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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. Amyloid fibril disruption by ultrasonic cavitation: nonequilibrium molecular dynamics simulations.

    PubMed

    Okumura, Hisashi; Itoh, Satoru G

    2014-07-30

    We describe the disruption of amyloid fibrils of Alzheimer's amyloid-β peptides by ultrasonic cavitation. For this purpose, we performed nonequilibrium all-atom molecular dynamics simulations with sinusoidal pressure and visualized the process with movies. When the pressure is negative, a bubble is formed, usually at hydrophobic residues in the transmembrane region. Most β-strands maintain their secondary structures in the bubble. When the pressure becomes positive, the bubble collapses, and water molecules crash against the hydrophilic residues in the nontransmembrane region to disrupt the amyloid. Shorter amyloids require longer sonication times for disruption because they do not have enough hydrophobic residues to serve as a nucleus to form a bubble. These results agree with experiments in which monodispersed amyloid fibrils were obtained by ultrasonication. PMID:24987794

  3. 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.

  4. 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.

  5. Equilibrium and nonequilibrium molecular-dynamics simulations of the central force model of water

    NASA Astrophysics Data System (ADS)

    Bresme, Fernando

    2001-10-01

    Equilibrium and nonequilibrium molecular-dynamics simulations of the central force model of water (CFM) [Lemberg and Stillinger, J. Chem. Phys. 62, 1677 (1975)] are presented. We consider a model based on a functional form introduced in theoretical studies of associating systems employing integral equations [F. Bresme, J. Chem. Phys. 108, 4505 (1998)]. Results on thermodynamic, dynamic, dielectric, and coexistence properties are presented. The central force model shows satisfactory agreement with the experimental results in all these cases. In addition, nonequilibrium molecular-dynamics simulations show that the CFM predicts a decrease of the thermal conductivity with temperature, as observed in the experiment, but this dependence is reproduced qualitatively at temperatures characteristic of supercooled states. These results emphasize the need for further studies of the heat conduction and properties of water in these conditions. Overall the present potential should provide a basis for further theoretical and simulation studies of complex systems where water is present.

  6. 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. PMID:26300709

  7. A localized momentum constraint for non-equilibrium molecular dynamics simulations.

    PubMed

    Smith, E R; Heyes, D M; Dini, D; Zaki, T A

    2015-02-21

    A method which controls momentum evolution in a sub-region within a molecular dynamics simulation is derived from Gauss's principle of least constraint. The technique for localization is founded on the equations by Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] expressed in a weak form according to the control volume (CV) procedure derived by Smith et al. [Phys. Rev. E. 85, 056705 (2012)]. A term for the advection of molecules appears in the derived constraint and is shown to be essential in order to exactly control the time evolution of momentum in the subvolume. The numerical procedure converges the total momentum in the CV to the target value to within machine precision in an iterative manner. The localized momentum constraint can prescribe essentially arbitrary flow fields in non-equilibrium molecular dynamics simulations. The methodology also forms a rigorous mathematical framework for introducing coupling constraints at the boundary between continuum and discrete systems. This functionality is demonstrated with a boundary-driven flow test case. PMID:25702005

  8. Periodic boundary conditions for long-time nonequilibrium molecular dynamics simulations of incompressible flows

    NASA Astrophysics Data System (ADS)

    Dobson, Matthew

    2014-11-01

    This work presents a generalization of the Kraynik-Reinelt (KR) boundary conditions for nonequilibrium molecular dynamics simulations. In the simulation of steady, homogeneous flows with periodic boundary conditions, the simulation box deforms with the flow, and it is possible for image particles to become arbitrarily close, causing a breakdown in the simulation. The KR boundary conditions avoid this problem for planar elongational flow and general planar mixed flow [T. A. Hunt, S. Bernardi, and B. D. Todd, J. Chem. Phys. 133, 154116 (2010)] through careful choice of the initial simulation box and by periodically remapping the simulation box in a way that conserves image locations. In this work, the ideas are extended to a large class of three-dimensional flows by using multiple remappings for the simulation box. The simulation box geometry is no longer time-periodic (which was shown to be impossible for uniaxial and biaxial stretching flows in the original work by Kraynik and Reinelt [Int. J. Multiphase Flow 18, 1045 (1992)]. The presented algorithm applies to all flows with nondefective flow matrices, and in particular, to uniaxial and biaxial flows.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Okumura, Hisashi

    2015-12-01

    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.

  15. 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.

  16. Nonequilibrium Molecular Dynamics Simulations of Organic Friction Modifiers Adsorbed on Iron Oxide Surfaces.

    PubMed

    Ewen, James P; Gattinoni, Chiara; Morgan, Neal; Spikes, Hugh A; Dini, Daniele

    2016-05-10

    For the successful development and application of lubricants, a full understanding of the nanoscale behavior of complex tribological systems is required, but this is difficult to obtain experimentally. In this study, we use nonequilibrium molecular dynamics (NEMD) simulations to examine the atomistic structure and friction properties of commercially relevant organic friction modifier (OFM) monolayers adsorbed on iron oxide surfaces and lubricated by a thin, separating layer of hexadecane. Specifically, acid, amide, and glyceride OFMs, with saturated and Z-unsaturated hydrocarbon tail groups, are simulated at various surface coverages and sliding velocities. At low and medium coverage, the OFMs form liquidlike and amorphous monolayers, respectively, which are significantly interdigitated with the hexadecane lubricant, resulting in relatively high friction coefficients. At high coverage, solidlike monolayers are formed for all of the OFMs, which, during sliding, results in slip planes between well-defined OFM and hexadecane layers, yielding a marked reduction in the friction coefficient. When present at equal surface coverage, OFMs with saturated and Z-unsaturated tail groups are found to yield similar structure and friction behavior. OFMs with glyceride head groups yield significantly lower friction coefficients than amide and particularly carboxylic acid head groups. For all of the OFMs and coverages simulated, the friction coefficient is found to increase linearly with the logarithm of sliding velocity; however, the gradient of this increase depends on the coverage. The structure and friction details obtained from these simulations agree well with experimental results and also shed light on the relative tribological performance of these OFMs through nanoscale structural variations. This has important implications in terms of the applicability of NEMD to aid the development of new formulations to control friction. PMID:27064962

  17. 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. PMID:27071540

  18. 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.

  19. Shear viscosity of a supercooled polymer melt via nonequilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Varnik, F.; Binder, K.

    2002-10-01

    Using nonequilibrium molecular dynamics simulations, we compute the shear viscosity, ηs, of a glass forming polymer melt at temperatures ranging from the normal liquid state down to the supercooled state. For this purpose, the polymer melt is confined between two solid walls and a constant force pointing in direction parallel to the walls is applied on each monomer thus giving rise to a Poiseuille flow. It is shown that ηs(T) does not exhibit an Arrhenius-type behavior but can be described both by a power law (mode coupling theory) and by a Vogel-Fulcher-Tammann law. A similar behavior is observed in recent experiments above the glass transition temperature. The diffusion coefficient is computed using the mean square displacements in direction perpendicular to the flow. Combined with the knowledge of ηs(T), it is then shown that the Stokes-Einstein relation is valid at high temperatures, whereas deviations are observed in the supercooled regime in agreement with experiments. Moreover, the local viscosity, η(z), is also computed and its reliability is discussed. Using the sharp rise of η(z) close to the wall, we estimate zwall, the effective position of the wall. It is found that zwall moves towards the film center at lower T thus leading to a decrease of the (hydrodynamic) width of the system. Furthermore, we observe that the curves for η(z)/ηs at various temperatures superimpose if the data are depicted versus z-zwall(T). This suggests that the spatial and temperature dependence of the local viscosity separate if the effective position of the wall is chosen as a new reference plane.

  20. 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.

  1. Non-equilibrium molecular dynamics simulation of nanojet injection with adaptive-spatial decomposition parallel algorithm.

    PubMed

    Shin, Hyun-Ho; Yoon, Woong-Sup

    2008-07-01

    An Adaptive-Spatial Decomposition parallel algorithm was developed to increase computation efficiency for molecular dynamics simulations of nano-fluids. Injection of a liquid argon jet with a scale of 17.6 molecular diameters was investigated. A solid annular platinum injector was also solved simultaneously with the liquid injectant by adopting a solid modeling technique which incorporates phantom atoms. The viscous heat was naturally discharged through the solids so the liquid boiling problem was avoided with no separate use of temperature controlling methods. Parametric investigations of injection speed, wall temperature, and injector length were made. A sudden pressure drop at the orifice exit causes flash boiling of the liquid departing the nozzle exit with strong evaporation on the surface of the liquids, while rendering a slender jet. The elevation of the injection speed and the wall temperature causes an activation of the surface evaporation concurrent with reduction in the jet breakup length and the drop size. PMID:19051924

  2. 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)

  3. Quantitatively analyzing phonon spectral contribution of thermal conductivity based on nonequilibrium molecular dynamics simulations. I. From space Fourier transform

    NASA Astrophysics Data System (ADS)

    Zhou, Yanguang; Zhang, Xiaoliang; Hu, Ming

    2015-11-01

    Probing detailed spectral dependence of phonon transport properties in bulk materials is critical to improve the function and performance of structures and devices in a diverse spectrum of technologies. Currently, such information can only be provided by the phonon spectral energy density (SED) or equivalently, time domain normal mode analysis (TDNMA) methods in the framework of equilibrium molecular dynamics simulations (EMD), but has not been realized in nonequilibrium molecular dynamics simulations (NEMD) so far. In this paper we generate a scheme directly based on NEMD and lattice dynamics theory, called the time domain direct decomposition method (TDDDM), to predict the phonon mode specific thermal conductivity. Two benchmark cases of Lennard-Jones (LJ) argon and Stillinger-Weber (SW) Si are studied by TDDDM to characterize contributions of individual phonon modes to overall thermal conductivity and the results are compared with that predicted using SED and TDNMA. Similar trends are found for both cases, which indicate that our TDDDM approach captures the major phonon properties in NEMD run. The biggest advantage of TDDDM is that it can be used to investigate the size effect of individual phonon modes in NEMD simulations, which cannot be tackled by SED and TDNMA in EMD simulations currently. We found that the phonon modes with mean free path larger than the system size are truncated in NEMD and contribute little to the overall thermal conductivity. The TDDDM provides direct physical origin for the well-known strong size effects in thermal conductivity prediction by NEMD. Moreover, the well-known common sense of the zero thermal conductivity contribution from the Γ point is rigorously proved by TDDDM. Since TDDDM inherently possesses the nature of both NEMD simulations and lattice dynamics, we anticipate that TDDDM is particularly useful for offering a deep understanding of phonon behaviors in nanostructures or under strong confinement, especially when the

  4. Quantitatively analyzing phonon spectral contribution of thermal conductivity based on nonequilibrium molecular dynamics simulations. II. From time Fourier transform

    NASA Astrophysics Data System (ADS)

    Zhou, Yanguang; Hu, Ming

    2015-11-01

    From a nanoscale heat transfer point of view, currently one of the most interesting and challenging tasks is to quantitatively analyze phonon mode specific transport properties in solid materials, which plays a vital role in many emerging and diverse technological applications. It has not been long that such information can be provided by the phonon spectral energy density (SED) or equivalently time domain normal mode analysis (TDNMA) methods in the framework of equilibrium molecular dynamics (EMD) simulations. However, few methods have been developed for nonequilibrium molecular dynamics (NEMD) simulations [Phys. Rev. B 91, 115426 (2015), 10.1103/PhysRevB.91.115426], the other widely used computational method for calculating thermal transport of materials in addition to EMD. In this work, a computational scheme based on time Fourier transform of atomistic heat current, called the frequency domain direct decomposed method (FDDDM), is proposed to analyze the contributions of frequency dependent thermal conductivity in NEMD simulations. The FDDDM results of Lennard-Jones argon and Stillinger-Weber Si are compared with the TDNMA method from EMD simulation. Similar trends are found for both cases, which confirm the validity of our FDDDM approach. Benefiting from the inherent nature of NEMD and the theoretical formula that does not require any temperature assumption, the FDDDM can be directly used to investigate the size and temperature effect. Moreover, the unique advantage of FDDDM prior to previous methods (such as SED and TDNMA) is that it can be straightforwardly used to characterize the phonon frequency dependent thermal conductivity of disordered systems, such as amorphous materials. The FDDDM approach can also be a good candidate to be used to understand the phonon behaviors and thus provides useful guidance for designing efficient structures for advanced thermal management.

