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Sample records for nonequilibrium molecular-dynamics simulation

  1. Nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W.G. . Dept. of Applied Science Lawrence Livermore National Lab., CA )

    1990-11-01

    The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.

  2. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

    SciTech Connect

    Radak, Brian K.; Roux, Benoît

    2016-10-07

    Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.

  3. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

    DOE PAGES

    Radak, Brian K.; Roux, Benoît

    2016-10-07

    Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance.more » An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.« less

  4. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Radak, Brian K.; Roux, Benoît

    2016-10-01

    Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Finally, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.

  5. Nonequilibrium adiabatic molecular dynamics simulations of methane clathrate hydrate decomposition.

    PubMed

    Alavi, Saman; Ripmeester, J A

    2010-04-14

    Nonequilibrium, constant energy, constant volume (NVE) molecular dynamics simulations are used to study the decomposition of methane clathrate hydrate in contact with water. Under adiabatic conditions, the rate of methane clathrate decomposition is affected by heat and mass transfer arising from the breakup of the clathrate hydrate framework and release of the methane gas at the solid-liquid interface and diffusion of methane through water. We observe that temperature gradients are established between the clathrate and solution phases as a result of the endothermic clathrate decomposition process and this factor must be considered when modeling the decomposition process. Additionally we observe that clathrate decomposition does not occur gradually with breakup of individual cages, but rather in a concerted fashion with rows of structure I cages parallel to the interface decomposing simultaneously. Due to the concerted breakup of layers of the hydrate, large amounts of methane gas are released near the surface which can form bubbles that will greatly affect the rate of mass transfer near the surface of the clathrate phase. The effects of these phenomena on the rate of methane hydrate decomposition are determined and implications on hydrate dissociation in natural methane hydrate reservoirs are discussed.

  6. Nonequilibrium adiabatic molecular dynamics simulations of methane clathrate hydrate decomposition

    NASA Astrophysics Data System (ADS)

    Alavi, Saman; Ripmeester, J. A.

    2010-04-01

    Nonequilibrium, constant energy, constant volume (NVE) molecular dynamics simulations are used to study the decomposition of methane clathrate hydrate in contact with water. Under adiabatic conditions, the rate of methane clathrate decomposition is affected by heat and mass transfer arising from the breakup of the clathrate hydrate framework and release of the methane gas at the solid-liquid interface and diffusion of methane through water. We observe that temperature gradients are established between the clathrate and solution phases as a result of the endothermic clathrate decomposition process and this factor must be considered when modeling the decomposition process. Additionally we observe that clathrate decomposition does not occur gradually with breakup of individual cages, but rather in a concerted fashion with rows of structure I cages parallel to the interface decomposing simultaneously. Due to the concerted breakup of layers of the hydrate, large amounts of methane gas are released near the surface which can form bubbles that will greatly affect the rate of mass transfer near the surface of the clathrate phase. The effects of these phenomena on the rate of methane hydrate decomposition are determined and implications on hydrate dissociation in natural methane hydrate reservoirs are discussed.

  7. Molecular rheology of perfluoropolyether lubricant via nonequilibrium molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Guo, Qian; Chung, Pil Seung; Chen, Haigang; Jhon, Myung S.

    2006-04-01

    Molecular rheology of perfluoropolyether (PFPE) systems is particularly important in designing effective lubricants that control the friction and wear in tribological applications. Using the coarse-grained, bead-spring model, equilibrium molecular dynamics based on the Langevin equation in a quiescent flow was first employed to examine the nanostructure of PFPE. Further, by integrating the modified Langevin equation and imposing the Lees-Edwards boundary condition, nonequilibrium molecular dynamics of steady shear was investigated. We observe that the shear viscosity of PFPE system depends strongly on molecular architecture (e.g., molecular weight and endgroup functionality) and external conditions (e.g., temperature and shear rate). Our study of the flow activation energy/entropy and their correlations with nanostructure visualization showed that the PFPE structure was substantially modified.

  8. Electrophoresis in Protein Crystal: Nonequilibrium Molecular Dynamics Simulations

    PubMed Central

    Hu, Zhongqiao; Jiang, Jianwen

    2008-01-01

    Electrophoresis of a mixture of NaCl and CaCl2 in a lysozyme crystal is investigated using nonequilibrium molecular dynamics (MD) simulations. Upon exposure to an electric field, the stability of lysozyme is found to decrease slightly. This finding is demonstrated by increases in the root mean-square deviations of the heavy atoms of lysozyme, in the solvent-accessible surface area of hydrophobic residues, and in the number of hydrogen bonds between lysozyme and water. The solvent-accessible surface area of hydrophilic residues changes marginally, and the number of hydrogen bonds between lysozyme molecules decreases. Water molecules tend to align preferentially parallel to the electric field, and the dipole moment along the pore axis increases linearly with increasing field strength. Two pronounced layered structures are observed for Na+ and Ca2+ in the vicinity of protein surface, but only one enriched layer is observed for Cl−. The number distributions of all ions are nearly independent of the electric field. The water coordination numbers of all ions are smaller in the crystal than in aqueous bulk solution; however, the reverse is found for the Cl− coordination numbers of cations. Both the water and the Cl− coordination numbers are insensitive to the electric field. Ion diffusivities in the crystal are ∼2 orders of magnitude smaller than those in aqueous bulk solution. The drift velocities of ions increase proportionally to the electric field, particularly at high strengths, and depend on ionic charge and coordination with oppositely charged ions. Electrical current exhibits a linear relationship with the field strength. The zero-field electrical conductivity is estimated to be 0.56 S/m, which is very close to 0.61 S/m as predicted by the Nernst-Einstein equation. PMID:18641079

  9. Classical molecular dynamics simulations for non-equilibrium correlated plasmas

    NASA Astrophysics Data System (ADS)

    Ferri, S.; Calisti, A.; Talin, B.

    2017-03-01

    A classical molecular dynamics model was recently extended to simulate neutral multi-component plasmas where various charge states of the same atom and electrons coexist. It is used to investigate the plasma effects on the ion charge and on the ionization potential in dense plasmas. Different simulated statistical properties will show that the concept of isolated particles is lost in such correlated plasmas. The charge equilibration is discussed for a carbon plasma at solid density and investigation on the charge distribution and on the ionization potential depression (IPD) for aluminum plasmas is discussed with reference to existing experiments.

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

    SciTech Connect

    Bresme, F.; Armstrong, J.

    2014-01-07

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

  11. Nanoscopic spontaneous motion of liquid trains: Nonequilibrium molecular dynamics simulation.

    PubMed

    Bahrami, Amir Houshang; Jalali, Mir Abbas

    2010-01-14

    Macroscale experiments show that a train of two immiscible liquid drops, a bislug, can spontaneously move in a capillary tube because of surface tension asymmetries. We use molecular dynamics simulation of Lennard-Jones fluids to demonstrate this phenomenon for NVT ensembles in submicron tubes. We deliberately tune the strength of intermolecular forces and control the velocity of bislug in different wetting and viscosity conditions. We compute the velocity profile of particles across the tube and explain the origin of deviations from the classical parabolae. We show that the self-generated molecular flow resembles the Poiseuille law when the ratio of the tube radius to its length is less than a critical value.

  12. Nonequilibrium molecular dynamics simulations of heat flow in one-dimensional lattices

    PubMed

    Zhang; Isbister; Evans

    2000-04-01

    We study the use of the Evans nonequilibrium molecular dynamics (NEMD) heat flow algorithm for the computation of the heat conductivity in one-dimensional lattices. For the well-known Fermi-Pasta-Ulam model, it is shown that when the heat field strength is greater than a certain critical value (which depends on the system size) solitons can be generated in molecular dynamics simulations starting from random initial conditions. Such solitons are stable and travel with supersonic speeds. For smaller heat fields, no solitons are generated in the molecular dynamics simulations; the heat conductivity obtained via the NEMD algorithm increases monotonically with the size of the system.

  13. Non-Equilibrium Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Ciccotti, Giovanni; Kapral, Raymond; Sergi, Alessandro

    Statistical mechanics provides a well-established link between microscopic equilibrium states and thermodynamics. If one considers systems out of equilibrium, the link between microscopic dynamical properties and non-equilibrium macroscopic states is more difficult to establish [1,2]. For systems lying near equilibrium, linear response theory provides a route to derive linear macroscopic laws and the microscopic expressions for the transport properties that enter the constitutive relations. If the system is displaced far from equilibrium, no fully general theory exists to treat such systems. By restricting consideration to a class of non-equilibrium states which arise from perturbations (linear or non-linear) of an equilibrium state, methods can be developed to treat non-equilibrium states. Furthermore, non-equilibrium molecular dynamics (NEMD) simulation methods can be devised to provide estimates for the transport properties of these systems.

  14. Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics-Monte Carlo simulations.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2015-01-14

    A family of hybrid simulation methods that combines the advantages of Monte Carlo (MC) with the strengths of classical molecular dynamics (MD) consists in carrying out short non-equilibrium MD (neMD) trajectories to generate new configurations that are subsequently accepted or rejected via an MC process. In the simplest case where a deterministic dynamic propagator is used to generate the neMD trajectories, the familiar Metropolis acceptance criterion based on the change in the total energy ΔE, min[1, exp{-βΔE}], guarantees that the hybrid algorithm will yield the equilibrium Boltzmann distribution. However, the functional form of the acceptance probability is more complex when the non-equilibrium switching process is generated via a non-deterministic stochastic dissipative propagator coupled to a heat bath. Here, we clarify the conditions under which the Metropolis criterion remains valid to rigorously yield a proper equilibrium Boltzmann distribution within hybrid neMD-MC algorithm.

  15. Slip length of water on graphene: limitations of non-equilibrium molecular dynamics simulations.

    PubMed

    Kannam, Sridhar Kumar; Todd, B D; Hansen, J S; Daivis, Peter J

    2012-01-14

    Data for the flow rate of water in carbon nanopores is widely scattered, both in experiments and simulations. In this work, we aim at precisely quantifying the characteristic large slip length and flow rate of water flowing in a planar graphene nanochannel. First, we quantify the slip length using the intrinsic interfacial friction coefficient between water and graphene, which is found from equilibrium molecular dynamics (EMD) simulations. We then calculate the flow rate and the slip length from the streaming velocity profiles obtained using non-equilibrium molecular dynamics (NEMD) simulations and compare with the predictions from the EMD simulations. The slip length calculated from NEMD simulations is found to be extremely sensitive to the curvature of the velocity profile and it possesses large statistical errors. We therefore pose the question: Can a micrometer range slip length be reliably determined using velocity profiles obtained from NEMD simulations? Our answer is "not practical, if not impossible" based on the analysis given as the results. In the case of high slip systems such as water in carbon nanochannels, the EMD method results are more reliable, accurate, and computationally more efficient compared to the direct NEMD method for predicting the nanofluidic flow rate and hydrodynamic boundary condition.

  16. Equilibrium and nonequilibrium molecular dynamics simulations of thermal conductance at solid-gas interfaces.

    PubMed

    Liang, Zhi; Evans, William; Keblinski, Pawel

    2013-02-01

    The thermal conductance at solid-gas interfaces with different interfacial bonding strengths is calculated through Green-Kubo equilibrium molecular dynamics (EMD) simulations. Due to the finite size of the simulation system, the long-time integral of the time correlation function of heat power across the solid-gas interface exhibits an exponential decay, which contains the information on interfacial thermal conductance. If an adsorbed gas layer is formed on the solid surface, it is found that the solid-gas interface needs to be defined at a plane outside the adsorbed layer so as to obtain the correct result from the Green-Kubo formula. The EMD simulation result agrees very well with that obtained from nonequilibrium molecular dynamics simulations. By calculating the average solid-gas interaction time as a function of solid-gas interaction strength, we find the incident gas atoms thermalize with the metal surface much more rapidly when the surface is covered by adsorbed gas molecules.

  17. On determining continuum quantities of non-equilibrium processes via molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Fu, Yao

    In this dissertation, a high-fidelity atomistic-to-continuum link for highly non-equilibrium processes has been established by making several modifications to Hardy's theory. Although Hardy's thermomechanical quantities were derived analytically to conserve mass, momentum and energy, they have not been rigorously tested and validated numerically in the past. Hence the first task was to investigate the effectiveness of ensemble averaging in removing thermal fluctuations and compare with conventional time averaging for fcc crystals simulated using both equilibrium and non-equilibrium molecular dynamics (MD) simulations, where the non-equilibrium process was introduced by a shock impact. It has been found that the ensemble averaging has better convergence than time averaging due to the statistical independence of the thermomechanical quantities computed using ensemble averaging. The second task was to test the validity of Hardy's theory by checking if it is able to conserve mass, momentum and energy numerically. A few highly non-equilibrium processes were simulated using MD, including Gaussian wave and shock impact propagation in 1D and 3D fcc crystals. Based on the test results, a new normalization rule has been proposed so that the computed thermomechanical quantities can conserve the fundamental properties more accurately. To a large extent, Hardy's theory has been found to be valid regardless of the width of the localization function, the interatomic potential and crystal structure, and with and without ensemble averaging. To further test the validity of Hardy's theory for more complex non-equilibrium processes, where plastic deformation is accomplished through dislocation glide and slip band emission, a crack propagation problem in iron crystal with a pre-created center crack is simulated using MD. The computed Hardy's thermomechanical quantities can generally conserve mass, momentum and energy. Exceptions have been found around the crack region, where the

  18. Plasticity induced by shock waves in nonequilibrium molecular-dynamics simulations

    PubMed

    Holian; Lomdahl

    1998-06-26

    Nonequilibrium molecular-dynamics simulations of shock waves in three-dimensional 10-million atom face-centered cubic crystals with cross-sectional dimensions of 100 by 100 unit cells show that the system slips along all of the available 111 slip planes, in different places along the nonplanar shock front. Comparison of these simulations with earlier ones on a smaller scale not only eliminates the possibility that the observed slippage is an artifact of transverse periodic boundary conditions, but also reveals the richness of the nanostructure left behind. By introducing a piston face that is no longer perfectly flat, mimicking a line or surface inhomogeneity in the unshocked material, it is shown that for weaker shock waves (below the perfect-crystal yield strength), stacking faults can be nucleated by preexisting extended defects.

  19. Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2015-08-11

    A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys. 2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD-MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD-MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems.

  20. Non-equilibrium molecular dynamics simulations of spall in single crystal tantalum

    NASA Astrophysics Data System (ADS)

    Hahn, Eric N.; Germann, Timothy C.; Ravelo, Ramon J.; Hammerberg, James E.; Meyers, Marc A.

    2017-01-01

    Ductile tensile failure of tantalum is examined through large scale non-equilibrium molecular dynamics simulations. Several loading schemes including flyer plate impact, decaying shock loading via a frozen piston, and quasi-isentropic (constant strain-rate) expansion are employed to span tensile strain-rates of 108 to 1014 per second. Single crystals of <001> orientation are specifically evaluated to eliminate grain boundary effects. Heterogeneous void nucleation occurs principally at the intersection of deformation twins in single crystals. At high strain rates, multiple spall events occur throughout the material and voids continue to nucleate until relaxation waves arrive from adjacent events. At ultra-high strain rates, those approaching or exceeding the atomic vibrational frequency, spall strength saturates near the maximum theoretical spall strength.

  1. Thermal diode in gas-filled nanogap with heterogeneous surfaces using nonequilibrium molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Avanessian, T.; Hwang, G.

    2016-10-01

    A thermal diode serves as a basic building block to design advanced thermal management systems in energy-saving applications. However, the main challenges of existing thermal diodes are poor steady-state performance, slow transient response, and/or extremely difficult manufacturing. In this study, the thermal diode is examined by employing an argon gas-filled nanogap with heterogeneous surfaces in the Knudsen regime, using nonequilibrium molecular dynamics simulation. The asymmetric gas pressure and thermal accommodation coefficients changes are found due to asymmetric adsorptions onto the heterogeneous nanogap with respect to the different temperature gradient directions, and these in turn result in the thermal diode. The maximum degree of diode (or rectification) is Rmax ˜ 7, at the effective gas-solid interaction ratio between the two surfaces of ɛ*= 0.75. This work could pave the way to designing advanced thermal management systems such as thermal switches (transistors).

  2. On the domain size effect of thermal conductivities from equilibrium and nonequilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wang, Zuyuan; Ruan, Xiulin

    2017-01-01

    Equilibrium molecular dynamics (EMD) simulations with the Green-Kubo formula and nonequilibrium molecular dynamics (NEMD) simulations with the Fourier's Law are two widely used methods for calculating thermal conductivities of materials. It is well known that both methods suffer from domain size effects, especially for NEMD. But the underlying mechanisms and their comparison have not been much quantitatively studied before. In this paper, we investigate their domain size effects by using crystalline silicon at 1000 K, graphene at 300 K, and silicene at 300 K as model material systems. The thermal conductivity of silicon from EMD simulations increases normally with the increasing domain size and converges at a size of around 4 ×4 ×4 nm3 . The converging trend agrees well with the wavelength-accumulated thermal conductivity. The thermal conductivities of graphene and silicene from EMD simulations decrease abnormally with the increasing domain size and converge at a size of around 10 ×10 nm2 . We ascribe the anomalous size effect to the fact that as the domain size increases, the effect of more phonon scattering processes (particularly the flexural phonons) dominates over the effect of more phonon modes contributing to the thermal conductivity. The thermal conductivities of the three material systems from NEMD simulations all show normal domain size effects, although their dependences on the domain size differ. The converging trends agree with the mean free path accumulation of thermal conductivity. This study provides new insights that other than some exceptions, the domain size effects of EMD and NEMD are generally associated with wavelength and mean free path accumulations of thermal conductivity, respectively. Since phonon wavelength spans over a much narrower range than mean free path, EMD usually has less significant domain size effect than NEMD.

  3. Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressure.

    PubMed

    Wang, Luying; Dumont, Randall S; Dickson, James M

    2012-07-28

    Nonequilibrium molecular dynamics (NEMD) simulations are used to investigate pressure-driven water flow passing through carbon nanotube (CNT) membranes at low pressures (5.0 MPa) typical of real nanofiltration (NF) systems. The CNT membrane is modeled as a simplified NF membrane with smooth surfaces, and uniform straight pores of typical NF pore sizes. A NEMD simulation system is constructed to study the effects of the membrane structure (pores size and membrane thickness) on the pure water transport properties. All simulations are run under operating conditions (temperature and pressure difference) similar to a real NF processes. Simulation results are analyzed to obtain water flux, density, and velocity distributions along both the flow and radial directions. Results show that water flow through a CNT membrane under a pressure difference has the unique transport properties of very fast flow and a non-parabolic radial distribution of velocities which cannot be represented by the Hagen-Poiseuille or Navier-Stokes equations. Density distributions along radial and flow directions show that water molecules in the CNT form layers with an oscillatory density profile, and have a lower average density than in the bulk flow. The NEMD simulations provide direct access to dynamic aspects of water flow through a CNT membrane and give a view of the pressure-driven transport phenomena on a molecular scale.

  4. Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressurea)

    NASA Astrophysics Data System (ADS)

    Wang, Luying; Dumont, Randall S.; Dickson, James M.

    2012-07-01

    Nonequilibrium molecular dynamics (NEMD) simulations are used to investigate pressure-driven water flow passing through carbon nanotube (CNT) membranes at low pressures (5.0 MPa) typical of real nanofiltration (NF) systems. The CNT membrane is modeled as a simplified NF membrane with smooth surfaces, and uniform straight pores of typical NF pore sizes. A NEMD simulation system is constructed to study the effects of the membrane structure (pores size and membrane thickness) on the pure water transport properties. All simulations are run under operating conditions (temperature and pressure difference) similar to a real NF processes. Simulation results are analyzed to obtain water flux, density, and velocity distributions along both the flow and radial directions. Results show that water flow through a CNT membrane under a pressure difference has the unique transport properties of very fast flow and a non-parabolic radial distribution of velocities which cannot be represented by the Hagen-Poiseuille or Navier-Stokes equations. Density distributions along radial and flow directions show that water molecules in the CNT form layers with an oscillatory density profile, and have a lower average density than in the bulk flow. The NEMD simulations provide direct access to dynamic aspects of water flow through a CNT membrane and give a view of the pressure-driven transport phenomena on a molecular scale.

  5. Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes.

    PubMed

    Wang, Luying; Dumont, Randall S; Dickson, James M

    2013-03-28

    Nonequilibrium molecular dynamics (NEMD) simulations are presented to investigate the effect of water-membrane interactions on the transport properties of pressure-driven water flow passing through carbon nanotube (CNT) membranes. The CNT membrane is modified with different physical properties to alter the van der Waals interactions or the electrostatic interactions between water molecules and the CNT membranes. The unmodified and modified CNT membranes are models of simplified nanofiltration (NF) membranes at operating conditions consistent with real NF systems. All NEMD simulations are run with constant pressure difference (8.0 MPa) temperature (300 K), constant pore size (0.643 nm radius for CNT (12, 12)), and membrane thickness (6.0 nm). The water flow rate, density, and velocity (in flow direction) distributions are obtained by analyzing the NEMD simulation results to compare transport through the modified and unmodified CNT membranes. The pressure-driven water flow through CNT membranes is from 11 to 21 times faster than predicted by the Navier-Stokes equations. For water passing through the modified membrane with stronger van der Waals or electrostatic interactions, the fast flow is reduced giving lower flow rates and velocities. These investigations show the effect of water-CNT membrane interactions on water transport under NF operating conditions. This work can help provide and improve the understanding of how these membrane characteristics affect membrane performance for real NF processes.

  6. Plasticity induced by shock waves in nonequilibrium molecular-dynamics simulation

    SciTech Connect

    Holian, B.L.

    1998-03-01

    Nonequilibrium molecular dynamics (NEMD) simulations of shock waves in single crystals have shown that, above a threshold strength, strongly shocked crystals deform in a very simple way. Rather than experiencing massive deformation, a simple slippage occurs at the shock front, relieving the peak shear stress, and leaving behind a stacking fault. Later calculations quantified the apparent threshold strength, namely the yield strength of the perfect crystal. Subsequently, pulsed x-ray experiments on shocked single crystals showed relative shifts in diffraction peaks, confirming the authors NEMD observations of stacking faults produced by shockwave passage. With the advent of massively parallel computers, the authors have been able to simulate shock waves in 10-million atom crystals with cross sectional dimensions of 100 x 100 fcc unit cells (compared to earlier 6 x 6 systems). They have seen that the increased cross-section allows the system to slip along all of the available {l_brace}111{r_brace} slip planes, in different places along the now non-planar shock front. These simulations conclusively eliminate the worry that the kind of slippage they have observed is somehow an artifact of transverse periodic boundary conditions. Moreover, they have introduced a piston face that is no longer perfectly flat, mimicking a line or surface inhomogeneity in the unshocked material, and show that for weaker shock waves (below the perfect crystal yield strength), stacking faults can be nucleated by preexisting extended defects.

  7. Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes

    NASA Astrophysics Data System (ADS)

    Wang, Luying; Dumont, Randall S.; Dickson, James M.

    2013-03-01

    Nonequilibrium molecular dynamics (NEMD) simulations are presented to investigate the effect of water-membrane interactions on the transport properties of pressure-driven water flow passing through carbon nanotube (CNT) membranes. The CNT membrane is modified with different physical properties to alter the van der Waals interactions or the electrostatic interactions between water molecules and the CNT membranes. The unmodified and modified CNT membranes are models of simplified nanofiltration (NF) membranes at operating conditions consistent with real NF systems. All NEMD simulations are run with constant pressure difference (8.0 MPa) temperature (300 K), constant pore size (0.643 nm radius for CNT (12, 12)), and membrane thickness (6.0 nm). The water flow rate, density, and velocity (in flow direction) distributions are obtained by analyzing the NEMD simulation results to compare transport through the modified and unmodified CNT membranes. The pressure-driven water flow through CNT membranes is from 11 to 21 times faster than predicted by the Navier-Stokes equations. For water passing through the modified membrane with stronger van der Waals or electrostatic interactions, the fast flow is reduced giving lower flow rates and velocities. These investigations show the effect of water-CNT membrane interactions on water transport under NF operating conditions. This work can help provide and improve the understanding of how these membrane characteristics affect membrane performance for real NF processes.

  8. Non-equilibrium molecular dynamics simulation of the unstirred layer in the osmotically driven flow

    NASA Astrophysics Data System (ADS)

    Konno, Keito; Itano, Tomoaki; Seki, Masako

    2015-11-01

    We studied the solvent flows driven by the osmotic pressure difference across the semi-permeable membrane. The flow penetrating from the low concentration side transports away solutes adjacent of the membrane, so that the concentration is reduced significantly only at the vicinity of the membrane. It is expected that the relatively low solute concentration develops into a thin boundary layer in the vicinity of the membrane in the case of absence of external stirring process, which is termed as un-stirred layer (USL). To investigate concentration distribution in USL, we carried out non-equilibrium molecular dynamics simulations. The flows driven by th osmotic pressure are idealized as 2 dimensional hard disk model, which is composed of solvent and solute molecules. The membrane is modeled as a medium composed of stationary parallel rods distributed by a spatial interval, which is less than the diameter of the solute molecules. The following results were obtained from the numerical simulation. First, the thickness of USL, which was estimated from the obtained concentration distribution, is on the order of a length determined by mean free path. Second, USL was semicircle the center of which is on the end of pore of membrane.

  9. Nonequilibrium molecular dynamics: The first 25 years

    SciTech Connect

    Hoover, W.G. |

    1992-08-01

    Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments.

  10. Nonequilibrium Molecular Dynamics Simulations of Steady-State Heat and Mass Transport in Condensation. II. Transfer Coefficients.

    PubMed

    Røsjorde, A.; Kjelstrup, S.; Bedeaux, D.; Hafskjold, B.

    2001-08-01

    We present coefficients for transfer of heat and mass across the liquid-vapor interface of a one-component fluid. The coefficients are defined for the Gibbs surface from nonequilibrium thermodynamics and determined by nonequilibrium molecular dynamics simulations. The main conductivity coefficients are found to become large near the critical point, consistent with the disappearance of the surface in this limit. The resistivities of transfer found by molecular dynamics simulations are compared to the values predicted by kinetic theory. The main resistivity to heat transfer is found to agree from the triple point to about halfway to the critical point. The resistivity to mass transfer was used to determine the condensation coefficient, which was found to be practically constant with a value of about 0.82. The resistivity coupling coefficient predicted by simulations also agrees with values predicted by kinetic theory from the triple point until about halfway to the critical point. Copyright 2001 Academic Press.

  11. Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril

    SciTech Connect

    Okumura, Hisashi

    2015-12-31

    Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. We perform all-atom molecular dynamics simulations of amyloid fibril assembly and disassembly.

  12. Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2014-09-21

    Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

  13. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    PubMed

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases.

  14. Thermal Conductivity of GaN Nanotubes Simulated by Nonequilibrium Molecular Dynamics

    SciTech Connect

    Wang, Zhiguo; Gao, Fei; Crocombette, J.-P.; Zu, Xiaotao; Yang, Li; Weber, William J.

    2007-04-15

    Thermal conductivity of GaN nanotubes along the tube axis is investigated over the temperature range of 600K-2300K using homogeneous nonequilibrium molecular dynamics. In general, the thermal conductivity of nanotubes is smaller than that for the bulk GaN single crystal. The thermal conductivity is also found to decrease with temperature and increase with increasing wall thickness of the nanotubes. The change of phonon spectrum and surface inelastic scattering may account for the reduction of thermal conductivity in the nanotubes, while thermal softening and high frequency phonon interactions at high temperatures may provide an explanation for its decrease with increasing temperature.

  15. Temperature control in molecular dynamic simulations of non-equilibrium processes

    NASA Astrophysics Data System (ADS)

    Toton, Dawid; Lorenz, Christian D.; Rompotis, Nikolaos; Martsinovich, Natalia; Kantorovich, Lev

    2010-02-01

    Thermostats are often used in various condensed matter problems, e.g. when a biological molecule undergoes a transformation in a solution, a crystal surface is irradiated with energetic particles, a crack propagates in a solid upon applied stress, two surfaces slide with respect to each other, an excited local phonon dissipates its energy into a crystal bulk, and so on. In all of these problems, as well as in many others, there is an energy transfer between different local parts of the entire system kept at a constant temperature. Very often, when modelling such processes using molecular dynamics simulations, thermostatting is done using strictly equilibrium approaches serving to describe the NVT ensemble. In this paper we critically discuss the applicability of such approaches to non-equilibrium problems, including those mentioned above, and stress that the correct temperature control can only be achieved if the method is based on the generalized Langevin equation (GLE). Specifically, we emphasize that a meaningful compromise between computational efficiency and a physically appropriate implementation of the NVT thermostat can be achieved, at least for solid state and surface problems, if the so-called stochastic boundary conditions (SBC), recently derived from the GLE (Kantorovich and Rompotis 2008 Phys. Rev. B 78 094305), are used. For SBC, the Langevin thermostat is only applied to the outer part of the simulated fragment of the entire system which borders the surrounding environment (not considered explicitly) serving as a heat bath. This point is illustrated by comparing the performance of the SBC and some of the equilibrium thermostats in two problems: (i) irradiation of the Si(001) surface with an energetic CaF2 molecule using an ab initio density functional theory based method, and (ii) the tribology of two amorphous SiO2 surfaces coated with self-assembled monolayers of methyl-terminated hydrocarbon alkoxylsilane molecules using a classical atomistic

  16. Vibrational mean free paths and thermal conductivity of amorphous silicon from non-equilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Sääskilahti, K.; Oksanen, J.; Tulkki, J.; McGaughey, A. J. H.; Volz, S.

    2016-12-01

    The frequency-dependent mean free paths (MFPs) of vibrational heat carriers in amorphous silicon are predicted from the length dependence of the spectrally decomposed heat current (SDHC) obtained from non-equilibrium molecular dynamics simulations. The results suggest a (frequency)- 2 scaling of the room-temperature MFPs below 5 THz. The MFPs exhibit a local maximum at a frequency of 8 THz and fall below 1 nm at frequencies greater than 10 THz, indicating localized vibrations. The MFPs extracted from sub-10 nm system-size simulations are used to predict the length-dependence of thermal conductivity up to system sizes of 100 nm and good agreement is found with independent molecular dynamics simulations. Weighting the SDHC by the frequency-dependent quantum occupation function provides a simple and convenient method to account for quantum statistics and provides reasonable agreement with the experimentally-measured trend and magnitude.

  17. Variable timestep algorithm for molecular dynamics simulation of non-equilibrium processes

    NASA Astrophysics Data System (ADS)

    Marks, Nigel A.; Robinson, Marc

    2015-06-01

    A simple, yet robust variable timestep algorithm is developed for use in molecular dynamics simulations of energetic processes. Single-particle Kepler orbits are studied to study the relationship between trajectory properties and the critical timestep for constant integration error. Over a wide variety of conditions the magnitude of the maximum force is found to correlate linearly with the inverse critical timestep. Other quantities used in the literature such as the time derivative of the force and the product of the velocity and force also show reasonable correlations, but not to the same extent. Application of the corresponding metric | |Fmax | | Δt in molecular dynamics simulation of radiation damage in graphite shows that the scheme is both straightforward to implement and effective. In tests on a 1 keV cascade the timestep varies by over two orders of magnitude with minimal loss of energy conservation.

  18. Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ngo, Son Tung; Nguyen, Minh Tung; Nguyen, Minh Tho

    2017-05-01

    The absolute binding free energy of an inhibitor to HIV-1 Protease (PR) was determined throughout evaluation of the non-bonded interaction energy difference between the two bound and unbound states of the inhibitor and surrounding molecules by the fast pulling of ligand (FPL) process using non-equilibrium molecular dynamics (NEMD) simulations. The calculated free energy difference terms help clarifying the nature of the binding. Theoretical binding affinities are in good correlation with experimental data, with R = 0.89. The paradigm used is able to rank two inhibitors having the maximum difference of ∼1.5 kcal/mol in absolute binding free energies.

  19. Flow and plasticity via nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W.G.

    1984-06-11

    The viscous flow of fluids and the plastic flow of solids, such as metals, are interesting from both the practical and the theoretical points of view. Atomistic molecular dynamics simulations provide a way of visualizing and understanding these flows in a detailed microscopic way. Simulations are necessarily carried out at relatively high rates of strain. For this reason they are ideally suited to the study of nonlinear flow phenomena: normal stresses induced by shear deformation, stress rotation, and the coupling of stress with heat flow, for instance. The simulations require appropriate boundary conditions, forces, and equations of motion. Newtonian mechanics is relatively inefficient for this simulation task. A modification, Nonequilibrium Molecular Dynamics, has been developed to simulate nonequilibrium flows. By now, many high-strain-rate rheological studies of flowing (viscous) fluids and (plastic) solids have been carried out. Here I describe the new methods used in the simulations and some results obtained in this way. A three-body shear-flow exercise is appended to make these ideas more concrete.

  20. Nonequilibrium molecular dynamics simulations of nanoconfined fluids at solid-liquid interfaces

    NASA Astrophysics Data System (ADS)

    Morciano, M.; Fasano, M.; Nold, A.; Braga, C.; Yatsyshin, P.; Sibley, D. N.; Goddard, B. D.; Chiavazzo, E.; Asinari, P.; Kalliadasis, S.

    2017-06-01

    We investigate the hydrodynamic properties of a Lennard-Jones fluid confined to a nanochannel using molecular dynamics simulations. For channels of different widths and hydrophilic-hydrophobic surface wetting properties, profiles of the fluid density, stress, and viscosity across the channel are obtained and analysed. In particular, we propose a linear relationship between the density and viscosity in confined and strongly inhomogeneous nanofluidic flows. The range of validity of this relationship is explored in the context of coarse grained models such as dynamic density functional-theory.

  1. Nonequilibrium molecular dynamics simulations of nanoconfined fluids at solid-liquid interfaces.

    PubMed

    Morciano, M; Fasano, M; Nold, A; Braga, C; Yatsyshin, P; Sibley, D N; Goddard, B D; Chiavazzo, E; Asinari, P; Kalliadasis, S

    2017-06-28

    We investigate the hydrodynamic properties of a Lennard-Jones fluid confined to a nanochannel using molecular dynamics simulations. For channels of different widths and hydrophilic-hydrophobic surface wetting properties, profiles of the fluid density, stress, and viscosity across the channel are obtained and analysed. In particular, we propose a linear relationship between the density and viscosity in confined and strongly inhomogeneous nanofluidic flows. The range of validity of this relationship is explored in the context of coarse grained models such as dynamic density functional-theory.

  2. Cell list algorithms for nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Dobson, Matthew; Fox, Ian; Saracino, Alexandra

    2016-06-01

    We present two modifications of the standard cell list algorithm that handle molecular dynamics simulations with deforming periodic geometry. Such geometry naturally arises in the simulation of homogeneous, linear nonequilibrium flow modeled with periodic boundary conditions, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. Previous works focused on the planar flows handled by Lees-Edwards or Kraynik-Reinelt boundary conditions, while the new versions of the cell list algorithm presented here are formulated to handle the general 3D deforming simulation geometry. As in the case of equilibrium, for short-ranged pairwise interactions, the cell list algorithm reduces the computational complexity of the force computation from O(N2) to O(N), where N is the total number of particles in the simulation box. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.

  3. Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ohmura, Satoshi; Nagaya, Kiyonobu; Shimojo, Fuyuki; Yao, Makoto

    2015-08-01

    The dynamic properties of liquid B2O3 under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B2O3 shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8).

  4. Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

    SciTech Connect

    Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki

    2015-08-17

    The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

  5. Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations.

    PubMed

    Fischer, Sean A; Aprà, Edoardo; Govind, Niranjan; Hess, Wayne P; El-Khoury, Patrick Z

    2017-02-16

    Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single-molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single-molecule SERS spectra and selection rules is a challenging task and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4'-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single-molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

  6. Evaluation of reptation-based modeling of entangled polymeric fluids including chain rotation via nonequilibrium molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Nafar Sefiddashti, Mohammad Hadi; Edwards, Brian J.; Khomami, Bamin

    2017-08-01

    Recent simulation results of a moderately entangled linear polyethylene C700H1402 liquid have confirmed prior simulation and experimental evidence that individual polymer molecules experience periodic rotation and retraction cycles under steady shear flow at high Weissenberg number. With this insight, theoreticians have begun to grapple with this additional complicating physical phenomenon that needs to be incorporated into rheological models to help explain the data under conditions of high shear. In this paper we examine these recent efforts by using nonequilibrium molecular dynamics simulations to provide insight into the requisite theoretical variables and their assigned evolution equations to evaluate the capability of these tube-based models to predict accurately the simulated data sets. This analysis reveals that the primary variables used in tube models to impart a conceptual basis to the theory, namely, the tube orientation tensor and the tube stretch, remain fundamental system properties even far away from equilibrium; however, the theory describing their evolution under flow is not well suited to quantitative prediction. Furthermore, it is demonstrated that key system properties, such as the entanglement number and disengagement time, should play a more significant role in model development since these quantities can change dramatically under flow, particularly at high Weissenberg number where the chain rotation and retraction cycles dominate the system physics.

  7. Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils

    NASA Astrophysics Data System (ADS)

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.

    2016-11-01

    The cavitation of gas bubbles in liquids has been applied to different disciplines in life and natural sciences, and in technologies. To obtain an appropriate theoretical description of effects induced by the bubble cavitation, we develop an all-atom nonequilibrium molecular-dynamics simulation method to simulate bubbles undergoing harmonic oscillation in size. This allows us to understand the mechanism of the bubble cavitation-induced liquid shear stress on surrounding objects. The method is then employed to simulate an Aβ fibril model in the presence of bubbles, and the results show that the bubble expansion and contraction exert water pressure on the fibril. This yields to the deceleration and acceleration of the fibril kinetic energy, facilitating the conformational transition between local free energy minima, and leading to the dissociation of the fibril. Our work, which is a proof-of-concept, may open a new, efficient way to dissociate amyloid fibrils using the bubble cavitation technique, and new venues to investigate the complex phenomena associated with amyloidogenesis.

  8. Nonequilibrium molecular dynamics simulations with a backward-forward trajectories sampling for multidimensional infrared spectroscopy of molecular vibrational modes

    NASA Astrophysics Data System (ADS)

    Hasegawa, Taisuke; Tanimura, Yoshitaka

    2008-02-01

    A full molecular dynamics (MD) simulation approach to calculate multidimensional third-order infrared (IR) signals of molecular vibrational modes is proposed. Third-order IR spectroscopy involves three-time intervals between three excitation and one probe pulses. The nonequilibrium MD (NEMD) simulation allows us to calculate molecular dipoles from nonequilibrium MD trajectories for different pulse configurations and sequences. While the conventional NEMD approach utilizes MD trajectories started from the initial equilibrium state, our approach does from the intermediate state of the third-order optical process, which leads to the doorway-window decomposition of nonlinear response functions. The decomposition is made before the second pump excitation for a two-dimensional case of IR photon echo measurement, while it is made after the second pump excitation for a three-dimensional case of three-pulse IR photon echo measurement. We show that the three-dimensional IR signals are efficiently calculated by using the MD trajectories backward and forward in time for the doorway and window functions, respectively. We examined the capability of the present approach by evaluating the signals of two- and three-dimensional IR vibrational spectroscopies for liquid hydrogen fluoride. The calculated signals might be explained by anharmonic Brownian model with the linear-linear and square-linear system-bath couplings which was used to discuss the inhomogeneous broadening and dephasing mechanism of vibrational motions. The predicted intermolecular librational spectra clearly reveal the unusually narrow inhomogeneous linewidth due to the one-dimensional character of HF molecule and the strong hydrogen bond network.

  9. Modelling of ion permeation in K+ channels by nonequilibrium molecular dynamics simulations: I. Permeation energetics and structure stability.

    PubMed

    Neamţu, A; Suciu, Daniela

    2004-01-01

    Because of the great importance of physiological and pathophysiological processes in which ion channels are involved and because their operation is described by physicochemical laws, there have been many attempts to develop physical models able to describe the membrane permeability and also the structural and functional properties of the channel protein structures. In this study (in two parts) we present a series of simulations on a K+ channel model (KcsA) using Nonequilibrium Molecular Dynamics simulations (NEMD), in order to follow structure stability, permeation energetics and the possibility of obtaining quantitative information about the permeation process using the Linear Response Theory (LRT). On K+ ions were applied external forces to determine them to pass through the channel in a relatively small amount of time, accessible computationally. We ascertained a high resistance of the protein to deformation even in conditions when great forces were applied on ions (the system was far from equilibrium). The estimation of energy profiles in the course of ions passage through the channel demonstrates that these proteins create a conductivity pathway with no energetic barriers for ions movement across the channel (which could be present due to ions dehydration). The dynamic model used demonstrates (as proposed before in the literature after the examination of the static KcsA structure obtained by X-Ray crystallography) that this is due to the interaction of ions with the negatively charged carbonyl oxygens of the main polypeptide chain in the selectivity filter region.

  10. Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations.

    PubMed

    Chen, Alan A; García, Angel E

    2012-06-12

    An RNA kissing loop from the Moloney murine leukemia virus (MMLV) exhibits unusual mechanical stability despite having only two intermolecular base pairs. Mutations at this junction have been shown to destabilize genome dimerization, with concomitant reductions in viral packaging efficiency and infectivity. Optical tweezers experiments have shown that it requires as much force to break the MMLV kissing-loop complex as is required to unfold an 11-bp RNA hairpin [Li PTX, Bustamante C, Tinoco I (2006) Proc Natl Acad Sci USA 103:15847-15852]. Using nonequilibrium all-atom molecular dynamics simulations, we have developed a detailed model for the kinetic intermediates of the force-induced dissociation of the MMLV dimerization initiation site kissing loop. Two hundred and eight dissociation events were simulated (approximately 16 μs total simulation time) under conditions of constant applied external force, which we use to construct a Markov state model for kissing-loop dissociation. We find that the complex undergoes a conformational rearrangement, which allows for equal distribution of the applied force among all of the intermolecular hydrogen bonds, which is intrinsically more stable than the sequential unzipping of an ordinary hairpin. Stacking interactions with adjacent, unpaired loop adenines further stabilize the complex by increasing the repair rate of partially broken H-bonds. These stacking interactions are prominently featured in the transition state, which requires additional coordinates orthogonal to the end-to-end extension to be uniquely identified. We propose that these stabilizing features explain the unusual stability of other retroviral kissing-loop complexes such as the HIV dimerization site.

  11. Nonequilibrium molecular dynamics simulation study on the orientation transition in the amphiphilic lamellar phase under shear flow.

    PubMed

    Guo, Hongxia

    2006-12-07

    By the extensive large-scale nonequilibrium molecular dynamics simulation on an effective generic model-A2B2 tetramer for amphiphiles, we investigate the shear-induced parallel to perpendicular orientation transition in the lamellar phase as a function of segregation degree and shear rate. Under low rate shear flow the evolution of parallel lamellar configurations at different segregation strengths shows a similar kinetic pathway independent of the segregation degree. While under high rate shear flow in which the lifetime of undulation instability exceeds the characteristic time of the applied shear flow, the kinetic pathway of the shear-induced parallel-to-perpendicular orientation transition in lamellar systems is the segregation degree dependent. Comparing the temporal mesoscopic domain morphology, the microscopic chain conformation, and macroscopic observable-viscosity changes with the experimentally proposed mechanisms, we find that the undulation instability, partial breakup of monodomain, grain rotation, and recombination combined with defect migration and annihilation are the kinetic pathway for the parallel-to-perpendicular orientation transition in the lamellar phase in or near the intermediate segregation limit, and that the undulation instability, domain dissolution, and reformation along the preferred direction combined with defect migration and annihilation are the kinetic pathway for the parallel-to-perpendicular orientation transition in the lamellar phase close to the order-to-disorder phase transition point. A detailed underlying microscopic picture of the alignment process illustrates that the orientation transition is driven by the alignment of molecules with shear flow. The orientation diagram that characterizes the steady-state orientations as a function of shear rate and attractive potential depth is built, in which the attractive potential depth takes the role of an inverse temperature, somewhat like the Flory-Huggins interaction parameter

  12. Anisotropic heat transport in nanoconfined polyamide-6,6 oligomers: atomistic reverse nonequilibrium molecular dynamics simulation.

    PubMed

    Eslami, Hossein; Mohammadzadeh, Laila; Mehdipour, Nargess

    2012-03-14

    While polymers are known as thermal insulators, recent studies show that stretched single chains of polymers have a very high thermal conductivity. In this work, our new simulation scheme for simulation of heat flow in nanoconfined fluids [H. Eslami, L. Mohammadzadeh, and N. Mehdipour, J. Chem. Phys. 135, 064703 (2011)] is employed to study the effect of chain ordering (stretching) on the rate of heat transfer in polyamide-6,6 nanoconfined between graphene surfaces. Our results for the heat flow in the parallel direction (the plane of surfaces) show that the coefficient of thermal conductivity depends on the intersurface distance and is much higher than that of the bulk polymer. A comparison of results in this work with our former findings on the heat flow in the perpendicular direction, with the coefficient of heat conductivity less than the bulk sample, reveal that well-organized polymer layers between the confining surfaces show an anisotropic heat conduction; the heat conduction in the direction parallel to the surfaces is much higher than that in the perpendicular direction. The origin of such anisotropy in nanometric heat flow is shown to be the dramatic anisotropy in chain conformations (chain stretching) beside the confining surfaces. The results indicate that the coefficients of heat conductivity in both directions, normal and parallel to the surfaces, depend on the degree of polymer layering between the surfaces and the pore width.

  13. Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Hoover, W. G.; Hoover, C. G.

    1993-08-01

    Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics 'smoothed-particle hydrodynamics,' in 1977. It is a likely contributor to 'hybrid' simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.

  14. Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W. G.; Hoover, C. G.

    1993-08-01

    Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.

  15. Molecular dynamics simulations.

    PubMed

    Lindahl, Erik

    2015-01-01

    Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform μs-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation.

  16. Elastic Barrier Dynamical Freezing in Free Energy Calculations: A Way To Speed Up Nonequilibrium Molecular Dynamics Simulations by Orders of Magnitude.

    PubMed

    Giovannelli, Edoardo; Cardini, Gianni; Chelli, Riccardo

    2016-03-08

    An important issue concerning computer simulations addressed to free energy estimates via nonequilibrium work theorems, such as the Jarzynski equality [Phys. Rev. Lett. 1997, 78, 2690], is the computational effort required to achieve results with acceptable accuracy. In this respect, the dynamical freezing approach [Phys. Rev. E 2009, 80, 041124] has been shown to improve the efficiency of this kind of simulations, by blocking the dynamics of particles located outside an established mobility region. In this report, we show that dynamical freezing produces a systematic spurious decrease of the particle density inside the mobility region. As a consequence, the requirements to apply nonequilibrium work theorems are only approximately met. Starting from these considerations, we have developed a simulation scheme, called "elastic barrier dynamical freezing", according to which a stiff potential-energy barrier is enforced at the boundaries of the mobility region, preventing the particles from leaving this region of space during the nonequilibrium trajectories. The method, tested on the calculation of the distance-dependent free energy of a dimer immersed into a Lennard-Jones fluid, provides an accuracy comparable to the conventional steered molecular dynamics, with a computational speedup exceeding a few orders of magnitude.

  17. Anisotropy of the thermal conductivity in a crystalline polymer: Reverse nonequilibrium molecular dynamics simulation of the δ phase of syndiotactic polystyrene

    NASA Astrophysics Data System (ADS)

    Rossinsky, Eddie; Müller-Plathe, Florian

    2009-04-01

    The thermal conductivity of the crystalline δ phase of syndiotactic polystyrene has been investigated by reverse nonequilibrium molecular dynamics simulations. The results are in the expected range. An anisotropy is found for the thermal conductivity, with the component in chain direction being 2.5-3 larger than perpendicular to it. Any increase in the density causes an increase also in the thermal conductivity, particularly in the perpendicular directions. As side results, the simulations confirm an earlier finding on the force field dependence of the thermal conductivity: The thermal conductivity has a tendency to decrease when the number of active degrees of freedom in the system is reduced by the introduction of constraints. This dependence is, however, weaker and more erratic than previously found for molecular liquids and amorphous polymers.

