; Crowley, Michael F
2014-01-01
We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. PMID:24302199
A Molecular Dynamics Study of Thermal Ablation
D. T. W. Lin; Yuh-Chung Hu
2006-01-01
The bio-heat transfer problem and the thermal ablation in bio-tissue require general solutions for the control of the external heating power. An algorithm based on the molecular dynamics (MD) and the GROMACS protein data bank is developed to solve the bio-heat transfer problem. The value of the thermal conductivity of alanine is calculated from the autocorrelation function of the Green-Kubo
Exploring Transmembrane Diffusion Pathways With Molecular Dynamics
NSDL National Science Digital Library
Yi Wang (University of Illinois at Urbana-Champaign)
2010-06-01
Transmembrane exchange of materials is a fundamental process in biology. Molecular dynamics provides a powerful method to investigate in great detail various aspects of the phenomenon, particularly the permeation of small uncharged molecules, which continues to pose a challenge to experimental studies. We will discuss some of the recent simulation studies investigating the role of lipid-mediated and protein-mediated mechanisms in permeation of water and gas molecules across the membrane.
NASA Astrophysics Data System (ADS)
Balucani, N.; Casavecchia, P.; Aoiz, F. J.; Bañares, L.; Castillo, J. F.; Herrero, V. J.
This paper describes crossed beam experiments and quasiclassical trajectory (QCT) calculations for the 'insertion' reaction O(1D)+D2 at a collision energy (Ec=25.9 kJ mol-1) much higher than the calculated barrier (˜8.4 kJ mol-1) for the competitive 'abstraction' mechanism, which takes place along the excited state potential energy surfaces (PES). Adiabatic QCT calculations were carried out on the ground 11A' and first excited 11A'' PESs developed by Dobbyn and Knowles. Non-adiabatic contributions from the excited 21A' PES to the reaction were considered by means of a trajectory surface hopping method. QCT calculations were also performed at Ec=22.2 kJ mol-1 to compare with previous experimental results. Excellent agreement was found between experiment and QCT predictions at Ec=22.2 kJ mol-1, while at the higher Ec of 25.9 kJ mol-1 only a qualitative agreement was noted. In all cases, the comparison was significantly improved with respect to QCT calculations on a previous version of the ground state PES.
Improving structure-based function prediction using molecular dynamics
Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.
2009-01-01
Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472
Control-volume representation of molecular dynamics
E. R. Smith; D. M. Heyes; D. Dini; T. A. Zaki
2012-05-24
A Molecular Dynamics (MD) parallel to the Control Volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood, J. Chem. Phys. 18, 817 (1950) over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' Transport Theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-Control-Volume (\\CV) conversion function $\\vartheta_{i}$, for each molecule $i$. The \\CV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the Volume Average (VA, Lutsko, J. Appl. Phys 64, 1152 (1988)) techniques and the Method of Planes (MOP, Todd et al, Phys. Rev. E 52, 1627 (1995)) emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and non-equilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative, and is therefore ideally suited to obtain macroscopic properties from a discrete system.
Equipartition Principle for Internal Coordinate Molecular Dynamics.
Jain, Abhinandan; Park, In-Hee; Vaidehi, Nagarajan
2012-08-14
The principle of equipartition of (kinetic) energy for all-atom Cartesian molecular dynamics states that each momentum phase space coordinate on the average has ½kT of kinetic energy in a canonical ensemble. This principle is used in molecular dynamics simulations to initialize velocities, and to calculate statistical properties such as entropy. Internal coordinate molecular dynamics (ICMD) models differ from Cartesian models in that the overall kinetic energy depends on the generalized coordinates and includes cross-terms. Due to this coupled structure, no such equipartition principle holds for ICMD models. In this paper we introduce non-canonical modal coordinates to recover some of the structural simplicity of Cartesian models and develop a new equipartition principle for ICMD models. We derive low-order recursive computational algorithms for transforming between the modal and physical coordinates. The equipartition principle in modal coordinates provides a rigorous method for initializing velocities in ICMD simulations thus replacing the ad hoc methods used until now. It also sets the basis for calculating conformational entropy using internal coordinates. PMID:23341754
Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics
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.
Molecular dynamics simulation: A tool for exploration and discovery
NASA Astrophysics Data System (ADS)
Rapaport, Dennis C.
2009-03-01
The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).
NASA Astrophysics Data System (ADS)
Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.
2015-02-01
We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7
Ungar, L W; Scherer, N F; Voth, G A
1997-01-01
Classical molecular dynamics simulations are used to investigate the nuclear motions associated with photoinduced electron transfer in plastocyanin. The blue copper protein is modeled using a molecular mechanics potential; potential parameters for the copper-protein interactions are determined using an x-ray crystallographic structure and absorption and resonance Raman spectra. Molecular dynamics simulations yield a variety of information about the ground (oxidized) and optically excited (charge-transfer) states: 1) The probability distribution of the potential difference between the states, which is used to determine the coordinate and energy displacements, places the states well within the Marcus inverted region. 2) The two-time autocorrelation function of the difference potential in the ground state and the average of the difference potential after instantaneous excitation to the excited state are very similar (confirming linear response in this system); their decay indicates that vibrational relaxation occurs in about 1 ps in both states. 3) The spectral densities of various internal coordinates begin to identify the vibrations that affect the optical transition; the spectral density of the difference potential correlation function should also prove useful in quantum simulations of the back electron transfer. 4) Correlation functions of the protein atomic motions with the difference potential show that the nuclear motions are correlated over a distance of more than 20 A, especially along proposed electron transport paths. Images FIGURE 1 FIGURE 7 PMID:8994588
Annihilation of craters: Molecular dynamic simulations on a silver surface
Henriksson, K. O. E.; Nordlund, K.; Keinonen, J. [Royal Institute of Technology, Department of Reactor Physics, S-10691 Stockholm (Sweden); Accelerator Laboratory, P.O. Box 43, FI-00014 University of Helsinki (Finland)
2007-12-15
The ability of silver cluster ions containing 13 atoms to fill in a preexisting crater with a radius of about 28 A ring on a silver (001) target has been investigated using molecular dynamics simulations and the molecular-dynamics-Monte Carlo corrected effective medium potential. The largest lateral distance r between crater and ion was about three times the radius of the preexisting crater, namely, 75 A ring . The results reveal that when r<20 A ring and r>60 A ring the preexisting crater is partially filled in, and for other distances there is a net growth of the crater. The lattice damage created by the cluster ions, the total sputtering yield, the cluster sputtering yield, and simulated transmission electron microscopy images of the irradiated targets are also presented.
Dynamic surface tension effects from molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Lukyanov, Alex; Likhtman, Alexei
2011-11-01
We will present results of our recent large scale molecular dynamics simulations of dynamic surface tension behaviour in the case of a liquid-gas interface. We will demonstrate the mechanism of surface tension relaxation from a non-equilibrium state in several representative cases: long-chain flexible molecules with Lennard-Jones beads connected by FENE springs and binary Lennard-Jones mixtures (Kob-Andersen model). The methodology of the surface tension evaluation has been successfully tested against the Laplace law in all the cases.
Thermal Transport in Carbon Nanotubes using Molecular Dynamics
NASA Astrophysics Data System (ADS)
Moore, Andrew; Khatun, Mahfuza
2011-10-01
We will present results of thermal transport phenomena in Carbon Nanotube (CNT) structures. CNTs have many interesting physical properties, and have the potential for device applications. Specifically, CNTs are robust materials with high thermal conductance and excellent electrical conduction properties. A review of electrical and thermal conduction of the structures will be discussed. The research requires analytical analysis as well as simulation. The major thrust of this study is the usage of the molecular dynamics (MD) simulator, LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). A significant investigation using the LAMMPS code is conducted on the existing Beowulf Computing Cluster at BSU. NanoHUB, an open online resource to the entire nanotechnology community developed by the researchers of Purdue University, is used for further supplementary resources. Results will include the time-dependence of temperature, kinetic energy, potential energy, heat flux correlation, and heat conduction.
(Molecular understanding of mutagenicity using potential energy methods)
Broyde, S.
1990-01-01
The objective of our work has been, for many year, to elucidate on a molecular level at atomic resolution the structures of DNAs modified by highly mutagenic polycyclic aromatic amines and hydrocarbons, and their less mutagenic chemically related analogs and unmodified DNAs, as controls. The ultimate purpose of this undertaking is to obtain an understanding of the relationship DNA structures and mutagenicity. Our methods for elucidating structures are computational, but we keep in close contact with experimental developments, and have, very recently, been able to incorporate the first experimental information from NMR studies by other workers in our calculations. The specific computational methods we employ are minimized potential energy calculations using the torsion angle space program DUPLEX, developed and written by Dr. Brain Hingerty to yield static views. Molecular dynamics simulations of the important static structures with full solvation and salt are carried out with the program AMBER; this yields mobile views in a milieu that best mimics the natural environment of the cell. In addition, we have been developing new strategies for searching conformation space and building DNA duplexes from favored subunit structures. 30 refs., 12 figs.
DYNAMICAL ANALYSIS OF HIGHLY EXCITED MOLECULAR SPECTRA
Michael E. Kellman
2005-06-17
Spectra and internal dynamics of highly excited molecules are essential to understanding processes of fundamental importance for combustion, including intramolecular energy transfer and isomerization reactions. The goal of our program is to develop new theoretical tools to unravel information about intramolecular dynamics encoded in highly excited experimental spectra. We want to understand the formations of ''new vibrational modes'' when the ordinary normal modes picture breaks down in highly excited vibrations. We use bifurcation analysis of semiclassical versions of the effective Hamiltonians used by spectroscopists to fit complex experimental spectra. Specific molecular systems are of interest for their relevance to combustion and the availability of high-quality experimental data. Because of its immense importance in combustion, the isomerizing acetylene/vinylidene system has been the object of long-standing experimental and theoretical research. We have made significant progress in systematically understanding the bending dynamics of the acetylene system. We have begun to make progress on extending our methodology to the full bend-stretch vibrational degrees of freedom, including dynamics with multiple wells and above barrier motion, and time-dependent dynamics. For this, development of our previous methods using spectroscopic fitting Hamiltonians is needed, for example, for systems with multiple barriers.
Implementing peridynamics within a molecular dynamics code.
Lehoucq, Richard B.; Silling, Stewart Andrew; Plimpton, Steven James; Parks, Michael L.
2007-12-01
Peridynamics (PD) is a continuum theory that employs a nonlocal model to describe material properties. In this context, nonlocal means that continuum points separated by a finite distance may exert force upon each other. A meshless method results when PD is discretized with material behavior approximated as a collection of interacting particles. This paper describes how PD can be implemented within a molecular dynamics (MD) framework, and provides details of an efficient implementation. This adds a computational mechanics capability to an MD code, enabling simulations at mesoscopic or even macroscopic length and time scales.
Bio-Molecular Dynamics Comes of Age
NSDL National Science Digital Library
Herman J. C. Berendsen (University of Groningen, Netherlands; Department of Biophysical Chemistry and the BIOSON Research Institute)
1996-02-16
Access to the article is free, however registration and sign-in are required. Atomic force microscopy has recently been used to measure the binding force between two biomolecules; complementing the experiments are computational molecular dynamics studies that seek to reveal the details of the binding and unbinding mechanisms. In his Perspective, Berendsen discusses the results reported in the same issue by GrubmÃ¼ller et al. (p. 997) on numerical simulations of the binding and separation of biotin from streptavidin, which show excellent agreement with measurements of the rupture force.
Molecular Dynamics Modeling of Actin Network Formation
NASA Astrophysics Data System (ADS)
Pandolfi, Ronald; Becich, Peter; Nguyen, Lam; Hirst, Linda
2011-03-01
Actin filaments are ubiquitous and critical in cellular functions. The polymer protein F-actin is a semi-flexible filament that forms networks in the presence of binding proteins (i.e. ?-actinin, filamin, fascin). Molecular dynamics modeling and simulation of the formation of these networks has revealed the dependence of network structure on the ratio of G-actin monomers to cross-linkers, cross-linker shape, and filament length. In this study we focus on the effects of filament length on the assembled system. Comparative experimental work informs the accuracy of the modeled systems. Fourier analysis of the simulated networks allows quantitative characterization of the network structure.
Exploring Hamiltonian dielectric solvent molecular dynamics
NASA Astrophysics Data System (ADS)
Bauer, Sebastian; Tavan, Paul; Mathias, Gerald
2014-09-01
Hamiltonian dielectric solvent (HADES) is a recent method [7,25], which enables Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric continua. Sample simulations of an ?-helical decapeptide with and without explicit solvent demonstrate the high efficiency of HADES-MD. Addressing the folding of this peptide by replica exchange MD we study the properties of HADES by comparing melting curves, secondary structure motifs and salt bridges with explicit solvent results. Despite the unoptimized ad hoc parametrization of HADES, calculated reaction field energies correlate well with numerical grid solutions of the dielectric Poisson equation.
Molecular dynamics simulations of dense plasmas
Collins, L.A.; Kress, J.D.; Kwon, I. [Los Alamos National Lab., NM (United States); Lynch, D.L. [Thinking Machines Corp., Cambridge, MA (United States); Troullier, N. [Minnesota Univ., Minneapolis, MN (United States)
1993-12-31
We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.
[Oligoglycine surface structures: molecular dynamics simulation].
Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V
2010-01-01
The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements. PMID:21063448
Molecular dynamics simulation of supercritical fluids
NASA Astrophysics Data System (ADS)
Branam, Richard D.
Axisymmetric injectors appear in a multitude of applications ranging from rocket engines to biotechnology. While experimentation is limited to larger injectors, much interest has been shown in the micro- and nano-scales as well. Experimentation at these scales can be cost prohibitive if even possible. Often, the operating regime involves supercritical fluids or complex geometries. Molecular dynamics modeling provides a unique way to explore these flow regimes, calculate hard to measure flow parameters accurately, and determine the value of potential improvements before investing in costly experiments or manufacturing. This research effort modeled sub- and supercritical fluid flow in a cylindrical tube being injected into a quiescent chamber. The ability of four wall models to provide an accurate simulation was compared. The simplest model, the diffuse wall, proved useful in getting results quickly but the results for the higher density cases are questionable, especially with respect to velocity profiles and density distributions. The one zone model, three layers of an fcc solid tethered to the lattice sites with a spring, proved very useful for this research primarily because it did not need as many CPU hours to equilibrate. The two zone wall uses springs as a two body potential and has a second stationary zone to hold the wall in place. The most complicated, the three zone wall, employed a reactionary zone, a stochastic zone and a stationary zone using a Lennard-Jones two body potential. Jet simulations were conducted on argon and nitrogen for liquid tube diameters from 20 to 65 A at both sub and supercritical temperatures (Ar: 130 K and 160 K, N2: 120 K and 130 K). The simulations focused on pressures above the critical pressure (Ar: 6 MPa, N2: 4 MPa). The diffusive wall showed some variation from the analytical velocity profile in the tube while the atomistically modeled walls performed very well. The walls were all able to maintain system temperature to reach the desired simulation conditions. The most dramatic differences between the models were evident in the jet flow into the chamber. The simulation results were strongly influenced by the size of the tube and the wall-fluid interactions. The diffuse wall and the explicitly modeled walls show the ability to compare with macroscaled systems for an issuing jet near the injector region when the behavior of the flow, in particular at the fluid-wall interface. The explicitly modeled walls performed very well for these locations but determining the appropriate fluid-wall interactions is critical. This interaction is the largest source of error for this research. Comparing the jet results to the available experimental data showed evidence these simulations accurately represent injection flow. Both the diffuse and one zone walls showed good agreement with the density profiles for the larger injection systems. The mass distribution into the chamber compares very well with experimental shadowgraphs. This evidence validates this simulation and suggests further work is possible and appropriate.
MOLECULAR ANALYSIS OF HUMAN SPERMATOZOA: POTENTIAL FOR INFERTILITY RESEARCH
Gordon Research Conference: Mammalian Gametogenesis and Embryogenesis New London, CT, July 1-6, 2000 Molecular Analysis of Human Spermatozoa: Potential for Infertility Research David Miller 1, David Dix2, Robert Reid 3, Stephen A Krawetz 3 1Reproductive ...
Exact dynamic properties of molecular motors
NASA Astrophysics Data System (ADS)
Boon, N. J.; Hoyle, R. B.
2012-08-01
Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.
Multiple branched adaptive steered molecular dynamics
NASA Astrophysics Data System (ADS)
Ozer, Gungor; Keyes, Thomas; Quirk, Stephen; Hernandez, Rigoberto
2014-08-01
Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by "rare events" from the ensemble of nonequilibrium trajectories. The recently proposed adaptive steered molecular dynamics, ASMD, introduced a new idea for selecting important events and eliminating the non-contributing trajectories, thus decreasing the overall computation needed. ASMD was shown to reduce the number of trajectories needed by a factor of 10 in a benchmarking study of decaalanine stretching. Here we propose a novel, highly efficient "multiple branching" (MB) version, MB-ASMD, which obtains a more complete enhanced sampling of the important trajectories, while still eliminating non-contributing segments. Compared to selecting a single configuration in ASMD, MB-ASMD offers to select multiple configurations at each segment along the reaction coordinate based on the distribution of work trajectories. We show that MB-ASMD has all benefits of ASMD such as faster convergence of the PMF even when pulling 1000 times faster than the reversible limit while greatly reducing the probability of getting trapped in a non-significant path. We also analyze the hydrogen bond breaking within the decaalanine peptide as we force the helix into a random coil and confirm ASMD results with less noise in the numerical averages.
ls1 mardyn: The massively parallel molecular dynamics code for large systems
Christoph Niethammer; Stefan Becker; Martin Bernreuther; Martin Buchholz; Wolfgang Eckhardt; Alexander Heinecke; Stephan Werth; Hans-Joachim Bungartz; Colin W. Glass; Hans Hasse; Jadran Vrabec; Martin Horsch
2014-08-20
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales which were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multi-center rigid potential models based on Lennard-Jones sites, point charges and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, e.g. for fluids at interfaces, as well as non-equilibrium molecular dynamics simulation of heat and mass transfer.
Molecular interferometer to decode attosecond electron-nuclear dynamics.
Palacios, Alicia; González-Castrillo, Alberto; Martín, Fernando
2014-03-18
Understanding the coupled electronic and nuclear dynamics in molecules by using pump-probe schemes requires not only the use of short enough laser pulses but also wavelengths and intensities that do not modify the intrinsic behavior of the system. In this respect, extreme UV pulses of few-femtosecond and attosecond durations have been recognized as the ideal tool because their short wavelengths ensure a negligible distortion of the molecular potential. In this work, we propose the use of two twin extreme UV pulses to create a molecular interferometer from direct and sequential two-photon ionization processes that leave the molecule in the same final state. We theoretically demonstrate that such a scheme allows for a complete identification of both electronic and nuclear phases in the wave packet generated by the pump pulse. We also show that although total ionization yields reveal entangled electronic and nuclear dynamics in the bound states, doubly differential yields (differential in both electronic and nuclear energies) exhibit in addition the dynamics of autoionization, i.e., of electron correlation in the ionization continuum. Visualization of such dynamics is possible by varying the time delay between the pump and the probe pulses. PMID:24591647
Molecular dynamics study of solid ?-N2
NASA Astrophysics Data System (ADS)
Klein, Michael L.; Lévesque, Dominique; Weis, Jean-Jacques
1981-02-01
A computer simulation study of orientationally disordered solid ?-N2 is reported for the state condition V=26.1 cm3/mol, T=47 K. We utilized an hexagonal system of 288 molecules interacting via a Raich-Gillis intermolecular potential. Particular attention is given to the dynamical structure factor S(Q,?) and its dependence on the momentum transfer h/Q. In this regard the present model agrees considerably better with experimental observations than previous work based upon a simple atom-atom potential with no electrostatic quadrupole-quadrupole interaction.
Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation
NASA Technical Reports Server (NTRS)
Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.
2007-01-01
The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.
Tjon effect for dense systems. A molecular-dynamics study
NASA Astrophysics Data System (ADS)
Brey, J. J.; Ordóñez, J. Gómez; Santos, A.
1982-11-01
The time evolution of an isolated, spatially homogeneous system, with an isotropic distribution of velocities and with particles interacting via a Lennard-Jones potential, has been analyzed by means of molecular dynamics. The initial velocity distribution is assumed to be zero except for two given speeds v? and v?. We have found an overpopulation phenomenon for high speeds, analogous to the one observed in the theoretical studies of model Boltzmann equations. The influence of v? and v? on this effect has been analyzed. A qualitative comparison with theoretical results is presented. Furthermore, we have observed a similar, less intense, overpopulation effect for low speeds.
Molecular dynamics calculations for sodium using pseudopotential theory
Swanson, R.E.
1981-06-01
The equation of state of sodium is studied using the molecular dynamics technique whereby the classical motion of a system of ions is solved with the aid of computers. The interaction potential between pairs of sodium ions consists of Coulomb and Born-Mayer repulsion terms and an effective ion-ion interaction derived from pseudopotential theory. This theory includes the effects of electron gas screening, exchange, and correlation. A model pseudopotential with parameters fit to experimental low-temperature data is used. By using this technique, an atomic description of a simple metal proceeds to the calculation of macroscopic thermodynamic properties.
Molecular dynamics simulations of shock-induced plasticity in tantalum
NASA Astrophysics Data System (ADS)
Tramontina, Diego; Erhart, Paul; Germann, Timothy; Hawreliak, James; Higginbotham, Andrew; Park, Nigel; Ravelo, Ramón; Stukowski, Alexander; Suggit, Mathew; Tang, Yizhe; Wark, Justin; Bringa, Eduardo
2014-03-01
We present Non-Equilibrium Molecular Dynamics (NEMD) simulations of shock wave compression along the [001] direction in monocrystalline Tantalum, including pre-existing defects which act as dislocation sources. We use a new Embedded Atom Model (EAM) potential and study the nucleation and evolution of dislocations as a function of shock pressure and loading rise time. We find that the flow stress and dislocation density behind the shock front depend on strain rate. We find excellent agreement with recent experimental results on strength and recovered microstructure, which goes from dislocations to a mixture of dislocations and twins, to twinning dominated response, as the shock pressure increases.
Higher-order symplectic Born-Oppenheimer molecular dynamics
Niklasson, Anders [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, Matt [Los Alamos National Laboratory; Odell, Anders [RIT; Delin, Anna [RIT; Johansson, Borje [RIT
2009-01-01
The extended Lagrangian formulation of time-reversible Born-Oppenheimer molecular dynamics (TR-BOMD) enables the use of geometric integrators in the propagation of both the nuclear and the electronic degrees of freedom on the Born-Oppenheimer potential energy surface. Different symplectic integrators up to the 6th order have been adapted and optimized to TR-BOMD in the framework of ab initio self-consistent-field theory. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements.
Molecular dynamics simulation of multivalent ion mediated DNA attraction
Dai, Liang; Nordenskiold, Lars; van der Maarel, Johan R C
2008-01-01
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e. multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.
Enhanced thermal characterization of silica aerogels through molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Yeo, J. J.; Liu, Z. S.; Ng, T. Y.
2013-10-01
Porous structures of silica aerogels are generated using classical molecular dynamics, with the Tersoff potential, which has been re-parametrized for modeling silicon dioxides. This work demonstrates that this potential is superior to the widely used BKS potential in terms of characterizing the thermal conductivities of amorphous silica, by comparing the vibrational density of states with previous experimental studies. Aerogel samples of increasing densities are obtained through an expanding, heating and quenching process. Reverse non-equilibrium molecular dynamics is applied at each density to determine the thermal conductivity. A power-law fit of the results is found to accurately reflect the power-law variation found in experimental bulk aerogels. The results are also of the same order of magnitude as experimental bulk aerogels, but they are consistently higher. By analyzing the pore size distribution on different simulation length scales, we show that such a disparity is due to finite sizes of pores that can be represented, where increasing simulation length scales lead to an increase in the largest pore size that can be modeled.
Molecular dynamics simulations of diffusion in mesoporous glass
Fernandes, N.E.; Gavalas, G.R. [California Inst. of Tech., Pasadena, CA (United States)] [California Inst. of Tech., Pasadena, CA (United States)
1999-03-01
The effect of gas-solid intrapore potential and surface roughness on diffusion in a single capillary was investigated by molecular dynamics simulations. Calculations were carried out for nitrogen and isobutane under free molecular flow conditions in pores of diameter 4--14 {angstrom} at temperatures of 200--800 K. The gases were treated as Lennard-Jones atoms and the pore surface was taken as cylindrical, exerting a 9-3 potential. No energy transfer was considered between the gas and solid, but interaction with the roughened pore wall provided the scattering required for diffusive transport. Two effects of the gas-solid potential were examined in some detail. One is the enhanced intrapore gas concentration which increases the flux, and the other is the bending of the molecular trajectories which decreases the flux. In pores of radius 20 {angstrom}, both effects were significant for temperatures as high as 500 K and were enhanced as the temperature decreased. For nitrogen, the two effects partially canceled each other over the temperature range examined, resulting in a temperature dependence similar to that of Knudsen diffusion. For isobutane, the partitioning effect dominated the path curvature effect at temperatures as high as 500 K.
Development of a Water Cluster Evaporation Model using Molecular Dynamics
NASA Astrophysics Data System (ADS)
Borner, Arnaud; Li, Zheng; Levin, Deborah A.
2011-05-01
A Monte Carlo simulation using the SPC potential model has been used to determine the potential energy and constant volume heat capacity of water dimers and trimers. It was found that the potential energy almost follows a linear trend versus temperature. The heat capacity fluctuates around 10 cal/mol/K and reaches a maximum around 220 K for the dimer and 240 K for the trimer. The Molecular Dynamics simulation has been used to evaporate water dimers and trimers. The cumulative evaporation probabilities were calculated for temperatures ranging from 240 K to 300 K. The cluster evaporation rates were calculated using Weerashinge's equation, and they were compared with the UDT rates. Both values were found to be in good agreement. Finally, vibrational frequencies were computed.