  5. 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.

  6. Thermal conductivity of carbon nanotube—polyamide-6,6 nanocomposites: Reverse non-equilibrium molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Alaghemandi, Mohammad; Müller-Plathe, Florian; Böhm, Michael C.

    2011-11-01

    The thermal conductivity of composites of carbon nanotubes and polyamide-6,6 has been investigated using reverse non-equilibrium molecular dynamics simulations in a full atomistic resolution. It is found, in line with experiments, that the composites have thermal conductivities, which are only moderately larger than that of pure polyamide. The composite conductivities are orders of magnitude less than what would be expected from naïve additivity arguments. This means that the intrinsic thermal conductivities of isolated nanotubes, which exceed the best-conducting metals, cannot be harnessed for heat transport, when the nanotubes are embedded in a polymer matrix. The main reason is the high interfacial thermal resistance between the nanotubes and the polymer, which was calculated in addition to the total composite thermal conductivity as well as that of the subsystem. It hinders heat to be transferred from the slow-conducting polymer into the fast-conducting nanotubes and back into the polymer. This interpretation is in line with the majority of recent simulation works. An alternative explanation, namely, the damping of the long-wavelength phonons in nanotubes by the polymer matrix is not supported by the present calculations. These modes provide most of the polymers heat conduction. An additional minor effect is caused by the anisotropic structure of the polymer phase induced by the nearby nanotube surfaces. The thermal conductivity of the polymer matrix increases slightly in the direction parallel to the nanotubes, whereas it decreases perpendicular to it.

  7. 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. PMID:22423855

  8. 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.

  9. The director and molecular dynamics of the field-induced alignment of a Gay-Berne nematic phase: An isothermal-isobaric nonequilibrium molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Luckhurst, Geoffrey R.; Satoh, Katsuhiko

    2010-05-01

    Isothermal-isobaric molecular dynamics simulations have been performed for the generic Gay-Berne (GB) mesogen, GB(4.4, 20.0, 1, 1), to investigate director and molecular rotational motion during the field-induced alignment of a nematic. The alignment process for the director is discussed within the context of a hydrodynamic analysis based on the Ericksen-Leslie theory and this is found to predict the simulated behavior well. The dependence of the relaxation time for the alignment on the field strength is also in good accord with the theory. The rotational viscosity coefficient estimated from the simulation is smaller than that typically observed for real nematics and the possible reasons for this are discussed. However, the simulation results are found to follow not only the theory but also the experiments, at least qualitatively. No significant variation in the local and long-range structure of the nematic phase is found during the field-induced alignment process. In addition, we have explored the molecular dynamics in the nematic phase in the presence of the field using the first- and second-rank time autocorrelation functions. More importantly we are able to show that the director relaxation time is longer than that for molecular rotation. It is also possible to use the two orientational correlation times to explore the relationship between the rotational viscosity coefficient and the rotational diffusion constant. The diffusion constants determined from the orientational correlation times, based on the short-time expansion of the autocorrelation functions, are found to be significantly different. In consequence it is not possible to test, unambiguously, the relationship between the rotational viscosity coefficient and the rotational diffusion constant. However, it would seem that the second-rank rotational correlation time provides the most reliable route to the rotational viscosity coefficient.

  10. Radiation in molecular dynamic simulations

    SciTech Connect

    Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M

    2008-10-13

    Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.

  11. Shear thinning and shear dilatancy of liquid n-hexadecane via equilibrium and nonequilibrium molecular dynamics simulations: Temperature, pressure, and density effects

    NASA Astrophysics Data System (ADS)

    Tseng, Huan-Chang; Wu, Jiann-Shing; Chang, Rong-Yeu

    2008-07-01

    Equilibrium and nonequilibrium molecular dynamics (MD) simulations have been performed in both isochoric-isothermal (NVT) and isobaric-isothermal (NPT) ensemble systems. Under steady state shearing conditions, thermodynamic states and rheological properties of liquid n-hexadecane molecules have been studied. Between equilibrium and nonequilibrium states, it is important to understand how shear rates (γ˙) affect the thermodynamic state variables of temperature, pressure, and density. At lower shear rates of γ˙<1×1011s-1, the relationships between the thermodynamic variables at nonequilibrium states closely approximate those at equilibrium states, namely, the liquid is very near its Newtonian fluid regime. Conversely, at extreme shear rates of γ˙>1×1011s-1, specific behavior of shear dilatancy is observed in the variations of nonequilibrium thermodynamic states. Significantly, by analyzing the effects of changes in temperature, pressure, and density on shear flow system, we report a variety of rheological properties including the shear thinning relationship between viscosity and shear rate, zero-shear-rate viscosity, rotational relaxation time, and critical shear rate. In addition, the flow activation energy and the pressure-viscosity coefficient determined through Arrhenius and Barus equations acceptably agree with the related experimental and MD simulation results.

  12. Molecular dynamics simulations

    SciTech Connect

    Alder, B.J.

    1985-07-01

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

  13. Nonlinearity and slip behavior of n-hexadecane in large amplitude oscillatory shear flow via nonequilibrium molecular dynamic simulation

    NASA Astrophysics Data System (ADS)

    Wang, Chen-Chieh; Chang, Rong-Yeu

    2012-03-01

    Molecular dynamic simulation is used to investigate the viscoelastic properties of n-hexadecane under oscillatory shear flow. Rheometric simulations of an ultra-thin molecular film are studied and compared with the results of a bulk simulation. Strain amplitude sweep tests at a fixed frequency show that strain thinning (the dynamic modulus monotonically decreases with increasing strain amplitude) exists at extreme strain for both bulk and thin film systems. Fourier analysis is performed to characterize the nonlinear behavior of the viscoelasticity. No even harmonic was found in our study even though wall slip occurs. Furthermore, we show that a Fourier series with odd harmonics can be used to perfectly describe the simulation results by plotting Lissajous loops. Shear wave propagation appears when the frequency is larger than a certain value. Moreover, the molecular orientation and molecular potential energies, including those for bonding potential, intra- and intermolecular van der Waals interactions are plotted against the strain amplitude to examine the changes in the microscopic structures with respect to the macroscopic thermodynamic states.

  14. 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.

  15. 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. PMID:24600690

  16. Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows

    NASA Astrophysics Data System (ADS)

    Wang, Guan M.; Sandberg, William C.

    2007-04-01

    In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels. The new methods were demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. The tethering of the linker molecule (6-mercapto-1-hexanol) to perfect Au(111) surfaces was parametrized based on density functional theory (DFT) calculations. Force field parameters were incorporated into the CHARMM database. Gold surfaces are simulated in a Lennard-Jones style model that was fitted to the Morse potential model of bulk gold. The bonding force of attachment of the DNA molecules to the gold substrate linker molecule was computed to be up to a few nN when the DNA molecules are fully stretched at high shear rates. For the first time, we calculated the relaxation time of DNA molecules in picoseconds (ps) and the hydrodynamic force up to a few nanoNewtons (nN) per base pair in a nanochannel flow. The velocity profiles in the solvent due to the presence of the tethered DNA molecules were found to be nonlinear only at high shear flow rates. Free ssDNA molecules in a shear flow were observed to behave differently from each other depending upon their initial orientation in the flow field. Both free and tethered DNA molecules are clearly observed to be stretching, rotating and relaxing. Methods developed in this initial work can be incorporated

  17. Molecular Dynamics Simulation of Shock Induced Detonation

    NASA Astrophysics Data System (ADS)

    Tomar, Vikas; Zhou, Min

    2004-07-01

    This research focuses on molecular dynamics (MD) simulation of shock induced detonation in Fe2O3+Al thermite mixtures. A MD model is developed to simulate non-equilibrium stress-induced reactions. The focus is on establishing a criterion for reaction initiation, energy content and rate of energy release as functions of mixture and reinforcement characteristics. A cluster functional potential is proposed for this purpose. The potential uses the electronegativity equalization to account for changes in the charge of different species according to local environment. Parameters in the potential are derived to fit to the properties of Fe, Al, Fe2O3, and Al2O3. NPT MD simulations are carried out to qualitatively check the energetics of the forward (Fe2O3+Al) as well as backward (Al2O3+Fe) thermite reactions. The results show that the potential can account for the energetics of thermite reactions.

  18. 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. PMID:27389206

  19. 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.

  20. Molecular Dynamics Simulations of Polymers

    NASA Astrophysics Data System (ADS)

    Han, Jie

    1995-01-01

    Molecular dynamics (MD) simulations have been undertaken in this work to explore structures and properties of polyethylene (PE), polyisobutylene (PIB), atactic polypropylene (aPP) and atactic polystyrene (aPS). This work has not only demonstrated the reliability of MD simulations by comparing results with available experiments, but more importantly has revealed structure-property relationships on a molecular level for these selected polymers. Structures of these amorphous polymers were characterized by radial distribution functions (RDFs) or scattering profiles, and properties of the polymers studied were pressure-volume -temperature (PVT) equation of state, enthalpy, cohesive energy, the diffusion coefficient of methane in the polymer, and glass transition temperature. Good agreement was found for these structures and properties between simulation and experiment. More importantly, the scientific understanding of structure-property relationships was established on a molecular level. In the order of aPP (PE), PIB and aPS, with the chain surface separation or free volume decreasing, the density increases and the diffusion coefficient decreases. Therefore, the effects of changes or modifications in the chemical structure of monomer molecules (substituting pendent hydrogen with methyl or phenyl) on polymeric materials performance were attributed to the effects of molecular chain structure on packing structure, which, in turn, affects the properties of these polymers. Local chain dynamics and relaxation have been studied for bulk PE and aPS. Cooperative transitions occur at second-neighbor bonds for PE, and first-neighbor bonds for aPS due to the role of side groups. The activation energy is a single torsional barrier for overall conformational transitions, and is single torsional barrier plus locally "trapped" barrier for relaxation. Temperature dependence is Arrhenius for transition time, and is WLF for relaxation time. The mean correlation times derived from

  1. Reduced thermal conductivity of a nanoparticle decorated nanowire: A non-equilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Masnoon, Ahmed Shafkat; Bipasha, Ferdaushi Alam; Morshed, A. K. M. M.

    2016-07-01

    The effect of nanoparticles decoration on the thermal conductivity of a nanowire is studied using Non Equilibrium Molecular Dynamics (NEMD) simulation. The simulation was conducted using simplified molecular model with Lennard-Jones potential. Argon-like solid was used as the material for both the nanowire and nanoparticles. Nanoparticles were placed on the surface of the nanowire and also embedded inside the structure. Non-equilibrium molecular dynamics simulation was conducted by imposing temperature gradient along the length of the nanowire and thermal conductivity of the nanowire was calculated. Nanowire without any nanoparticles was used as the baseline data. Due to presence of nanoparticles thermal conductivity of the nanowire was observed to decrease and up to 40% reduction in thermal conductivity was observed. With the increase in number of the nanoparticles, thermal conductivity was observed to decrease; however size of nanoparticles has little effect.