  18. Molecular dynamics simulations.

    PubMed

    Lindahl, Erik R

    2008-01-01

    Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary hardware and software, how to obtain suitable starting molecular structures, immersing it in a solvent, choosing good simulation parameters, and energy minimization. The chapter also describes how to analyze the simulation in terms of potential energies, structural fluctuations, coordinate stability, geometrical features, and, finally, how to create beautiful ray-traced movies that can be used in presentations.

  19. Nonequilibrium solvent effects in Born-Oppenheimer molecular dynamics for ground and excited electronic states

    SciTech Connect

    Bjorgaard, Josiah August; Velizhanin, Kirill A.; Tretiak, Sergei

    2016-04-15

    The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited state molecular dynamics. In this paper, we describe methods of simulating nonequilibrium solvent effects in excited state molecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Finally, molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission.

  20. Nonequilibrium solvent effects in Born-Oppenheimer molecular dynamics for ground and excited electronic states

    NASA Astrophysics Data System (ADS)

    Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

    2016-04-01

    The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited state molecular dynamics. In this work, we describe methods of simulating nonequilibrium solvent effects in excited state molecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission.

  1. Floating orbital molecular dynamics simulations.

    PubMed

    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.

  2. Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2015-08-11

    Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up

  3. Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer.

    PubMed

    Zhang, Yue; Barnes, George L; Yan, Tianying; Hase, William L

    2010-05-07

    Model non-equilibrium molecular dynamics (MD) simulations are presented of heat transfer from a hot Au {111} substrate to an alkylthiolate self-assembled monolayer (H-SAM) to assist in obtaining an atomic-level understanding of experiments by Wang et al. (Z. Wang, J. A. Carter, A. Lagutchev, Y. K. Koh, N.-H. Seong, D. G. Cahill, and D. D. Dlott, Science, 2007, 317, 787). Different models are considered to determine how they affect the heat transfer dynamics. They include temperature equilibrated (TE) and temperature gradient (TG) thermostat models for the Au(s) surface, and soft and stiff S/Au(s) models for bonding of the S-atoms to the Au(s) surface. A detailed analysis of the non-equilibrium heat transfer at the heterogeneous interface is presented. There is a short time temperature gradient within the top layers of the Au(s) surface. The S-atoms heat rapidly, much faster than do the C-atoms in the alkylthiolate chains. A high thermal conductivity in the H-SAM, perpendicular to the interface, results in nearly identical temperatures for the CH(2) and CH(3) groups versus time. Thermal-induced disorder is analyzed for the Au(s) substrate, the S/Au(s) interface and the H-SAM. Before heat transfer occurs from the hot Au(s) substrate to the H-SAM, there is disorder at the S/Au(s) interface and within the alkylthiolate chains arising from heat-induced disorder near the surface of hot Au(s). The short-time rapid heating of the S-atoms enhances this disorder. The increasing disorder of H-SAM chains with time results from both disorder at the Au/S interface and heat transfer to the H-SAM chains.

  4. Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

    2017-10-01

    Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.

  5. Full quantification of frequency-dependent interfacial thermal conductance contributed by two- and three-phonon scattering processes from nonequilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zhou, Yanguang; Hu, Ming

    2017-03-01

    Understanding phonon transport across interfaces serves as a major tool to advance a diverse spectrum of fundamental and applied research. Unlike bulk materials, where the three-phonon scattering process is relatively straightforward to investigate, little research has been dedicated to the detailed analysis of the three-phonon scattering process at interfaces due to the complexity of interfaces and the mismatch of phonon dispersions of the two connecting parts. Based on the nonequilibrium molecular dynamics simulation, which is one of the most popular approaches to investigate the thermal conductance, we develop an explicit theoretical framework by considering the full third-order force constants field to quantify the two- and three-phonon scattering at interfaces. Bulk Ar is used as a benchmark to validate the computational scheme by comparing the results with those using the all-order phonon scattering method [frequency-dependent directly decomposed method; Y. Zhou and M. Hu, Phys. Rev. B 92, 195205 (2015), 10.1103/PhysRevB.92.195205]. Then, Ar-heavy Ar and Si-Ge interfaces are studied and the respective role of two- and three-phonon scattering processes is quantitatively characterized at different temperatures. Moreover, all four different types of the three-phonon scattering process are explicitly evaluated. The method developed herein for splitting the two- and three-phonon scattering processes in the interfacial heat transport is expected to advance our understanding of the phonon process at interfaces, and will facilitate designing high-performance interfacial structures in terms of efficient thermal management.

  6. Nonequilibrium solvent effects in Born-Oppenheimer molecular dynamics for ground and excited electronic states

    DOE PAGES

    Bjorgaard, Josiah August; Velizhanin, Kirill A.; Tretiak, Sergei

    2016-04-15

    The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited state molecular dynamics. In this paper, we describe methods of simulating nonequilibrium solvent effects in excited state molecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Finally, molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibriummore » due to photoexcitation and emission.« less

  7. Molecular dynamics simulation of pyridine

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił

    2015-04-01

    Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.

  8. Nonequilibrium molecular dynamics simulations of the thermal conductivity of water: a systematic investigation of the SPC/E and TIP4P/2005 models.

    PubMed

    Römer, Frank; Lervik, Anders; Bresme, Fernando

    2012-08-21

    We report an extensive nonequilibrium molecular dynamics investigation of the thermal conductivity of water using two of the most accurate rigid nonpolarizable empirical models available, SPC/E and TIP4P/2005. Our study covers liquid and supercritical states. Both models predict the anomalous increase of the thermal conductivity with temperature and the thermal conductivity maximum, hence confirming their ability to reproduce the complex anomalous behaviour of water. The performance of the models strongly depends on the thermodynamic state investigated, and best agreement with experiment is obtained for states close to the liquid coexistence line and at high densities and temperatures. Considering the simplicity of these two models the overall agreement with experiments is remarkable. Our results show that explicit polarizability and molecular flexibility are not needed to reproduce the anomalous heat conduction of water.

  9. Nonequilibrium solvent effects in Born-Oppenheimer molecular dynamics for ground and excited electronic states.

    PubMed

    Bjorgaard, J A; Velizhanin, K A; Tretiak, S

    2016-04-21

    The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited statemolecular dynamics. In this work, we describe methods of simulating nonequilibrium solvent effects in excited statemolecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission.

  10. Modeling Molecular Dynamics from Simulations

    SciTech Connect

    Hinrichs, Nina Singhal

    2009-01-28

    Many important processes in biology occur at the molecular scale. A detailed understanding of these processes can lead to significant advances in the medical and life sciences. For example, many diseases are caused by protein aggregation or misfolding. One approach to studying these systems is to use physically-based computational simulations to model the interactions and movement of the molecules. While molecular simulations are computationally expensive, it is now possible to simulate many independent molecular dynamics trajectories in a parallel fashion by using super- or distributed- computing methods such as Folding@Home or Blue Gene. The analysis of these large, high-dimensional data sets presents new computational challenges. In this seminar, I will discuss a novel approach to analyzing large ensembles of molecular dynamics trajectories to generate a compact model of the dynamics. This model groups conformations into discrete states and describes the dynamics as Markovian, or history-independent, transitions between the states. I will discuss why the Markovian state model (MSM) is suitable for macromolecular dynamics, and how it can be used to answer many interesting and relevant questions about the molecular system. I will also discuss many of the computational and statistical challenges in building such a model, such as how to appropriately cluster conformations, determine the statistical reliability, and efficiently design new simulations.

  11. Molecular dynamics simulation of benzene

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił B. J.

    2016-03-01

    Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.

  12. Microwave-driven zeolite-guest systems show athermal effects from nonequilibrium molecular dynamics.

    PubMed

    Blanco, Cristian; Auerbach, Scott M

    2002-06-05

    Nonequilibrium molecular dynamics simulations show that steady-state systems obtained by microwave heating are qualitatively different from those at thermal equilibrium. This difference arises because energy transfer from hotter to colder species is not efficient enough to equilibrate the distribution of energy. Under nonequilibrium conditions, we found that microwave radiation can selectively heat methanol in a binary mixture of methanol-benzene adsorbed in faujasite zeolite. The difference in steady-state temperatures follows the trend Tmethanol > Tbenzene > Tzeolite, which is qualitatively consistent with recent experimental results.

  13. Novel methods for molecular dynamics simulations.

    PubMed

    Elber, R

    1996-04-01

    In the past year, significant progress was made in the development of molecular dynamics methods for the liquid phase and for biological macromolecules. Specifically, faster algorithms to pursue molecular dynamics simulations were introduced and advances were made in the design of new optimization algorithms guided by molecular dynamics protocols. A technique to calculate the quantum spectra of protein vibrations was introduced.

  14. Non-equilibrium molecular dynamics simulations of the transient Ludwig-Soret effect in a binary Lennard-Jones/spline mixture.

    PubMed

    Hafskjold, Bjørn

    2017-01-01

    A binary isotope mixture of Lennard-Jones/spline particles at equilibrium was perturbed by a sudden change in the system's boundary temperatures. The system's response was determined by non-equilibrium molecular dynamics (NEMD). Three transient processes were studied: 1) The propagation of a pressure (shock) wave, 2) heat diffusivity and conduction, and 3) thermal diffusion (the Ludwig-Soret effect). These three processes occur at different time scales, which makes it possible to separate them in one single NEMD run. The system was studied in liquid, supercritical, and dense gas states with various forms and strengths of the thermal perturbation. The results show that heat was initially transported by two separate mechanisms: 1) heat diffusion as described by the transient heat equation and 2) as a consequence of a pressure wave. The pressure wave travelled faster than the speed of sound, generating a shock wave in the system. Local equilibrium was found in the transient phase, even with very strong perturbations and in the shock front. Although the mass separation due to the Ludwig-Soret effect developed much slower than the pressure and temperature fields in the system at large, it was found that the Soret coefficient could be accurately determined from the initial phase of the transient and close to the heat source. This opens the possibility of a new way to analyse results from transient experiments and thereby minimize effects of gravity and convection due to buoyancy.

  15. Modeling Nanocomposites for Molecular Dynamics (MD) Simulations

    DTIC Science & Technology

    2015-01-01

    Maximum 200 Words) The minimum energy configuration for Molecular Dynamics (MD) simulations is found for a carbon nanotube (CNT)/polymer... Carbon Nanotubes (CNTs), Molecular Dynamics Simulations 15. NUMBER OF PAGES 18 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT... Carbon Nanotubes ,” Macromolecules, Volume 39, Number 16, pp. 5194-5205, July 2006. 6. “VMD-Visual Molecular Dynamics ,” March 2014, http

  16. Computer simulation of nonequilibrium processes

    SciTech Connect

    Wallace, D.C.

    1985-07-01

    The underlying concepts of nonequilibrium statistical mechanics, and of irreversible thermodynamics, will be described. The question at hand is then, how are these concepts to be realize in computer simulations of many-particle systems. The answer will be given for dissipative deformation processes in solids, on three hierarchical levels: heterogeneous plastic flow, dislocation dynamics, an molecular dynamics. Aplication to the shock process will be discussed.

  17. Molecular dynamics simulations of microscale fluid transport

    SciTech Connect

    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.

  18. 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

  19. A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity

    NASA Astrophysics Data System (ADS)

    Müller-Plathe, Florian

    1997-04-01

    A nonequilibrium molecular dynamics method for calculating the thermal conductivity is presented. It reverses the usual cause and effect picture. The "effect," the heat flux, is imposed on the system and the "cause," the temperature gradient is obtained from the simulation. Besides being very simple to implement, the scheme offers several advantages such as compatibility with periodic boundary conditions, conservation of total energy and total linear momentum, and the sampling of a rapidly converging quantity (temperature gradient) rather than a slowly converging one (heat flux). The scheme is tested on the Lennard-Jones fluid.

  20. Molecular Dynamics Simulation of Supercritical Spray Phenomena

    DTIC Science & Technology

    2008-09-26

    Dynamics of the Rheological and Structural Properties of Linear and Branched Molecules. Simple Shear and Poiseuille Flows ; Instabilities and Slip...Michael Barrucco Publications: "Comparison of Wall Models for the Molecular Dynamics Simulation of Micro flows ," R. D. Branam and M. M...Performance 3. DATES COVERED (From - To) 1 Dec. 2003 - 31 May 2008 4. TITLE AND SUBTITLE Molecular Dynamics Simulation of Supercritical

  1. Verification of Onsager's reciprocal relations for evaporation and condensation using non-equilibrium molecular dynamics.

    PubMed

    Xu, J; Kjelstrup, S; Bedeaux, D; Røsjorde, A; Rekvig, L

    2006-07-01

    Non-equilibrium molecular dynamic (NEMD) simulations have been used to study heat and mass transfer across a vapor-liquid interface for a one-component system using a Lennard-Jones spline potential. It was confirmed that the relation between the surface tension and the surface temperature in the non-equilibrium system was the same as in equilibrium (local equilibrium). Interfacial transfer coefficients were evaluated for the surface, which expressed the heat and mass fluxes in temperature and chemical potential differences across the interfacial region (film). In this analysis it was assumed that the Onsager reciprocal relations were valid. In this paper we extend the number of simulations such that we can calculate all four interface film transfer coefficients along the whole liquid-vapor coexistence curve. We do this analysis both for the case where we use the measurable heat flux on the vapor side and for the case where we use the measurable heat flux on the liquid side. The most important result we found is that the coupling coefficients within the accuracy of the calculation are equal. This is the first verification of the validity of the Onsager relations for transport through a surface using molecular dynamics. The interfacial film transfer coefficients are found to be a function of the surface temperature alone. New expressions are given for the kinetic theory values of these coefficients which only depend on the surface temperature. The NEMD values were found to be in good agreement with these expressions.

  2. Effective interactions in molecular dynamics simulations of lysozyme solutions

    NASA Astrophysics Data System (ADS)

    Pellicane, Giuseppe; Sarkisov, Lev

    2014-09-01

    In this article we explore a problem of effective interactions between two rotationally restrained lysozyme molecules forming a crystal contact in aqueous solution. We perform non-equilibrium molecular dynamics simulations in order to estimate the interaction energy as a function of the distance between the two proteins obtained from direct application of the Jarzynski equality (JE), and compare it with that calculated by means of another non-equilibrium approach (Forward-Reverse method) and constrained force methods. The performance of the JE equality when applied to solvated protein interactions is discussed. All of the equilibrium and non-equilibrium methods show clear evidence that the potentials of mean force (PMF) are short-ranged, do not exceed few kTs, and that there is an accumulation of anions in the presence of hydrophobic surfaces.

  3. Molecular dynamics simulations of substitutional diffusion

    DOE PAGES

    Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob

    2016-12-18

    In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example,more » we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.« less

  4. Molecular dynamics simulations of substitutional diffusion

    SciTech Connect

    Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob

    2016-12-18

    In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example, we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.

  5. 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.

  6. 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.

  7. Molecular dynamics simulations: advances and applications

    PubMed Central

    Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

    2015-01-01

    Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800

  8. Molecular dynamics on nonequilibrium motion of a colloidal particle driven by an external torque

    NASA Astrophysics Data System (ADS)

    Yoo, Donghwan; Jung, Youngkyun; Kwon, Chulan

    2017-03-01

    We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use molecular dynamics simulation as an alternative to the Langevin dynamics. We prepare a heat bath composed of thousands of particles interacting with each other through the Lennard–Jones potential and impose the Langevin thermostat to maintain the heat bath in equilibrium. We consider a single colloidal particle interacting with with the particles of the heat bath also by the Lennard–Jones potential, without applying any types of dissipative or fluctuating forces used in Langevin dynamics. We set up simulation protocol fit for the overdamped limit as in real experiments, by increasing the size and mass of the colloidal particle. We study nonequilibrium fluctuations for work and heat produced incessantly in time and compare the results with those obtained from the previous studies via the overdamped Langevin dynamics. We confirm the Gallavotti–Cohen symmetry and the fluctuation theorem.

  9. The "Collisions Cube" Molecular Dynamics Simulator.

    ERIC Educational Resources Information Center

    Nash, John J.; Smith, Paul E.

    1995-01-01

    Describes a molecular dynamics simulator that employs ping-pong balls as the atoms or molecules and is suitable for either large lecture halls or small classrooms. Discusses its use in illustrating many of the fundamental concepts related to molecular motion and dynamics and providing a three-dimensional perspective of molecular motion. (JRH)

  10. Discrete Molecular Dynamics Simulation of Biomolecules

    NASA Astrophysics Data System (ADS)

    Ding, Feng

    2011-10-01

    Discrete molecular dynamics (DMD) simulation of hard spheres was the first implementation of molecular dynamics (MD) in history. DMD simulations are computationally more efficient than continuous MD simulations due to simplified interaction potentials. However, also due to these simplified potentials, DMD has often been associated with coarse-grained modeling, and hence continuous MD has become the dominant approach used to study the internal dynamics of biomolecules. With the recent advances in DMD methodology, including the development of high-resolution models for biomolecules and approaches to increase DMD efficiency, DMD simulations are emerging as an important tool in the field of molecular modeling, including the study of protein folding, protein misfolding and aggregation, and protein engineering. Recently, DMD methodology has been applied to modeling RNA folding and protein-ligand recognition. With these improvements to DMD methodology and the continuous increase in available computational power, we expect a growing role of DMD simulations in our understanding of biology.

  11. Molecular dynamic simulations of ocular tablet dissolution.

    PubMed

    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.

  12. Molecular dynamics study of CO2 hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis

    NASA Astrophysics Data System (ADS)

    English, Niall J.; Clarke, Elaine T.

    2013-09-01

    Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.

  13. Thermal conductance at the interface between crystals using equilibrium and nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Merabia, Samy; Termentzidis, Konstantinos

    2012-09-01

    In this article, we compare the results of nonequilibrium (NEMD) and equilibrium (EMD) molecular dynamics methods to compute the thermal conductance at the interface between solids. We propose to probe the thermal conductance using equilibrium simulations measuring the decay of the thermally induced energy fluctuations of each solid. We also show that NEMD and EMD give generally speaking inconsistent results for the thermal conductance: Green-Kubo simulations probe the Landauer conductance between two solids which assumes phonons on both sides of the interface to be at equilibrium. On the other hand, we show that NEMD give access to the out-of-equilibrium interfacial conductance consistent with the interfacial flux describing phonon transport in each solid. The difference may be large and reaches typically a factor 5 for interfaces between usual semiconductors. We analyze finite size effects for the two determinations of the interfacial thermal conductance, and show that the equilibrium simulations suffer from severe size effects as compared to NEMD. We also compare the predictions of the two above-mentioned methods—EMD and NEMD—regarding the interfacial conductance of a series of mass mismatched Lennard-Jones solids. We show that the Kapitza conductance obtained with EMD can be well described using the classical diffuse mismatch model (DMM). On the other hand, NEMD simulation results are consistent with an out-of-equilibrium generalization of the acoustic mismatch model (AMM). These considerations are important in rationalizing previous results obtained using molecular dynamics, and help in pinpointing the physical scattering mechanisms taking place at atomically perfect interfaces between solids, which is a prerequisite to understand interfacial heat transfer across real interfaces.

  14. Non-equilibrium phase behavior and friction of confined molecular films under shear: A non-equilibrium molecular dynamics study.

    PubMed

    Maćkowiak, Sz; Heyes, D M; Dini, D; Brańka, A C

    2016-10-28

    The phase behavior of a confined liquid at high pressure and shear rate, such as is found in elastohydrodynamic lubrication, can influence the traction characteristics in machine operation. Generic aspects of this behavior are investigated here using Non-equilibrium Molecular Dynamics (NEMD) simulations of confined Lennard-Jones (LJ) films under load with a recently proposed wall-driven shearing method without wall atom tethering [C. Gattinoni et al., Phys. Rev. E 90, 043302 (2014)]. The focus is on thick films in which the nonequilibrium phases formed in the confined region impact on the traction properties. The nonequilibrium phase and tribological diagrams are mapped out in detail as a function of load, wall sliding speed, and atomic scale surface roughness, which is shown can have a significant effect. The transition between these phases is typically not sharp as the external conditions are varied. The magnitude of the friction coefficient depends strongly on the nonequilibrium phase adopted by the confined region of molecules, and in general does not follow the classical friction relations between macroscopic bodies, e.g., the frictional force can decrease with increasing load in the Plug-Slip (PS) region of the phase diagram owing to structural changes induced in the confined film. The friction coefficient can be extremely low (∼0.01) in the PS region as a result of incommensurate alignment between a (100) face-centered cubic wall plane and reconstructed (111) layers of the confined region near the wall. It is possible to exploit hysteresis to retain low friction PS states well into the central localization high wall speed region of the phase diagram. Stick-slip behavior due to periodic in-plane melting of layers in the confined region and subsequent annealing is observed at low wall speeds and moderate external loads. At intermediate wall speeds and pressure values (at least) the friction coefficient decreases with increasing well depth of the LJ potential

  15. Non-equilibrium phase behavior and friction of confined molecular films under shear: A non-equilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Maćkowiak, Sz.; Heyes, D. M.; Dini, D.; Brańka, A. C.

    2016-10-01

    The phase behavior of a confined liquid at high pressure and shear rate, such as is found in elastohydrodynamic lubrication, can influence the traction characteristics in machine operation. Generic aspects of this behavior are investigated here using Non-equilibrium Molecular Dynamics (NEMD) simulations of confined Lennard-Jones (LJ) films under load with a recently proposed wall-driven shearing method without wall atom tethering [C. Gattinoni et al., Phys. Rev. E 90, 043302 (2014)]. The focus is on thick films in which the nonequilibrium phases formed in the confined region impact on the traction properties. The nonequilibrium phase and tribological diagrams are mapped out in detail as a function of load, wall sliding speed, and atomic scale surface roughness, which is shown can have a significant effect. The transition between these phases is typically not sharp as the external conditions are varied. The magnitude of the friction coefficient depends strongly on the nonequilibrium phase adopted by the confined region of molecules, and in general does not follow the classical friction relations between macroscopic bodies, e.g., the frictional force can decrease with increasing load in the Plug-Slip (PS) region of the phase diagram owing to structural changes induced in the confined film. The friction coefficient can be extremely low (˜0.01) in the PS region as a result of incommensurate alignment between a (100) face-centered cubic wall plane and reconstructed (111) layers of the confined region near the wall. It is possible to exploit hysteresis to retain low friction PS states well into the central localization high wall speed region of the phase diagram. Stick-slip behavior due to periodic in-plane melting of layers in the confined region and subsequent annealing is observed at low wall speeds and moderate external loads. At intermediate wall speeds and pressure values (at least) the friction coefficient decreases with increasing well depth of the LJ potential

  16. Choice of timestep in molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Fincham, David

    1986-06-01

    In molecular dynamics computer simulation of liquids it is important to use as large a timestep as possible in order to sample phase space rapidly and save on computer expense. The effect of the resulting algorithm errors in the trajectories of the molecules is not well understood. An empirical investigation into this question is reported. Several simulations differing only in the timestep used are compared. It is found that much larger timesteps than usual can be employed without producing significant errors in observed thermodynamic, structural or dynamic properties.

  17. Accelerated molecular dynamics simulations of protein folding.

    PubMed

    Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew

    2015-07-30

    Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.

  18. Molecular Dynamics Simulations of Acoustic Properties of Colloidal Suspensions

    NASA Astrophysics Data System (ADS)

    Noguez, Cecilia; Esquivel-Sirvent, Raul; Ramírez-Santiago, Guillermo

    1998-03-01

    Recent experiments of ultrasound waves in colloidal suspensions [1] have found that the acoustic velocity and attenuation exhibit an anomalous behavior close to the solid volume concentration of 40%. Currently, there appears that there is no clear understanding of these results. Motivated by these observations we have carried out extensive non-equilibrium molecular dynamics simulations to study the propagation of pressure waves through a colloidal suspension. The simulations consider the far from equilibrium corrections and calculate the viscosity and attenuation of sound waves traveling in the suspension. These quantities are studied as functions of frecuency and volume fraction. The possible relation between the results from the simulations and the experimental observatios is briefly discussed. [1] R. Esquivel-Sirvent and D. H. Green, Appl. Phys. Lett. 67, 3087 (1995); ibid, Mat. Res. Soc. Symp. 407, p. 99 (1996).

  19. MDLab: a molecular dynamics simulation prototyping environment.

    PubMed

    Cickovski, Trevor; Chatterjee, Santanu; Wenger, Jacob; Sweet, Christopher R; Izaguirre, Jesús A

    2010-05-01

    Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net. Copyright 2009 Wiley Periodicals, Inc.

  20. Molecular Dynamics Simulations of Interface Failure

    NASA Astrophysics Data System (ADS)

    Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.

    2007-03-01

    The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.

  1. Molecular dynamics simulations of dense plasmas

    SciTech Connect

    Collins, L.A.; Kress, J.D.; Kwon, I.; Lynch, D.L.; Troullier, N.

    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.

  2. Nanodrop contact angles from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim

    2016-11-01

    The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.

  3. Classical Molecular Dynamics Simulation of Nuclear Fuel

    SciTech Connect

    Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

    2015-10-10

    Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.

  4. 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.

  5. Water Flow inside Polamide Reverse Osmosis Membranes: A Non-Equilibrium Molecular Dynamics Study.

    PubMed

    Song, Yang; Xu, Fang; Wei, Mingjie; Wang, Yong

    2017-02-23

    Water flow inside polyamide (PA) reverse osmosis (RO) membranes is studied by steady state nonequilibrium molecular dynamics (NEMD) simulations in this work. The PA RO membrane is constructed with the all-atom model, and the density and average pore size obtained thereby are consistent with the latest experimental results. To obtain the time-independent water flux, a steady state NEMD method is used under various pressure drops. The water flux in our simulations, which is calculated under higher pressure drops, is in a linear relation with the pressure drops. Hence, the water flux in lower pressure drops can be reliably estimated, which could be compared with the experimental results. The molecular details of water flowing inside the membrane are considered. The radial distribution function and residence time of water around various groups of polyamide are introduced to analyze the water velocities around these groups, and we find that water molecules flow faster around benzene rings than around carboxyl or amino groups in the membrane, which implies that the main resistance of mass transport of water molecules comes from the carboxyl or amino groups inside the membranes. This finding is in good consistency with experimental results and suggests that less free carboxyl or amino groups should be generated inside RO membranes to enhance water permeance.

  6. Monoamine transporters: insights from molecular dynamics simulations

    PubMed Central

    Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185

  7. Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry.

    PubMed

    Luk, Hoi Ling; Feist, Johannes; Toppari, J Jussi; Groenhof, Gerrit

    2017-09-12

    When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control. However, designing cavity parameters to control chemistry requires a theoretical model with which the effect of the light-matter coupling on the molecular dynamics can be predicted accurately. Here we present a multiscale quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation model for photoactive molecules that are strongly coupled to confined light in optical cavities or surface plasmons. Using this model we have performed simulations with up to 1600 Rhodamine molecules in a cavity. The results of these simulations reveal that the contributions of the molecules to the polariton are time-dependent due to thermal fluctuations that break symmetry. Furthermore, the simulations suggest that in addition to the cavity quality factor, also the Stokes shift and number of molecules control the lifetime of the polariton. Because large numbers of molecules interacting with confined light can now be simulated in atomic detail, we anticipate that our method will lead to a better understanding of the effects of strong coupling on chemical reactivity. Ultimately the method may even be used to systematically design cavities to control photochemistry.

  8. Nonequilibrium ab initio molecular dynamics determination of Ti monovacancy migration rates in B 1 TiN

    NASA Astrophysics Data System (ADS)

    Gambino, D.; Sangiovanni, D. G.; Alling, B.; Abrikosov, I. A.

    2017-09-01

    We use the color diffusion (CD) algorithm in nonequilibrium (accelerated) ab initio molecular dynamics simulations to determine Ti monovacancy jump frequencies in NaCl-structure titanium nitride (TiN), at temperatures ranging from 2200 to 3000 K. Our results show that the CD method extended beyond the linear-fitting rate-versus-force regime [Sangiovanni et al., Phys. Rev. B 93, 094305 (2016), 10.1103/PhysRevB.93.094305] can efficiently determine metal vacancy migration rates in TiN, despite the low mobilities of lattice defects in this type of ceramic compound. We propose a computational method based on gamma-distribution statistics, which provides unambiguous definition of nonequilibrium and equilibrium (extrapolated) vacancy jump rates with corresponding statistical uncertainties. The acceleration-factor achieved in our implementation of nonequilibrium molecular dynamics increases dramatically for decreasing temperatures from 500 for T close to the melting point Tm, up to 33 000 for T ≈0.7 Tm .

  9. Molecular dynamics simulation of aluminium melting

    NASA Astrophysics Data System (ADS)

    Novak, Jakob

    2016-06-01

    Solid-liquid phase transition has been simulated by the molecular dynamics method, using isobaric-isoenthalpic ensemble. For interatomic potential, glue potential has been selected. The original algorithm for bookkeeping of the information on neighbouring relationships of the atoms has been developed and used in this research. Time consumption for calculation of interatomic forces has been reduced from o(N2) to o(N) by the use of this algorithm. Calculations show that phase transition from solid to liquid occurs between 1,000 K and 1,300 K. The simulated temperature of phase transition is higher than the experimental value due to the absence of crystal defects. If constant heat flux is supplied, temperature decreases during melting because the superheated state becomes unstable. During the cooling process, no significant changes of the observed variables were detected due to the high cooling rate, which prevents crystallisation.

  10. Molecular dynamics simulations of magnetized dusty plasmas

    NASA Astrophysics Data System (ADS)

    Piel, Alexander; Reichstein, Torben; Wilms, Jochen

    2012-10-01

    The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)

  11. Molecular Dynamics Simulations of Hypervelocity Impacts

    NASA Astrophysics Data System (ADS)

    Owens, Eli T.; Bachlechner, Martina E.

    2007-03-01

    Outer space silicon solar cells are exposed to impacts with micro meteors that can destroy the surface leading to device failure. A protective coating of silicon nitride will protect against such failure. Large-scale molecular dynamics simulations are used to study how silicon/silicon nitride fails due to hypervelocity impacts. Three impactors made of silicon nitride are studied. Their cross-sectional areas, relative to the target, are as follows: the same as the target, half of the target, and a quarter of the target. Impactor speeds from 5 to 11 km/second yield several modes of failure, such as deformation of the target by the impactor and delimitation of the silicon nitride from the silicon at the interface. These simulations will give a much clearer picture of how solar cells composed of a silicon/silicon nitride interface will respond to impacts in outer space. This will ultimately lead to improved devices with longer life spans.

  12. Thermal resistance of twist boundaries in silicon nanowires by nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bohrer, Jan K.; Schröer, Kevin; Brendel, Lothar; Wolf, Dietrich E.

    2017-04-01

    The thermal boundary resistance (Kapitza resistance) of (001) twist boundaries in silicon is investigated by nonequilibrium molecular dynamics simulations. In order to enable continuous adjustment of the mismatch angle, a cylindrical geometry with fixed atomic positions at the boundaries is devised. The influence of the boundary conditions on the Kapitza resistance is removed by means of a finite size analysis. Due to the diamond structure of silicon, twist boundaries with mismatch angles ϕ and 90 ° - ϕ are not equivalent, whereas those with ± ϕ or with 90 ° ± ϕ are. The Kapitza resistance increases with mismatch angle up to 45 ° , where it reaches a plateau around 1.56 ± 0.05 K m 2 / GW . Between 80 ° and the 90 ° Σ 1 grain boundary it drops by about 30%. Surprisingly, lattice coincidence at other angles ( Σ 5 , Σ 13 , Σ 27 , Σ 25 ) has no noticable effect on the Kapitza resistance. However, there is a clear correlation between the Kapitza resistance and the width of a non-crystalline layer at the twist boundaries.

  13. Molecular dynamics simulation of fractal aggregate diffusion

    NASA Astrophysics Data System (ADS)

    Pranami, Gaurav; Lamm, Monica H.; Vigil, R. Dennis

    2010-11-01

    The diffusion of fractal aggregates constructed with the method by Thouy and Jullien [J. Phys. A 27, 2953 (1994)10.1088/0305-4470/27/9/012] comprised of Np spherical primary particles was studied as a function of the aggregate mass and fractal dimension using molecular dynamics simulations. It is shown that finite-size effects have a strong impact on the apparent value of the diffusion coefficient (D) , but these can be corrected by carrying out simulations using different simulation box sizes. Specifically, the diffusion coefficient is inversely proportional to the length of a cubic simulation box, and the constant of proportionality appears to be independent of the aggregate mass and fractal dimension. Using this result, it is possible to compute infinite dilution diffusion coefficients (Do) for aggregates of arbitrary size and fractal dimension, and it was found that Do∝Np-1/df , as is often assumed by investigators simulating Brownian aggregation of fractal aggregates. The ratio of hydrodynamic radius to radius of gyration is computed and shown to be independent of mass for aggregates of fixed fractal dimension, thus enabling an estimate of the diffusion coefficient for a fractal aggregate based on its radius of gyration.

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

    SciTech Connect

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

    2015-02-14

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

  15. Molecular dynamics simulation in virus research

    PubMed Central

    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

  16. Microsecond Molecular Dynamics Simulations of Lipid Mixing

    PubMed Central

    2015-01-01

    Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na+ ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes. PMID:25237736

  17. Quantum molecular dynamics simulations of dense matter

    SciTech Connect

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I.

    1997-12-31

    The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.

  18. Molecular Dynamics Simulation of a RNA Aptasensor.

    PubMed

    Ruan, Min; Seydou, Mahamadou; Noel, Vincent; Piro, Benoit; Maurel, François; Barbault, Florent

    2017-04-14

    Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.

  19. Molecular Dynamics Simulations of Ferroelectric Phase Transitions

    NASA Astrophysics Data System (ADS)

    Yu, Rici; Krakauer, Henry

    1997-03-01

    Based on an analysis of the wavevector dependence of the lattice instabilities in KNbO_3, we proposed a real-space chain-like instability and a scenario of sequential freezing out or onset of coherence of these instabilities, which qualitatively explains the sequence of observed temperature-dependent ferroelectric phases.(R. Yu and H. Krakauer, Phys. Rev. Lett. 74), 4067 (1995). We suggested that this chain-like instability should also be found in BaTiO_3, and this has been subsequently confirmed by Ghosez et al.(P. Ghosez et al.), Proc. 4th Williamsburg Workshop on First-Principles Calculations for Ferroelectrics, to be published We will present molecular dynamics simulations on BaTiO_3, using effective Hamiltonians constructed from first-principles calculations,(W. Zhong, D. Vanderbilt, and K. M. Rabe, Phys. Rev. Lett. 73), 1861 (1994). that reproduce the essential features of diffuse x-ray scattering measurements in the cubic, tetragonal, orthorhombic, and rhombohedral phases. The good agreement supports the interpretation of real-space chain-formation. Simulations for KNbO3 may also be reported.

  20. Detecting Allosteric Networks Using Molecular Dynamics Simulation.

    PubMed

    Bowerman, S; Wereszczynski, J

    2016-01-01

    Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. © 2016 Elsevier Inc. All rights reserved.

  1. Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.

    PubMed

    Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C; Roux, Benoît

    2013-10-01

    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 β-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.

  2. Studying the unfolding kinetics of proteins under pressure using long molecular dynamic simulation runs.

    PubMed

    Chara, Osvaldo; Grigera, José Raúl; McCarthy, Andrés N

    2007-12-01

    The usefulness of computational methods such as molecular dynamics simulation has been extensively established for studying systems in equilibrium. Nevertheless, its application to complex non-equilibrium biological processes such as protein unfolding has been generally regarded as producing results which cannot be interpreted straightforwardly. In the present study, we present results for the kinetics of unfolding of apomyoglobin, based on the analysis of long simulation runs of this protein in solution at 3 kbar (1 atm = 1.01325, bar = 101,325 Pa). We hereby demonstrate that the analysis of the data collected within a simulated time span of 0.18 mus suffices for producing results, which coincide remarkably with the available unfolding kinetics experimental data. This not only validates molecular dynamics simulation as a valuable alternative for studying non-equilibrium processes, but also enables a detailed analysis of the actual structural mechanism which underlies the unfolding process of proteins under elusive denaturing conditions such as high pressure.

  3. Nanoscale deicing by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-07-01

    Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice

  4. Coarse-grained protein molecular dynamics simulations.

    PubMed

    Derreumaux, Philippe; Mousseau, Normand

    2007-01-14

    A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Abeta16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four Abeta16-22 peptides can form a three-stranded beta sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.

  5. Coarse-grained protein molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Derreumaux, Philippe; Mousseau, Normand

    2007-01-01

    A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.

  6. Molecular Dynamics Simulations of Coulomb Explosion

    SciTech Connect

    Bringa, E M

    2002-05-17

    A swift ion creates a track of electronic excitations in the target material. A net repulsion inside the track can cause a ''Coulomb Explosion'', which can lead to damage and sputtering of the material. Here we report results from molecular-dynamics (MD) simulations of Coulomb explosion for a cylindrical track as a function of charge density and neutralization/quenching time, {tau}. Screening by the free electrons is accounted for using a screened Coulomb potential for the interaction among charges. The yield exhibits a prompt component from the track core and a component, which dominates at higher excitation density, from the heated region produced. For the cases studied, the number of atoms ejected per incident ion, i.e. the sputtering yield Y, is quadratic with charge density along the track as suggested by simple models. Y({tau} = 0.2 Debye periods) is nearly 20% of the yield when there is no neutralization ({tau} {yields} {infinity}). The connections between ''Coulomb explosions'', thermal spikes and measurements of electronic sputtering are discussed.

  7. Atomistic molecular dynamics simulations of shock compressed quartz

    NASA Astrophysics Data System (ADS)

    Farrow, M. R.; Probert, M. I. J.

    2011-07-01

    Atomistic non-equilibrium molecular dynamics simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer, and van Santen [Phys. Rev. B 43, 5068 (1991)], 10.1103/PhysRevB.43.5068 to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geometry optimised system of a polar slab in a three-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under representative pressure conditions of the Earth core, but unsuitable for high-pressure shock wave simulations. We also find that the BKS potential incorrectly prefers the β-quartz phase over the α-quartz phase at zero-temperature, and that there is a β → α phase-transition at 6 GPa.

  8. Molecular dynamics simulations of xDNA.

    PubMed

    Varghese, Mathew K; Thomas, Renjith; Unnikrishnan, N V; Sudarsanakumar, C

    2009-05-01

    xDNA is a modified DNA, which contains natural as well as expanded bases. Expanded bases are generated by the addition of a benzene spacer to the natural bases. A set of AMBER force-field parameters were derived for the expanded bases and the structural dynamics of the xDNA decamer (xT5' G xT A xC xG C xA xG T3').(xA5' C T xG C G xT A xC A3') was explored using a 22 ns molecular dynamics simulation in explicit solvent. During the simulation, the duplex retained its Watson-Crick base-pairing and double helical structure, with deviations from the starting B-form geometry towards A-form; the deviations are mainly in the backbone torsion angles and in the helical parameters. The sugar pucker of the residues were distributed among a variety of modes; C2' endo, C1' exo, O4' endo, C4' exo, C2' exo, and C3' endo. The enhanced stacking interactions on account of the modification in the bases could help to retain the duplex nature of the helix with minor deviations from the ideal geometry. In our simulation, the xDNA showed a reduced minor groove width and an enlarged major groove width in comparison with the NMR structure. Both the grooves are larger than that of standard B-DNA, but major groove width is larger than that of A-DNA with almost equal minor groove width. The enlarged groove widths and the possibility of additional hydration in the grooves makes xDNA a potential molecule for various applications. Copyright (c) 2009 Wiley Periodicals, Inc.

  9. 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

  10. Spectral analysis of nonequilibrium molecular dynamics: Spectral phonon temperature and local nonequilibrium in thin films and across interfaces

    NASA Astrophysics Data System (ADS)

    Feng, Tianli; Yao, Wenjun; Wang, Zuyuan; Shi, Jingjing; Li, Chuang; Cao, Bingyang; Ruan, Xiulin

    2017-05-01

    Although extensive experimental and theoretical works have been conducted to understand the ballistic and diffusive phonon transport in nanomaterials recently, direct observation of temperature and thermal nonequilibrium of different phonon modes has not been realized. Herein, we have developed a method within the framework of molecular dynamics to calculate the temperatures of phonons in both real and phase spaces. Taking silicon thin film and graphene as examples, we directly obtained the spectral phonon temperature (SPT) and observed the local thermal nonequilibrium between the ballistic and diffusive phonons. Such nonequilibrium also generally exists across interfaces and is surprisingly large, and it provides a significant additional thermal interfacial resistance mechanism besides phonon reflection. Our SPT results directly show that the vertical thermal transport across the dimensionally mismatched graphene-substrate interface is through the coupling between flexural acoustic phonons of graphene and the longitudinal phonons in the substrate with mode conversion. In the dimensionally matched interfaces, e.g., graphene-graphene junction and graphene-boron nitride planar interfaces, strong coupling occurs between the acoustic phonon modes on both sides, and the coupling decreases with interfacial mixing. The SPT method together with the spectral heat flux can eliminate the size effect of the thermal conductivity prediction induced from ballistic transport.

  11. 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..

  12. Molecular Dynamics Simulation of Disordered Zircon

    SciTech Connect

    Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin

    2004-02-27

    The melting of zircon and the amorphous state produced by quenching from the melt were simulated by molecular dynamics using a new partial charge model combined with the Ziegler-Biersack-Littmark potential. The model has been established for the description of the crystalline and aperiodic structures of zircon in order to be used for the simulation of displacement cascades. It provides an excellent fit to the structure, and accounts with convenient precision the mechanical and thermodynamic properties of zircon. The calculated melting temperature is about 2100 K. The activation energy for self-diffusion of ions in the liquid state was determined to be 190-200 kJ/mole. Melt quenching was employed to produce two different disordered states with distinct densities and structures. In the high density disordered state, the zircon structure is intact but the bond angle distributions are broader, 4% of the Si units are polymerized, and the volume swelling is about 8%. In the low density amorphous state, the Zr and Si coordination numbers are lower, and the Zr-O and Si-O bond lengths are shorter than corresponding values for the crystal. In addition, a highly polymerized Si network, with average connectivity of two, is observed in the low density amorphous state. These features have all been experimentally observed in natural metamict zircon. The present findings, when considered in light of experimental radiation effects studies, suggest that the swelling in zircon arises initially from disorder in the zircon crystal, and at high doses the disordered crystal is unable to accommodate the volume expansion and transforms to the amorphous state.

  13. Molecular Dynamics Simulations of Thermal Induced Chemistry in TATB

    NASA Astrophysics Data System (ADS)

    Quenneville, Jason; Germann, Timothy

    2006-03-01

    Equilibrium molecular dynamics (MD) simulation of high explosives can provide important information on their thermal decomposition by helping to characterize processes with timescales that are much longer than those attainable with non-equilibrium MD shock studies. A reactive force field is used with MD to probe the chemisty induced by intense heating (`cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). The force field (ReaxFF) was developed by van Duin, Goddard and coworkers^ at CalTech and has already shown promise in predicting the chemistry in small samples of RDX under either shock compression or intense heat. Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. We will show results of 100,000-particle simulations at several temperatures, carried out with the massively parallel GRASP MD software developed at Sandia National Lab. Finally, we will compare the reactions and reaction timescales with those of RDX and HMX. ^ A. C. T. Van Duin, et al, J. Phys. Chem. A, 1005, 9396 (2001).

  14. Shock waves simulated using the dual domain material point method combined with molecular dynamics

    NASA Astrophysics Data System (ADS)

    Zhang, Duan Z.; Dhakal, Tilak R.

    2017-04-01

    In this work we combine the dual domain material point method with molecular dynamics in an attempt to create a multiscale numerical method to simulate materials undergoing large deformations with high strain rates. In these types of problems, the material is often in a thermodynamically nonequilibrium state, and conventional constitutive relations or equations of state are often not available. In this method, the closure quantities, such as stress, at each material point are calculated from a molecular dynamics simulation of a group of atoms surrounding the material point. Rather than restricting the multiscale simulation in a small spatial region, such as phase interfaces, or crack tips, this multiscale method can be used to consider nonequilibrium thermodynamic effects in a macroscopic domain. This method takes the advantage that the material points only communicate with mesh nodes, not among themselves; therefore molecular dynamics simulations for material points can be performed independently in parallel. The dual domain material point method is chosen for this multiscale method because it can be used in history dependent problems with large deformation without generating numerical noise as material points move across cells, and also because of its convergence and conservation properties. To demonstrate the feasibility and accuracy of this method, we compare the results of a shock wave propagation in a cerium crystal calculated using the direct molecular dynamics simulation with the results from this combined multiscale calculation.

  15. Shock waves simulated using the dual domain material point method combined with molecular dynamics

    DOE PAGES

    Zhang, Duan Z.; Dhakal, Tilak Raj

    2017-01-17

    Here in this work we combine the dual domain material point method with molecular dynamics in an attempt to create a multiscale numerical method to simulate materials undergoing large deformations with high strain rates. In these types of problems, the material is often in a thermodynamically nonequilibrium state, and conventional constitutive relations or equations of state are often not available. In this method, the closure quantities, such as stress, at each material point are calculated from a molecular dynamics simulation of a group of atoms surrounding the material point. Rather than restricting the multiscale simulation in a small spatial region,more » such as phase interfaces, or crack tips, this multiscale method can be used to consider nonequilibrium thermodynamic effects in a macroscopic domain. This method takes the advantage that the material points only communicate with mesh nodes, not among themselves; therefore molecular dynamics simulations for material points can be performed independently in parallel. The dual domain material point method is chosen for this multiscale method because it can be used in history dependent problems with large deformation without generating numerical noise as material points move across cells, and also because of its convergence and conservation properties. In conclusion, to demonstrate the feasibility and accuracy of this method, we compare the results of a shock wave propagation in a cerium crystal calculated using the direct molecular dynamics simulation with the results from this combined multiscale calculation.« less

  16. Transport properties of dense fluid mixtures using nonequilibrium molecular dynamics. Final report, September 15, 1987--March 14, 1997

    SciTech Connect

    Murad, S.

    1997-05-01

    Computer Simulation Studies were carried out using the method of equilibrium and nonequilibrium molecular dynamics (NEMD) to examine a wide range of transport processes in both fluids and fluid mixtures. This included testing a wide range of mixing rules for thermal conductivity and viscosity. In addition a method was developed to calculate the internal rotational contributions to thermal conductivity and the accuracy of current methods for predicting these contributions were examined. These comparisons were then used to suggest possible ways of improving these theories. The method of NEMD was also used to examine the critical enhancements of thermal conductivity. Finally, molecular simulations were carried out to study the various transport coefficients of fluids confined by membranes, as well as important transport processes such as osmosis, and reverse osmosis.

  17. Molecular dynamics simulations of glycoclusters and glycodendrimers.

    PubMed

    von der Lieth, Claus W; Frank, Martin; Lindhorst, Thisbe K

    2002-05-01

    Protein-carbohydrate recognition plays a crucial role in a wide range of biological processes, required both for normal physiological functions and the onset of disease. Nature uses multivalency in carbohydrate-protein interactions as a strategy to overcome the low affinity found for singular binding of an individual saccharide epitope to a single carbohydrate recognition domain of a lectin. To mimic the complex multi-branched oligosaccharides found in glycoconjugates, which form the structural basis of multivalent carbohydrate-protein interactions, so-called glycoclusters and glycodendrimers have been designed to serve as high-affinity ligands of the respective receptor proteins. To allow a rational design of glycodendrimer-type molecules with regard to the receptor structures involved in carbohydrate recognition, a deeper knowledge of the dynamics of such molecules is desirable. Most glycodendrimers have to be considered highly flexible molecules with their conformational preferences most difficult to elucidate by experimental methods. Longtime molecular dynamics (MD) simulations with inclusion of explicit solvent molecules are suited to explore the conformational space accessible to glycodendrimers. Here, a detailed geometric and conformational analysis of 15 glycodendrimers and glycoclusters has been accomplished, which differ with regard to their core moieties, spacer characteristics and the type of terminal carbohydrate units. It is shown that the accessible conformational space depends strongly on the structural features of the core and spacer moieties and even on the type of terminating sugars. The obtained knowledge about possible spatial distributions of the sugar epitopes exposed on the investigated hyperbranched neoglycoconjugates is detailed for all examples and forms important information for the interpretation and prediction of affinity data, which can be deduced from biological testing of these multivalent neoglycoconjugates.