NASA Astrophysics Data System (ADS)
Chelli, Riccardo; Cardini, Gianni; Procacci, Piero; Righini, Roberto; Califano, Salvatore
2003-07-01
Structural and dynamical properties of liquid and supercooled liquid m-toluidine are studied by molecular dynamics simulations. Approaching the liquid-glass transition, dynamical heterogeneities, a characteristic common to all supercooled glass formers, are observed. We prove the occurrence of strict correlation between these heterogeneities and the potential energy landscape of the system, expressed in terms of molecule-molecule interactions. A slowing down of the self-diffusive motion of the molecular centers of mass is observed for particular arrangements of pairs of H-bonded molecules. Previous studies on model systems provided evidence of the correlation between dynamical heterogeneities and potential energy landscape, described in terms of the inherent structure of the system. While in this last case the structure is viewed as a collective property of the system, in m-toluidine short-range interactions are sufficient to explain the dynamical behavior in a satisfactory way. This result agrees with the view, supported also by experimental observations, that m-toluidine can be considered as an ensemble of H-bonded subsystems weakly interacting among them.
On-the-fly free energy parameterization via temperature accelerated molecular dynamics
Abrams, Cameron F.; Vanden-Eijnden, Eric
2012-01-01
We discuss a method for parametric calculation of free energy functions in arbitrary collective variables using molecular simulations. The method uses a variant of temperature accelerated molecular dynamics to evolve on-the-fly the parameters of the free energy function to their optimum values by minimization of a cumulative gradient error. We illustrate how the method performs using simple examples and discuss its application in the derivation of effective pairwise potentials for multiscale molecular simulations. PMID:23226688
TOPICAL REVIEW: Current-driven dynamics in molecular-scale devices
NASA Astrophysics Data System (ADS)
Seideman, Tamar
2003-04-01
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.
Anisotropic magnetic molecular dynamics of cobalt nanowires
NASA Astrophysics Data System (ADS)
Beaujouan, David; Thibaudeau, Pascal; Barreteau, Cyrille
2012-11-01
An investigation of thermally induced spin and lattice dynamics of a cobalt nanowire on a (111)Pt substrate is presented via magnetic molecular dynamics. This dynamical simulation model treats each atom as a particle supporting a classical spin. A coordinate dependent on both exchange and anisotropic functions ensures a minimal coupling between the spin and the lattice degrees of freedom to translate the magnetostrictive behavior of most magnetic materials. A spin-pair model of anisotropy is proposed to connect to the lattice thermodynamics. In order to solve linked spin-coordinate equations of motion, the efficiencies of algorithms based on Suzuki-Trotter decompositions are compared. The temperature dependence of the magnetic behavior of Co nanowires is investigated through thermal stochastic connections with mechanical and spin Langevin noises. From a magnetic Hamiltonian parametrized on ab initio calculations, the size dependence of the energy barriers and characteristic time scales of the magnetization relaxation are computed. In the superparamagnetic limit, it is shown that all spins in a nanowire evolve in a coherent rotation. When the size of the single nanowire increases, nucleations of domain walls let the activation energy be independent of the length of the wire.
Atomistic molecular dynamic simulations of multiferroics.
Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L
2012-08-10
A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings. PMID:23006300
Nonlinear Dynamics in Double Square Well Potential
Ramaz Khomeriki; Jerome Leon; Stefano Ruffo; Sandro Wimberger
2007-11-15
Considering the coherent nonlinear dynamics in double square well potential we find the example of coexistence of Josephson oscillations with a self-trapping regime. This macroscopic bistability is explained by proving analytically the simultaneous existence of symmetric, antisymmetric and asymmetric stationary solutions of the associated Gross-Pitaevskii equation. The effect is illustrated and confirmed by numerical simulations. This property allows to make suggestions on possible experiments using Bose-Einstein condensates in engineered optical lattices or weakly coupled optical waveguide arrays.
Structure factor and rheology of chain molecules from molecular dynamics
NASA Astrophysics Data System (ADS)
Castrejón-González, Omar; Castillo-Tejas, Jorge; Manero, Octavio; Alvarado, Juan F. J.
2013-05-01
Equilibrium and non-equilibrium molecular dynamics were performed to determine the relationship between the static structure factor, the molecular conformation, and the rheological properties of chain molecules. A spring-monomer model with Finitely Extensible Nonlinear Elastic and Lennard-Jones force field potentials was used to describe chain molecules. The equations of motion were solved for shear flow with SLLOD equations of motion integrated with Verlet's algorithm. A multiple time scale algorithm extended to non-equilibrium situations was used as the integration method. Concentric circular patterns in the structure factor were obtained, indicating an isotropic Newtonian behavior. Under simple shear flow, some peaks in the structure factor were emerged corresponding to an anisotropic pattern as chains aligned along the flow direction. Pure chain molecules and chain molecules in solution displayed shear-thinning regions. Power-law and Carreau-Yasuda models were used to adjust the generated data. Results are in qualitative agreement with rheological and light scattering experiments.
Molecular Dynamics Simulations of Non-accreting Neutron Star Crusts
NASA Astrophysics Data System (ADS)
Hoffman, Kelsey L.; Heyl, J. S.
2010-02-01
Neutron stars which do not accrete material can still have impurities in their crust, due to nuclear reactions in the crust. These impurities in the crust could affect the mechanical properties of the neutron star crust. In order to investigate the properties of the crust of a non-accreting neutron star we are performing molecular dynamic simulations of the crust. We are using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), where simulations are run at fixed energy and volume, with the isotopes interacting via a repulsive Yukawa potential. Here we are presenting the preliminary results of the equilibrium structure of the solid neutron star crust using abundances of a non-accreting source.
A scheme to combine molecular dynamics and dislocation dynamics
NASA Astrophysics Data System (ADS)
Brinckmann, Steffen; Mahajan, Dhiraj K.; Hartmaier, Alexander
2012-06-01
Many engineering challenges occur on multiple interacting length scales, e.g. during fracture atoms separate on the atomic scale while plasticity develops on the micrometer scale. To investigate the details of these events, a concurrent multiscale model is required which studies the problem at appropriate length- and time-scales: the atomistic scale and the dislocation dynamics scale. The AtoDis multiscale model is introduced, which combines atomistics and dislocation dynamicsinto a fully dynamic model that is able to simulate deformation mechanisms at finite temperature. The model uses point forces to ensure mechanical equilibrium and kinematic continuity at the interface. By resolving each interface atom analytically, and not numerically, the framework uses a coarse FEM mesh and intrinsically filters out atomistic vibrations. This multiscale model allows bi-directional dislocation transition at the interface of both models with no remnant atomic disorder. Thereby, the model is able to simulate a larger plastic zone than conventional molecular dynamics while reducing the need for constitutive dislocation dynamics equations. This contribution studies dislocation nucleation at finite temperature and investigates the absorption of dislocations into the crack wake.
Molecular dynamics, spin dynamics study of phonon-magnon interactions in BCC iron
NASA Astrophysics Data System (ADS)
Perera, Dilina; Landau, David P.; Stocks, G. Malcolm; Nicholson, Don; Eisenbach, Markus; Yin, Junqi
2013-03-01
By combining an atomistic many-body potential (Finnis-Sinclair) with a classical Heisenberg-like spin Hamiltonian, we perform combined molecular and spin dynamics simulations to investigate phonon-magnon interactions in BCC iron. The coupling between atomic and spin degrees of freedom is established via a distance dependent exchange interaction derived from first principles electronic structure calculations. Coupled equations of motion are integrated using a second order Suzuki-Trotter decomposition of the exponential time evolution operator. To investigate the effect of lattice vibrations on spin wave spectrum, we calculate spin-spin and density-density dynamic structure factors S(q, ?), and compare that to the results obtained from pure spin dynamics simulations performed on a rigid lattice. In the presence of lattice vibrations, we observe an additional peak in the longitudinal spin-spin dynamic structure factor which coincides with the peak position in density-density dynanmic structure factor.
Molecular Dynamics of a Protein Surface: Ion-Residues Interactions
Friedman, Ran; Nachliel, Esther; Gutman, Menachem
2005-01-01
Time-resolved measurements indicated that protons could propagate on the surface of a protein or a membrane by a special mechanism that enhanced the shuttle of the proton toward a specific site. It was proposed that a suitable location of residues on the surface contributes to the proton shuttling function. In this study, this notion was further investigated by the use of molecular dynamics simulations, where Na+ and Cl? are the ions under study, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using as a model a few Na+ and Cl? ions enclosed in a fully hydrated simulation box with a small globular protein (the S6 of the bacterial ribosome). Three independent 10-ns-long simulations indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. However, it was noted that close to some domains the ions extended their duration near the surface, thus suggesting that the local electrostatic potential hindered their diffusion to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of the molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed. PMID:15894639
Nonequilibrium molecular dynamics for bulk materials and nanostructures
NASA Astrophysics Data System (ADS)
Dayal, Kaushik; James, Richard D.
2010-02-01
We describe a method of constructing exact solutions of the equations of molecular dynamics in non-equilibrium settings. These solutions correspond to some viscometric flows, and to certain analogs of viscometric flows for fibers and membranes that have one or more dimensions of atomic scale. This work generalizes the method of objective molecular dynamics (OMD) ( Dumitric? and James, 2007). It allows us to calculate viscometric properties from a molecular-level simulation in the absence of a constitutive equation, and to relate viscometric properties directly to molecular properties. The form of the solutions is partly independent of the form of the force laws between atoms, and therefore these solutions have implications for coarse-grained theories. We show that there is an exact reduction of the Boltzmann equation corresponding to one family of OMD solutions. This reduction includes most known exact solutions of the equations of the moments for special kinds of molecules and gives the form of the molecular density function corresponding to such flows. This and other consequences leads us to propose an addition to the principle of material frame indifference, a cornerstone of nonlinear continuum mechanics. The method is applied to the failure of carbon nanotubes at an imposed strain rate, using the Tersoff potential for carbon. A large set of simulations with various strain rates, initial conditions and two choices of fundamental domain (unit cell) give the following unexpected results: Stone-Wales defects play no role in the failure (though Stone-Wales partials are sometimes seen just prior to failure), a variety of failure mechanisms is observed, and most simulations give a strain at failure of 15-20%, except those done with initial temperature above about 1200 K and at the lower strain rates. The latter have a strain at failure of 1-2%.
Singh, S.B.
1992-01-01
The structures of the adducts of (+)- and (-)trans-7,8,dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo (a)pyrene (anti-BPDE) formed by trans addition to N[sup 2] of guanine have been of great interest because the high biological activity of BPDE in mammalian mutagenesis and tumorigenesis has been attributed to the predominant (+)-adduct, while the (-)-adduct is inactive. Molecular mechanics and dynamics calculations have been employed to elucidate the structural difference between this mirror image adduct pair in a duplex dodecamer, d(5' GCGCGCG-(BPDE)CGCGC3') [center dot] d(5'GCGCGCGCGCGC3'). Minimized potential energy calculations using the program DUPLEX were employed to locate starting structures for the dynamics. Three types of structures were found in the energy minimized conformation space searches for each enantiomer: pyrenyl moiety in the minor groove of a Watson-Crick base paired B-DNA duplex, pyrenyl moiety in the major groove of a B-DNA duplex with syn guanine and Hoogsteen base pairs at the modification site, and intercalation type structures. The minor groove structure is energetically preferred for the (+) enantiomer while both minor groove and major groove structures are favored and of comparable energy in the (-) enantiomer. These energy-minimized duplex dodecamers, as well as an unmodified B-DNA control of the same sequence, were subjected to 100 ps molecular dynamics simulations with solvent and salt with the program AMBER. The duplex dodecamer, d(CGCGAATTCGCG)[sub 2], was subjected to a similar simulation using the crystal structure as starting coordinates. Detailed analysis of the dynamic evolution of the conformational and the helical parameters of all the dodecamer simulations were carried out with Molecular Dynamics Analysis Toolchest.
Fiber lubrication: A molecular dynamics simulation study
NASA Astrophysics Data System (ADS)
Liu, Hongyi
Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence of water increases the attractive interaction energy of the diblock copolymer on the cellulose surface, compared with that on the PP surface. Water decreases the interaction energy of the triblock copolymer on the cellulose surface, compared with that on the PP surface. MesoDyn was adopted to investigate the self-assembled morphology of the triblock copolymer, in aqueous solution, confined and sheared at solid-liquid interfaces. In a bulk aqueous solution, when the polymer concentration reached 10% v/v, micelles were observed with PPO blocks in the core and PEO blocks in the shell of the micelles. At the concentrations of 25% and 50%, worm-like micelles and irregular cylinders were observed in solutions, respectively. The micelles were formed faster in aqueous solutions confined by cellulose surfaces than that in the bulk. The formed micelles were broken under shearing, which led to a depletion of polymers at the interfaces. During the shearing on the PP surfaces, the polymers were adsorbed on the surfaces protecting the PP surfaces. This simulation study in the fiber lubrication was in good agreement with the experimental results and so provided an approach to visualize the polymer configuration at the liquid-solid interface, predict the lubricant-surface systems, and theoretically guide the experiments of designing new/efficient lubricants for fibers.
Ion Mobility Analysis of Molecular Dynamics
NASA Astrophysics Data System (ADS)
Wyttenbach, Thomas; Pierson, Nicholas A.; Clemmer, David E.; Bowers, Michael T.
2014-04-01
The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1&-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated.
Molecular dynamics investigation of carbon nanotube resonance
NASA Astrophysics Data System (ADS)
Chang, I.-Ling
2013-06-01
In this work, a methodology to directly extract resonant information from an equilibrium molecular dynamics simulation is proposed and demonstrated by analyzing the vibrational behavior of carbon nanotubes (CNTs). Different vibrational motions, i.e. longitudinal, transverse, rotational and radial, could be easily distinguished and computed through the time sequence of the velocity components of atoms at the equilibrating process. Fast Fourier transform is adopted to perform the transformation of vibration information from time to frequency domain. The effects of CNT length, radius and boundary condition on the resonant behaviors of CNTs are systematically investigated. Moreover, the simulation results are compared with those predicted based on the Euler-Bernoulli beam theory. Note that the simulated longitudinal and rotational resonant behaviors agree quite well with the theoretical prediction and a slight deviation is observed in the transverse prediction.
Nonequilibrium molecular dynamics: The first 25 years
Hoover, W.G. [Univ. of California, Davis, CA (United States); [Lawrence Livermore National Lab., CA (United States)
1992-08-01
Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments.
Ion mobility analysis of molecular dynamics.
Wyttenbach, Thomas; Pierson, Nicholas A; Clemmer, David E; Bowers, Michael T
2014-01-01
The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated. PMID:24328447
Molecular dynamics simulations of microscale fluid transport
Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.
1998-02-01
Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.
Molecular Dynamic Simulation of Failure of Ettringite
NASA Astrophysics Data System (ADS)
Sun, W.; Wang, D.; Wang, L.
2013-03-01
Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.
Effective Pair Potential for Solid Molecular Hydrogen at High Pressures
NASA Astrophysics Data System (ADS)
Moraldi, Massimo
2012-09-01
An effective pair potential for molecular hydrogen in the solid phase is presented. It is able to reproduce the measured equation of state up to 120 GPa. At short intermolecular distances, this potential is softer than previously proposed potentials. The calculations of the equation of state at high pressures are performed by a simple method involving a single frequency as a variational parameter. The accuracy of the calculation is estimated by treating perturbatively the difference of the real Hamiltonian and the harmonic one.
Minnesota, University of
of cathepsin K is characterized by a catalytic triad, consisting of Cys25, His162, and Asn182 residuesMolecular Dynamics Simulations of the Catalytic Pathway of a Cysteine Protease: A Combined QM: Molecular dynamics simulations using a combined QM/MM potential have been performed to study the catalytic
Molecular dynamics study of solvation differences between cis- and transplatin molecules in water
Cen-Feng Fu; Shan Xi Tian
2010-01-01
The classical molecular dynamics (MD) simulations for the solvation properties of cis- and transplatins in water are performed with the Lennard-Jones plus Coulomb electrostatic potential parameters that are optimized with ab initio potential energies of the water-platin systems. Two hydration shells are found both for cis- and transplatins. The first shell of water molecules is closer to transplatin than cisplatin.
Dynamics of dewetting at the nanoscale using molecular dynamics.
Bertrand, E; Blake, T D; Ledauphin, V; Ogonowski, G; Coninck, J De; Fornasiero, D; Ralston, J
2007-03-27
Large-scale molecular dynamics simulations are used to model the dewetting of solid surfaces by partially wetting thin liquid films. Two levels of solid-liquid interaction are considered that give rise to large equilibrium contact angles. The initial length and thickness of the films are varied over a wide range at the nanoscale. Spontaneous dewetting is initiated by removing a band of molecules either from each end of the film or from its center. As observed experimentally and in previous simulations, the films recede at an initially constant speed, creating a growing rim of liquid with a constant receding dynamic contact angle. Consistent with the current understanding of wetting dynamics, film recession is faster on the more poorly wetted surface to an extent that cannot be explained solely by the increase in the surface tension driving force. In addition, the rates of recession of the thinnest films are found to increase with decreasing film thickness. These new results imply not only that the mobility of the liquid molecules adjacent to the solid increases with decreasing solid-liquid interactions, but also that the mobility adjacent to the free surface of the film is higher than in the bulk, so that the effective viscosity of the film decreases with thickness. PMID:17328565
Molecular Dynamics Modeling of Ionic Liquids in Electrospray Propulsion
of Technology. 1 #12;2 #12;Molecular Dynamics Modeling of Ionic Liquids in Electrospray Propulsion by NanakoMolecular Dynamics Modeling of Ionic Liquids in Electrospray Propulsion Nanako Takahashi, Paulo C Propulsion Nanako Takahashi, Paulo C. Lozano June 2010 SSL # 6-10 This work is based on the unaltered text
Molecular dynamics and the accuracy of numerically computed averages
Stephen D. Bond; Benedict J. Leimkuhler
2007-01-01
Molecular dynamics is discussed from a mathematical perspective. The re- cent history of method development is briefly surveyed with an emphasis on the use of geometric integration as a guiding principle. The recovery of sta- tistical mechanical averages from molecular dynamics is then introduced, and the use of backward error analysis as a technique for analysing the accuracy of numerical
How Dynamic Visualization Technology Can Support Molecular Reasoning
ERIC Educational Resources Information Center
Levy, Dalit
2013-01-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…
Molecular dynamics simulation in virus research
Ode, Hirotaka; Nakashima, Masaaki; Kitamura, Shingo; Sugiura, Wataru; Sato, Hironori
2012-01-01
Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique. PMID:22833741
Molecular beam studies of reaction dynamics
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Zendlová, Lucie; Hobza, Pavel; Kabelác, Martin
2007-03-15
The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations. PMID:17302446
Isomorphic phase transformation in shocked cerium using molecular dynamics
Dupont, Virginie [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; Chen, Shao - Ping [Los Alamos National Laboratory
2010-08-12
Cerium (Ce) undergoes a significant ({approx}16%) volume collapse associated with an isomorphic fcc-fcc phase transformation when subject to compressive loading. We present here a new Embedded Atom Method (EAM) potential for Cerium that models two minima for the two fcc phases. We show results from its use in Molecular Dynamics (MD) simulations of Ce samples subjected to shocks with pressures ranging from 0.5 to 25 GPa. A split wave structure is observed, with an elastic precursor followed by a plastic wave. The plastic wave causes the expected fcc-fcc phase transformation. Comparisons to experiments and MD simulations on Cesium (Cs) indicate that three waves could be observed. The construction of the EAM potential may be the source of the difference.
The MOLDY short-range molecular dynamics package
NASA Astrophysics Data System (ADS)
Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.
2011-12-01
We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as 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.
Internal coordinate molecular dynamics: a foundation for multiscale dynamics.
Vaidehi, Nagarajan; Jain, Abhinandan
2015-01-29
Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406
Accelerated molecular dynamics methods: introduction and recent developments
Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO
2009-01-01
A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what reaction pathways may be important, we return instead to a molecular dynamics treatment, in which the trajectory itself finds an appropriate way to escape from each state of the system. Since a direct integration of the trajectory would be limited to nanoseconds, while we are seeking to follow the system for much longer times, we modify the dynamics in some way to cause the first escape to happen much more quickly, thereby accelerating the dynamics. The key is to design the modified dynamics in a way that does as little damage as possible to the probability for escaping along a given pathway - i.e., we try to preserve the relative rate constants for the different possible escape paths out of the state. We can then use this modified dynamics to follow the system from state to state, reaching much longer times than we could reach with direct MD. The dynamics within any one state may no longer be meaningful, but the state-to-state dynamics, in the best case, as we discuss in the paper, can be exact. We have developed three methods in this accelerated molecular dynamics (AMD) class, in each case appealing to TST, either implicitly or explicitly, to design the modified dynamics. Each of these methods has its own advantages, and we and others have applied these methods to a wide range of problems. The purpose of this article is to give the reader a brief introduction to how these methods work, and discuss some of the recent developments that have been made to improve their power and applicability. Note that this brief review does not claim to be exhaustive: various other methods aiming at similar goals have been proposed in the literature. For the sake of brevity, our focus will exclusively be on the methods developed by the group.
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.
Zhang, Lin; Tang, Ronghong; Bai, Shu; Connors, Natalie K; Lua, Linda H L; Chuan, Yap P; Middelberg, Anton P J; Sun, Yan
2013-05-01
Virus-like particles (VLPs) are highly organized nanoparticles that have great potential in vaccinology, gene therapy, drug delivery, and materials science. However, the application of VLPs is hindered by obstacles in their design and production due to low efficiency of self-assembly. In the present study, all-atom (AA) molecular dynamics (MD) simulations coupled with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method are utilized to examine the molecular interactions in the capsomere of a murine polyomavirus (MPV) VLP. It is found that both low ionic strength and the intracapsomere disulfide bonds are favorable for maintaining a stable capsomere. Simulation results examining the effects of solution conditions on the stabilization of a capsomere were verified by calorimetry experiments. Simulation results of free energy decomposition indicate that hydrophobic interaction is favorable for the formation of a capsomere, whereas electrostatic interaction is unfavorable. With increasing ionic strength, the dominant interaction for the stabilization of a capsomere changes from hydrophobic to electrostatic. By comprehensive analyses, the key amino acid residues (hot spots) in VP1 protein aiding formation of a capsomere in different solution conditions have been identified. These results provide molecular insights into the stabilization of building blocks for VLP and are expected to have implications in their partitioning between the correct and off-pathway reactions in VLP assembly. PMID:23586433
Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review
Paquet, Eric; Viktor, Herna L.
2015-01-01
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262
NASA Astrophysics Data System (ADS)
Banuelos, E. U.; Amarillas, A. P.
2004-02-01
In this work we studied the temperature-induced changes in the structural and dynamical properties of liquid Ag using molecular dynamics (DM) computer simulation. The atomic interactions are modeled through a semiempirical potential function which incorporates n-body effects and is based on the second moments approximation of the density of states of a tight-binding Hamiltonian. The caloric curve was used to calculate the latent heat of fusion and the pair distribution function, g(r), was calculated from a set of atomic configurations collected at several time-steps. The dynamical properties are studied through the velocity autocorrelation function and the mean-square displacement. The self-diffusion coefficient and its behavior with the temperature, obtained from our simulations, shows the typical behavior of the simple liquids. Our results are compared to available experimental data.
Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.
Graziani, F R; Bauer, J D; Murillo, M S
2014-09-01
Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD. The STLS contribution produces an effective electron-proton interaction that involves the electron-proton structure factor, thereby extending the usual mean-field theory to correlated but near equilibrium systems. Finally, a third variant of KTMD is derived. It includes dynamical electrons and their correlations coupled to a MD description for the ions. A set of coupled equations for the one-particle electron Wigner function and the electron-electron and electron-proton correlation functions are coupled to a classical Liouville equation for the protons. This latter variation has both time and momentum dependent correlations. PMID:25314544
Kinetic theory molecular dynamics and hot dense matter: Theoretical foundations
NASA Astrophysics Data System (ADS)
Graziani, F. R.; Bauer, J. D.; Murillo, M. S.
2014-09-01
Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD. The STLS contribution produces an effective electron-proton interaction that involves the electron-proton structure factor, thereby extending the usual mean-field theory to correlated but near equilibrium systems. Finally, a third variant of KTMD is derived. It includes dynamical electrons and their correlations coupled to a MD description for the ions. A set of coupled equations for the one-particle electron Wigner function and the electron-electron and electron-proton correlation functions are coupled to a classical Liouville equation for the protons. This latter variation has both time and momentum dependent correlations.
IBIsCO: a molecular dynamics simulation package for coarse-grained simulation.
Karimi-Varzaneh, Hossein Ali; Qian, Hu-Jun; Chen, Xiaoyu; Carbone, Paola; Müller-Plathe, Florian
2011-05-01
IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors. PMID:21425295
Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations
Cai, Wei
Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations-4040, USA a r t i c l e i n f o Article history: Received 19 February 2010 Received in revised form 16 April t The orientation dependent plasticity in metal nanowires is investigated using molecular dynamics and dislocation
A quantum molecular dynamics study of aqueous solvation dynamics.
Videla, Pablo E; Rossky, Peter J; Laria, D
2013-10-28
Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E , and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ?20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case. PMID:24182048
A quantum molecular dynamics study of aqueous solvation dynamics
NASA Astrophysics Data System (ADS)
Videla, Pablo E.; Rossky, Peter J.; Laria, D.
2013-10-01
Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E, and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ˜20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.
Molecular and chemical engineering of bacteriophages for potential medical applications.
Hodyra, Katarzyna; D?browska, Krystyna
2015-04-01
Recent progress in molecular engineering has contributed to the great progress of medicine. However, there are still difficult problems constituting a challenge for molecular biology and biotechnology, e.g. new generation of anticancer agents, alternative biosensors or vaccines. As a biotechnological tool, bacteriophages (phages) offer a promising alternative to traditional approaches. They can be applied as anticancer agents, novel platforms in vaccine design, or as target carriers in drug discovery. Phages also offer solutions for modern cell imaging, biosensor construction or food pathogen detection. Here we present a review of bacteriophage research as a dynamically developing field with promising prospects for further development of medicine and biotechnology. PMID:25048831
A new shared-memory programming paradigm for molecular dynamics simulations on the Intel Paragon
D`Azevedo, E.F.; Romine, C.H.