  2. 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.

  3. 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.

  4. Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading

    NASA Astrophysics Data System (ADS)

    Aghaei, Amin; Dayal, Kaushik

    2011-06-01

    We report on non-equilibrium molecular dynamics calculations of chiral single-wall carbon nanotubes using the framework of Objective Structures. This enables us to adapt molecular dynamics to the symmetry of chiral nanotubes and efficiently simulate these systems with small unit cells. We outline the method and the adaptation of a conventional thermostat and barostat to this setting. We then apply the method in order to examine the behavior of nanotubes with various chiralities subject to a constant extensional strain rate. We examine the effects of temperature, strain rate, and pre-compression/pre-tension. We find a range of failure mechanisms, including the formation of Stone-Wales defects, the opening of voids, and the motion of atoms out of the cross-section.

  5. Buckybomb: Reactive Molecular Dynamics Simulation.

    PubMed

    Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V

    2015-03-01

    Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material. PMID:26262672

  6. Molecular dynamics simulations of large macromolecular complexes

    PubMed Central

    Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

    2015-01-01

    Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770

  7. Molecular dynamics simulations of supramolecular polymer rheology

    NASA Astrophysics Data System (ADS)

    Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.

    2010-11-01

    Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate β and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.

  8. 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.

  9. 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.

  10. 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)

  11. Optimizing Water Transport through Graphene-Based Membranes: Insights from Nonequilibrium Molecular Dynamics.

    PubMed

    Muscatello, Jordan; Jaeger, Frederike; Matar, Omar K; Müller, Erich A

    2016-05-18

    Recent experimental results suggest that stacked layers of graphene oxide exhibit strong selective permeability to water. To construe this observation, the transport mechanism of water permeating through a membrane consisting of layered graphene sheets is investigated via nonequilibrium and equilibrium molecular dynamics simulations. The effect of sheet geometry is studied by changing the offset between the entrance and exit slits of the membrane. The simulation results reveal that the permeability is not solely dominated by entrance effects; the path traversed by water molecules has a considerable impact on the permeability. We show that contrary to speculation in the literature, water molecules do not pass through the membrane as a hydrogen-bonded chain; instead, they form well-mixed fluid regions confined between the graphene sheets. The results of the present work are used to provide guidelines for the development of graphene and graphene oxide membranes for desalination and solvent separation. PMID:27121070

  12. Disorder-driven nonequilibrium melting studied by electron diffraction, brillouis scattering, and molecular dynamics

    SciTech Connect

    Okamoto, P. R.; Lam, N. Q.; Grimsditch, M.

    1999-12-21

    In the present paper, a brief overview of the electron diffraction, Brillouin scattering and molecular dynamics studies of radiation-induced amorphization of ordered intermetallic compounds is presented. In these studies, measured changes in the velocity of surface acoustic phonons, lattice constant, and the Bragg-Williams long-range order parameter induced by irradiation were compared with the results of computer simulations of defect-induced amorphization. The results indicate that progressive chemical disordering of the superlattice structure during irradiation is accompanied by an expansion of the lattice and a large change in sound velocity corresponding to a {approximately} 50% decrease in the average shear modulus. The onset of amorphization occurs when the average shear modulus of the crystalline compound becomes equal to that of the amorphous phase. This elastic softening criterion for the onset of amorphization and the dependence of the average shear modulus on the long-range-order parameter are in excellent agreement with molecular dynamics simulations. Both the experimental observations and computer simulations confirm the predictions of the generalized Lindemann melting criterion which stipulates that thermodynamic melting of a defective crystal occurs when the sum of the dynamic and static mean-square atomic displacements reaches a critical value identical to that for melting of the defect-free crystal. In this broader view of melting, the crystal-to-glass transformation is a disorder-driven nonequilibrium melting process occurring at temperatures below the Kauzmann isentropic glass-transition temperature.

  13. 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. PMID:24073784

  14. ADAPTIVE MULTILEVEL SPLITTING IN MOLECULAR DYNAMICS SIMULATIONS*

    PubMed Central

    Aristoff, David; Lelièvre, Tony; Mayne, Christopher G.; Teo, Ivan

    2014-01-01

    Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling method that has been used successfully in high-dimensional stochastic simulations to identify trajectories across a high potential barrier separating one metastable state from another, and to estimate the probability of observing such a trajectory. An attractive feature of AMS is that, in the limit of a large number of replicas, it remains valid regardless of the choice of reaction coordinate used to characterize the trajectories. Previous studies have shown AMS to be accurate in Monte Carlo simulations. In this study, we extend the application of AMS to molecular dynamics simulations and demonstrate its effectiveness using a simple test system. Our conclusion paves the way for useful applications, such as molecular dynamics calculations of the characteristic time of drug dissociation from a protein target. PMID:26005670

  15. Nanoindentation of Zr by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Lu (芦子哲), Zizhe; Chernatynskiy, Aleksandr; Noordhoek, Mark J.; Sinnott, Susan B.; Phillpot, Simon R.

    2015-12-01

    Molecular dynamics simulations of nanoindentation are used to study the deformation behaviors of single crystal Zr for four different surface orientations. The comparison of results for two different potentials, an embedded atom method potential and a charged optimized many body potential, reveals the influence of stable and unstable stacking fault energy on dislocation behaviors under nanoindentation. The load-displacement curve, hardness and deformation behaviors of the various surface orientations Zr are compared and the elastic and plastic deformation behaviors are analyzed.

  16. Molecular dynamics simulation of ice XII

    NASA Astrophysics Data System (ADS)

    Borzsák, István; Cummings, Peter T.

    1999-02-01

    Molecular dynamics simulations have been performed on the newly discovered metastable ice XII. This new crystalline ice phase [C. Lobban, J.L. Finney, W.F. Kuhs, Nature (London) 391 (1998) 268] is proton-disordered. Thus 90 possible configurations of the unit cell can be constructed which differ only in the orientations of the water molecules. The simulation used the TIP4P potential model for water at constant temperature and density. About one-quarter of the initial configurations did not melt in the course of the simulation. This result is supportive of the experimental structure and also demonstrates the ability of this water model to study ice phases.

  17. Novel procedure for thermal equilibration in molecular dynamics simulation.

    PubMed

    Gallo, Marco T; Grant, Barry J; Teodoro, Miguel L; Melton, Julia; Cieplak, Piotr; Phillips, George N; Stec, Boguslaw

    2009-04-01

    We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797

  18. Novel procedure for thermal equilibration in molecular dynamics simulation

    PubMed Central

    Gallo, Marco T.; Grant, Barry J.; Teodoro, Miguel L.; Melton, Julia; Cieplak, Piotr; Phillips, George N.; Stec, Boguslaw

    2014-01-01

    We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797

  19. 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.

  20. Thermostability of Enzymes from Molecular Dynamics Simulations.

    PubMed

    Zeiske, Tim; Stafford, Kate A; Palmer, Arthur G

    2016-06-14

    Thermodynamic stability is a central requirement for protein function, and one goal of protein engineering is improvement of stability, particularly for applications in biotechnology. Herein, molecular dynamics simulations are used to predict in vitro thermostability of members of the bacterial ribonuclease HI (RNase H) family of endonucleases. The temperature dependence of the generalized order parameter, S, for four RNase H homologues, from psychrotrophic, mesophilic, and thermophilic organisms, is highly correlated with experimentally determined melting temperatures and with calculated free energies of folding at the midpoint temperature of the simulations. This study provides an approach for in silico mutational screens to improve thermostability of biologically and industrially relevant enzymes. PMID:27123810

  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. Shockwave-induced plasticity via large-scale nonequilibrium molecular dynamics

    SciTech Connect

    Holian, B.L.

    1998-07-01

    Nonequilibrium molecular-dynamics (MD) 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 our MD observations of stacking faults produced by shockwave passage. With the advent of massively parallel computers, we have been able to simulate shock waves in 10-million atom crystals with cross-sectional dimensions of 100{times}100 fcc unit cells (compared to earlier 6{times}6 systems). We 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 we have observed is somehow an artifact of transverse periodic boundary conditions. Thus, future simulations are much more likely to show that weak-shock plasticity is nucleated by pre-existing extended defects embedded in the sample. {copyright} {ital 1998 American Institute of Physics.}

  3. Electronic continuum model for molecular dynamics simulations.

    PubMed

    Leontyev, I V; Stuchebrukhov, A A

    2009-02-28

    A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627

  4. Polymer Brushes under Shear: Molecular Dynamics Simulations Compared to Experiments.

    PubMed

    Singh, Manjesh K; Ilg, Patrick; Espinosa-Marzal, Rosa M; Kröger, Martin; Spencer, Nicholas D

    2015-04-28

    Surfaces coated with polymer brushes in a good solvent are known to exhibit excellent tribological properties. We have performed coarse-grained equilibrium and nonequilibrium molecular dynamics (MD) simulations to investigate dextran polymer brushes in an aqueous environment in molecular detail. In a first step, we determined simulation parameters and units by matching experimental results for a single dextran chain. Analyzing this model when applied to a multichain system, density profiles of end-tethered polymer brushes obtained from equilibrium MD simulations compare very well with expectations based on self-consistent field theory. Simulation results were further validated against and correlated with available experimental results. The simulated compression curves (normal force as a function of surface separation) compare successfully with results obtained with a surface forces apparatus. Shear stress (friction) obtained via nonequilibrium MD is contrasted with nanoscale friction studies employing colloidal-probe lateral force microscopy. We find good agreement in the hydrodynamic regime and explain the observed leveling-off of the friction forces in the boundary regime by means of an effective polymer-wall attraction. PMID:25830715

  5. 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

  6. 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.

  7. Effects of vacancy defects on thermal conductivity in crystalline silicon: A nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Lee, Yongjin; Lee, Sangheon; Hwang, Gyeong S.

    2011-03-01

    We examine the effects of vacancy defects on thermal conductivity in bulk crystalline silicon (c-Si) using nonequilibrium molecular dynamics simulations. While most vacancies are thought to remain in the form of clusters in bulk c-Si, recent theoretical studies have predicted that small vacancy clusters energetically prefer to be fourfold coordinated by nullifying dangling bonds. Hence, in this work, we consider three different-sized fourfold vacancy clusters, tetra- (V4), hexa- (V6), and dodeca-vacancy (V12), with particular interest in studying how phonon transport is affected by vacancy concentration and cluster size in association with fourfold coordination-induced lattice distortions. Our simulations show that thermal conductivity (κ) rapidly drops with vacancy concentration (nv) with an inverse power-law relation (κ∝nv-α, with α ≈ 0.7-1.1 depending on cluster size); the presence of 1.5% vacancies leads to a 95% reduction in κ as compared to the defect free c-Si. When nv is low (<1%), the reduction of κ with nv appears to be a function of cluster size, and the size effect becomes unimportant as nv increases above 1%. We discuss the correlation between phone scattering and cluster size, based on the relative rates of phonon-vacancy scattering associated with defect-induced strain fields. We also estimate the dependence of phonon mean free path on vacancy concentration and cluster size.

  8. Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

    NASA Astrophysics Data System (ADS)

    Stella, L.; Lorenz, C. D.; Kantorovich, L.