  18. Molecular Dynamics Simulation of the Phonon Conductivity in Cu-Ni Binary Alloy

    NASA Astrophysics Data System (ADS)

    Konishi, Yusuke; Fukushima, Tetsuya; Sato, Kazunori; Asai, Yoshihiro; Katayama-Yoshida, Hiroshi

    2014-03-01

    In 2010, a giant Peltier effect was observed in a Cu-Ni/Au junction. It is considered that this giant Peltier effect is caused by nano-scale phase separation formed in the sputtering process. The giant Peltier coefficient in the Cu-Ni/Au junction indicates the great Seebeck coefficient in Cu-Ni alloy. Although this alloy is a prospective thermoelectric material because of its great Seebeck coefficient, the low phonon thermal conductivity is also necessary for a large thermoelectric coefficient ZT. In order to find conditions for the low phonon conductivity, we calculate the thermal conductivity in Cu-Ni Alloy in various shapes with or without nanostructures by using nonequilibrium molecular dynamics simulation. In this simulation, we use a semi-empirical potential and the reverse nonequilibrium molecular dynamics method.

  19. Frontiers in molecular dynamics simulations of DNA.

    PubMed

    Pérez, Alberto; Luque, F Javier; Orozco, Modesto

    2012-02-21

    It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global

  20. Nonequilibrium molecular dynamics study of electric and low-frequency microwave fields on hen egg white lysozyme

    NASA Astrophysics Data System (ADS)

    English, Niall J.; Solomentsev, Gleb Y.; O'Brien, Paul

    2009-07-01

    Nonequilibrium molecular dynamics simulations of various mutants of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of both external static electric and low-frequency microwave (2.45 GHz) fields of varying intensity. Significant nonthermal field effects were noted, such as marked changes in the protein's secondary structure relative to the zero-field state, depending on the field conditions, mutation, and orientation with respect to the applied field. This occurred primarily as a consequence of alignment of the protein's total dipole moment with the external field, although the dipolar alignment of water molecules in both the solvation layer and the bulk was also found to be influential. Substantial differences in behavior were found for proteins with and without overall net charges, particularly with respect to translational motion. Localized motion and perturbation of hydrogen bonds were also found to be evident for charged residues.

  1. Determination of the distance-dependent viscosity of mixtures in parallel slabs using non-equilibrium molecular dynamics.

    PubMed

    Pařez, Stanislav; Předota, Milan

    2012-03-14

    We generalize a technique for determination of the shear viscosity of mixtures in planar slabs using non-equilibrium computer simulations by applying an external force parallel to the surface generating Poiseuille flow. The distance-dependent viscosity of the mixture, given as a function of the distance from the surface, is determined by analysis of the resulting velocity profiles of all species. We present results for a highly non-ideal water + methanol mixture in the whole concentration range between rutile (TiO(2)) walls. The bulk results are compared to the existing equilibrium molecular dynamics and experimental data while the inhomogeneous viscosity profiles at the interface are interpreted using the structural data and information on hydrogen bonding.

  2. Molecular dynamics simulations of evaporation-induced nanoparticle assembly

    NASA Astrophysics Data System (ADS)

    Cheng, Shengfeng; Grest, Gary S.

    2013-02-01

    While evaporating solvent is a widely used technique to assemble nano-sized objects into desired superstructures, there has been limited work on how the assembled structures are affected by the physical aspects of the process. We present large scale molecular dynamics simulations of the evaporation-induced assembly of nanoparticles suspended in a liquid that evaporates in a controlled fashion. The quality of the nanoparticle crystal formed just below the liquid/vapor interface is found to be better at relatively slower evaporation rates, as less defects and grain boundaries appear. This trend is understood as the result of the competition between the accumulation and diffusion times of nanoparticles at the liquid/vapor interface. When the former is smaller, nanoparticles are deposited so fast at the interface that they do not have sufficient time to arrange through diffusion, which leads to the prevalence of defects and grain boundaries. Our results have important implications in understanding assembly of nanoparticles and colloids in non-equilibrium liquid environments.

  3. Multimillion atom molecular dynamics simulations of glasses and ceramic materials

    NASA Astrophysics Data System (ADS)

    Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro

    1999-11-01

    Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed.

  4. A nonequilibrium molecular dynamics method for thermal conductivities based on thermal noise

    NASA Astrophysics Data System (ADS)

    Terao, Takamichi; Müller-Plathe, Florian

    2005-02-01

    We developed a nonequilibrium molecular dynamics (NEMD) method for calculating thermal conductivities. In contrast to other NEMD algorithms, here only the heat sink is localized, whereas the heat source can be uniformly distributed throughout the system. The noise due to cutting off the pair forces or to integration errors is such a uniform heat source. In traditional NEMD methods it is normally considered a nuisance factor. The new algorithm accounts for it and uses it. The algorithm is easy to derive, analyse and implement. Moreover, it circumvents the need to calculate energy fluxes. It is tested on the enhanced simple-point charge model for liquid water and reproduces the known thermal conductivity of this model liquid of 0.81Wm-1K-1. It can be generalized to situations, where the thermal noise is replaced by another uniform heat source, or to the inverse situation, where the heat source is localized but the heat sink extends over the entire system.

  5. A nonequilibrium molecular dynamics method for thermal conductivities based on thermal noise.

    PubMed

    Terao, Takamichi; Müller-Plathe, Florian

    2005-02-22

    We developed a nonequilibrium molecular dynamics (NEMD) method for calculating thermal conductivities. In contrast to other NEMD algorithms, here only the heat sink is localized, whereas the heat source can be uniformly distributed throughout the system. The noise due to cutting off the pair forces or to integration errors is such a uniform heat source. In traditional NEMD methods it is normally considered a nuisance factor. The new algorithm accounts for it and uses it. The algorithm is easy to derive, analyse and implement. Moreover, it circumvents the need to calculate energy fluxes. It is tested on the enhanced simple-point charge model for liquid water and reproduces the known thermal conductivity of this model liquid of 0.81 W m(-1) K(-1). It can be generalized to situations, where the thermal noise is replaced by another uniform heat source, or to the inverse situation, where the heat source is localized but the heat sink extends over the entire system.

  6. A uniform source-and-sink scheme for calculating thermal conductivity by nonequilibrium molecular dynamics.

    PubMed

    Cao, Bing-Yang; Li, Yuan-Wei

    2010-07-14

    A uniform source-and-sink (USS) scheme, which combines features of the reverse [F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997)] and improved relaxation [B. Y. Cao, J. Chem. Phys. 129, 074106 (2008)] methods, is developed to calculate the thermal conductivity by nonequilibrium molecular dynamics (NEMD). The uniform internal heat source and sink are realized by exchanging the velocity vectors of individual atoms in the right half and left half systems, and produce a periodically quadratic temperature profile throughout the system. The thermal conductivity can be easily extracted from the mean temperatures of the right and left half systems rather than by fitting the temperature profiles. In particular, this scheme greatly increases the relaxation of the exited localized phonon modes which often worsen the calculation accuracy and efficiency in most other NEMD methods. The calculation of the thermal conductivities of solid argon shows that the simple USS scheme gives accurate results with fast convergence.

  7. A uniform source-and-sink scheme for calculating thermal conductivity by nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Cao, Bing-Yang; Li, Yuan-Wei

    2010-07-01

    A uniform source-and-sink (USS) scheme, which combines features of the reverse [F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997)] and improved relaxation [B. Y. Cao, J. Chem. Phys. 129, 074106 (2008)] methods, is developed to calculate the thermal conductivity by nonequilibrium molecular dynamics (NEMD). The uniform internal heat source and sink are realized by exchanging the velocity vectors of individual atoms in the right half and left half systems, and produce a periodically quadratic temperature profile throughout the system. The thermal conductivity can be easily extracted from the mean temperatures of the right and left half systems rather than by fitting the temperature profiles. In particular, this scheme greatly increases the relaxation of the exited localized phonon modes which often worsen the calculation accuracy and efficiency in most other NEMD methods. The calculation of the thermal conductivities of solid argon shows that the simple USS scheme gives accurate results with fast convergence.

  8. Molecular dynamics simulations of granular compaction: The single granule case

    NASA Astrophysics Data System (ADS)

    Sanchez-Castillo, Francisco X.; Anwar, Jamshed; Heyes, David M.

    2003-03-01

    We have carried out nonequilibrium molecular dynamics simulations of the compaction of a single three-dimensional granule composed of over 1000 Lennard-Jones (LJ) particles. The granule was contained within an orthorhombic box with repulsive walls and deformed by a vertically moving top wall. The compaction cycle adopted was intended to mimic the procedure employed in industrial tabletting processes, by compressing the granule during the downward movement of the top wall (compaction) followed by an upward movement of the top wall (decompaction). We have explored the effects of different compression rates on the deformation, microstructure, and the final integrity of the granule. Although the simulations are formally atomistic, we believe a mesoscopic significance can be attached to the results that makes them relevant to the larger scale compaction involved in industrially relevant processes. The cluster representation of the granule allows for significant deformation during the process, and the simulations reproduce a number of well-known effects found in the pharmaceutical tabletting and other literature. Rapid compaction resulted in an essentially elastic response and even break up of the formed tablet during the decompaction stage, an effect known as lamination. Slower compaction speeds, which enabled greater internal rearrangement of the LJ particles through plastic deformation, produced a more structurally uniform tablet at the end of the cycle. For the faster compaction speed the top wall moved away faster than the compacted material could recover, giving rise to misleadingly low values of the apparent elastic response of the material as measured by the force from the material on the top wall. We believe this could be an important issue when interpreting experimental data. These simulations were able to capture the transition between the fast and slow compaction rate regimes and reveal some rudiments of the lamination problem that plagues the industrial

  9. On Mechanical Properties of Graphene Sheet Estimated Using Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Das, D. K.; Ghosh, M. M.

    2017-09-01

    This work reports estimation of mechanical properties, particularly Young's modulus of a single-layered graphene sheet by molecular dynamics (MD) simulation-based four different approaches, viz. tensile modeling, bending modeling, oscillation modeling and equilibrium MD modeling. The Young's modulus is estimated to be of the order of some TPa. The equilibrium MD method has yielded a Young's modulus value lower than the other non-equilibrium methods, due to the absence of any external forcing factor. Among the non-equilibrium MD methods, the bending modeling is found to predict the highest value of Young's modulus. Comparison among different non-equilibrium methods has established the effect of strain rate on the estimated value of the Young's modulus. The MD simulation-based approaches adopted here can be useful for the design of graphene and graphene-based materials in advanced mechanical applications.

  10. Methods for molecular dynamics simulations of protein folding/unfolding in solution.

    PubMed

    Beck, David A C; Daggett, Valerie

    2004-09-01

    All atom molecular dynamics simulations have become a standard method for mapping equilibrium protein dynamics and non-equilibrium events like folding and unfolding. Here, we present detailed methods for performing such simulations. Generic protocols for minimization, solvation, simulation, and analysis derived from previous studies are also presented. As a measure of validation, our water model is compared with experiment. An example of current applications of these methods, simulations of the ultrafast folding protein Engrailed Homeodomain are presented including the experimental evidence used to verify their results. Ultrafast folders are an invaluable tool for studying protein behavior as folding and unfolding events measured by experiment occur on timescales accessible with the high-resolution molecular dynamics methods we describe. Finally, to demonstrate the prospect of these methods for folding proteins, a temperature quench simulation of a thermal unfolding intermediate of the Engrailed Homeodomain is described.

  11. Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Non-equilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    English, Niall J.; Garate, José-A.

    2016-08-01

    An extensive suite of non-equilibrium molecular-dynamics simulation has been performed for ˜0.85-0.9 μs of human aquaporin 4 in the absence and presence of externally applied static and alternating electric fields applied along the channels (in both axial directions in the static case, taken as the laboratory z-axis). These external fields were of 0.0065 V/Å (r.m.s.) intensity (of the same order as physiological electrical potentials); alternating fields ranged in frequency from 2.45 to 500 GHz. In-pore gating dynamics was studied, particularly of the relative propensities for "open" and "closed" states of the conserved arginines in the arginine/aromatic area (itself governed in no small part by external-field response of the dipolar alignment of the histidine-201 residue in the selectivity filter). In such a manner, the intimate connection of field-response governing "two-state" histidine states was established statistically and mechanistically. Given the appreciable size of the energy barriers for histidine-201 alignment, we have also performed non-equilibrium metadynamics/local-elevation of static fields applied along both directions to construct the free-energy landscape thereof in terms of external-field direction, elucidating the importance of field direction on energetics. We conclude from direct measurement of deterministic molecular dynamics in conjunction with applied-field metadynamics that the intrinsic electric field within the channel points along the +z-axis, such that externally applied static fields in this direction serve to "open" the channel in the selectivity-filter and the asparagine-proline-alanine region.

  12. Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Non-equilibrium molecular dynamics.

    PubMed

    English, Niall J; Garate, José-A

    2016-08-28

    An extensive suite of non-equilibrium molecular-dynamics simulation has been performed for ∼0.85-0.9 μs of human aquaporin 4 in the absence and presence of externally applied static and alternating electric fields applied along the channels (in both axial directions in the static case, taken as the laboratory z-axis). These external fields were of 0.0065 V/Å (r.m.s.) intensity (of the same order as physiological electrical potentials); alternating fields ranged in frequency from 2.45 to 500 GHz. In-pore gating dynamics was studied, particularly of the relative propensities for "open" and "closed" states of the conserved arginines in the arginine/aromatic area (itself governed in no small part by external-field response of the dipolar alignment of the histidine-201 residue in the selectivity filter). In such a manner, the intimate connection of field-response governing "two-state" histidine states was established statistically and mechanistically. Given the appreciable size of the energy barriers for histidine-201 alignment, we have also performed non-equilibrium metadynamics/local-elevation of static fields applied along both directions to construct the free-energy landscape thereof in terms of external-field direction, elucidating the importance of field direction on energetics. We conclude from direct measurement of deterministic molecular dynamics in conjunction with applied-field metadynamics that the intrinsic electric field within the channel points along the +z-axis, such that externally applied static fields in this direction serve to "open" the channel in the selectivity-filter and the asparagine-proline-alanine region.

  13. Hydration dynamics in water clusters via quantum molecular dynamics simulations

    SciTech Connect

    Turi, László

    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

  14. Energy flow and long-range correlations in guanine-binding riboswitch: a nonequilibrium molecular dynamics study.

    PubMed

    Nguyen, Phuong H; Derreumaux, Philippe; Stock, Gerhard

    2009-07-09

    A nonequilibrium molecular dynamics (MD) study of the temperature-induced energy flow in a RNA-ligand complex is presented, which employs extensive all-atom explicit solvent MD simulations of the aptamer domain of the guanine-sensing riboswitch (GRA). Since the few existing MD investigations of biomolecular energy flow have used quite different computational approaches, the applicability and performance of the various methods are compared first. In particular, a nonequilibrium correlation function C(ij)(tau) is introduced that describes the cumulative response of residue j at delay time tau to the energy source at residue i. Employing this analysis, the anisotropic energy flow and long-range correlations in GRA are studied, which can be monitored over distances up to approximately 4 nm. To test whether these long-range correlations are relevant for molecular function, the unbinding-induced conformational changes of GRA are calculated using the linear-response theory, assuming that the unbinding of the guanine ligand represents the first step responsible for the function of GRA. Interestingly, it is found that the same residues that are of functional importance are also prominently involved in the energy transfer. In particular, significant correlations between the guanine ligand and the distant "kissing" loops of GRA are found. This finding is in line with recent experiments which indicate that these long-range interactions may be important for the induced-fit binding of the ligand.

  15. 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.

  16. AceCloud: Molecular Dynamics Simulations in the Cloud.

    PubMed

    Harvey, M J; De Fabritiis, G

    2015-05-26

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

  17. Enhanced sampling techniques in molecular dynamics simulations of biological systems.

    PubMed

    Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

    2015-05-01

    Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. In Silico Determination of Gas Permeabilities by Non-Equilibrium Molecular Dynamics: CO2 and He through PIM-1

    PubMed Central

    Frentrup, Hendrik; Hart, Kyle E.; Colina, Coray M.; Müller, Erich A.

    2015-01-01

    We study the permeation dynamics of helium and carbon dioxide through an atomistically detailed model of a polymer of intrinsic microporosity, PIM-1, via non-equilibrium molecular dynamics (NEMD) simulations. This work presents the first explicit molecular modeling of gas permeation through a high free-volume polymer sample, and it demonstrates how permeability and solubility can be obtained coherently from a single simulation. Solubilities in particular can be obtained to a very high degree of confidence and within experimental inaccuracies. Furthermore, the simulations make it possible to obtain very specific information on the diffusion dynamics of penetrant molecules and yield detailed maps of gas occupancy, which are akin to a digital tomographic scan of the polymer network. In addition to determining permeability and solubility directly from NEMD simulations, the results shed light on the permeation mechanism of the penetrant gases, suggesting that the relative openness of the microporous topology promotes the anomalous diffusion of penetrant gases, which entails a deviation from the pore hopping mechanism usually observed in gas diffusion in polymers. PMID:25764366

  19. In Silico Determination of Gas Permeabilities by Non-Equilibrium Molecular Dynamics: CO2 and He through PIM-1.

    PubMed

    Frentrup, Hendrik; Hart, Kyle E; Colina, Coray M; Müller, Erich A

    2015-03-10

    We study the permeation dynamics of helium and carbon dioxide through an atomistically detailed model of a polymer of intrinsic microporosity, PIM-1, via non-equilibrium molecular dynamics (NEMD) simulations. This work presents the first explicit molecular modeling of gas permeation through a high free-volume polymer sample, and it demonstrates how permeability and solubility can be obtained coherently from a single simulation. Solubilities in particular can be obtained to a very high degree of confidence and within experimental inaccuracies. Furthermore, the simulations make it possible to obtain very specific information on the diffusion dynamics of penetrant molecules and yield detailed maps of gas occupancy, which are akin to a digital tomographic scan of the polymer network. In addition to determining permeability and solubility directly from NEMD simulations, the results shed light on the permeation mechanism of the penetrant gases, suggesting that the relative openness of the microporous topology promotes the anomalous diffusion of penetrant gases, which entails a deviation from the pore hopping mechanism usually observed in gas diffusion in polymers.

  20. Soft-spring wall based non-periodic boundary conditions for non-equilibrium molecular dynamics of dense fluids

    SciTech Connect

    Ghatage, Dhairyashil; Tomar, Gaurav Shukla, Ratnesh K.

    2015-03-28

    Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient.

  1. Modelling transient heat conduction in solids at multiple length and time scales: A coupled non-equilibrium molecular dynamics/continuum approach

    SciTech Connect

    Jolley, Kenny; Gill, Simon P.A.

    2009-10-20

    A method for controlling the thermal boundary conditions of non-equilibrium molecular dynamics simulations is presented. The method is simple to implement into a conventional molecular dynamics code and independent of the atomistic model employed. It works by regulating the temperature in a thermostatted boundary region by feedback control to achieve the desired temperature at the edge of an inner region where the true atomistic dynamics are retained. This is necessary to avoid intrinsic boundary effects in non-equilibrium molecular dynamics simulations. Three thermostats are investigated: the global deterministic Nose-Hoover thermostat and two local stochastic thermostats, Langevin and stadium damping. The latter thermostat is introduced to avoid the adverse reflection of phonons that occurs at an abrupt interface. The method is then extended to allow atomistic/continuum models to be thermally coupled concurrently for the analysis of large steady state and transient heat conduction problems. The effectiveness of the algorithm is demonstrated for the example of heat flow down a three-dimensional atomistic rod of uniform cross-section subjected to a variety of boundary conditions.

  2. Molecular dynamics simulation of an argon cluster filled inside carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Cui, Shu-Wen; Zhu, Ru-Zeng; Wang, Xiao-Song; Yang, Hong-Xiu

    2014-10-01

    The effects of the diameters of single-walled carbon nanotubes (SWCNTs) (7.83 Å to 27.40 Å) and temperature (20 K-45 K) on the equilibrium structure of an argon cluster are systematically studied by molecular dynamics simulation with consideration of the SWCNTs to be fixed. Since the diameters of SWCNTs with different chiralities increase when temperature is fixed at 20 K, the equilibrium structures of the argon cluster transform from monoatomic chains to helical and then to multishell coaxial cylinders. Chirality has almost no noticeable influence on these cylindrosymmetric structures. The effects of temperature and a non-equilibrium sudden heating process on the structures of argon clusters in SWCNTs are also studied by molecular dynamics simulation.

  3. Molecular-dynamics approach for studying the nonequilibrium behavior of x-ray-heated solid-density matter

    NASA Astrophysics Data System (ADS)

    Abdullah, Malik Muhammad; Anurag, Jurek, Zoltan; Son, Sang-Kil; Santra, Robin

    2017-08-01

    When matter is exposed to a high-intensity x-ray free-electron-laser pulse, the x rays excite inner-shell electrons leading to the ionization of the electrons through various atomic processes and creating high-energy-density plasma, i.e., warm or hot dense matter. The resulting system consists of atoms in various electronic configurations, thermalizing on subpicosecond to picosecond timescales after photoexcitation. We present a simulation study of x-ray-heated solid-density matter. For this we use XMDYN, a Monte Carlo molecular-dynamics-based code with periodic boundary conditions, which allows one to investigate nonequilibrium dynamics. XMDYN is capable of treating systems containing light and heavy atomic species with full electronic configuration space and three-dimensional spatial inhomogeneity. For the validation of our approach we compare for a model system the electron temperatures and the ion charge-state distribution from XMDYN to results for the thermalized system based on the average-atom model implemented in XATOM, an ab initio x-ray atomic physics toolkit extended to include a plasma environment. Further, we also compare the average charge evolution of diamond with the predictions of a Boltzmann continuum approach. We demonstrate that XMDYN results are in good quantitative agreement with the above-mentioned approaches, suggesting that the current implementation of XMDYN is a viable approach to simulate the dynamics of x-ray-driven nonequilibrium dynamics in solids. To illustrate the potential of XMDYN for treating complex systems, we present calculations on the triiodo benzene derivative 5-amino-2,4,6-triiodoisophthalic acid (I3C), a compound of relevance of biomolecular imaging, consisting of heavy and light atomic species.

  4. Nonholonomic Hamiltonian method for molecular dynamics simulations of reacting shocks

    NASA Astrophysics Data System (ADS)

    Bass, Joseph; Fahrenthold, Eric P.

    2017-01-01

    Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general the potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new nonholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations, and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted parameters.

  5. Investigation of Ribosomes Using Molecular Dynamics Simulation Methods.

    PubMed

    Makarov, G I; Makarova, T M; Sumbatyan, N V; Bogdanov, A A

    2016-12-01

    The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.

  6. Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems

    PubMed Central

    Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus

    2014-01-01

    Background Molecular Dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Major Conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. General Significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. PMID:25450171

  7. A Molecular Dynamics Simulation of C60-C60 Collision

    NASA Astrophysics Data System (ADS)

    Liu, Lei; Chen, Kaitai; Li, Yufen

    1993-12-01

    The formation process of C120-complex in C60-C60 collision has been clearly demonstrated by a molecular dynamics simulation. The complex, with a peanut-shell-like structure, is in a quite stable dynamical state. The results are consistent with recent observations.

  8. Molecular dynamics simulation of aqueous solutions of glycine betaine

    NASA Astrophysics Data System (ADS)

    Civera, Monica; Fornili, Arianna; Sironi, Maurizio; Fornili, Sandro L.

    2003-01-01

    Molecular dynamics simulation is used to investigate hydration properties of glycine betaine in a large range of solute concentrations. Statistical analyses of the system trajectories evidence microscopic details suggesting an interpretation of experimental results recently obtained for aqueous solutions of trimethylamine- N-oxide, a bioprotectant closely related to glycine betaine.

  9. Semiconductor nanostructure properties. Molecular Dynamic Simulations

    NASA Astrophysics Data System (ADS)

    Podolska, N. I.; Zhmakin, A. I.

    2013-08-01

    The need for research is based on the fact that development of non-planar semiconductor nanosystems and nanomaterials with controlled properties is an important scientific and industrial problem. So, final scientific and technological problem is the creation of adequate modern methods and software for growth and properties simulation and optimization of various III-V (GaAs, InAs, InP, InGaAs etc.) nanostructures (e.g. nanowires) with controlled surface morphology, crystal structure, optical, transport properties etc. Accordingly, now we are developing a specialized computer code for atomistic simulation of structural (distribution of atoms and impurities, elastic and force constants, strain distribution etc.) and thermodynamic (mixing energy, interaction energy, surface energy etc.) properties of the nanostructures. Some simulation results are shown too.

  10. Real-world predictions from ab initio molecular dynamics simulations.

    PubMed

    Kirchner, Barbara; di Dio, Philipp J; Hutter, Jürg

    2012-01-01

    In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.

  11. Solvent-Driven Preferential Association of Lignin with Regions of Crystalline Cellulose in Molecular Dynamics Simulation

    SciTech Connect

    Lindner, Benjamin; Petridis, Loukas; Schulz, Roland; Smith, Jeremy C

    2013-01-01

    The precipitation of lignin onto cellulose after pretreatment of lignocellulosic biomass is an obstacle to economically viable cellulosic ethanol production. Here, 750 ns nonequilibrium molecular dynamics simulations are reported of a system of lignin and cellulose in aqueous solution. Lignin is found to strongly associate with itself and the cellulose. However, noncrystalline regions of cellulose are observed to have a lower tendency to associate with lignin than crystalline regions, and this is found to arise from stronger hydration of the noncrystalline chains. The results suggest that the recalcitrance of crystalline cellulose to hydrolysis arises not only from the inaccessibility of inner fibers but also due to the promotion of lignin adhesion.

  12. Molecular dynamics simulation of crystal growth in Al50Ni50: The generation of defects

    NASA Astrophysics Data System (ADS)

    Kuhn, Philipp; Horbach, Jürgen

    2013-01-01

    The ordering processes in the interface of a solidifying binary alloy (Al50Ni50) are studied by molecular dynamics computer simulation. At various temperatures below the melting point, inhomogeneous systems with planar crystal-melt interfaces in (100) orientation are prepared. The growth of a new crystalline Al or Ni layer proceeds through different time-delayed ordering processes. Before the onset of crystallization, there is a segregation process of Al and Ni atoms in the region where a new layer forms. We show that the interplay between segregation and crystallization supports the formation of a high nonequilibrium concentration of point defects.

  13. Molecular dynamics simulation of propagating cracks

    NASA Technical Reports Server (NTRS)

    Mullins, M.

    1982-01-01

    Steady state crack propagation is investigated numerically using a model consisting of 236 free atoms in two (010) planes of bcc alpha iron. The continuum region is modeled using the finite element method with 175 nodes and 288 elements. The model shows clear (010) plane fracture to the edge of the discrete region at moderate loads. Analysis of the results obtained indicates that models of this type can provide realistic simulation of steady state crack propagation.

  14. Molecular dynamics simulation of propagating cracks

    NASA Technical Reports Server (NTRS)

    Mullins, M.

    1982-01-01

    Steady state crack propagation is investigated numerically using a model consisting of 236 free atoms in two (010) planes of bcc alpha iron. The continuum region is modeled using the finite element method with 175 nodes and 288 elements. The model shows clear (010) plane fracture to the edge of the discrete region at moderate loads. Analysis of the results obtained indicates that models of this type can provide realistic simulation of steady state crack propagation.

  15. New ways to boost molecular dynamics simulations.

    PubMed

    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.

  16. Molecular Dynamics Simulations of Network Glasses

    NASA Astrophysics Data System (ADS)

    Drabold, David A.

    The following sections are included: * Introduction and Background * History and use of MD * The role of the potential * Scope of the method * Use of a priori information * Appraising a model * MD Method * Equations of motion * Energy minimization and equilibration * Deeper or global minima * Simulated annealing * Genetic algorithms * Activation-relaxation technique * Alternate dynamics * Modeling infinite systems: Periodic boundary conditions * The Interatomic Interactions * Overview * Empirical classical potentials * Potentials from electronic structure * The tight-binding method * Approximate methods based on tight-binding * First principles * Local basis: "ab initio tight binding" * Plane-waves: Car-Parrinello methods * Efficient ab initio methods for large systems * The need for locality of electron states in real space * Avoiding explicit orthogonalization * Connecting Simulation to Experiment * Structure * Network dynamics * Computing the harmonic modes * Dynamical autocorrelation functions * Dynamical structure factor * Electronic structure * Density of states * Thermal modulation of the electron states * Transport * Applications * g-GeSe2 * g-GexSe1-x glasses * Amorphous carbon surface * Where to Get Codes to Get Started * Acknowledgments * References

  17. Studying the Unfolding Kinetics of Proteins under Pressure Using Long Molecular Dynamic Simulation Runs

    PubMed Central

    Chara, Osvaldo; Grigera, José Raúl

    2008-01-01

    The usefulness of computational methods such as molecular dynamics simulation has been extensively established for studying systems in equilibrium. Nevertheless, its application to complex non-equilibrium biological processes such as protein unfolding has been generally regarded as producing results which cannot be interpreted straightforwardly. In the present study, we present results for the kinetics of unfolding of apomyoglobin, based on the analysis of long simulation runs of this protein in solution at 3 kbar (1 atm = 1.01325, bar = 101 325 Pa). We hereby demonstrate that the analysis of the data collected within a simulated time span of 0.18 μs suffices for producing results, which coincide remarkably with the available unfolding kinetics experimental data. This not only validates molecular dynamics simulation as a valuable alternative for studying non-equilibrium processes, but also enables a detailed analysis of the actual structural mechanism which underlies the unfolding process of proteins under elusive denaturing conditions such as high pressure. PMID:19669536

  18. Molecular dynamics simulation of interfacial adhesion

    SciTech Connect

    Yarovsky, I.; Chaffee, A.L.

    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.

  19. Free energy of adsorption for a peptide at a liquid/solid interface via nonequilibrium molecular dynamics.

    PubMed

    Mijajlovic, Milan; Penna, Matthew J; Biggs, Mark J

    2013-03-05

    Protein adsorption is of wide interest including in many technological applications such as tissue engineering, nanotechnology, biosensors, drug delivery, and vaccine production among others. Understanding the fundamentals of such technologies and their design would be greatly aided by an ability to efficiently predict the conformation of an adsorbed protein and its free energy of adsorption. In the study reported here, we show that this is possible when data obtained from nonequilibrium thermodynamic integration (NETI) combined with steered molecular dynamics (SMD) is subject to bootstrapping. For the met-enkephalin pentapeptide at a water-graphite interface, we were able to obtain accurate predictions for the location of the adsorbed peptide and its free energy of adsorption from around 50 and 80 SMD simulations, respectively. It was also shown that adsorption in this system is both energetically and entropically driven. The free energy of adsorption was also decomposed into that associated with formation of the cavity in the water near the graphite surface sufficient to accommodate the adsorbed peptide and that associated with insertion of the peptide into this cavity. This decomposition reveals that the former is modestly energetically and entropically unfavorable, whereas the latter is the opposite in both regards to a much greater extent.

  20. Nonequilibrium molecular dynamics study of ring polymer melts under shear and elongation flows: A comparison with their linear analogs

    SciTech Connect

    Yoon, Jeongha; Kim, Jinseong; Baig, Chunggi

    2016-07-15

    We present detailed results for the structural and rheological properties of unknotted and unconcatenated ring polyethylene (PE) melts under shear and elongation flows via direct atomistic nonequilibrium molecular dynamics simulations. Short (C{sub 78}H{sub 156}) and long (C{sub 400}H{sub 800}) ring PE melts were subjected to planar Couette flow (PCF) and planar elongational flow (PEF) across a wide range of strain rates from linear to highly nonlinear flow regimes. The results are analyzed in detail through a direct comparison with those of the corresponding linear polymers. We found that, in comparison to their linear analogs, ring melts possess rather compact chain structures at or near the equilibrium state and exhibit a considerably lesser degree of structural deformation with respect to the applied flow strength under both PCF and PEF. The large structural resistance of ring polymers against an external flow field is attributed to the intrinsic closed-loop configuration of the ring and the topological constraint of nonconcatenation between ring chains in the melt. As a result, there appears to be a substantial discrepancy between ring and linear systems in terms of their structural and rheological properties such as chain orientation, the distribution of chain dimensions, viscosity, flow birefringence, hydrostatic pressure, the pair correlation function, and potential interaction energies. The findings and conclusions drawn in this work would be a useful guide in future exploration of the characteristic dynamical and relaxation mechanisms of ring polymers in bulk or confined systems under flowing conditions.

  1. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: A non-equilibrium molecular dynamics study.

    PubMed

    Lemarchand, Claire A; Bailey, Nicholas P; Todd, Billy D; Daivis, Peter J; Hansen, Jesper S

    2015-06-28

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed.

  2. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: A non-equilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Lemarchand, Claire A.; Bailey, Nicholas P.; Todd, Billy D.; Daivis, Peter J.; Hansen, Jesper S.

    2015-06-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed.

  3. Nonlinear Resonance Artifacts in Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Schlick, Tamar; Mandziuk, Margaret; Skeel, Robert D.; Srinivas, K.

    1998-02-01

    The intriguing phenomenon of resonance, a pronounced integrator-induced corruption of a system's dynamics, is examined for simple molecular systems subject to the classical equations of motion. This source of timestep limitation is not well appreciated in general, and certainly analyses of resonance patterns have been few in connection to biomolecular dynamics. Yet resonances are present in the commonly used Verlet integrator, in symplectic implicit schemes, and also limit the scope of current multiple-timestep methods that are formulated as symplectic and reversible. The only general remedy to date has been to reduce the timestep. For this purpose, we derive method-dependent timestep thresholds (e.g., Tables 1 and 2) that serve as useful guidelines in practice for biomolecular simulations. We also devise closely related symplectic implicit schemes for which the limitation on the discretization stepsize is much less severe. Specifically, we design methods to remove third-order, or both the third- and fourth-order, resonances. These severe low-order resonances can lead to instability or very large energies. Our tests on two simple molecular problems (Morse and Lennard-Jones potentials), as well as a 22-atom molecule, N-acetylalanyl-N '-methylamide, confirm this prediction; our methods can delay resonances so that they occur only at larger timesteps (EW method) or are essentially removed (LIM2 method). Although stable for large timesteps by this approach, trajectories show large energy fluctuations, perhaps due to the coupling with other factors that induce instability in complex nonlinear systems. Thus, the methods developed here may be more useful for conformational sampling of biomolecular structures. The analysis presented here for the blocked alanine model emphasizes that one-dimensional analysis of resonances can be applied to a more complex, multimode system to analyze resonance behavior, but that resonance due to frequency coupling is more complex to pinpoint

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

    SciTech Connect

    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.; Winey, J. Michael; Gupta, Yogendra Mohan; Lane, J. Matthew D.; Ditmire, Todd; Quevedo, Hernan J.

    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.

  5. Nonequilibrium phenomena in N{sub 2}-cluster-surface collisions: A molecular-dynamics study of fragmentation, lateral jetting, and nonequilibrium energy distributions

    SciTech Connect

    Zimmermann, Steffen; Urbassek, Herbert M.

    2006-12-15

    Using molecular-dynamics simulation, we study the impact of (N{sub 2}){sub 2869} clusters on a flat rigid wall. We study the cluster fragmentation process, the formation of lateral jets, the energy redistribution among the resulting fragments, and the ratio of internal and translational energy of the emerging free molecules as a function of cluster impact energy in the range of 0.076-1520 meV/molecule. We find the fragmentation threshold energy to be in agreement with that found previously for (N{sub 2}){sub 13} clusters; the (scaled) number of fragments, however, increases more slowly with impact energy. Also the energy redistribution of the cluster impact energy among the internal and translational energy of the fragments is similar to that found for the small cluster. This means in particular that free molecules show a strong nonequilibrium energy partitioning in which the internal degrees of freedom are considerably less excited than the translational degrees of freedom. We also find that at impact energies above the fragmentation threshold the angular distribution of fragments is peaked parallel to the surface--i.e., the formation of lateral surface jets.

  6. Molecular dynamics simulation of carbon disulphide with a Gaussian correction

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił B. J.

    2017-02-01

    Molecular Dynamics (MD) simulations of liquid carbon disulphide (CS2) in the temperature range 164-318 K under normal pressure and at experimental density were performed using an expa-6 potential with a Gaussian correction plus electrostatic interactions. This correction allowed to modify the curvature of the potential. The results of the MD simulation are compared with available experimental data. The agreement is good.

  7. Molecular dynamics simulation of a nanoscopic nematic twist cell

    NASA Astrophysics Data System (ADS)

    Mirantsev, Leonid V.; Virga, Epifanio G.

    2007-08-01

    We present molecular dynamics simulations of a nanoscopic nematic twist cell confined within two bounding substrates with conflicting anchoring conditions. The results of our simulations show that the torque transmitted through the cell drops significantly below a certain critical cell’s thickness, thus confirming the predictions of the continuum Landau theory extrapolated down to the nanoscopic scale [F. Bisi, E. G. Virga, and G. E. Durand, Phys. Rev. E 70, 042701 (2004)].

  8. Studies of thermal transport properties using molecular dynamics simulation techniques

    NASA Astrophysics Data System (ADS)

    Ratanapisit, Juraivan

    The purpose of this research has been to investigate the transport properties of fluids using novel techniques in molecular dynamics simulations: symplectic integration algorithms for equations of motion, Baranyai's thermostatted fluid wall algorithm, and Rapaport's algorithm for hard chain fluids. In the symplectic integration study, an extensive series of equilibrium molecular dynamic simulations have been performed to investigate the accuracy, stability and efficiency of second order explicit symplectic integrators: position Verlet, velocity Verlet, and the McLauchlan-Atela algorithms. To our knowledge, previous studies of the symplectic integrators have only looked at the thermodynamic energy using a simple model fluid. Our work presents realistic but perhaps the simplest simulations possible to test the effect of the integrators on the three main transport properties. Our results suggest that if an algorithm fails to adequately conserve energy, it will also show significant uncertainties in transport property calculations. A large portion of the simulation study focused on a new algorithm for thermal conductivity based on Baranyai's fluid wall method. This algorithm is stable enough to perform simulations even using large time steps and provides reasonable values and uncertainties for the thermal conductivity. The investigation was conducted using two different thermostat algorithms: the Gaussian and Nosé-Hoover thermostats. The final part of this research focused on the viscosity of hard chain fluids. This study was initiated with an investigation of the equilibrium molecular dynamic simulations of pure hard-sphere molecules. The natural extension of that work was to hard chain fluids. (Abstract shortened by UMI.)

  9. 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).

  10. Molecular dynamics simulations on PGLa using NMR orientational constraints.

    PubMed

    Sternberg, Ulrich; Witter, Raiker

    2015-11-01

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

  11. Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

    PubMed

    Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

    2017-01-01

    Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

  12. Description of ferrocenylalkylthiol SAMs on gold by molecular dynamics simulations.

    PubMed

    Goujon, F; Bonal, C; Limoges, B; Malfreyt, P

    2009-08-18

    Molecular dynamics simulations of mixed monolayers consisting of Fc(CH2)12S-/C10S-Au SAMs are carried out to calculate structural (density profiles, angular distributions, positions of atoms) and energetic properties. The purpose of this paper is to explore the possible inhomogeneity of the neutral ferrocene moieties within the monolayer. Five systems have been studied using different grafting densities for the ferrocenylalkylthiolates. The angular distributions are described in terms of the relative contributions from isolated and clustered ferrocene moieties in the binary SAMs. It is shown that the energetic contributions strongly depend on the state of the ferrocene. The ability of molecular dynamics simulations to enable better understanding the SAM structure is illustrated in this work.

  13. Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.

    SciTech Connect

    Lau, E Y; Krishnan, V V

    2007-07-18

    The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.

  14. Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.

    PubMed

    Omelyan, I P

    2006-09-01

    A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations.

  15. Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates.

    PubMed

    Markegard, Cade B; Mazaheripour, Amir; Jocson, Jonah-Micah; Burke, Anthony M; Dickson, Mary N; Gorodetsky, Alon A; Nguyen, Hung D

    2015-09-03

    Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks.

  16. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

    PubMed

    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.

  17. 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.

  18. Molecular dynamics simulations of ordering of polydimethylsiloxane under uniaxial extension

    SciTech Connect

    Lacevic, N M; Gee, R H

    2005-03-11

    Molecular dynamics simulations of a bulk melts of polydimethylsiloxane (PDMS) are utilized to study chain conformation and ordering under constant uniaxial tension. We find that large extensions induce chain ordering in the direction of applied tension. We also find that voids are created via a cavitation mechanism. This study represents a validation of the current model for PDMS and benchmark for the future study of mechanical properties of PDMS melts enriched with fillers under tension.

  19. Understanding mechanical properties of polymer nanocomposites with molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Sen, Suchira

    Equilibrium Molecular Dynamics (MD) simulations are used extensively to study various aspects of polymer nanocomposite (PNC) behavior in the melt state---the key focus is on understanding mechanisms of mechanical reinforcement. Mechanical reinforcement of the nanocomposite is believed to be caused by the formation of a network-like structure---a result of polymer chains bridging particles to introduce network elasticity. In contrast, in traditional composites, where the particle size range is hundreds of microns and high loadings of particle are used, the dominant mechanism is the formation of a percolated filler structure. The difference in mechanism with varying particle sizes, at similar particle loading, arises from the polymer-particle interfacial area available, which increases dramatically as the particle size decreases. Our interest in this work is to find (a) the kind of polymer-particle interactions necessary to facilitate the formation of a polymer network in a nanocomposite, and (b) the reinforcing characteristics of such a polymer network. We find that very strong polymer-particle binding is necessary to create a reinforcing network. The strength of the binding has to be enough to immobilize polymer on the particle surface for timescales comparable and larger than the terminal relaxation time of the stress of the neat melt. The second finding, which is a direct outcome of very strong binding, is that the method of preparation plays a critical role in determining the reinforcement of the final product. The starting conformations of the polymer chains determine the quality of the network. The strong binding traps the polymer on the particle surface which gets rearranged to a limited extent, within stress relaxation times. Significant aging effects are seen in system relaxation; the inherent non-equilibrium consequences of such strong binding. The effect of the polymer immobilization slows down other relaxation processes. The diffusivity of all chains is

  20. Comparison of the Green-Kubo and homogeneous non-equilibrium molecular dynamics methods for calculating thermal conductivity

    NASA Astrophysics Data System (ADS)

    Dongre, B.; Wang, T.; Madsen, G. K. H.

    2017-07-01

    Different molecular dynamics methods like the direct method, the Green-Kubo (GK) method and homogeneous non-equilibrium molecular dynamics (HNEMD) method have been widely used to calculate lattice thermal conductivity ({κ }{\\ell }). While the first two methods have been used and compared quite extensively, there is a lack of comparison of these methods with the HNEMD method. Focusing on the underlying computational parameters, we present a detailed comparison of the GK and HNEMD methods for both bulk and vacancy Si using the Stillinger-Weber potential. For the bulk calculations, we find both methods to perform well and yield {κ }{\\ell } within acceptable uncertainties. In case of the vacancy calculations, HNEMD method has a slight advantage over the GK method as it becomes computationally cheaper for lower {κ }{\\ell } values. This study could promote the application of HNEMD method in {κ }{\\ell } calculations involving other lattice defects like nanovoids, dislocations, interfaces.

  1. Enhancing protein adsorption simulations by using accelerated molecular dynamics.

    PubMed

    Mücksch, Christian; Urbassek, Herbert M

    2014-01-01

    The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s) and experiment (up to hours), and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.

  2. Enhancing Protein Adsorption Simulations by Using Accelerated Molecular Dynamics

    PubMed Central

    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

  3. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

    PubMed

    De Jong, Djurre H; Schäfer, Lars V; De Vries, Alex H; Marrink, Siewert J; Berendsen, Herman J C; Grubmüller, Helmut

    2011-07-15

    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.

  4. Bulk viscosity of the Lennard-Jones system at the triple point by dynamical nonequilibrium molecular dynamics.

    PubMed

    Palla, Pier Luca; Pierleoni, Carlo; Ciccotti, Giovanni

    2008-08-01

    Nonequilibrium molecular dynamics (NEMD) calculations of the bulk viscosity of the triple point Lennard-Jones fluid are performed with the aim of investigating the origin of the observed disagreement between Green-Kubo estimates and previous NEMD data. We show that a careful application of the Doll's perturbation field, the dynamical NEMD method, the instantaneous form of the perturbation and the "subtraction technique" provides a NEMD estimate of the bulk viscosity at zero field in full agreement with the value obtained by the Green-Kubo formula. As previously reported for the shear viscosity, we find that the bulk viscosity exhibits a large linear regime with the field intensity.

  5. Molecular dynamics simulation of dipalmitoylphosphatidylserine bilayer with Na+ counterions.

    PubMed Central

    Pandit, Sagar A; Berkowitz, Max L

    2002-01-01

    We performed a molecular dynamics simulation of dipalmitoylphosphatidylserine (DPPS) bilayer with Na+ counterions. We found that hydrogen bonding between the NH group and the phosphate group leads to a reduction in the area per headgroup when compared to the area in dipalmitoylphosphatidylcholine bilayer. The Na+ ions bind to the oxygen in the carboxyl group of serine, thus giving rise to a dipolar bilayer similar to dipalmitoylphosphatidylethanolamine bilayer. The results of the simulation show that counterions play a crucial role in determining the structural and electrostatic properties of DPPS bilayer. PMID:11916841

  6. Superionicity in Na3 PO4 : A molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Yin, Wei-Guo; Liu, Jianjun; Duan, Chun-Gang; Mei, W. N.; Smith, R. W.; Hardy, J. R.

    2004-08-01

    Fast ionic conduction in solid Na3PO4 is studied by use of molecular dynamics simulation based on the modified Lu -Hardy approach. We obtain reasonable agreement with experiment for the structural transition and diffusion of the sodium ions. All the sodium ions are found to contribute comparably to the high ionic conductivity. The results of the simulation are discussed in terms of the relative magnitude of the two proposed transport mechanisms: percolation and paddle-wheel. It appears to us that the percolation mechanism dominates the sodium diffusion.

  7. Using collective variables to drive molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme

    2013-12-01

    A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.

  8. Molecular Dynamics Simulations of Gas Transport in Polymer Films

    NASA Astrophysics Data System (ADS)

    Whitley, David; Butler, Simon; Adolf, David

    2010-03-01

    Parallel molecular dynamics simulations have been carried out to determine the permeability of O2 and N2 through polyethylene terephthalate, polypropylene and cis(1-4) polybutadiene. The permeability of both mixed and unmixed gas penetrants is studied within films of these well known gas barrier polymers. Results are obtained either through the solubility and diffusion (i.e. P=D*S) or via the permeability directly. Encouraging results are obtained. Additional analysis focuses on ``unmixed/mixed gas'' intracomparisons of the simulated permeability data in addition to corresponding penetrant and host polymer local dynamics.

  9. Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.

  10. Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.

  11. Molecular dynamics simulation of threshold displacement energies in zircon

    SciTech Connect

    Moreira, Pedro A.; Devanathan, Ramaswami; Yu, Jianguo; Weber, William J.

    2009-10-15

    Molecular-dynamics simulations were used to examine the displacement threshold energy (Ed) surface for Zr, Si and O in zircon using two different interatomic potentials. For each sublattice, the simulation was repeated from different initial conditions to estimate the uncertainty in the calculated value of Ed. The displacement threshold energies vary considerably with crystallographic direction and sublattice. The average displacement energy calculated with a recently developed transferable potential is about 120 and 60 eV for cations and anions, respectively. The oxygen displacement energy shows good agreement with experimental estimates in ceramics.