1994-12-01
This report describes the use of shared memory emulation with DOLIB (Distributed Object Library) to simplify parallel programming on the Intel Paragon. A molecular dynamics application is used as an example to illustrate the use of the DOLIB shared memory library. SOTON-PAR, a parallel molecular dynamics code with explicit message-passing using a Lennard-Jones 6-12 potential, is rewritten using DOLIB primitives. The resulting code has no explicit message primitives and resembles a serial code. The new code can perform dynamic load balancing and achieves better performance than the original parallel code with explicit message-passing.
Huge-scale molecular dynamics simulation of multibubble nuclei
NASA Astrophysics Data System (ADS)
Watanabe, Hiroshi; Suzuki, Masaru; Ito, Nobuyasu
2013-12-01
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers.
Molecular Dynamics Simulation of Binary Fluid in a Nanochannel
NASA Astrophysics Data System (ADS)
Mullick, Shanta; Pathania, Y.; Ahluwalia, P. K.
2011-12-01
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 12?, 14? and 16? 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.
Molecular Dynamics Simulation of Binary Fluid in a Nanochannel
Mullick, Shanta; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, SummerHill, Shimla - 171005 (India); Pathania, Y. [Chitkara University, Atal Shiksha Kunj, Atal Nagar, Barotiwala, Dist Solan, Himachal Pradesh - 174103 (India)
2011-12-12
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 12{sigma}, 14{sigma} and 16{sigma} 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.
Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Laghaei, Rozita; Mousseau, Normand
2010-04-01
Expansion of polyglutamine (polyQ) beyond the pathogenic threshold (35-40 Gln) is associated with several neurodegenerative diseases including Huntington's disease, several forms of spinocerebellar ataxias and spinobulbar muscular atrophy. To determine the structure of polyglutamine aggregates we perform replica-exchange molecular dynamics simulations coupled with the optimized potential for effective peptide forcefield. Using a range of temperatures from 250 to 700 K, we study the aggregation kinetics of the polyglutamine monomer and dimer with chain lengths from 30 to 50 residues. All monomers show a similar structural change at the same temperature from ?-helical structure to random coil, without indication of any significant ?-strand. For dimers, by contrast, starting from random structures, we observe spontaneous formation of antiparallel ?-sheets and triangular and circular ?-helical structures for polyglutamine with 40 residues in a 400 ns 50 temperature replica-exchange molecular dynamics simulation (total integrated time 20 ?s). This ˜32 Å diameter structure reorganizes further into a tight antiparallel double-stranded ˜22 Å nanotube with 22 residues per turn close to Perutz' model for amyloid fibers as water-filled nanotubes. This diversity of structures suggests the existence of polymorphism for polyglutamine with possibly different pathways leading to the formation of toxic oligomers and to fibrils.
Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing
2012-01-01
The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs. PMID:22761821
Molecularly imprinted polymers—potential and challenges in analytical chemistry
J. O. Mahony; K. Nolan; M. R. Smyth; B. Mizaikoff
2005-01-01
Among the variety of biomimetic recognition schemes utilizing supramolecular approaches molecularly imprinted polymers (MIPs) have proven their potential as synthetic receptors in numerous applications ranging from liquid chromatography to assays and sensor technology. Their inherent advantages compared to biochemical\\/biological recognition systems include robustness, storage endurance and lower costs. However, until recently only few contributions throughout the relevant literature describe quantitative
Integrating influenza antigenic dynamics with molecular evolution
Bedford, Trevor; Suchard, Marc A; Lemey, Philippe; Dudas, Gytis; Gregory, Victoria; Hay, Alan J; McCauley, John W; Russell, Colin A; Smith, Derek J; Rambaut, Andrew
2014-01-01
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001 PMID:24497547
Fracture simulations via massively parallel molecular dynamics
NASA Astrophysics Data System (ADS)
Holian, B. L.; Abraham, F. F.; Ravelo, R.
Fracture simulations at the atomistic level have been carried out for relatively small systems of particles, typically 10,000 or less. In order to study anything approaching a macroscopic system, massively parallel molecular dynamics (MD) must be employed. In two spatial dimensions (2D), it is feasible to simulate a sample that is 0.1 microns on a side. Recent MD simulations of mode 1 crack extension under tensile loading at high strain rates are reported. The method of uniaxial, homogeneously expanding periodic boundary conditions was employed to represent tensile stress conditions near the crack tip. The effects of strain rate, temperature, material properties (equation of state and defect energies), and system size were examined. It was found that, in order to mimic a bulk sample, several tricks (in addition to expansion boundary conditions) need to be employed: (1) the sample must be pre-strained to nearly the condition at which the crack will spontaneously open; (2) to relieve the stresses at free surfaces, such as the initial notch, annealing by kinetic-energy quenching must be carried out to prevent unwanted rarefactions; (3) sound waves emitted as the crack tip opens and dislocations emitted from the crack tip during blunting must be absorbed by special reservoir regions. The tricks described briefly will be especially important to carrying out feasible massively parallel 3D simulations via MD.
Molecular chaperone-mediated nuclear protein dynamics.
Echtenkamp, Frank J; Freeman, Brian C
2014-05-01
Homeostasis requires effective action of numerous biological pathways including those working along a genome. The variety of processes functioning in the nucleus is considerable, yet the number of employed factors eclipses this total. Ideally, individual components assemble into distinct complexes and serially operate along a pathway to perform work. Adding to the complexity is a multitude of fluctuating internal and external signals that must be monitored to initiate, continue or halt individual activities. While cooperative interactions between proteins of the same process provide a mechanism for rapid and precise assembly, the inherent stability of such organized structures interferes with the proper timing of biological events. Further prolonging the longevity of biological complexes are crowding effects resulting from the high concentration of intracellular macromolecules. Hence, accessory proteins are required to destabilize the various assemblies to efficiently transition between structures, avoid off-pathway competitive interactions, and to terminate pathway activity. We suggest that molecular chaperones have evolved, in part, to manage these challenges by fostering a general and continuous dynamic protein environment within the nucleus. PMID:24694369
Molecular dynamics simulation of flow in pores
NASA Astrophysics Data System (ADS)
Blömer, Jan
2001-08-01
The gaseous flow in nano-scale pores is of wide interest for many today's industrial applications, e.g., in microelectronics, nano-mechanical devices (Knudsen compressor) and reaction and adsorption at porous surfaces. This can be seen from a variety of papers of recent RGD Symposia. Furthermore it is possible to separate gases by porous membranes. Although the fundamental problem of all these applications is same, namely the important role of the gas-surface interaction in such small structures, we will primarily concentrate on the separation of different gas species by porous membranes. These membranes are typically very robust (temperature, chemical resistance) because they are made from ceramics which offers new application fields. Porous flow can roughly be divided in several flow regimes by the Knudsen number: From viscous flow to Knudsen diffusion to surface diffusion and up to capillary condensation. A Molecular Dynamics (MD) model for the gas as well as the surface is formulated to investigate the interaction of gas atoms or molecules with internal degrees of freedom and the pore. The MD method seems to be well suited to study these phenomena because it can deal with the high density and the many-body-interactions, which occur during the multilayer adsorption and condensation at the surface, although it is clear that it is limited to a small physical space because of its high computational consumption.
Phonostat: thermostatting phonons in molecular dynamics simulations.
Raghunathan, Rajamani; Greaney, P Alex; Grossman, Jeffrey C
2011-06-01
Thermostat algorithms in a molecular dynamics simulation maintain an average temperature of a system by regulating the atomic velocities rather than the internal degrees of freedom. Herein, we present a "phonostat" algorithm that can regulate the total energy in a given internal degree of freedom. In this algorithm, the modal energies are computed at each time step using a mode-tracking scheme and then the system is driven by an external driving force of desired frequency and amplitude. The rate and amount of energy exchange between the phonostat and the system is controlled by two distinct damping parameters. Two different schemes for controlling the external driving force amplitude are also presented. In order to test our algorithm, the method is applied initially to a simple anharmonic oscillator for which the role of various phonostat parameters can be carefully tested. We then apply the phonostat to a more realistic (10,0) carbon nanotube system and show how such an approach can be used to regulate energy of highly anharmonic modes. PMID:21663354
Ultrafast dynamics in the power stroke of a molecular rotary motor
NASA Astrophysics Data System (ADS)
Conyard, Jamie; Addison, Kiri; Heisler, Ismael A.; Cnossen, Arjen; Browne, Wesley R.; Feringa, Ben L.; Meech, Stephen R.
2012-07-01
Light-driven molecular motors convert light into mechanical energy through excited-state reactions. Unidirectional rotary molecular motors based on chiral overcrowded alkenes operate through consecutive photochemical and thermal steps. The thermal (helix inverting) step has been optimized successfully through variations in molecular structure, but much less is known about the photochemical step, which provides power to the motor. Ultimately, controlling the efficiency of molecular motors requires a detailed picture of the molecular dynamics on the excited-state potential energy surface. Here, we characterize the primary events that follow photon absorption by a unidirectional molecular motor using ultrafast fluorescence up-conversion measurements with sub 50 fs time resolution. We observe an extraordinarily fast initial relaxation out of the Franck-Condon region that suggests a barrierless reaction coordinate. This fast molecular motion is shown to be accompanied by the excitation of coherent excited-state structural motion. The implications of these observations for manipulating motor efficiency are discussed.
NASA Astrophysics Data System (ADS)
Pérez, Alejandro; Tuckerman, Mark E.
2011-08-01
Higher order factorization schemes are developed for path integral molecular dynamics in order to improve the convergence of estimators for physical observables as a function of the Trotter number. The methods are based on the Takahashi-Imada and Susuki decompositions of the Boltzmann operator. The methods introduced improve the averages of the estimators by using the classical forces needed to carry out the dynamics to construct a posteriori weighting factors for standard path integral molecular dynamics. The new approaches are straightforward to implement in existing path integral codes and carry no significant overhead. The Suzuki higher order factorization was also used to improve the end-to-end distance estimator in open path integral molecular dynamics. The new schemes are tested in various model systems, including an ab initio path integral molecular dynamics calculation on the hydrogen molecule and a quantum water model. The proposed algorithms have potential utility for reducing the cost of path integral molecular dynamics calculations of bulk systems.
Multiscale molecular dynamics using the matched interface and boundary method
Geng, Weihua; Wei, G.W.
2010-01-01
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. PMID:21088761
Enhanced molecular dynamics for simulating porous interphase layers in batteries.
Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan (Rice University, Houston, TX)
2009-10-01
Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media.
Multiscale molecular dynamics using the matched interface and boundary method
Geng Weihua [Department of Mathematics, Michigan State University, East Lansing, MI 48824 (United States); Wei, G.W., E-mail: wei@math.msu.ed [Department of Mathematics, Michigan State University, East Lansing, MI 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824 (United States)
2011-01-20
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.
Phonon dispersion measured directly from molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Kong, Ling Ti
2011-10-01
A method to measure the phonon dispersion of a crystal based on molecular dynamics simulation is proposed and implemented as an extension to an open source classical molecular dynamics simulation code LAMMPS. In the proposed method, the dynamical matrix is constructed by observing the displacements of atoms during molecular dynamics simulation, making use of the fluctuation-dissipation theory. The dynamical matrix can then be employed to compute the phonon spectra by evaluating its eigenvalues. It is found that the proposed method is capable of yielding the phonon dispersion accurately, while taking into account the anharmonic effect on phonons simultaneously. The implementation is done in the style of fix of LAMMPS, which is designed to run in parallel and to exploit the functions provided by LAMMPS; the measured dynamical matrices could be passed to an auxiliary postprocessing code to evaluate the phonons.
Surface properties of water clusters: a molecular dynamics study
NASA Astrophysics Data System (ADS)
Zakharov Elena, Viktor V.; Brodskaya Aatto Laaksonen, N.
1998-10-01
Radial local densities, local energies per molecule, orientational distribution functions, normal component of the pressure tensor and other surface properties of water are calculated, based on molecular dynamics simulations of water clusters at 300K. Three different water models are evaluated: the rigid five-site ST2 and four-site TIP4P models; and the three-site SPC/E model, which is made flexible with respect to the angle bending. The size of the clusters is varied from 64 to 1000 water molecules. It is concluded that surface properties are highly sensitive to the choice of potential model. On the basis of the dependence of the work of cluster formation on the cluster size, the influence of the water model on the surface tension of the plane surface is discussed. None of the three models considered gives a proper value for the surface tension of water at room temperature.
Molecular dynamics simulation of dislocations in uranium dioxide
NASA Astrophysics Data System (ADS)
Fossati, Paul; Van Brutzel, Laurent; Devincre, Benoît
2013-11-01
The plasticity of the fluorite structure in UO2 is investigated with molecular dynamics simulation and empirical potential. The stacking fault energies and the dislocation core structures with Burgers vector a2<110> are systematically calculated. All dislocation core structures show a significant increase of the oxygen sub-lattice disorder at temperatures higher than 1500 K. The threshold stress for dislocation glide is found to decrease with increasing temperature but its values is always very high, several GPa at 0 K and several hundred of MPa at 2000 K. A relation between the dislocation mobility dependence with temperature and the increase of the oxygen sub-lattice disorder in the dislocation cores is established.
Masses, luminosities and dynamics of galactic molecular clouds
NASA Technical Reports Server (NTRS)
Solomon, P. M.; Rivolo, A. R.; Mooney, T. J.; Barrett, J. W.; Sage, L. J.
1987-01-01
Star formation in galaxies takes place in molecular clouds and the Milky Way is the only galaxy in which it is possible to resolve and study the physical properties and star formation activity of individual clouds. The masses, luminosities, dynamics, and distribution of molecular clouds, primarily giant molecular clouds in the Milky Way are described and analyzed. The observational data sets are the Massachusetts-Stony Brook CO Galactic Plane Survey and the IRAS far IR images. The molecular mass and infrared luminosities of glactic clouds are then compared with the molecular mass and infrared luminosities of external galaxies.
Fracture simulations using large-scale molecular dynamics
NASA Astrophysics Data System (ADS)
Holian, Brad Lee; Ravelo, Ramon
1995-05-01
We report on recent molecular-dynamics (MD) fracture simulations of mode-I tensile loading at high strain rates. Because cracks emit sound waves, previous simulations became unreliable beyond one sound traversal time. Using massively parallel MD, we show how to eliminate unwanted boundary effects and study unimpeded crack propagation mechanisms. In order to represent tensile stress conditions near the crack tip, we employ uniaxial, homogeneously expanding periodic boundary conditions, examining the effects of strain rate, temperature, and interaction potential. Because our samples are sufficiently large, we see dislocations being emitted from the crack tip at nearly the shear-wave sound speed cs. As they move many lattice spacings away from the crack, they slow down, finally moving at about 2/3cs. Each time dislocations are emitted, the crack tip ``fishtails,'' and at sufficiently high strain, the crack can fork; dislocations can climb and become nucleation sites for additional microcracks. We find that we can suppress ductile behavior by including viscous damping in the equations of motion, thereby demonstrating a transition to brittle crack propagation as static, zero-strain-rate conditions are approached. Finally, we show that, by altering only the attractive tail of the pair potential, we can change a ductile material into a brittle one. Under dynamic crack propagation, the distinction between ductile and brittle behavior is blurred: in brittle materials, dislocations are asymptotically bound to the crack tip, while in ductile materials, they can escape.
Surface Diffusion of Single Polymer Chain Using Molecular Dynamics SIMULATION*
NASA Astrophysics Data System (ADS)
Desai, Tapan; Keblinski, Pawel; Kumar, Sanat; Granick, Steve
2004-05-01
Results of recent experiments on polymer chains adsorbed from dilute solution at solid-liquid interface show the power scaling law dependence of the chain diffusivity, D, as a function of the degree of polymerization, N, D ˜ N^3/2. By contrast, DNA molecules bound to fluid cationic lipid bilayers follows Rouse dynamics with D ˜ N^1. We used molecular dynamics simulations to gain an understanding of these dissimilar scaling behaviors. Our model systems contain chains comprised of N monomers connected by anharmonic springs described by the finite extendible nonlinear elastic, FENE potential, embedded into a solvent of N=1 monomers. Two types of simulations we performed: (i) the chain is confined to two dimensions, (ii) the three dimensional chain in the solvent is confined between two solids plates. With randomly placed impenetrable obstacles on the surface, the diffusion of 2D chains exhibits, D ˜ N^3/2 behavior, when the chain radius of gyration, Rg, is larger than half the distance between obstacles, and D ˜ N^1 for shorter chains. In the presence of an athermal solvent, the scaling exponent is 0.75 due to hydrodynamic forces, for the two-dimensional system. We will also discuss the nature of dynamic adsorption transition and effects of hydrodynamics forces on chain diffusion for the three-dimensional simulations.
Molecular Dynamics Simulation of Homogeneous Crystal Nucleation in Polyethylene
Yi, Peng
Using a realistic united-atom force field, molecular dynamics simulations were performed to study homogeneous nucleation of the crystal phase at about 30% supercooling from the melts of n-pentacontahectane (C150) and a ...
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the ...
Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films
Kim, Bo Hung
2010-07-14
Molecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal interactions at the wall-fluid interface...
CHARACTERIZING COUPLED CHARGE TRANSPORT WITH MULTISCALE MOLECULAR DYNAMICS
Swanson, Jessica
2011-08-31
This is the final progress report for Award DE-SC0004920, entitled 'Characterizing coupled charge transport with multi scale molecular dynamics'. The technical abstract will be provided in the uploaded report.
The stressstrain behavior of polymernanotube composites from molecular dynamics simulation
Brenner, Donald W.
. Stress/strain curves; C. Computational simulation; Carbon nano- tubes 1. Introduction In the last few and geo- metry. In particular, molecular dynamics (MD) simula- tions can predict the effect of mechanical
A combined molecular dynamics and diffusion model of single proton conduction through gramicidin.
Schumaker, M F; Pomès, R; Roux, B
2000-01-01
We develop a model for proton conduction through gramicidin based on the molecular dynamics simulations of Pomès and Roux (Biophys. J. 72:A246, 1997). The transport of a single proton through the gramicidin pore is described by a potential of mean force and diffusion coefficient obtained from the molecular dynamics. In addition, the model incorporates the dynamics of a defect in the hydrogen bonding structure of pore waters without an excess proton. Proton entrance and exit were not simulated by the molecular dynamics. The single proton conduction model includes a simple representation of these processes that involves three free parameters. A reasonable value can be chosen for one of these, and the other two can be optimized to yield a good fit to the proton conductance data of, Ann. N.Y. Acad. Sci. 339:8-20) for pH > or = 1.7. A sensitivity analysis shows the significance of this fit. PMID:11106593
Fast Parallel Algorithms for Short-Range Molecular Dynamics
Steve Plimpton
1995-01-01
Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors
Zaccarelli, Emanuela
Confirmation of anomalous dynamical arrest in attractive colloids: A molecular dynamics study E studies have indicated that particles with a short-ranged attraction exhibit a range of dynamical arrest phenomena. These include very pronounced reentrance in the dynamical arrest curve, a logarithmic singularity
Molecular dynamics simulations of yttrium-stabilized zirconia
Xiaoyun Li; B. Hafskjold
1995-01-01
The electric conductivity of yttrium-stabilized zirconia exhibits a maximum as a function of dopant (Y3+) cation concentration in isothermal and isobaric conditions. In order to improve the conductivity of this important solid electrolyte, it is essential to understand the ion transport mechanisms at the molecular level. This was investigated by the molecular dynamics simulations method in the present study. The
Molecular dynamics simulation of ultrafast laser ablation of fused silica
Xu, Xianfan
Molecular dynamics simulation of ultrafast laser ablation of fused silica C Cheng, A Q Wu and X Xu-mail: xxu@ecn.purdue.edu Abstract. Ultrafast laser ablation of fused silica is studied using molecular that ultrafast laser is capable of microscale fabrication of glass. The process of "laser ablation
Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics
M’Koma, Amosy E
2014-01-01
Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn’s colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed. PMID:25429322
Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics.
M'Koma, Amosy E
2014-11-27
Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn's colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed. PMID:25429322
Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis†
Feng, Yaoyu; Xiao, Lihua
2011-01-01
Summary: Molecular diagnostic tools have been used recently in assessing the taxonomy, zoonotic potential, and transmission of Giardia species and giardiasis in humans and animals. The results of these studies have firmly established giardiasis as a zoonotic disease, although host adaptation at the genotype and subtype levels has reduced the likelihood of zoonotic transmission. These studies have also identified variations in the distribution of Giardia duodenalis genotypes among geographic areas and between domestic and wild ruminants and differences in clinical manifestations and outbreak potentials of assemblages A and B. Nevertheless, our efforts in characterizing the molecular epidemiology of giardiasis and the roles of various animals in the transmission of human giardiasis are compromised by the lack of case-control and longitudinal cohort studies and the sampling and testing of humans and animals living in the same community, the frequent occurrence of infections with mixed genotypes and subtypes, and the apparent heterozygosity at some genetic loci for some G. duodenalis genotypes. With the increased usage of multilocus genotyping tools, the development of next-generation subtyping tools, the integration of molecular analysis in epidemiological studies, and an improved understanding of the population genetics of G. duodenalis in humans and animals, we should soon have a better appreciation of the molecular epidemiology of giardiasis, the disease burden of zoonotic transmission, the taxonomy status and virulences of various G. duodenalis genotypes, and the ecology of environmental contamination. PMID:21233509
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.
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. PMID:24277840
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
Yoo, Jejoong; Aksimentiev, Aleksei
2013-01-01
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. PMID:24277840
Johnston, Jennifer M.
2014-01-01
The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field. PMID:24158803
Graphitization of small diamond cluster --Molecular dynamics simulation A. Brdka a,, T.W. Zerda b
Powles, Rebecca
Graphitization of small diamond cluster -- Molecular dynamics simulation A. BrÃ³dka a,, T.W. Zerda b simulation was used to study graphitization process of a small diamond cluster at 1200, 1500, and 1800 K was described by the reactive bond order potential. Results obtained for 1500 K showed transformation of diamond
Annihilation of craters: Molecular dynamic simulations on a silver surface K. O. E. Henriksson*
Nordlund, Kai
Annihilation of craters: Molecular dynamic simulations on a silver surface K. O. E. Henriksson of silver cluster ions containing 13 atoms to fill in a preexisting crater with a radius of about 28 Ã?ÂMonte Carlo corrected effective medium potential. The largest lateral distance r between crater and ion
On the potential for molecular imaging with Cerenkov luminescence
Lewis, Matthew A.; Kodibagkar, Vikram D.; Öz, Orhan K.; Mason, Ralph P.
2011-01-01
Recent observation of optical luminescence due to beta decay from suitable radiotracers has led to the possible development of new preclinical optical imaging methods. The generation of photons that can be detected using instrumentation optimized for bioluminescence imaging has been putatively associated with the Cerenkov effect. We describe the simultaneous utilization of fluorescence reporters to convert the Cerenkov luminescence to longer wavelengths for better tissue penetration and also for modulating the luminescence spectrum for potential molecular imaging strategies. PMID:21124555
Molecular Dynamics in Self-Assembled Monolayers
Jason Bochinski; Derrick Stevens; Mary Scott; Laura Guy; Casey Dedeugd; Laura Clarke
2007-01-01
Silane self-assembled monolayers (SAMs) are an important tool for both scientific research and technological applications. Despite their widespread use, few experimental investigations have addressed molecular motion within these films, which offer a unique and useful physical system for fundamental scientific studies, such as observing dipolar and other glass transitions in two-dimensions. In addition, relaxations such as ``rotator'' phases where molecular
Boyer, Edmond
1 Dynamic viscosity estimation of hydrogen sulfide using a predictive scheme based on molecular on molecular dynamics results on Lennard-Jones spheres is proposed to model the viscosity of hydrogen sulfide is that the adjustment does not involve any viscosity data because only density values have been used in order
Bohm's Quantum Potential and the Visualization of Molecular Structure
NASA Technical Reports Server (NTRS)
Levit, Creon; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.
Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations
Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C.
2013-01-01
A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific ?-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient. The calculated reversal potential of 28.6 mV is found to be in excellent agreement with the values of 26–27 mV measured from lipid bilayer experiments, thereby demonstrating that the method allows realistic simulations of nonequilibrium membrane transport with quantitative accuracy. As a final example, the pore domain of Kv1.2, a highly selective voltage-activated K+ channel, is simulated in a lipid bilayer under conditions that recreate, for the first time, the physiological K+ and Na+ concentration gradients and the electrostatic potential difference of living cells. PMID:24081985
Atomistic modeling of the aluminum and iron oxide material system using classical molecular dynamics
Vikas Tomar
2005-01-01
In the current research, a framework based on classical molecular dynamics (MD) is developed for computational mechanical analyses of complex nanoscale materials. The material system of focus is a combination of fcc-Al and alpha-Fe2O3. The framework includes the development of an interatomic potential, a scalable parallel MD code, nanocrystalline composite structures, and methodologies for the quasistatic and dynamic strength analyses.
NASA Astrophysics Data System (ADS)
Curchod, Basile; Penfold, Thomas; Rothlisberger, Ursula; Tavernelli, Ivano
2013-09-01
We review our recent work on ab initio nonadiabatic molecular dynamics, based on linear-response timedependent density functional theory for the calculation of the nuclear forces, potential energy surfaces, and nonadiabatic couplings. Furthermore, we describe how nuclear quantum dynamics beyond the Born-Oppenheimer approximation can be performed using quantum trajectories. Finally, the coupling and control of an external electromagnetic field with mixed quantum/classical trajectory surface hopping is discussed.
Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam
2011-01-01
An extended accelerated molecular dynamics (AMD) methodology called adaptive AMD is presented. Adaptive AMD (Ad-AMD) is an efficient and robust conformational space sampling algorithm that is particularly-well suited to proteins with highly structured potential energy surfaces exhibiting complex, large-scale collective conformational transitions. Ad-AMD simulations of substrate-free P450cam reveal that this system exists in equilibrium between a fully and partially open conformational state. The mechanism for substrate binding depends on the size of the ligand. Larger ligands enter the P450cam binding pocket, and the resulting substrate-bound system is trapped in an open conformation via a population shift mechanism. Small ligands, which fully enter the binding pocket, cause an induced-fit mechanism, resulting in the formation of an energetically stable closed conformational state. These results are corroborated by recent experimental studies and potentially provide detailed insight into the functional dynamics and conformational behavior of the entire cytochrome-P450 superfamily. PMID:21307966
NASA Astrophysics Data System (ADS)
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 spatial instrumental scales, understanding experimental results involves extensive and difficult data analysis based on liquid theory and condensed matter physics. Therefore, a model that successfully describes the inter- and intra-dendrimer correlations is crucial in obtaining and delivering reliable information. On the other hand, making meaningful comparisons between molecular dynamics and neutron scattering is a fundamental challenge to link simulations and experiments at the nano-scale. This challenge stems from our approach to utilize MD simulation to explain the underlying mechanism of experimental observation. The SANS measurements were conducted on a series of SANS spectrometers including the Extended Q-Range Small-Angle Neutron Scattering Diffractometer (EQ-SANS) and the General-Purpose Small-Angle Neutron Scattering Diffractometer (GP-SANS) at the Oak Ridge National Laboratory (ORNL), and NG7 Small Angle Neutron Scattering Spectrometer at National Institute of Standards (NIST) and Technology in U.S.A., large dynamic range small-angle diffractometer D22 at Institut Laue-Langevin (ILL) in France, and 40m-SANS Spectrometer at Korea Atomic Energy Research Institute (KAERI) in Korea. On the other hand, the Amber molecular dynamics simulation package is utilized to carry out the computational study. In this dissertation, the following observations have been revealed. The previously developed theoretical model for polyelectrolyte dendrimers are adopted to analyze SANS measurements and superb model fitting quality is found. Coupling with advanced contrast variation small angle neutron scattering (CVSANS) data analysis scheme reported recently, the intra-dendrimer hydration and hydrocarbon components distributions are revealed experimentally. The results indeed indicate that the maximum density is located in the molecular center rather than periphery, which is consistent to previous SANS studies and the back-folding picture of PAMAM dendrimers. According to this picture, at neutral condition, the exterior residues folding back into interior would necessarily
OPTIMAL CONTROL OF ATOMIC, MOLECULAR AND ELECTRON DYNAMICS
Kassel, UniversitÃ¤t
, the dream was realized to actively exert control over quantum systems. Active control over the dynamicsChapter 9 OPTIMAL CONTROL OF ATOMIC, MOLECULAR AND ELECTRON DYNAMICS WITH TAILORED FEMTOSECOND on adaptive femtosecond quantum control where a learning algorithm and direct experimental feedback signals
The Computer Simulation of Liquids by Molecular Dynamics.
ERIC Educational Resources Information Center
Smith, W.
1987-01-01
Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)
Changes in molecular dynamics of apomyoglobin during amyloid formation
NASA Astrophysics Data System (ADS)
Stadler, Andreas Maximilian; Fabiani, Elisa; Zaccai, Giuseppe
2012-02-01
Changes of molecular dynamics associated with amyloid fibril formation were explored using apomyoglobin as a model system. Protein dynamics was measured using elastic incoherent neutron scattering. The formation of amyloid fibres was evidenced by the presence of characteristic signatures in the X-ray diffraction pattern.
Molecular dynamics simulation of Li surface erosion and bubble formation
Z. Insepov; A. Hassanein
2005-01-01
Structure and dynamical properties of liquid Li containing He atoms were studied by the Molecular Dynamics method at various temperatures and densities and the diffusion coefficients were calculated. A new model of liquid Li surface is developed that shows the stratification of surface layers. The liquid Li sputtering yield, due to bombardment by slow He ions, was calculated for the
Molecular dynamics simulation of nanomaterials using an artificial neural net
Mark Benedict; John F. Maguire
2004-01-01
We report a method of conducting molecular dynamics (MD) simulations that uses an artificial neural net (ANN) to significantly increase computational speed. The technique enables dynamical simulation of hard objects with essentially arbitrarily complex geometry and is well suited to the simulation of granular matter over a wide range of densities. In hard systems, binary collisions are well defined and
Self Diffusion in Nano Filled Polymer Melts: a Molecular Dynamics Simulation Study
NASA Astrophysics Data System (ADS)
Desai, Tapan; Keblinski, Pawel
2003-03-01
SELF DIFFUSION IN NANO FILLED POLYMER MELTS: A MOLECULAR DYNAMICS SIMULATION STUDY* T. G. Desai,P. Keblinski, Material Science and Engineering Department, Rensselaer Polytechnic Institute, Troy, NY. Using molecular dynamics simulations, we studied the dynamics of the polymeric systems containing immobile and analytically smooth spherical nanoparticles. Each chain consisted of N monomers connected by an anharmonic springs described by the finite extendible nonlinear elastic, FENE potential. The system comprises of 3nanoparticles and the rest by freely rotating but not overlapping chains. The longest chain studied has a Radius of gyration equal to particle size radius and comparable to inter-particle distance. There is no effect on the structural characteristics such as Radius of gyration or end to end distance due to the nanoparticles. Diffusion of polymeric chains is not affected by the presence of either attractive or repulsive nanoparticles. In all cases Rouse dynamics is observed for short chains with a crossover to reptation dynamics for longer chains.
Molecular dynamics of the water liquid-vapor interface
NASA Technical Reports Server (NTRS)
Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)
1987-01-01
The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.
Molecular dynamics simulation of pervaporation in zeolite membranes
NASA Astrophysics Data System (ADS)
Jia, W.; Murad, S.
The pervaporation separation of liquid mixtures of water/ethanol and water/methanol using three zeolite (Silicalite, NaA and Chabazite) membranes has been examined using the method of molecular dynamics. The main goal of this study was to identify intermolecular interactions between water, methanol, ethanol and the membrane surface that play a critical role in the separations. This would then allow better membranes to be designed more efficiently and systematically than the trial-and-error procedures often being used. Our simulations correctly exhibited all the qualitative experimental observations for these systems, including the hydrophobic or hydrophilic behaviour of zeolite membranes. The simulations showed that, for Silicalite zeolite, the separation is strongly influenced by the selective adsorption of ethanol. The separation factor, as a consequence, increases almost exponentially as the ethanol composition decreases. For ethanol dehydration in NaA and Chabazite, pore size was found to play a very important role in the separation; very high separation factors were therefore possible. Simulations were also used to investigate the effect of pore structure, feed compositions and operating conditions on the pervaporation efficiency. Finally, our simulations also demonstrated that molecular simulations could serve as a useful screening tool to determine the suitability of a membrane for potential pervaporation separation applications. Simulations can cost only a small fraction of an experiment, and can therefore be used to design experiments most likely to be successful.
A steered molecular dynamics mediated hit discovery for histone deacetylases.
Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe
2014-02-28
The inhibitors of class I histone deacetylases (HDACIs) have gained significant interest in cancer therapeutics. Virtual high throughput screening (vHTS) is one of the popular approaches used in the identification of novel scaffolds of HDACIs. However, an accurate description of ligand-protein flexibilities in the vHTS remains challenging. In this work, we implement an integrated approach, which combines the vHTS with the 'state-of-the-art' steered molecular dynamics (SMD). This approach serves as an efficient tool to identify potential hits and characterize their binding potencies against the class I HDACs in a flexible solvent environment. A hybrid pharmacophore-based and structure-based vHTS method identifies the hits with more favourable physico-chemical features against the class I HDACs. Our pharmacophore-based screening enhanced the quality of the vHTS outcomes. Further, the molecular interactions between the hits and the HDACs are investigated using the SMD-driven force profiles, which in turn resulted in filtering the hits with higher binding potencies against the HDACs. Our results, therefore, reveal that vHTS and SMD can be a complementary and effective analytical tool for accelerating the hit identification phase in structure-based drug design. PMID:24429775
Unfixed cryosections of striated muscle to study dynamic molecular events.
Ménétret, J F; Craig, R
1994-01-01
The structures of the actin and myosin filaments of striated muscle have been studied extensively in the past by sectioning of fixed specimens. However, chemical fixation alters molecular details and prevents biochemically induced structural changes. To overcome these problems, we investigate here the potential of cryosectioning unfixed muscle. In cryosections of relaxed, unfixed specimens, individual myosin filaments displayed the characteristic helical organization of detached cross-bridges, but the filament lattice had disintegrated. To preserve both the filament lattice and the molecular structure of the filaments, we decided to section unfixed rigor muscle, stabilized by actomyosin cross-bridges. The best sections showed periodic, angled cross-bridges attached to actin and their Fourier transforms displayed layer lines similar to those in x-ray diffraction patterns of rigor muscle. To preserve relaxed filaments in their original lattice, unfixed sections of rigor muscle were picked up on a grid and relaxed before negative staining. The myosin and actin filaments showed the characteristic helical arrangements of detached cross-bridges and actin subunits, and Fourier transforms were similar to x-ray patterns of relaxed muscle. We conclude that the rigor structure of muscle and the ability of the filament lattice to undergo the rigor-relaxed transformation can be preserved in unfixed cryosections. In the future, it should be possible to carry out dynamic studies of active sacromeres by cryo-electron microscopy. Images FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 FIGURE 8 PMID:7819493
Mixtures of protic ionic liquids and molecular cosolvents: a molecular dynamics simulation.
Docampo-Álvarez, Borja; Gómez-González, Víctor; Méndez-Morales, Trinidad; Carrete, Jesús; Rodríguez, Julio R; Cabeza, Óscar; Gallego, Luis J; Varela, Luis M
2014-06-01
In this work, the effect of molecular cosolvents (water, ethanol, and methanol) on the structure of mixtures of these compounds with a protic ionic liquid (ethylammonium nitrate) is analyzed by means of classical molecular dynamics simulations. Included are as-yet-unreported measurements of the densities of these mixtures, used to test our parameterized potential. The evolution of the structure of the mixtures throughout the concentration range is reported by means of the calculation of coordination numbers and the fraction of hydrogen bonds in the system, together with radial and spatial distribution functions for the various molecular species and molecular ions in the mixture. The overall picture indicates a homogeneous mixing process of added cosolvent molecules, which progressively accommodate themselves in the network of hydrogen bonds of the protic ionic liquid, contrarily to what has been reported for their aprotic counterparts. Moreover, no water clustering similar to that in aprotic mixtures is detected in protic aqueous mixtures, but a somehow abrupt replacing of [NO3](-) anions in the first hydration shell of the polar heads of the ionic liquid cations is registered around 60% water molar concentration. The spatial distribution functions of water and alcohols differ in the coordination type, since water coordinates with [NO3](-) in a bidentate fashion in the equatorial plane of the anion, while alcohols do it in a monodentate fashion, competing for the oxygen atoms of the anion. Finally, the collision times of the different cosolvent molecules are also reported by calculating their velocity autocorrelation functions, and a caging effect is observed for water molecules but not in alcohol mixtures. PMID:24908021
Mixtures of protic ionic liquids and molecular cosolvents: A molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Docampo-Álvarez, Borja; Gómez-González, Víctor; Méndez-Morales, Trinidad; Carrete, Jesús; Rodríguez, Julio R.; Cabeza, Óscar; Gallego, Luis J.; Varela, Luis M.
2014-06-01
In this work, the effect of molecular cosolvents (water, ethanol, and methanol) on the structure of mixtures of these compounds with a protic ionic liquid (ethylammonium nitrate) is analyzed by means of classical molecular dynamics simulations. Included are as-yet-unreported measurements of the densities of these mixtures, used to test our parameterized potential. The evolution of the structure of the mixtures throughout the concentration range is reported by means of the calculation of coordination numbers and the fraction of hydrogen bonds in the system, together with radial and spatial distribution functions for the various molecular species and molecular ions in the mixture. The overall picture indicates a homogeneous mixing process of added cosolvent molecules, which progressively accommodate themselves in the network of hydrogen bonds of the protic ionic liquid, contrarily to what has been reported for their aprotic counterparts. Moreover, no water clustering similar to that in aprotic mixtures is detected in protic aqueous mixtures, but a somehow abrupt replacing of [NO3]- anions in the first hydration shell of the polar heads of the ionic liquid cations is registered around 60% water molar concentration. The spatial distribution functions of water and alcohols differ in the coordination type, since water coordinates with [NO3]- in a bidentate fashion in the equatorial plane of the anion, while alcohols do it in a monodentate fashion, competing for the oxygen atoms of the anion. Finally, the collision times of the different cosolvent molecules are also reported by calculating their velocity autocorrelation functions, and a caging effect is observed for water molecules but not in alcohol mixtures.
Reactive Molecular Dynamics Simulations at the Petascale (Invited)
NASA Astrophysics Data System (ADS)
Nakano, A.
2013-12-01
We are developing a divide-conquer-recombine algorithmic framework into a metascalable (or 'design once, scale on new architectures') parallelization scheme to perform large spatiotemporal-scale reactive molecular dynamics simulations. The scheme has achieved parallel efficiency well over 0.9 on 786,432 IBM BlueGene/Q processors for 8.5 trillion-atom molecular dynamics and 1.9 trillion electronic degrees-of-freedom quantum molecular dynamics in the framework of density functional theory. Simulation results reveal intricate interplay between photoexcitation, mechanics, flow, and chemical reactions at the nanoscale. Specifically, we will discuss atomistic mechanisms of: (1) rapid hydrogen production from water using metallic alloy nanoparticles; (2) molecular control of charge transfer, charge recombination, and singlet fission for efficient solar cells; and (3) mechanically enhanced reaction kinetics in nanobubbles and nanojets.
D. Sugny; Stéphane Vranckx; Mamadou Ndong; Nathalie Vaeck; Osman Atabek; Michèle Desouter-Lecomte
2014-12-15
The constraint of time-integrated zero-area on the laser field is a fundamental, both theoretical and experimental requirement in the control of molecular dynamics. By using techniques of local and optimal control theory, we show how to enforce this constraint on two benchmark control problems, namely molecular orientation and photofragmentation. The origin and the physical implications on the dynamics of this zero-area control field are discussed.
Molecular dynamics simulation of gas clusters impact on solid targets
Insepov, Z. [Kazakh National Technical Univ., Almaty (Kazakhstan)
1994-12-31
The interaction of a cluster of Ar{sub n} (n=87-300) on a gold and silicon substrate was simulated by use of ordinary and Langevin Molecular Dynamics. The cluster was prepared by cutting out of a spherical f.c.c. block of Dynamics. The Buckingham potential was used for an interaction between the argon atoms. The excitation of the argon atoms due to high temperature and/or high pressure inside the cluster have been taken into account by use of a Monte-Carlo procedure. The N-body potential proposed by Rosato for gold and Axilrod-Teller 3-body potential for silicon was used, which describes well equilibrium properties of bulk material. The substrate was modeled using a b.c.c. lattice (for gold) and diamond (for silicon) of about 30000 atoms. These atoms were separated into three regions, depending on how near they are the impact zone. The atoms of central impact zone are being described by NM. The next zone consists of several semi-spherical layers of a thermal bath, for which the LMD was used. All the other atoms represent the movable (in radial direction) or rigid framework. The kinetic energy of the clusters is varied from 10 to 100 eV/atom. It has been shown that the impact of energetic Ar cluster with the kinetic energy of 100 eV/atom on a gold target sputters not only single atoms but also small gold clusters in the 10 atoms range. Lateral sputtering of gold target material has been predicted. Preliminary results for argon clusters implantation into the silicon (111) shows that this process seems to be quite small due to the very weak bond energy between argon and silicon atoms.
Volume Determination of Globular Proteins by Molecular Dynamics
Jonathan L. Belof; Edward W. Lowe; Randy W. Larsen; Brian Space
2014-04-06
Molecular dynamics simulations of myoglobin and aspartate aminotransferase, with explicit solvent, are shown to accurately reproduce the experimentally measured molar volumes. Single amino-acid substitution at VAL39 of aspartate aminotransferase is known to produce large volumetric changes in the enzyme, and this effect is demonstrated in simulation as well. This molecular dynamics approach, while more computationally expensive that extant computational methods of determining the apparent volume of biological systems, is quite feasible with modern computer hardware and is shown to yield accurate volumetric data with as little as several nanoseconds of dynamics.
Hydrogen bond lifetime for water in classic and quantum molecular dynamics
NASA Astrophysics Data System (ADS)
Antipova, M. L.; Petrenko, V. E.
2013-07-01
The lifetime of hydrogen bonds in water at T = 298 K and p = 0.1 MPa is computed by means of classic molecular dynamics with eight different potentials of pair lifetime interaction and Car-Parinello molecular dynamics. The results obtained using various computational techniques for hydrogen bond life-times are compared. It is shown that they can differ from one another by several times. The dependence for the hydrogen bond lifetime computed in our numerical experiment upon the method of its determination is found.
NASA Astrophysics Data System (ADS)
Ohta, S.; Nakano, M.; Kishi, R.; Takahashi, H.; Furukawa, S.
2006-02-01
We develop the second-order Monte Carlo wavefunction (MCWF) approach to the exciton dynamics of molecular aggregate systems composed of dipole-coupled two-state monomers. The explicit form of Lindblad operator, which is indispensable for applying the MCWF approach, for population relaxation among exciton states is derived based on the quantum master equation involving weak exciton-phonon coupling. The exciton migration behaviors obtained by the MCWF approach are turned out to coincide with those by the conventional master equation approach, indicating the high potential of the MCWF approach to the dissipative exciton dynamics of extended molecular aggregates or supermolecules.
Integrating Molecular Dynamics Simulations with Chemical Probing Experiments Using SHAPE-FIT.
Kirmizialtin, Serdal; Hennelly, Scott P; Schug, Alexander; Onuchic, Jose N; Sanbonmatsu, Karissa Y
2015-01-01
Integration and calibration of molecular dynamics simulations with experimental data remain a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2'-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the force field according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. PMID:25726467
Ming Liu; Minggui Yuan; Minxian Luo; Xianzhang Bu; Hai-Bin Luo; Xiaopeng Hu
2010-01-01
Glyoxalase I (GLOI) is a key metalloenzyme in glycolytic pathway by detoxifying reactive ?-ketoaldehydes such as methylglyoxal. Recent studies demonstrate that the nature product curcumin is an efficient inhibitor of GLOI, but its binding mechanism towards GLOI is still unclear. In the present study, molecular docking and molecular dynamics (MD) simulations were performed to better understand the inhibitory mechanism of
Fragment Molecular Orbital-Based Molecular Dynamics Study on Hydrated Ln(III) Ions
NASA Astrophysics Data System (ADS)
Fujiwara, Takayuki; Mori, Hirotoshi; Komeiji, Yuto; Mochizuki, Yuji
Hydration structures of Ln(III) ions were investigated by the fragment molecular orbital-based molecular dynamics simulations. The gadolinium break in changes of coordination numbers from nine to eight was of special interest. No clear "break" at gadolinium was observed in characteristics of both radial and angular distribution functions.
Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber
Luchko, Tyler; Gusarov, Sergey; Roe, Daniel R.; Simmerling, Carlos; Case, David A.; Tuszynski, Jack; Kovalenko, Andriy
2010-01-01
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G. PMID:20440377
Attosecond molecular dynamics: fact or fiction?
NASA Astrophysics Data System (ADS)
Lépine, Franck; Ivanov, Misha Y.; Vrakking, Marc J. J.
2014-03-01
The emerging application of attosecond techniques to molecular systems allows the role of electronic coherence in the control of chemical reactions to be investigated. Prompt ionization of molecules by an attosecond pulse may induce charge migration across a molecular structure on attosecond to few-femtosecond timescales, thereby possibly determining the subsequent relaxation pathways that a molecule may take. We discuss how proposals for this 'charge-directed reactivity' fit within the current understanding of quantum control and review the current state of the art of attosecond molecular science. Specifically, we review the role of electronic coherence and coupling of the electronic and nuclear degrees of freedom in high-harmonic spectroscopy and in the first attosecond pump-probe experiments on molecular systems.
Molecular dynamics simulation of interfacial adhesion
Yarovsky, I.; Chaffee, A.L. [BHP Research, Mulgrave (Australia)
1996-12-31
Chromium salts are often used in the pretreatment stages of steel painting processes in order to improve adhesion at the metal oxide/primer interface. Although well established empirically, the chemical basis for the improved adhesion conferred by chromia is not well understood. A molecular level understanding of this behaviour should provide a foundation for the design of materials offering improved adhesion control. Molecular modelling of adhesion involves simulation and analysis of molecular behaviour at the interface between two interacting phases. The present study concerns behaviour at the boundary between the metal coated steel surface (with or without chromium pretreatment) and an organic primer based on a solid epoxide resin produced from bisphenol A and epichlorohydrin. An epoxy resin oligomer of molecular weight 3750 was used as the model for the primer.
Dynamical analysis of highly excited molecular spectra
Kellman, M.E. [Univ. of Oregon, Eugene (United States)
1993-12-01
The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.
Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics.
Petsev, Nikolai D; Leal, L Gary; Shell, M Scott
2015-01-28
We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling. PMID:25637963
Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2015-01-01
We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.
NASA Astrophysics Data System (ADS)
Calvo, F.; Parneix, P.; Van-Oanh, N.-T.
2010-03-01
The vibrational spectra of the naphthalene, pyrene, and coronene molecules have been computed in the 0-3500 cm-1 infrared range using classical and quantum molecular dynamics simulations based on a dedicated tight-binding potential energy surface. The ring-polymer molecular dynamics (RPMD) and partially adiabatic centroid molecular dynamics (CMD) methods have been employed to account for quantum nuclear effects. The contributions of quantum delocalization to the line shift and broadening are significant in the entire spectral range and of comparable magnitude as pure thermal effects. While the two methods generally produce similar results, the CMD method may converge slower at low temperature with increasing Trotter discretization number. However, and contrary to the CMD method, the RPMD approach suffers from serious resonance problems at high frequencies and low temperatures.
Free energy calculations using dual-level Born-Oppenheimer molecular dynamics
Retegan, Marius; Martins-Costa, Marilia; Ruiz-Lopez, Manuel F. [Theoretical Chemistry and Biochemistry Group, SRSMC, CNRS, Nancy-University, BP 70239, 54506 Vandoeuvre-les-Nancy (France)
2010-08-14
We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.
Dynamic Structure of a Molecular Liquid S0.5Cl0.5: Ab initio Molecular-Dynamics Simulations
NASA Astrophysics Data System (ADS)
Ohmura, Satoshi; Shimakura, Hironori; Kawakita, Yukinobu; Shimojo, Fuyuki; Yao, Makoto
2013-07-01
The static and dynamic structures of a molecular liquid S0.5Cl0.5 consisting of Cl--S--S--Cl (S2Cl2) type molecules are studied by means of ab initio molecular dynamics simulations. Both the calculated static and dynamic structure factors are in good agreement with experimental results. The dynamic structures are discussed based on van-Hove distinct correlation functions, molecular translational mean-square displacements (TMSD) and rotational mean-square displacements (RMSD). In the TMSD and RMSD, there are ballistic and diffusive regimes in the sub-picosecond and picosecond time regions, respectively. These time scales are consistent with the decay time observed experimentally. The interaction between molecules in the liquid is also discussed in comparison with that in another liquid chalcogen--halogen system Se0.5Cl0.5.
Fayer, Michael D.
Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level
Molecular kinetic theory of boundary slip on textured surfaces by molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Wang, LiYa; Wang, FengChao; Yang, FuQian; Wu, HengAn
2014-11-01
A theoretical model extended from the Frenkel-Eyring molecular kinetic theory (MKT) was applied to describe the boundary slip on textured surfaces. The concept of the equivalent depth of potential well was adopted to characterize the solid-liquid interactions on the textured surfaces. The slip behaviors on both chemically and topographically textured surfaces were investigated using molecular dynamics (MD) simulations. The extended MKT slip model is validated by our MD simulations under various situations, by constructing different complex surfaces and varying the surface wettability as well as the shear stress exerted on the liquid. This slip model can provide more comprehensive understanding of the liquid flow on atomic scale by considering the influence of the solid-liquid interactions and the applied shear stress on the nano-flow. Moreover, the slip velocity shear-rate dependence can be predicted using this slip model, since the nonlinear increase of the slip velocity under high shear stress can be approximated by a hyperbolic sine function.
Lühmann, Dirk-Sören; Sengstock, Klaus
2015-01-01
In the 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 pi electron system with special regard to localization and spin order. The dynamical timescale of ultracold atom simulators are on the order milliseconds which allow for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated pi system of the artificial benzene molecule.
Modeling ramp compression experiments using large-scale molecular dynamics simulation.
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.