    2014-04-01

    The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

  9. A nonequilibrium molecular dynamics study of the rheology of alkanes

    SciTech Connect

    Gupta, S.A.; Cui, S.T.; Cummings, P.T.; Cochran, H.D. |

    1996-05-01

    We examine the rheological properties of four different alkanes: n-decane, n-hexadecane, n-tetracosane, and squalane. Simulations of Couette flow are performed for a range of shear rates with 100 molecules in each case using a replicated data version of our code. Number of interaction sites ranges from 1000 to 3000. We have performed extremely long simulations required to obtain acceptable statistics at low shear rates. The alkanes show a transition from non-Newtonian to Newtonian behavior as the shear rate decreases to low values. 1 tab, 1 fig, 17 refs.

  10. Ionic conductivity in Gd-doped CeO2: Ab initio color-diffusion nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Nilsson, Johan O.; Vekilova, Olga Yu.; Hellman, Olle; Klarbring, Johan; Simak, Sergei I.; Skorodumova, Natalia V.

    2016-01-01

    A first-principles nonequilibrium molecular dynamics (NEMD) study employing the color-diffusion algorithm has been conducted to obtain the bulk ionic conductivity and the diffusion constant of gadolinium-doped cerium oxide (GDC) in the 850-1150 K temperature range. Being a slow process, ionic diffusion in solids usually requires simulation times that are prohibitively long for ab initio equilibrium molecular dynamics. The use of the color-diffusion algorithm allowed us to substantially speed up the oxygen-ion diffusion. The key parameters of the method, such as field direction and strength as well as color-charge distribution, have been investigated and their optimized values for the considered system have been determined. The calculated ionic conductivity and diffusion constants are in good agreement with available experimental data.

  11. Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.

    PubMed

    Schwabe, Tobias

    2015-08-20

    For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273

  12. Molecular Dynamics Simulations of Graphene Oxide Frameworks

    SciTech Connect

    Zhu, Pan; Sumpter, Bobby G; Meunier, V.; Nicolai, Adrien

    2013-01-01

    We use quantum mechanical calculations to develop a full set of force field parameters in order to perform molecular dynamics simulations to understand and optimize the molecular storage properties inside Graphene Oxide Frameworks (GOFs). A set of boron-related parameters for commonly used empirical force fields is determined to describe the non-bonded and bonded interactions between linear boronic acid linkers and graphene sheets of GOF materials. The transferability of the parameters is discussed and their validity is quantified by comparing quantum mechanical and molecular mechanical structural and vibrational properties. The application of the model to the dynamics of water inside the GOFs reveals significant variations in structural flexibility of GOF depending on the linker density, which is shown to be usable as a tuning parameter for desired diffusion properties.

  13. Molecular Dynamics Simulations of Water Evaporation

    NASA Astrophysics Data System (ADS)

    Wen, Chengyuan; Grest, Gary; Cheng, Shengfeng

    2015-03-01

    The evaporation of water from the liquid/vapor interface is studied via large-scale molecular dynamics simulations for systems of more than a million atoms at 550K and 600K. The TIP4P-2005 water model whose liquid/vapor surface tension is in excellent agreement with experiments is used. Evaporative cooling at the interface is observed from temperature profiles determined from both translational and rotational kinetic energy. During evaporation, the density of water is slightly enhanced near the liquid-vapor interface. The velocity distribution of water molecules in the vapor phase during evaporation at various distances relative to the interface fit a Maxwell-Boltzmann distribution. While our results indicate an imbalance between evaporating and condensing water molecules, local thermal equilibrium is found to hold in addition to mechanical equilibrium. Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.

  14. Molecular dynamics simulations of weak detonations.

    PubMed

    Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie

    2011-12-01

    Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055

  15. Nonlinear rheological behavior associated with structural transitions in block copolymer solutions via nonequilibrium molecular dynamics.

    PubMed

    Rychkov, Igor; Yoshikawa, Kenichi

    2004-02-15

    The nonequilibrium molecular dynamics computer simulation method was used to study microsegregated block copolymer systems in a selective solvent under a shear flow field. Two polymer concentrations were considered, 0.3 and 0.4, corresponding to the body centered cubic spherical and hexagonal cylindrical zero-shear phases, respectively. As the shear rate increased, both systems exhibited two-stage shear thinning, a peak in the scalar pressure, and normal stress differences. Microscopic connections were investigated by calculating the gyration and bond orientation tensors and the interaction energies per particle. At high shear rates, polymer chains elongate and orient along the direction of shear, and this is accompanied by the breaking-up of domains. The structure-rheology relation was discussed with regard to the morphological changes reported in our last study for the same systems. In particular, the structurally relevant critical values of the shear rate were found to delimit different behaviors of the shear rate-dependencies obtained in this work. PMID:15268506

  16. Investigation of tensile response and thermal conductivity of boron-nitride nanosheets using molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mortazavi, Bohayra; Rémond, Yves

    2012-06-01

    In this paper, we employed classical molecular dynamics simulations using the Tersoff potential for the evaluation of thermal conductivity and tensile response of single-layer boron-nitride sheets (SBNS). By carrying out uniaxial tension simulations, the elastic moduli of SBNS structures are predicted to be close to those of boron-nitride nanotubes in a range between 0.8 and 0.85 TPa for different chirality directions. Performing non-equilibrium molecular dynamics simulations, the thermal conductivity of SBNS is predicted to be around 80 W/m-K, which is shown to be independent of chirality directions.

  17. 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.

  18. Local Refinements in Classical Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Fackeldey, Konstantin; Weber, Marcus

    2014-03-01

    Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.

  19. 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.

  20. Molecular dynamics simulation of liquid sulfur dioxide.

    PubMed

    Ribeiro, Mauro C C

    2006-05-01

    A previously proposed model for molecular dynamics (MD) simulation of liquid sulfur dioxide, SO(2), has been reviewed. Thermodynamic, structural, and dynamical properties were calculated for a large range of thermodynamic states. Predicted (P,V,T) of simulated system agrees with an elaborated equation of state recently proposed for liquid SO(2). Calculated heat capacity, expansion coefficient, and isothermal compressibility are also in good agreement with experimental data. Calculated equilibrium structure agrees with X-ray and neutron scattering measurements on liquid SO(2). The model also predicts the same (SO(2))(2) dimer structure as previously determined by ab initio calculations. Detailed analysis of equilibrium structure of liquid SO(2) is provided, indicating that, despite the rather large dipole moment of the SO(2) molecule, the structure is mainly determined by the Lennard-Jones interactions. Both single-particle and collective dynamics are investigated. Temperature dependency of dynamical properties is given. The MD results are compared with previous findings obtained from the analysis of inelastic neutron scattering spectra of liquid SO(2), including wave-vector dependent structural relaxation, tau(k), and viscosity, eta(k). PMID:16640437

  1. 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

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

    PubMed Central

    Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C.

    2013-01-01

    A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific 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. PMID:24081985

  3. Atomistic molecular dynamic simulations of multiferroics.

    PubMed

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L

    2012-08-10

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings. PMID:23006300

  4. Atomistic Molecular Dynamic Simulations of Multiferroics

    NASA Astrophysics Data System (ADS)

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.

    2012-08-01

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.

  5. 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.

  6. Nanoscale deicing by molecular dynamics simulation.

    PubMed

    Xiao, Senbo; He, Jianying; Zhang, Zhiliang

    2016-08-14

    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. PMID:27431975

  7. 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

  8. 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.

  9. 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..

  10. Molecular dynamics simulation of amorphous indomethacin.

    PubMed

    Xiang, Tian-Xiang; Anderson, Bradley D

    2013-01-01

    Molecular dynamics (MD) simulations have been conducted using an assembly consisting of 105 indomethacin (IMC) molecules and 12 water molecules to investigate the underlying dynamic (e.g., rotational and translational diffusivities and conformation relaxation rates) and structural properties (e.g., conformation, hydrogen-bonding distributions, and interactions of water with IMC) of amorphous IMC. These properties may be important in predicting physical stability of this metastable material. The IMC model was constructed using X-ray diffraction data with the force-field parameters mostly assigned by analogy with similar groups in Amber-ff03 and atomic charges calculated with the B3LYP/ccpVTZ30, IEFPCM, and RESP models. The assemblies were initially equilibrated in their molten state and cooled through the glass transition temperature to form amorphous solids. Constant temperature dynamic runs were then carried out above and below the T(g) (i.e., at 600 K (10 ns), 400 K (350 ns), and 298 K (240 ns)). The density (1.312 ± 0.003 g/cm(3)) of the simulated amorphous solid at 298 K was close to the experimental value (1.32 g/cm(3)) while the estimated T(g) (384 K) was ~64 degrees higher than the experimental value (320 K) due to the faster cooling rate. Due to the hindered rotation of its amide bond, IMC can exist in different diastereomeric states. Different IMC conformations were sufficiently sampled in the IMC melt or vapor, but transitions occurred rarely in the glass. The hydrogen-bonding patterns in amorphous IMC are more complex in the amorphous state than in the crystalline polymorphs. Carboxylic dimers that are dominant in α- and γ-crystals were found to occur at a much lower probability in the simulated IMC glasses while hydrogen-bonded IMC chains were more easily identified patterns in the simulated amorphous solids. To determine molecular diffusivity, a novel analytical method is proposed to deal with the non-Einsteinian behavior, in which the temporal

  11. 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).

  12. Thermal Transport in Fullerene Derivatives Using Molecular Dynamics Simulations

    PubMed Central

    Chen, Liang; Wang, Xiaojia; Kumar, Satish

    2015-01-01

    In order to study the effects of alkyl chain on the thermal properties of fullerene derivatives, we perform molecular dynamics (MD) simulations to predict the thermal conductivity of fullerene (C60) and its derivative phenyl-C61-butyric acid methyl ester (PCBM). The results of non-equilibrium MD simulations show a length-dependent thermal conductivity for C60 but not for PCBM. The thermal conductivity of C60, obtained from the linear extrapolation of inverse conductivity vs. inverse length curve, is 0.2  W m−1 K−1 at room temperature, while the thermal conductivity of PCBM saturates at ~0.075  W m−1 K−1 around 20 nm. The different length-dependence behavior of thermal conductivity indicates that the long-wavelength and low-frequency phonons have large contribution to the thermal conduction in C60. The decrease in thermal conductivity of fullerene derivatives can be attributed to the reduction in group velocities, the decrease of the frequency range of acoustic phonons, and the strong scattering of low-frequency phonons with the alkyl chains due to the significant mismatch of vibrational density of states in low frequency regime between buckyball and alkyl chains in PCBM. PMID:26238607

  13. Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: A nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Solomentsev, Gleb Y.; English, Niall J.; Mooney, Damian A.

    2010-12-01

    Nonequilibrium molecular dynamics simulations of a charge-neutral mutant of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of external microwave fields (2.45 to 100 GHz) of an rms electric field intensity of 0.05 V Å-1. A systematic study was carried out of the distributions of persistence times and energies of each intraprotein hydrogen bond in between breakage and reformation, in addition to overall persistence over 20 ns simulations, vis-à-vis equilibrium, zero-field conditions. It was found that localized translational motion for formally charged residues led to greater disruption of associated hydrogen bonds, although induced rotational motion of strongly dipolar residues also led to a degree of hydrogen bond perturbation. These effects were most apparent in the solvent exposed exterior of hen egg white lysozyme, in which the intraprotein hydrogen bonds tend to be weaker.