  12. Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.

    PubMed

    Frank, Martin

    2015-01-01

    Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).

  13. The molecular dynamics simulation of ion-induced ripple growth

    NASA Astrophysics Data System (ADS)

    Süle, P.; Heinig, K.-H.

    2009-11-01

    The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength (λ) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths (λ <35 nm) the adatom yield drops hence no surface diffusion takes place which is sufficient for ripple growth. The MD simulations predict that the growth of ripples with λ >35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in λ long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for λ >35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.

  14. Molecular-dynamics simulation of mechanical alloying for the Al50Ti50 alloy

    NASA Astrophysics Data System (ADS)

    Lu, J.; Szpunar, J. A.

    1993-07-01

    The structural ordering development during mechanical alloying of the Al50Ti50 alloy was investigated by using molecular-dynamics computer simulations. Random external forces with both random orientations and magnitudes were used to simulate the mechanical alloying processes and pseudopotential was used as a model for the interaction between the atoms. The results indicate that the final nonequilibrium phase obtained through simulation of mechanical alloying is an amorphous state which can be formed experimentally in the laboratory. The transformation from crystals to amorphous state may locally be a first-order-like phase transition, but statistically it is a gradual phase transition due to the characteristics of random external forces which help atoms to overcome their energetic barrier during the mechanical alloying. This means that the transformation occurs in random sites and is discontinuous.

  15. Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

    PubMed

    Janowski, Pawel A; Liu, Chunmei; Deckman, Jason; Case, David A

    2016-01-01

    Molecular dynamics simulations of crystals can enlighten interpretation of experimental X-ray crystallography data and elucidate structural dynamics and heterogeneity in biomolecular crystals. Furthermore, because of the direct comparison against experimental data, they can inform assessment of molecular dynamics methods and force fields. We present microsecond scale results for triclinic hen egg-white lysozyme in a supercell consisting of 12 independent unit cells using four contemporary force fields (Amber ff99SB, ff14ipq, ff14SB, and CHARMM 36) in crystalline and solvated states (for ff14SB only). We find the crystal simulations consistent across multiple runs of the same force field and robust to various solvent equilibration schemes. However, convergence is slow compared with solvent simulations. All the tested force fields reproduce experimental structural and dynamic properties well, but Amber ff14SB maintains structure and reproduces fluctuations closest to the experimental model: its average backbone structure differs from the deposited structure by 0.37Å; by contrast, the average backbone structure in solution differs from the deposited by 0.65Å. All the simulations are affected by a small progressive deterioration of the crystal lattice, presumably due to imperfect modeling of hydrogen bonding and other crystal contact interactions; this artifact is smallest in ff14SB, with average lattice positions deviating by 0.20Å from ideal. Side-chain disorder is surprisingly low with fewer than 30% of the nonglycine or alanine residues exhibiting significantly populated alternate rotamers. Our results provide helpful insight into the methodology of biomolecular crystal simulations and indicate directions for future work to obtain more accurate energy models for molecular dynamics. © 2015 The Protein Society.

  16. Reverse Non-Equilibrium Molecular Dynamics Demonstrate That Surface Passivation Controls Thermal Transport at Semiconductor-Solvent Interfaces.

    PubMed

    Hannah, Daniel C; Gezelter, J Daniel; Schaller, Richard D; Schatz, George C

    2015-06-23

    We examine the role played by surface structure and passivation in thermal transport at semiconductor/organic interfaces. Such interfaces dominate thermal transport in semiconductor nanomaterials owing to material dimensions much smaller than the bulk phonon mean free path. Utilizing reverse nonequilibrium molecular dynamics simulations, we calculate the interfacial thermal conductance (G) between a hexane solvent and chemically passivated wurtzite CdSe surfaces. In particular, we examine the dependence of G on the CdSe slab thickness, the particular exposed crystal facet, and the extent of surface passivation. Our results indicate a nonmonotonic dependence of G on ligand-grafting density, with interfaces generally exhibiting higher thermal conductance for increasing surface coverage up to ∼0.08 ligands/Å(2) (75-100% of a monolayer, depending on the particular exposed facet) and decreasing for still higher coverages. By analyzing orientational ordering and solvent penetration into the ligand layer, we show that a balance of competing effects is responsible for this nonmonotonic dependence. Although the various unpassivated CdSe surfaces exhibit similar G values, the crystal structure of an exposed facet nevertheless plays an important role in determining the interfacial thermal conductance of passivated surfaces, as the density of binding sites on a surface determines the ligand-grafting densities that may ultimately be achieved. We demonstrate that surface passivation can increase G relative to a bare surface by roughly 1 order of magnitude and that, for a given extent of passivation, thermal conductance can vary by up to a factor of ∼2 between different surfaces, suggesting that appropriately tailored nanostructures may direct heat flow in an anisotropic fashion for interface-limited thermal transport.

  17. Symplectic molecular dynamics simulations on specially designed parallel computers.

    PubMed

    Borstnik, Urban; Janezic, Dusanka

    2005-01-01

    We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

  18. Petascale Molecular Dynamics Simulations of Polymers and Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Nguyen, Trung Dac; Carrillo, Jan-Michael; Brown, W. Michael

    2014-03-01

    The availability of faster and larger supercomputers and more efficient parallel algorithms now enable us to perform unprecedented simulations approaching experimental scales. Here we present two examples of our latest large-scale molecular dynamics simulations using the Titan supercomputer in the Oak Ridge Leadership Computing Facility (OLCF). In the first study, we address the rupture origin of liquid crystal thin films wetting a solid substrate. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top of thermal nucleation. Importantly, we found evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. In the second study, we used coarse-grained molecular dynamics to simulate the thermal annealing of poly(3-hexylthiophene) (P3HT) and Phenyl-C61-butyric acid methyl ester (PCBM) blends in the presence of a silicon substrate found in organic solar cells. Our simulations show different phase segregated morphologies dependent on the P3HT chain length and PCBM volume fraction in the blend. Furthermore, the ternary blend of short and long P3HT chains with PCBM affects the vertical phase segregation of PCBM decreasing its concentration in the vicinity of the substrate. U.S. DOE Contract No. DE-AC05-00OR22725.

  19. Ice formation on kaolinite: Insights from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Sosso, Gabriele C.; Tribello, Gareth A.; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

    2016-12-01

    The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.

  20. Massively Parallel Reactive and Quantum Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Vashishta, Priya

    2015-03-01

    In this talk I will discuss two simulations: Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near silica surface. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. Quantum molecular dynamics (QMD) simulations are performed on 786,432-processor Blue Gene/Q to study on-demand production of hydrogen gas from water using Al nanoclusters. QMD simulations reveal rapid hydrogen production from water by an Al nanocluster. We find a low activation-barrier mechanism, in which a pair of Lewis acid and base sites on the Aln surface preferentially catalyzes hydrogen production. I will also discuss on-demand production of hydrogen gas from water using and LiAl alloy particles. Research reported in this lecture was carried in collaboration with Rajiv Kalia, Aiichiro Nakano and Ken-ichi Nomura from the University of Southern California, and Fuyuki Shimojo and Kohei Shimamura from Kumamoto University, Japan.

  1. Scaling laws for thermal conductivity of crystalline nanoporous silicon based on molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Fang, Jin; Pilon, Laurent

    2011-09-01

    This study establishes that the effective thermal conductivity keff of crystalline nanoporous silicon is strongly affected not only by the porosity f ν and the system's length Lz but also by the pore interfacial area concentration Ai. The thermal conductivity of crystalline nanoporous silicon was predicted using non-equilibrium molecular dynamics simulations. The Stillinger-Weber potential for silicon was used to simulate the interatomic interactions. Spherical pores organized in a simple cubic lattice were introduced in a crystalline silicon matrix by removing atoms within selected regions of the simulation cell. Effects of the (i) system length ranging from 13 to 130 nm, (ii) pore diameter varying between 1.74 and 5.86 nm, and (iii) porosity ranging from 8% to 38%, on thermal conductivity were investigated. A physics-based model was also developed by combining kinetic theory and the coherent potential approximation. The effective thermal conductivity was proportional to (1 - 1.5f ν) and inversely proportional to the sum (Ai/4 + 1/Lz). This model was in excellent agreement with the thermal conductivity of nanoporous silicon predicted by molecular dynamics simulations for spherical pores (present study) as well as for cylindrical pores and vacancy defects reported in the literature. These results will be useful in designing nanostructured materials with desired thermal conductivity by tuning their morphology.

  2. A multi-scale approach to molecular dynamics simulations of shock waves

    SciTech Connect

    Reed, E J; Fried, L E; Manaa, M R; Joannopoulos, J D

    2004-09-03

    Study of the propagation of shock waves in condensed matter has led to new discoveries ranging from new metastable states of carbon [1] to the metallic conductivity of hydrogen in Jupiter, [2] but progress in understanding the microscopic details of shocked materials has been extremely difficult. Complications can include the unexpected formation of metastable states of matter that determine the structure, instabilities, and time-evolution of the shock wave. [1,3] The formation of these metastable states can depend on the time-dependent thermodynamic pathway that the material follows behind the shock front. Furthermore, the states of matter observed in the shock wave can depend on the timescale on which observation is made. [4,1] Significant progress in understanding these microscopic details has been made through molecular dynamics simulations using the popular non-equilibrium molecular dynamics (NEMD) approach to atomistic simulation of shock compression. [5] The NEMD method involves creating a shock at one edge of a large system by assigning some atoms at the edge a fixed velocity. The shock propagates across the computational cell to the opposite side. The computational work required by NEMD scales at least quadratically in the evolution time because larger systems are needed for longer simulations to prevent the shock wave from reflecting from the edge of the computational cell and propagating back into the cell. When quantum mechanical methods with poor scaling of computational effort with system size are employed, this approach to shock simulations rapidly becomes impossible.

  3. Molecular dynamics simulation of hollow thick-walled cylinder collapse

    SciTech Connect

    Nikonov, A. Yu.

    2015-10-27

    The generation and evolution of plastic deformation in a hollow single-crystal cylinder under high-rate axisymmetric loading were studied. An advantage of the proposed loading scheme is that all loading modes are applied simultaneously within the chosen crystallographic plane of the cylinder base and different strain degrees are achieved along the specimen cross section. Molecular dynamics simulation was performed to show that the achievement of a certain strain causes the formation of structural defects on the inner surface of the specimen. The obtained results can be used to explain the main plastic deformation mechanisms of crystalline solids.

  4. Molecular dynamics simulation of bicrystalline metal surface treatment

    SciTech Connect

    Nikonov, A. Yu.

    2015-10-27

    The paper reports the molecular dynamics simulation results on the behavior of a copper crystallite in local frictional contact. The crystallite has a perfect defect-free structure and contains a high-angle grain boundary of type Σ5. The influence of the initial structure on the specimen behavior under loading was analyzed. It is shown that nanoblocks are formed in the subsurface layer. The atomic mechanism of nanofragmentation was studied. A detailed analysis of atomic displacements in the blocks showed that the displacements are rotational. Calculations revealed that the misorientation angle of formed nanoblocks along different directions does not exceed 2 degrees.

  5. Molecular dynamics simulations studies of laser ablation in metals

    SciTech Connect

    Roth, Johannes; Sonntag, Steffen; Karlin, Johannes; Paredes, Carolina Trichet; Sartison, Marc; Krauss, Armin; Trebin, Hans-Rainer

    2012-07-30

    An overview of several aspects of our recent molecular dynamics simulations of femtosecond laser ablation is presented. This includes the study of phase diagrams for suitable interactions, analysis of ablated material and bubble formation below threshold, study of two-pulse ablation and the classification of materials with respect to electron properties and electron-phonon coupling in the two-temperature model. A treatment of boundary conditions and of an extended twotemperature model is also included. Most of the results apply to aluminum, others also to copper and iron, and to metals in general.

  6. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps.

    PubMed

    Ruggerone, Paolo; Vargiu, Attilio V; Collu, Francesca; Fischer, Nadine; Kandt, Christian

    2013-01-01

    Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

  7. Molecular Dynamics Simulation of Telomere and TRF1

    NASA Astrophysics Data System (ADS)

    Kaburagi, Masaaki; Fukuda, Masaki; Yamada, Hironao; Miyakawa, Takeshi; Morikawa, Ryota; Takasu, Masako; Kato, Takamitsu A.; Uesaka, Mitsuru

    Telomeres play a central role in determining longevity of a cell. Our study focuses on the interaction between telomeric guanines and TRF1 as a means to observe the telomeric based mechanism of the genome protection. In this research, we performed molecular dynamics simulations of a telomeric DNA and TRF1. Our results show a stable structure with a high affinity for the specific protein. Additionally, we calculated the distance between guanines and the protein in their complex state. From this comparison, we found the calculated values of distance to be very similar, and the angle of guanines in their complex states was larger than that in their single state.

  8. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

    NASA Astrophysics Data System (ADS)

    Mugnai, Mauro L.; Elber, Ron

    2015-01-01

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide.

  9. Thermal stability of marks gold nanoparticles: A molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Jia, Yanlin; Li, Siqi; Qi, Weihong; Wang, Mingpu; Li, Zhou; Wang, Zhixing

    2017-03-01

    Molecular dynamics (MDs) simulations were used to explore the thermal stability of Au nanoparticles (NPs) with decahedral, cuboctahedral, icosahedral and Marks NPs. According to the calculated cohesive energy and melting temperature, the Marks NPs have a higher cohesive energy and melting temperature compared to these other shapes. The Lindemann index, radial distribution function, deformation parameters, mean square displacement and self-diffusivity have been used to characterize the structure variation during heating. This work may inspire researchers to prepare Marks NPs and apply them in different fields.

  10. Limits of hardness at the nanoscale: Molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Vo, Nhon Q.; Averback, Robert S.; Bellon, Pascal; Caro, Alfredo

    2008-12-01

    Contrary to the often reported findings from molecular dynamics computer simulation that metals soften as their grain sizes fall below 10-15 nm, we do not observe such softening in nanocrystalline specimens when they are first thermally relaxed. We offer a simple model that illustrates that the increased hardening is a consequence of grain-boundary relaxation, which suppresses grain-boundary sliding and forces the material to deform by dislocation glide. These observations provide an explanation for why some experiments observe an inverse Hall-Petch relationship at grain sizes below 10-20 nm while others do not.

  11. Molecular dynamical simulations of melting behaviors of metal clusters

    SciTech Connect

    Hamid, Ilyar; Fang, Meng; Duan, Haiming

    2015-04-15

    The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002)] for the statically stable structures.

  12. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

    SciTech Connect

    Mugnai, Mauro L.; Elber, Ron

    2015-01-07

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide.

  13. Accelerating ab initio molecular dynamics simulations by linear prediction methods

    NASA Astrophysics Data System (ADS)

    Herr, Jonathan D.; Steele, Ryan P.

    2016-09-01

    Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps' Fock or density matrix elements. In this work, the recursive Burg 'linear prediction' technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8-3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.

  14. Interfacial interaction between polypropylene and nanotube: A molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Danhui; Yang, Houbo; Liu, Zhongkui; Liu, Anmin; Li, Yunfang

    2017-09-01

    The interfacial interaction between polypropylene (PE) and single walled carbon nanotube (SWCNT) was studied using molecular dynamics (MD) simulations. The result showed that the PE chain could stabilize the SWCNT and then extended along the direction of SWCNT. The mechanism of interfacial interaction between PE and SWCNT was also discussed. Furthermore, the interfacial interaction between more PE and SWCNT was also investigated and the position also deeply influenced the interaction. This will be beneficial to understanding the interfacial interaction between polymer and CNT in solution, and also guiding the fabrication of high performance polymer/CNT nanocomposites.

  15. Hypervelocity Impact on Interfaces: A Molecular-Dynamics Simulations Study

    NASA Astrophysics Data System (ADS)

    Bachlechner, Martina E.; Owens, Eli T.; Leonard, Robert H.; Cockburn, Bronwyn C.

    2008-03-01

    Silicon/silicon nitride interfaces are found in micro electronics and solar cells. In either application the mechanical integrity of the interface is of great importance. Molecular-dynamics simulations are performed to study the failure of interface materials under the influence of hypervelocity impact. Silicon nitride plates impacting on silicon/silicon nitride interface targets of different thicknesses result in structural phase transformation and delamination at the interface. Detailed analyses of atomic velocities, bond lengths, and bond angles are used to qualitatively examine the respective failure mechanisms.

  16. Molecular-dynamics simulation of thermal conductivity in amorphous silicon

    NASA Astrophysics Data System (ADS)

    Lee, Young Hee; Biswas, R.; Soukoulis, C. M.; Wang, C. Z.; Chan, C. T.; Ho, K. M.

    1991-03-01

    The temperature-dependent thermal conductivity κ(T) of amorphous silicon has been calculated from equilibrium molecular-dynamics simulations using the time correlations of the heat flux operator in which anharmonicity is explicitly incorporated. The Stillinger-Weber two- and three-body Si potential and the Wooten-Weaire-Winer a-Si model were utilized. The calculations correctly predict an increasing thermal conductivity at low temperatures (below 400 K). The κ(T), for T>400 K, is affected by the thermally generated coordination-defect states. Comparisons to both experiment and previous calculations will be described.

  17. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

    PubMed Central

    Ruggerone, Paolo; Vargiu, Attilio V.; Collu, Francesca; Fischer, Nadine; Kandt, Christian

    2013-01-01

    Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa. PMID:24688701

  18. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.

    PubMed

    Mugnai, Mauro L; Elber, Ron

    2015-01-07

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system-the diffusion along the backbone torsions of a solvated alanine dipeptide.

  19. Molecular dynamics simulations of high speed rarefied gas flows

    NASA Astrophysics Data System (ADS)

    Dongari, Nishanth; Zhang, Yonghao; Reese, Jason M.

    2012-11-01

    To understand the molecular behaviour of gases in high speed rarefied conditions, we perform molecular dynamics (MD) numerical experiments using the open source code Open FOAM. We use shear-driven Couette flows as test cases, where the two parallel plates are moving with a speed of Uw in opposite directions with their temperatures set to Tw. The gas rarefaction conditions vary from slip to transition, and compressibility conditions vary from low speed isothermal to hypersonic flow regimes, i.e. Knudsen number (Kn) from 0.01 to 1 and Mach number (Ma) from 0.05 to 10. We measure the molecular velocity distribution functions, the spatial variation of gas mean free path profiles and other macroscopic properties. Our MD results convey that flow properties in the near-wall non-equilibrium region do not merely depend on Kn, but they are also significantly affected by Ma. These results may yield new insight into diffusive transport in rarefied gases at high speeds.

  20. Semi-analytical solution for the generalized absorbing boundary condition in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lee, Chung-Shuo; Chen, Yan-Yu; Yu, Chi-Hua; Hsu, Yu-Chuan; Chen, Chuin-Shan

    2017-02-01

    We present a semi-analytical solution of a time-history kernel for the generalized absorbing boundary condition in molecular dynamics (MD) simulations. To facilitate the kernel derivation, the concept of virtual atoms in real space that can conform with an arbitrary boundary in an arbitrary lattice is adopted. The generalized Langevin equation is regularized using eigenvalue decomposition and, consequently, an analytical expression of an inverse Laplace transform is obtained. With construction of dynamical matrices in the virtual domain, a semi-analytical form of the time-history kernel functions for an arbitrary boundary in an arbitrary lattice can be found. The time-history kernel functions for different crystal lattices are derived to show the generality of the proposed method. Non-equilibrium MD simulations in a triangular lattice with and without the absorbing boundary condition are conducted to demonstrate the validity of the solution.

  1. Osmotic and diffusio-osmotic flow generation at high solute concentration. II. Molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Yoshida, Hiroaki; Marbach, Sophie; Bocquet, Lydéric

    2017-05-01

    In this paper, we explore osmotic transport by means of molecular dynamics (MD) simulations. We first consider osmosis through a membrane and investigate the reflection coefficient of an imperfectly semi-permeable membrane, in the dilute and high concentration regimes. We then explore the diffusio-osmotic flow of a solute-solvent fluid adjacent to a solid surface, driven by a chemical potential gradient parallel to the surface. We propose a novel non-equilibrium MD (NEMD) methodology to simulate diffusio-osmosis, by imposing an external force on every particle, which properly mimics the chemical potential gradient on the solute in spite of the periodic boundary conditions. This NEMD method is validated theoretically on the basis of linear-response theory by matching the mobility with their Green-Kubo expressions. Finally, we apply the framework to more realistic systems, namely, a water-ethanol mixture in contact with a silica or a graphene surface.

  2. Semi-analytical solution for the generalized absorbing boundary condition in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lee, Chung-Shuo; Chen, Yan-Yu; Yu, Chi-Hua; Hsu, Yu-Chuan; Chen, Chuin-Shan

    2017-07-01

    We present a semi-analytical solution of a time-history kernel for the generalized absorbing boundary condition in molecular dynamics (MD) simulations. To facilitate the kernel derivation, the concept of virtual atoms in real space that can conform with an arbitrary boundary in an arbitrary lattice is adopted. The generalized Langevin equation is regularized using eigenvalue decomposition and, consequently, an analytical expression of an inverse Laplace transform is obtained. With construction of dynamical matrices in the virtual domain, a semi-analytical form of the time-history kernel functions for an arbitrary boundary in an arbitrary lattice can be found. The time-history kernel functions for different crystal lattices are derived to show the generality of the proposed method. Non-equilibrium MD simulations in a triangular lattice with and without the absorbing boundary condition are conducted to demonstrate the validity of the solution.

  3. Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

    PubMed

    Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao

    2017-08-24

    Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Copyright © 2017. Published by Elsevier Ltd.

  4. Molecular-dynamics simulation of thin-film growth

    NASA Astrophysics Data System (ADS)

    Schneider, M.; Schuller, I. K.; Rahman, A.

    1987-01-01

    The epitaxial growth of thin films has been studied by molecular-dynamics computer simulation. In these simulations atoms are projected towards a temperature-controlled substrate, and the equations of motion of all atoms are solved for a given interaction potential. The calculations give insight into the microscopic structure of thin films, the dynamics of the adsorption process, and they help answer the way in which substrate temperature, form of the substrate, flux of impinging atoms, and form of the interaction potential, affect epitaxial growth. Simulations were performed for monatomic and binary systems with spherically symmetric atomic interactions, and for systems in which the atoms are interacting via a three-body potential to simulate the epitaxial growth of silicon.

  5. Molecular dynamics simulation of amplitude modulation atomic force microscopy.

    PubMed

    Hu, Xiaoli; Egberts, Philip; Dong, Yalin; Martini, Ashlie

    2015-06-12

    Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip-substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip-sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement.

  6. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    NASA Technical Reports Server (NTRS)

    Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

    2000-01-01

    We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

  7. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    NASA Technical Reports Server (NTRS)

    Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

    2000-01-01

    We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

  8. Molecular-dynamics simulation of a ceramide bilayer

    NASA Astrophysics Data System (ADS)

    Pandit, Sagar A.; Scott, H. Larry

    2006-01-01

    Ceramide is the simplest lipid in the biologically important class of glycosphingolipids. Ceramide is an important signaling molecule and a major component of the strateum corneum layer in the skin. In order to begin to understand the biophysical properties of ceramide, we have carried out a molecular-dynamics simulation of a hydrated 16:0 ceramide lipid bilayer at 368K (5° above the main phase transition). In this paper we describe the simulation and present the resulting properties of the bilayer. We compare the properties of the simulated ceramide bilayer to an earlier simulation of 18:0 sphingomyelin, and we discuss the results as they relate to experimental data for ceramide and other sphingolipids. The most significant differences arise at the lipid/water interface, where the lack of a large ceramide polar group leads to a different electron density and a different electrostatic potential but, surprisingly, not a different overall "dipole potential," when ceramide is compared to sphingomyelin.

  9. Molecular Dynamics Simulation of Binary Fluid in a Nanochannel

    SciTech Connect

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

    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.

  10. Molecular dynamics simulation of TCDD adsorption on organo-montmorillonite.

    PubMed

    Zhu, Runliang; Hu, Wenhao; You, Zhimin; Ge, Fei; Tian, Kaixun

    2012-07-01

    In this work, molecular dynamics simulation was applied to investigate the adsorption of Tetrachlorodibenzo-p-Dioxin (TCDD) on tetramethylammonium (TMA) and tetrapropylammonium (TPA) modified montmorillonite, with the aim of providing novel information for understanding the adsorptive characteristics of organo-montmorillonite toward organic contaminants. The simulation results showed that on both outer surface and interlayer space of TPA modified montmorillonite (TPA-mont), TCDD was adsorbed between the TPA cations with the molecular edge facing siloxane surface. Similar result was observed for the adsorption on the outer surface of TMA modified montmorillonite (TMA-mont). These results indicated that TCDD had stronger interaction with organic cation than with siloxane surface. While in the interlayer space of TMA-mont, TCDD showed a coplanar orientation with the siloxane surfaces, which could be ascribed to the limited gallery height within TMA-mont interlayer. Comparing with TMA-mont, TPA-mont had larger adsorption energy toward TCDD but smaller interlayer space to accommodate TCDD. Our results indicated that molecular dynamics simulation can be a powerful tool in characterizing the adsorptive characteristics of organoclays and provided additional proof that for the organo-montmorillonite synthesized with small organic cations, the available interlayer space rather than the attractive force plays the dominant role for their adsorption capacity toward HOCs.

  11. Molecular dynamic simulations of the water absorbency of hydrogels.

    PubMed

    Ou, Xiang; Han, Qiang; Dai, Hui-Hui; Wang, Jiong

    2015-09-01

    A polymer gel can imbibe solvent molecules through surface tension effect. When the solvent happens to be water, the gel can swell to a large extent and forms an aggregate called hydrogel. The large deformation caused by such swelling makes it difficult to study the behaviors of hydrogels. Currently, few molecular dynamic simulation works have been reported on the water absorbing mechanism of hydrogels. In this paper, we first use molecular dynamic simulation to study the water absorbing mechanism of hydrogels and propose a hydrogel-water interface model to study the water absorbency of the hydrogel surface. Also, the saturated water content and volume expansion rate of the hydrogel are investigated by building a hydrogel model with different cross-linking degree and by comparing the water absorption curves under different temperatures. The sample hydrogel model used consists of Polyethylene glycol diglycidyl ether (PEGDGE) as epoxy and the Jeffamine, poly-oxy-alkylene-amines, as curing agent. The conclusions obtained are useful for further investigation on PEGDGE/Jeffamine hydrogel. Moreover, the simulation methods, including hydrogel-water interface modeling, we first propose are also suitable to study the water absorbing mechanism of other hydrogels.

  12. Molecular dynamics simulations through GPU video games technologies

    PubMed Central

    Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia

    2016-01-01

    Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251

  13. Molecular dynamics simulations through GPU video games technologies.

    PubMed

    Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia

    Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations.

  14. Trypsinogen activation as observed in accelerated molecular dynamics simulations

    PubMed Central

    Boechi, Leonardo; Pierce, Levi; Komives, Elizabeth A; McCammon, J Andrew

    2014-01-01

    Serine proteases are involved in many fundamental physiological processes, and control of their activity mainly results from the fact that they are synthetized in an inactive form that becomes active upon cleavage. Three decades ago Martin Karplus’s group performed the first molecular dynamics simulations of trypsin, the most studied member of the serine protease family, to address the transition from the zymogen to its active form. Based on the computational power available at the time, only high frequency fluctuations, but not the transition steps, could be observed. By performing accelerated molecular dynamics (aMD) simulations, an interesting approach that increases the configurational sampling of atomistic simulations, we were able to observe the N-terminal tail insertion, a crucial step of the transition mechanism. Our results also support the hypothesis that the hydrophobic effect is the main force guiding the insertion step, although substantial enthalpic contributions are important in the activation mechanism. As the N-terminal tail insertion is a conserved step in the activation of serine proteases, these results afford new perspective on the underlying thermodynamics of the transition from the zymogen to the active enzyme. PMID:25131668

  15. Ab initio molecular dynamics simulations of nitromethane under shock initiation conditions

    NASA Astrophysics Data System (ADS)

    Decker, S. A.; Chau, D.; Woo, T. K.; Zhang, F.

    Detonation theories for homogeneous, condensed energetic materials have focused on 1-d analysis in which the detonation ignition physics forms the most difficult part. The classic ZND model considers detonation ignition through a frozen shock transition followed by an induction period, in which the shock temperature induces vibrational, rotational and electronic excitation followed by molecular dissociation (i.e., thermal decomposition). The frozen shock assumption has been the topic of debate and an alternative model has been proposed whereby detonation ignition arises from excitation of the translational degrees of freedom in the shock front [1]. This raises an important postulation of detonation ignition of molecular condensed matter being initiated by non-equilibrium kinetic events within the shock front rather than equilibrium thermal molecular dissociation due to the shock temperature. Experimental support for this hypothesis must be derived from observations inside the shock front thereby requiring measurements on the time scale of 10-2-1 ps, which remains beyond the scope of current experimental techniques. However, the recent development of ab initio molecular dynamics simulations offers an alternative approach to elucidate possible mechanisms of detonation ignition. These methods are based on first-principle quantum mechanical calculations that allow for the simulation of chemical processes at the atomic level. Molecular dynamics simulations of bimolecular collisions using density functional theories serve as a most simplified model for shock-induced dissociation [2-3], while multimolecular collisions including neighbourhood molecules serve as a simple model for shock dissociation in bulk liquid [4].

  16. Molecular dynamics simulation of rupture in glassy polymer bridges within filler aggregates

    NASA Astrophysics Data System (ADS)

    Froltsov, Vladimir A.; Klüppel, Manfred; Raos, Guido

    2012-10-01

    We present a series of nonequilibrium molecular dynamics simulations, investigating the rupture mechanisms in glassy polymer films confined between two solid surfaces. Such systems provide a useful model for the strong nonlinear reinforcement of rubber by colloidal filler particles. Depending on the degree of confinement three qualitatively different rupture modes have been found, which originate from the interplay of internal (polymer-polymer) and external (polymer-wall) interactions. In very thin films we observe the formation and stretching of many single-chain bridges between the confining surfaces. Progressing to thicker samples we observe fewer bridges, consisting of bundled polymer chains, and eventually just one large bridge in thick specimens. The yield stress and the elongational modulus of the polymer films have been calculated from the stress-strain curves at various temperatures and confinements and their behavior has been analyzed in terms of polymer-polymer and polymer-surface interaction energies. The thinnest films (5 monomer diameters) are always glassy in our simulations, while the others display a glass transition temperature around 0.50-0.55 (in units ɛ0/kB of the Lennard-Jones interaction energy), depending on their thickness. This range of values, which has been determined using both the nonequilibrium tensile simulations and equilibrium diffusion data, agrees with the transition temperature previously found by shear simulations [Baljon and Robbins, ScienceSCIEAS0036-807510.1126/science.271.5248.482 271, 482 (1996)].

  17. Molecular dynamics simulation of rupture in glassy polymer bridges within filler aggregates.

    PubMed

    Froltsov, Vladimir A; Klüppel, Manfred; Raos, Guido

    2012-10-01

    We present a series of nonequilibrium molecular dynamics simulations, investigating the rupture mechanisms in glassy polymer films confined between two solid surfaces. Such systems provide a useful model for the strong nonlinear reinforcement of rubber by colloidal filler particles. Depending on the degree of confinement three qualitatively different rupture modes have been found, which originate from the interplay of internal (polymer-polymer) and external (polymer-wall) interactions. In very thin films we observe the formation and stretching of many single-chain bridges between the confining surfaces. Progressing to thicker samples we observe fewer bridges, consisting of bundled polymer chains, and eventually just one large bridge in thick specimens. The yield stress and the elongational modulus of the polymer films have been calculated from the stress-strain curves at various temperatures and confinements and their behavior has been analyzed in terms of polymer-polymer and polymer-surface interaction energies. The thinnest films (5 monomer diameters) are always glassy in our simulations, while the others display a glass transition temperature around 0.50-0.55 (in units ε(0)/k(B) of the Lennard-Jones interaction energy), depending on their thickness. This range of values, which has been determined using both the nonequilibrium tensile simulations and equilibrium diffusion data, agrees with the transition temperature previously found by shear simulations [Baljon and Robbins, Science 271, 482 (1996)].

  18. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    SciTech Connect

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

    1994-12-31

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

  19. Lightweight computational steering of very large scale molecular dynamics simulations

    SciTech Connect

    Beazley, D.M.; Lomdahl, P.S.

    1996-09-01

    We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.

  20. A molecular dynamics simulation study of coaxial stacking in RNA.

    PubMed

    Schneider, C; Sühnel, J

    2000-12-01

    We report on unrestrained molecular dynamics simulations of an RNA tetramer binding to a tetra-nucleotide overhang at the 5'-end of an RNA hairpin (nicked structure) and of the corresponding continuous hairpin with Na+ as counterions. The simulations lead to stable structures and in this way a structural model for the coaxially stacked RNA hairpin is generated. The stacking interface in the coaxially stacked nicked hairpin structure is characterized by a reduced twist and shift and a slightly increased propeller twist as compared to the continuous system. This leads to an increased overlap between C22 and G23 in the stacking interface of the nicked structure. In the simulations the continuous RNA hairpin has an almost straight helical axis. On the other hand, the corresponding axis for the nicked structure exhibits a marked kink of 39 degrees. The stacking interface exhibits no increased flexibility as compared to the corresponding base pair step in the continuous structure.

  1. Molecular dynamics simulation of gold cluster growth during sputter deposition

    NASA Astrophysics Data System (ADS)

    Abraham, J. W.; Strunskus, T.; Faupel, F.; Bonitz, M.

    2016-05-01

    We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.

  2. Comment on molecular dynamics simulations of monolayers of fluorinated amphiphiles

    NASA Astrophysics Data System (ADS)

    Shin, Seokmin; Collazo, Nancy; Rice, Stuart A.

    1993-02-01

    We report the results of new molecular dynamics simulations of liquid-supported monolayers of perfluorinated and partially fluorinated amphiphiles such as F(CF2)11COOH and F(CF2)10CH2COOH. The new simulations include a representation of the superhelical structure of the perfluoroalkane portion of the amphiphile chain in the intramolecular potential energy; in addition, the calculation of the collective tilt angle of the monolayer is improved to include the effect of the azimuthal distribution of individual molecular tilt angles. The results of the simulations are in agreement with the available experimental data. In particular, the packing structure and the observed breakup of the homogeneous ordered monolayer into ordered islands with the same collective tilt of the molecules are correctly predicted as are the very small collective tilt angles. These new results remove the discrepancy between predicted and observed collective tilt angles reported in our previous papers [J. Chem. Phys. 96, 1352, 4735 (1992)].

  3. Molecular dynamics simulation of gold cluster growth during sputter deposition

    SciTech Connect

    Abraham, J. W. Bonitz, M.; Strunskus, T.; Faupel, F.

    2016-05-14

    We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.

  4. Network Visualization of Conformational Sampling during Molecular Dynamics Simulation

    PubMed Central

    Ahlstrom, Logan S.; Baker, Joseph Lee; Ehrlich, Kent; Campbell, Zachary T.; Patel, Sunita; Vorontsov, Ivan I.; Tama, Florence; Miyashita, Osamu

    2013-01-01

    Effective data reduction methods are necessary for uncovering the inherent conformational relationships present in large molecular dynamics (MD) trajectories. Clustering algorithms provide a means to interpret the conformational sampling of molecules during simulation by grouping trajectory snapshots into a few subgroups, or clusters, but the relationships between the individual clusters may not be readily understood. Here we show that network analysis can be used to visualize the dominant conformational states explored during simulation as well as the connectivity between them, providing a more coherent description of conformational space than traditional clustering techniques alone. We compare the results of network visualization against 11 clustering algorithms and principal component conformer plots. Several MD simulations of proteins undergoing different conformational changes demonstrate the effectiveness of networks in reaching functional conclusions. PMID:24211466

  5. A hybrid algorithm for parallel molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mangiardi, Chris M.; Meyer, R.

    2017-10-01

    This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

  6. Molecular dynamics simulation of friction of hydrocarbon thin films

    SciTech Connect

    Tamura, Hiroyuki; Yoshida, Muneo; Kusakabe, Kenichi

    1999-10-26

    Molecular Dynamics (MD) simulations were performed to investigate the dynamic behavior of hydrocarbon molecules under shear conditions. Frictional properties of cyclohexane, n-hexane, and iso-hexane thin films confirmed between two solid surfaces were calculated. Because the affinity of the solid surfaces in these simulations is strong, slippages occurred at inner parts of the confined films, whereas no slippages were observed at the solid boundaries. The hexagonal closest packing structure was observed for the adsorbed cyclohexane molecular layers. The branched methyl groups in the iso-hexane molecules increase the shear stress between the molecular layers. For the n-hexane monolayer, molecules were observed to roll during the sliding simulations. Rolling of the n-hexane molecules decreased the shear stress.

  7. Molecular Dynamics Simulation of Iron — A Review

    NASA Astrophysics Data System (ADS)

    Chui, C. P.; Liu, Wenqing; Xu, Yongbing; Zhou, Yan

    2015-12-01

    Molecular dynamics (MD) is a technique of atomistic simulation which has facilitated scientific discovery of interactions among particles since its advent in the late 1950s. Its merit lies in incorporating statistical mechanics to allow for examination of varying atomic configurations at finite temperatures. Its contributions to materials science from modeling pure metal properties to designing nanowires is also remarkable. This review paper focuses on the progress of MD in understanding the behavior of iron — in pure metal form, in alloys, and in composite nanomaterials. It also discusses the interatomic potentials and the integration algorithms used for simulating iron in the literature. Furthermore, it reveals the current progress of MD in simulating iron by exhibiting some results in the literature. Finally, the review paper briefly mentions the development of the hardware and software tools for such large-scale computations.

  8. Molecular dynamics simulations of solutions at constant chemical potential

    NASA Astrophysics Data System (ADS)

    Perego, C.; Salvalaglio, M.; Parrinello, M.

    2015-04-01

    Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

  9. Molecular Dynamics Simulation of Carbon Nanotube Based Gears

    NASA Technical Reports Server (NTRS)

    Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)

    1996-01-01

    We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.

  10. 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 α-helical structure to random coil, without indication of any significant β-strand. For dimers, by contrast, starting from random structures, we observe spontaneous formation of antiparallel β-sheets and triangular and circular β-helical structures for polyglutamine with 40 residues in a 400 ns 50 temperature replica-exchange molecular dynamics simulation (total integrated time 20 μs). 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.

  11. Molecular Dynamics Simulation of Carbon Nanotube Based Gears

    NASA Technical Reports Server (NTRS)

    Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)

    1996-01-01

    We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.

  12. Dihedral angle principal component analysis of molecular dynamics simulations.

    PubMed

    Altis, Alexandros; Nguyen, Phuong H; Hegger, Rainer; Stock, Gerhard

    2007-06-28

    It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements. To account for the circular statistics of angular variables, a transformation from the space of dihedral angles {phi(n)} to the metric coordinate space {x(n)=cos phi(n),y(n)=sin phi(n)} was employed. To study the validity and the applicability of the approach, in this work the theoretical foundations underlying the dihedral angle principal component analysis (dPCA) are discussed. It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide. Furthermore, a complex version of the dPCA is introduced, in which N angular variables naturally lead to N eigenvalues and eigenvectors. Applying the methodology to the construction of the free energy landscape of decaalanine from a 300 ns molecular dynamics simulation, a critical comparison of the various methods is given.

  13. Molecular dynamics simulation of amorphous SiO2 nanoparticles.

    PubMed

    Hoang, Vo Van

    2007-11-08

    Molecular dynamics simulation of amorphous SiO2 spherical nanoparticles has been carried out in a model with different sizes, 2, 4, and 6 nm, under non-periodic boundary conditions. We use the pair interatomic potentials which have weak Coulomb interaction and Morse type short-range interaction. Models have been obtained by cooling from the melt via molecular dynamics (MD) simulation. Structural properties of amorphous nanoparticles obtained at 350 K have been studied via partial radial distribution functions (PRDFs), mean interatomic distances, coordination numbers, and bond-angle distributions, which are compared with those observed in the bulk. Calculations of the radial density profile in nanoparticles show the tendency of oxygen to concentrate at the surface as observed previously in other amorphous clusters or thin films. Size effects on structure of nanosized models are significant. The calculations show that if the size is larger than 4 nm, amorphous SiO2 nanoparticles have a distorted tetrahedral network structure with the mean coordination number ZSi-O approximately 4.0 and ZO-Si approximately 2.0 like those observed in the bulk. Surface structure, surface energy, and glass transition temperature of SiO2 nanoparticles have been obtained and presented.

  14. Molecular Dynamics Simulations of Adhesion at Epoxy Interfaces

    NASA Technical Reports Server (NTRS)

    Frankland, Sarah-Jane V.; Clancy, Thomas C.; Hinkley, J. A.; Gates. T. S.

    2008-01-01

    The effect of moisture on adhesives used in aerospace applications can be modeled with chemically specific techniques such as molecular dynamics simulation. In the present study, the surface energy and work of adhesion are calculated for epoxy surfaces and interfaces, respectively, by using molecular dynamics simulation. Modifications are made to current theory to calculate the work of adhesion at the epoxy-epoxy interface with and without water. Quantitative agreement with experimental values is obtained for the surface energy and work of adhesion at the interface without water. The work of adhesion agrees qualitatively with the experimental values for the interface with water: the magnitude is reduced 15% with respect to the value for the interface without water. A variation of 26% in the magnitude is observed depending on the water configuration at a concentration of 1.6 wt%. The methods and modifications to the method that are employed to obtain these values are expected to be applicable for other epoxy adhesives to determine the effects of moisture uptake on their work of adhesion.

  15. Enhanced heat transfer through filler-polymer interface by surface-coupling agent in heat-dissipation material: A non-equilibrium molecular dynamics study

    SciTech Connect

    Tanaka, Kouichi; Ogata, Shuji; Kobayashi, Ryo; Tamura, Tomoyuki; Kitsunezuka, Masashi; Shinma, Atsushi

    2013-11-21

    Developing a composite material of polymers and micrometer-sized fillers with higher heat conductance is crucial to realize modular packaging of electronic components at higher densities. Enhancement mechanisms of the heat conductance of the polymer-filler interfaces by adding the surface-coupling agent in such a polymer composite material are investigated through the non-equilibrium molecular dynamics (MD) simulation. A simulation system is composed of α-alumina as the filler, bisphenol-A epoxy molecules as the polymers, and model molecules for the surface-coupling agent. The inter-atomic potential between the α-alumina and surface-coupling molecule, which is essential in the present MD simulation, is constructed to reproduce the calculated energies with the electronic density-functional theory. Through the non-equilibrium MD simulation runs, we find that the thermal resistance at the interface decreases significantly by increasing either number or lengths of the surface-coupling molecules and that the effective thermal conductivity of the system approaches to the theoretical value corresponding to zero thermal-resistance at the interface. Detailed analyses about the atomic configurations and local temperatures around the interface are performed to identify heat-transfer routes through the interface.

  16. Molecular dynamics simulations of hydrogen diffusion in aluminum

    SciTech Connect

    Zhou, X. W.; El Gabaly, F.; Stavila, V.; Allendorf, M. D.

    2016-03-23

    In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear how they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.

  17. Molecular dynamics simulations of hydrogen diffusion in aluminum

    DOE PAGES

    Zhou, X. W.; El Gabaly, F.; Stavila, V.; ...

    2016-03-23

    In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear howmore » they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.« less

  18. Crossover from equilibration to aging: Nonequilibrium theory versus simulations

    NASA Astrophysics Data System (ADS)

    Mendoza-Méndez, P.; Lázaro-Lázaro, E.; Sánchez-Díaz, L. E.; Ramírez-González, P. E.; Pérez-Ángel, G.; Medina-Noyola, M.

    2017-08-01

    Understanding glasses and the glass transition requires comprehending the nature of the crossover from the ergodic (or equilibrium) regime, in which the stationary properties of the system have no history dependence, to the mysterious glass transition region, where the measured properties are nonstationary and depend on the protocol of preparation. In this work we use nonequilibrium molecular dynamics simulations to test the main features of the crossover predicted by the molecular version of the recently developed multicomponent nonequilibrium self-consistent generalized Langevin equation theory. According to this theory, the glass transition involves the abrupt passage from the ordinary pattern of full equilibration to the aging scenario characteristic of glass-forming liquids. The same theory explains that this abrupt transition will always be observed as a blurred crossover due to the unavoidable finiteness of the time window of any experimental observation. We find that within their finite waiting-time window, the simulations confirm the general trends predicted by the theory.

  19. Flow alignment phenomena in liquid crystals studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Sarman, Sten; Laaksonen, Aatto

    2009-10-01

    The flow alignment of a nematic liquid crystal has been studied as a function of temperature, beginning at high temperature in the nematic phase and down to the nematic-smectic A phase transition. The alignment angle is obtained by estimating the twist viscosities by nonequilibrium molecular dynamics (NEMD) methods. These estimates are cross-checked by evaluating the corresponding equilibrium fluctuation relations. As a further comparison, shear flow simulations are carried out by application of the SLLOD equations of motion (so named because of their close relationship to the Doll's equation of motion, which can be derived from the Doll's tensor Hamiltonian), whereby the alignment angle is obtained directly. All these methods give consistent results for the alignment angle. At low temperatures near the nematic-smectic A transition the system becomes flow unstable. In this region the alignment angle has been calculated as a function of time.

  20. Hot spot and temperature analysis of shocked hydrocarbon polymer foams using molecular dynamics simulation

    SciTech Connect

    Lane, J. Matthew D.; Grest, Gary S.; Mattsson, Thomas R.

    2013-11-01

    Hydrocarbon polymers, foams and nanocomposites are increasingly being subjected to extreme environments. Molecular scale modeling of these materials offers insight into failure mechanisms and complex response. Prior classical molecular dynamics (MD) simulations of the principal shock Hugoniot for two hydrocarbon polymers, polyethylene (PE) and poly (4-methyl-1-pentene) (PMP) have shown good agreement with density functional theory (DFT) calculations and experiments conducted at Sandia National Laboratories. We extended these results to include low-density polymer foams using nonequilibrium MD techniques and found good quantitative agreement with experiment. Here, we have measured the local temperature during void collapse to investigate the formation of hot spots and their relationship to polymer dissociation in foams.

  1. Molecular dynamics simulation of effective thermal conductivity of vapor-filled nanogap and nanocavity

    NASA Astrophysics Data System (ADS)

    Hwang, G. S.; Kaviany, M.

    2009-07-01

    The effect of adsorption on momentum au and thermal aT accommodation coefficients and effective thermal conductivity ⟨kf⟩ of Ar vapor-filled Pt nanogap and nanocavity is examined using nonequilibrium molecular dynamics (MD) simulations. For the accommodation coefficients, the increase in solid-fluid or fluid-fluid interatomic interactions within adsorbed layer causes transitions in magnitudes of au and aT near Ar triple-point temperature. In the nanogap, ⟨kf⟩ MD results are in close agreement with the available closed-form solution for transition-flow regime, i.e., Knudsen number 0.1

  2. Unraveling Hydrophobic Interactions at the Molecular Scale Using Force Spectroscopy and Molecular Dynamics Simulations.

    PubMed

    Stock, Philipp; Monroe, Jacob I; Utzig, Thomas; Smith, David J; Shell, M Scott; Valtiner, Markus

    2017-03-28

    Interactions between hydrophobic moieties steer ubiquitous processes in aqueous media, including the self-organization of biologic matter. Recent decades have seen tremendous progress in understanding these for macroscopic hydrophobic interfaces. Yet, it is still a challenge to experimentally measure hydrophobic interactions (HIs) at the single-molecule scale and thus to compare with theory. Here, we present a combined experimental-simulation approach to directly measure and quantify the sequence dependence and additivity of HIs in peptide systems at the single-molecule scale. We combine dynamic single-molecule force spectroscopy on model peptides with fully atomistic, both equilibrium and nonequilibrium, molecular dynamics (MD) simulations of the same systems. Specifically, we mutate a flexible (GS)5 peptide scaffold with increasing numbers of hydrophobic leucine monomers and measure the peptides' desorption from hydrophobic self-assembled monolayer surfaces. Based on the analysis of nonequilibrium work-trajectories, we measure an interaction free energy that scales linearly with 3.0-3.4 kBT per leucine. In good agreement, simulations indicate a similar trend with 2.1 kBT per leucine, while also providing a detailed molecular view into HIs. This approach potentially provides a roadmap for directly extracting qualitative and quantitative single-molecule interactions at solid/liquid interfaces in a wide range of fields, including interactions at biointerfaces and adhesive interactions in industrial applications.