Prokop, Alexandr; Vacek, Jaroslav; Michl, Josef
2012-03-27
Friction in molecular rotors is examined by classical molecular dynamics simulations for grid-mounted azimuthal dipolar molecular rotors, whose rotation is either allowed to decay freely or is driven at GHz frequencies by a flow of rare gas or by a rotating electric field. The rotating parts (rotators) are propeller-shaped. Their two to six blades consist of condensed aromatic rings and are attached to a deltahedral carborane hub, whose antipodal carbons carry [n]staffane axles mounted on a square molecular grid. The dynamic friction constant ? has been derived in several independent ways with similar results. Analysis of free rotation decay yields ? as a continuous exponentially decreasing function of rotor frequency. The calculated dependence of friction torque on frequency resembles the classical macroscopic Stribeck curve. Its relation to rotational potential energy barriers and the key role of the rate of intramolecular vibrational redistribution (IVR) of energy and angular momentum from rotator rotation to other modes are considered in two limiting regimes. (i) In the strongly overdamped regime, rotation is much slower than IVR, and effective friction can be expressed through potential barriers to rotation. (ii) In the strongly underdamped regime, rotation is much faster than IVR, whose rate then determines friction. PMID:22299637
Priya Doss, C George; Nagasundaram, N
2014-02-01
Excision repair cross complementation group 1 (ERCC1) is an important protein in the nucleotide excision repair (NER) pathway, which is responsible for removing DNA adducts induced by platinum based compounds. The heterodimer ERCC1-XPF is one of two endonucleases required for NER. Genetic variations or polymorphisms in ERCC1 gene alter DNA repair capacity. Reduced DNA repair (NER) capacity may result in tumors and enhances cisplatin chemotherapy in cancer patients, which functions by causing DNA damage. Therefore, ERCC1 variants have the potential to be used as a strong candidate biomarker in cancer treatments. In this study we identified five variants V116M, R156Q, A199T, S267P, and R322C of ERCC1 gene as highly deleterious. Further structural and functional analysis has been conducted for ERCC1 protein in the presence of three variants V116M, R156Q, and A199T. Occurrence of theses variations adversely affected the regular interaction between ERCC1 and XPF protein. Analysis of 20 ns molecular dynamics simulation trajectories reveals that the predicted deleterious variants altered the ERCC1-XPF complex stability, flexibility, and surface area. Notably, the number of hydrogen bonds in ERCC1-XPF mutant complexes decreased in the molecular dynamic simulation periods. Overall, this study explores the link between the ERCC1 deleterious variants and cisplatin chemotherapy for various cancers with the help of molecular docking and molecular dynamic approaches. PMID:24158589
Population Dynamics and Harvest Potential of Mountain
SANDRA HAMEL; STEEVE D. COTE; MARCO FESTA-BIANCHET
The understanding of population dynamics is a central issue for managing large mammals. Modeling has allowed population ecologists to increase their knowledge about complex systems and better predict population responses to diverse perturbations. Mountain goats (Oreamnos americanus) appear sensitive to harvest, but the relative influence of survival and reproductive rates on their population dynamics are not well understood. Using longitudinal
Shu-Qun Liu; Zhao-Hui Meng; Yun-Xin Fu; Ke-Qin Zhang
2010-01-01
Serine protease proteinase K, a member of the subtilisin family of enzymes, is of significant industrial, agricultural and\\u000a biotechnological importance. Despite the wealth of structural information about proteinase K provided by static X-ray structures,\\u000a a full understanding of the enzymatic mechanism requires further insight into the dynamic properties of this enzyme. Molecular\\u000a dynamics simulations and essential dynamics (ED) analysis were
NASA Astrophysics Data System (ADS)
Grest, Gary S.
2008-03-01
Twenty years ago at the APS March Meeting, Kurt Kremer and I presented the first numerical evidence from computer simulations that the reptation model of Edwards and de Gennes correctly describes the dynamics of entangled linear polymer melts. For chains longer than the entanglement length Ne, the monomers of a chain move predominantly along their own contour. The distinctive signature of reptation dynamics, which we observed, was that on intermediate time scales, the mean squared displacement of a monomer increases with time as t^ 1/4. Though these early simulations were limited to chains of a few Ne, they demonstrated the potential of computer simulations to contribute to our understanding of polymer dynamics. Here I will review the progress over the past twenty years and present an outlook for the future in modeling entangled polymer melts and networks. With present day computers coupled with efficient parallel molecular dynamics codes, it is now possible to follow the equilibrium dynamics of chains of length 10-20Ne from the early Rouse regime to the long time diffusive regime. Result of these simulations support the earlier results obtained on chains of only a few Ne. Further evidence for the tube models of polymer dynamics has been obtained by identifying the primitive path mesh that characterizes the microscopic topological state of the computer- generated conformations of the chains. In particular, the plateau moduli derived on the basis of this analysis quantitatively reproduce experimental data for a wide spectrum of entangled polymer liquids including semi-dilute theta solutions of synthetic polymers, the corresponding dense melts, and solutions of semi-flexible (bio)polymers such as f-actin or suspensions of rodlike viruses. We also find that in agreement with the reptation model, the stress, end-to-end distance and entanglement length of an entangled melt subjected to uniaxial elongation, all relax on the same time scale.
Dynamic Trace-Based Analysis of Vectorization Potential of Applications
Rountev, Atanas "Nasko"
develop an approach to infer a program's SIMD parallelization potential by analyzing the dynamic dataDynamic Trace-Based Analysis of Vectorization Potential of Applications Justin Holewinski of production compilers such as GNU gcc, In- tel icc, PGI pgcc, and IBM xlc have invested considerable effort
Classical Fluid Dynamics Under Molecular Scale Confinement
NASA Astrophysics Data System (ADS)
Percus, J. K.
This is a review of some recent developments in the theory of classical nanoscale fluid dynamics, with tagged particle dynamics as the signature of transport properties. A heuristic analysis of the time asymptotic regime in strictly one-dimensional flow is followed by an exact treatment of the same system, with arbitrary non-interacting point particle dynamics. Stretched time and space coordinates allow us to obtain a universal form — the telegrapher's equation — for the self-dynamics after transients have died down. Attention then shifts to one-particle diffusion in a spatially modulated tubular enclosure, which is analyzed by increasingly sophisticated approximation methods. With this background, single-file fluid flow in modulated enclosures is studied, and preliminary analysis of the "passing region" carried out as well.
Design Challenges for Control of Molecular Dynamics
Peirce, Anthony
of modem control techniques at the level of quantum systems should open up a new domain of technological or an attacking reagent to preferentially react at the activated site. A number of clever variations on this theme]-[3] into optimal con- trol of molecular motion attempts to put the subject on a sound theoretical footing and open
Structure and Dynamics of Magnetized Dark Molecular Clouds
NASA Astrophysics Data System (ADS)
Li, P. S.; McKee, C. F.; Klein, R. I.
2015-03-01
Massive infrared dark clouds (IRDCs) are believed to be the precursors to star clusters and massive stars (e.g. Bergin & Tafalla 2007). The supersonic, turbulent nature of molecular clouds in the presence of magnetic fields poses a great challenge in understanding the structure and dynamics of magnetized molecular clouds and the star formation therein. Using the high-order radiation-magneto-hydrodynamic adaptive mesh refinement (AMR) code ORION2 (Li et al. 2012), we perform a large-scale driven-turbulence simulation to reveal the 3D filamentary structure and dynamical state of a highly supersonic (thermal Mach number = 10) and strongly magnetized (plasma ?=0.02) massive infrared dark molecular cloud. With the high resolution afforded by AMR, we follow the dynamical evolution of the cloud in order to understand the roles of strong magnetic fields, turbulence, and self-gravity in shaping the cloud and in the formation of dense cores.
Molecular dynamics simulation of liquid-vapor phase equilibria in polar fluids
NASA Astrophysics Data System (ADS)
Eslami, Hossein; Dargahi, Ali; Behnejad, Hassan
2009-04-01
A new molecular dynamics simulation technique in the grand canonical ensemble [H. Eslami, F. Müller-Plathe, J. Comput. Chem. 28 (2007) 1763], has been employed to calculate the chemical potentials in the coexisting liquid and vapor phases of pure water, methanol, and acetonitrile. Calculating the chemical potentials in the liquid phase, a new method [J. Vrabec, H. Hasse, Mol. Phys. 100 (2002) 3375], has been employed to calculate the phase coexistence point. In this method just two independent simulations in the grand canonical ensemble are needed to be performed and the molecules are inserted into or deleted from the system in a dynamical way.
Femtosecond molecular dynamics studied with vacuum ultraviolet pulse pairs
NASA Astrophysics Data System (ADS)
Allison, Thomas K., III
Atoms and molecules have most of their oscillator strength in the vacuum ultraviolet (VUV) and extreme ultraviolet (XUV), between the wavelengths of 200 nm and 30 nm. However, most femtosecond spectroscopy has been restricted to the visible and infrared due to a lack of sufficiently intense VUV and XUV femtosecond light sources. This thesis discusses extensions of pump/probe spectroscopy to the VUV and XUV, and its application to the dynamics of ethylene and oxygen molecules excited at 161 nm. I begin with a detailed discussion of the short wavelength light source used in this work. The source is based on the high order harmonics of a near infrared laser and can deliver > 1010 photons per shot in femtosecond pulses, corresponding to nearly 10 MW peak power in the XUV. Measurements of the harmonic yields as a function of the generation conditions reveal the roles of phase matching and ionization gating in the high order harmonic generation process. Pump/probe measurements are conducted using a unique VUV interferometer, capable of combining two different harmonics at a focus with variable delay. Measurements of VUV multiphoton ionization allows for characterization of the source and the interferometer. In molecules, time resolved measurements of fragment ion yields reveal the femtosecond dynamics of the system. The range of wavelengths available for pump and probe allows the dynamics to be followed from photo-excitation all the way to dissociation without detection window effects. The dynamics in ethylene upon pi ? pi* excitation are protypical of larger molecules and have thus served as an important test case for advanced ab initio molecular dynamics theories. Femtosecond measurements to date, however, have been extremely lacking. In the present work, through a series of pump probe experiments using VUV and XUV pulses, time scales for the non-adiabatic relaxation of the electronic excitation, hydrogen migration across the double bond, and H2 molecule elimination are measured and compared to theory. In the simpler oxygen molecule, excitation in the Schuman-Runge continuum leads to direct dissociation along the B S-u3 potential energy curve. The time resolved photoion spectra show that the total photoionization cross section of the molecule resembles two oxygen atoms within 50 fs after excitation.
Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.
Cawkwell, M J; Niklasson, Anders M N
2012-10-01
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. PMID:23039583
Driving Ordering Processes in Molecular-Dynamics Simulations
NASA Astrophysics Data System (ADS)
Dittmar, Harro; Kusalik, Peter G.
2014-05-01
Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized.
State-to-state dynamics of molecular energy transfer
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.
Dynamic Nanodevices Based on Protein Molecular Motors
Dan V. Nicolau
Most of the present micro\\/nano biodevices are designed for a single use, as opposed to ‘classical’ non-biodevices (e.g., from\\u000a the steam engine to the microchip). Once their function, be that simple molecular recognition like in microarrays or even\\u000a biomolecular computation as in DNA computation arrays, is fulfilled and the information is passed further to signal and information\\u000a processing systems, the
VUV studies of molecular photofragmentation dynamics
White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)
1993-12-01
State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.
Chinnasamy, Sathishkumar; Chinnasamy, Selvakkumar; Nagamani, Selvaraman; Muthusamy, Karthikeyan
2014-09-30
Snake venom metalloproteinase (SVMP) (Echis coloratus (Carpet viper) is a multifunctional enzyme that is involved in producing several symptoms that follow a snakebite, such as severe local hemorrhage, nervous system effects and tissue necrosis. Because the three-dimensional (3D) structure of SVMP is not known, models were constructed, and the best model was selected based on its stereo-chemical quality. The stability of the modeled protein was analyzed through molecular dynamics (MD) simulation studies. Structure-based virtual screening was performed, and 15 potential molecules with the highest binding energies were selected. Further analysis was carried out with induced fit docking, Prime/MM-GBSA (?GBind calculations), quantum-polarized ligand docking, and density functional theory calculations. Further, the stability of the lead molecules in the SVMP-active site was examined using MD simulation. The results showed that the selected lead molecules were highly stable in the active site of SVMP. Hence, these molecules could potentially be selective inhibitors of SVMP. These lead molecules can be experimentally validated, and their backbone structural scaffold could serve as building blocks in designing drug-like molecules for snake antivenom. PMID:25192471
Molecular Dynamics Simulations of Supported Pt Nanoclusters
Washington at Seattle, University of - Department of Physics, Electroweak Interaction Research Group
high activity Â· low energy consumption Â· long lifetime. Applications: Â· Catalytic converters for increasing catalytic activity. Increase surface area of catalyst. Objectives: Â· 100% selectivity Â· extremely of nanoscale catalytic processes Dynamic structure in supported Pt nanoclusters: Real-time density functional
Spreading dynamics of chain-like monolayers: a molecular dynamics study.
Bertrand, E; Blake, T D; De Coninck, J
2005-07-01
Using large-scale molecular dynamics simulations, we have shown previously that the spreading dynamics of sessile drops on solid surfaces can be described in detail using the molecular-kinetic theory of dynamic wetting. Here we present our first steps in extending this approach to investigate the spreading dynamics of Langmuir-Blodgett monolayers. We make use of a monolayer model originally developed by Karaborni and Toxvaerd, but somewhat simplified to facilitate large-scale simulations. Our preliminary results are in good agreement with recent experimental observations and also support a molecular-kinetic interpretation in which the driving force for spreading is the lateral pressure in the monolayer. Away from equilibrium, initial spreading rates are constant and logarithmically dependent on pressure. However, near equilibrium, spreading is pseudo-diffusive and follows the square root of time. In both regimes the controlling factor is the equilibrium frequency of molecular displacements within the monolayer. PMID:15982076
Molecular dynamics study of proton binding to silica surfaces
Rustad, J.R.; Wasserman, E.; Felmy, A.R.; Wilke, C. [Pacific Northwest National Lab., Richland, WA (United States). Environmental and Molecular Sciences Lab.] [Pacific Northwest National Lab., Richland, WA (United States). Environmental and Molecular Sciences Lab.
1998-02-01
Molecular statics calculations on gas-phase and solvated clusters and on gas-phase and solvated slabs representing aqueous species and surfaces were applied to investigate acid/base reactions on silica surfaces. The gas-phase approach, which was previously applied to goethite, predicts a surface pK{sub a} of 8.5 for the reaction > SiOH {yields} > SiO{sup {minus}} + H{sup +} which is in good agreement with estimates based on potentiometric titration. However, the model gives an unrealistically large pK{sub a} for the reaction > SiOH{sub 2}{sup +} {yields} > SiOH + H{sup +}. The model dependence of this result was checked by using two different types of interaction potentials, one based on quantum mechanical calculations on H{sub 4}SiO{sub 4} clusters, and another empirical model fitted to the structure and elastic properties of {alpha}-quartz. Because these models gave similar results, the authors hypothesize that the failure of the gas-phase models is due to intrinsic solvation effects not accounted for by previously developed correlations. They tested this idea by carrying out energy minimization calculations on gas-phase clusters with one hydration shell as well as molecular dynamics simulations on fully-solvated H{sub 5}SiO{sub 4}{sup +} and a fully solvated (0001) surface of {beta}-quartz. Though the authors are unable to establish a quantitative measure of the pK{sub a} of SiOH{sub 2} groups, the solvated systems do indicate that SiOH groups do not protonate in any of the solvated models.
Molecular dynamics modelling of radiation damage in zircon
NASA Astrophysics Data System (ADS)
Grechanovsky, A. E.
2009-04-01
Zircon (ZrSiO4) is among actinide-bearing phases which has been proposed as a crystalline confinement matrix for nuclear waste management, especially for weapon-grade plutonium and UO2 spent fuel in the USA. Zircon is also widely used in geochronology. But, with accumulating ?-decay damage, zircon undergoes a radiation induced transition to an amorphous (or metamict) state. So, in the present work molecular dynamics simulations (MD simulations) of zircon structure have been performed to study radiation damage in zircon. In this technique, one simulates the propagation of an energetic particle in a system of atoms interacting via model potentials, by integrating the Newton equations of motion. Author has used version 3.09 of the DL_POLY molecular simulation package. Zircon structure containing 181944 atoms (19x19x21 unit cells) was equilibrated at 300 K for 10 ps, and one Zr atom (usually called the primary knock-on atom, PKA) was given a velocity corresponding to an implantation energy of about 20 keV. MD simulations were performed in the microcanonical ensemble that is under conditions of constant particle number, volume and energy. Results of the MD simulations show that the number of interstitials is equal to 840 atoms. This is very close (4000-5000 atoms for 70 keV recoil atom 234Th) to what is measured in the diffuse x-ray scattering and NMR experiments on amorphous metamict samples (damaged by natural irradiation) of geological age. It has been shown that the damaged structure contains several depleted regions with characteristic sized up to 2,5 nm after single event and up to 4,5 nm after three overlapping events. Furthermore, these events produce channels of depleted matter between the overlapping damaged regions. These channels provide a high-diffusivity path for radiogenic Pb (percolation effect). Loss of radiogenic Pb may result in to incorrect dating of rocks.
Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes
Orsi, Mario; Noro, Massimo G.; Essex, Jonathan W.
2011-01-01
Triclocarban and triclosan, two potent antibacterial molecules present in many consumer products, have been subject to growing debate on a number of issues, particularly in relation to their possible role in causing microbial resistance. In this computational study, we present molecular-level insights into the interaction between these antimicrobial agents and hydrated phospholipid bilayers (taken as a simple model for the cell membrane). Simulations are conducted by a novel ‘dual-resolution’ molecular dynamics approach which combines accuracy with efficiency: the antimicrobials, modelled atomistically, are mixed with simplified (coarse-grain) models of lipids and water. A first set of calculations is run to study the antimicrobials' transfer free energies and orientations as a function of depth inside the membrane. Both molecules are predicted to preferentially accumulate in the lipid headgroup–glycerol region; this finding, which reproduces corresponding experimental data, is also discussed in terms of a general relation between solute partitioning and the intramembrane distribution of pressure. A second set of runs involves membranes incorporated with different molar concentrations of antimicrobial molecules (up to one antimicrobial per two lipids). We study the effects induced on fundamental membrane properties, such as the electron density, lateral pressure and electrical potential profiles. In particular, the analysis of the spontaneous curvature indicates that increasing antimicrobial concentrations promote a ‘destabilizing’ tendency towards non-bilayer phases, as observed experimentally. The antimicrobials' influence on the self-assembly process is also investigated. The significance of our results in the context of current theories of antimicrobial action is discussed. PMID:21131331
Dynamical Higgs potentials with a landscape
J. L. F. Barbon; C. Hoyos
2006-02-28
We consider one-loop effective potentials for adjoint Higgs fields that originate from flat holonomies in toroidal compactification of gauge theories. We show that such potentials are "landscape-like" for large gauge groups and generic non-supersymmetric matter representations. In particular, there is a large number of vacua with similar local properties, scanning a broad band of vacuum energies.
NASA Astrophysics Data System (ADS)
Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C.
2013-11-01
Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.
Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics
NASA Astrophysics Data System (ADS)
Ehrlicher, Allen
2012-02-01
Mechanical stresses elicit cellular reactions mediated by chemical signals. Defective responses to forces underlie human medical disorders, such as cardiac failure and pulmonary injury. Despite detailed knowledge of the cytoskeleton's structure, the specific molecular switches that convert mechanical stimuli into chemical signals have remained elusive. Here we identify the actin-binding protein, filamin A (FLNa) as a central mechanotransduction element of the cytoskeleton by using Fluorescence Loss After photoConversion (FLAC), a novel high-speed alternative to FRAP. We reconstituted a minimal system consisting of actin filaments, FLNa and two FLNa-binding partners: the cytoplasmic tail of ß-integrin, and FilGAP. Integrins form an essential mechanical linkage between extracellular and intracellular environments, with ß integrin tails connecting to the actin cytoskeleton by binding directly to filamin. FilGAP is a FLNa-binding GTPase-activating protein specific for Rac, which in vivo regulates cell spreading and bleb formation. We demonstrate that both externally-imposed bulk shear and myosin II driven forces differentially regulate the binding of integrin and FilGAP to FLNa. Consistent with structural predictions, strain increases ß-integrin binding to FLNa, whereas it causes FilGAP to dissociate from FLNa, providing a direct and specific molecular basis for cellular mechanotransduction. These results identify the first molecular mechanotransduction element within the actin cytoskeleton, revealing that mechanical strain of key proteins regulates the binding of signaling molecules. Moreover, GAP activity has been shown to switch cell movement from mesenchymal to amoeboid motility, suggesting that mechanical forces directly impact the invasiveness of cancer.
NASA Astrophysics Data System (ADS)
Zimmerman, J. A.; Winey, J. M.; Gupta, Y. M.
2011-06-01
Molecular dynamics (MD) simulations were used to examine elastic shock wave propagation in aluminum single crystals along [100], [110] and [111] directions using four different embedded-atom method potentials. Continuum variables extracted from MD results show that stresses, densities, and temperatures for [100] shock propagation are significantly different for the various potentials, while the results for [110] and [111] propagation are similar for three of the four potentials. Overall, the recent potential by Winey, Kubota and Gupta [MSMSE 17, 055004 (2009)] provides the best agreement with nonlinear elastic calculations that include elastic constants up to fourth order. Our MD-continuum approach provides a key step in establishing the applicability of classical MD potentials for dynamic compression. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Molecular Dynamics Study of Polymer Separation Using a Nanofluidic Staircase
NASA Astrophysics Data System (ADS)
Phelan, Frederick, Jr.; Forrey, Christopher
2013-03-01
The diffusive behavior of isolated polymer chains in a nanofluidic staircase has recently been studied experimentally [Strychalski et al., Macromolecules, 45(3), 1602, (2012); Stavis et al., Lab Chip, 12(19), 1174, (2012)] and by simulation [Phelan et al., in preparation, (2012)]. Chains are observed to exhibit spontaneous 1-D biased diffusion from regions of high to low confinement, without the use of external forces, under conditions where the local confinement lies in either the Odijk or de Gennes regimes. The transport mechanism is that of a Brownian motor, where the polymer free energy is used to generate directed transport using thermal fluctuations and the biased structural features of the device. The nanostaircase has potential for a number of applications in polymer measurement science and transport, an important one of which could be separations. To study this, we examine polymer separation in the nanofluidic staircase using the molecular dynamics simulation software LAMMPS. Length based separations of linear polymers as applicable to DNA separations are the main topic of the study, but the effect of more complex architectures such as branching are also examined.
Helium diffusion in tungsten: A molecular dynamics study
NASA Astrophysics Data System (ADS)
Shu, Xiaolin; Tao, Peng; Li, Xiaochun; Yu, Yi
2013-05-01
The diffusion process of He in W is simulated by a molecular dynamics (MD) method with self-developed W-H-He analytic bond-order potentials. The mean squared displacement (MSD) method is employed to determine diffusivity at different temperatures, and then the diffusivity-temperature (D-T) relationship is fitted by the Arrhenius equation to obtain the prefactor and the diffusion barrier. We show the diffusivity of He and the corresponding prefactor and diffusion barrier are different at different temperature ranges. The diffusivities are 9.50 × 10-9 exp(-0.021 eV/kT) m2/s in the temperature range of 50-300 K, 3.61 × 10-8 exp(-0.057 eV/kT) m2/s in 300-1500 K, and 8.562 × 10-8 exp(-0.157 eV/kT) m2/s in 1500-3000 K, respectively, which correspond to different diffusion mechanisms. At a lower temperature, He diffuses directly from one tetrahedral interstitial site (TIS) to another TIS through the diagonal interstitial site with a lower diffusion barrier, while it can diffuse from one TIS to other TIS through the octahedral interstitial site with higher barrier at higher temperature.
Novel morphologies for laterally decorated metaparticles: Molecular dynamics simulation
A. Y. Slyusarchuk; J. M. Ilnytskyi
2015-01-12
We consider a mesoscale model for nano-sized metaparticles (MPs) composed of a central sphere decorated by polymer chains with laterally attached spherocylinder. The latter mimics the mesogenic (e.g., cyanobiphenyl) group. Molecular dynamics simulations of $100$ MPs reveal the existence of two novel morphologies: $\\textrm{uCol}_\\mathrm{h}$ (hexagonal columnar arrangement of MPs with strong uniaxial order of mesogens collinear to the columns axis) and $\\mathrm{wCol}_\\mathrm{h}$ [the same arrangement of MPs but with weak or no liquid crystalline (LC) order]. Collinearity of the LC director and the columnar axis in $\\textrm{uCol}_\\mathrm{h}$ morphology indicates its potentially different opto-mechanical response to an external perturbation as compared to the columnar phase for the terminally attached mesogens. Preliminary analysis of the structures of both phases is performed by studying the order parameters and by visualisation of the MPs arrangements. Different mechanisms for the mesogens reorientation are pointed out for the cases of their terminal and lateral attachment.
Molecular dynamics model of carbon nanotubes in EPON 862/DETDA polymer
NASA Astrophysics Data System (ADS)
Ingvason, Guttormur Arnar
The aerospace industry is interested in increasing the strength while reducing the weight of carbon fiber composite materials. Adding single walled carbon nanotubes (SWCNT) to a polymer matrix can achieve that goal by improving delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential to represent the interactions between the atoms of the polymer and the SWCNT. This potential includes non-bonded interactions (9-6 Lennard-Jones), bond interaction (class2), angles (class2) and dihedrals (class2) to create a molecular dynamics model for single-walled carbon nanotubes and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the potential. The first one is a tensile test on a SWCNT, leading to a Young's modulus of 1.4 TPa at 300K. The second one is a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.
H-Bond in methanol: a molecular dynamics study
NASA Astrophysics Data System (ADS)
Alonso, J.; Bermejo, F. J.; Garciá-Hernández, M.; Martínez, J. L.; Howells, W. S.
1991-11-01
A set of molecular dynamics (MD) simulations of methanol- d4 at three temperatures in the liquid range (200, 250 and 300K) have been carried out. The equations of motion of 256 molecules interacting through a potential model due to Haughney et al. [J. Phys. Chem., 91 (1987) 4934] were solved using the velocity version of the Verlet algorithm. This rather large number of molecules was required for studying the behaviour of the system at momentum transfers as low as 0.25 Å -1. It was found that the system experiences long period fluctuations, and therefore very long MD runs (of the order of 100 ps) are necessary in order to obtain accurate statistical averages. Computed static properties are in good agreement with those reported by Haughney et al. and the neutron weighted g( r) and the static structure factor compare favourably with available neutron diffraction data. The study of time-dependent properties through centre-of-mass autocorrelation functions (VACF, Fs( Q,t) and F( Q,t)) and their memory functions reveals features unknown in simple liquids and very similar to those found in liquid water. A close agreement between centre-of-mass single-particle autocorrelation functions and the translational part of QENS data is also observed. The dynamic structure factor for the centres of mass show distinctive side peaks in the same region of the ( Q,?) plane where recently collective excitations have been studied using coherent neutron scattering thus establishing the presence of propagating short wavelength modes. fa]Presented at the International Symposium on Hydrogen Bond Physics held at Il Ciocco, Barga, Italy, 11-14 September 1990.
Molecular dynamic analysis of the structure of dendrimers
NASA Astrophysics Data System (ADS)
Canetta, E.; Maino, G.