  14. Shockwave-Induced Plasticity Via Large-Scale Nonequilibrium Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Holian, Brad Lee

    1997-07-01

    In nonequilibrium molecular-dynamics (MD) simulations of shock waves in single crystals, carried out in 1979 at Los Alamos,(B.L. Holian and G.K. Straub, Phys. Rev. Lett. 43), 1598 (1979). we discovered 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. We realized, of course, that real materials could yield at much lower thresholds, and speculated then that pre-existing defects could nucleate plastic flow at lower shock strengths than those characteristic of pure single crystals. (Historical note: at about the same time as our earliest dynamical shockwave simulations, Mogilevsky, working independently in the Soviet Union, carried out relaxation MD calculations under uniaxial strain, and observed spontaneous production of dislocations.(M.A. Mogilevsky, in Shock Waves and High Strain Rate Phenomena in Metals) (Plenum, New York, 1981), p.531.) Further Los Alamos calculations, carried out nearly a decade later in five-times larger systems (up to 10,000 atoms), confirmed this observation and quantified the threshold strength, namely the yield strength of the perfect crystal.(B.L. Holian, Phys. Rev. A 37), 2562 (1988); for a review, see B.L. Holian, Shock Waves 5, 149 (1995). Subsequently, Zaretskii and co-workers,(E.B. Zaretskii, G.I. Kanel, P.A. Mogilevskii, and V.E. Fortov, Sov. Phys. Dokl. 36), 76 (1991). using x-ray diffraction of shocked single crystals, confirmed our MD observations of stacking faults produced by shockwave passage. With the advent of massively parallel computers, we have recently studied systems with over six-times larger cross-sectional area and four-times longer distance of run to the steady state (approximately 270,000 atoms). We have seen that the increased cross-section allows the system to slip along both available forward slip systems, in

  15. Thermodiffusion in model nanofluids by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Galliero, G.; Volz, S.

    2008-02-01

    In this work, a new algorithm is proposed to compute single particle (infinite dilution) thermodiffusion using nonequilibrium molecular dynamics simulations through the estimation of the thermophoretic force that applies on a solute particle. This scheme is shown to provide consistent results for model nanofluids in the liquid state (spherical nonmetallic nanoparticles+Lennard-Jones fluid) where it appears that thermodiffusion amplitude, as well as thermal conductivity, decreases with nanoparticle concentration. Then, by changing the nature of the nanoparticle (size, mass, and internal stiffness) and that of the solvent (quality and viscosity), various trends are exhibited. In all cases, the single particle thermodiffusion is positive, i.e., the nanoparticle tends to migrate toward the cold area. The single particle thermal diffusion coefficient is shown to be independent of the size of the nanoparticle (diameter of 0.8-4nm), whereas it increases with the quality of the solvent and is inversely proportional to the viscosity of the fluid. In addition, this coefficient is shown to be independent of the mass of the nanoparticle and to increase with the stiffness of the nanoparticle internal bonds. Besides, for these configurations, the mass diffusion coefficient behavior appears to be consistent with a Stokes-Einstein-like law.

  16. Shear thinning behavior of linear polymer melts under shear flow via nonequilibrium molecular dynamics

    NASA Astrophysics Data System (ADS)

    Xu, Xiaolei; Chen, Jizhong; An, Lijia

    2014-05-01

    The properties of both untangled and entangled linear polymer melts under shear flow are studied by nonequilibrium molecular dynamics simulations. The results reveal that the dependence of shear viscosity η on shear rate dot{γ }, expressed by η ˜ dot{γ }^{-n}, exhibits three distinct regimes. The first is the well-known Newtonian regime, namely, η independent of shear rate at small shear rates dot{γ }<τ 0^{-1} (where τ0 is the longest polymer relaxation time at equilibrium). In the non-Newtonian regime (dot{γ }>τ 0^{-1}), the shear dependence of viscosity exhibits a crossover at a critical shear rate dot{γ }c dividing this regime into two different regimes, shear thinning regime I (ST-I) and II (ST-II), respectively. In the ST-I regime (τ ^{-1}_0dot{γ }c) a universal power law η ˜ dot{γ }^{-0.37} is found for considered chain lengths. Furthermore, the longer the polymer chain is, the smaller the shear viscosity for a given shear rate in the ST-II regime. The simulation also shows that a characteristic chain length, below which dot{γ }c will be equal to τ 0^{-1}, lies in the interval 30 < N < 50. For all considered chain lengths in the ST-II regime, we also find that the first and second normal stress differences N1 and N2 follow power laws of N1 ˜ dot{γ }^{2/3} and N2 ˜ dot{γ }^{0.82}, respectively; the orientation resistance parameter mG follows the relation mG ˜ dot{γ }^{0.75} and the tumbling frequency ftb follows f_{tb} ˜ dot{γ }^{0.75}. These results imply that the effects of entanglement on the shear dependences of these properties may be negligible in the ST-II regime. These findings may shed some light on the nature of shear thinning in flexible linear polymer melts.

  17. Molecular dynamics simulations of pressure shocks in liquid phase nitromethane

    NASA Astrophysics Data System (ADS)

    McNatt, Michael David

    The dynamic energy transfer processes present in liquid nitromethane (NM) under pressure shock loading conditions have been investigated by nonequilibrium molecular dynamics methods using a previously developed, fully flexible NM force field (Sorescu, D. C.; Rice, B. M.; Thompson, D. L. J. Phys. Chem. B 2000, 104, 8406). Generally good qualitative agreement with the corresponding experimental values was found for sound speeds (C) as a function of temperature. This is true as well for the PVT Hugoniot data calculated for the shock compressed zones behind our simulated shock fronts. The predicted C( T) are, however, ˜13--30% higher than experiment (Lysne, P. C.; Hardesty, D. R. J. Chem. Phys. 1973, 59, 6512) and our predicted densities for the shock compressed area behind fronts are consistently 4--10% lower than experiment (Winey, J. M.; Duvall, G. E.; Knudson, M. D.; Gupta, Y. M. J. Chem. Phys. 2000, 113, 7492). Accurate Hugoniot pressures are predicted by our simulations at all three initial temperatures (T i) studied. The Ti simulated for this work (255, 300, 350 K) span virtually the entire experimental ambient pressure liquid temperature range of NM (˜ 244--373 K). Thus combining and comparing our results with those of Winey et al. based on empirical equations of state work, opens up a considerable range of possible further tests and developments of our NM force field. This is particularly important in regards to the intermolecular force field due to its intended purpose of being applicable to a wide range of nitro and nitramine energetic compounds. Also, within the timeframes of our simulations (< 10 ps) the kinetic energy behind our shock fronts does not achieve equilibrium conditions as determined by the classical theory of equipartition.

  18. Development of semiclassical molecular dynamics simulation method.

    PubMed

    Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi

    2016-04-28

    Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383

  19. 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. PMID:27586951

  20. Molecular dynamics simulations of water permeation across Nafion membrane interfaces.

    PubMed

    Daly, Kevin B; Benziger, Jay B; Panagiotopoulos, Athanassios Z; Debenedetti, Pablo G

    2014-07-24

    Permeation of water across the membrane/vapor and membrane/liquid-water interfaces of Nafion is studied using nonequilibrium molecular dynamics (NEMD) simulations, providing direct calculations of mass-transfer resistance. Water mass transfer within one nanometer of the vapor interface is shown to be 2 orders of magnitude slower than at any other point within the membrane, in qualitative agreement with permeation experiments. This interfacial resistance is much stronger than the resistance suggested by prior simulation work calculating self-diffusivity near the interface. The key difference between the prior approach and the NEMD approach is that the NEMD approach implicitly incorporates changes in solubility in the direction normal to the interface. Water is shown to be very insoluble near the vapor interface, which is rich in hydrophobic perfluorocarbon chains, in agreement with advancing contact angle experiments. Hydrophilic side chains are buried beneath this hydrophobic layer and aligned toward the interior of the membrane. Hydrophilic pores are not exposed to the vapor interface as proposed in prior theoretical work. At the membrane/liquid-water interface, highly swollen polymer chains extend into the liquid-water phase, forming a nanoscopically rough interface that is consistent with atomic force microscopy experiments. In these swollen conformations, hydrophilic side chains are exposed to the liquid-water phase, suggesting that the interface is hydrophilic, in agreement with receding contact angle experiments. The mass-transfer resistance of this interface is negligible compared to that of the bulk, in qualitative agreement with permeation experiments. The water activity at the vapor and liquid-water interfaces are nearly the same, yet large conformational and transport differences are observed, consistent with a mass-transfer-based understanding of Schroeder's paradox for Nafion. PMID:24971638

  1. Accelerated electronic structure-based molecular dynamics simulations of shock-induced chemistry

    NASA Astrophysics Data System (ADS)

    Cawkwell, Marc

    2015-06-01

    The initiation and progression of shock-induced chemistry in organic materials at moderate temperatures and pressures are slow on the time scales available to regular molecular dynamics simulations. Accessing the requisite time scales is particularly challenging if the interatomic bonding is modeled using accurate yet expensive methods based explicitly on electronic structure. We have combined fast, energy conserving extended Lagrangian Born-Oppenheimer molecular dynamics with the parallel replica accelerated molecular dynamics formalism to study the relatively sluggish shock-induced chemistry of benzene around 13-20 GPa. We model interatomic bonding in hydrocarbons using self-consistent tight binding theory with an accurate and transferable parameterization. Shock compression and its associated transient, non-equilibrium effects are captured explicitly by combining the universal liquid Hugoniot with a simple shrinking-cell boundary condition. A number of novel methods for improving the performance of reactive electronic structure-based molecular dynamics by adapting the self-consistent field procedure on-the-fly will also be discussed. The use of accelerated molecular dynamics has enabled us to follow the initial stages of the nucleation and growth of carbon clusters in benzene under thermodynamic conditions pertinent to experiments.

  2. Studying Interactions by Molecular Dynamics Simulations at High Concentration

    PubMed Central

    Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro

    2012-01-01

    Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. PMID:22500085

  3. Reactive Molecular Dynamics Simulations at the Petascale (Invited)

    NASA Astrophysics Data System (ADS)

    Nakano, A.

    2013-12-01

    We are developing a divide-conquer-recombine algorithmic framework into a metascalable (or 'design once, scale on new architectures') parallelization scheme to perform large spatiotemporal-scale reactive molecular dynamics simulations. The scheme has achieved parallel efficiency well over 0.9 on 786,432 IBM BlueGene/Q processors for 8.5 trillion-atom molecular dynamics and 1.9 trillion electronic degrees-of-freedom quantum molecular dynamics in the framework of density functional theory. Simulation results reveal intricate interplay between photoexcitation, mechanics, flow, and chemical reactions at the nanoscale. Specifically, we will discuss atomistic mechanisms of: (1) rapid hydrogen production from water using metallic alloy nanoparticles; (2) molecular control of charge transfer, charge recombination, and singlet fission for efficient solar cells; and (3) mechanically enhanced reaction kinetics in nanobubbles and nanojets.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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.

  6. 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

  7. 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.

  8. 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

  9. Chain networking revealed by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing

    Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)

  10. 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.

  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. Self-interstitial clusters in radiation damage accumulation: coupled molecular dynamics and metadynamics simulations

    NASA Astrophysics Data System (ADS)

    Monasterio, Paul R.; Yip, Sidney; Yildiz, Bilge

    2013-04-01

    Self-interstitial interactions causing volume expansion in bcc Fe are studied through an idealized microstructure evolution model in which only self-interstial atoms (SIAs) are inserted. Using a combination of non-equilibrium molecular dynamics simulations and a metadynamics algorithm, meta-stable SIA clusters are observed to nucleate and grow into dislocation loops or localized amorphous phases, both contributing to swelling behavior persisting well beyond the atomistic time scale. A non-monotonic local density variation with dose rate is found and attributed to competing evolutions of different defective structures.

  13. 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.