  3. Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

    PubMed Central

    2015-01-01

    Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron–sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specific interactions that occur in its catalytic center. The results suggest that the architecture of the active site is stabilized by key hydrogen bonds, and Asn258 positions the substrate for oxidation. Analysis of protein–water interactions reveal the presence of a network of solvent molecules at the entrance to the active site, which could be of potential catalytic importance. PMID:24955078

  4. Temperature fluctuations in canonical systems: Insights from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Hickman, J.; Mishin, Y.

    2016-11-01

    Molecular dynamics simulations of a quasiharmonic solid are conducted to elucidate the meaning of temperature fluctuations in canonical systems and validate a well-known but frequently contested equation predicting the mean square of such fluctuations. The simulations implement two virtual and one physical (natural) thermostat and examine the kinetic, potential, and total energy correlation functions in the time and frequency domains. The results clearly demonstrate the existence of quasiequilibrium states in which the system can be characterized by a well-defined temperature that follows the mentioned fluctuation equation. The emergence of such states is due to the wide separation of time scales between thermal relaxation by phonon scattering and slow energy exchanges with the thermostat. The quasiequilibrium states exist between these two time scales when the system behaves as virtually isolated and equilibrium.

  5. Molecular dynamics simulation of radiation damage cascades in diamond

    SciTech Connect

    Buchan, J. T.; Robinson, M.; Christie, H. J.; Roach, D. L.; Ross, D. K.; Marks, N. A.

    2015-06-28

    Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

  6. Structural Modeling and Molecular Dynamics Simulation of the Actin Filament

    SciTech Connect

    Splettstoesser, Thomas; Holmes, Kenneth; Noe, Frank; Smith, Jeremy C

    2011-01-01

    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.

  7. Molecular Dynamics Simulations of Homogeneous Crystallization in Polymer Melt

    NASA Astrophysics Data System (ADS)

    Kong, Bin

    2015-03-01

    Molecular mechanisms of homogeneous nucleation and crystal growth from the melt of polyethylene-like polymer were investigated by molecular dynamics simulations. The crystallinity was determined by using the site order parameter method (SOP), which described local order degree around an atom. Snapshots of the simulations showed evolution of the nucleation and the crystal growth through SOP images clearly. The isothermal crystallization kinetics was determined at different temperatures. The rate of crystallization, Kc, and the Avrami exponents, n, were determined as a function of temperature. The forming of nucleis was traced to reveal that the nucleis were formed with more ordered cores and less ordered shells. A detailed statistical analysis of the MD snapshots and trajectories suggested conformations of the polymer chains changed smoothly from random coil to chain folded lamella in the crystallization processes.

  8. A model for including thermal conduction in molecular dynamics simulations

    NASA Technical Reports Server (NTRS)

    Wu, Yue; Friauf, Robert J.

    1989-01-01

    A technique is introduced for including thermal conduction in molecular dynamics simulations for solids. A model is developed to allow energy flow between the computational cell and the bulk of the solid when periodic boundary conditions cannot be used. Thermal conduction is achieved by scaling the velocities of atoms in a transitional boundary layer. The scaling factor is obtained from the thermal diffusivity, and the results show good agreement with the solution for a continuous medium at long times. The effects of different temperature and size of the system, and of variations in strength parameter, atomic mass, and thermal diffusivity were investigated. In all cases, no significant change in simulation results has been found.

  9. Molecular Dynamics Simulation of MgSiO3 Perovskite

    NASA Astrophysics Data System (ADS)

    Lin-xiang, Zhou; L, Zhou X.; J, Hardy R.; Xin, Xu; X, Xu

    1998-06-01

    Using molecular dynamics to simulate MgSiO3 perovskite is performed to investigate its phase transitions and superionicity. These simulations has used parameter-free Gordon-Kim potentials and a novel technique to monitor the motion of ions which clearly demonstrates the sublattice melting of ions O2- and the rotations of SiO6 octahedra. MgSiO3 has to undergo a few of phase transitions, then enter into the cubic phase. In particular, there is a transitional phase between orthorhombic phase and cubic phase. There are a superionic phase and the cubic phase in magnesium-rich silicate perovskite. This superionic phase occurs after the onset of cubic phase before the melting point. The onset temparature Tc for superionicity is about 200-700 K below the melting point Tm, Tc / Tm similar 0.92.

  10. Homogeneous Nucleation of Methane Hydrate in Microsecond Molecular Dynamics Simulations.

    PubMed

    Sarupria, Sapna; Debenedetti, Pablo G

    2012-10-18

    We report atomistically detailed molecular dynamics simulations of homogeneous nucleation of methane hydrate in bulk aqueous phase in the absence of any interface. Subcritical clusters of water and methane molecules are formed in the initial segment of the simulations, which then aggregate to give the critical hydrate nucleus. This occurs over time scales of several hundred nanoseconds, indicating that the formation and aggregation of subcritical clusters can contribute significantly to the overall rate of hydrate nucleation. The clusters have elements of sI hydrate structure, such as 5(12) and 5(12)6(2) cages as well as other uncommon 5(12)6(3) and 5(12)6(4) cages, but do not possess long-range order. Clusters are dynamic in nature and undergo continuous structural rearrangements.

  11. Molecular dynamics simulations of field emission from a planar nanodiode

    SciTech Connect

    Torfason, Kristinn; Valfells, Agust; Manolescu, Andrei

    2015-03-15

    High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission in planar nanodiodes. The effects of space-charge and emitter radius are examined and compared to previous results concerning transition from Fowler-Nordheim to Child-Langmuir current [Y. Y. Lau, Y. Liu, and R. K. Parker, Phys. Plasmas 1, 2082 (1994) and Y. Feng and J. P. Verboncoeur, Phys. Plasmas 13, 073105 (2006)]. The Fowler-Nordheim law is used to determine the current density injected into the system and the Metropolis-Hastings algorithm to find a favourable point of emission on the emitter surface. A simple fluid like model is also developed and its results are in qualitative agreement with the simulations.

  12. Molecular Dynamic Simulations on Surface Tension of Methanol

    NASA Astrophysics Data System (ADS)

    Obeidat, Abdalla

    2015-04-01

    Molecular dynamic simulations have been performed to study the surface tension of methanol at low temperatures. Six different models of methanol have been studied to compute the surface tension of different models. The models have been used to predict the surface tensions are: OPLS, Gromos 96, H1, J1, J2, and van Leeuwen model. Our results show that the most accurate model compared to true methanol was van Leeuwen model. The results were fitted to a straight line to predict other data of surface tension at specific temperature. The simulation were performed using the Gromacs package at temperatures: 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, and 300 K. This work is supported by JUST.

  13. Pasta Elasticity: Molecular dynamics simulations of nuclear pasta deformations

    NASA Astrophysics Data System (ADS)

    Caplan, M. E.; Horowitz, C. J.; Berry, D. K.

    2015-04-01

    Nuclear pasta is expected in the inner crust of neutron stars at densities near the nuclear saturation density. In this work, the elastic properties of pasta are calculated from large scale molecular dynamics simulations by deforming the simulation volume. Our model uses a semi-classical two-nucleon potential that reproduces nuclear saturation. We report the shear modulus and breaking strain of a variety of pasta phases for different temperatures, densities, and proton fractions. The presence of pasta in neutron stars could have significant effects on crustal oscillations and could be inferred from observations of soft-gamma repeaters. Additionally, these elastic parameters will enable us to improve estimates of the maximum size and lifetime of ``mountains'' on the crust, which could efficiently radiate gravitational waves.

  14. Molecular dynamics simulation of wetting on modified amorphous silica surface

    NASA Astrophysics Data System (ADS)

    Chai, Jingchun; Liu, Shuyan; Yang, Xiaoning

    2009-08-01

    The microscopic wetting of water on amorphous silica surfaces has been investigated by molecular dynamics simulation. Different degrees of surface hydroxylation/silanization were considered. It was observed that the hydrophobicity becomes enhanced with an increase in the degree of surface silanization. A continuous transformation from hydrophilicity to hydrophobicity can be attained for the amorphous silica surfaces through surface modification. From the simulation result, the contact angle can exceed 90° when surface silanization percentage is above 50%, showing a hydrophobic character. It is also found that when the percentage of surface silanization is above 70% on the amorphous silica surface, the water contact angle almost remains unchanged (110-120°). This phenomenon is a little different from the wetting behavior on smooth quartz plates in previous experimental report. This change in the wettability on modified amorphous silica surfaces can be interpreted in terms of the interaction between water molecules and the silica surfaces.

  15. Homogenous mixing of ionic liquids: molecular dynamics simulations.

    PubMed

    Payal, Rajdeep Singh; Balasubramanian, Sundaram

    2013-12-28

    Binary mixtures of room temperature ionic liquids (IL) with a common cation were investigated using atomistic molecular dynamics (MD) simulations. Two different binary ILs, viz., [C4mim][PF6]-[C4mim][Cl] and [C4mim][PF6]-[C4mim][BF4], were studied with varying fractions of either anion. The coordination environment of an anion around the cation is altered in the presence of another type of anion. The extent of change is larger for anions with much different radii. Atomistic MD and coarse grain MD simulations do not show any evidence for the clustering of like anions at any concentration. The binary liquids are well mixed at the molecular level.

  16. Molecular dynamics simulations of field emission from a planar nanodiode

    NASA Astrophysics Data System (ADS)

    Torfason, Kristinn; Valfells, Agust; Manolescu, Andrei

    2015-03-01

    High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission in planar nanodiodes. The effects of space-charge and emitter radius are examined and compared to previous results concerning transition from Fowler-Nordheim to Child-Langmuir current [Y. Y. Lau, Y. Liu, and R. K. Parker, Phys. Plasmas 1, 2082 (1994) and Y. Feng and J. P. Verboncoeur, Phys. Plasmas 13, 073105 (2006)]. The Fowler-Nordheim law is used to determine the current density injected into the system and the Metropolis-Hastings algorithm to find a favourable point of emission on the emitter surface. A simple fluid like model is also developed and its results are in qualitative agreement with the simulations.

  17. A model for including thermal conduction in molecular dynamics simulations

    NASA Technical Reports Server (NTRS)

    Wu, Yue; Friauf, Robert J.

    1989-01-01

    A technique is introduced for including thermal conduction in molecular dynamics simulations for solids. A model is developed to allow energy flow between the computational cell and the bulk of the solid when periodic boundary conditions cannot be used. Thermal conduction is achieved by scaling the velocities of atoms in a transitional boundary layer. The scaling factor is obtained from the thermal diffusivity, and the results show good agreement with the solution for a continuous medium at long times. The effects of different temperature and size of the system, and of variations in strength parameter, atomic mass, and thermal diffusivity were investigated. In all cases, no significant change in simulation results has been found.

  18. Transient molecular dynamics simulations of liquid viscosity for nonpolar and polar fluids.

    PubMed

    Thomas, Jason C; Rowley, Richard L

    2011-01-14

    A transient molecular dynamics (TMD) method for obtaining fluid viscosity is extended to multisite, force-field models of both nonpolar and polar liquids. The method overlays a sinusoidal velocity profile over the peculiar particle velocities and then records the transient decay of the velocity profile. The viscosity is obtained by regression of the solution of the momentum equation with an appropriate constitutive equation and initial and boundary conditions corresponding to those used in the simulation. The transient velocity decays observed appeared to include both relaxation and retardation effects. The Jeffreys viscoelastic model was found to model accurately the transient responses obtained for multisite models for n-butane, isobutane, n-hexane, water, methanol, and 1-hexanol. TMD viscosities obtained for saturated liquids over a wide range of densities agreed well for the polar fluids, both with nonequilibrium molecular dynamics (NEMD) results using the same force-field models and with correlations based on experimental data. Viscosities obtained for the nonpolar fluids agreed well with the experimental and NEMD results at low to moderate densities, but underpredicted experimental values at higher densities where shear-thinning effects and viscous heating may impact the TMD simulations.

  19. Quantum molecular dynamics simulations of hydrogen production and solar cells

    NASA Astrophysics Data System (ADS)

    Mou, Weiwei

    The global energy crisis presents two major challenges for scientists around the world: Producing cleaner energy which is sustainable for the environment; And improving the efficiency of energy production as well as consumption. It is crucial and yet elusive to understand the atomistic mechanisms and electronic properties, which are needed in order to tackle those challenges. Quantum molecular dynamics simulations and nonadiabatic quantum molecular dynamics are two of the dominant methods used to address the atomistic and electronic properties in various energy studies. This dissertation is an ensemble of three studies in energy research: (1) Hydrogen production from the reaction of aluminum clusters with water to provide a renewable energy cycle; (2) The photo-excited charge transfer and recombination at a quaterthiophene/zinc oxide interface to improve the power conversion efficiency of hybrid poly(3-hexylthiophene) (P3HT) /ZnO solar cells; and (3) the charge transfer at a rubrene/C60 interface to understand why phenyl groups in rubrene improve the performance of rubrene/C60 solar cells.

  20. Molecular dynamics of silicon indentation

    NASA Astrophysics Data System (ADS)

    Kallman, J. S.; Hoover, W. G.; Hoover, C. G.; de Groot, A. J.; Lee, S. M.; Wooten, F.

    1993-04-01

    We use nonequilibrium molecular dynamics to simulate the elastic-plastic deformation of silicon under tetrahedral nanometer-sized indentors. The results are described in terms of a rate-dependent and temperature-dependent phenomenological yield strength. We follow the structural change during indentation with a computer technique that allows us to model the dynamic simulation of diffraction patterns.

  1. Molecular dynamics simulations of ballistic He penetration into W fuzz

    NASA Astrophysics Data System (ADS)

    Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M.

    2016-12-01

    Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called ‘fuzz’ structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers than He diffusion through fuzz nanorods. Instead of trying to grow a fuzz layer starting from a flat piece of bulk W, a new approach of creating a fully formed fuzz structure 0.43 µm thick out of ellipsoidal pieces of W is employed. Lack of detailed experimental knowledge of the 3D structure of fuzz is dealt with by simulating He bombardment on five different structures of 15 vol% W and determining the variation in He penetration for each case. The results show that by far the most important factor determining He penetration is the amount of open channels through which He ions can travel unimpeded. For a more or less even W density distribution He penetration into fuzz falls off exponentially with distance and can thus be described by a ‘half depth’. In a 15 vol% fuzz structure, the half depth can reach 0.18 µm. In the far sparser fuzz structures that were recently reported, the half depth might be 1 µm or more. This means that ballistic He penetration offers a more likely scenario than He diffusion through nanorods for how He moves through fuzz and may provide an adequate explanation for how He penetrates through the thickest fuzz layers reported so far. Furthermore, the exponential decrease in penetration with depth would follow a logarithmic dependence on fluence which is compatible with experiments. A comparison of these results and molecular dynamics calculations carried out in the recoil interaction approximation shows that results for W fuzz are qualitatively very different from conventional stopping power calculations on W with a similarly low but homogeneous density distribution.

  2. Perturbation of hydration layer in solvated proteins by external electric and electromagnetic fields: Insights from non-equilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Nandi, Prithwish K.; Futera, Zdenek; English, Niall J.

    2016-11-01

    Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ˜220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical

  3. Perturbation of hydration layer in solvated proteins by external electric and electromagnetic fields: Insights from non-equilibrium molecular dynamics.

    PubMed

    Nandi, Prithwish K; Futera, Zdenek; English, Niall J

    2016-11-28

    Given the fundamental role of water in governing the biochemistry of enzymes, and in regulating their wider biological activity (e.g., by local water concentration surrounding biomolecules), the influence of extraneous electric and electromagnetic (e/m) fields thereon is of central relevance to biophysics and, more widely, biology. With the increase in levels of local and atmospheric microwave-frequency radiation present in modern life, as well as other electric-field exposure, the impact upon hydration-water layers surrounding proteins, and biomolecules generally, becomes a particularly pertinent issue. Here, we present a (non-equilibrium) molecular-dynamics-simulation study on a model protein (hen egg-white lysozyme) hydrated in water, in which we determine, inter alia, translational self-diffusivities for both hen egg-white lysozyme and its hydration layer together with relaxation dynamics of the hydrogen-bond network between the protein and its hydration-layer water molecules on a residue-per-residue basis. Crucially, we perform this analysis both above and below the dynamical-transition temperature (at ∼220 K), at 300 and 200 K, respectively, and we compare the effects of external static-electric and e/m fields with linear-response-régime (r.m.s.) intensities of 0.02 V/Å. It was found that the translational self-diffusivity of hen egg-white lysozyme and its hydration-water layer are increased substantially in static fields, primarily due to the induced electrophoretic motion, whilst the water-protein hydrogen-bond-network-rearrangement kinetics can also undergo rather striking accelerations, primarily due to the enhancement of a larger-amplitude local translational and rotational motion by charged and dipolar residues, which serves to promote hydrogen-bond breakage and re-formation kinetics. These external-field effects are particularly evident at 200 K, where they serve to induce the protein- and solvation-layer-response effects redolent of dynamical

  4. 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.

  5. Molecular Dynamics of Dense Fluids: Simulation-Theory Symbiosis

    NASA Astrophysics Data System (ADS)

    Yip, Sidney

    35 years ago Berni J. Alder showed the Boltzmann-Enskog kinetic theory failed to adequately account for the viscosity of fluids near solid density as determined by molecular dynamics simulation. This work, along with other notable simulation findings, provided great stimulus to the statistical mechanical studies of transport phenomena, particularly in dealing with collective effects in the time correlation functions of liquids. An extended theoretical challenge that remains partially resolved at best is the shear viscosity of supercooled liquids. How can one give a unified explanation of the so-called fragile and strong characteristic temperature behavior, with implications for the dynamics of glass transition? In this tribute on the occasion of his 90th birthday symposium, we recount a recent study where simulation, combined with heuristic (transition-state) and first principles (linear response) theories, identifies the molecular mechanisms governing glassy-state relaxation. Such an interplay between simulation and theory is progress from the early days; instead of simulation challenging theory, now simulation and theory complement each other.

  6. Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations

    NASA Astrophysics Data System (ADS)

    Vijaykumar, Adithya; Bolhuis, Peter G.; ten Wolde, Pieter Rein

    2015-12-01

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

  7. Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Levine, Zachary Alan

    Computer simulations of physical, chemical, and biological systems have improved tremendously over the past five decades. From simple studies of liquid argon in the 1960s to fully atomistic simulations of entire viruses in the past few years, recent advances in high-performance computing have continuously enabled simulations to bridge the gap between scientific theory and experiment. Molecular dynamics simulations in particular have allowed for the direct observation of spatial and temporal events which are at present inaccessible to experiments. For this dissertation I employ all-atom molecular dynamics simulations to study the transient, electric field-induced poration (or electroporation) of phospholipid bilayers at MV/m electric fields. Phospholipid bilayers are the dominant constituents of cell membranes and act as both a barrier and gatekeeper to the cell interior. This makes their structural integrity and susceptibility to external perturbations an important topic for study, especially as the density of electromagnetic radiation in our environment is increasing steadily. The primary goal of this dissertation is to understand the specific physical and biological mechanisms which facilitate electroporation, and to connect our simulated observations to experiments with live cells and to continuum models which seek to describe the underlying biological processes of electroporation. In Chapter 1 I begin with a brief introduction to phospholipids and phospholipid bilayers, followed by an extensive overview of electroporation and atomistic molecular dynamics simulations. The following chapters will then focus on peer-reviewed and published work we performed, or on existing projects which are currently being prepared for submission. Chapter 2 looks at how external electric fields affect both oxidized and unoxidized lipid bilayers as a function of oxidation concentration and oxidized lipid type. Oxidative damage to cell membranes represents a physiologically relevant

  8. Direct molecular dynamics simulation of liquid-solid phase equilibria for two-component plasmas.

    PubMed

    Schneider, A S; Hughto, J; Horowitz, C J; Berry, D K

    2012-06-01

    We determine the liquid-solid phase diagram for carbon-oxygen and oxygen-selenium plasma mixtures using two-phase molecular dynamics simulations. We identify liquid, solid, and interface regions using a bond angle metric. To study finite-size effects, we perform 27,648- and 55,296-ion simulations. To help monitor nonequilibrium effects, we calculate diffusion constants D(i). For the carbon-oxygen system we find that D(O) for oxygen ions in the solid is much smaller than D(C) for carbon ions and that both diffusion constants are 80 or more times smaller than diffusion constants in the liquid phase. There is excellent agreement between our carbon-oxygen phase diagram and that predicted by Medin and Cumming. This suggests that errors from finite-size and nonequilibrium effects are small and that the carbon-oxygen phase diagram is now accurately known. The oxygen-selenium system is a simple two-component model for more complex rapid proton capture nucleosynthesis ash compositions for an accreting neutron star. Diffusion of oxygen, in a predominantly selenium crystal, is remarkably fast, comparable to diffusion in the liquid phase. We find a somewhat lower melting temperature for the oxygen-selenium system than that predicted by Medin and Cumming. This is probably because of electron screening effects.

  9. Thermal conductivity of carbon dioxide from non-equilibrium molecular dynamics: A systematic study of several common force fields

    NASA Astrophysics Data System (ADS)

    Trinh, Thuat T.; Vlugt, Thijs J. H.; Kjelstrup, Signe

    2014-10-01

    We report a systematic investigation of the thermal conductivity of various three-site models of carbon dioxide (CO2) using nonequilibrium molecular dynamics in the temperature range 300-1000 K and for pressures up to 200 MPa. A direct comparison with experimental data is made. Three popular CO2 force fields (MSM, EPM2, and TraPPE) and two flexible models (based on EPM2) were investigated. All rigid force fields accurately predict the equation of state for carbon dioxide for the given range of variables. They can also reproduce the thermal conductivity of CO2 at room temperature and predict a decrease of the thermal conductivity with increasing temperature. At high temperatures, the rigid models underestimate the thermal conductivity.

  10. Thermal conductivity of carbon dioxide from non-equilibrium molecular dynamics: a systematic study of several common force fields.

    PubMed

    Trinh, Thuat T; Vlugt, Thijs J H; Kjelstrup, Signe

    2014-10-07

    We report a systematic investigation of the thermal conductivity of various three-site models of carbon dioxide (CO2) using nonequilibrium molecular dynamics in the temperature range 300-1000 K and for pressures up to 200 MPa. A direct comparison with experimental data is made. Three popular CO2 force fields (MSM, EPM2, and TraPPE) and two flexible models (based on EPM2) were investigated. All rigid force fields accurately predict the equation of state for carbon dioxide for the given range of variables. They can also reproduce the thermal conductivity of CO2 at room temperature and predict a decrease of the thermal conductivity with increasing temperature. At high temperatures, the rigid models underestimate the thermal conductivity.

  11. Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.

    2016-10-01

    SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.

  12. Molecular-dynamics simulation of two-dimensional thermophoresis

    PubMed

    Paredes; Idler; Hasmy; Castells; Botet

    2000-11-01

    A numerical technique is presented for the thermal force exerted on a solid particle by a gaseous medium between two flat plates at different temperatures, in the free molecular or transition flow. This is a two-dimensional molecular-dynamics simulation of hard disks in a inhomogeneous thermal environment. All steady-state features exhibited by the compressible hard-disk gas are shown to be consistent with the expected behaviors. Moreover the thermal force experienced by a large solid disk is investigated, and compared to the analytical case of cylinders moving perpendicularly to the constant temperature gradient for an infinite Knudsen number and in an infinite medium. We show precise examples of how this technique can be used simply to investigate more difficult practical problems, in particluar the influence of nonlinear gradients for large applied differences of temperature, of proximity of the walls, and of smaller Knudsen numbers.

  13. Protein unfolding pathways explored through molecular dynamics simulations.

    PubMed

    Daggett, V; Levitt, M

    1993-07-20

    Herein we describe the results of molecular dynamics simulations of the bovine pancreatic trypsin inhibitor (BPTI) in solution at a variety of temperatures both with and without disulfide bonds. The reduced form of the protein unfolded at high temperature to an ensemble of conformations with all the properties of the molten globule state. In this account we outline the structural details of the actual unfolding process between the native and molten globule states. The first steps of unfolding involved expansion of the protein, which disrupted packing interactions. The solvent-accessible surface area also quickly increased. The unfolding was localized mostly to the turn and loop regions of the molecule, while leaving the secondary structure intact. Then, there was more gradual unfolding of the secondary structure and non-native turns became prevalent. This same trajectory was continued and more drastic unfolding occurred that resulted in a relatively compact state devoid of stable secondary structure.

  14. Car-parrinello molecular dynamics simulation of liquid formic acid.

    PubMed

    Bakó, I; Hutter, J; Pálinkás, G

    2006-02-16

    First-principles molecular dynamics has been used to investigate the structural, vibrational, and energetic properties of formic acid, formic acid-formate anion dimers, and liquid formic acid in a periodically repeated box with 32 formic acid molecules. We found that in liquid formic acid the hydrogen-bonded clusters mainly consist of linear branching chains. From our simulation, we got good agreement with the available structural and dynamical data. We also studied the proton transfer in the cis-formic acid-formate anion dimer, and we showed that this proton transfer does not have any potential barrier. The hydrogen bonding statistics as well as the mean lifetime of the hydrogen bonds are analyzed.

  15. 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.

  16. Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin.

    PubMed Central

    Leenders, R; van Gunsteren, W F; Berendsen, H J; Visser, A J

    1994-01-01

    Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin in water have been performed in a sphere of 1.4-nm radius surrounded by a restrained shell of 0.8 nm. The flavin binding site, comprising the active site of the flavodoxin, was in the center of the sphere. No explicit information about protein-bound water molecules was included. An analysis is made of the motional characteristics of residues located in the active site. Positional fluctuations, hydrogen bonding patterns, dihedral angle transitions, solvent behavior, and time-dependent correlations are examined. The 375-ps trajectories show that both oxidized and reduced protein-bound flavins are immobilized within the protein matrix, in agreement with earlier obtained time-resolved fluorescence anisotropy data. The calculated time-correlated behavior of the tryptophan residues reveals significant picosecond mobility of the tryptophan side chain located close to the reduced isoalloxazine part of the flavin. PMID:8011895

  17. Molecular dynamics simulation of annealed ZnO surfaces

    SciTech Connect

    Min, Tjun Kit; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    The effect of thermally annealing a slab of wurtzite ZnO, terminated by two surfaces, (0001) (which is oxygen-terminated) and (0001{sup ¯}) (which is Zn-terminated), is investigated via molecular dynamics simulation by using reactive force field (ReaxFF). We found that upon heating beyond a threshold temperature of ∼700 K, surface oxygen atoms begin to sublimate from the (0001) surface. The ratio of oxygen leaving the surface at a given temperature increases as the heating temperature increases. A range of phenomena occurring at the atomic level on the (0001) surface has also been explored, such as formation of oxygen dimers on the surface and evolution of partial charge distribution in the slab during the annealing process. It was found that the partial charge distribution as a function of the depth from the surface undergoes a qualitative change when the annealing temperature is above the threshold temperature.

  18. Molecular dynamics computer simulation of permeation in solids

    SciTech Connect

    Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M.

    1997-12-31

    In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.

  19. Molecular Dynamics Simulations of Anti-Aggregation Effect of Ibuprofen

    PubMed Central

    Chang, Wenling E.; Takeda, Takako; Raman, E. Prabhu; Klimov, Dmitri K.

    2010-01-01

    Abstract Using implicit solvent molecular dynamics and replica exchange simulations, we study the impact of ibuprofen on the growth of wild-type Aβ fibrils. We show that binding of ibuprofen to Aβ destabilizes the interactions between incoming peptides and the fibril. As a result, ibuprofen interference modifies the free energy landscape of fibril growth and reduces the free energy gain of Aβ peptide binding to the fibril by ≃2.5 RT at 360 K. Furthermore, ibuprofen interactions shift the thermodynamic equilibrium from fibril-like locked states to disordered docked states. Ibuprofen's anti-aggregation effect is explained by its competition with incoming Aβ peptides for the same binding site located on the fibril edge. Although ibuprofen impedes fibril growth, it does not significantly change the mechanism of fibril elongation or the structure of Aβ peptides bound to the fibril. PMID:20513411

  20. Molecular dynamics simulation of shock melting of aluminum single crystal

    NASA Astrophysics Data System (ADS)

    Ju, Yuanyuan; Zhang, Qingming; Gong, Zizheng; Ji, Guangfu; Zhou, Lin

    2013-09-01

    Molecular dynamics method in conjunction with multi-scale shock technique is employed to study the melting characteristics of aluminum single crystal under dynamic conditions. The simulated results show that a linear relationship exists between the shock wave velocity and particle velocity, in good agreement with the experimental data. Comparing the Lindemann melting curve with the two Hugoniot curves for the solid and liquid phases, the Hugoniot melting is found to begin at 93.6 GPa and end at 140 GPa, which is consistent with the theoretical calculations. The impact of crystal defects on the melting characteristics of aluminum single crystal is also studied, and the results indicate that the pressure and temperature increase slightly for the system experiencing the same dynamic loading due to the crystal defects.

  1. Diffusion and structure in silica liquid: a molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Hung, P. K.; Hong, N. V.; Vinh, L. T.

    2007-11-01

    Diffusion and structure in liquid silica under pressure have been investigated by a molecular dynamics model of 999 atoms with the inter-atomic potentials of van Beest, Kramer and van Santen. The simulation reveals that silica liquid is composed of the species SiO4, SiO5 and SiO6 with a fraction dependent on pressure. The density as well as volume of voids can be expressed as a linear function of the fraction of those species. Low-density liquid is mainly constructed of SiO4 and has a large number of O- and Si-voids and a large void tube. This tube contains most O-voids and is spread over the whole system. The anomalous diffusion behavior is observed and discussed.

  2. Molecular dynamics simulations of cluster nucleation during inert gas condensation.

    PubMed

    Krasnochtchekov, Pavel; Averback, R S

    2005-01-22

    Molecular dynamics simulations of vapor-phase nucleation of germanium in an argon atmosphere were performed and a unexpected channel of nucleation was observed. This channel, vapor-induced cluster splitting, is important for more refractory materials since the critical nucleus size can fall below the size of a dimer. As opposed to conventional direct vapor nucleation of the dimer, which occurs by three-body collisions, cluster-splitting nucleation is a second-order reaction. The most important cluster-splitting reaction is the collision of a vapor atom and a trimer that leads to the formation of two dimers. The importance of the cluster-splitting nucleation channel relative to the direct vapor nucleation channel is observed to increase with decreasing vapor density and increasing ratio of vapor to carrier gas atoms.

  3. Molecular Dynamics Simulation of FCC Metallic Nanowires: A Review

    NASA Astrophysics Data System (ADS)

    Lao, Jijun; Naghdi Tam, Mehdi; Pinisetty, Dinesh; Gupta, Nikhil

    2013-02-01

    Molecular dynamic simulation studies are reviewed to understand the influence of strain rate, temperature, and cross-section size on the mechanical properties of face-centered cubic (FCC) metallic nanowires (MNWs). The yield stress of FCC MNWs is found to be 100 times higher than that of the corresponding bulk metals. The yield strain and fracture stress of MNWs are also found to be significantly higher compared with those of the bulk metals. The influence of deformation mechanisms (slip and twinning) on the mechanical properties of FCC MNWs is discussed. FCC MNWs are found to exhibit novel structural reorientation, phase transformation, elastic recovery, pseudoelasticity, and shape memory effect. MNWs with body-centered cubic (BCC) and hexagonal closed-packed crystal structures are compared with the FCC MNWs. Pseudoelasticity was also observed in BCC MNWs similar to that of FCC MNWs. Dense nano-twin arrays were found in Mg nanowires despite the high twin boundary energy.

  4. Molecular Dynamics Simulation of Energetic Uranium Recoil Damage in Zircon

    SciTech Connect

    Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin

    2006-10-11

    Defect production and amorphization due to energetic uranium recoils in zircon (ZrSiO4), which is a promising ceramic nuclear waste form, is studied using molecular dynamics simulations with a partial charge model. An algorithm that distinguishes between undamaged crystal, crystalline defects and amorphous regions is used to develop a fundamental understanding of the primary damage state. The amorphous cascade core is separated from the surrounding crystal by a defect-rich region. Small, chemically inhomogeneous amorphous clusters are also produced around the core. The amorphous regions consist of under-coordinated Zr and polymerized Si leading to amorphization and phase separation on a nanometer scale into Zr- and Si-rich regions. This separation could play an important role in the experimentally observed formation of nanoscale ZrO2 in ZrSiO4 irradiated at elevated temperatures.

  5. Molecular dynamics simulation of binary mixtures of molten alkali carbonates

    NASA Astrophysics Data System (ADS)

    Tissen, J. T. W. M.; Janssen, G. J. M.; van der Eerden, P.

    Molecular dynamics simulations have been performed on three binary eutectic mixtures: Li/NaCO3 (53-47 mol%), Li/KCO3 (62-38 mol%) and KCO3 (43-57 mol%) at 1200 K. The short-range order in the mixtures differs in many respects from the short-range order found in the pure components. The Li+ ions are coordinated by a smaller number of oxygen atoms, the Na+ and K+ ions by a larger number. The Li+ ions become trapped in their first coordination shell, leaving relatively more space for the larger atoms. This feature is the cause of the often-observed non-additivity of the dynamic properties of these mixtures, such as the Chemla effect in Li/KCO3, the large negative deviations from linear additivity for the electrical conductivity, as well as the dependence of the self-diffusion coefficient of the cations on the Li2CO3 content.

  6. Molecular dynamics simulations of crystallization of Lennard-Jones nanoparticles

    NASA Astrophysics Data System (ADS)

    Thi Thuy Huong, Ta; Van Hoang, Vo; Khuong Cat, Phan Ngoc

    2014-07-01

    Crystallization of Lennard-Jones nanoparticles has been studied by molecular dynamics (MD) simulations. Spherical models with free surface are cooled from the melt to crystalline state. In the cooling process, thermodynamics, structural properties and atomic mechanism of the crystallization are investigated. We found that crystallization in nanoparticles follows the Ostwald's step rule like that found in the past. Due to free surface contribution, the solidification exhibits non-homogeneous behavior which proceeds in different manners between core and surface: homogeneous crystallization in the core and heterogeneous one in the surface layer of nanoparticles. It is due to the discrepancy between structures of two parts: highly ordered structure dominates in the core region while the surface exhibits defective one with a high fraction of undercoordinated sites. Also, our results are consistent with previous ones about the free surface-induced phenomena.

  7. Relationship between nanocrystalline and amorphous microstructures by molecular dynamics simulation

    SciTech Connect

    Keblinski, P.; Phillpot, S.R.; Wolf, D.; Gleiter, H.

    1996-08-01

    A recent molecular dynamics simulation method for growth of fully dense nanocrystalline materials crystallized from melt was used with the Stillinger-Weber three-body potential to synthesize nanocrystalline Si with a grain size up to 75{Angstrom}. Structures of the highly constrained grain boundaries (GBs), triple lines, and point grain junctions were found to be highly disordered and similar to the structure of amorphous Si. These and earlier results for fcc metals suggest that a nanocrystalline microstructure may be viewed as a two-phase system, namely an ordered crystalline phase in the grain interiors connected by an amorphous, intergranular, glue-like phase. Analysis of the structures of bicrystalline GBs in the same materials reveals the presence of an amorphous intergranular equilibrium phase only in the high-energy but not the low-energy GBs, suggesting that only high-energy boundaries are present in nanocrystalline microstructures.

  8. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

    PubMed Central

    Mugnai, Mauro L.; Elber, Ron

    2015-01-01

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide. PMID:25573551

  9. Coarse-graining RNA nanostructures for molecular dynamics simulations

    PubMed Central

    Paliy, Maxim; Melnik, Roderick; Shapiro, Bruce A

    2013-01-01

    A series of coarse-grained models have been developed for study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in full atomistic modeling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the three-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4′ dihedrals taken from a reference structure are included. These findings are discussed in the context of RNA conformation classes. PMID:20577037

  10. Molecular dynamics simulations of electron irradiated PVDF nanofibers

    NASA Astrophysics Data System (ADS)

    Miao, Jiayuan; Bhatta, Ram; Kisielowski, Christian; Lolla, Dinesh; Reneker, Darrell; Tsige, Mesfin; Taylor, Philip

    2014-03-01

    High-resolution, aberration corrected transmission electron microscopy was used to observe morphological changes and segmental motion of electrospun poly(vinylidene fluoride) nanofibers in an 80 kilovolt electron beam. Atomic and molecular scale high-resolution images of fibers were made with an aberration corrected electron microscope. Chemical and morphological changes, which include the breaking of the fiber, loss of fluorine atoms and cross-linking of chains, caused by the high-energy electron beam were observed. We present the results of molecular dynamics (MD) simulations of such atomic and molecular level observations. The calculational models include the influence of chain scission, chain recoiling, and torsional defects on the morphology of a nanofiber. The effects of the loss of fluorine atoms and the applied tension on the morphology of the fibers were also investigated. Work supported by the Petroleum Research Fund of the American Chemical Society.

  11. Interactions in charged colloidal suspensions: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Padidela, Uday Kumar; Behera, Raghu Nath

    2017-07-01

    Colloidal suspensions are extensively used in everyday life and find several applications in the pharmaceutical, chemical, food industries, etc. We present the classical molecular dynamics simulation results of the structural and transport properties of charged colloidal suspensions as a function of its size, charge and concentration. The system is viewed as a two-component (colloids and counterions) primitive model consisting of spherical colloid particle (macroion) and the counterions (micro-particles), which are treated explicitly. The solvent is treated as dielectric continuum. A systematic trend in the radial distribution functions g(r), potential of mean force W(r), different thermodynamic properties and diffusion coefficients is obtained as a function of colloid charge, size and concentration. An attractive minimum in W(r) is obtained at short interparticle distance.

  12. "Like-charge attraction" between anionic polyelectrolytes: molecular dynamics simulations.

    PubMed

    Molnar, Ferenc; Rieger, Jens

    2005-01-18

    "Like-charge attraction" is a phenomenon found in many biological systems containing DNA or proteins, as well as in polyelectrolyte systems of industrial importance. "Like-charge attraction" between polyanions is observed in the presence of mobile multivalent cations. At a certain limiting concentration of cations, the negatively charged macroions cease to repel each other and even an attractive force between the anions is found. With classical molecular dynamics simulations it is possible to elucidate the processes that govern the attractive behavior with atomistic resolution. As an industrially relevant example we study the interaction of negatively charged carboxylate groups of sodium polyacrylate molecules with divalent cationic Ca2+ counterions. Here we show that Ca2+ ions initially associate with single chains of polyacrylates and strongly influence sodium ion distribution; shielded polyanions approach each other and eventually "stick" together (precipitate), contrary to the assumption that precipitation is initially induced by intermolecular Ca2+ bridging.

  13. Molecular dynamics simulations on networks of heparin and collagen.

    PubMed

    Kulke, Martin; Geist, Norman; Friedrichs, Wenke; Langel, Walter

    2017-06-01

    Synthetic scaffolds containing collagen (Type I) are of increasing interest for bone tissue engineering, especially for highly porous biomaterials in combination with glycosaminoglycans. In experiments the integration of heparin during the fibrillogenesis resulted in different types of collagen fibrils, but models for this aggregation on a molecular scale were only tentative. We conducted molecular dynamic simulations investigating the binding of heparin to collagen and the influence of the telopeptides during collagen aggregation. This aims at explaining experimental findings on a molecular level. Novel structures for N- and C-telopeptides were developed with the TIGER2 replica exchange algorithm and dihedral principle component analysis. We present an extended statistical analysis of the mainly electrostatic interaction between heparin and collagen and identify several binding sites. Finally, we propose a molecular mechanism for the influence of glycosaminoglycans on the morphology of collagen fibrils. Proteins 2017; 85:1119-1130. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  14. Molecular dynamics simulations of lysozyme in water/sugar solutions

    NASA Astrophysics Data System (ADS)

    Lerbret, A.; Affouard, F.; Bordat, P.; Hédoux, A.; Guinet, Y.; Descamps, M.

    2008-04-01

    Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.

  15. Clustering effects in ionic polymers: Molecular dynamics simulations

    SciTech Connect

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing the electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.

  16. Clustering effects in ionic polymers: Molecular dynamics simulations

    DOE PAGES

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing themore » electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.« less

  17. Continuum and molecular-dynamics simulation of nanodroplet collisions.

    PubMed

    Bardia, Raunak; Liang, Zhi; Keblinski, Pawel; Trujillo, Mario F

    2016-05-01

    The extent to which the continuum treatment holds in binary droplet collisions is examined in the present work by using a continuum-based implicit surface capturing strategy (volume-of-fluid coupled to Navier-Stokes) and a molecular dynamics methodology. The droplet pairs are arranged in a head-on-collision configuration with an initial separation distance of 5.3 nm and a velocity of 3 ms^{-1}. The size of droplets ranges from 10-50 nm. Inspecting the results, the collision process can be described as consisting of two periods: a preimpact phase that ends with the initial contact of both droplets, and a postimpact phase characterized by the merging, deformation, and coalescence of the droplets. The largest difference between the continuum and molecular dynamics (MD) predictions is observed in the preimpact period, where the continuum-based viscous and pressure drag forces significantly overestimate the MD predictions. Due to large value of Knudsen number in the gas (Kn_{gas}=1.972), this behavior is expected. Besides the differences between continuum and MD, it is also observed that the continuum simulations do not converge for the set of grid sizes considered. This is shown to be directly related to the initial velocity profile and the minute size of the nanodroplets. For instance, for micrometer-size droplets, this numerical sensitivity is not an issue. During the postimpact period, both MD and continuum-based simulations are strikingly similar, with only a moderate difference in the peak kinetic energy recorded during the collision process. With values for the Knudsen number in the liquid (Kn_{liquid}=0.01 for D=36nm) much closer to the continuum regime, this behavior is expected. The 50 nm droplet case is sufficiently large to be predicted reasonably well with the continuum treatment. However, for droplets smaller than approximately 36 nm, the departure from continuum behavior becomes noticeably pronounced, and becomes drastically different for the 10 nm

  18. Systematic Coarse-graining of Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Voth, Gregory

    2015-03-01

    Coarse-grained (CG) models can provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms that are correlated over distance scales of many covalent bond lengths and at long time scales. Systematic variational coarse-graining methods based on information from molecular dynamics simulations of finer-grained (e.g., all-atom) models provide attractive tools for the systematic development of CG models. Examples include the multiscale coarse-graining (MS-CG) and relative entropy minimization methods, and results from the former theory will be presented in this talk. In addition, a new approach will be presented that is appropriate for the ``ultra coarse-grained'' (UCG) regime, e.g., at a coarse-grained resolution that is much coarser than one amino acid residue per CG particle in a protein. At this level of coarse-graining, one is faced with the possible existence of multiple metastable states ``within'' the CG sites for a given UCG model configuration. I will therefore describe newer systematic variational UCG methods specifically designed to CG entire protein domains and subdomains into single effective CG particles. This is accomplished by augmenting existing effective particle CG schemes to allow for discrete state transitions and configuration-dependent resolution. Additionally, certain aspects of this work connect back to single-state force matching and open up new avenues for method development. This general body of theory and algorithm provides a formal statistical mechanical basis for the coarse-graining of fine-grained molecular dynamics simulation data at various levels of CG resolution. Representative applications will be described as time allows.

  19. Molecular Dynamics Simulations of Hugoniot Relations for Poly[methyl methacrylate

    DTIC Science & Technology

    2011-11-01

    Molecular Dynamics Simulations of Hugoniot Relations for Poly[ methyl methacrylate ] by Tanya L. Chantawansri, Edward F. C. Byrd, Betsy M. Rice...Ground, MD 21005-5066 ARL-TR-5819 November 2011 Molecular Dynamics Simulations of Hugoniot Relations for Poly[ methyl methacrylate ...4. TITLE AND SUBTITLE Molecular Dynamics Simulations of Hugoniot Relations for Poly[ methyl methacrylate ] 5a. CONTRACT NUMBER 5b. GRANT NUMBER

  20. Molecular dynamic simulations on TKX-50/RDX cocrystal.

    PubMed

    Xiong, Shuling; Chen, Shusen; Jin, Shaohua

    2017-06-01

    Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) is a newly synthesized energetic material with excellent comprehensive properties. Cyclotrimethylenetrinitramine (RDX) is currently one of the most widely used energetic materials in the world. TKX-50 and RDX supercell models and TKX-50/RDX cocrystal model were constructed based on their crystal cell parameters and the formation mechanism of cocrystal, respectively, then they were simulated by molecular dynamics (MD) simulations. The maximum trigger bond (NNO2) length(Lmax), binding energy (Ebind), radial distribution function (RDF), cohesive energy density(CED) and mechanical properties were simulated at different temperatures based on the simulated equilibrium structures of the models. The simulated results indicate that hydrogen bond and van der Waals force interactions exist in the cocrystal system and the hydrogen bonds are mainly derived from the hydrogen atom of TKX-50 with the oxygen or nitrogen atom of RDX. Moreover, TKX-50/RDX cocrystal structure significantly reduces the sensitivity and improves the thermodynamic stability of RDX, and it also shows better mechanical properties than pure TKX-50 and RDX, indicating that it will vastly expand the application scope of the single compound explosives. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Acoustic properties in glycerol glass-former: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Busselez, Remi; Pezeril, Thomas; Institut des Materiaux et Molecules du Mans Team

    2013-03-01

    Study of high-frequency collective dynamics around TeraHertz region in glass former has been a subject of intense investigations and debates over the past decade. In particular, the presence of the Boson peak characteristic of glassy material and its relation to other glass anomalies. Recently, experiments and simulations have underlined possible relation between Boson peak and transverse acoustic modes in glassy materials. In particular, simulations of simple Lennard Jones glass former have shown a relation between Ioffe-Regel criterion in transverse modes and Boson peak. We present here molecular dynamics simulation on high frequency dynamics of glycerol. In order to study mesoscopic order (0.5-5nm-1), we made use of large simulation box containing 80000 atoms. Analysis of collective longitudinal and transverse acoustic modes shows striking similarities in comparison with simulation of Lennard-Jones particles. In particular, it seems that a connection may exist between Ioffe-Regel criterion for transverse modes and Bose Peak frequency. However,in our case we show that this connection may be related with structural correlation arising from molecular clusters.

  2. Anharmonic force constants extracted from first-principles molecular dynamics: applications to heat transfer simulations.

    PubMed

    Tadano, T; Gohda, Y; Tsuneyuki, S

    2014-06-04

    A systematic method to calculate anharmonic force constants of crystals is presented. The method employs the direct-method approach, where anharmonic force constants are extracted from the trajectory of first-principles molecular dynamics simulations at high temperature. The method is applied to Si where accurate cubic and quartic force constants are obtained. We observe that higher-order correction is crucial to obtain accurate force constants from the trajectory with large atomic displacements. The calculated harmonic and anharmonic force constants are, then, combined with the Boltzmann transport equation (BTE) and non-equilibrium molecular dynamics (NEMD) methods in calculating the thermal conductivity. The BTE approach successfully predicts the lattice thermal conductivity of bulk Si, whereas NEMD shows considerable underestimates. To evaluate the linear extrapolation method employed in NEMD to estimate bulk values, we analyze the size dependence in NEMD based on BTE calculations. We observe strong nonlinearity in the size dependence of NEMD in Si, which can be ascribed to acoustic phonons having long mean-free-paths and carrying considerable heat. Subsequently, we also apply the whole method to a thermoelectric material Mg2Si and demonstrate the reliability of the NEMD method for systems with low thermal conductivities.