2004-01-01
We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.
Evidence for dynamically important magnetic fields in molecular clouds
Hua-Bai Li; Raymond Blundell; Abigail Hedden; Jonathan Kawamura; Scott Paine; Edward Tong
2011-01-01
Recent observational evidence that magnetic fields are dynamically important in molecular clouds, compared to self-gravity and turbulence, is reviewed and illustrated with data from the NGC 2024 region. One piece of evidence, turbulence anisotropy, was found in the diffuse envelope of a cloud (Av≈ 1; Heyer et al. 2008); our data further suggest turbulence anisotropy in the cloud (Av >
Molecular dynamics simulations of implantation damage and recovery in semiconductors
M. Sayed; J. H. Jefferson; A. B. Walker; A. G. Cullis
1995-01-01
Numerous experiments on damage in semiconductors due to ion bombardment have shown quite varied material-dependent behaviour. In particular after the recovery phase, the residual damage can vary from almost crystalline to amorphous for given ion bombardment conditions [1]. We have studied both the initial cascade damage and the subsequent recovery using approximate and full molecular dynamics techniques for Si, GaAs
NAMD: a Parallel, Object-Oriented Molecular Dynamics Program
Mark T. Nelson; William Humphrey; Attila Gursoy; Andrew Dalke; Laxmikant V. Kalé; Robert D. Skeel; Klaus Schulten
1996-01-01
NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design imple mented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decom position coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors. Also, NAMD incorporates the distributed par
Granular Media on a Vibrating Plate:. a Molecular Dynamics Simulation
Jason A. C. Gallas; Hans J. Herrmann; Stefan Sokolowski
1993-01-01
When sand or other granular materials are shaken, poured or sheared many intriguing phenomena can be observed. We will model the granular medium by a packing of elastic spheres and simulate it via Molecular Dynamics. Dissipation of energy and shear friction at collisions are included. The onset of fluidization can be determined and is in good agreement with experiments. On
Molecular dynamics of liquid benzene via femtosecond pulses laser excitation
Paris-Sud XI, Université de
1749 Molecular dynamics of liquid benzene via femtosecond pulses laser excitation J. Etchepare, G moléculaires. Abstract. 2014 We analyse the complex response of liquid benzene to the applied 45 fs FHWM new results obtained by the transient grating temporal behaviour analysis of benzene, a molecule
Extended Thomas-Fermi molecular dynamics of sodium clusters
P. Blaise; S. A. Blundell; C. Guet
1997-01-01
We describe a semiclassical molecular-dynamics procedure suitable for charged or neutral clusters of sodium containing up to several hundred atoms. The charged liquid drop energy parameters of the model are extracted, and shown to be in good agreement with empirically inferred values. Vertical ionization energies are also found to be in good agreement with experiment. We find that the time-averaged
Little evidence for dynamic divergences in ultraviscous molecular liquids
Loss, Daniel
and relaxation time is observed on continued cooling, and the liquid eventually solidifies into a glass--a frozen liquid. Which of the two scenarios that prevails depends on the cooling rate. The ultraviscous liquidARTICLES Little evidence for dynamic divergences in ultraviscous molecular liquids TINA HECKSHER
Molecular dynamics in arbitrary geometries: Parallel evaluation of pair forces
Graham B. Macpherson; Jason M. Reese
2008-01-01
A new algorithm for calculating intermolecular pair forces in molecular dynamics (MD) simulations on a distributed parallel computer is presented. The arbitrary interacting cells algorithm (AICA) is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh that has been spatially decomposed into irregular portions for parallelisation. It is intended for nano scale fluid mechanics simulation by
Structure and Molecular Dynamics of Multilayered Polycarbonate/Polystyrene Films
Paris-Sud XI, Université de
Structure and Molecular Dynamics of Multilayered Polycarbonate/Polystyrene Films M. Walczak,1 W (wileyonlinelibrary.com). ABSTRACT: Multilayered film polycarbonate/polysty- rene (PC/PS) comprising 257 layers Periodi- cals, Inc. J Appl Polym Sci 000: 000000, 2012 Key words: interface; polystyrene; polycarbonate
Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments
De Paris, Renata; Quevedo, Christian V.; Ruiz, Duncan D.; Norberto de Souza, Osmar; Barros, Rodrigo C.
2015-01-01
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 simulation of shocks in porous TATB crystals
Laurence E. Fried; Craig Tarver
1996-01-01
We report molecular dynamics results on the shock structure of two dimensional crystals of triaminotrinitrobenzene (TATB). We find that the shock front broadens to approximately 30 nm in materials with a 20 percent random void distribution. As expected from bulk experiments, the shock velocity decreases with increasing porosity and the temperature behind the shock front increases with increasing porosity. Shock
Ethanol and water capacities of alcohols: a molecular dynamics study
Technology Transfer Automated Retrieval System (TEKTRAN)
The extended hydrogen bond networks formed by alcohols are good indicators of their capacities to hold water. Results from molecular dynamics simulations on 24 linear alcohol isomers containing from 6 to 12 carbon atoms show the effects of the hydroxyl location on bulk hydrogen-bonded structures. ...
Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions
NASA Technical Reports Server (NTRS)
Menon, Madhu
1998-01-01
In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.
Laser opto-microactuators rotated by molecular gas dynamics effects
M. Ota; T. Nakao; M. Sakamoto
1998-01-01
Summary form only given. Laser opto-microactuators are discussed in this study. The actuators are rotated by the effects of molecular gas dynamics such as the forces by a thermal creep force and a radiometric force. The effects are induced by heating of the rotor surface of the actuators with a laser beam. It is elucidated that the maximum torque of
Time resolved measurements of molecular orientational dynamics in liquids
Righini, R. [LENS, University of Florence, 50125 Florence (Italy)]|[Department of Chemistry, University of Basilicata, 85100 Potenza (Italy)
1996-04-01
Time resolved optical experiments on different molecular liquids in the proximity of disorder-order phase transitions show the appearance of relatively slow collective dynamics associated to the set-up of long range intermolecular correlation. The data are discussed on the basis of the available microscopic and phenomenological theories. {copyright} {ital 1996 American Institute of Physics.}
MOLECULAR DYNAMICS SIMULATIONS OF HMX CRYSTAL POLYMORPHS USING
Utah, University of
MOLECULAR DYNAMICS SIMULATIONS OF HMX CRYSTAL POLYMORPHS USING A FLEXIBLE MOLECULE FORCE FIELD a recently developed quantum chemistry-based atomistic force field [J. Phys. Chem. B 103 (1999) 3570] were published, fully flexible, quantum chemistry-based atomistic force field for HMX. 5 In this paper we present
Heermann, Dieter W.
be a Hamiltonian, Lagrangian or expressed directly in Newton's equations of motion. In the first two cases of molecules which individually obey classical laws of motion. Note that this includes not only point . . . . . . . . . . . . 20 1.1.3 Isothermal-Isobaric Knsemble Molecular Dynamics . . . 25 1.2 Density Functional Method
A Molecular Dynamics Simulation of Hydrogen Storage with SWNTs
Maruyama, Shigeo
A Molecular Dynamics Simulation of Hydrogen Storage with SWNTs S. Maruyama and T. Kimura, Bunkyo-ku, Tokyo 113-8656, Japan The mechanism of efficient hydrogen storage (1) with SWNTs (2, and the storage amount became about 5 wt % regardless of the tube radius. The number of absorbed hydrogen
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
Rapaport, Dennis C.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine D 2009; published 30 April 2009 A nanoscale-sized Stirling engine with an atomistic working fluid has s : 02.70.Ns, 05.70.Ln, 47.61. k The Stirling engine, an external combustion engine in- vented almost two
Fragmentation by molecular dynamics: The microscopic ''big bang''
Brad Holian; Dennis Grady
1988-01-01
We propose and test a new molecular-dynamics method to study fragmentation of condensed matter under homogeneous adiabatic expansion. Our atomistic simulations give significant insight into the nature of fragment distributions. We also find that a simple continuum model based on energy balance gives a reasonably good estimate of the average fragment mass.
Molecular Dynamics Simulation of Hexamine and Suberic Acid
Yuansheng Pan; David Brown; Gervais Chapuis
2003-01-01
In order to perform a molecular dynamics (MD) simulation of the incommensurate crystalline structure hexamethylenetetramine suberate (C 6 H 12 N 4 )(HOOC-(CH 2 ) 6 -COOH), we present in a first step the separate simulations of the crystalline structure of each of the two pure components, hexamethylenetetramine (HMT) and suberic acid. The domain decomposition parallel MD program ddgmq is
Molecular Dynamics Simulations of Alumina Addition in Sodium Silicate Glasses
M. Montorsi; M. C. Menziani; C. Leonelli; G. C. Pellacani; A. N. Cormack
2000-01-01
Molecular dynamics simulations of alumina containing silicate glasses have been performed in order to determine the influence of that ion on the final properties of the glasses. In particular, short- and mid-range structures were analyzed in terms of the distribution of non bridging oxygen, bridging oxygen, three bridging oxygen species in the glasses, along with the coordination number distribution (cn)
Molecular Dynamics of Coat Proteins of the Human Rhinovirus
Wan F. Lau; B. Montgomery Pettitt; Terry P. Lybrand
1988-01-01
The effects of the oxazole antiviral WIN 52084 on the thermal vibrations of the coat proteins of the human rhinovirus were studied by means of a comparison of two molecular dynamics simulations. One simulation involved only a protomeric unit (cluster of four proteins) of the viral coat, while the other included the antiviral drug bound to the protein cluster. Analysis
Hydrogen Raman shifts in carbon nanotubes from molecular dynamics simulation
Brenner, Donald W.
Hydrogen Raman shifts in carbon nanotubes from molecular dynamics simulation S.J.V. Frankland *, D hydrogen in individual single-shell carbon nanotubes and nanotube ropes using a semiclassical model. The calculations predict that isolated hydrogen molecules inside of nanotubes have a Raman frequency that increases
Karthick, T; Balachandran, V; Perumal, S
2015-04-15
Thiophene derivatives have been focused in the past decades due to their remarkable biological and pharmacological activities. In connection with that the conformational stability, spectroscopic characterization, molecular (inter- and intra-) interactions, and molecular docking studies on thiophene-2-carboxylicacid have been performed in this work by experimental FT-IR and theoretical quantum chemical computations. Experimentally recorded FT-IR spectrum in the region 4000-400cm(-1) has been compared with the scaled theoretical spectrum and the spectral peaks have been assigned on the basis of potential energy distribution results obtained from MOLVIB program package. The conformational stability of monomer and dimer conformers has been examined. The presence of inter- and intramolecular interactions in the monomer and dimer conformers have been explained by natural bond orbital analysis. The UV-Vis spectra of the sample in different solvents have been simulated and solvent effects were predicted by polarisable continuum model with TD-DFT/B3LYP/6-31+G(d,p) method. To test the biological activity of the sample, molecular docking (ligand-protein) simulations have been performed using SWISSDOCK web server. The full fitness (FF) score and binding affinity values revealed that thiophene-2-carboxylicacid can act as potential inhibitor against inflammation. PMID:25677530
Liu, Qixin; Cai, Zhiyong
2014-01-01
This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745
Numerical methods for molecular dynamics. Progress report
Skeel, R.D.
1991-12-31
This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.
Nonadiabatic Molecular Dynamics Simulations: Synergies between Theory and Experiments.
Tavernelli, Ivano
2015-03-17
Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics/molecular mechanics (QM/MM) approach has the advantage of providing an atomistic (even though approximated) description of the solvent molecules, which is crucial for the characterization of all ultrafast relaxation phenomena that depend on the geometrical arrangement at the interface between a molecule and the solvent, for example, the hydrogen bond network. After a short description of the TDDFT-based implementation of Ehrenfest and trajectory surface hopping dynamics, I will present applications in different domains of molecular chemistry and physics: the analysis and the understanding of (time-resolved) X-ray absorption spectra, the interpretation of the ultrafast relaxation dynamics of photoexcited dyes in solution, and the design of specific laser pulses (capable of inducing desired chemical reactions) using local control theory. PMID:25647401
Ingólfsson, Helgi I.; Li, Yuhui; Vostrikov, Vitaly V.; Gu, Hong; Hinton, James F.; Koeppe, Roger E.; Roux, Benoît; Andersen, Olaf S.
2011-01-01
Gramicidin A (gA) channels provide an ideal system to test molecular dynamics (MD) simulations of membrane proteins. The peptide backbone lines a cation-selective pore and, due to the small channel size, the average structure and extent of fluctuations of all atoms in the peptide will influence ion permeation. This raises the question of how well molecular mechanical force fields used in MD simulations and potential of mean force (PMF) calculations can predict structure and dynamics as well as ion permeation. To address this question, we undertook a comparative study of nuclear magnetic resonance (NMR) observables predicted by fully atomistic MD simulations on a gA dimer embedded in a sodium dodecyl sulfate (SDS) micelle with measurements of the gA dimer backbone and tryptophan side chain dynamics using solution state 15N-NMR on gA dimers in SDS micelles. This comparison enables us to examine the robustness of the MD simulations done using different force fields, as well as their ability to predict important features of the gA channel. We find that MD is able to predict NMR observables, including the generalized order parameters (S2), the 15N spin-lattice (T1), spin-spin (T2) relaxation times, and the 1H-15N nuclear Overhauser effect (NOE), with remarkable accuracy. To examine further how differences in the force fields can affect the channel conductance, we calculated the PMF for K+ and Na+ permeation through a gA channel in a dimyristoylphosphatidylcholine (DMPC) bilayer. In this case, we find that MD is less successful in quantitatively predicting the single-channel conductance. PMID:21574563
Molecular Dynamics of a Water-Lipid Bilayer Interface
NASA Technical Reports Server (NTRS)
Wilson, Michael A.; Pohorille, Andrew
1994-01-01
We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.
Drugs That Target Dynamic Microtubules: A New Molecular Perspective
Stanton, Richard A.; Gernert, Kim M.; Nettles, James H.; Aneja, Ritu
2011-01-01
Microtubules have long been considered an ideal target for anticancer drugs because of the essential role they play in mitosis, forming the dynamic spindle apparatus. As such, there is a wide variety of compounds currently in clinical use and in development that act as antimitotic agents by altering microtubule dynamics. Although these diverse molecules are known to affect microtubule dynamics upon binding to one of the three established drug domains (taxane, vinca alkaloid, or colchicine site), the exact mechanism by which each drug works is still an area of intense speculation and research. In this study, we review the effects of microtubule-binding chemotherapeutic agents from a new perspective, considering how their mode of binding induces conformational changes and alters biological function relative to the molecular vectors of microtubule assembly or disassembly. These “biological vectors” can thus be used as a spatiotemporal context to describe molecular mechanisms by which microtubule-targeting drugs work. PMID:21381049
Sheng-Nian Luo; Thomas J. Ahrens; Tahir Çagin; Alejandro Strachan; William A. Goddard; Damian C. Swift
2003-01-01
The maximum superheating and undercooling achievable at various heating (or cooling) rates were investigated based on classical nucleation theory and undercooling experiments, molecular dynamics (MD) simulations, and dynamic experiments. The highest (or lowest) temperature Tc achievable in a superheated solid (or an undercooled liquid) depends on a dimensionless nucleation barrier parameter beta and the heating (or cooling) rate Q. beta
Sheng-Nian Luo; Thomas J. Ahrens; Tahir Ca; Alejandro Strachan; William A. Goddard III; Damian C. Swift
2003-01-01
The maximum superheating and undercooling achievable at various heating ~or cooling! rates were inves- tigated based on classical nucleation theory and undercooling experiments, molecular dynamics ~MD! simu- lations, and dynamic experiments. The highest ~or lowest! temperature Tc achievable in a superheated solid ~or an undercooled liquid! depends on a dimensionless nucleation barrier parameter b and the heating ~or cooling! rate
Lisal, Martin
Reaction ensemble molecular dynamics: Direct simulation of the dynamic equilibrium properties of chemically reacting mixtures John K. Brennan,1, * Martin Lísal,2,3 Keith E. Gubbins,4 and Betsy M. Rice1 1 U 21005-5066, USA 2 E. Hála Laboratory of Thermodynamics, Institute of Chemical Process Fundamentals
Self-consistent field theory based molecular dynamics with linear system-size scaling
NASA Astrophysics Data System (ADS)
Richters, Dorothee; Kühne, Thomas D.
2014-04-01
We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.
Self-consistent field theory based molecular dynamics with linear system-size scaling
Richters, Dorothee [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany)] [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany); Kühne, Thomas D., E-mail: kuehne@uni-mainz.de [Institute of Physical Chemistry and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz (Germany); Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn (Germany)
2014-04-07
We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.
Hu, Xiaohu [ORNL; Elghobashi-Meinhardt, Nadia [Karlsruhe Institute of Technology, Karlsruhe, Germany; Gembris, Daniel [Bruker Bio-Spin MRI GmbH, Ettling, Germany; Smith, Jeremy C [ORNL
2011-01-01
The electric field dependence of the structure and dynamics of water at 77 K, i.e., below the glass transition temperature (136 K), is investigated using molecular dynamics simulations. Transitions are found at two critical field strengths, denoted E1 and E2. The transition around E1 3.5 V/nm is characterized by the onset of significant structural disorder, a rapid increase in the orientational polarization, and a maximum in the dynamical fluctuations. At E2 40 V/nm, the system crystallizes in discrete steps into a body-centered-cubic unit cell that minimizes the potential energy by simultaneous superpolarization of the water molecular dipoles and maximization of the intermolecular hydrogen bonds. The stepwise and discontinuous increase of the orientational polarization with the increasing electric field indicates that the dipole relaxation in the electric field is highly cooperative.
Equilibrium and nonequilibrium molecular-dynamics simulations of the central force model of water
NASA Astrophysics Data System (ADS)
Bresme, Fernando
2001-10-01
Equilibrium and nonequilibrium molecular-dynamics simulations of the central force model of water (CFM) [Lemberg and Stillinger, J. Chem. Phys. 62, 1677 (1975)] are presented. We consider a model based on a functional form introduced in theoretical studies of associating systems employing integral equations [F. Bresme, J. Chem. Phys. 108, 4505 (1998)]. Results on thermodynamic, dynamic, dielectric, and coexistence properties are presented. The central force model shows satisfactory agreement with the experimental results in all these cases. In addition, nonequilibrium molecular-dynamics simulations show that the CFM predicts a decrease of the thermal conductivity with temperature, as observed in the experiment, but this dependence is reproduced qualitatively at temperatures characteristic of supercooled states. These results emphasize the need for further studies of the heat conduction and properties of water in these conditions. Overall the present potential should provide a basis for further theoretical and simulation studies of complex systems where water is present.
An estimation of molecular dynamic behaviour in a liquid using core-loss spectroscopy
Matsui, Yoshiki; Seki, Koichiro; Hibara, Akihide; Mizoguchi, Teruyasu
2013-01-01
We report an effective approach for estimating the dynamic behaviour of molecules in liquid from their core-loss spectra by combining molecular dynamics simulations and first-principles band-structure calculations. The carbon K-edge of the technologically important methanol was calculated, and the experimental spectra were well reproduced using the presented calculation method, which effectively included multiple-molecule interactions. Several peaks arose from the methanol molecules with different C-O bonding modes, and the splitting of those peaks was sensitively altered by the magnitude of the dynamic behaviour of molecules. These findings allow for estimation of the dynamic behaviour of molecules in liquids using core-loss spectroscopy, and the method offers the potential to identify the dynamic behaviour of the molecules in liquids with high spatial resolution, temporal resolution, and sensitivity. PMID:24356101
Membrane potential dynamics of grid cells.
Domnisoru, Cristina; Kinkhabwala, Amina A; Tank, David W
2013-03-14
During navigation, grid cells increase their spike rates in firing fields arranged on a markedly regular triangular lattice, whereas their spike timing is often modulated by theta oscillations. Oscillatory interference models of grid cells predict theta amplitude modulations of membrane potential during firing field traversals, whereas competing attractor network models predict slow depolarizing ramps. Here, using in vivo whole-cell recordings, we tested these models by directly measuring grid cell intracellular potentials in mice running along linear tracks in virtual reality. Grid cells had large and reproducible ramps of membrane potential depolarization that were the characteristic signature tightly correlated with firing fields. Grid cells also demonstrated intracellular theta oscillations that influenced their spike timing. However, the properties of theta amplitude modulations were not consistent with the view that they determine firing field locations. Our results support cellular and network mechanisms in which grid fields are produced by slow ramps, as in attractor models, whereas theta oscillations control spike timing. PMID:23395984
Water harvesting using a conducting polymer: A study by molecular dynamics simulation
Ostwal, Mayur M.; Sahimi, Muhammad; Tsotsis, Theodore T. [Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211 (United States)
2009-06-15
The results of extensive molecular simulations of adsorption and diffusion of water vapor in polyaniline, made conducting by doping it with HCl or HBr over a broad range of temperatures, are reported. The atomistic model of the polymers was generated using energy minimization, equilibrium molecular dynamics simulations, and two different force fields. The computed sorption isotherms are in excellent agreement with the experimental data. The computed activation energies for the diffusion of water molecules in the polymers also compare well with what has been reported in the literature. The results demonstrate the potential of conducting polyaniline for water harvesting from air.
Dynamics of Quantum Vorticity in a Random Potential
Link, Bennett [Department of Physics, Montana State University, Bozeman Montana 59717 (United States)
2009-04-03
I study the dynamics of a superfluid vortex in a random potential, as in the inner crust of a neutron star. Below a critical flow velocity of the ambient superfluid, a vortex is effectively immobilized by lattice forces even in the limit of zero dissipation. Low-velocity, translatory motion is not dynamically possible, a result with important implications for understanding neutron star precession and the dynamical properties of superfluid nuclear matter.
Dynamics of Quantum Vorticity in a Random Potential
Bennett Link
2009-03-27
I study the dynamics of a superfluid vortex in a random potential, as in the inner crust of a neutron star. Below a critical flow velocity of the ambient superfluid, a vortex is effectively immobilized by lattice forces even in the limit of zero dissipation. Low-velocity, translatory motion is not dynamically possible, a result with important implications for understanding neutron star precession and the dynamical properties of superfluid nuclear matter.
Molecular Dynamics Simulations of Sonic Hedgehog-Receptor and Inhibitor Complexes and Their
Lee, Keun Woo
Molecular Dynamics Simulations of Sonic Hedgehog-Receptor and Inhibitor Complexes), Gyeongsang National University (GNU), Jinju, Republic of Korea Abstract The sonic hedgehog (Shh) signaling) Molecular Dynamics Simulations of Sonic Hedgehog-Receptor and Inhibitor Complexes and Their Applications
Crack Formation and Propagation in Molecular Dynamics Simulations of Polymer Liquid Crystals
North Texas, University of
308 Crack Formation and Propagation in Molecular Dynamics Simulations of Polymer Liquid Crystals: computer modeling; fracture; molecular dynamics; polymer liquid crystals (PLC); structure to distinguish between monomer liquid crystals (MLCs) and polymer liquid crystals (PLCs).[4] PLCs
NASA Astrophysics Data System (ADS)
Georgescu, IonuÅ£; Deckman, Jason; Fredrickson, Laura J.; Mandelshtam, Vladimir A.
2011-05-01
A new method, here called thermal Gaussian molecular dynamics (TGMD), for simulating the dynamics of quantum many-body systems has recently been introduced [I. Georgescu and V. A. Mandelshtam, Phys. Rev. B 82, 094305 (2010)]. As in the centroid molecular dynamics (CMD), in TGMD the N-body quantum system is mapped to an N-body classical system. The associated both effective Hamiltonian and effective force are computed within the variational Gaussian wave-packet approximation. The TGMD is exact for the high-temperature limit, accurate for short times, and preserves the quantum canonical distribution. For a harmonic potential and any form of operator hat{A}, it provides exact time correlation functions CAB(t) at least for the case of hat{B}, a linear combination of the position, hat{x}, and momentum, hat{p}, operators. While conceptually similar to CMD and other quantum molecular dynamics approaches, the great advantage of TGMD is its computational efficiency. We introduce the many-body implementation and demonstrate it on the benchmark problem of calculating the velocity time auto-correlation function for liquid para-hydrogen, using a system of up to N = 2592 particles.
Georgescu, Ionut; Deckman, Jason; Fredrickson, Laura J; Mandelshtam, Vladimir A
2011-05-01
A new method, here called thermal Gaussian molecular dynamics (TGMD), for simulating the dynamics of quantum many-body systems has recently been introduced [I. Georgescu and V. A. Mandelshtam, Phys. Rev. B 82, 094305 (2010)]. As in the centroid molecular dynamics (CMD), in TGMD the N-body quantum system is mapped to an N-body classical system. The associated both effective Hamiltonian and effective force are computed within the variational Gaussian wave-packet approximation. The TGMD is exact for the high-temperature limit, accurate for short times, and preserves the quantum canonical distribution. For a harmonic potential and any form of operator A?, it provides exact time correlation functions C(AB)(t) at least for the case of B, a linear combination of the position, x, and momentum, p, operators. While conceptually similar to CMD and other quantum molecular dynamics approaches, the great advantage of TGMD is its computational efficiency. We introduce the many-body implementation and demonstrate it on the benchmark problem of calculating the velocity time auto-correlation function for liquid para-hydrogen, using a system of up to N = 2592 particles. PMID:21548675
Simple Method to Compute Pair Distribution Function from Molecular Dynamics Data
NASA Astrophysics Data System (ADS)
Uno, Toshiaki; Sogo, Kiyoshi
2015-04-01
A new simple method to compute the pair distribution function from molecular dynamics data is proposed, which is applied to two examples to determine the crystal structure in the solid phase. It is found that the short-range order of a two-dimensional repulsive system is a triangular lattice, and the crystal structure of a three-dimensional finite-range potential (including both repulsive and attractive parts) system is a hexagonal-close-packed lattice.