  14. Multi-petaflop/s quantum and reactive molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Nakano, Aiichiro

    We have developed a divide-conquer-recombine algorithmic framework for large quantum molecular dynamics (QMD) and reactive molecular dynamics (RMD) simulations. The algorithms have achieved parallel efficiency over 0.98 on 786,432 IBM Blue Gene/Q processors for 39.8 trillion electronic degrees-of-freedom QMD in the framework of density functional theory and 67.6 billion-atom RMD. We will discuss several applications including (1) 16,616-atom QMD simulation of rapid hydrogen production from water using metallic alloy nanoparticles, (2) 6,400-atom nonadiabatic QMD simulation of exciton dynamics for efficient solar cells, and (3) 112 million-atom RMD simulation of nanocarbon synthesis by high temperature oxidation of SiC nanoparticles.

  15. Improving the performance of molecular dynamics simulations on parallel clusters.

    PubMed

    Borstnik, Urban; Hodoscek, Milan; Janezic, Dusanka

    2004-01-01

    In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds. PMID:15032512

  16. 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. PMID:19669536

  17. 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.

  18. 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.

  19. Nonequilibrium-molecular-dynamics measurement of the Leslie coefficients of a Gay-Berne nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Qian, Tiezheng

    2007-03-01

    We carried out nonequilibrium molecular dynamics (MD) simulations to measure the six Leslie coefficients of a nematic liquid crystal composed of molecules interacting via the Gay-Berne potential. In the presence of a simple shear flow, an external field is applied to control the molecular orientation, and a uniform director is stabilized in the central region of the channel in which the liquid crystal is confined and sheared. With the director tuned by varying the applied field, a number of orientational states are stabilized in the presence of a shear flow, and various viscous stress components are measured in these states of different directors. The six Leslie coefficients αi are determined by interpreting the MD measurement data for viscous stress according to the constitutive relations in the Ericksen-Leslie-Parodi (ELP) theory. The Parodi relation α2+α3=α6-α5 is well satisfied. Given the values of the Leslie coefficients, liquid crystal orientations are evaluated for different field directions and shear rates. Comparison with those directly measured in MD simualtions demonstrates a quantitative agreement, showing that in the Gay-Berne nematic liquid crystal, the viscous stress and the coupling between orientation and flow are well described by the ELP theory.

  20. 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.

  1. Computer simulation of nonequilibrium processes

    SciTech Connect

    Hoover, W.G.; Moran, B.; Holian, B.L.; Posch, H.A.; Bestiale, S.

    1987-01-01

    Recent atomistic simulations of irreversible macroscopic hydrodynamic flows are illustrated. An extension of Nose's reversible atomistic mechanics makes it possible to simulate such non-equilibrium systems with completely reversible equations of motion. The new techniques show that macroscopic irreversibility is a natural inevitable consequence of time-reversible Lyapunov-unstable microscopic equations of motion.

  2. 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. PMID:17025782

  3. Nonholonomic Hamiltonian Method for Molecular Dynamics Simulations of Reacting Shocks

    NASA Astrophysics Data System (ADS)

    Fahrenthold, Eric; Bass, Joseph

    2015-06-01

    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 these 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 noholonomic 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 model parameters. Example applications of the method show molecular level shock to detonation simulations in nitromethane and RDX. Research supported by the Defense Threat Reduction Agency.

  4. Annihilation of craters: Molecular dynamic simulations on a silver surface

    SciTech Connect

    Henriksson, K. O. E.; Nordlund, K.; Keinonen, J.

    2007-12-15

    The ability of silver cluster ions containing 13 atoms to fill in a preexisting crater with a radius of about 28 A ring on a silver (001) target has been investigated using molecular dynamics simulations and the molecular-dynamics-Monte Carlo corrected effective medium potential. The largest lateral distance r between crater and ion was about three times the radius of the preexisting crater, namely, 75 A ring . The results reveal that when r<20 A ring and r>60 A ring the preexisting crater is partially filled in, and for other distances there is a net growth of the crater. The lattice damage created by the cluster ions, the total sputtering yield, the cluster sputtering yield, and simulated transmission electron microscopy images of the irradiated targets are also presented.

  5. Time series analysis of molecular dynamics simulation using wavelet

    NASA Astrophysics Data System (ADS)

    Toda, Mikito

    2012-08-01

    A new method is presented to extract nonstationary features of slow collective motion toward time series data of molecular dynamics simulation for proteins. The method consists of the following two steps: (1) the wavelet transformation and (2) the singular value decomposition (SVD). The wavelet transformation enables us to characterize time varying features of oscillatory motions and SVD enables us to reduce the degrees of freedom of the movement. We apply the method to molecular dynamics simulation of various proteins such as Adenylate Kinase from Escherichia coli (AKE) and Thermomyces lanuginosa lipase (TLL). Moreover, we introduce indexes to characterize collective motion of proteins. These indexes provide us with information of nonstationary deformation of protein structures. We discuss future prospects of our study involving "intrinsically disordered proteins".

  6. 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.

  7. 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. PMID:19449821

  8. 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. PMID:19518394

  9. 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.

  10. Molecular dynamic simulation of non-melt laser annealing process

    NASA Astrophysics Data System (ADS)

    Liren, Yan; Dai, Li; Wei, Zhang; Zhihong, Liu; Wei, Zhou; Quan, Wang

    2016-03-01

    Molecular dynamic simulation is performed to study the process of material annealing caused by a 266 nm pulsed laser. A micro-mechanism describing behaviors of silicon and impurity atoms during the laser annealing at a non-melt regime is proposed. After ion implantation, the surface of the Si wafer is acted by a high energy laser pulse, which loosens the material and partially frees both Si and impurity atoms. While the residual laser energy is absorbed by valence electrons, these atoms are recoiled and relocated to finally form a crystal. Energy-related movement behavior is observed by using the molecular dynamic method. The non-melt laser anneal appears to be quite sensitive to the energy density of the laser, as a small excess energy may causes a significant impurity diffusion. Such a result is also supported by our laser anneal experiment.

  11. 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.

  12. 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.

  13. 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.

  14. Error and efficiency of replica exchange molecular dynamics simulations

    PubMed Central

    Rosta, Edina; Hummer, Gerhard

    2009-01-01

    We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977

  15. Error and efficiency of replica exchange molecular dynamics simulations.

    PubMed

    Rosta, Edina; Hummer, Gerhard

    2009-10-28

    We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977

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

    SciTech Connect

    Suele, P.; Heinig, K.-H.

    2009-11-28

    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 ({lambda}) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths ({lambda}<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 {lambda}>35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in {lambda} long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for {lambda}>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.

  17. Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts.

    PubMed

    Frank, Martin; Gutbrod, Peter; Hassayoun, Chokri; von Der Lieth, Claus-W

    2003-10-01

    Molecular dynamics is a rapidly developing field of science and has become an established tool for studying the dynamic behavior of biomolecules. Although several high quality programs for performing molecular dynamic simulations are freely available, only well-trained scientists are currently able to make use of the broad scientific potential that molecular dynamic simulations offer to gain insight into structural questions at an atomic level. The "Dynamic Molecules" approach is the first internet portal that provides an interactive access to set up, perform and analyze molecular dynamic simulations. It is completely based on standard web technologies and uses only publicly available software. The aim is to open molecular dynamics techniques to a broader range of users including undergraduate students, teachers and scientists outside the bioinformatics field. The time-limiting factors are the availability of free capacity on the computing server to run the simulations and the time required to transport the history file through the internet for the animation mode. The interactive access mode of the portal is acceptable for animations of molecules having up to about 500 atoms. PMID:12908101

  18. 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. PMID:26013419

  19. Setting up and running molecular dynamics simulations of membrane proteins.

    PubMed

    Kandt, Christian; Ash, Walter L; Tieleman, D Peter

    2007-04-01

    Molecular dynamics simulations have become a popular and powerful technique to study lipids and membrane proteins. We present some general questions and issues that should be considered prior to embarking on molecular dynamics simulation studies of membrane proteins and review common simulation methods. We suggest a practical approach to setting up and running simulations of membrane proteins, and introduce two new (related) methods to embed a protein in a lipid bilayer. Both methods rely on placing lipids and the protein(s) on a widely spaced grid and then 'shrinking' the grid until the bilayer with the protein has the desired density, with lipids neatly packed around the protein. When starting from a grid based on a single lipid structure, or several potentially different lipid structures (method 1), the bilayer will start well-packed but requires more equilibration. When starting from a pre-equilibrated bilayer, either pure or mixed, most of the structure of the bilayer stays intact, reducing equilibration time (method 2). The main advantages of these methods are that they minimize equilibration time and can be almost completely automated, nearly eliminating one time consuming step in MD simulations of membrane proteins. PMID:17367719

  20. 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. PMID:26358333

  1. Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo

    SciTech Connect

    Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.

    2000-10-10

    Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.

  2. 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.

  3. A reduced basis method for molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Vincent-Finley, Rachel Elisabeth

    In this dissertation, we develop a method for molecular simulation based on principal component analysis (PCA) of a molecular dynamics trajectory and least squares approximation of a potential energy function. Molecular dynamics (MD) simulation is a computational tool used to study molecular systems as they evolve through time. With respect to protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds. To capture motion at all levels, time steps on the order of a femtosecond are employed when solving the equations of motion and simulations must continue long enough to capture the desired large-scale motion. To date, simulations of solvated proteins on the order of nanoseconds have been reported. It is typically the case that simulations of a few nanoseconds do not provide adequate information for the study of large-scale motions. Thus, the development of techniques that allow longer simulation times can advance the study of protein function and dynamics. In this dissertation we use principal component analysis (PCA) to identify the dominant characteristics of an MD trajectory and to represent the coordinates with respect to these characteristics. We augment PCA with an updating scheme based on a reduced representation of a molecule and consider equations of motion with respect to the reduced representation. We apply our method to butane and BPTI and compare the results to standard MD simulations of these molecules. Our results indicate that the molecular activity with respect to our simulation method is analogous to that observed in the standard MD simulation with simulations on the order of picoseconds.

  4. Identifying the mechanisms of polymer friction through molecular dynamics simulation.

    PubMed

    Dai, Ling; Minn, M; Satyanarayana, N; Sinha, Sujeet K; Tan, V B C

    2011-12-20

    Mechanisms governing the tribological behavior of polymer-on-polymer sliding were investigated by molecular dynamics simulations. Three main mechanisms governing frictional behavior were identified. Interfacial "brushing" of molecular chain ends over one another was observed as the key contribution to frictional forces. With an increase of the sliding speed, fluctuations in frictional forces reduced in both magnitude and periodicity, leading to dynamic frictional behavior. While "brushing" remained prevalent, two additional irreversible mechanisms, "combing" and "chain scission", of molecular chains were observed when the interfaces were significantly diffused. PMID:22044344

  5. 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.

  6. 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.

  7. Analysis of motion features for molecular dynamics simulation of proteins

    NASA Astrophysics Data System (ADS)

    Kamada, Mayumi; Toda, Mikito; Sekijima, Masakazu; Takata, Masami; Joe, Kazuki

    2011-01-01

    Recently, a new method for time series analysis using the wavelet transformation has been proposed by Sakurai et al. We apply it to molecular dynamics simulation of Thermomyces lanuginosa lipase (TLL). Introducing indexes to characterize collective motion of the protein, we have obtained the following two results. First, time evolution of the collective motion involves not only the dynamics within a single potential well but also takes place wandering around multiple conformations. Second, correlation of the collective motion between secondary structures shows that collective motion exists involving multiple secondary structures. We discuss future prospects of our study involving 'disordered proteins'.

  8. 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.

  9. Molecular Dynamics Simulations Of Nanometer-Scale Feature Etch

    SciTech Connect

    Vegh, J. J.; Graves, D. B.