  3. Molecular dynamics simulations: Parameter evaluation, application and development

    NASA Astrophysics Data System (ADS)

    Zhou, Jin

    Molecular dynamics (MD) simulation is a theoretical technique for investigating the physical properties of a wide variety of molecules. This dissertation contains my studies on three important parts of the MD simulation: evaluation of parameters in empirical energy functions widely used in MD simulations, application of MD simulation on experimentally interested biological molecules and development of new methods for constraint dynamics simulations. All the work in this thesis made use of CHARMM as an MD simulation tool. The MD simulation uses empirical energy functions parameterized by a set of parameters. These parameters play an important role in the quality of the simulations. I evaluated nine parameter sets from Harvard University and Molecular Simulations, Inc. for protein simulations by the MD simulations of hydrated form of carboxy- myoglobin and interleukin-1/beta, which are rich in two typical protein structure motifs, helix and β sheet structures respectively. It is found that some sets are good at representing helical structure proteins while others are good at β sheet proteins. But all of them need improvement on representing motions at low temperature. Experimental evidence indicates that the 1A coiled-coil domains of the Intermediate Filament (IF) proteins consisting of coiled human keratins 1 and 10 (K1 and K10) are 'hot spots' for substitutional mutations. Some of these mutations are correlated to the human skin diseases-epidermolytic hyperkeratiosis (EH) and epidermolysis bullosa simplex (EBS). The MD simulation technique is used here for the first time to model and simulate these proteins to elucidate the molecular-level effects of these mutations. Lacking the experimental crystal structures, the initial structure of 1A domain of the wild type Intermediate Filament protein and its mutants were modeled from scratch to reproduce the well- known properties of the proteins of this kind followed by identical MD simulations. The important result is

  4. Molecular dynamics simulation of biomembranes in aqueous solution

    NASA Astrophysics Data System (ADS)

    Bostick, David Lee

    In recent years, the developments in classical molecular dynamics simulation have allowed for an atomistic depiction of mesoscopic biological systems. With the awareness of such developments, the natural strive of the scientific community has been to increase the size of such simulated systems [70]. Nonetheless, the subtleties in the properties of biomembranes require an unusually thoughtful approach [70, 203]. In this work, a hierarchical approach is taken, with respect to system complexity, in the classical molecular dynamics simulation of biomembrane systems in aqueous solution. A progression of simulation studies is presented that begins with the analysis of the interfacial properties of neat bilayers composed of zwitterionic (phosphatidylcholine) lipids in both pure water and in electrolyte. We move on to study mixed bilayers containing zwitterionic (phosphatidylcholine) and acidic (phosphatidylserine) lipids with counterions immersed in electrolyte. Yet another layer of complexity is added to the problem by studying hydrated bilayers containing phosphatidylcholine lipids and cholesterol. Finally, we address the semipermeable nature of biomembranes by studying two membrane-channel systems. We start with a simple model membrane-channel consisting of a six-helix alamethicin bundle embedded in a hydrated phosphatidylcholine bilayer. The knowledge gained from this study is then carried over to the simulation of a large membrane-embedded prokaryotic ClC Cl-/H + antiporter, utilizing a free-energetic analysis to reveal the role of protons in the Cl- transport mechanism. Throughout the progression, methods are developed and used in the analysis of interfacial aqueous solution structure, ion-membrane binding, lipid structural properties, inter-lipid hydrogen bonded complexation, and electrostatics at the membrane interface. The developments reveal the layered nature of water near the rugged, molecularscale aqueous solution/membrane interface and its electrostatic

  5. An undergraduate laboratory activity on molecular dynamics simulations.

    PubMed

    Spitznagel, Benjamin; Pritchett, Paige R; Messina, Troy C; Goadrich, Mark; Rodriguez, Juan

    2016-01-01

    Vision and Change [AAAS, 2011] outlines a blueprint for modernizing biology education by addressing conceptual understanding of key concepts, such as the relationship between structure and function. The document also highlights skills necessary for student success in 21st century Biology, such as the use of modeling and simulation. Here we describe a laboratory activity that allows students to investigate the dynamic nature of protein structure and function through the use of a modeling technique known as molecular dynamics (MD). The activity takes place over two lab periods that are 3 hr each. The first lab period unpacks the basic approach behind MD simulations, beginning with the kinematic equations that all bioscience students learn in an introductory physics course. During this period students are taught rudimentary programming skills in Python while guided through simple modeling exercises that lead up to the simulation of the motion of a single atom. In the second lab period students extend concepts learned in the first period to develop skills in the use of expert MD software. Here students simulate and analyze changes in protein conformation resulting from temperature change, solvation, and phosphorylation. The article will describe how these activities can be carried out using free software packages, including Abalone and VMD/NAMD. © 2016 The International Union of Biochemistry and Molecular Biology.

  6. Ab-Initio Molecular Dynamics Simulation of Graphene Sheet

    NASA Astrophysics Data System (ADS)

    Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.

    2017-01-01

    The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.

  7. How to identify dislocations in molecular dynamics simulations?

    NASA Astrophysics Data System (ADS)

    Li, Duo; Wang, FengChao; Yang, ZhenYu; Zhao, YaPu

    2014-12-01

    Dislocations are of great importance in revealing the underlying mechanisms of deformed solid crystals. With the development of computational facilities and technologies, the observations of dislocations at atomic level through numerical simulations are permitted. Molecular dynamics (MD) simulation suggests itself as a powerful tool for understanding and visualizing the creation of dislocations as well as the evolution of crystal defects. However, the numerical results from the large-scale MD simulations are not very illuminating by themselves and there exist various techniques for analyzing dislocations and the deformed crystal structures. Thus, it is a big challenge for the beginners in this community to choose a proper method to start their investigations. In this review, we summarized and discussed up to twelve existing structure characterization methods in MD simulations of deformed crystal solids. A comprehensive comparison was made between the advantages and disadvantages of these typical techniques. We also examined some of the recent advances in the dynamics of dislocations related to the hydraulic fracturing. It was found that the dislocation emission has a significant effect on the propagation and bifurcation of the crack tip in the hydraulic fracturing.

  8. Multipole Algorithms for Molecular Dynamics Simulation on High Performance Computers.

    NASA Astrophysics Data System (ADS)

    Elliott, William Dewey

    1995-01-01

    A fundamental problem in modeling large molecular systems with molecular dynamics (MD) simulations is the underlying N-body problem of computing the interactions between all pairs of N atoms. The simplest algorithm to compute pair-wise atomic interactions scales in runtime {cal O}(N^2), making it impractical for interesting biomolecular systems, which can contain millions of atoms. Recently, several algorithms have become available that solve the N-body problem by computing the effects of all pair-wise interactions while scaling in runtime less than {cal O}(N^2). One algorithm, which scales {cal O}(N) for a uniform distribution of particles, is called the Greengard-Rokhlin Fast Multipole Algorithm (FMA). This work describes an FMA-like algorithm called the Molecular Dynamics Multipole Algorithm (MDMA). The algorithm contains several features that are new to N-body algorithms. MDMA uses new, efficient series expansion equations to compute general 1/r^{n } potentials to arbitrary accuracy. In particular, the 1/r Coulomb potential and the 1/r^6 portion of the Lennard-Jones potential are implemented. The new equations are based on multivariate Taylor series expansions. In addition, MDMA uses a cell-to-cell interaction region of cells that is closely tied to worst case error bounds. The worst case error bounds for MDMA are derived in this work also. These bounds apply to other multipole algorithms as well. Several implementation enhancements are described which apply to MDMA as well as other N-body algorithms such as FMA and tree codes. The mathematics of the cell -to-cell interactions are converted to the Fourier domain for reduced operation count and faster computation. A relative indexing scheme was devised to locate cells in the interaction region which allows efficient pre-computation of redundant information and prestorage of much of the cell-to-cell interaction. Also, MDMA was integrated into the MD program SIgMA to demonstrate the performance of the program over

  9. Molecular Dynamics Simulation of Membranes and a Transmembrane Helix

    NASA Astrophysics Data System (ADS)

    Duong, Tap Ha; Mehler, Ernest L.; Weinstein, Harel

    1999-05-01

    Three molecular dynamics (MD) simulations of 1.5-ns length were carried out on fully hydrated patches of dimyristoyl phosphatidylcholine (DMPC) bilayers in the liquid-crystalline phase. The simulations were performed using different ensembles and electrostatic conditions: a microcanonical ensemble or constant pressure-temperature ensemble, with or without truncated electrostatic interactions. Calculated properties of the membrane patches from the three different protocols were compared to available data from experiments. These data include the resulting overall geometrical dimensions, the order characteristics of the lipid hydrocarbon chains, as well as various measures of the conformations of the polar head groups. The comparisons indicate that the simulation carried out within the microcanonical ensemble with truncated electrostatic interactions yielded results closest to the experimental data, provided that the initial equilibration phase preceding the production run was sufficiently long. The effects of embedding a non-ideal helical protein domain in the membrane patch were studied with the same MD protocols. This simulation was carried out for 2.5 ns. The protein domain corresponds to the seventh transmembrane segment (TMS7) of the human serotonin 5HT 2Areceptor. The peptide is composed of two α-helical segments linked by a hinge domain around a perturbing Asn-Pro motif that produces at the end of the simulation a kink angle of nearly 80° between the two helices. Several aspects of the TMS7 structure, such as the bending angle, backbone Φ and Ψ torsion angles, the intramolecular hydrogen bonds, and the overall conformation, were found to be very similar to those determined by NMR for the corresponding transmembrane segment of the tachykinin NK-1 receptor. In general, the simulations were found to yield structural and dynamic characteristics that are in good agreement with experiment. These findings support the application of simulation methods to the study

  10. Molecular dynamics simulations of He bubble nucleation at grain boundaries.

    PubMed

    Zhang, Yongfeng; Millett, Paul C; Tonks, Michael; Zhang, Liangzhe; Biner, Bulent

    2012-08-01

    The nucleation behavior of He bubbles in single-crystal (sc) and nano-grain body-centered-cubic (bcc) Mo is simulated using molecular dynamics (MD) simulations, focusing on the effects of the grain boundary (GB) structure. In sc Mo, the nucleation behavior of He bubbles depends on irradiation conditions. He bubbles nucleate by either clustering of He atoms with pre-existing vacancies or self-interstitial-atom (SIA) punching without initial vacancies. In nano-grain Mo, strong precipitation of He at the GBs is observed, and the density, size and spatial distribution of He bubbles vary with the GB structure. The corresponding He bubble density is higher in nano-grain Mo than that in sc Mo and the average bubble size is smaller. In the GB plane, He bubbles distribute along the dislocation cores for GBs consisting of GB dislocations and randomly for those without distinguishable dislocation structures. The simulation results in nano-grain Mo are in agreement with previous experiments in metal nano-layers, and they are further explained by the effect of excess volume associated with the GBs.

  11. Molecular dynamics simulation of liquid water: Hybrid density functionals

    SciTech Connect

    Todorova, T; Seitsonen, A; Hutter, J; Kuo, W; Mundy, C

    2005-09-12

    The structure, dynamical and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta functional, four gradient corrected functionals, the local density and Hartree-Fock approximation. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and under-structured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller averaged numbers of hydrogen bonds and similar hydrogen bond populations as pure density functionals. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than from the corresponding pure density functionals.

  12. Molecular dynamics simulation of graphene bombardment with Si ion

    NASA Astrophysics Data System (ADS)

    Qin, Xin-Mao; Gao, Ting-Hong; Yan, Wan-Jun; Guo, Xiao-Tian; Xie, Quan

    2014-03-01

    Molecular dynamics simulations with Tersoff-Ziegler-Biersack-Littmark (Tersoff-ZBL) potential and adaptive intermolecular reactive empirical bond order (AIREBO) potential are performed to study the effect of irradiated graphene with silicon ion at several positions and energy levels of 0.1-1000 eV. The simulations reveal four processes: absorption, replacement, transmission and damage. At energies below 110 eV, the dominant process is absorption. For atom in group (a), the process that takes place is replacement, in which the silicon ion removes one carbon atom and occupies the place of the eliminated atom at the incident energy of 72-370 eV. Transmission is present at energies above 100 eV for atom in group (d). Damage is a very important process in current bombardment, and there are four types of defects: single vacancy, replacement-single vacancy, double vacancy and nanopore. The simulations provide a fundamental understanding of the silicon bombardment of graphene, and the parameters required to develop graphene-based devices by controlling defect formation.

  13. Sequence-dependent DNA deformability studied using molecular dynamics simulations

    PubMed Central

    Fujii, Satoshi; Kono, Hidetoshi; Takenaka, Shigeori; Go, Nobuhiro; Sarai, Akinori

    2007-01-01

    Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein–DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein–DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids. PMID:17766249

  14. Molecular Dynamics Simulations of Ion Equilibration in Ultracold Neutral Plasmas

    NASA Astrophysics Data System (ADS)

    Maksimovic, Nikola; Langin, Thomas; Strickler, Trevor; Killian, Thomas

    2015-11-01

    Understanding transport and equilibration in strongly coupled plasmas is important for modeling plasmas found in extreme environments like inertial confinement fusion plasmas and interiors of gas-giant planets. We use molecular dynamics simulations of Yukawa one component plasmas under periodic boundary conditions to study the evolution of strongly coupled ultracold neutral plasmas (UNPs) at early times. Simulations provide access to observable quantities in strongly coupled plasmas, namely correlation functions. Experimentally, the average velocity of an ion subset with a skewed velocity profile has been used to measure velocity autocorrelation functions and provide access to diffusion coefficients and other transport processes in UNPs. Using the simulation, we verify the experimental measurements of average velocities of ion subsets in UNPs and confirm their agreement with the velocity autocorrelation function. Finally, we examine the collective mode behavior of the ions during their equilibration phase by calculating the longitudinal current correlation function at various times during equilibration. This allows us to study the collective mode coupling behavior of the equilibration of ions in UNPs and its dependence on screening parameter.

  15. An alamethicin channel in a lipid bilayer: molecular dynamics simulations.

    PubMed Central

    Tieleman, D P; Berendsen, H J; Sansom, M S

    1999-01-01

    We present the results of 2-ns molecular dynamics (MD) simulations of a hexameric bundle of Alm helices in a 1-palmitoyl-2-oleoylphosphatidylcholine bilayer. These simulations explore the dynamic properties of a model of a helix bundle channel in a complete phospholipid bilayer in an aqueous environment. We explore the stability and conformational dynamics of the bundle in a phospholipid bilayer. We also investigate the effect on bundle stability of the ionization state of the ring of Glu18 side chains. If all of the Glu18 side chains are ionised, the bundle is unstable; if none of the Glu18 side chains are ionized, the bundle is stable. pKA calculations suggest that either zero or one ionized Glu18 is present at neutral pH, correlating with the stable form of the helix bundle. The structural and dynamic properties of water in this model channel were examined. As in earlier in vacuo simulations (Breed et al., 1996 .Biophys. J. 70:1643-1661), the dipole moments of water molecules within the pore were aligned antiparallel to the helix dipoles. This contributes to the stability of the helix bundle. PMID:10096876

  16. Molecular dynamics simulation of thionated hen egg white lysozyme.

    PubMed

    Huang, Wei; Eichenberger, Andreas P; van Gunsteren, Wilfred F

    2012-08-01

    Understanding of the driving forces of protein folding is a complex challenge because different types of interactions play a varying role. To investigate the role of hydrogen bonding involving the backbone, the effect of thio substitutions in a protein, hen egg white lysozyme (HEWL), was investigated through molecular dynamics simulations of native as well as partly (only residues in loops) and fully thionated HEWL using the GROMOS 54A7 force field. The results of the three simulations show that the structural properties of fully thionated HEWL clearly differ from those of the native protein, while for partly thionated HEWL they only changed slightly compared with native HEWL. The analysis of the torsional-angle distributions and hydrogen bonds in the backbone suggests that the α-helical segments of native HEWL tend to show a propensity to convert to 3(10)-helical geometry in fully thionated HEWL. A comparison of the simulated quantities with experimental NMR data such as nuclear overhauser effect (NOE) atom-atom distance bounds and (3)J((H)(N)(H)(α))-couplings measured for native HEWL illustrates that the information content of these quantities with respect to the structural changes induced by thionation of the protein backbone is rather limited.

  17. Molecular dynamics simulation of thionated hen egg white lysozyme

    PubMed Central

    Huang, Wei; Eichenberger, Andreas P; van Gunsteren, Wilfred F

    2012-01-01

    Understanding of the driving forces of protein folding is a complex challenge because different types of interactions play a varying role. To investigate the role of hydrogen bonding involving the backbone, the effect of thio substitutions in a protein, hen egg white lysozyme (HEWL), was investigated through molecular dynamics simulations of native as well as partly (only residues in loops) and fully thionated HEWL using the GROMOS 54A7 force field. The results of the three simulations show that the structural properties of fully thionated HEWL clearly differ from those of the native protein, while for partly thionated HEWL they only changed slightly compared with native HEWL. The analysis of the torsional-angle distributions and hydrogen bonds in the backbone suggests that the α-helical segments of native HEWL tend to show a propensity to convert to 310-helical geometry in fully thionated HEWL. A comparison of the simulated quantities with experimental NMR data such as nuclear overhauser effect (NOE) atom–atom distance bounds and 3JHNHα-couplings measured for native HEWL illustrates that the information content of these quantities with respect to the structural changes induced by thionation of the protein backbone is rather limited. PMID:22653637

  18. Molecular dynamics simulations of Li transport between cathode crystals

    NASA Astrophysics Data System (ADS)

    Garofalini, S. H.

    The molecular dynamics (MD) computer simulation technique has been used to study the effect of an amorphous intergranular film (IGF) present in a polycrystalline cathode on Li transport. The solid electrolyte is a model lithium silicate glass while the cathode is a nanocrystalline vanadia with an amorphous V 2O 5 IGF separating the crystals. Thin (˜1 to a few nanometer thick) IGFs are known to be present in most polycrystalline oxide materials. However, the role of such a film on Li transport in oxide cathodes has not been addressed. Current scanning probe microscopy (SPM) studies have shown that the orientation of the layered nanocrystalline vanadia crystals near the cathode/solid electrolyte interface is not optimized for Li ion transport. While the precise structure of the material between the crystals has not been identified, initially it can be initially considered as likely to be a thin non-crystalline (amorphous) film. This is based on the ubiquitous presence of such a structure in other polycrystalline oxides. Also, and with more relevance to the materials used in thin film batteries, an amorphous film can be expected to form between nanocrystals that crystallized from an amorphous matrix, as would be the case in a deposited thin film cathode. Consistent with simulations of Li transport in amorphous vanadia, the current simulations show that Li ions diffuse more rapidly into the amorphous intergranular thin film than into the layered vanadia with the (0 0 1) planes parallel to the cathode/electrolyte interface.

  19. Energy conservation in molecular dynamics simulations of classical systems.

    PubMed

    Toxvaerd, Søren; Heilmann, Ole J; Dyre, Jeppe C

    2012-06-14

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete "Verlet" algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence of a "shadow Hamiltonian" H [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the original H with the property that the discrete positions of the Verlet algorithm for H lie on the analytic trajectories of H. The shadow Hamiltonian can be obtained from H by an asymptotic expansion in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show analytically as well as numerically that energy conservation is not sensitive to round-off errors.

  20. A combined Event-Driven/Time-Driven molecular dynamics algorithm for the simulation of shock waves in rarefied gases

    SciTech Connect

    Valentini, Paolo Schwartzentruber, Thomas E.

    2009-12-10

    A novel combined Event-Driven/Time-Driven (ED/TD) algorithm to speed-up the Molecular Dynamics simulation of rarefied gases using realistic spherically symmetric soft potentials is presented. Due to the low density regime, the proposed method correctly identifies the time that must elapse before the next interaction occurs, similarly to Event-Driven Molecular Dynamics. However, each interaction is treated using Time-Driven Molecular Dynamics, thereby integrating Newton's Second Law using the sufficiently small time step needed to correctly resolve the atomic motion. Although infrequent, many-body interactions are also accounted for with a small approximation. The combined ED/TD method is shown to correctly reproduce translational relaxation in argon, described using the Lennard-Jones potential. For densities between {rho}=10{sup -4}kg/m{sup 3} and {rho}=10{sup -1}kg/m{sup 3}, comparisons with kinetic theory, Direct Simulation Monte Carlo, and pure Time-Driven Molecular Dynamics demonstrate that the ED/TD algorithm correctly reproduces the proper collision rates and the evolution toward thermal equilibrium. Finally, the combined ED/TD algorithm is applied to the simulation of a Mach 9 shock wave in rarefied argon. Density and temperature profiles as well as molecular velocity distributions accurately match DSMC results, and the shock thickness is within the experimental uncertainty. For the problems considered, the ED/TD algorithm ranged from several hundred to several thousand times faster than conventional Time-Driven MD. Moreover, the force calculation to integrate the molecular trajectories is found to contribute a negligible amount to the overall ED/TD simulation time. Therefore, this method could pave the way for the application of much more refined and expensive interatomic potentials, either classical or first-principles, to Molecular Dynamics simulations of shock waves in rarefied gases, involving vibrational nonequilibrium and chemical reactivity.

  1. Hybrid molecular dynamics simulation for plasma induced damage analysis

    NASA Astrophysics Data System (ADS)

    Matsukuma, Masaaki

    2016-09-01

    In order to enable further device size reduction (also known as Moore's law) and improved power performance, the semiconductor industry is introducing new materials and device structures into the semiconductor fabrication process. Materials now include III-V compounds, germanium, cobalt, ruthenium, hafnium, and others. The device structure in both memory and logic has been evolving from planar to three dimensional (3D). One such device is the FinFET, where the transistor gate is a vertical fin made either of silicon, silicon-germanium or germanium. These changes have brought renewed interests in the structural damages caused by energetic ion bombardment of the fin sidewalls which are exposed to the ion flux from the plasma during the fin-strip off step. Better control of the physical damage of the 3D devices requires a better understanding of the damage formation mechanisms on such new materials and structures. In this study, the damage formation processes by ion bombardment have been simulated for Si and Ge substrate by Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid simulations and compared to the results from the classical molecular dynamics (MD) simulations. In our QM/MM simulations, the highly reactive region in which the structural damage is created is simulated with the Density Functional based Tight Binding (DFTB) method and the region remote from the primary region is simulated using classical MD with the Stillinger-Weber and Moliere potentials. The learn on the fly method is also used to reduce the computational load. Hence our QM/MM simulation is much faster than the full QC-MD simulations and the original QM/MM simulations. The amorphous layers profile simulated with QM/MM have obvious differences in their thickness for silicon and germanium substrate. The profile of damaged structure in the germanium substrate is characterized by a deeper tail then in silicon. These traits are also observed in the results from the mass selected ion beam

  2. Molecular dynamics simulation of silicate glasses and their surfaces

    NASA Astrophysics Data System (ADS)

    Yuan, Xianglong

    1999-12-01

    The bulk and surface structures of vitreous silica and silicate glasses have been modeled using the molecular dynamics technique. An extensive preliminary study, on the influences of different potential models and of different simulation approaches on the final bulk and surface structures, concludes that good result can be obtained using the constant volume simulation with a modified pair-wise potential from van Beest and coworkers, together with alkali-oxygen potential models developed in this study. Glass structures with the reliability factors, Rchi of 7.2% for vitreous silica and 5.6% for sodium silicate have been achieved. The environments of O, Si and Na in silicate glasses have been thoroughly examined. Considerable similarities in local structures exist between crystalline and the simulated glass structures. It is found that our simulated glasses more resemble high-pressured experimental glasses, which is implied by the existence of fivefold silicon species. Based on bulk structures studied, glass surfaces were created by a fracture process. It is speculated that surface defect concentrations depend on the topological characteristics of the network structure, and are essential for the viability of surfaces. Analysis of local structures for difference species implies that the sodium silicate surfaces resemble more the Na-rich regions in the bulk structures. An efficient algorithm for finding primitive rings in a topological network has been developed. Analysis using this algorithm shows that reconstruction of Na-rich regions occurs on extending simulation size, demonstrating simulation size influence on modeled glass structures. Finally, our detailed analysis of Si-O-Si bond angle distributions demonstrates that vitreous silica glass has a broader Si-O-Si BAD, whilst sodium silicate glasses favor narrower distributions.

  3. Insights from molecular dynamics simulations for computational protein design.

    PubMed

    Childers, Matthew Carter; Daggett, Valerie

    2017-02-01

    A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

  4. Molecular Dynamics Simulations of Diffusion in a Silica Melt

    NASA Astrophysics Data System (ADS)

    Gemmell, A.; Fraser, D.; Refson, K.

    2003-12-01

    Computer modelling of silicate melts enables the study of pressure-temperature conditions not easily obtainable by traditional experimentation (e.g. 1). Diffusion in melts under various conditions is critical to our understanding of a variety of processes such as melt crystallisation, magma mixing and the behaviour of trace elements during magma ascent that underpins the field of igneous petrogenesis. It can also provide information on melt structure via diffusion mechanisms and their activation energies. In the present paper, the magnitude and mechanism of diffusion of silicon and oxygen in molten silica has been investigated by molecular dynamics using a modified BKS potential (2). A range of melt temperatures and pressures were studied with a view to understanding the relationship between temperature, pressure, diffusion and melt structure. At each P-T point studied, the system was equilibrated for between 1 million and 40 million 1fs steps depending on the conditions, with data collection over the same time range. The potential was adjusted to overcome problems with instability in the particle velocities at high temperature. The simulations were run at the Oxford University Supercomputing centre, UK. Systems of 144, 288, 576 and 1152 particles were investigated. In addition, two different sets of periodic boundary conditions were used - cubic and truncated octahedral. The latter was found to provide a better ratio of simulated time to compute time. The present data extend the range of data available and indicate a pronounced non-linearity in the temperature dependence of diffusion, as shown by plots of log10D with 1/T. The second derivative is greatest around 3500K. At least two different diffusion mechanisms may operate at lower and higher temperatures with differing activation energies. Comparison with previous molecular dynamics data shows broad agreement with most studies. Although the data presented do include some low temperature runs, comparison with

  5. Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.

    PubMed

    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

  6. The Art of Molecular Dynamics Simulation (by D. C. Rapaport)

    NASA Astrophysics Data System (ADS)

    Molner, Stephen P.

    1999-02-01

    Cambridge University Press: New York, 1996. 400 pp. ISBN 0 521 44561 2. $74.95. This book describes the extremely powerful techniques of molecular dynamics simulation. The techniques involve solving the classical many-body problems in contexts relevant to the study of matter at the atomic level. The method allows the prediction of static and dynamics properties of substances directly from the underlying interactions between molecules. This is, of course, a very broad subject and the author has adopted a dual approach in that the text is partly tutorial and also contains a large number of computer programs for practical use. Rapaport has adopted the attitude of trying the simplest method first. Atoms are modeled as point particles interacting through point potentials. Molecules are represented by atoms with orientation dependent forces, or as extended structures each containing several interaction sites. The molecules may be rigid, flexible, or somewhere in between, and if there are internal degrees of freedom there will be internal forces as well. The intent of the book is not to discuss the design of molecular models, but rather to make use of existing models, and from a pedagogical viewpoint the simpler the model the better. The aim of the book is to demonstrate the general methodology of molecular dynamics simulation by example, not to review the large body of literature covering the many different kinds of models developed for specific applications. The text is partly tutorial, but also contains a large number of computer programs for practical use. This volume will serve as an introduction to the subject for beginners and as a reference manual for the more experienced practitioner. The material covers a wide range of practical methods and real applications and is organized as a series of case studies. The typical case study includes a summary of the theoretical background used for the formulation of the computational approach. That is described by either a

  7. Molecular Dynamics Simulations of Spinodal-Assisted Polymer Crystallization

    SciTech Connect

    Gee, R H; Lacevic, N M; Fried, L

    2005-07-08

    Large scale molecular dynamics simulations of bulk melts of polar (poly(vinylidene fluoride) (pVDF)) polymers are utilized to study chain conformation and ordering prior to crystallization under cooling. While the late stages of polymer crystallization have been studied in great detail, recent theoretical and experimental evidence indicates that there are important phenomena occurring in the early stages of polymer crystallization that are not understood to the same degree. When the polymer melt is quenched from a temperature above the melting temperature to the crystallization temperature, crystallization does not occur instantaneously. This initial interval without crystalline order is characterized as an induction period. It has been thought of as a nucleation period in the classical theories of polymer crystallization, but recent experiments, computer simulations, and theoretical work suggest that the initial period in polymer crystallization is assisted by a spinodal decomposition type mechanism. In this study we have achieved physically realistic length scales to study early stages of polymer ordering, and show that spinodal-assisted ordering prior to crystallization is operative in polar polymers suggesting general applicability of this process.

  8. The superspreading mechanism unveiled via molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Theodorakis, Panagiotis; Muller, Erich; Craster, Richard; Matar, Omar

    2014-11-01

    Superspreading, by which aqueous droplets laden with specific surfactants wet hydrophobic substrates, is an unusual and dramatic phenomenon. This is attributed to various factors, e.g., a particular surfactant geometry, Marangoni flow, unique solid-fluid interactions, however, direct evidence for a plausible mechanism for superspreading has not yet been provided. Here, we use molecular dynamics simulations of a coarse-grained model with force fields obtained from the SAFT- γ equation of state to capture the superspreading mechanism of water drops with surfactants on model surfaces. Our simulations highlight and monitor the main features of the molecular behavior that lead to the superspreading mechanism, and reproduce and explain the experimentally-observed characteristic maxima of the spreading rate of the droplet vs. surfactant concentration and wettability. We also present a comparison between superspreading and non-superspreading surfactants underlining the main morphological and energetic characteristics of superspreaders. We believe that this is the first time a plausible superspreading mechanism based on a microscopic description is proposed; this will enable the design of surfactants with enhanced spreading ability specifically tailored for applications. EPSRC Grant Number EP/J010502/1.

  9. Energetics of a heat engine: a molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Tadele, Kumneger; Tatek, Yergou B.; Bekele, Mulugeta

    2016-11-01

    We perform a classical molecular dynamics simulation study of a heat engine operating between two heat reservoirs and performing a Carnot-like cycle in a finite time over a wide range of process rates. The working substance of the heat engine is made of highly concentrated interacting Lennard-Jones particles with the aim to simulate a real gas. The piston speed and temperature ratio of the cold and hot heat reservoirs are used as control parameters whereas efficiency and power output per cycle are the physical quantities of interest. The variation of these quantities as a function of the independent parameters is studied with the objective to investigate the validity of relevant theoretical predictions. For instance, for small process rates, the linear dependence of the heat engine efficiency with temperature ratio, in agreement with theory, has been demonstrated. Finally, a unified optimization criterion is applied to determine optimum operation conditions of the engine that make the best trade-off between efficiency and power output.

  10. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

    PubMed

    Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver

    2011-07-30

    MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.

  11. Local structure in anisotropic systems determined by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Komolkin, Andrei V.; Maliniak, Arnold

    In the present communication we describe the investigation of local structure using a new visualization technique. The approach is based on two-dimensional pair correlation functions derived from a molecular dynamics computer simulation. We have used this method to analyse a trajectory produced in a simulation of a nematic liquid crystal of 4-n-pentyl-4'-cyanobiphenyl (5CB) (Komolkin et al., 1994, J. chem. Phys., 101, 4103). The molecule is assumed to have cylindrical symmetry, and the liquid crystalline phase is treated as uniaxial. The pair correlation functions or cylindrical distribution functions (CDFs) are calculated in the molecular (m) and laboratory (l) frames, gm2(z1 2, d1 2) and g12(Z1 2, D1 2). Anisotropic molecular organization in the liquid crystal is reflected in laboratory frame CDFs. The molecular excluded volume is determined and the effect of the fast motion in the alkyl chain is observed. The intramolecular distributions are included in the CDFs and indicate the size of the motional amplitude in the chain. Absence of long range order was confirmed, a feature typical for a nematic liquid crystal.

  12. Post-processing interstitialcy diffusion from molecular dynamics simulations

    SciTech Connect

    Bhardwaj, U.; Bukkuru, S.; Warrier, M.

    2016-01-15

    An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:.

  13. Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution

    PubMed Central

    Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E.; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W.

    2011-01-01

    Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly-developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions. PMID:21812485

  14. Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations

    PubMed Central

    2013-01-01

    Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins. PMID:23298176

  15. Simulating Heat Flux and Bubble Nucleation using Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Karayiannis, Tassos; Smith, Edward; Sefiane, Khellil; Matar, Omar

    2016-11-01

    Modelling the heat flux in multiphase flow situations must account for nucleation of bubbles, non-linear heat transfer coefficients, complex molecular interaction at the surface, detailed surface textures as well as build up of material on the surface. These complex factors combine to define the well known boiling curve, which characterises the heat flux for a given temperature gradient. Understanding and optimisation of this boiling curve, and its critical heat flux (CHF), is a problem of great importance. Molecular dynamics (MD), by modelling the motion of the individual molecules, can replicate the bubble nucleation and heat flux. Details of the wall-fluid interaction are represented with complex textures and the surface materials can be explicitly reproduced. In this talk, MD simulation results are presented for bubble nucleation and heat flux. The heat flux is matched to experimental results and the process of nucleation explored for both fractal and textured surfaces. The unique insights from the molecular scale are discussed and potential applications including surface design and coupled molecular to continuum simulation are presented. EPSRC UK platform Grant MACIPh (EP/L020564/1).

  16. Structural properties of CHAPS micelles, studied by molecular dynamics simulations.

    PubMed

    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.

  17. Self-pinning of a nanosuspension droplet: Molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Shi, Baiou; Webb, Edmund B.

    2016-07-01

    Results are presented from molecular dynamics simulations of Pb(l) nanodroplets containing dispersed Cu nanoparticles (NPs) and spreading on solid surfaces. Three-dimensional simulations are employed throughout, but droplet spreading and pinning are reduced to two-dimensional processes by modeling cylindrical NPs in cylindrical droplets; NPs have radius RNP≅3 nm while droplets have initial R0≅42 nm . At low particle loading explored here, NPs in sufficient proximity to the initial solid-droplet interface are drawn into advancing contact lines; entrained NPs eventually bind with the underlying substrate. For relatively low advancing contact angle θadv, self-pinning on entrained NPs occurs; for higher θadv, depinning is observed. Self-pinning and depinning cases are compared and forces on NPs at the contact line are computed during a depinning event. Though significant flow in the droplet occurs in close proximity to the particle during depinning, resultant forces are relatively low. Instead, forces due to liquid atoms confined between the particles and substrate dominate the forces on NPs; that is, for the NP size studied here, forces are interface dominated. For pinning cases, a precursor wetting film advances ahead of the pinned contact line but at a significantly slower rate than for a pure droplet. This is because the precursor film is a bilayer of liquid atoms on the substrate surface but it is instead a monolayer film as it crosses over pinning particles; thus, mass delivery to the bilayer structure is impeded.

  18. Microstructure evolution of polycrystalline silicon by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Chen, Xiao; Ding, Jianning; Jiang, Cunhua; Liu, Zunfeng; Yuan, Ningyi

    2017-06-01

    Polycrystalline silicon is the dominant material in solar cells and plays an important role in photovoltaic industry. It is important for not only the conventional production of silicon ingots but also the direct growth of silicon wafers to control crystallization for obtaining the desired polycrystalline silicon. To the best of our knowledge, few studies have systematically reported about the effects of crystalline planes on the solidification behavior of liquid silicon and the analysis of the microstructural features of the polysilicon structure. In this study, molecular dynamics simulations were employed to investigate the solidification and microstructure evolution of polysilicon, with focus on the effects of the seed distribution and cooling rate on the growth of polycrystalline silicon. The (110), (111), and (112) planes were extruded by the (100) plane and formed the inclusion shape. The crystallization of silicon consisted of diamond-type structures is relatively high at a low cooling rate. The simulations provide substantial information regarding microstructures and serve as guidance for the growth of polycrystalline silicon.

  19. Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems.

    PubMed

    Chiu, Matt; Herbordt, Martin C

    2010-11-01

    The acceleration of molecular dynamics (MD) simulations using high-performance reconfigurable computing (HPRC) has been much studied. Given the intense competition from multicore and GPUs, there is now a question whether MD on HPRC can be competitive. We concentrate here on the MD kernel computation: determining the short-range force between particle pairs. In one part of the study, we systematically explore the design space of the force pipeline with respect to arithmetic algorithm, arithmetic mode, precision, and various other optimizations. We examine simplifications and find that some have little effect on simulation quality. In the other part, we present the first FPGA study of the filtering of particle pairs with nearly zero mutual force, a standard optimization in MD codes. There are several innovations, including a novel partitioning of the particle space, and new methods for filtering and mapping work onto the pipelines. As a consequence, highly efficient filtering can be implemented with only a small fraction of the FPGA's resources. Overall, we find that, for an Altera Stratix-III EP3ES260, 8 force pipelines running at nearly 200 MHz can fit on the FPGA, and that they can perform at 95% efficiency. This results in an 80-fold per core speed-up for the short-range force, which is likely to make FPGAs highly competitive for MD.

  20. Molecular dynamics simulation of dipalmitoylphosphatidylcholine membrane with cholesterol sulfate.

    PubMed Central

    Smondyrev, A M; Berkowitz, M L

    2000-01-01

    Using the molecular dynamics simulation technique, we studied the changes occurring in a dipalmitoylphosphatidylcholine (DPPC):cholesterol (CH) membrane at 50 mol% sterol when cholesterol is replaced with cholesterol sulfate (CS). Our simulations were performed at constant pressure and temperature on a nanosecond time scale. We found that 1) the area per DPPC:CS heterodimer is greater than the area of the DPPC:CH heterodimer; 2) CS increases ordering of DPPC acyl chains, but to a lesser extent than CH; 3) the number of hydrogen bonds between DPPC and water is decreased in a CS-containing membrane, but CS forms more water hydrogen bonds than CH; and 4) the membrane dipole potential reverses its sign for a DPPC-CS membrane compared to a DPPC-CH bilayer. We also studied the changes occurring in lipid headgroup conformations and determined the location of CS molecules in the membrane. Our results are in good agreement with the data available from experiments. PMID:10733950

  1. Molecular dynamics simulations of polymer crystallization via self-seeding

    NASA Astrophysics Data System (ADS)

    Luo, Chuanfu; Sommer, Jens-Uwe

    2010-03-01

    We use large scale molecular dynamics (MD) to simulate the processes of polymer crystallization with a coarse-grained model. In total we are able to simulate 1000 polymer chains made of 1000 monomers each, a system large enough to compare to experimental relevant, entangled melts. It is found that some micro crystalline domains (MCDs) can survive slightly above the apparent melting temperature after a consistent cooling and reheating cycle. We chose the stablest MCD as a baby seed and let it grow at a constant quenched temperature. A single lamella can be formed via this self-seeding process. We observe the growth pathway and analyze the chain dynamics especially at the growth front.[4pt] [1] C. Luo and J. Sommer, Comp Phys. Comm. 180, 1382 (2009)[0pt] [2] C. Luo and J. Sommer, Phys. Rev. Lett. 102, 147801 (2009)[0pt] [3] J-J. Xu, Y. Ma, W.B. Hu, M. Rehahn and G. Reiter, Nature Materials 8, 348 (2009)

  2. Simulation of Gold Functionalization with Cysteine by Reactive Molecular Dynamics.

    PubMed

    Monti, Susanna; Carravetta, Vincenzo; Ågren, Hans

    2016-01-21

    The anchoring mechanism of cysteine to gold in water solution is characterized in detail by means of a combination of quantum chemistry (QC) and reactive classical molecular dynamics (RC-MD) calculations. A possible adsorption-reaction route is proposed, through RC-MD simulations based on a modified version of the protein reactive force field (ReaxFF), in which gold-protein interactions have been included after accurate parametrization at the QC level. The computational results confirm recent experimental findings regarding the mechanism as a two-step binding, namely, a slow physisorption followed by a fast chemisorption. The reaction barriers are estimated through the nudged elastic band approach and checked by QC calculations. Surface reconstructions, induced by the strong adsorption of the molecule, are identified, and their role, as further adsorbate stabilizers, is properly disclosed. The satisfactory agreement with QC data and experiments confirm the reliability of the simulations and the unique opportunity they provide to follow locally molecule adsorption on selected materials.

  3. Enhanced molecular dynamics for simulating porous interphase layers in batteries.

    SciTech Connect

    Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan

    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.

  4. Virtual-Wall Model for Molecular Dynamics Simulation.

    PubMed

    Qian, Lijuan; Tu, Chengxu; Bao, Fubing; Zhang, Yonghao

    2016-12-09

    A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the atomic wall causes the periodicity of the force acting on a fluid molecule from the wall molecules. This force is first calculated and then stored in the memory. A fluid molecule appearing in the wall force field is subjected to the force from the wall molecules. The force can then be determined by the position of the molecule relative to the wall. This model avoids excessive calculations of fluid-wall interactions and reduces the computational time drastically. The time reduction is significant for small fluid density and channel height. The virtual-wall model is applied to Poiseuille and Couette flows, and to a flow in a channel with a rough surface. Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. The appropriate bin size and cut-off radius in the virtual-wall model are also discussed.

  5. Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lu, Yan; Salsbury, Freddie R.

    2015-01-01

    ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.

  6. Molecular Dynamics Simulations of Fracture of Model Epoxies

    SciTech Connect

    STEVENS,MARK J.

    2000-01-18

    The failure of thermosetting polymer adhesives is an important problem which particularly lacks understanding from the molecular viewpoint. While linear elastic fracture mechanics works well for such polymers far from the crack tip, the method breaks down near the crack tip where large plastic deformation occurs and the molecular details become important [1]. Results of molecular dynamics simulations of highly crosslinked polymer networks bonded to a solid surface are presented here. Epoxies are used as the guide for modeling. The focus of the simulations is the network connectivity and the interfacial strength. In a random network, the bond stress is expected to vary, and the most stressed bonds will break first [2]. Crack initiation should occur where a cluster of highly constrained bonds exists. There is no reason to expect crack initiation to occur at the interface. The results to be presented show that the solid surface limits the interfacial bonding resulting in stressed interfacial bonds and interfacial fracture. The bonds in highly-crosslinked random networks do not become stressed as expected. The sequence of molecular structural deformations that lead to failure has been determined and found to be strongly dependent upon the network connectivity. The structure of these networks and its influence on the stress-strain behavior will be discussed in general. A set of ideal, ordered networks have been constructed to manipulate the deformation sequence to achieve different fracture modes (i.e. cohesive vs. adhesive).

  7. GPU-enabled molecular dynamics simulations of ankyrin kinase complex

    NASA Astrophysics Data System (ADS)

    Gautam, Vertika; Chong, Wei Lim; Wisitponchai, Tanchanok; Nimmanpipug, Piyarat; Zain, Sharifuddin M.; Rahman, Noorsaadah Abd.; Tayapiwatana, Chatchai; Lee, Vannajan Sanghiran

    2014-10-01

    The ankyrin repeat (AR) protein can be used as a versatile scaffold for protein-protein interactions. It has been found that the heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. Using ILK-AR with high affinity for the PINCH1 as our model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. In this study, the long time scale dynamics simulations with GPU accelerated molecular dynamics (MD) simulations in AMBER12 have been performed to locate the hot spots of protein-protein interaction by the analysis of the Molecular Mechanics-Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA) of the MD trajectories. Our calculations suggest good binding affinity of the complex and also the residues critical in the binding.

  8. The collapsing bubble in a liquid by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Xiao, C.; Heyes, D. M.; Powles, J. G.

    Molecular dynamics simulations have been made of a collapsing bubble or cavity in a simple liquid. Simulations of a Lennard-Jones liquid reveal that the collapsing process takes place in a series of stages. First, the 'hottest' molecules from the high kinetic energy tail in the Maxwell-Boltzmann distribution diffuse into the empty cavity. This is followed by a gradual filling in of the cavity until the density in the centre is a little lower than that of the bulk liquid. The system eventually reaches a final new equilibrium liquid state through a subsequent slower equilibration phase. The bubble fills in an oscillatory manner, by partly filling in, and then partially emptying, and so on, with ever decreasing amplitude towards the final uniform liquid state. These density oscillations are more obvious in systems with a larger bubble. Similar oscillations are observed in the kinetic energy of the molecules at selected radii from the centre of the initial bubble. The maximum temperature occurs typically at the end of the initial fillingin stage during which the density of the core undergoes a vapour-to-liquid phase transition, the released latent heat probably contributing to the temperatures achieved in this region. The average maximum temperature found in the smallest system examined is about nine times the critical temperature, which is about 6000K for water, thus suggesting a simple mechanism for producing molecules with the sorts of kinetic energies and lifetimes required for sonoluminescence.

  9. Orbital-Free Molecular Dynamics Simulations at Extreme Conditions

    NASA Astrophysics Data System (ADS)

    Kress, J. D.; Collins, L. A.; Ticknor, C.

    2015-06-01

    Large-scale molecular dynamics (MD) simulations in an orbital-free (OF) density-functional theory (DFT) formulation have been performed for pure and mixed species over a broad range of temperatures (T) and densities (ρ) that includes the warm, dense matter and high-energy density physics regimes. A finite-temperature Thomas-Fermi-Dirac form with a local-density exchange-correlation potential and a regularized electron-ion interaction represents the quantum nature of the electrons. In particular, we examine the efficacy of the OFMD approach as an effective bridge between Kohn-Sham DFT MD at low temperatures and simple, fully-ionized plasma models at high temperatures. Comparisons against intermediate-range constructions such as the Yukawa and one-component plasmas are also made. We examine the mass transport (diffusion, viscosity) properties of various systems, ranging from light to heavy elements, including lithium hydride (LiH), mixtures of LiH with uranium, mixtures of deuterium-tritium (DT) with plutonium and mixtures of DT with plastic (CH). The OFMD mass transport results have been fitted to simple functions of ρ and T suitable for use in hydrodynamics simulation codes.

  10. Molecular dynamics simulations of He bubble nucleation at grain boundaries

    SciTech Connect

    Yongfeng Zhang; Paul C Millett; Michael Tonks; Liangzhe Zhang; Bulent Biner

    2012-08-01

    The nucleation behavior of He bubbles in nano-grained body-centered-cubic (BCC) Mo is simulated using molecular dynamics (MD) simulations with a bicrystal model, focusing on the effect of grain boundary (GB) structure. Three types of GBs, the (100) twist S29, the ?110? symmetrical tilt (tilt angle of 10.1?), and the (112) twin boundaries, are studied as representatives of random GB, low angle GB with misfit dislocations, and special sigma boundaries. With the same amount of He, more He clusters form in nano-grained Mo with smaller average size compared to that in bulk. The effects of the GB structure originate from the excess volume in GBs. Trapping by excess volume results in reduction in mobility of He atoms, which enhances the nucleation with higher density of bubbles, and impedes the growth of He bubbles by absorption of mobile He atoms. Furthermore, the distribution of excess volume in GBs determines the distribution of He clusters. The effect of GBs becomes less pronounced with increasing vacancy concentration in the matrix.

  11. Molecular dynamics simulations of cavitation bubble collapse and sonoluminescence

    NASA Astrophysics Data System (ADS)

    Schanz, Daniel; Metten, Burkhard; Kurz, Thomas; Lauterborn, Werner

    2012-11-01

    The dynamics of the medium within a collapsing and rebounding cavitation bubble is investigated by means of molecular dynamics (MD) simulations adopting a hard sphere model for the species inside the bubble. The dynamics of the surrounding liquid (water) is modelled using a Rayleigh-Plesset (RP)-type equation coupled to the bubble interior by the gas pressure at the wall obtained from the MD calculations. Water vapour and vapour chemistry are included in the RP-MD model as well as mass and energy transfer through the bubble wall. The calculations reveal the evolution of temperature, density and pressure within a bubble at conditions typical of single-bubble sonoluminescence and predict how the particle numbers and densities of different vapour dissociation and reaction products in the bubble develop in space and time. Among the parameters varied are the sound pressure amplitude of a sonoluminescence bubble in water, the noble gas mixture in the bubble and the accommodation coefficients for mass and energy exchange through the bubble wall. Simulation particle numbers up to 10 million are used; most calculations, however, are performed with one million particles to save computer run time. Validation of the MD code was done by comparing MD results with solutions obtained by continuum mechanics calculations for the Euler equations.