Three-dimensional molecular dynamics study of aperture shape effect on nanojet ejection
Chin-Tien Lin; Jenn-Kun Kuo; Tzu-Hsiang Yen
2011-01-01
Three-dimensional molecular dynamics (MD) simulations of nanojet ejection with different aperture shapes are reported. The simulations use the Lennard-Jones 12-6 (LJ) potential to describe the intermolecular interaction. Using non-equilibrium MD, argon nanojet ejection is simulated under vacuum conditions. According to the analysis, different aperture shapes influence the ejection processes. The ejection speeds were 23.7 and 63.2?m\\/s respectively in the simulation.
Short-range dislocation interactions using molecular dynamics: Annihilation of screw dislocations
S. Swaminarayan; R. Lesar; P. Lomdahl; D. Beazley
1998-01-01
We present results of a large-scale atomistic study of the annihilation of oppositely signed screw dislocations in an fcc metal using molecular dynamics (MD) and an Embedded-Atom-Method (EAM) potential for Cu. The mechanisms of the annihilation process are studied in detail. From the simulation results, we determined the interaction energy between the dislocations as a function of separation. These results
A Molecular Dynamics Simulation of Phase Transitions: Thermodynamics and Transport Coefficients
NASA Astrophysics Data System (ADS)
Uno, Toshiaki; Sogo, Kiyoshi
2015-03-01
Molecular dynamics simulations are performed by using the Nosé-Poincaré thermostat for N = 103 particles system. A new finite range potential function with both attractive and repulsive forces is employed to investigate the phase transitions covering three phases of gas, liquid and solid. Besides the thermodynamic properties, transport coefficients such as diffusion constant, shear and bulk viscosities and thermal conductivity are computed from simulation data. A phase diagram is constructed by locating the phase boundaries from these quantities.
Carbon atom, dimer and trimer chemistry on diamond surfaces from molecular dynamics simulations
Valone, S.M.
1995-07-01
Spectroscopic studies of various atmospheres appearing in diamond film synthesis suggest evidence for carbon atoms, dimers, or trimers. Molecular dynamics simulations with the Brenner hydrocarbon potential are being used to investigate the elementary reactions of these species on a hydrogen-terminated diamond (111) surface. In principle these types of simulations can be extended to simulations of growth morphologies, in the 1-2 monolayer regime presently.
New ways to boost molecular dynamics simulations.
Krieger, Elmar; Vriend, Gert
2015-05-15
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time-step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a "densostat," and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org. © 2015 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25824339
Broyde, S.; Shapiro, R.
1993-09-01
Our objective has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by highly mutagenic aromatic amines and hydrocarbons. The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence but it may be enhanced greatly after covalent modification by a mutagenic substance. The methods that we use to elucidate structures are computational, but we keep in close contact with experimental developments, and we incorporate data from NMR studies in our calculations when they are available. X-ray and low resolution spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. Even the high resolution NMR method cannot alone yield molecular views, though it does so in combination with our computations. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations of static structures with solvent and salt can be carried out with the program AMBER; this yields mobile views in a medium that mimics aspects of the natural aqueous environment of the cell.
Molecular docking and molecular dynamics studies on ?-lactamases and penicillin binding proteins.
Kumar, K M; Anbarasu, Anand; Ramaiah, Sudha
2014-04-01
Bacterial resistance to ?-lactam antibiotics poses a serious threat to human health. Penicillin binding proteins (PBPs) and ?-lactamases are involved in both antibacterial activity and mediation of ?-lactam antibiotic resistance. The two major reasons for resistance to ?-lactams include: (i) pathogenic bacteria expressing drug insensitive PBPs rendering ?-lactam antibiotics ineffective and (ii) production of ?-lactamases along with alteration of their specificities. Thus, there is an urgent need to develop newer ?-lactams to overcome the challenge of bacterial resistance. Therefore the present study aims to identify the binding affinity of ?-lactam antibiotics with different types of PBPs and ?-lactamases. In this study, cephalosporins and carbapenems are docked into PBP2a of Staphylococcus aureus, PBP2b and PBP2x of Streptococcus pneumoniae and SHV-1 ?-lactamase of Escherichia coli. The results reveal that Ceftobiprole can efficiently bind to PBP2a, PBP2b and PBP2x and not strongly to SHV-1 ?-lactamase. Furthermore, molecular dynamics (MD) simulations are performed to refine the binding mode of the docked complex structure and to observe the differences in the stability of free PBP2x and Ceftobiprole bound PBP2x. MD simulation supports the greater stability of the Ceftobiprole-PBP2x complex compared to free PBP2x. This work demonstrates that potential ?-lactam antibiotics can efficiently bind to different types of PBPs for circumventing ?-lactam resistance and opens avenues for the development of newer antibiotics that can target bacterial pathogens. PMID:24503740
Special issue on ultrafast electron and molecular dynamics
NASA Astrophysics Data System (ADS)
Martin, Fernando; Hishikawa, Akiyoshi; Vrakking, Marc
2014-06-01
In the last few years, the advent of novel experimental and theoretical approaches has made possible the investigation of (time-resolved) molecular dynamics in ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation (HHG) and XUV/x-ray free electron lasers, and the emergence of novel detection strategies, such as time-resolved electron/x-ray diffraction and the fully coincident detection of electrons and fragment ions in reaction microscopes, has significantly expanded the arsenal of available techniques, and has taken studies of molecular dynamics into new domains of spectroscopic, spatial and temporal resolution, the latter including first explorations into the attosecond domain, thus opening completely new avenues for imaging electronic and nuclear dynamics in molecules. Along the way, particular types of molecular dynamics, e.g., dynamics around conical intersections, have gained an increased prominence, sparked by the realization of the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. In the short term, this will allow one to uncover and control the dynamics of elementary chemical processes such as, e.g., ultrafast charge migration, proton transfer, isomerization or multiple ionization, and to address new key questions about the role of attosecond coherent electron dynamics in chemical reactivity. The progress on the theoretical side has been no less impressive. Novel generations of supercomputers and a series of novel computational strategies have allowed nearly exact calculations in small molecules, as well as highly successful approximate calculations in large, polyatomic molecules, including biomolecules. Frequent and intensive collaborations involving both theory and experiment have been essential for the progress that has been accomplished. The special issue 'Ultrafast electron and molecular dynamics' seeks to provide an overview of the current developments, as well as new concepts that are emerging in this field when studying molecular dynamics at attosecond or few-femtosecond time-scales. It also aims at indicating how such studies are likely to evolve in the coming years. In this context, the present special issue contains contributions from recognized experts on HHG, free electron lasers, attosecond and femtosecond pump-probe spectroscopy, electron and x-ray diffraction methods, photoionization and theoretical methods specially designed for the analysis of experiments in this field. Seven review articles report on the present status of some selected topics, namely, table-top and free-electron lasers operating in the XUV and x-ray wavelength regimes to investigate ultrafast molecular dynamics, imaging methods to visualize electron and nuclear dynamics, nonlinear optics applications, and recent theoretical developments. These and other topics are covered by 32 research papers, in which new exciting results show the path for future developments in this field.
Zuo, Zhili; Gang, Chen; Zou, Hanjun; Mok, Puah Chum; Zhu, Weiliang; Chen, Kaixian; Jiang, Hualiang
2007-06-01
Beta-secretase is a potential target for inhibitory drugs against Alzheimer's disease as it cleaves amyloid precursor protein (APP) to form insoluble amyloid plaques and vascular deposits in the brain. Beta-secretase is matured from its precursor protein, called beta-secretase zymogen, which, different from most of other zymogens, is also partially active in cleaving APP. Hence, it is important to study on the mechanism of the zymogen's activation process. This study was to model the 3-D structure of the zymogen, followed by intensive molecular dynamics (MD) simulations to identify the most probable 3-D model and to study the dynamic structural behavior of the zymogen for understanding the effects of pro-segment on the function of the enzyme. The results revealed that the dropping in catalytic activity of the beta-secretase zymogen could be attributed to the occupation of the entrance of the catalytic site of the zymogen by its pro-segment. On the other hand, the partial catalytic activity of the zymogen could be explained by high fluctuation of the pro-segment in comparison with that of other zymogens, resulting in the occasionally exposure of the catalytic site for access its substrate APP. Indeed, steered MD (SMD) simulation revealed a weak pulling force at quasi-equilibrium state for the pro-segment of the zymogen leaving from the entrance, indicating that this swinging process could take place spontaneously. Furthermore, MM-PBSA calculation revealed a small change of free energy of 10.56 kal/mol between the initial and final states of the process of pro-segment swung outside the binding pocket of beta-secretase zymogen. These results not only account for the partial catalytic activity of beta-secretase zymogen, but also provide useful clues for discovering new potent ligands, as new type of drug leads for curing Alzheimer's disease, to prevent the pro-segment of the zymogen from leaving its catalytic site. PMID:17500040
Liu, Qixin; Cai, Zhiyong
2014-01-01
This paper presents studies on the characteristics of gas molecular mean freepath in nanopores by molecular dynamics simulation. Our study results indicate that themean free path of all molecules in nanopores depend on both the radius of the nanoporeand the gas-solid interaction strength. Besides mean free path of all molecules in thenanopore, this paper highlights the gas molecular mean free path at different positions ofthe nanopore and the anisotropy of the gas molecular mean free path at nanopores. Themolecular mean free path varies with the molecule's distance from the center of thenanopore. The least value of the mean free path occurs at the wall surface of the nanopore.The present paper found that the gas molecular mean free path is anisotropic when gas isconfined in nanopores. The radial gas molecular mean free path is much smaller than themean free path including all molecular collisions occuring in three directions. Our studyresults also indicate that when gas is confined in nanopores the gas molecule number densitydoes not affect the gas molecular mean free path in the same way as it does for the gas inunbounded space. These study results may bring new insights into understanding the gasflow's characteristic at nanoscale. PMID:25046745
Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation
2014-01-01
Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585
ERIC Educational Resources Information Center
Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.
2010-01-01
As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…
Nakata, Hiroya [Tokyo Institute of Technology; Schmidt, Michael W [Ames Laboratory; Fedorov, Dmitri G [National Institute of Advanced Industrial Science and Technology (AIST); Kitaura, Kazuo [Kobe University; Nakamura, Shinichiro [Nakamura Lab; Gordon, Mark S [Ames Laboratory
2014-10-16
The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.
Dynamical Casimir-Polder potentials in non-adiabatic conditions
Riccardo Messina; Roberto Passante; Lucia Rizzuto; Salvatore Spagnolo; Ruggero Vasile
2014-04-09
In this paper we review different aspects of the dynamical Casimir- Polder potential between a neutral atom and a perfectly conducting plate under nonequilibrium conditions. In order to calculate the time evolution of the atom-wall Casimir-Polder potential, we solve the Heisenberg equations describing the dynamics of the coupled system using an iterative technique. Different nonequilibrium initial states are considered, such as bare and partially dressed states. The partially dressed states considered are obtained by a sudden change of a physical parameter of the atom or of its position relative to the conducting plate. Experimental feasibility of detecting the considered dynamical effects is also discussed.
A molecular dynamics study of polymer/graphene interfacial systems
Rissanou, Anastassia N.; Harmandaris, Vagelis [Department of Mathematics and Applied Mathematics, University of Crete, GR-71409, Heraklion, Crete, Greece and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-71110, Heraklion, Cret (Greece)
2014-05-15
Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.
Anomalous flow behavior in nanochannels: A molecular dynamics study
NASA Astrophysics Data System (ADS)
Murad, Sohail; Luo, Lin; Chu, Liang-Yin
2010-06-01
We report molecular dynamics simulations of flow of water in nanochannels with a range of surface wettability characteristics (hydrophobic to strongly hydrophilic) and driving forces (pressures). Our results show apparently anomalous behavior. At low pressures, the rate is higher in nanochannels with hydrophilic surfaces than that with hydrophobic surfaces; however, with high pressure driven flow we observe opposite trends. This apparently anomalous behavior can be explained on the basis of molecular thermodynamics and fluid mechanics considerations. Understanding such behavior is important in many nanofluidic devices such as nanoreactors, nanosensors, and nanochips that are increasingly being designed and used.
Brown, Alex
Normal mode analysis using the driven molecular dynamics method. II. An application to biological of biological molecules is the method of molecular dynamics MD simulations. This computational method predicts 2004; accepted 8 June 2004 The driven molecular-dynamics DMD method, recently proposed by Bowman, Zhang
Maruyama, Shigeo
Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes * Shigeo-8656 The hydrogen storage mechanism of SWNTs was studied through molecular dynamics simulations. Assuming the simple : Molecular Dynamics Method, Hydrogen Storage, Single Walled Carbon Nanotubes, Lennard-Jones, Adsorption
2014-01-01
Background SG2NA is a member of the striatin sub-family of WD-40 repeat proteins. Striatin family members have been associated with diverse physiological functions. SG2NA has also been shown to have roles in cell cycle progression, signal transduction etc. They have been known to interact with a number of proteins including Caveolin and Calmodulin and also propagate the formation of a multimeric protein unit called striatin-interacting phosphatase and kinase. As a pre-requisite for such interaction ability, these proteins are known to be unstable and primarily disordered in their arrangement. Earlier we had identified that it has multiple isoforms (namely 35, 78, 87 kDa based on its molecular weight) which are generated by alternative splicing. However, detailed structural information of SG2NA is still eluding the researchers. Results This study was aimed towards three-dimensional molecular modeling and characterization of SG2NA protein and its isoforms. One structure out of five was selected for each variant having the least value for C score. Out of these, m35 kDa with a C score value of ?3.21was the most poorly determined structure in comparison to m78 kDa and m87 kDa variants with C scores of ?1.16 and ?1.97 respectively. Further evaluation resulted in about 61.6% residues of m35 kDa, 76.6% residues of m78 kDa and 72.1% residues of m87 kDa falling in the favorable regions of Ramchandran Plot. Molecular dynamics simulations were also carried out to obtain biologically relevant structural models and compared with previous atomic coordinates. N-terminal region of all variants was found to be highly disordered. Conclusion This study provides first-hand detailed information to understand the structural conformation of SG2NA protein variants (m35 kDa, m78 kDa and m87 kDa). The WD-40 repeat domain was found to constitute antiparallel strands of ?-sheets arranged circularly. This study elucidates the crucial structural features of SG2NA proteins which are involved in various protein-protein interactions and also reveals the extent of disorder present in the SG2NA structure crucial for excessive interaction and multimeric protein complexes. The study also potentiates the role of computational approaches for preliminary examination of unknown proteins in the absence of experimental information. PMID:25015106
Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R.; Shalashilin, Dmitrii V.
2014-01-01
In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely. PMID:24982247
Neural Dynamics Underlying Event-Related Potentials
NASA Technical Reports Server (NTRS)
Shah, Ankoor S.; Bressler, Steven L.; Knuth, Kevin H.; Ding, Ming-Zhou; Mehta, Ashesh D.; Ulbert, Istvan; Schroeder, Charles E.
2003-01-01
There are two opposing hypotheses about the brain mechanisms underlying sensory event-related potentials (ERPs). One holds that sensory ERPs are generated by phase resetting of ongoing electroencephalographic (EEG) activity, and the other that they result from signal averaging of stimulus-evoked neural responses. We tested several contrasting predictions of these hypotheses by direct intracortical analysis of neural activity in monkeys. Our findings clearly demonstrate evoked response contributions to the sensory ERP in the monkey, and they suggest the likelihood that a mixed (Evoked/Phase Resetting) model may account for the generation of scalp ERPs in humans.
Communication: Multiple-timestep ab initio molecular dynamics with electron correlation
NASA Astrophysics Data System (ADS)
Steele, Ryan P.
2013-07-01
A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Møller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.
Amorphization in the vicinity of a grain boundary: A molecular-dynamics approach
NASA Astrophysics Data System (ADS)
Gutiérrez, Gonzalo; Kiwi, Miguel; Ramírez, Ricardo
1996-10-01
The dynamics of the melting process of a binary system (such as the one formed by Co and Zr) that contains a grain boundary is investigated by means of molecular dynamics using Lennard-Jones-type interatomic potentials. The evolution of the disordering sequence, as the temperature is increased, is quantitatively studied and graphically illustrated. It is found that the presence of the defect acts like a seed for the disordering, with the genesis of an intermediate amorphous phase. The latter is properly identified and characterized and constitutes an intermediate stage before the proper melting process sets in.
MOLECULAR EPIDEMIOLOGY: POTENTIAL IMPACTS ON THE ASSESSMENT OF PUBLIC HEALTH
Introduction The term "molecular epidemiology" has been used to cover a broad range of scientific activities, often without specific reference to epidemiology. In fact, as noted by Foxman and Riley [1],molecular epidemiology has often been described almost exclusively in...
Quantum dynamics of bio-molecular systems in noisy environments
M. B. Plenio; S. F. Huelga
2012-02-05
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical description of system-environment interaction in the non-perturbative regime and present a promising new method that can overcome some limitations of existing methods. Thirdly, we present an approach towards deciding and quantifying the non-classicality of the action of the environment and the observed system-dynamics. We stress the relevance of these tools for strengthening the interplay between theoretical and experimental research in this field.
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.
2010-03-14
Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.
Concise NMR approach for molecular dynamics characterizations in organic solids.
Aliev, Abil E; Courtier-Murias, Denis
2013-08-22
Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the ? and ? polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics. PMID:23879450
Molecular dynamics simulations on the local order of liquid and amorphous ZnTe
NASA Astrophysics Data System (ADS)
Rino, José Pedro; Borges, Denilson; Mota, Rita C.; Silva, Maurício A. P.
2008-05-01
Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has successfully described the structural, dynamical, and structural phase transformation induced by pressure in ZnTe [D. S. Borges and J. P. Rino, Phys. Rev. B 72, 014107 (2005)]. The two-body term of the interaction potential consists of Coulomb interaction resulting from charge transfer, steric repulsion due to atomic sizes, charge-dipole interaction to include the effect of electronic polarizability of anions, and dipole-dipole (van der Waals) interactions. The three-body covalent term is a modification of the Stillinger-Weber potential. Molecular dynamics simulations in isobaric-isenthalpic ensemble have been performed for systems amounting to 4096 and 64 000 particles. Starting from a crystalline zinc-blende (ZB) structure, the system is initially heated until a very homogeneous liquid is obtained. The vitreous zinc telluride phase is attained by cooling the liquid at sufficiently fast cooling rates, while slower cooling rates lead to a disordered ZB crystalline structure. Two- and three-body correlations for the liquid and vitreous phases are analyzed through pair distribution functions, static structure factors, and bond angle distributions. In particular, the neutron static structure factor for the liquid phase is in very good agreement with both the reported experimental data and first-principles simulations.
Dynamics of a classical particle in a quasi periodic potential
NASA Astrophysics Data System (ADS)
Tenenbaum Katan, Yaniv; Kachman, Tal; Fishman, Shmuel; Soffer, Avy
2015-03-01
We study the dynamics of a one-dimensional classical particle in a space and time dependent potential with randomly chosen parameters. The focus of this work is a quasi-periodic potential, which only includes a finite number of Fourier components. The momentum is calculated analytically for short time within a self-consistent approximation, under certain conditions. We find that the dynamics can be described by a model of a random walk between the Chirikov resonances, which are resonances between the particle momentum and the Fourier components of the potential. We use numerical methods to test these results and to evaluate the important properties, such as the characteristic hopping time between the resonances. This work sheds light on the short time dynamics induced by potentials which are relevant for optics and atom optics.
Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.
Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms
Dupuy, L; Tadmor, E B; Miller, R E; Phillips, R
2005-02-02
Using a combination of statistical mechanics and finite-element interpolation, the authors develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasi-continuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nanoindentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.
Schrödinger Operators with Dynamically Defined Potentials: A Survey
David Damanik
2014-10-09
In this survey we discuss spectral and quantum dynamical properties of discrete one-dimensional Schr\\"odinger operators whose potentials are obtained by real-valued sampling along the orbits of an ergodic invertible transformation. After an introductory part explaining basic spectral concepts and fundamental results, we present the general theory of such operators, and then provide an overview of known results for specific classes of potentials. Here we focus primarily on the cases of random and almost periodic potentials.
Peptide Folding Kinetics from Replica Exchange Molecular Dynamics
Nicolae-Viorel Buchete; Gerhard Hummer
2008-02-11
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica exchanges, we estimate short-time propagators in conformation space and use them to construct a master equation. For a helical peptide in explicit water, we determine the rates of transitions both locally between microscopic conformational states and globally for folding and unfolding. We show that accurate rates in the ~1/(100 ns) to ~1/(1 ns) range can be obtained from REMD with exchange times of 5 ps, in excellent agreement with results from long equilibrium molecular dynamics.
Enhancing Protein Adsorption Simulations by Using Accelerated Molecular Dynamics
Mücksch, Christian; Urbassek, Herbert M.
2013-01-01
The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ( s) and experiment (up to hours), and the accordingly different ‘final’ adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces. PMID:23755156
Statistical identification of structural rearrangement events in molecular dynamics trajectories
NASA Astrophysics Data System (ADS)
Bingemann, Dieter
2013-03-01
We describe a statistical analysis method to detect simultaneous break points of the mean in multiple observables with Gaussian fluctuations as often observed in single molecule experiments and molecular dynamics trajectories. The maximum likelihood method finds the most likely break point in a given sequence of normally distributed multivariate observations using Hotteling's T2 statistic. In stochastic simulations we determine the threshold F-values for the acceptance of a break point in three dimensions and test the sensitivity and accuracy of the method. We present an algorithm that systematically identifies the most likely break points in a trajectory in a self-consistent manner. We test the method and algorithm with trajectories from molecular dynamics simulations on a prototypical atomistic glass former.
Time series analysis of molecular dynamics simulation using wavelet
NASA Astrophysics Data System (ADS)
Toda, Mikito
2012-08-01
A new method is presented to extract nonstationary features of slow collective motion toward time series data of molecular dynamics simulation for proteins. The method consists of the following two steps: (1) the wavelet transformation and (2) the singular value decomposition (SVD). The wavelet transformation enables us to characterize time varying features of oscillatory motions and SVD enables us to reduce the degrees of freedom of the movement. We apply the method to molecular dynamics simulation of various proteins such as Adenylate Kinase from Escherichia coli (AKE) and Thermomyces lanuginosa lipase (TLL). Moreover, we introduce indexes to characterize collective motion of proteins. These indexes provide us with information of nonstationary deformation of protein structures. We discuss future prospects of our study involving "intrinsically disordered proteins".
Excitation dynamics and relaxation in a molecular heterodimer
NASA Astrophysics Data System (ADS)
Balevi?ius, V.; Gelzinis, A.; Abramavicius, D.; Man?al, T.; Valkunas, L.
2012-08-01
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.
Long Timestep Molecular Dynamics on the Graphical Processing Unit
Sweet, James C.; Nowling, Ronald J.; Cickovski, Trevor; Sweet, Christopher R.; Pande, Vijay S.; Izaguirre, Jesús A.
2013-01-01
Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 ?s/day using implicit solvent models. PMID:24436689
Elastic Green's function techniques for molecular dynamics. Applications to tribology
NASA Astrophysics Data System (ADS)
Campana Cue, Carlos E.
The contact mechanics of solid bodies with rough surfaces is a topic of great practical importance because it affects, among other quantities, friction, adhesion, wear and heat transfer at the interface between two solids. Calculating pressure distributions in contacts has proven difficult due to the complex, multiscale topographies of real surfaces. Being able to predict the distribution of loads in mechanical components within industrial applications bears potential for an improved design of the components' surfaces. For example, unraveling the contact mechanics of aluminum-silicon alloys used in engines of fuel-efficient, lightweight cars, could constitute a big step towards designing an alloy with a reasonable safety factor to avoid aluminum adhesion and scuffing. In this thesis we introduce a new multiscale technique recently developed by us for the simulation of rough, semi-infinite elastic solids. With its help, we address open questions concerning contact mechanics. Pressure profiles, pressure distributions as well as areas of contact are calculated for single and multi-asperites interfaces with both idealized self-affine and experimentally-measured topographies. The methodology is also employed to shed light on the contact mechanics of aluminum-silicon alloys. Our numerical results are compared to the predictions of the analytical theories by Greenwood and Persson. We show how the theory by Greenwood is unable to predict the correct contact morphologies while Perssons' theory fails when predicting the pressure tails on individual silicon grains within aluminum-silicon alloys. Keywords. Contact Mechanics, Molecular Dynamics, Green's Functions, Tribology, Multiscale Techniques, Linear Elasticity, Rough Surfaces.
NASA Astrophysics Data System (ADS)
Ono, Junichi; Ando, Koji
2012-11-01
A semiquantal (SQ) molecular dynamics (MD) simulation method based on an extended Hamiltonian formulation has been developed using multi-dimensional thawed Gaussian wave packets (WPs), and applied to an analysis of hydrogen-bond (H-bond) dynamics in liquid water. A set of Hamilton's equations of motion in an extended phase space, which includes variance-covariance matrix elements as auxiliary coordinates representing anisotropic delocalization of the WPs, is derived from the time-dependent variational principle. The present theory allows us to perform real-time and real-space SQMD simulations and analyze nuclear quantum effects on dynamics in large molecular systems in terms of anisotropic fluctuations of the WPs. Introducing the Liouville operator formalism in the extended phase space, we have also developed an explicit symplectic algorithm for the numerical integration, which can provide greater stability in the long-time SQMD simulations. The application of the present theory to H-bond dynamics in liquid water is carried out under a single-particle approximation in which the variance-covariance matrix and the corresponding canonically conjugate matrix are reduced to block-diagonal structures by neglecting the interparticle correlations. As a result, it is found that the anisotropy of the WPs is indispensable for reproducing the disordered H-bond network compared to the classical counterpart with the use of the potential model providing competing quantum effects between intra- and intermolecular zero-point fluctuations. In addition, the significant WP delocalization along the out-of-plane direction of the jumping hydrogen atom associated with the concerted breaking and forming of H-bonds has been detected in the H-bond exchange mechanism. The relevance of the dynamical WP broadening to the relaxation of H-bond number fluctuations has also been discussed. The present SQ method provides the novel framework for investigating nuclear quantum dynamics in the many-body molecular systems in which the local anisotropic fluctuations of nuclear WPs play an essential role.