    2008-09-23

    Molecular dynamics (MD) simulations have been carried out to examine fundamental etch limitations. Beams of Ar{sup +}, Ar{sup +}/F and CF{sub x}{sup +} (x = 2,3) with 2 nm diameter cylindrical confinement were utilized to mimic 'perfect' masks for small feature etching in silicon. The holes formed during etch exhibit sidewall damage and passivation as a result of ion-induced mixing. The MD results predict a minimum hole diameter of {approx}5 nm after post-etch cleaning of the sidewall.

  10. Tight-binding molecular-dynamics simulation of buckyball collisions

    SciTech Connect

    Zhang, B.L.; Wang, C.Z.; Chan, C.T.; Ho, K.M. )

    1993-04-01

    The collisions between C[sub 60] molecules are studied by tight-binding molecular-dynamics simulations. We observe three different regimes of behavior as the collisions become more and more energetic: bouncing, fusion, and fragmentation. The critical energies for fusion and fragmentation as well as details of the energy transfer during the collision process for the bouncing regime are investigated. The collisions at several specific energies and orientations produce interesting novel molecules, such as small baby cages, caps, and even a Russian-Doll molecule in which a small cage is trapped in a bigger one. 28 refs., 5 figs., 2 tabs.

  11. A sampling problem in molecular dynamics simulations of macromolecules.

    PubMed Central

    Clarage, J B; Romo, T; Andrews, B K; Pettitt, B M; Phillips, G N

    1995-01-01

    Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled. Images Fig. 1 Fig. 2 Fig. 3 PMID:7724554

  12. 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.

  13. Molecular dynamics simulations of nanoidentation of silicon nitride

    SciTech Connect

    Walsh, P.; Omeltchenko, A.; Kikuchi, Hideaki; Kalia, R.K.; Nakano, Aiichiro; Vashishta, P.

    1999-08-01

    This is a report of work in progress on 10 million atom Molecular Dynamics (MD) simulations of nanoindentation of crystalline and amorphous silicon nitride (Si{sub 3}N{sub 4}). Nanoindentation is used to determine mechanical properties of extremely thin films such as hardness and elastic moduli. The authors report load-displacement curves for several Si{sub 3}N{sub 4} configurations using an idealized non-deformable indenter and analyze the local stress distributions in the vicinity of the indenter tip. Preliminary results for surface adhesion using Si{sub 3}N{sub 4} for both tip and substrate are also reported.

  14. 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.

  15. 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.

  16. Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers

    SciTech Connect

    Vashishta, Priya; Kalia, Rajiv

    2005-02-24

    Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report.

  17. 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.

  18. Insights into Buforin II Membrane Translocation from Molecular Dynamics Simulations

    PubMed Central

    Elmore, Donald E.

    2012-01-01

    Buforin II is a histone-derived antimicrobial peptide that readily translocates across lipid membranes without causing significant membrane permeabilization. Previous studies showed that mutating the sole proline of buforin II dramatically decreases its translocation. As well, researchers have proposed that the peptide crosses membranes in a cooperative manner through forming transient toroidal pores. This paper reports molecular dynamics simulations designed to investigate the structure of buforin II upon membrane entry and evaluate whether the peptide is able to form toroidal pore structures. These simulations showed a relationship between protein-lipid interactions and increased structural deformations of the buforin N-terminal region promoted by proline. Moreover, simulations with multiple peptides show how buforin II can embed deeply into membranes and potentially form toroidal pores. Together, these simulations provide structural insight into the translocation process for buforin II in addition to providing more general insight into the role proline can play in antimicrobial peptides. PMID:23022591

  19. 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.

  20. 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

  1. 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.

  2. Transport properties of dense fluid mixtures using nonequilibrium molecular dynamics. [Viscosity and thermal conductivity of continuous, or polydisperse mixtures

    SciTech Connect

    Murad, S.

    1990-09-01

    This progress report covers research carried out during the period September 15, 1987--September 15, 1990. The main emphasis of the work was on dense fluid mixtures, although in some cases work had to be done on pure fluids before we could study mixtures in a meaningful way. A summary of our results is given. (1) An algorithm was developed and used to calculate the viscosity and thermal conductivity of continuous, or polydisperse mixtures with various distributions (e.g. linear, several gaussian distributions including unsymmetric, etc.) using nonequilibrium molecular dynamics (NEMD). (2) A method was developed to calculate the thermal conductivity of nonspherical (rigid) molecules using NEMD. (3) The NEMD method for thermal conductivity of nonspherical molecules was used to have a careful look at the contributions due to internal rotational degrees of freedom in linear compounds such as chlorine, nitrogen, etc. (4) It has long been speculated that polar fluids exhibit heat induced birefringence, i.e., the molecules will tend to align themselves along the direction of an external heat field. Using nonequilibrium molecular dynamics we were able to conclusively confirm this. (5) We completed a preliminary study of the viscosity of homonuclear diatomics and their mixtures (e.g. N{sub 2}, Cl{sub 2}, etc.). (6) We completed a study of the various flexibility (vibrational) effects, such as bond bending, bond stretching etc., on linear and nonlinear model triatomics. To examine these effects in our preliminary study, we looked at the pressure second virial coefficients.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Byutner, Oleksiy; Smith, Grant

    2001-03-01

    In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.

  8. Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen

    SciTech Connect

    Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M; Benedict, L; Hau-Riege, S; Langdon, A; London, R

    2008-02-14

    The temperature equilibration rate in dense hydrogen (for both T{sub i} > T{sub e} and T{sub i} < T{sub e}) has been calculated with large-scale molecular dynamics simulations for temperatures between 10 and 300 eV and densities between 10{sup 20}/cc to 10{sup 24}/cc. Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L {approx}> 1, Brown-Preston-Singleton [Brown et al., Phys. Rep. 410, 237 (2005)] with the sub-leading corrections and the fit of Gericke-Murillo-Schlanges [Gericke et al., PRE 65, 036418 (2003)] to the T-matrix evaluation of the collision operator, agrees with the MD data to within the error bars of the simulation. For more strongly-coupled plasmas where L {approx}< 1, our numerical results are consistent with the fit of Gericke-Murillo-Schlanges.

  9. 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.

  10. 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.

  11. 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.

  12. Molecular dynamics simulations of a lithium/sodium carbonate mixture.

    PubMed

    Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo

    2016-03-01

    The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates. PMID:26897519

  13. Molecular dynamics simulations of detonation on the roadrunner supercomputer

    NASA Astrophysics Data System (ADS)

    Mniszewski, Susan; Cawkwell, Marc; Germann, Timothy C.

    2012-03-01

    The temporal and spatial scales intrinsic to a real detonating explosive are extremely difficult to capture using molecular dynamics (MD) simulations. Nevertheless, MD remains very attractive since it allows for the resolution of dynamic phenomena at the atomic scale. Large-scale reactive MD simulations in three dimensions require immense computational resources even when simple reactive force fields are employed. We focus on the REBO force field for 'AB' since it has been shown to support a detonation while being simple, analytic, and short-ranged. The transition from two-to three- dimensional simulations is being facilitated by the port of the REBO force field in the parallel MD code SPaSM to LANL's petaflop supercomputer 'Roadrunner'. We provide a detailed discussion of the challenges associated with computing interatomic forces on a hybrid Opteron/Cell BE computational architecture.

  14. Implementation of the force decomposition machine for molecular dynamics simulations.

    PubMed

    Borštnik, Urban; Miller, Benjamin T; Brooks, Bernard R; Janežič, Dušanka

    2012-09-01

    We present the design and implementation of the force decomposition machine (FDM), a cluster of personal computers (PCs) that is tailored to running molecular dynamics (MD) simulations using the distributed diagonal force decomposition (DDFD) parallelization method. The cluster interconnect architecture is optimized for the communication pattern of the DDFD method. Our implementation of the FDM relies on standard commodity components even for networking. Although the cluster is meant for DDFD MD simulations, it remains general enough for other parallel computations. An analysis of several MD simulation runs on both the FDM and a standard PC cluster demonstrates that the FDM's interconnect architecture provides a greater performance compared to a more general cluster interconnect. PMID:23085166

  15. Structure and dynamics of complex liquid water: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    S, Indrajith V.; Natesan, Baskaran

    2015-06-01

    We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

  16. Molecular Dynamics Simulation of Electrophoresis of a Telehelic Polymer Chain

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Aniket

    2002-08-01

    We report the conformational and the dynamical properties of an end-labeled polymer chain embedded in a porous medium made of randomly distributed immobile spherical obstacles using a stochastic Molecular Dynamic(MD) simulation method for several obstacle densities and for various bias strenghts applied only to one end of the chain. First, various properties of the chain are studied when the external bias is set to zero. We then extend the stochastic MD simulation to study the electrophresis of a polymer chain driven by (i) a steady and (ii) a time dependent electric field. These studies are relevant for various time dependent gel electrophoresis methods widely used to separate DNA molecules. The qualitative features are compared with experiments, analytic theories, and recent Monte Carlo Simulation results.

  17. Parallel Molecular Dynamics Stencil : a new parallel computing environment for a large-scale molecular dynamics simulation of solids

    NASA Astrophysics Data System (ADS)

    Shimizu, Futoshi; Kimizuka, Hajime; Kaburaki, Hideo

    2002-08-01

    A new parallel computing environment, called as ``Parallel Molecular Dynamics Stencil'', has been developed to carry out a large-scale short-range molecular dynamics simulation of solids. The stencil is written in C language using MPI for parallelization and designed successfully to separate and conceal parts of the programs describing cutoff schemes and parallel algorithms for data communication. This has been made possible by introducing the concept of image atoms. Therefore, only a sequential programming of the force calculation routine is required for executing the stencil in parallel environment. Typical molecular dynamics routines, such as various ensembles, time integration methods, and empirical potentials, have been implemented in the stencil. In the presentation, the performance of the stencil on parallel computers of Hitachi, IBM, SGI, and PC-cluster using the models of Lennard-Jones and the EAM type potentials for fracture problem will be reported.

  18. Thermal conductivity of liquid argon in nanochannels from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    HyŻorek, Krzysztof; Tretiakov, Konstantin V.

    2016-05-01

    The thermal conductivity of liquid argon in nanochannels has been calculated over a wide range of densities using two independent methods—the Green-Kubo approach in equilibrium molecular dynamics simulations and the Müller-Plathe method in non-equilibrium molecular dynamics simulations. The Lennard-Jones potential was used to model interatomic interactions. The influence of transversal size and shape of a nanochannel on the thermal conductivity of liquid argon along the length of the channel has been investigated. The transversal size of nanochannel varied from 2.25 nm to 15 nm. The simulations revealed that the thermal conductivity weakly depends on the shape (square vs circular) of channel and scales with a cross-sectional area of nanochannel. It has been observed that thermal conductivity increases with an increase of the transversal size of the channel. Also, it reaches bulk values for some characteristic size of channel that depends strongly on density. Good agreement of the computed thermal conductivities of liquid argon over a wide density range with the experimental data allowed the value of the characteristic size of channel as a function of density to be estimated. This value depends on density and varies from 5 nm to 11 nm.