  12. Path-integral molecular dynamics simulation of diamond

    NASA Astrophysics Data System (ADS)

    Ramírez, Rafael; Herrero, Carlos P.; Hernández, Eduardo R.

    2006-06-01

    Diamond is studied by path-integral molecular dynamics simulations of the atomic nuclei in combination with a tight-binding Hamiltonian to describe its electronic structure and total energy. This approach allows us to quantify the influence of quantum zero-point vibrations and finite temperatures on both the electronic and vibrational properties of diamond. The electron-phonon coupling mediated by the zero-point vibration reduces the direct electronic gap of diamond by 10%. The calculated decrease of the direct gap with temperature shows good agreement with the experimental data available up to 700K . Anharmonic vibrational frequencies of the crystal have been obtained from a linear-response approach based on the path integral formalism. In particular, the temperature dependence of the zone-center optical phonon has been derived from the simulations. The anharmonicity of the interatomic potential produces a red shift of this phonon frequency. At temperatures above 500K , this shift is overestimated in comparison to available experimental data. The predicted temperature shift of the elastic constant c44 displays reasonable agreement with the available experimental results.

  13. Molecular dynamics simulation of solvated protein at high pressure.

    PubMed

    Kitchen, D B; Reed, L H; Levy, R M

    1992-10-20

    We have completed a molecular dynamics simulation of protein (bovine pancreatic trypsin inhibitor, BPTI) in solution at high pressure (10 kbar). The structural and energetic effects of the application of high pressure to solvated protein are analyzed by comparing the results of the high-pressure simulation with a corresponding simulation at low pressure. The volume of the simulation cell containing one protein molecule plus 2943 water molecules decreases by 24.7% at high pressure. This corresponds to a compressibility for the protein solution of beta = 1.8 x 10(-2) kbar-1. The compressibility of the protein is estimated to be about one-tenth that of bulk water, while the protein hydration layer water is found to have a greater compressibility as compared to the bulk, especially for water associated with hydrophobic groups. The radius of gyration of BPTI decreases by 2% and there is a one third decrease in the protein backbone atomic fluctuations at high pressure. We have analyzed pressure effects on the hydration energy of the protein. The total hydration energy is slightly (4%) more favorable at high pressure even though the surface accessibility of the protein has decreased by a corresponding amount. Large pressure-induced changes in the structure of the hydration shell are observed. Overall, the solvation shell waters appear more ordered at high pressure; the pressure-induced ordering is greatest for nonpolar surface groups. We do not observe evidence of pressure-induced unfolding of the protein over the 100-ps duration of the high-pressure simulation. This is consistent with the results of high-pressure optical experiments on BPTI.(ABSTRACT TRUNCATED AT 250 WORDS)

  14. Car-Parrinello molecular dynamics simulation of Fe 3+ (aq).

    PubMed

    Amira, Sami; Spångberg, Daniel; Zelin, Viktor; Probst, Michael; Hermansson, Kersti

    2005-07-28

    The optimized geometry and energetic properties of Fe(D2O)n 3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe 3+ ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell...second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.

  15. Thermophysical properties of energetic ionic liquids/nitric acid mixtures: insights from molecular dynamics simulations.

    PubMed

    Hooper, Justin B; Smith, Grant D; Bedrov, Dmitry

    2013-09-14

    Molecular dynamics (MD) simulations of mixtures of the room temperature ionic liquids (ILs) 1-butyl-4-methyl imidazolium [BMIM]/dicyanoamide [DCA] and [BMIM][NO3(-)] with HNO3 have been performed utilizing the polarizable, quantum chemistry based APPLE&P(®) potential. Experimentally it has been observed that [BMIM][DCA] exhibits hypergolic behavior when mixed with HNO3 while [BMIM][NO3(-)] does not. The structural, thermodynamic, and transport properties of the IL/HNO3 mixtures have been determined from equilibrium MD simulations over the entire composition range (pure IL to pure HNO3) based on bulk simulations. Additional (non-equilibrium) simulations of the composition profile for IL/HNO3 interfaces as a function of time have been utilized to estimate the composition dependent mutual diffusion coefficients for the mixtures. The latter have been employed in continuum-level simulations in order to examine the nature (composition and width) of the IL/HNO3 interfaces on the millisecond time scale.

  16. Nonequilibrium molecular dynamics of the rheological and structural properties of linear and branched molecules. Simple shear and poiseuille flows; instabilities and slip.

    PubMed

    Castillo-Tejas, Jorge; Alvarado, Juan F J; González-Alatorre, Guillermo; Luna-Bárcenas, Gabriel; Sanchez, Isaac C; Macias-Salinas, Ricardo; Manero, Octavio

    2005-08-01

    Nonequilibrium molecular-dynamics simulations are performed for linear and branched chain molecules to study their rheological and structural properties under simple shear and Poiseuille flows. Molecules are described by a spring-monomer model with a given intermolecular potential. The equations of motion are solved for shear and Poiseuille flows with Lees and Edward's [A. W. Lees and S. F. Edwards, J. Phys. C 5, 1921 (1972)] periodic boundary conditions. A multiple time-scale algorithm extended to nonequilibrium situations is used as the integration method, and the simulations are performed at constant temperature using Nose-Hoover [S. Nose, J. Chem. Phys. 81, 511 (1984)] dynamics. In simple shear, molecules with flow-induced ellipsoidal shape, having significant segment concentrations along the gradient and neutral directions, exhibit substantial flow resistance. Linear molecules have larger zero-shear-rate viscosity than that of branched molecules, however, this behavior reverses as the shear rate is increased. The relaxation time of the molecules is associated with segment concentrations directed along the gradient and neutral directions, and hence it depends on structure and molecular weight. The results of this study are in qualitative agreement with other simulation studies and with experimental data. The pressure (Poiseuille) flow is induced by an external force F(e) simulated by confining the molecules in the region between surfaces which have attractive forces. Conditions at the boundary strongly influence the type of the slip flow predicted. A parabolic velocity profile with apparent slip on the wall is predicted under weakly attractive wall conditions, independent of molecular structure. In the case of strongly attractive walls, a layer of adhered molecules to the wall produces an abrupt distortion of the velocity profile which leads to slip between fluid layers with magnitude that depends on the molecular structure. Finally, the molecular deformation

  17. Protein Under Pressure: Molecular Dynamics Simulation of the Arc Repressor

    SciTech Connect

    Trzesniak, Daniel Rodrigo F.; Lins, Roberto D.; van Gunsteren, Wilfred F.

    2006-10-01

    Experimental nuclear magnetic resonance results for the Arc Repressor have shown that this dimeric protein dissociates into a molten globule at high pressure. This structural change is accompanied by a modification of the hydrogenbonding pattern of the intermolecular -sheet: it changes its character from intermolecular to intramolecular with respect to the two monomers. Molecular dynamics simulations of the Arc Repressor, as a monomer and a dimer, at elevated pressure have been performed with the aim to study this hypothesis and to identify the major structural and dynamical changes of the protein under such conditions. The monomer appears less stable than the dimer. However, the complete dissociation has not been seen because of the long timescale needed to observe this phenomenon. In fact, the protein structure altered very little when increasing the pressure. It became slightly compressed and the dynamics of the side-chains and the unfolding process slowed down. Increasing both, temperature and pressure, a tendency of conversion of intermolecular into intramolecular hydrogen bonds in the -sheet region has been detected, supporting the mentioned hypothesis. Also, the onset of denaturation of the separated chains was observed.

  18. Nucleation of Salt Crystals in Clay Minerals: Molecular Dynamics Simulation.

    PubMed

    Dashtian, Hassan; Wang, Haimeng; Sahimi, Muhammad

    2017-07-20

    Nucleation of salt crystals in confined media occurs in many processes of high importance, such as injection of CO2 in geological formations for its sequestration. In particular, salt precipitation in clays, a main component of sedimentary rock, is an important phenomenon. The crystals precipitate on the pores' surface, modify the pore space morphology, and reduce its flow and transport properties. Despite numerous efforts to understand the mechanisms of nucleation of salt crystals in confined media, the effect of the clay's chemistry on the growth, distribution, and properties of the crystals is not well understood. We report the results of extensive molecular dynamics simulation of nucleation and growth of NaCl crystals in a clay pore using molecular models of two types of clay minerals, Na-montmorillonite and kaolinite. Clear evidence is presented for the nucleation of the salt crystals that indicates that the molecular structure of clay minerals affects their spatial distribution, although the nucleation mechanism is the same in both types of clays.

  19. Thermophoresis in liquids: a molecular dynamics simulation study.

    PubMed

    Han, Minsub

    2005-04-01

    Thermophoresis in liquids is studied by molecular dynamics simulation (MD). A theory is developed that divides the problem in the way consistent with the characteristic scales. MD is then conducted to obtain the solution of each problem, which is to be all combined for macroscopic predictions. It is shown that when the temperature gradient is applied to the nonconducting liquid bath that contains neutral particles, there occurs a pressure gradient tangential to the particle surface at the particle-liquid interface. This may induce the flow in the interfacial region and eventually the particle to move. This applies to the material system that interacts through van der Waals forces and may be a general source of the thermophoresis phenomenon in liquids. The particle velocity is linearly proportional to the temperature gradient. And, in a large part of the given temperature range, the particle motion is in the direction toward the cold end and decreases with respect to the temperature. It is also shown that the particle velocity decreases or even reverses its sign in the lowest limit of the temperature range or with a particle of relatively weak molecular interactions with the liquid. The characteristics of the phenomenon are analyzed in molecular details.

  20. Hydrotropic Solubilization by Urea Derivatives: A Molecular Dynamics Simulation Study

    PubMed Central

    Cui, Yong

    2013-01-01

    Hydrotropy is a phenomenon where the presence of a large quantity of one solute enhances the solubility of another solute. The mechanism of this phenomenon remains a topic of debate. This study employed molecular dynamics simulation to investigate the hydrotropic mechanism of a series of urea derivatives, that is, urea (UR), methylurea (MU), ethylurea (EU), and butylurea (BU). A poorly water-soluble compound, nifedipine (NF), was used as the model solute that was solubilized. Structural, dynamic, and energetic changes upon equilibration were analyzed to supply insights to the solubilization mechanism. The study demonstrated that NF and urea derivatives underwent significant nonstoichiometric molecular aggregation in the aqueous solution, a result consistent with the self-aggregation of urea derivatives under the same conditions. The analysis of hydrogen bonding and energy changes revealed that the aggregation was driven by the partial restoration of normal water structure. The energetic data also suggested that the promoted solubilization of NF is favored in the presence of urea derivatives. While the solutes aggregated to a varying degree, the systems were still in single-phase liquid state as attested by their active dynamics. PMID:26555993

  1. Molecular dynamics simulation of UO 2 nanocrystals surface

    NASA Astrophysics Data System (ADS)

    Boyarchenkov, A. S.; Potashnikov, S. I.; Nekrasov, K. A.; Kupryazhkin, A. Ya.

    2012-02-01

    In this article we investigated surface of nanocrystals (NCs) of uranium dioxide (UO 2) using molecular dynamics (MD) under isolated (non-periodic) boundary conditions in the approximation of rigid ions and pair potentials (RIPI). It is shown that a cubic shape of NCs is metastable and equilibrium is reached in the process of structural relaxation to the octahedral shape during long simulations of 1000 ns (200 million MD steps), which increase with the size of NC. We measured the size dependences of the lattice parameter and the surface energy density of cubic and octahedral NCs with volumes up to 1000 nm 3 (50 000 particles) at temperatures of 2200 K and 2300 K. For the surfaces {1 0 0} and {1 1 1} we obtained the energy densities σ100 = 1.60 ± 0.02 J/m 2, σ111 = 1.14 ± 0.03 J/m 2 and surface tension constant γ111 = 0.841 ± 0.008 J/m 2. The resulting ratio of σ100/ σ111 = 1.41 ± 0.04 within the error coincides with the experimental value of 1.42 ± 0.05 measured for microscopic cavities in UO 2 monocrystals.

  2. Molecular dynamics simulations of DNA-polycation complexes

    NASA Astrophysics Data System (ADS)

    Ziebarth, Jesse; Wang, Yongmei

    2008-03-01

    A necessary step in the preparation of DNA for use in gene therapy is the packaging of DNA with a vector that can condense DNA and provide protection from degrading enzymes. Because of the immunoresponses caused by viral vectors, there has been interest in developing synthetic gene therapy vectors, with polycations emerging as promising candidates. Molecular dynamics simulations of the DNA duplex CGCGAATTCGCG in the presence of 20 monomer long sequences of the polycations, poly-L-lysine (PLL) and polyethyleneimine (PEI), with explicit counterions and TIP3P water, are performed to provide insight into the structure and formation of DNA polyplexes. After an initial separation of approximately 50 å, the DNA and polycation come together and form a stable complex within 10 ns. The DNA does not undergo any major structural changes upon complexation and remains in the B-form. In the formed complex, the charged amine groups of the polycation mainly interact with DNA phosphate groups, and rarely occupy electronegative sites in either the major or minor grooves. Differences between complexation with PEI and PLL will be discussed.

  3. Protein under pressure: molecular dynamics simulation of the arc repressor.

    PubMed

    Trzesniak, Daniel; Lins, Roberto D; van Gunsteren, Wilfred F

    2006-10-01

    Experimental nuclear magnetic resonance results for the Arc Repressor have shown that this dimeric protein dissociates into a molten globule at high pressure. This structural change is accompanied by a modification of the hydrogen-bonding pattern of the intermolecular beta-sheet: it changes its character from intermolecular to intramolecular with respect to the two monomers. Molecular dynamics simulations of the Arc Repressor, as a monomer and a dimer, at elevated pressure have been performed with the aim to study this hypothesis and to identify the major structural and dynamical changes of the protein under such conditions. The monomer appears less stable than the dimer. However, the complete dissociation has not been seen because of the long timescale needed to observe this phenomenon. In fact, the protein structure altered very little when increasing the pressure. It became slightly compressed and the dynamics of the side-chains and the unfolding process slowed down. Increasing both, temperature and pressure, a tendency of conversion of intermolecular into intramolecular hydrogen bonds in the beta-sheet region has been detected, supporting the mentioned hypothesis. Also, the onset of denaturation of the separated chains was observed.

  4. Recovering position-dependent diffusion from biased molecular dynamics simulations

    SciTech Connect

    Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez

    2014-02-28

    All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.

  5. Kinetic distance and kinetic maps from molecular dynamics simulation.

    PubMed

    Noé, Frank; Clementi, Cecilia

    2015-10-13

    Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly interconverting states. Here, we build upon diffusion map theory and define a kinetic distance metric for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here, we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine. We find that the total kinetic variance (TKV) is an excellent indicator of model quality and can be used to rank different input feature sets.

  6. Phonon properties of graphene derived from molecular dynamics simulations

    PubMed Central

    Koukaras, Emmanuel N.; Kalosakas, George; Galiotis, Costas; Papagelis, Konstantinos

    2015-01-01

    A method that utilises atomic trajectories and velocities from molecular dynamics simulations has been suitably adapted and employed for the implicit calculation of the phonon dispersion curves of graphene. Classical potentials widely used in the literature were employed. Their performance was assessed for each individual phonon branch and the overall phonon dispersion, using available inelastic x-ray scattering data. The method is promising for systems with large scale periodicity, accounts for anharmonic effects and non-bonding interactions with a general environment, and it is applicable under finite temperatures. The temperature dependence of the phonon dispersion curves has been examined with emphasis on the doubly degenerate Raman active Γ-E2g phonon at the zone centre, where experimental results are available. The potentials used show diverse behaviour. The Tersoff-2010 potential exhibits the most systematic and physically sound behaviour in this regard, and gives a first-order temperature coefficient of χ = −0.05 cm−1/K for the Γ-E2g shift in agreement with reported experimental values. PMID:26316252

  7. Excipient-assisted vinpocetine nanoparticles: experiments and molecular dynamic simulations.

    PubMed

    Li, Cai-Xia; Wang, Hao-Bo; Oppong, Daniel; Wang, Jie-Xin; Chen, Jian-Feng; Le, Yuan

    2014-11-03

    Hydrophilic excipients can be used to increase the solubility and bioavailability of poorly soluble drugs. In this work, the conventional water-soluble pharmaceutical excipients hydroxypropylmethylcellulose (HPMC), polyvinylpyrrolidone (PVP), and lactose (LAC) were used as solid supports to prevent drug nanoparticles from aggregation and enhance drug dissolution. Excipient-assisted vinpocetine (VIN) nanoparticles were prepared by reactive precipitation. The analysis results indicated that HPMC was a suitable excipient to prepare VIN nanoparticles. VIN/HPMC nanoparticles had a mean size of 130 nm within a narrow distribution. The dissolution rate of VIN nanoparticles was significantly faster than those of a physical mixture of VIN/HPMC and raw VIN. VIN/HPMC nanoparticles had a higher dissolution profile than VIN/PVP and VIN/LAC nanoparticles. Besides, molecular dynamics (MD) simulation was applied to investigate the molecular interactions between VIN and excipients. The calculated results revealed that VIN interacted with excipients by Coulomb and Lennard-Jones (LJ) interactions. Few hydrogen bonds were formed between VIN and excipients. The HPMC affording smaller particle size may be a result of the stronger interactions between VIN and HPMC (mainly LJ interaction) and the property of HPMC. These characteristics may greatly influence the adsorption behavior and may be the crucial parameter for the better performance of HPMC.

  8. Molecular dynamics simulations of alkyl substituted nanographene crystals

    NASA Astrophysics Data System (ADS)

    Ziogos, Orestis George; Theodorou, Doros Nicolas

    2015-09-01

    Discotic polyaromatic molecules, similar to nanometric graphene flakes, constitute an interesting class of materials for organic electronic applications. Grafting flexible side chains around the periphery of such molecules enhances their processability and gives rise to diverse behaviours, such as the manifestation of liquid-crystalline character and anisotropic mechanical response. In this work, we examine by means of molecular dynamics simulations the properties of molecular crystals comprised of alkyl-substituted hexa-peri-hexabenzocoronene mesogens. Pristine and mono-substituted systems by hydrogen or iodine atoms are modelled, with variable side chain length. A general structural and mechanical robustness to peripheral substitution is reported, with the mesogens forming tightly packed molecular wires even at elevated temperature and pressure. In their discotic ordering, the molecules present relatively low translational mobility, a beneficial phenomenon for charge transport. A thermotropic dependence of the mechanical response is identified, with the systems behaving differently in their room-temperature crystalline phase and in their liquid-crystalline phase at elevated temperatures. The melting process is also examined, elucidating an initial negative expansion along a high symmetry direction and the existence of a metastable state, before falling into the final liquid-crystalline state. Dedicated to Professor Jean-Pierre Hansen, with deepest appreciation of his outstanding contributions to liquid and soft matter theory.

  9. Molecular Dynamics Simulations of Highly Charged Green Fluorescent Proteins

    SciTech Connect

    Lau, E Y; Phillips, J L; Colvin, M E

    2009-03-26

    A recent experimental study showed that green fluorescent protein (GFP) that has been mutated to have ultra-high positive or negative net charges, retain their native structure and fluorescent properties while gaining resistance to aggregation under denaturing conditions. These proteins also provide an ideal test case for studying the effects of surface charge on protein structure and dynamics. They have performed classical molecular dynamics (MD) simulations on the near-neutral wildtype GFP and mutants with net charges of -29 and +35. They analyzed the resulting trajectories to quantify differences in structure and dynamics between the three GFPs. This analyses shows that all three proteins are stable over the MD trajectory, with the near-neutral wild type GFP exhibiting somewhat more flexibility than the positive or negative GFP mutants, as measured by the order parameter and changes in phi-psi angles. There are more dramatic differences in the properties of the water and counter ions surrounding the proteins. The water diffusion constant near the protein surface is closer to the value for bulk water in the positively charged GFP than in the other two proteins. Additionally, the positively charged GFP shows a much greater clustering of the counter ions (CL-) near its surface than corresponding counter ions (Na+) near the negatively charged mutant.

  10. Insights into channel dysfunction from modelling and molecular dynamics simulations.

    PubMed

    Musgaard, Maria; Paramo, Teresa; Domicevica, Laura; Andersen, Ole Juul; Biggin, Philip C

    2017-06-29

    Developments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use of computational modelling can provide complementary information that can refine working hypotheses of both wild type and mutant ion channels. The simplest but still powerful tool is homology modelling. Many structures are available now that can provide suitable templates for many different types of ion channels, allowing a full three-dimensional interpretation of mutational effects. These structural models, and indeed the structures themselves obtained by X-ray crystallography, and more recently cryo-electron microscopy, can be subjected to molecular dynamics simulations, either as a tool to help explore the conformational dynamics in detail or simply as a means to refine the models further. Here we review how these approaches have been used to improve our understanding of how diseases might be linked to specific mutations in ion channel proteins. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. Cold-active enzymes studied by comparative molecular dynamics simulation.

    PubMed

    Spiwok, Vojtech; Lipovová, Petra; Skálová, Tereza; Dusková, Jarmila; Dohnálek, Jan; Hasek, Jindrich; Russell, Nicholas J; Králová, Blanka

    2007-04-01

    Enzymes from cold-adapted species are significantly more active at low temperatures, even those close to zero Celsius, but the rationale of this adaptation is complex and relatively poorly understood. It is commonly stated that there is a relationship between the flexibility of an enzyme and its catalytic activity at low temperature. This paper gives the results of a study using molecular dynamics simulations performed for five pairs of enzymes, each pair comprising a cold-active enzyme plus its mesophilic or thermophilic counterpart. The enzyme pairs included alpha-amylase, citrate synthase, malate dehydrogenase, alkaline protease and xylanase. Numerous sites with elevated flexibility were observed in all enzymes; however, differences in flexibilities were not striking. Nevertheless, amino acid residues common in both enzymes of a pair (not present in insertions of a structure alignment) are generally more flexible in the cold-active enzymes. The further application of principle component analysis to the protein dynamics revealed that there are differences in the rate and/or extent of opening and closing of the active sites. The results indicate that protein dynamics play an important role in catalytic processes where structural rearrangements, such as those required for active site access by substrate, are involved. They also support the notion that cold adaptation may have evolved by selective changes in regions of enzyme structure rather than in global change to the whole protein.

  12. Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.

    PubMed

    Tao, Peng; Wu, Xiongwu; Brooks, Bernard R

    2012-10-07

    An algorithm is presented to maintain rigid structures in Verlet based cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program suite, avoids the calculations of Lagrange multipliers, so that the complexity of computation does not increase with the number of particles in a rigid structure. The implementation of this algorithm does not require significant modification of propagation integrator, and can be plugged into any cartesian based MD integration scheme. A unique feature of the SHAPE method is that it is interchangeable with SHAKE for any object that can be constrained as a rigid structure using multiple SHAKE constraints. Unlike SHAKE, the SHAPE method can be applied to large linear (with three or more centers) and planar (with four or more centers) rigid bodies. Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency.

  13. Molecular dynamics simulations of the mammalian glutamate transporter EAAT3.

    PubMed

    Heinzelmann, Germano; Kuyucak, Serdar

    2014-01-01

    Excitatory amino acid transporters (EAATs) are membrane proteins that enable sodium-coupled uptake of glutamate and other amino acids into neurons. Crystal structures of the archaeal homolog GltPh have been recently determined both in the inward- and outward-facing conformations. Here we construct homology models for the mammalian glutamate transporter EAAT3 in both conformations and perform molecular dynamics simulations to investigate its similarities and differences from GltPh. In particular, we study the coordination of the different ligands, the gating mechanism and the location of the proton and potassium binding sites in EAAT3. We show that the protonation of the E374 residue is essential for binding of glutamate to EAAT3, otherwise glutamate becomes unstable in the binding site. The gating mechanism in the inward-facing state of EAAT3 is found to be different from that of GltPh, which is traced to the relocation of an arginine residue from the HP1 segment in GltPh to the TM8 segment in EAAT3. Finally, we perform free energy calculations to locate the potassium binding site in EAAT3, and find a high-affinity site that overlaps with the Na1 and Na3 sites in GltPh.

  14. Recovering position-dependent diffusion from biased molecular dynamics simulations.

    PubMed

    Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez

    2014-02-28

    All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica(®) package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics. Given known free energy and D, the package can also generate diffusive trajectories.

  15. Molecular dynamics simulation of fluorine cluster ion impact

    NASA Astrophysics Data System (ADS)

    Aoki, Takaaki; Matsuo, Jiro; Yamada, Isao

    2000-04-01

    Molecular dynamics (MD) simulations of fluorine atoms, molecules and clusters impacting a silicon substrate were performed in order to investigate the impact process of a reactive cluster ion. This result shows that when the incident energy of the impacting fluorine atom or molecule is less than 10 eV/atom, the species are only adsorbed on the surface and sputtering of substrate atoms does not occur. On the other hand, a fluorine cluster consisting of 30 molecules produces sputtering even at a low incident energy of 1 eV/atom. At these conditions, the surface atoms are desorbed as fluorine-containing species, such as SiF or SiF 2, indicating that chemical desorption is enhanced by irradiation with fluorine clusters. As the incident energy of the cluster increases to values as high as 100 eV/atom, almost all the fluorine atoms penetrate the surface and a crater-shaped damage is formed. The incident F atoms reside at the bottom region of the crater. In this case, silicon atoms leave the surface as monomers, dimers or clusters without F atoms, i.e., in this regime physical sputtering through atomic collisions has a higher probability than chemical reactions, like in the case of Ne or Ar cluster impact.

  16. Hidden Markov models from molecular dynamics simulations on DNA.

    PubMed

    Thayer, Kelly M; Beveridge, D L

    2002-06-25

    An enhanced bioinformatics tool incorporating the participation of molecular structure as well as sequence in protein DNA recognition is proposed and tested. Boltzmann probability models of sequence-dependent DNA structure from all-atom molecular dynamics simulations were obtained and incorporated into hidden Markov models (HMMs) that can recognize molecular structural signals as well as sequence in protein-DNA binding sites on a genome. The binding of catabolite activator protein (CAP) to cognate DNA sequences was used as a prototype case for implementation and testing of the method. The results indicate that even HMMs based on probabilistic roll/tilt dinucleotide models of sequence-dependent DNA structure have some capability to discriminate between known CAP binding and nonbinding sites and to predict putative CAP binding sites in unknowns. Restricting HMMs to sequence only in regions of strong consensus in which the protein makes base specific contacts with the cognate DNA further improved the discriminatory capabilities of the HMMs. Comparison of results with controls based on sequence only indicates that extending the definition of consensus from sequence to structure improves the transferability of the HMMs, and provides further supportive evidence of a role for dynamical molecular structure as well as sequence in genomic regulatory mechanisms.

  17. Molecular dynamics simulations of polymer transport in nanocomposites

    NASA Astrophysics Data System (ADS)

    Desai, Tapan; Keblinski, Pawel; Kumar, Sanat K.

    2005-04-01

    Molecular dynamics simulations on the Kremer-Grest bead-spring model of polymer melts are used to study the effect of spherical nanoparticles on chain diffusion. We find that chain diffusivity is enhanced relative to its bulk value when polymer-particle interactions are repulsive and is reduced when polymer-particle interactions are strongly attractive. In both cases chain diffusivity assumes its bulk value when the chain center of mass is about one radius of gyration Rg away from the particle surface. This behavior echoes the behavior of polymer melts confined between two flat surfaces, except in the limit of severe confinement where the surface influence on polymer mobility is more pronounced for flat surfaces. A particularly interesting fact is that, even though chain motion is strongly speeded up in the presence of repulsive boundaries, this effect can be reversed by pinning one isolated monomer onto the surface. This result strongly stresses the importance of properly specifying boundary conditions when the near surface dynamics of chains are studied.

  18. Molecular dynamics simulation of NaCl dissolution.

    PubMed

    Lanaro, Gabriele; Patey, G N

    2015-03-19

    Molecular dynamics simulations are used to investigate the dissolution of NaCl nanocrystals (containing ∼2400 ions) in water. We focus on systems under sink conditions at 300 K, but the influences of concentration and temperature are also investigated. Cubical, spherical, tablet-shaped, and rod-shaped nanocrystals are considered, and it is shown that the initial shape can influence the dissolution process. Dissolution is observed to occur in three stages: an initial period where the most exposed ions are removed from the crystal surface, and the crystal takes on a solution-annealed shape which persists throughout the second stage of dissolution; a second long intermediate stage where dissolution roughly follows a fixed rate law; and a final stage where the small residual crystal (≲200 ions) dissolves at an ever increasing rate until it disappears. The second stage of dissolution which applies for most of the dissolution process is well described by classical rate equations which simply assume that the dissolution rate is proportional to an active surface area from which ions are most easily detached from the crystal. The active area depends on the initial crystal shape. We show that for our model NaCl nanocrystals the rate-determining step for dissolution under sink conditions is ion detachment from the crystal, and that diffusion layers do not exist for these systems.

  19. Molecular dynamics simulation of photodissociation of carbon monoxide from hemoglobin

    SciTech Connect

    Henry, E.R.; Levitt, M.; Eaton, W.A.

    1985-04-01

    A molecular dynamics simulation of the photodissociation of carbon monoxide from the alpha subunit of hemoglobin is described. To initiate photodissociation, trajectories of the liganded molecule were interrupted, the iron-carbon monoxide bond was broken, and the parameters of the iron-nitrogen bonds were simultaneously altered to produce a deoxyheme conformation. Heme potential functions were used that reproduce the energies and forces for the iron out-of-plane motion obtained from quantum mechanical calculations. The effect of the protein on the rate and extent of the displacement of the iron from the porphyrin plane was assessed by comparing the results with those obtained for an isolated complex of heme with imidazole and carbon monoxide. The half-time for the displacement of the iron from the porphyrin plane was found to be 50-150 fs for both the protein and the isolated complex. These results support the interpretation of optical absorption studies using 250-fs laser pulses that the iron is displaced from the porphyrin plane within 350 fs in both hemoglobin and a free heme complex in solution.

  20. Molecular Dynamics Simulations of the Mammalian Glutamate Transporter EAAT3

    PubMed Central

    Heinzelmann, Germano; Kuyucak, Serdar

    2014-01-01

    Excitatory amino acid transporters (EAATs) are membrane proteins that enable sodium-coupled uptake of glutamate and other amino acids into neurons. Crystal structures of the archaeal homolog GltPh have been recently determined both in the inward- and outward-facing conformations. Here we construct homology models for the mammalian glutamate transporter EAAT3 in both conformations and perform molecular dynamics simulations to investigate its similarities and differences from GltPh. In particular, we study the coordination of the different ligands, the gating mechanism and the location of the proton and potassium binding sites in EAAT3. We show that the protonation of the E374 residue is essential for binding of glutamate to EAAT3, otherwise glutamate becomes unstable in the binding site. The gating mechanism in the inward-facing state of EAAT3 is found to be different from that of GltPh, which is traced to the relocation of an arginine residue from the HP1 segment in GltPh to the TM8 segment in EAAT3. Finally, we perform free energy calculations to locate the potassium binding site in EAAT3, and find a high-affinity site that overlaps with the Na1 and Na3 sites in GltPh. PMID:24643009

  1. Dynamic transitions in molecular dynamics simulations of supercooled silicon

    NASA Astrophysics Data System (ADS)

    Mei, Xiaojun; Eapen, Jacob

    2013-04-01

    Two dynamic transitions or crossovers, one at a low temperature (T* ≈ 1006 K) and the other at a high temperature (T0 ≈ 1384 K), are shown to emerge in supercooled liquid silicon using molecular dynamics simulations. The high-temperature transition (T0) marks the decoupling of stress, density, and energy relaxation mechanisms. At the low-temperature transition (T*), depending on the cooling rate, supercooled silicon can either undergo a high-density-liquid to low-density-liquid (HDL-LDL) phase transition or experience an HDL-HDL crossover. Dynamically heterogeneous domains that emerge with supercooling become prominent across the HDL-HDL transition at 1006 K, with well-separated mobile and immobile regions. Interestingly, across the HDL-LDL transition, the most mobile atoms form large prominent aggregates while the least mobile atoms get spatially dispersed akin to that in a crystalline state. The attendant partial return to spatial uniformity with the HDL-LDL phase transition indicates a dynamic mechanism for relieving the frustration in supercooled states.

  2. Pressure denaturation of apomyoglobin: a molecular dynamics simulation study.

    PubMed

    McCarthy, Andrés N; Grigera, J Raúl

    2006-03-01

    The effect of pressure on the structure and mobility of Sperm Wale Apomyoglobin was studied by Molecular Dynamics computer simulation at 1 bar and 3 kbar (1 atm=1.01325 bar=101.325 kPa). The results are in good agreement with the available experimental data, allowing further analysis of other features of the effect of pressure on the protein solution. From the analysis of Secondary Structures (SS) along the trajectories it is observed that alpha-helixes are favoured under pressure at the expense of bends, turns and 3-helixes. The studies of mobility show that although the general mobility is restricted under pressure this is not true for some particular residues. The studies of tertiary structure show important conformational changes. The evolution of the Solvent Accessed Surface (SAS) with pressure shows a notorious increase due almost completely to a biased raise in the hydrophobic area exposed, which consequently shows that the hydrophobic interaction is considerably weaker under high hydrostatic pressure conditions.

  3. Oleic acid phase behavior from molecular dynamics simulations.

    PubMed

    Janke, J Joel; Bennett, W F Drew; Tieleman, D Peter

    2014-09-09

    Fatty acid aggregation is important for a number of diverse applications: from origins of life research to industrial applications to health and disease. Experiments have characterized the phase behavior of oleic acid mixtures, but the molecular details are complex and hard to probe with many experiments. Coarse-grained molecular dynamics computer simulations and free energy calculations are used to model oleic acid aggregation. From random dispersions, we observe the aggregation of oleic acid monomers into micelles, vesicles, and oil phases, depending on the protonation state of the oleic acid head groups. Worm-like micelles are observed when all the oleic acid molecules are deprotonated and negatively charged. Vesicles form spontaneously if significant amounts of both neutral and negative oleic acid are present. Oil phases form when all the fatty acids are protonated and neutral. This behavior qualitatively matches experimental observations of oleic acid aggregation. To explain the observed phase behavior, we use umbrella sampling free energy calculations to determine the stability of individual monomers in aggregates compared to water. We find that both neutral and negative oleic acid molecules prefer larger aggregates, but neutral monomers prefer negatively charged aggregates and negative monomers prefer neutral aggregates. Both neutral and negative monomers are most stable in a DOPC bilayer, with implications on fatty acid adsorption and cellular membrane evolution. Although the CG model qualitatively reproduces oleic acid phase behavior, we show that an updated polarizable water model is needed to more accurately predict the shift in pKa for oleic acid in model bilayers.

  4. Modeling of RNA nanotubes using molecular dynamics simulation.

    PubMed

    Badu, S R; Melnik, R; Paliy, M; Prabhakar, S; Sebetci, A; Shapiro, B A

    2014-11-01

    In this study, we construct novel RNA nanoclusters, RNA nanotubes made of several nanorings up to the size of 20 nm, utilizing the molecular dynamics simulation, and study their structural properties [i.e., the root mean square deviation, the radius of gyration and the radial distribution function (RDF)] in physiological solutions that can be used for drug delivery into the human body. The patterns of energy and temperature variations of the systems are also discussed. Furthermore, we study the concentration of ions around the tube as a function of time at a particular temperature. We have found that when the temperature increases, the number of ions increases within a certain distance of the tube. We report that the number of ions within this distance around the tubes decreases in quenched runs. This indicates that some ions evaporate with decrease in temperature, as has been observed in the case of the nanoring. RDF plots also demonstrate a similar trend with temperature, as was found in the case of RNA nanorings.

  5. Homology model and molecular dynamics simulation of carp ovum cystatin.

    PubMed

    Su, Yuan-Chen; Lin, Jin-Chung; Liu, Hsuan-Liang

    2005-01-01

    In this study, a homology model of carp ovum cystatin was constructed based on the crystal structure of chicken egg white cystatin. The results of amino acid sequence alignment indicate that these two proteins exhibit 36.11% of sequence identity. The resultant homology model reveals that carp ovum cystatin shares similar folds as chicken egg white cystatin, particularly in the conserved regions of Q48-V49-G52 and P98-W99 and the locations of two disulfide bonds, C67-C76 and C90-C110. However, the results of 1 ns molecular dynamics simulations show that carp ovum cystatin exhibits less structural integrity than chicken egg white cystatin in explicit water at 300 K. The relatively hydrophilic Met62 of carp ovum cystatin, corresponding to the hydrophobic Leu68 of human cystatin C and Ile66 of chicken egg white cystatin, may destabilize the hydrophobic core and form a dimeric structure more easily through domain swapping. A total of 16 positively charged residues are equally distributed on the surface of carp ovum cystatin, resulting in agglutination with the negatively charged spermatozoa via electrostatic interaction. Thus, carp ovum cystatin is considered to be important in preventing carp eggs from polyspermy.

  6. Molecular Dynamics Simulations of Nanoparticles Coated with Charged Polymers

    NASA Astrophysics Data System (ADS)

    Wen, Chengyuan; Cheng, Shengfeng

    Polymer coating is frequently used to stabilize colloidal and nano-sized particles. We employ molecular dynamics simulations to study nanoparticles coated with polymer chains that contain ionizable groups. In a polar solvent, the chains become charged with counterions dissociated. In the computational model, we treat the solvent as a uniform dielectric background and use the bead-spring model for the polymer chains. Counterions are explicitly included as mobile beads. The nanoparticle is modeled as a layer of sites uniformly distributed on a spherical surface with a certain fraction of sites serving as the tether points of the grafted polymer brush. We vary the grafting density and calculate the distribution of polymer beads and counterions around the nanoparticle. Our results indicate that charged chains adopt extended conformations because of their mutual repulsions. We further study the interactions between two polymer-coated nanoparticles and obtain the potential of mean force. We also find an interesting transition of a confined single layer of such polymer-coated nanoparticles into two layers when the confinement is removed. Results show that the brush-brush contact has a nonuniform distribution and the nanoparticles tend to form dipole-like structures.

  7. Improvement in Empirical Potential Functions for Increasing the Utility of Molecular Dynamics Simulations

    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.

  8. Multicanonical Molecular Dynamics Simulations of the N-terminal Domain of Protein L9

    PubMed Central

    Yaşar, Fatih; Jiang, Ping; Hansmann, Ulrich H. E.

    2014-01-01

    We describe multicanonical molecular dynamic simulations of the N-terminal domain of the protein L9. Analyzing free energy landscapes and thermal ordering, we propose a possible folding mechanism for the protein. By comparing our results with that of molecular dynamics runs of the protein at constant temperature, we find that multicanonical molecular dynamics leads to orders of magnitude higher sampling of folding transitions. PMID:25253918

  9. Molecular dynamics simulations of bubble nucleation in dark matter detectors.

    PubMed

    Denzel, Philipp; Diemand, Jürg; Angélil, Raymond

    2016-01-01

    Bubble chambers and droplet detectors used in dosimetry and dark matter particle search experiments use a superheated metastable liquid in which nuclear recoils trigger bubble nucleation. This process is described by the classical heat spike model of F. Seitz [Phys. Fluids (1958-1988) 1, 2 (1958)PFLDAS0031-917110.1063/1.1724333], which uses classical nucleation theory to estimate the amount and the localization of the deposited energy required for bubble formation. Here we report on direct molecular dynamics simulations of heat-spike-induced bubble formation. They allow us to test the nanoscale process described in the classical heat spike model. 40 simulations were performed, each containing about 20 million atoms, which interact by a truncated force-shifted Lennard-Jones potential. We find that the energy per length unit needed for bubble nucleation agrees quite well with theoretical predictions, but the allowed spike length and the required total energy are about twice as large as predicted. This could be explained by the rapid energy diffusion measured in the simulation: contrary to the assumption in the classical model, we observe significantly faster heat diffusion than the bubble formation time scale. Finally we examine α-particle tracks, which are much longer than those of neutrons and potential dark matter particles. Empirically, α events were recently found to result in louder acoustic signals than neutron events. This distinction is crucial for the background rejection in dark matter searches. We show that a large number of individual bubbles can form along an α track, which explains the observed larger acoustic amplitudes.

  10. Nucleation Rate Analysis of Methane Hydrate from Molecular Dynamics Simulations

    SciTech Connect

    Yuhara, Daisuke; Barnes, Brian C.; Suh, Donguk; Knott, Brandon C.; Beckham, Gregg T.; Yasuoka, Kenji; Wu, David T.; Amadeu K. Sum

    2015-01-06

    Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Moreover, various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP) methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates were calculated by MFPT and SP methods and are within 5%; the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.

  11. Contact angles from Young's equation in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Jiang, Hao; Müller-Plathe, Florian; Panagiotopoulos, Athanassios Z.

    2017-08-01

    We propose a method to calculate the equilibrium contact angle of heterogeneous 3-phase solid/fluid/fluid systems using molecular dynamics simulations. The proposed method, which combines the phantom-wall method [F. Leroy and F. Müller-Plathe, J. Chem. Phys. 133, 044110 (2010)] and Bennett's acceptance ratio approach [C. H. Bennett, J. Comput. Phys. 22, 245 (1976)], is able to calculate the solid/fluid surface tension relative to the solid surface energy. The calculated relative surface tensions can then be used in Young's equation to estimate the equilibrium contact angle. A fluid droplet is not needed for the proposed method, in contrast to the situation for direct simulations of contact angles. In addition, while prior free-energy based methods for contact angles mainly focused on the wetting of fluids in coexistence with their vapor on solid surfaces, the proposed approach was designed to study the contact angles of fluid mixtures on solid surfaces above the fluid saturation pressures. Using the proposed approach, the contact angles of binary Lennard-Jones fluid mixtures on a non-polar solid substrate were calculated at various interaction parameters and the contact angle of water in equilibrium with CO2 on a hydrophilic polar silica surface was obtained. For both non-polar and polar systems, the calculated contact angles from the proposed method were in agreement with those obtained from the geometry of a cylindrical droplet. The computational cost of the proposed method was found to be comparable to that of simulations that use fluid droplets, but the new method provides a way to calculate the contact angle directly from Young's equation without ambiguity.

  12. Combining docking and molecular dynamic simulations in drug design.

    PubMed

    Alonso, Hernán; Bliznyuk, Andrey A; Gready, Jill E

    2006-09-01

    A rational approach is needed to maximize the chances of finding new drugs, and to exploit the opportunities of potential new drug targets emerging from genomic and proteomic initiatives, and from the large libraries of small compounds now readily available through combinatorial chemistry. Despite a shaky early history, computer-aided drug design techniques can now be effective in reducing costs and speeding up drug discovery. This happy outcome results from development of more accurate and reliable algorithms, use of more thoughtfully planned strategies to apply them, and greatly increased computer power to allow studies with the necessary reliability to be performed. Our review focuses on applications and protocols, with the main emphasis on critical analysis of recent studies where docking calculations and molecular dynamics (MD) simulations were combined to dock small molecules into protein receptors. We highlight successes to demonstrate what is possible now, but also point out drawbacks and future directions. The review is structured to lead the reader from the simpler to more compute-intensive methods. Thus, while inexpensive and fast docking algorithms can be used to scan large compound libraries and reduce their size, more accurate but expensive MD simulations can be applied when a few selected ligand candidates remain. MD simulations can be used: during the preparation of the protein receptor before docking, to optimize its structure and account for protein flexibility; for the refinement of docked complexes, to include solvent effects and account for induced fit; to calculate binding free energies, to provide an accurate ranking of the potential ligands; and in the latest developments, during the docking process itself to find the binding site and correctly dock the ligand a priori.

  13. Nucleation Rate Analysis of Methane Hydrate from Molecular Dynamics Simulations

    DOE PAGES

    Yuhara, Daisuke; Barnes, Brian C.; Suh, Donguk; ...

    2015-01-06

    Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Moreover, various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP)more » methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates were calculated by MFPT and SP methods and are within 5%; the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.« less

  14. Molecular dynamics simulations of bubble nucleation in dark matter detectors

    NASA Astrophysics Data System (ADS)

    Denzel, Philipp; Diemand, Jürg; Angélil, Raymond

    2016-01-01

    Bubble chambers and droplet detectors used in dosimetry and dark matter particle search experiments use a superheated metastable liquid in which nuclear recoils trigger bubble nucleation. This process is described by the classical heat spike model of F. Seitz [Phys. Fluids (1958-1988) 1, 2 (1958), 10.1063/1.1724333], which uses classical nucleation theory to estimate the amount and the localization of the deposited energy required for bubble formation. Here we report on direct molecular dynamics simulations of heat-spike-induced bubble formation. They allow us to test the nanoscale process described in the classical heat spike model. 40 simulations were performed, each containing about 20 million atoms, which interact by a truncated force-shifted Lennard-Jones potential. We find that the energy per length unit needed for bubble nucleation agrees quite well with theoretical predictions, but the allowed spike length and the required total energy are about twice as large as predicted. This could be explained by the rapid energy diffusion measured in the simulation: contrary to the assumption in the classical model, we observe significantly faster heat diffusion than the bubble formation time scale. Finally we examine α -particle tracks, which are much longer than those of neutrons and potential dark matter particles. Empirically, α events were recently found to result in louder acoustic signals than neutron events. This distinction is crucial for the background rejection in dark matter searches. We show that a large number of individual bubbles can form along an α track, which explains the observed larger acoustic amplitudes.

  15. Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

    PubMed Central

    Sutton, Rebecca; Sposito, Garrison

    2002-01-01

    Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers) provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.

  16. Contact angles from Young's equation in molecular dynamics simulations.

    PubMed

    Jiang, Hao; Müller-Plathe, Florian; Panagiotopoulos, Athanassios Z

    2017-08-28

    We propose a method to calculate the equilibrium contact angle of heterogeneous 3-phase solid/fluid/fluid systems using molecular dynamics simulations. The proposed method, which combines the phantom-wall method [F. Leroy and F. Müller-Plathe, J. Chem. Phys. 133, 044110 (2010)] and Bennett's acceptance ratio approach [C. H. Bennett, J. Comput. Phys. 22, 245 (1976)], is able to calculate the solid/fluid surface tension relative to the solid surface energy. The calculated relative surface tensions can then be used in Young's equation to estimate the equilibrium contact angle. A fluid droplet is not needed for the proposed method, in contrast to the situation for direct simulations of contact angles. In addition, while prior free-energy based methods for contact angles mainly focused on the wetting of fluids in coexistence with their vapor on solid surfaces, the proposed approach was designed to study the contact angles of fluid mixtures on solid surfaces above the fluid saturation pressures. Using the proposed approach, the contact angles of binary Lennard-Jones fluid mixtures on a non-polar solid substrate were calculated at various interaction parameters and the contact angle of water in equilibrium with CO2 on a hydrophilic polar silica surface was obtained. For both non-polar and polar systems, the calculated contact angles from the proposed method were in agreement with those obtained from the geometry of a cylindrical droplet. The computational cost of the proposed method was found to be comparable to that of simulations that use fluid droplets, but the new method provides a way to calculate the contact angle directly from Young's equation without ambiguity.

  17. Molecular dynamics simulation studies of tailored nanostructured polymers

    NASA Astrophysics Data System (ADS)

    Liu, Lixin

    With recent advancements in the synthesis and characterization of polymeric materials, scientists are able to create multi-scale novel polymers with various cases of chemical functionalities, diversified topologies, as well as cross-linking networks. Due to those remarkable achievements, there are a broad range of possible applications of smart polymers in catalysis, in environmental remediation, and especially in drug-delivery. Because of rising interest in developing therapeutic drug binding to specific treating target, polymer chemists are in particular interests in design and engineering the drug delivery materials to be not only bio-compatible, but also to be capable of self-assembly at various in-vivo physiological stimulus. Both experimental and theoretical work indicate that the thermodynamic properties relating to the hydrophobic effect play an important role in determining self-assembly process. At the same time, computational simulation and modeling are powerful instruments to contribute to microscopic thermodynamics' understanding toward self-assembly phenomenon. Along with statistical approaches, constructing empirical model based on simulation results would also help predict for further development of tailored nano-structured materials. My Research mainly focused on investigating physical and chemical characteristics of polymer materials through molecular dynamics simulation and probing the fundamental thermodynamic driving force of self-assembly behavior. We tried to surmount technological obstacles in computational chemistry and build an efficient scheme to identify the physical and chemical Feature of molecules, to reproduce underlying properties, to understand the origin of thermodynamic signatures, and to speed up current trial and error process in screening new materials.