Molecular Dynamics Studies on the Buffalo Prion Protein
Zhang, Jiapu
2015-01-01
It was reported that buffalo is a low susceptibility species resisting to TSEs (Transmissible Spongiform Encephalopathies) (same as rabbits, horses and dogs). TSEs, also called prion diseases, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species (in humans prion diseases are (v)CJDs, GSS, FFI, and kulu etc). It was reported that buffalo is a low susceptibility species resisting to prion diseases (as rabbits, dogs, horses). In molecular structures, these neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein, predominantly with alpha-helices, into insoluble abnormally folded infectious prions, rich in beta-sheets. This paper studies the molecular structure and structural dynamics of buffalo prion protein, in order to find out the reason why buffaloes are resistant to prion diseases. We first did molecular modeling a homology structure constructed by one mutation at residue 143 from the Nuclear Magnetic Resonanc...
Molecular Dynamic Simulation of Disorder Induced Amorphization in Pyrochlore
Chartier, Alain; Meis, Constantin; Crocombette, J.-P.; Weber, William J.; Corrales, Louis R.
2005-01-21
The defect accumulation of amorphization has been studied for the La2Zr2O7 pyrochlore by means of classical molecular dynamic simulations. Present calculations show that the accumulation of cation Frenkel pairs is the main driving parameter for the amorphization process, while the oxygen atoms simply rearrange around cations. Under Frenkel pair accumulation, the structure follows the pyrochlore-amorphous sequence. Present results consequently provide atomic-level interpretation to previous experimental irradiation observations of the two-step phase transitions.
Replica-exchange molecular dynamics method for protein folding
Yuji Sugita; Yuko Okamoto
1999-01-01
We have developed a formulation for molecular dynamics algorithm for the replica-exchange method. The effectiveness of the method for the protein-folding problem is tested with the penta-peptide Met-enkephalin. The method can overcome the multiple-minima problem by exchanging non-interacting replicas of the system at several temperatures. From only one simulation run, one can obtain probability distributions in canonical ensemble for a
Molecular Dynamics Simulation of DPPC Bilayer in DMSO
Alexander M. Smondyrev; Max L. Berkowitz
1999-01-01
We performed molecular dynamics simulations on dipalmitoylphosphatidylcholine (DPPC)\\/dimethylsulfoxide (DMSO) system that has the same lipid:solvent weight ratio as in our previous simulation done on DPPC\\/water. We did not observe a large change in the size of DPPC membrane when the solvent was changed from water to DMSO. Also, we did not observe that a large number of DMSO molecules is
Calculating Conductance of Ion Channels – Linking Molecular Dynamics and Electrophysiology
NASA Astrophysics Data System (ADS)
Wilson, Michael A.; Pohorille, Andrew
2015-01-01
Molecular dynamics computer simulations were combined with an electrodiffusion model to compute conduction of simple ion channels. The main assumptions of the model, and the consistency, efficiency and accuracy of the ion current calculations were tested and found satisfactory. The calculated current-voltage dependence for a synthetic peptide channel is in agreement with experiments and correctly captures the asymmetry of current with respect to applied field.
Molecular dynamics simulation of chains mobility in polyethylene crystal
V. I. Sultanov; V. V. Atrazhev; D. V. Dmitriev; S. F. Burlatsky
2014-01-17
The mobility of polymer chains in perfect polyethylene (PE) crystal was calculated as a function of temperature and chain length through Molecular dynamics (MD) in united atom approximation. The results demonstrate that the chain mobility drastically increases in the vicinity of the phase transition from the orthorhombic to quasi-hexagonal phase. In the quasi-hexagonal phase, the chain mobility is almost independent on temperature and inversely proportional to the chain length.
Molecular dynamics simulation of shocks in porous TATB crystals
Fried, L.E.; Tarver, C.
1995-08-01
We report molecular dynamics results on the shock structure of 2-D crystals of triaminotrinitrobenzene (TATB). We find that the shock front broadens to approx. 30 nm in materials with a 20% random void distribution. As expected from bulk experiments, the shock velocity decreases with increasing porosity and the temperature behind the shock front increases with increasing porosity. Shock equilibration times increase from 1 ps to greater than 10 ps.
A molecular dynamics study on sI hydrogen hydrate.
Mondal, S; Ghosh, S; Chattaraj, P K
2013-07-01
A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen. PMID:23093389
Surface-directed spinodal decomposition: a molecular dynamics study.
Jaiswal, Prabhat K; Puri, Sanjay; Das, Subir K
2012-05-01
We use molecular dynamics simulations to study surface-directed spinodal decomposition in unstable binary AB fluid mixtures at wetting surfaces. The thickness of the wetting layer R1 grows with time t as a power law (R1?t?). We find that hydrodynamic effects result in a crossover of the growth exponent from ??1/3 to 1. We also present results for the layerwise correlation functions and domain length scales. PMID:23004733
Molecular dynamics simulation of cluster ion bombardment of solid surfaces
Z. Insepov; I. Yamada
1995-01-01
The Molecular Dynamics Method (MMD) is used for a simulation of interactions with gold and silicon surfaces of accelerated Arn(n ? 55–200) cluster ions with energies of 10 to 100 eV per cluster atom. The gold target sputtering yield Y can be described by a power dependence Y ? E2.35 on the Ar cluster total energy. The result of this
Ab initio molecular dynamics for open-shell transition metals
G. Kresse; J. Hafner
1993-01-01
We show that quantum-mechanical molecular-dynamics simulations in a finite-temperature local-density approximation based on the calculation of the electronic ground state and of the Hellmann-Feynman forces after each time step are feasible for liquid noble and transition metals. This is possible with the use of Vanderbilt-type ``ultrasoft'' pseudopotentials and efficient conjugate-gradient techniques for the determination of the electronic ground state. Results
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
Rapaport, D C
2009-01-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine
NASA Astrophysics Data System (ADS)
Rapaport, D. C.
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency. PMID:19518394
Molecular Orientation Dynamics of Polymer-Stabilized Ferroelectric Liquid Crystals
Hirokazu Furue; Mizuho Gonda; Jun Hatano
2005-01-01
The dynamic behavior of ferroelectric liquid crystal molecules can be studied in terms of the phase difference angle and the angle of the relative amplitude ratio of elliptically polarized light, measured by time-resolved transmission ellipsometry. It has been known that the phase difference angle and the angle of the relative amplitude ratio indicate qualitatively the out-of-plane and in-plane molecular rotations
Silvia Arrese-Igor; Angel Alegria; Angel J. Moreno; Juan Colmenero
2012-02-23
We address the general question of how the molecular weight dependence of chain dynamics in unentangled polymers is modified by blending. By dielectric spectroscopy we measure the normal mode relaxation of polyisoprene in blends with a slow matrix of poly(ter-butylstyrene). Unentangled polyisoprene in the blend exhibits strong deviations from Rouse scaling, approaching 'entangled-like' behavior at low temperatures in concomitance with the increase of the dynamic asymmetry in the blend. The obtained results are discussed in the framework of the generalized Langevin equation formalism. On this basis, a non trivial relationship between the molecular weight dependence of the longest chain relaxation time and the nonexponentiality of the corresponding Rouse correlator is found. This result is confirmed by molecular dynamics simulations.
Molecular-level dynamics of refractory dissolved organic matter
NASA Astrophysics Data System (ADS)
Niggemann, J.; Gerdts, G.; Dittmar, T.
2012-04-01
Refractory dissolved organic matter (DOM) accounts for most of the global oceanic organic carbon inventory. Processes leading to its formation and factors determining its stability are still largely unknown. We hypothesize that refractory DOM carries a universal molecular signature. Characterizing spatial and temporal variability in this universal signature is a key to understanding dynamics of refractory DOM. We present results from a long-term study of the DOM geo-metabolome in the open North Sea. Geo-metabolomics considers the entity of DOM as a population of compounds, each characterized by a specific function and reactivity in the cycling of energy and elements. Ten-thousands of molecular formulae were identified in DOM by ultrahigh resolution mass spectrometry analysis (FT-ICR-MS, Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry). The DOM pool in the North Sea was influenced by a complex interplay of processes that produced, transformed and degraded dissolved molecules. We identified a stable fraction in North Sea DOM with a molecular composition similar to deep ocean DOM. Molecular-level changes in this stable fraction provide novel information on dynamics and interactions of refractory DOM.
Hu, Hao; Liu, Haiyan
2013-05-30
Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem. PMID:23642216
Density-potential mappings in quantum dynamics
NASA Astrophysics Data System (ADS)
Ruggenthaler, M.; Giesbertz, K. J. H.; Penz, M.; van Leeuwen, R.
2012-05-01
In a recent paper [Europhys. Lett.EULEEJ0295-507510.1209/0295-5075/95/13001 95, 13001 (2011)] the question of whether the density of a time-dependent quantum system determines its external potential was reformulated as a fixed-point problem. This idea was used to generalize the existence and uniqueness theorems underlying time-dependent density-functional theory. In this work we extend this proof to allow for more general norms and provide a numerical implementation of the fixed-point iteration scheme. We focus on the one-dimensional case because it allows for a more in-depth analysis using singular Sturm-Liouville theory and at the same time provides an easy visualization of the numerical applications in space and time. We give an explicit relation between the boundary conditions on the density and the convergence properties of the fixed-point procedure via the spectral properties of the associated Sturm-Liouville operator. We show precisely under which conditions discrete and continuous spectra arise and give explicit examples. These conditions are then used to show that, in the most physically relevant cases, the fixed-point procedure converges. This is further demonstrated with an example.
Molecular Structure and Transport Dynamics in Perfluoro Sulfonyl Imide Membranes
Idupulapati, Nagesh B.; Devanathan, Ramaswami; Dupuis, Michel
2011-05-25
We report a detailed and comprehensive analysis of the nanostructure, transport dynamics of water and hydronium and water percolation in hydrated perfluoro sulfonyl imides (PFSI), a polymer considered for proton transport in PEM fuel cells, using classical molecular dynamics simulations. The dynamical changes are related to the changes in the membrane nanostructure. Water network percolation threshold, the level at which a consistent spanning water network starts to develop in the membrane, lies between hydration level (?) 6 and 7. The higher acidity of the sulfonyl imide acid group of PFSI compared to Nafion reported in our earlier ab initio study, translates into more free hydronium ions at low hydration levels. Nevertheless, the calculated diffusion coefficients of the H3O+ ions and H2O molecules as a function the hydration level were observed to be almost the same as that of Nafion, indicating similar conductivity and consistent with the experimental observations. This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory, a U.S. Department of Energy (DOE) national scientific user facility located at the Pacific Northwest National Laboratory (PNNL). This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
Hall, G.E.
2011-05-31
This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.
Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs
NASA Astrophysics Data System (ADS)
Morozov, I. V.; Kazennov, A. M.; Bystryi, R. G.; Norman, G. E.; Pisarev, V. V.; Stegailov, V. V.
2011-09-01
We report on simulation technique and benchmarks for molecular dynamics simulations of the relaxation processes in solids and liquids using the graphics processing units (GPUs). The implementation of a many-body potential such as the embedded atom method (EAM) on GPU is discussed. The benchmarks obtained by LAMMPS and HOOMD packages for simple Lennard-Jones liquids and metals using EAM potentials are presented for both Intel CPUs and Nvidia GPUs. As an example the crystallization rate of the supercooled Al melt is computed.
First results on oxygen self-diffusion in ?-Pu2O3 investigated by molecular dynamics
NASA Astrophysics Data System (ADS)
Yu, Huilong; Meng, Daqiao; Huang, He; Li, Gan
2014-09-01
The oxygen self-diffusion of ?-Pu2O3 has been investigated by molecular dynamics method. The empirical potential of ?-Pu2O3 has been fitted. Based on this new potential, the calculation results, such as cell parameters, bulk modulus and dielectric constants, are well consistent with experimental data and previous reports. In this study, we systematically calculated the oxygen self-diffusion coefficients of ?-Pu2O3 in the temperature range of 750-2100 K and the activation energy of ?-Pu2O3 was obtained from these calculations.
Dynamics in molecular structures: Instabilities, transport, and transformation
NASA Astrophysics Data System (ADS)
Reardon, Brian Joseph
The purpose of this research was to elicit a greater understanding of atomic motion in disordered crystalline solids, glasses, and liquids. The work carried out to this end is described in three main sections. In the first section the theory of normal mode analysis (NMA) is introduced and it is proposed that, rather than normal modes of vibration, the eigenvalues of a force constant matrix and the corresponding eigenvectors be thought of as reflecting the degrees of freedom along which a dynamical system at an arbitrary point in phase space can evolve. This change in perception is necessary when NMA is applied to nonequilibrium systems in which negative eigenvalues manifest themselves after diagonalization. In this section, the concept of Lyapunov coefficients will also be introduced as a measure of chaotic behavior in a dynamical system. An important aspect in this context will be to show that there is a direct relationship between these criteria of chaos theory, and the eigenvalues which describe the trajectory of a configuration of atoms in phase space. This connection is only possible if the traditional realm of normal mode analysis is enhanced with the concept that the eigenvalues represent degrees of freedom of motion, and that the negative eigenvalues are responsible for either relaxation or evasion from one region in phase space to another. As such, these negative eigenvalues can be associated with the instability of crystalline phases and the mobility of structural defects. The second section of this thesis is devoted to the experimental determination of the dielectric response of alkali borate glasses. The purpose of this investigation was to characterize ionic motion on a time scale comparable to the one that can be achieved in computer simulations. Naturally, this requires high temperatures. Hence, the work described here involved the construction of an impedance spectrometer with furnace for the study of ionic conductivity in high-temperature liquids, including the design of a special sample holder. In particular, these experiments served to complement the numerical studies, by exposing phenomena which would be interesting to reconstruct numerically. During the study of the lithium, sodium, and potassium borates, numerous compositions showed the development of a secondary peak higher in frequency than the main peak for the glass. This phenomenon was characterized following various thermal histories of the glass, and it was found that the appearance of the high-frequency peak correlated almost exactly with the onset of the crystallization exotherm, as defined using differential scanning calorimetry. Thus, it is proposed that impedance spectroscopy can be used to elucidate information regarding the crystallization behavior of glasses. The third section of this work describes the development of an adaptive algorithm to optimize the parameters of the potential energy function used in both molecular dynamics and normal mode analysis. The methodology used allows for the simultaneous optimization of numerous variables of numerous objective functions derived from the potential energy function. The positive aspects of such an approach are addressed (fast, easy, efficient) along with some of the negative aspects (the algorithm is not self-tuning, a distribution of answers is often generated). Furthermore, the realistic limiting conditions of such an algorithm are pointed out. For example, niching is only effective in attribute space and is detrimental in phenotype space. The appendices list all of the computer codes developed in this work.
Molecular dynamics study of hydrated imogolite. 2. Structure and dynamics of confined water.
Creton, Benoît; Bougeard, Daniel; Smirnov, Konstantin S; Guilment, Jean; Poncelet, Olivier
2008-08-28
The behaviour of water confined in an imogolite nanotube was studied by means of molecular dynamics simulations. The results of the study show an important difference between the interaction of water molecules with the internal and external surfaces of the nanotube. The analysis of the density profiles of confined molecules, of their spatial organisation, of the size of molecular clusters, of the lifetime of H-bonds in the system and of dynamical characteristics of molecules permits us to qualify the external imogolite surface as hydrophobic, whereas the internal surface reveals a hydrophilic character. PMID:18688532
Tensile testing of Fe and FeCr nanowires using molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Byggmästar, J.; Granberg, F.; Kuronen, A.; Nordlund, K.; Henriksson, K. O. E.
2015-01-01
Using molecular dynamics, we have studied the behaviour of cylindrical [001]-oriented Fe and FeCr nanowires under uniaxial tensile strain with both an embedded atom method (EAM) and a Tersoff-like bond order potential. The mechanical properties were analysed and the deformation mechanism was studied and compared between the potentials. The effects of chromium content and size of the wire were studied. Both potentials show elongation by deformation twinning in the <111 >/{211 } system resulting in a significantly stiffer and stronger [110]-axial nanowire. The pure iron nanowires are elastically softer than bulk iron and an addition of chromium has both a softening and weakening effect. The bond order potential shows a strong dependence on chromium concentration, while the dependence is considerably weaker for the EAM potential.
Sakkiah, Sugunadevi; Arooj, Mahreen; Kumar, Manian Rajesh; Eom, Soo Hyun; Lee, Keun Woo
2013-01-01
The ability to identify the site of a protein that can bind with high affinity to small, drug-like compounds has been an important goal in drug design. Sirtuin 2 (SIRT2), histone deacetylase protein family, plays a central role in the regulation of various pathways. Hence, identification of drug for SIRT2 has attracted great interest in the drug discovery community. To elucidate the molecular basis of the small molecules interactions to inhibit the SIRT2 function we employed the molecular docking, molecular dynamics simulations, and the molecular mechanism Poisson-Boltzmann/surface area (MM-PBSA) calculations. Five well know inhibitors such as suramin, mol-6, sirtinol, 67, and nf675 were selected to establish the nature of the binding mode of the inhibitors in the SIRT2 active site. The molecular docking and dynamics simulations results revealed that the hydrogen bonds between Arg97 and Gln167 are crucial to inhibit the function of SIRT2. In addition, the MM-PBSA calculations revealed that binding of inhibitors to SIRT2 is mainly driven by van der Waals/non-polar interactions. Although the five inhibitors are very different in structure, shape, and electrostatic potential, they are able to fit in the same binding pocket. These findings from this study provide insights to elucidate the binding pattern of SIRT2 inhibitors and help in the rational structure-based design of novel SIRT2 inhibitors with improved potency and better resistance profile. PMID:23382805
Sakkiah, Sugunadevi; Arooj, Mahreen; Kumar, Manian Rajesh; Eom, Soo Hyun; Lee, Keun Woo
2013-01-01
The ability to identify the site of a protein that can bind with high affinity to small, drug-like compounds has been an important goal in drug design. Sirtuin 2 (SIRT2), histone deacetylase protein family, plays a central role in the regulation of various pathways. Hence, identification of drug for SIRT2 has attracted great interest in the drug discovery community. To elucidate the molecular basis of the small molecules interactions to inhibit the SIRT2 function we employed the molecular docking, molecular dynamics simulations, and the molecular mechanism Poisson-Boltzmann/surface area (MM-PBSA) calculations. Five well know inhibitors such as suramin, mol-6, sirtinol, 67, and nf675 were selected to establish the nature of the binding mode of the inhibitors in the SIRT2 active site. The molecular docking and dynamics simulations results revealed that the hydrogen bonds between Arg97 and Gln167 are crucial to inhibit the function of SIRT2. In addition, the MM-PBSA calculations revealed that binding of inhibitors to SIRT2 is mainly driven by van der Waals/non-polar interactions. Although the five inhibitors are very different in structure, shape, and electrostatic potential, they are able to fit in the same binding pocket. These findings from this study provide insights to elucidate the binding pattern of SIRT2 inhibitors and help in the rational structure-based design of novel SIRT2 inhibitors with improved potency and better resistance profile. PMID:23382805
Structural properties of CHAPS micelles, studied by molecular dynamics simulations.
Herrera, Fernando E; Garay, A Sergio; Rodrigues, Daniel E
2014-04-10
Detergents are essential tools to study biological membranes, and they are frequently used to solubilize lipids and integral membrane proteins. Particularly the nondenaturing zwitterionic detergent usually named CHAPS was designed for membrane biochemistry and integrates the characteristics of the sulfobetaine-type detergents and bile salts. Despite the available experimental data little is known about the molecular structure of its micelles. In this work, molecular dynamics simulations were performed to study the aggregation in micelles of several numbers of CHAPS (? 18) starting from a homogeneous water dilution. The force field parameters to describe the interactions of the molecule were developed and validated. After 50 ns of simulation almost all the systems result in the formation of stable micelles. The molecular shape (gyration radii, volume, surface) and the molecular structure (RDF, salt bridges, H-bonds, SAS) of the micelles were characterized. It was found that the main interactions that lead to the stability of the micelles are the electrostatic ones among the polar groups of the tails and the OH's from the ring moiety. Unlike micelles of other compounds, CHAPS show a grainlike heterogeneity with hydrophobic micropockets. The results are in complete agreement with the available experimental information from NMR, TEM, and SAXS studies, allowing the modeling of the molecular structure of CHAPS micelles. Finally, we hope that the new force field parameters for this detergent will be a significant contribution to the knowledge of such an interesting molecule. PMID:24650115
Dynamic heterogeneities in a supercooled diatomic molecular system
NASA Astrophysics Data System (ADS)
Palomar, Ricardo; Sesé, Gemma
2007-01-01
Dynamic heterogeneities in a supercooled system of diatomic molecules with an associated dipole moment have been investigated. To this end, three-time correlation functions have been evaluated. Correlations between molecular displacements performed during consecutive time intervals are apparent at low temperatures in the ? -relaxation regime, whereas they tend to disappear during the ? -relaxation regime. These correlations maximize when the deviation from Gaussian dynamics takes a maximum, and they reveal the existence of different dynamic domains. Directionality of translational motions has also been studied. At low temperatures, and in the ? -relaxation zone, the molecular vector displacement in a given time interval has an important component in the opposite direction of the vector displacement corresponding to the initial time interval. The amplitudes associated with this quasi-oscillatory behavior become larger as the system is cooled. Dynamic heterogeneities in reorientation have been observed in the ? -relaxation regime, and it has been obtained that molecules that perform faster translational motions experience faster reorientational motions too. This effect increases as temperature decreases.
Goddard III, William A.
Molecular Dynamics Study of a Surfactant-Mediated Decane-Water Interface: Effect of Molecular; In Final Form: May 25, 2004 The effect of molecular architecture of a surfactant, particularly was investigated using atomistic MD simulations. We consider a series of surfactant isomers in the family of alkyl
NASA Astrophysics Data System (ADS)
Satoh, Katsuhiko
2013-08-01
The thermodynamic scaling of molecular dynamic properties of rotation and thermodynamic parameters in a nematic phase was investigated by a molecular dynamic simulation using the Gay-Berne potential. A master curve for the relaxation time of flip-flop motion was obtained using thermodynamic scaling, and the dynamic property could be solely expressed as a function of TV^{? _? }, where T and V are the temperature and volume, respectively. The scaling parameter ?? was in excellent agreement with the thermodynamic parameter ?, which is the logarithm of the slope of a line plotted for the temperature and volume at constant P2. This line was fairly linear, and as good as the line for p-azoxyanisole or using the highly ordered small cluster model. The equivalence relation between ? and ?? was compared with results obtained from the highly ordered small cluster model. The possibility of adapting the molecular model for the thermodynamic scaling of other dynamic rotational properties was also explored. The rotational diffusion constant and rotational viscosity coefficients, which were calculated using established theoretical and experimental expressions, were rescaled onto master curves with the same scaling parameters. The simulation illustrates the universal nature of the equivalence relation for liquid crystals.
Assessment of the convergence of molecular dynamics simulations of lipopolysaccharide membranes
Soares, Thereza A.; Straatsma, TP
2008-03-01
The outer membrane of Gram-negative bacteria is composed of a phospholipid inner leaflet and a lipopolysaccharide outer leaflet. The chemical structure of lipopolysaccharide confers an asymmetric character to outer membranes that has been shown to play an important role in the in the electrical properties of porins, low permeability and intrinsic antibiotic resistance of Gram-negative bacteria. In the present work, atomistic molecular dynamics simulations of two different configurations of the outer membrane of Pseudomonas aeruginosa under periodic boundary conditions were carried out in order to i) validate model-derived properties against the available experimental data, ii) identify the properties whose dynamics can be sampled on nanosecond timescales, and iii) evaluate the dependence of the convergence of structural and dynamical properties on the initial configuration of the system, within the chosen force field and simulation conditions. Because the relaxation times associated with the motions of individual LPS monomers in outer membranes is very slow, the two initial configurations do not converge to a common ensemble of configuration on the nanosecond time scale. However, a number of properties of the outer membrane that will significantly impact the structural and internal dynamics of transmembrane proteins, most notably the electrostatic potential and molecular density, do converge within the simulated time scale. For these properties, a good agreement with the available experimental data was found. Such molecular model, capable of accounting for the high asymmetry and low fluidity characteristics of outer membranes, will certainly benefit future atomistic simulations of outer membrane proteins.
Collective excitation dynamics and polaron formation in molecular aggregates
NASA Astrophysics Data System (ADS)
Dahlbom, M.; Beenken, W.; Sundström, V.; Pullerits, T.
2002-10-01
Real-space collective excitation dynamics in molecular aggregates is studied using a model where the electronic system is described via exciton theory with surface hopping. The nuclear dynamics are included using the Langevin equation where temperature and zero-point motions are entered via the fluctuation-dissipation theorem. Dynamic processes like exciton relaxation, localization, polaron formation and diffusion of self-trapped excitons, which commonly require different theories, are simultaneously described with our approach. Numerical simulations of small linear aggregates are performed. Contrary to the common view we show that exciton relaxation can temporarily increase exciton delocalization. The results are discussed based on the photosynthetic light-harvesting pigment-protein complexes.
Dynamic coherence in excitonic molecular complexes under various excitation conditions
NASA Astrophysics Data System (ADS)
Chenu, Aurélia; Malý, Pavel; Man?al, Tomáš
2014-08-01
We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity - an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna-Matthews-Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.
Molecular dynamics studies of interfacial water at the alumina surface.
Argyris, Dr. Dimitrios [University of Oklahoma; Ho, Thomas [ORNL; Cole, David [Ohio State University
2011-01-01
Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior at distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.
Sequence heterogeneity and the dynamics of molecular motors
Yariv Kafri; David R. Nelson
2005-06-30
The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand of DNA or RNA on the dynamics of the motors. We stress how the predicted behavior might be observed experimentally in anomalous drift and diffusion of motors over a wide range of parameters near the stall force and discuss the extreme limit of strongly biased motors with one-way hopping. We then consider the dynamics in an environment containing a variety of different fuels which supply chemical energy for the motor motion, either on a heterogeneous or on a periodic track. The results for motion along a periodic track are relevant to kinesin motors in a solution with a mixture of different nucleotide triphosphate fuel sources.