  18. Nucleation rate analysis of methane hydrate from molecular dynamics simulations.

    PubMed

    Yuhara, Daisuke; Barnes, Brian C; Suh, Donguk; Knott, Brandon C; Beckham, Gregg T; Yasuoka, Kenji; Wu, David T; Sum, Amadeu K

    2015-01-01

    Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP) methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates calculated by MFPT and SP methods are within 5%, and the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.

  19. Probing Polyoxometalate-Protein Interactions Using Molecular Dynamics Simulations.

    PubMed

    Solé-Daura, Albert; Goovaerts, Vincent; Stroobants, Karen; Absillis, Gregory; Jiménez-Lozano, Pablo; Poblet, Josep M; Hirst, Jonathan D; Parac-Vogt, Tatjana N; Carbó, Jorge J

    2016-10-17

    The molecular interactions between the Ce(IV) -substituted Keggin anion [PW11 O39 Ce(OH2 )4 ](3-) (CeK) and hen egg-white lysozyme (HEWL) were investigated by molecular dynamics simulations. The analysis of CeK was compared with the Ce(IV) -substituted Keggin dimer [(PW11 O39 )2 Ce](10-) (CeK2 ) and the Zr(IV) -substituted Lindqvist anion [W5 O18 Zr(OH2 )(OH)](3-) (ZrL) to understand how POM features such as shape, size, charge, or type of incorporated metal ion influence the POM⋅⋅⋅protein interactions. Simulations revealed two regions of the protein in which the CeK anion interacts strongly: cationic sites formed by Arg21 and by Arg45 and Arg68. The POMs chiefly interact with the side chains of the positively charged (arginines, lysines) and the polar uncharged residues (tyrosines, serines, aspargines) via electrostatic attraction and hydrogen bonding with the oxygen atoms of the POM framework. The CeK anion shows higher protein affinity than the CeK2 and ZrL anions, because it is less hydrophilic and it has the right size and shape for establishing interactions with several residues simultaneously. The larger, more negatively charged CeK2 anion has a high solvent-accessible surface, which is sub-optimal for the interaction, while the smaller ZrL anion is highly hydrophilic and cannot efficiently interact with several residues simultaneously. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Molecular dynamics simulations of shock waves using the absorbing boundary condition: A case study of methane

    NASA Astrophysics Data System (ADS)

    Bolesta, Alexey V.; Zheng, Lianqing; Thompson, Donald L.; Sewell, Thomas D.

    2007-12-01

    We report a method that enables long-time molecular dynamics (MD) simulations of shock wave loading. The goal is to mitigate the severe interference effects that arise at interfaces or free boundaries when using standard nonequilibrium MD shock wave approaches. The essence of the method is to capture between two fixed pistons the material state at the precise instant in time when the shock front, initiated by a piston with velocity up at one end of the target sample, traverses the contiguous boundary between the target and a second, stationary piston located at the opposite end of the sample, at which point the second piston is also assigned velocity up and the simulation is continued. Thus, the target material is captured in the energy-volume Hugoniot state resulting from the initial shock wave, and can be propagated forward in time to monitor any subsequent chemistry, plastic deformation, or other time-dependent phenomena compatible with the spatial scale of the simulation. For demonstration purposes, we apply the method to shock-induced chemistry in methane based on the adaptive intermolecular reactive empirical bond order force field [S. J. Stuart , J. Chem. Phys. 112, 6472 (2000)].

  1. Homogeneous nucleation and growth in supersaturated zinc vapor investigated by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Römer, F.; Kraska, T.

    2007-12-01

    Homogeneous nucleation and growth of zinc from supersaturated vapor are investigated by nonequilibrium molecular dynamics simulations in the temperature range from 400to800K and for a supersaturation ranging from logS =2 to 11. Argon is added to the vapor phase as carrier gas to remove the latent heat from the forming zinc clusters. A new parametrization of the embedded atom method for zinc is employed for the interaction potential model. The simulation data are analyzed with respect to the nucleation rates and the critical cluster sizes by two different methods, namely, the threshold method of Yasuoka and Matsumoto [J. Chem. Phys. 109, 8451 (1998)] and the mean first passage time method for nucleation by Wedekind et al. [J. Chem. Phys. 126, 134103 (2007)]. The nucleation rates obtained by these methods differ approximately by one order of magnitude. Classical nucleation theory fails to describe the simulation data as well as the experimental data. The size of the critical cluster obtained by the mean first passage time method is significantly larger than that obtained from the nucleation theorem.

  2. Diffusion behavior in a liquid-liquid interfacial crystallization by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Kitayama, Akira; Yamanaka, Shinya; Kadota, Kazunori; Shimosaka, Atsuko; Shirakawa, Yoshiyuki; Hidaka, Jusuke

    2009-11-01

    Interfacial crystallization, such as surface crystallization in solution (solid-liquid) and liquid-liquid crystallization, gives us an asymmetric reaction field and is a technique for morphology control of crystals. In the liquid-liquid crystallization, the concentration distribution of solute ions and solvent molecules at the liquid-liquid interface directly relates to nucleation, crystal growth, and crystal morphology. Nonequilibrium molecular dynamics (MD) simulations have been performed at interfaces in NaCl solution/1-butanol and KCl solution/1-butanol system in order to clarify diffusion behavior of solute ions and solvent molecules. As simulation results, the hydrated solute ions were dehydrated with the diffusion of water from solution phase into 1-butanol phase. The different dehydration behaviors between NaCl and KCl solution can be also obtained from MD simulation results. Aggregated ions or clusters were formed by the dehydration near the solution/1-butanol interface. By comparison on the normalized number of total solute ions, the size and number of generated cluster in KCl solution/1-butanol interface are larger than those in the NaCl system. This originates in the difference hydration structures in the each solute ion.

  3. Grain boundary migration in metals: Molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zhang, Hao

    Grain boundary migration is key to materials microstructural processes such as grain growth and recrystallization. Quantitative boundary dynamic data is difficult to obtain, yet important for quantitative prediction of microstructural evolution and understanding migration fundamentals. Our molecular dynamics simulations first focus on curvature driven grain boundary migration to extract the reduced mobility and activation energy for migration as a function of boundary misorientation in aluminum. Simulation results are in good agreement with experimental observations except that the activation energy for migration found is much smaller than in experiment. This discrepancy led to a more systematic study of the absolute mobility and atomistic level mechanism for boundary migration. To study the mobility of a flat, fully defined boundary, we developed a strain-energy-anisotropy-driven migration simulation method. We applied this method to a series of Sigma5 [010] asymmetric tilt grain boundaries and extracted the absolute mobility as a function of temperature and inclination. Simulation results suggest that the mobility is a sensitive function of temperature and inclination. The boundary mobility tends to be minimized when one of the grain boundary planes has low Miller indices. Meanwhile, the comparison between grain boundary mobility, grain boundary self-diffusivity and energy suggests strong correlation at special inclinations, when one of the boundary planes is a high symmetry plane. In addition, we derive the grain boundary stiffness and reduced mobility as a function of boundary inclination. The grain boundary stiffness exhibits a large anisotropy, which is of the same order of magnitude as that of the grain boundary mobility. However, these two anisotropies nearly cancel, leaving the reduced mobility nearly isotropic. Finally, we identify the migration mechanism through frequent quenches and analysis of the atomic displacements, local and global excess volume

  4. A steady-state non-equilibrium molecular dynamics approach for the study of evaporation processes

    NASA Astrophysics Data System (ADS)

    Zhang, Jianguo; Müller-Plathe, Florian; Yahia-Ouahmed, Méziane; Leroy, Frédéric

    2013-10-01

    Two non-equilibrium methods (called bubble method and splitting method, respectively) have been developed and tested to study the steady state evaporation of a droplet surrounded by its vapor, where the evaporation continuously occurs at the vapor-liquid interface while the droplet size remains constant. In the bubble method, gas molecules are continuously reinserted into a free volume (represented by a bubble) located at the centre of mass of the droplet to keep the droplet size constant. In the splitting method, a molecule close to the centre of mass of the droplet is split into two: In this way, the droplet size is also maintained during the evaporation. By additional local thermostats confined to the area of insertion, the effect of frequent insertions on properties such as density and temperature can be limited to the immediate insertion area. Perturbations are not observed in other parts of the droplet. In the end, both the bubble method and the splitting method achieve steady-state droplet evaporation. Although these methods have been developed using an isolated droplet, we anticipate that they will find a wide range of applications in the study of the evaporation of isolated films and droplets or thin films on heated substrates or under confinement. They can in principle also be used to study the steady-state of other physical processes, such as the diffusion or permeation of gas molecules or ions in a pressure gradient or a concentration gradient.

  5. Molecular dynamics simulation of nonlinear spectroscopies of intermolecular motions in liquid water.

    PubMed

    Yagasaki, Takuma; Saito, Shinji

    2009-09-15

    Water is the most extensively studied of liquids because of both its ubiquity and its anomalous thermodynamic and dynamic properties. The properties of water are dominated by hydrogen bonds and hydrogen bond network rearrangements. Fundamental information on the dynamics of liquid water has been provided by linear infrared (IR), Raman, and neutron-scattering experiments; molecular dynamics simulations have also provided insights. Recently developed higher-order nonlinear spectroscopies open new windows into the study of the hydrogen bond dynamics of liquid water. For example, the vibrational lifetimes of stretches and a bend, intramolecular features of water dynamics, can be accurately measured and are found to be on the femtosecond time scale at room temperature. Higher-order nonlinear spectroscopy is expressed by a multitime correlation function, whereas traditional linear spectroscopy is given by a one-time correlation function. Thus, nonlinear spectroscopy yields more detailed information on the dynamics of condensed media than linear spectroscopy. In this Account, we describe the theoretical background and methods for calculating higher order nonlinear spectroscopy; equilibrium and nonequilibrium molecular dynamics simulations, and a combination of both, are used. We also present the intermolecular dynamics of liquid water revealed by fifth-order two-dimensional (2D) Raman spectroscopy and third-order IR spectroscopy. 2D Raman spectroscopy is sensitive to couplings between modes; the calculated 2D Raman signal of liquid water shows large anharmonicity in the translational motion and strong coupling between the translational and librational motions. Third-order IR spectroscopy makes it possible to examine the time-dependent couplings. The 2D IR spectra and three-pulse photon echo peak shift show the fast frequency modulation of the librational motion. A significant effect of the translational motion on the fast frequency modulation of the librational motion is

  6. Molecular dynamics simulations of nanoindentation and nanoscratching of silicon carbide

    NASA Astrophysics Data System (ADS)

    Noreyan, Alisa A.

    Parallel molecular dynamics simulations were carried out to investigate the interaction between a diamond indenter and silicon carbide during nanoindentation and nanoscratching. The dependence of the critical depth and pressure for the elastic-to-plastic transition on indentation velocity, tip size, and workpiece temperature was studied along with the nature of the deformation due to indentation and scratching. The two most widely used polytypes---cubic silicon carbide (3C-SiC) and hexagonal silicon carbide (6H-SiC)---were considered while the Si-terminated (001) ((0001)) surface was used in each case. Simulations were implemented using the Tersoff SiC potential, which accurately reproduces the lattice and elastic constants of 3C-SiC and 6H-SiC. Nanoindentation experiments were also carried out for 6H-SiC. For the 3C polytype, both the critical pressure and indentation depth for the elastic-to-plastic transition were found to decrease with increasing indenter size over the nanoscale range of indenter sizes used in our simulations. As a result, the measured hardness was found to be significantly higher than obtained experimentally for significantly larger indenter sizes. In addition, for indentation depths beyond the critical depth a phase transition to the rocksalt structure was observed. A similar phase transition was observed for the 6H polytype, but the transition pressure was found to be somewhat higher than for 3C-SiC. Both of these results are in good agreement with experimental results for bulk SiC. Thus, for nanoscale indentation of 3C and 6H-SiC, the onset of plastic behavior is related to the existence of a phase transition under the indenter tip. For the 6H case a weak dependence on indentation velocity was also observed. This claim was also confirmed by nanoindentation experiments, in which the strain rate sensitivity of mono-crystal 6H was investigated. Simulations of the nanoscratching of 3C-SiC were also carried out. Significant anisotropy in the

  7. Molecular Dynamics Simulation of Argon and Ammonia Physisorbed on Graphite.

    NASA Astrophysics Data System (ADS)

    Cheng, Ailan

    Molecular dynamics simulations are reported for argon and ammonia adsorbed on graphite. Potential models for the Ar-Ar and Ar-graphite interactions are taken to be sums of site-site Lennard -Jones(12-6) energies. Ammonia-ammonia and ammonia-graphite interactions are modeled by site-site interaction, with discrete fractional charges used to describe the electrostatic interactions and the Lennard-Jones(12-6) model used for the non-electrostatic part. The simulations of tri-layer and monolayer film of Ar/Gr were performed for temperatures ranging from 50K to 120K. Layer energies, layer densities, pair distribution functions and orientational bond correlation functions are calculated to characterize the melting transitions and the structures. The results show that the tri-layer film melts layer by layer. The chemical potential of the tri-layer film of argon is calculated at T = 103K by using the test particle, the real particle and the ratio methods. Chemical potentials are calculated for small bins in z direction perpendicular to the surface. The variation of Boltzmann factor with z provides a criterion of the accuracy of the chemical potential obtained. The ratio method provides more precise values than the test particle and real particle methods. Simulations of the monolayer, partial bilayer and complete bilayers at T = 96K were carried out. The results show that the variation of the molecular orientations with coverage are dramatic. The centers of mass of ammonia form a triangular lattice with lattice spacing equal 3.55 A. The unit cell for a monolayer contains four molecules. Electrostatic interactions played an important part in determining the orientations of the molecules. These interactions include both dipole-dipole and dipole-quadrupole interactions, which were roughly equal in magnitude. Melting transition for the submonolayer and monolayer NH_3/Gr were studied also. The role of the orientational order in determining the melting behaviors is discussed

  8. Boundary-controlled barostats for slab geometries in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Gattinoni, C.; Maćkowiak, Sz.; Heyes, D. M.; Brańka, A. C.; Dini, D.

    2014-10-01

    Molecular dynamics simulation barostat schemes are derived for achieving a given normal pressure for a thin liquid or solid layer confined between two parallel walls. This work builds on the boundary-controlled barostat scheme of Lupkowski and van Swol [J. Chem. Phys. 93, 737 (1990), 10.1063/1.459524]. Two classes of barostat are explored, one in which the external load is applied to a virtual regular lattice to which the wall atoms are bound using a tethering potential. The other type of barostat applies the external force directly to the wall atoms, which are not tethered. The extent to which the wall separation distribution is Gaussian is shown to be an effective measure of the quality of the barostat. The first class of barostat can suffer from anomalous dynamical signatures, even resonances, which are sensitive to the effective mass of the virtual lattice, whose value lacks any rigorous definition. The second type of barostat performs much better under equilibrium and wall-sliding nonequilibrium conditions and in not being so prone to resonance instabilities in the wall separation and does not require so many largely arbitrary parameters. The results of exploratory simulations which characterize the dynamical response of the model systems for both dry and wet or lubricated systems using the different barostats are presented. The barostats which have an inherent damping mechanism, such as the ones analogous to a damped harmonic oscillator, reduce the occurrence of large fluctuations and resonances in the separation between the two walls, and they also achieve a new target pressure more quickly. Near a nonequilibrium phase boundary the attributes of the barostat can have a marked influence on the observed behavior.

  9. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

    SciTech Connect

    Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.

    2010-11-01

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  10. Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations

    SciTech Connect

    P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li

    2011-12-31

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  11. Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes

    PubMed Central

    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

  12. Molecular dynamics simulations of water within models of ion channels.

    PubMed

    Breed, J; Sankararamakrishnan, R; Kerr, I D; Sansom, M S

    1996-04-01

    The transbilayer pores formed by ion channel proteins contain extended columns of water molecules. The dynamic properties of such waters have been suggested to differ from those of water in its bulk state. Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes of channel model are investigated: a) parallel bundles of hydrophobic (Ala20) alpha-helices; b) eight-stranded hydrophobic (Ala10) antiparallel beta-barrels; and c) parallel bundles of amphipathic alpha-helices (namely, delta-toxin, alamethicin, and nicotinic acetylcholine receptor M2 helix). The self-diffusion coefficients of water molecules within the pores are reduced significantly relative to bulk water in all of the models. Water rotational reorientation rates are also reduced within the pores, particularly in those pores formed by alpha-helix bundles. In the narrowest pore (that of the Ala20 pentameric helix bundle) self-diffusion coefficients and reorientation rates of intra-pore waters are reduced by approximately an order of magnitude relative to bulk solvent. In Ala20 helix bundles the water dipoles orient antiparallel to the helix dipoles. Such dipole/dipole interaction between water and pore may explain how water-filled ion channels may be formed by hydrophobic helices. In the bundles of amphipathic helices the orientation of water dipoles is modulated by the presence of charged side chains. No preferential orientation of water dipoles relative to the pore axis is observed in the hydrophobic beta-barrel models.

  13. Amorphous silicene—a view from molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Van Hoang, Vo; Long, N. T.

    2016-05-01

    Models of amorphous silicene (a-silicene) containing 104 atoms are obtained by cooling from the melt via molecular dynamics (MD) simulation. The evolution of various kinds of structural and thermodynamic behavior in models upon cooling from the melt is found, including total energy, radial distribution function (RDF), interatomic distance, coordination number, and ring and bond-angle distributions. We also show the buckling distribution and a 2D visualization of the atomic configurations. The diffraction pattern shows that a glass state is indeed formed in the system. The glass transition temperature of 2D silicon ({{T}\\text{g}}=1350 K) has a reasonable value compared to that of its 3D counterpart. Calculations show that although most atoms in a-silicene obtained at 300 K have a three-fold coordination and mainly evolve into six-fold rings, a-silicene also contains various structural defects including those not found in crystalline silicene (c-silicene) such as adatoms, clusters of small-membered rings, large-membered rings and local linear defects. The concentration of defects in a-silicene is much higher than that of the crystalline version. We find that buckling is not unique for all the atoms in the model. The strong distorted structure of a-silicene compared to that of the crystalline version may lead to physico-chemical properties, including the possibility of opening the band gap in the former compared to the zero band gap of the latter. Note that due to the fixed length being equal to buckling of 0.44 Å in the z direction with the elastic reflection behavior boundary, our models are relevant for a-silicene formed in confinement between two planar simple hard walls.

  14. Classical molecular dynamics simulation of electronically non-adiabatic processes.

    PubMed

    Miller, William H; Cotton, Stephen J

    2016-12-22

    Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).

  15. Molecular Dynamics Simulations of Responsive Semi-Fluorinated Interfaces

    NASA Astrophysics Data System (ADS)

    Pierce, Flint

    2010-03-01

    Responsive polymeric thin films with controlled surface energies, dielectric constants and structure are critical for a variety of emerging nano and micro-scale technologies including fluidics, electro-optical devices and biotechnology. Introducing nanometer sized fluorinated segments offers a means to tune the polymer properties while significantly enhancing chemical and thermal stability. The interfacial structure and dynamics of multiblock semi fluorinated copolymers at their liquid/vapor interface and at interfaces with water and protonated alkanes has been studied using explicit atom molecular dynamic simulations. For semifluorinated diblocks H3C(CH2)n-1(CF2)m-1CF3 of varying fluorine content, fluorinated groups proliferate and reside longer at the liquid/vapor interface as expected for the lower surface tension components. Aqueous interfaces of these diblocks are sharp and well defined with an enhanced density of protonated groups owing to their reduced hydrophobicity in comparison to fluorinated groups. The enhancement increases with temperature. Protonated alkanes are found to be mutually miscible with the semifluorinated diblock copolymers. Similar surface behavior is observed in semifluorinated multiblock copolymers of the form H-[(CH2)n (CF2)n]m-F where m varies from 3 to 48 with nxm=48. The fluorine enhancement at the liquid-vapor interface depends on both the temperature and block length, with the longest blocks showing the greatest enhancement. Due to mutual phobicity of protonated and fluorinated groups, nm-scale fluorine and hydrogen rich regions occur at the surfaces of these materials, with sizes that also depend on block length and temperature. Work in collaboration with Dvora Perahia and Gary S. Grest.

  16. Shock response of nanoporous Cu--A molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Zhao, Fengpeng

    2015-06-01

    Shock response of porous materials can be of crucial significance for shock physics and bears many practical applications in materials synthesis and engineering. Molecular dynamics simulations are carried out to investigate shock response of nanoporous metal materials, including elastic-plastic deformation, Hugoniot states, shock-induced melting, partial or complete void collapse, hotspot formation, nanojetting, and vaporization. A model nanoporous Cu with cylindrical voids and a high porosity under shocking is established to investigate such physical properties as velocity, temperature, density, stress and von Mises stress at different stages of compression and release. The elastic-plastic and overtaking shocks are observed at different shock strengths. A modified power-law P- α model is proposed to describe the Hugoniot states. The Grüneisen equation of state is validated. Shock-induced melting shows no clear signs of bulk premelting or superheating. Void collapse via plastic flow nucleated from voids, and the exact processes are shock strength dependent. With increasing shock strengths, void collapse transits from the ``geometrical'' mode (collapse of a void is dominated by crystallography and void geometry and can be different from that of one another) to ``hydrodynamic'' mode (collapse of a void is similar to one another). The collapse may be achieved predominantly by plastic flows along the {111} slip planes, by way of alternating compression and tension zones, by means of transverse flows, via forward and transverse flows, or through forward nano-jetting. The internal jetting induces pronounced shock front roughening, leading to internal hotspot formation and sizable high speed jets on atomically flat free surfaces. P. O. Box 919-401, Mianyang, 621900, Sichuan, PRC.

  17. Polymer deformation in Brownian ratchets: theory and molecular dynamics simulations.

    PubMed

    Kenward, Martin; Slater, Gary W

    2008-11-01

    We examine polymers in the presence of an applied asymmetric sawtooth (ratchet) potential which is periodically switched on and off, using molecular dynamics (MD) simulations with an explicit Lennard-Jones solvent. We show that the distribution of the center of mass for a polymer in a ratchet is relatively wide for potential well depths U0 on the order of several kBT. The application of the ratchet potential also deforms the polymer chains. With increasing U0 the Flory exponent varies from that for a free three-dimensional (3D) chain, nu=35 (U0=0), to that corresponding to a 2D compressed (pancake-shaped) polymer with a value of nu=34 for moderate U0. This has the added effect of decreasing a polymer's diffusion coefficient from its 3D value D3D to that of a pancaked-shaped polymer moving parallel to its minor axis D2D. The result is that a polymer then has a time-dependent diffusion coefficient D(t) during the ratchet off time. We further show that this suggests a different method to operate a ratchet, where the off time of the ratchet, toff, is defined in terms of the relaxation time of the polymer, tauR. We also derive a modified version of the Bader ratchet model [Bader, Proc. Natl. Acad. Sci. U.S.A. 96, 13165 (1999)] which accounts for this deformation and we present a simple expression to describe the time dependent diffusion coefficient D(t). Using this model we then illustrate that polymer deformation can be used to modulate polymer migration in a ratchet potential.

  18. Molecular dynamics simulations on the hydration of fluoroalcohols

    NASA Astrophysics Data System (ADS)

    Kinugawa, Kenichi; Nakanishi, Koichiro

    1988-11-01

    Molecular dynamics (MD) calculations have been carried out for aqueous solutions of isopropyl alcohol (IPA) and its fluorinated compounds, 1,1,1-trifluoro-2-propanol (TFIPA) and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIPA). The simulated systems were canonical ensembles containing 216 molecules in each, one of which was alcohol and the temperature was set to 298.15 K. The MCY (Matsuoka-Clementi-Yoshimine) potential was used for water-water interaction, whereas new potential functions were determined for alcohol-water interactions, on the basis of ab initio molecular orbital calculations on more than 1100 different dimeric configurations for each alcohol-water pair. The static properties of solvent water in the vicinity of each functional group of solute were obtained from MD calculations. It is found that the promotion of water structure and the increase of hydrogen bond between water molecules occurs not only near the fluoroalkyl group but also even near hydroxyl group of fluoroalcohols. Furthermore, the alcohol-water interaction is stronger for fluoroalcohols than for aliphatic alcohols, owing to the electronegativity and the electron withdrawing effect of fluorine atoms. The enthalpies of hydration for fluoroalcohols include the contributions from these features of both water-water and alcohol-water interactions. This is not the case for the hydration of aliphatic alcohols, and is the reason for the lack of regular change of enthalpies of hydration with the degree of the substitution of CH3 by the CF3 group. The hydration of IPA is similar to that of other aliphatic alcohols; hydrophobic hydration near the apolar group and the energetic unstabilization of water near the hydroxyl group are observed.

  19. Communication: A method to compute the transport coefficient of pure fluids diffusing through planar interfaces from equilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume

    2017-09-01

    The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.

  20. Communication: A method to compute the transport coefficient of pure fluids diffusing through planar interfaces from equilibrium molecular dynamics simulations.

    PubMed

    Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume

    2017-09-14

    The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.

  1. Mott Transition in a Metallic Liquid: Gutzwiller Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Chern, Gia-Wei; Barros, Kipton; Batista, Cristian D.; Kress, Joel D.; Kotliar, Gabriel

    2017-06-01

    We present a formulation of quantum molecular dynamics that includes electron correlation effects via the Gutzwiller method. Our new scheme enables the study of the dynamical behavior of atoms and molecules with strong electron interactions. The Gutzwiller approach goes beyond the conventional mean-field treatment of the intra-atomic electron repulsion and captures crucial correlation effects such as band narrowing and electron localization. We use Gutzwiller quantum molecular dynamics to investigate the Mott transition in the liquid phase of a single-band metal and uncover intriguing structural and transport properties of the atoms.

  2. Correlation between thermal conductivity and bond length alternation in carbon nanotubes: a combined reverse nonequilibrium molecular dynamics--crystal orbital analysis.

    PubMed

    Alaghemandi, Mohammad; Schulte, Joachim; Leroy, Frédéric; Müller-Plathe, Florian; Böhm, Michael C

    2011-01-15

    The thermal conductivity (λ) of carbon nanotubes (CNTs) with chirality indices (5,0), (10,0), (5,5), and (10,10) has been studied by reverse nonequilibrium molecular dynamics (RNEMD) simulations as a function of different bond length alternation patterns (Δr(i) ). The Δr(i) dependence of the bond force constant (k(rx) ) in the molecular dynamics force field has been modeled with the help of an electronic band structure approach. These calculations show that the Δr(i) dependence of k(rx) in tubes with not too small a diameter can be mapped by a simple linear bond length-bond order correlation. A bond length alternation with an overall reduction in the length of the nanotube causes an enhancement of λ, whereas an alternation scheme leading to an elongation of the tube is coupled to a decrease of the thermal conductivity. This effect is more pronounced in carbon nanotubes with larger diameters. The formation of a polyene-like structure in the direction of the longitudinal axis has a negligible influence on λ. A comparative analysis of the RNEMD and crystal orbital results indicates that Δr(i) -dependent modifications of λ and the electrical conductivity are uncorrelated. This behavior is in-line with a heat transfer that is not carried by electrons. Modifications of λ as a function of the bond alternation in the (10,10) nanotube are explained with the help of power spectra, which provide access to the density of vibrational states. We have suggested longitudinal low-energy modes in the spectra that might be responsible for the Δr(i) dependence of λ. Copyright © 2010 Wiley Periodicals, Inc.

  3. Communication: Influence of external static and alternating electric fields on water from long-time non-equilibrium ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Futera, Zdenek; English, Niall J.

    2017-07-01

    The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.

  4. 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)

  5. 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.

  6. 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)

  7. Extended Lagrangian quantum molecular dynamics simulations of shock-induced chemistry in hydrocarbons

    SciTech Connect

    Sanville, Edward J; Bock, Nicolas; Challacombe, William M; Cawkwell, Marc J; Niklasson, Anders M N; Dattelbaum, Dana M; Sheffield, Stephen; Sewell, Thomas D

    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.

  8. Molecular dynamics simulation study of binary fullerene mixtures

    NASA Astrophysics Data System (ADS)

    Ruberto, R.; Abramo, M. C.; Caccamo, C.

    2004-10-01

    We report constant-pressure molecular dynamics (MD) simulations of binary C60/Cn fullerene-mixtures ( n=70 , 76, 84, 96) modeled in terms of a spherically symmetric two-body potential. By starting from a liquid configuration of the system, we cool mixtures down to freezing and beyond, until room temperature is reached, in order to verify the formation of solid solutions, namely, of configurations characterized by a unique crystalline lattice whose sites are randomly occupied by the two component fullerene species. We first explore the entire concentration range of the C60x/C70(1-x)(0simulate forms substitutional solid solutions over a wide range of concentrations except for 0.3⩽x⩽0.5 ; over such an interval, it turns out that the initially liquid mixture can be supercooled down to relatively low temperatures, until eventually a glassy phase is formed. The study is then extended to fullerene mixtures of molecular diameter ratio α=σC60/σCn smaller than in C60/C70 (where α=0.93 ), as is the case for C60/C76 (α=0.89) , C60/C84(α=0.85) and C60/C96 (α=0.79) . The effect of the size mismatch between the two species is dramatic: The solid immiscibility region rapidly expands even upon a tiny reduction of α , with formation of an amorphous phase at sufficiently low temperature, as found for the C60/C70 mixture. For the smallest α(C60/C96) cocrystallization of the two components turns out to be forbidden over the whole concentration axis. A mapping of the MD evidences of the fullerene mixtures’ phase behavior onto the phase diagram of binary hard-sphere mixtures (determined by other authors) turns out to be worthwhile and enlightnening. In particular, size ratio effects and the onset of glassy phases emerge in qualitative good agreement

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

    NASA Astrophysics Data System (ADS)

    Dizkirici, Ayten; Tekpinar, Mustafa

    2015-03-01

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

  10. Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

    PubMed

    Dalby, Andrew; Shamsir, Mohd Shahir

    2015-01-01

    Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation.

  11. Molecular dynamics simulations of ice nucleation by electric fields.

    PubMed

    Yan, J Y; Patey, G N

    2012-07-05

    Molecular dynamics simulations are used to investigate heterogeneous ice nucleation in model systems where an electric field acts on water molecules within 10-20 Å of a surface. Two different water models (the six-site and TIP4P/Ice models) are considered, and in both cases, it is shown that a surface field can serve as a very effective ice nucleation catalyst in supercooled water. Ice with a ferroelectric cubic structure nucleates near the surface, and dipole disordered cubic ice grows outward from the surface layer. We examine the influences of temperature and two important field parameters, the field strength and distance from the surface over which it acts, on the ice nucleation process. For the six-site model, the highest temperature where we observe field-induced ice nucleation is 280 K, and for TIP4P/Ice 270 K (note that the estimated normal freezing points of the six-site and TIP4P/Ice models are ∼289 and ∼270 K, respectively). The minimum electric field strength required to nucleate ice depends a little on how far the field extends from the surface. If it extends 20 Å, then a field strength of 1.5 × 10(9) V/m is effective for both models. If the field extent is 10 Å, then stronger fields are required (2.5 × 10(9) V/m for TIP4P/Ice and 3.5 × 10(9) V/m for the six-site model). Our results demonstrate that fields of realistic strength, that act only over a narrow surface region, can effectively nucleate ice at temperatures not far below the freezing point. This further supports the possibility that local electric fields can be a significant factor influencing heterogeneous ice nucleation in physical situations. We would expect this to be especially relevant for ice nuclei with very rough surfaces where one would expect local fields of varying strength and direction.

  12. A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

    PubMed Central

    Ewen, James P.; Gattinoni, Chiara; Thakkar, Foram M.; Morgan, Neal; Spikes, Hugh A.; Dini, Daniele

    2016-01-01

    For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently

  13. Molecular Dynamics Simulation for the Dynamics and Kinetics of Folding Peptides in the Gas Phase.

    PubMed

    Litinas, Iraklis; Koutselos, Andreas D

    2015-12-31

    The conformations of flexible molecular species, such as oligomers and oligopeptides, and their interconversion in the gas phase have been probed by ion mobility spectrometry measurements. The ion motion is interpreted through the calculation of effective cross sections in the case of stable conformations of the macromolecules. However, when the molecular structures transform to each other as the ions collide with gas atoms during their flight through the drift tube, the introduction of an average cross section is required. To provide a direct way for the reproduction of the ion motion, we employ a nonequilibrium molecular dynamics simulation method and consider a molecular model that consists of two connected stiff cylindrical bodies interacting through an intramolecular model potential. With this procedure we have calculated the ion mobility as a function of temperature for a prototype peptide that converts between a helical and an extended globular form. The results are in good agreement with ion mobility spectrometry data confirming that an angular vibration coordinate can be used for the interpretation of the shifting of the drift-time distributions at high temperatures. The approach produces mean kinetic energies as well as various combined distributions of the ion degrees of freedom. It is easily applied to flexible macromolecular ions and can be extended to include additional degrees of freedom.

  14. Hydrogen bonding and vibrational energy relaxation of interfacial water: A full DFT molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Jeon, Jonggu; Hsieh, Cho-Shuen; Nagata, Yuki; Bonn, Mischa; Cho, Minhaeng

    2017-07-01

    The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm-1); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.

  15. Hydrogen bonding and vibrational energy relaxation of interfacial water: A full DFT molecular dynamics simulation.

    PubMed

    Jeon, Jonggu; Hsieh, Cho-Shuen; Nagata, Yuki; Bonn, Mischa; Cho, Minhaeng

    2017-07-28

    The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm(-1)); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.

  16. Adiabatic molecular-dynamics-simulation-method studies of kinetic friction

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Sokoloff, J. B.

    2005-06-01

    An adiabatic molecular-dynamics method is developed and used to study the Muser-Robbins model for dry friction (i.e., nonzero kinetic friction in the slow sliding speed limit). In this model, dry friction between two crystalline surfaces rotated with respect to each other is due to mobile molecules (i.e., dirt particles) adsorbed at the interface. Our adiabatic method allows us to quickly locate interface potential-well minima, which become unstable during sliding of the surfaces. Since dissipation due to friction in the slow sliding speed limit results from mobile molecules dropping out of such unstable wells, our method provides a way to calculate dry friction, which agrees extremely well with results found by conventional molecular dynamics for the same system, but our method is more than a factor of 10 faster.

  17. Atomistic molecular dynamics simulations of model C36 fullerite

    NASA Astrophysics Data System (ADS)

    Abramo, Maria C.; Caccamo, C.

    2008-02-01

    We report atomistic molecular dynamics investigations of a model C36 fullerite in which the fullerene molecules are modeled as rigid cages over which the carbon atoms occupy fixed interaction sites, distributed in space according to the experimentally known atomic positions in the molecule. Carbon sites belonging to different molecules are assumed to interact via a 12-6 Lennard-Jones-type potential; the parameters of the latter are employed in the framework of a molecular dynamics fitting procedure, through which the ambient condition physical quantities characterizing the hcp structure of solid C36 are eventually reproduced. We discuss applications of the adopted modelization to the C36 phases in a temperature range spanning from 300to1500K, and compare the obtained results to the available data for C36 and other fullerenes, and to the predictions of the well known Girifalco central potential modelization of interactions in fullerenes, as applied to the C36 case.

  18. Accelerating molecular dynamic simulation on graphics processing units.

    PubMed

    Friedrichs, Mark S; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L; Ensign, Daniel L; Bruns, Christopher M; Pande, Vijay S

    2009-04-30

    We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. (c) 2009 Wiley Periodicals, Inc.

  19. Large scale molecular dynamics simulations of a liquid crystalline droplet with fast multipole implementations

    SciTech Connect

    Wang, Z.; Lupo, J.; Patnaik, S.S.; McKenney, A.; Pachter, R.

    1999-07-01

    The Fast Multipole Method (FMM) offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus enabling more realistic molecular dynamics simulations of large molecular systems. The performance of the fast molecular dynamics (FMD) code, a parallel MD code being developed in the group, using the three-dimensional fast multipole method, shows a good speedup. The application to the full atomic-scale molecular dynamics simulation of a liquid crystalline droplet of 4-n-pentyl-4{prime}-cyanobiphenyl (5CB) molecules, of size 35,872 atoms, shows strong surface effects on various orientational order parameters.

  20. Carbon dioxide in silicate melts: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Guillot, Bertrand; Sator, Nicolas

    2011-04-01

    We have performed a series of molecular dynamics simulations aimed at the evaluation of the solubility of CO 2 in silicate melts of natural composition (from felsic to ultramafic). In making in contact within the simulation cell a supercritical CO 2 phase with a silicate melt of a given composition, we have been able to evaluate (i) the solubility of CO 2 in the P- T range 1473-2273 K and 20-150 kbar, (ii) the density change experienced by the CO 2-bearing melt, (iii) the respective concentrations of CO 2 and CO32- species in the melt, (iv) the lifetime and the diffusivity of these species and (v) the structure of the melt around the carbonate groups. The main results are the following: (1) The solubility of CO 2 increases markedly with the pressure in the three investigated melts (a rhyolite, a mid-ocean ridge basalt and a kimberlite) from about ˜2 wt% CO 2 at 20 kbar to ˜25 wt% at 100 kbar and 2273 K. The solubility is found to be weakly dependent on the melt composition (as far as the present compositions are concerned) and it is only at very high pressure (above ˜100 kbar) that a clear hierarchy between solubilities occurs (rhyolite < MORB < kimberlite). Furthermore at a given pressure the calculated solubility is negatively correlated with the temperature. (2) In CO 2-saturated melts, the proportion of carbonate ions (CO32-) is positively correlated with the pressure at isothermal condition and is negatively correlated with the temperature at isobaric condition (and vice versa for molecular CO 2). Furthermore, at fixed ( P, T) conditions the proportion of carbonate ions is higher in CO 2-undersaturated melts than in the CO 2-saturated melt. Although the proportion of molecular CO 2 decreases when the degree of depolymerization of the melt increases, it is still significant in CO 2-saturated basic and ultrabasic compositions at high temperatures. This finding is at variance with experimental data on CO 2-bearing glasses which show no evidence of molecular CO

  1. Exploiting molecular dynamics in Nested Sampling simulations of small peptides

    NASA Astrophysics Data System (ADS)

    Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor

    2016-04-01

    Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.

  2. Full molecular dynamics simulations of liquid water and carbon tetrachloride for two-dimensional Raman spectroscopy in the frequency domain

    NASA Astrophysics Data System (ADS)

    Jo, Ju-Yeon; Ito, Hironobu; Tanimura, Yoshitaka

    2016-12-01

    Frequency-domain two-dimensional (2D) Raman signals, which are equivalent to coherent two-dimensional Raman scattering (COTRAS) signals, for liquid water and carbon tetrachloride were calculated using an equilibrium-nonequilibrium hybrid molecular dynamics (MD) simulation algorithm. An appropriate representation of the 2D Raman spectrum obtained from MD simulations provides an easy-to-understand depiction of structural and dynamical properties. We elucidate mechanisms governing the 2D signal profiles involving anharmonic mode-mode coupling and the nonlinearities of the polarizability for the intermolecular and intramolecular vibrational modes. The predicted signal profiles and intensities can be utilized to analyze recently developed single-beam 2D spectra, whose signals are generated from a coherently controlled pulse, allowing the single-beam measurement to be carried out more efficiently. Moreover, the MD simulation results allow us to visualize the molecular structure and dynamics by comparing the accurately calculated spectrum with experimental result.

  3. Xenon Implantation in Nanodiamonds: In Situ Transmission Electron Microscopy Study and Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Shiryaev, A. A.; Hinks, J.; Marks, N.; Greaves, G.; Donnelly, S.; Fisenko, A. V.; Kiwi, M.

    2016-08-01

    We present results of the first investigation of the Xe implantation process into nanodiamonds of various sizes studied in situ in transmission electron microscope (TEM), complemented by advanced molecular dynamics simulations.

  4. Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

    PubMed

    Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

    2016-03-01

    Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

  5. Equilibrium sampling by reweighting nonequilibrium simulation trajectories

    NASA Astrophysics Data System (ADS)

    Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

    2016-03-01

    Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

  6. Molecular Dynamics Simulations of Hexadecane/Silicalite Interfaces

    SciTech Connect

    Grest, G.S.; Webb, E.B.

    1999-01-20

    The interface between liquid hexadecane and the (010) surface of silicalite was studied by molecular dynamics. The structure of molecules in the interracial region is influenced by the presence of pore mouths on the silicalite surface. For this surface, whose pores are the entrances to straight channels, the concentration profile for partially absorbed molecules is peaked around 10 monomers inside the zeolite. No preference to enter or exit the zeolite based on absorption length is observed except for very small or very large absorption lengths. We also found no preferential conformation of the unabsorbed tails for partially absorbed molecules.

  7. Simulation of shock-induced melting of Ni using molecular dynamics coupled to a two-temperature model

    NASA Astrophysics Data System (ADS)

    Koči, L.; Bringa, E. M.; Ivanov, D. S.; Hawreliak, J.; McNaney, J.; Higginbotham, A.; Zhigilei, L. V.; Belonoshko, A. B.; Remington, B. A.; Ahuja, R.

    2006-07-01

    Using nonequilibrium molecular dynamics (MD) simulations we study shock-induced melting in Ni with an embedded atom method (EAM). Dynamic melting is probed by the pair correlation function, and we find a melting lattice temperature of Tmelt=6400±300K for a melting pressure of Pmelt=275±10GPa . When a combined MD+TTM (two-temperature model) approach is used to include electronic heat conduction and electron-phonon coupling, Pmelt and Tmelt change. For a given pressure, the temperature behind the shock decreases due to electronic heat diffusion into the cold, unshocked material. This cooling of the material behind the shock slightly increases the melting pressure compared to simulations without electronic heat conduction and electron-phonon coupling. The decrease in the temperature behind the shock front is enhanced if the electron-phonon coupling is artificially made larger. We also explore the feasibility of using x-ray diffraction to detect melting.

  8. Effect of surface roughness and size of beam on squeeze-film damping—Molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Kim, Hojin; Strachan, Alejandro

    2015-11-01

    We use large-scale molecular dynamics (MD) to characterize fluid damping between a substrate and an approaching beam. We focus on the near contact regime where squeeze film (where fluid gap is comparable to the mean free path of the gas molecules) and many-body effects in the fluid become dominant. The MD simulations provide explicit description of many-body and non-equilibrium processes in the fluid as well as the surface topography. We study how surface roughness and beam width increases the damping coefficient due to their effect on fluid mobility. We find that the explicit simulations are in good agreement with prior direct simulation Monte Carlo results except at near-contact conditions where many-body effects in the compressed fluid lead the increased damping and weaker dependence on beam width. We also show that velocity distributions near the beam edges and for short gaps deviate from the Boltzmann distribution indicating a degree of local non-equilibrium. These results will be useful to parameterize compact models used for microsystem device-level simulations and provide insight into mesoscale simulations of near-contact damping.

  9. Effect of surface roughness and size of beam on squeeze-film damping—Molecular dynamics simulation study

    SciTech Connect

    Kim, Hojin; Strachan, Alejandro

    2015-11-28

    We use large-scale molecular dynamics (MD) to characterize fluid damping between a substrate and an approaching beam. We focus on the near contact regime where squeeze film (where fluid gap is comparable to the mean free path of the gas molecules) and many-body effects in the fluid become dominant. The MD simulations provide explicit description of many-body and non-equilibrium processes in the fluid as well as the surface topography. We study how surface roughness and beam width increases the damping coefficient due to their effect on fluid mobility. We find that the explicit simulations are in good agreement with prior direct simulation Monte Carlo results except at near-contact conditions where many-body effects in the compressed fluid lead the increased damping and weaker dependence on beam width. We also show that velocity distributions near the beam edges and for short gaps deviate from the Boltzmann distribution indicating a degree of local non-equilibrium. These results will be useful to parameterize compact models used for microsystem device-level simulations and provide insight into mesoscale simulations of near-contact damping.

  10. Thermal conductance of carbon nanotube contacts: Molecular dynamics simulations and general description of the contact conductance

    NASA Astrophysics Data System (ADS)

    Salaway, Richard N.; Zhigilei, Leonid V.

    2016-07-01

    The contact conductance of carbon nanotube (CNT) junctions is the key factor that controls the collective heat transfer through CNT networks or CNT-based materials. An improved understanding of the dependence of the intertube conductance on the contact structure and local environment is needed for predictive computational modeling or theoretical description of the effective thermal conductivity of CNT materials. To investigate the effect of local structure on the thermal conductance across CNT-CNT contact regions, nonequilibrium molecular dynamics (MD) simulations are performed for different intertube contact configurations (parallel fully or partially overlapping CNTs and CNTs crossing each other at different angles) and local structural environments characteristic of CNT network materials. The results of MD simulations predict a stronger CNT length dependence present over a broader range of lengths than has been previously reported and suggest that the effect of neighboring junctions on the conductance of CNT-CNT junctions is weak and only present when the CNTs that make up the junctions are within the range of direct van der Waals interaction with each other. A detailed analysis of the results obtained for a diverse range of intertube contact configurations reveals a nonlinear dependence of the conductance on the contact area (or number of interatomic intertube interactions) and suggests larger contributions to the conductance from areas of the contact where the density of interatomic intertube interactions is smaller. An empirical relation accounting for these observations and expressing the conductance of an arbitrary contact configuration through the total number of interatomic intertube interactions and the average number of interatomic intertube interactions per atom in the contact region is proposed. The empirical relation is found to provide a good quantitative description of the contact conductance for various CNT configurations investigated in the MD

  11. Simulating Nonequilibrium Radiation via Orthogonal Polynomial Refinement

    DTIC Science & Technology

    2015-01-07

    resolution orthogonal polynomial refinement technique for this multi-disciplinary science. Through the computational mathematics basic research, a...thus the phenomenon must be modeled [1-4]. In addition, the chemical species concentrations and its associated thermodynamic states of an inhomogeneous... thermodynamic state and compositions of the flow medium. The required optical parameters for the nonequilibrium phenomena simulation need to be determined

  12. Uranyl-Glutardiamidoxime Binding from First-Principles Molecular Dynamics, Classical Molecular Dynamics, and Free-Energy Simulations.

    PubMed

    Priest, Chad; Li, Bo; Jiang, De-En

    2017-08-21

    Exploring the structural interplay of ligands with uranyl can provide important knowledge for technology advances in uranium extraction from seawater. However, obtaining such chemical information is not an easy endeavor experimentally. From a plethora of computational methods, this work provides both microscopic insights and free-energy profiles of the binding between uranyl and deprotonated glutardiamidoxime (H2B) for which experimental structural information is not available, despite H2B being an important model ligand with an open-chain conformation for understanding aqueous uranium extraction chemistry. In our molecular dynamics (MD) simulations, we explicitly accounted for the water solvent as well as the Na(+) and Cl(-) ions. We found that hydrogen bonding plays a critical role in dictating the binding configurations of B(2-) and HB(-) with uranyl. Simulated free energies of sequential ligand binding to form UO2B, [UO2B2](2-), and [UO2(HB)B](-) show very good agreement with the experimental values, lending support to our structural insights. The potential of mean force simulations showed the common feature of an important intermediate state where one end of the ligand binds to uranyl while the other end is solvated in water. Bringing the loose end of the ligand to bind with uranyl has a free-energy barrier of 15-25 kJ/mol. The present work shows that the combined simulation approach can reveal key structural and thermodynamic insights toward a better understanding of aqueous complexation chemistry for uranium extraction from the sea.

  13. Simulation of Screw Dislocation Motion in Iron by Molecular