  19. Thermal conductivity of liquid argon in nanochannels from molecular dynamics simulations.

    PubMed

    Hyżorek, Krzysztof; Tretiakov, Konstantin V

    2016-05-21

    The thermal conductivity of liquid argon in nanochannels has been calculated over a wide range of densities using two independent methods-the Green-Kubo approach in equilibrium molecular dynamics simulations and the Müller-Plathe method in non-equilibrium molecular dynamics simulations. The Lennard-Jones potential was used to model interatomic interactions. The influence of transversal size and shape of a nanochannel on the thermal conductivity of liquid argon along the length of the channel has been investigated. The transversal size of nanochannel varied from 2.25 nm to 15 nm. The simulations revealed that the thermal conductivity weakly depends on the shape (square vs circular) of channel and scales with a cross-sectional area of nanochannel. It has been observed that thermal conductivity increases with an increase of the transversal size of the channel. Also, it reaches bulk values for some characteristic size of channel that depends strongly on density. Good agreement of the computed thermal conductivities of liquid argon over a wide density range with the experimental data allowed the value of the characteristic size of channel as a function of density to be estimated. This value depends on density and varies from 5 nm to 11 nm. PMID:27208958

  20. Molecular dynamics simulations of hydrogen diffusion in aluminum

    DOE PAGESBeta

    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 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

  1. 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%.

  2. 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.

  3. 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.

  4. Molecular Dynamics Simulations of Phospholipid Bilayers with Cholesterol

    PubMed Central

    Hofsäß, Christofer; Lindahl, Erik; Edholm, Olle

    2003-01-01

    To investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different levels of cholesterol content. The simulations extend to 10 ns, and were performed with hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. The bilayers contain 1024 lipids of which 0–40% were cholesterol and the rest DPPC. The effects of cholesterol on the structure and mesoscopic dynamics of the bilayer were monitored as a function of cholesterol concentration. The main effects observed are a significant ordering of the DPPC chains (as monitored by NMR type order parameters), a reduced fraction of gauche bonds, a reduced surface area per lipid, less undulations—corresponding to an increased bending modulus for the membrane, smaller area fluctuations, and a reduced lateral diffusion of DPPC-lipids as well as cholesterols. PMID:12668428

  5. 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.

  6. Phase transitions in electrorheological fluids using molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lapenta, Giovanni; Maizza, Giovanni; Palmieri, Antonio; Boretto, Gianmarco; Debenedetti, Massimo

    1999-10-01

    A parametric study of the properties of electrorheological fluids is conducted using molecular dynamics (MD) simulations. The MD model is based on the solution of the Langevin equation for a number of suspended particles. The equations of motion include inertial effects, polarization forces, Stokes' drag, short range repulsion, and Brownian forces. Different polarization forces are considered to include the effect of enhancements at short range due to multipole moments induced by the suspended particles and other effects. The model is used to investigate the structural changes induced by external electric fields and by shear strains imposed on the system. The response times are studied as a function of two characteristic parameters describing the physical status of the system (temperature and external electric field). Finally, the stress-strain characteristics are studied and the yield stress is calculated as a function of the external electric field. The simulated response is compared with experimental findings.

  7. Molecular dynamics simulations of dislocation instability in a stress gradient

    NASA Astrophysics Data System (ADS)

    Li, Ming; Selinger, Robin L.

    2003-04-01

    We present simulation studies of a morphological instability arising in dislocation dynamics. When an initially straight dislocation line is driven by a stress whose magnitude grows along the direction of dislocation motion, vibrational modes of the dislocation line with wavelength above a threshold value become linearly unstable. Molecular dynamics simulation studies of screw dislocations in Al demonstrate the onset of the instability during dislocation pair annihilation and annihilation at a crack tip. The wavelength of the unstable vibrational mode observed in each case agrees with the predictions of theoretical analysis. We discuss the role of temperature in nucleating the instability and speculate about how instabilities in dislocation motion could affect the density of threading dislocations during growth of heteroepitaxial thin films.

  8. 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.

  9. A molecular dynamics simulation study of defect production in vanadium

    SciTech Connect

    Morishita, K. |; Diaz de la Rubia, T.

    1995-01-23

    We performed molecular dynamics simulations to investigate the process of defect production in pure vanadium. The interaction of atoms was described by the EAM interatomic potential modified at short range to merge smoothly with the universal potential for description of the high energy recoils in cascades. The melting point of this EAM model of vanadium was found to be consistent with the experimental melting temperature. The threshold energies of displacement events in the model system are also consistent with experimental minimum threshold in vanadium, and its average was found to be 44 eV. We evaluated the efficiencies of defect production in the displacement events initiated by recoils with kinetic energy up to 5 keV, and found that the probability of cluster formation is smaller than that of simulated events in fcc metals reported in the literature.

  10. Quantum Thermal Bath for Path Integral Molecular Dynamics Simulation.

    PubMed

    Brieuc, Fabien; Dammak, Hichem; Hayoun, Marc

    2016-03-01

    The quantum thermal bath (QTB) method has been recently developed to account for the quantum nature of the nuclei by using standard molecular dynamics (MD) simulation. QTB-MD is an efficient but approximate method when dealing with strongly anharmonic systems, while path integral molecular dynamics (PIMD) gives exact results but in a huge amount of computation time. The QTB and PIMD methods have been combined in order to improve the PIMD convergence or correct the failures of the QTB-MD technique. Therefore, a new power spectral density of the random force within the QTB has been developed. A modified centroid-virial estimator of the kinetic energy, especially adapted to QTB-PIMD, has also been proposed. The method is applied to selected systems: a one-dimensional double-well system, a ferroelectric phase transition, and the position distribution of an hydrogen atom in a fuel cell material. The advantage of the QTB-PIMD method is its ability to give exact results with a more reasonable computation time for strongly anharmonic systems. PMID:26799437

  11. 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.

  12. Study on the thermal resistance in secondary particles chain of silica aerogel by molecular dynamics simulation

    SciTech Connect

    Liu, M.; Qiu, L. E-mail: jzzhengxinghua@163.com; Zheng, X. H. E-mail: jzzhengxinghua@163.com; Zhu, J.; Tang, D. W.

    2014-09-07

    In this article, molecular dynamics simulation was performed to study the heat transport in secondary particles chain of silica aerogel. The two adjacent particles as the basic heat transport unit were modelled to characterize the heat transfer through the calculation of thermal resistance and vibrational density of states (VDOS). The total thermal resistance of two contact particles was predicted by non-equilibrium molecular dynamics simulations (NEMD). The defects were formed by deleting atoms in the system randomly first and performing heating and quenching process afterwards to achieve the DLCA (diffusive limited cluster-cluster aggregation) process. This kind of treatment showed a very reasonable prediction of thermal conductivity for the silica aerogels compared with the experimental values. The heat transport was great suppressed as the contact length increased or defect concentration increased. The constrain effect of heat transport was much significant when contact length fraction was in the small range (<0.5) or the defect concentration is in the high range (>0.5). Also, as the contact length increased, the role of joint thermal resistance played in the constraint of heat transport was increasing. However, the defect concentration did not affect the share of joint thermal resistance as the contact length did. VDOS of the system was calculated by numerical method to characterize the heat transport from atomic vibration view. The smaller contact length and greater defect concentration primarily affected the longitudinal acoustic modes, which ultimately influenced the heat transport between the adjacent particles.

  13. Temperature Dependence Study of Noncontact Afm Images Using Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Nejat Pishkenari, Hossein; Meghdari, Ali

    The effect of temperature on the noncontact atomic force microscopy (NC-AFM) surface imaging is investigated with the aid of molecular dynamics (MD) analysis based on the Sutton-Chen (SC) interatomic potential. Particular attention is devoted to the tip and sample flexibility at different temperatures. When a gold coated probe is brought close to the Au (001) surface at high temperatures, the tip and surface atoms are pulled together and their distance becomes smaller. The tip and sample atoms displacement varies in the different environment temperatures and this leads to the different interaction forces. Along this line, to study the effect of temperature on the resulting images, we have employed the well-known NC-AFM model and carried out realistic non-equilibrium MD 3D simulations of atomic scale imaging at different close approach positions to the surface.

  14. Molecular dynamics simulations of displacement cascades in GaAs.

    SciTech Connect

    Foiles, Stephen Martin

    2010-04-01

    The quantification of the production of primary defects via displacement cascades is an important ingredient in the prediction of the influence of radiation on the performance of electronic components in radiation environments. Molecular dynamics simulations of displacement cascades are performed for GaAs The interatomic interactions are described using a recently proposed Bond Order Potential, and a simple model of electronic stopping is incorporated. The production of point defects is quantified as a function of recoil energy and recoil species. Correlations in the point defects are examined. There are a large number of anti-site defects nearest-neighbor pairs as well as di-vacancies and larger order vacancy clusters. Radiation damage and ion implantation in materials have been studied via molecular dynamics for many years. A significant challenge in these simulations is the detailed identification and quantification of the primary defect production. For the present case of a compound semiconductor, GaAs, there are a larger number of possible point defects compared to elemental materials; two types of vacancies, two types of interstitials and antisite defects. This is further complicated by the fact that, in addition to the formation of point defects, amorphous zones may also be created. The goal of the current work is to quantify the production of primary defects in GaAs due to radiation exposures. This information will be used as part of an effort to predict the influence of radiation environments on the performance of electronic components and circuits. The data provide the initial state for continuum-level analysis of the temporal evolution of defect populations. For this initial state, it is important to know both the number of the various point defects that may be produced as well as the initial spatial correlations between the primary defects. The molecular dynamics simulations employ a recently developed Bond Order Potential (BOP) for GaAs. The analysis

  15. Thermal conductivity of model zeolites: molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Murashov, Vladimir V.

    1999-02-01

    The thermal conductivity of model zeolites was investigated using non-equilibrium molecular dynamics calculations. This type of calculation was found to overestimate the thermal conductivity of low-density silica polymorphs. A better reproduction of the experimental results was found for zeolites, and this was related to the lower phonon mean free path. The thermal conductivity of framework silicates was shown to be determined primarily by the vibrations of the continuous oxygen sublattice. Thus, the most drastic suppression of the heat transfer was related to alterations of the O-O distances; for example, a sixfold reduction in thermal conductivity compared to that of siliceous LTA zeolite was found for LTA-A1PO4. Framework cations were shown to affect the heat transfer by changing the vibrational modes of the structural building units of the framework and non-framework counter-cations, by disturbing the oxygen sublattice locally and acting as Rayleigh and resonant scatterers. A model assuming the heat transfer to be due only to non-dispersive acoustic phonons failed to reproduce the dependence of the thermal conductivity on the mass of the cations and the unit-cell dimension, thus suggesting a more sophisticated mechanism of heat transfer to be operative in framework materials. The effect of non-framework non-ionic species on the thermal conductivity was shown to be determined by their effect on the characteristics of the oxygen framework vibrations. Thus, repulsive interactions between the oxygen sublattice and Xe8 clusters, reducing the anisotropy and anharmonicity of the oxygen vibrations, give rise to enhanced heat transfer in LTA-SiO2 at ambient conditions.

  16. 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

  17. 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.

  18. Molecular Dynamics Simulation on Stability of Insulin on Graphene

    NASA Astrophysics Data System (ADS)

    Liang, Li-jun; Wang, Qi; Wu, Tao; Shen, Jia-wei; Kang, Yu

    2009-12-01

    The adsorption dynamics of a model protein (the human insulin) onto graphene surfaces with different sizes was investigated by molecular dynamics simulations. During the adsorption, it has different effect on the stability of the model protein in the fixed and non-fixed graphene systems. The tertiary structure of the protein was destroyed or partially destroyed, and graphene surfaces shows the selective protection for some α-helices in non-fixed systems but not in fixed systems by reason of the flexibility of graphene. As indicated by the interaction energy curve and trajectory animation, the conformation and orientation selection of the protein were induced by the properties and the texture of graphene surfaces. The knowledge of protein adsorption on graphene surfaces would be helpful to better understand stability of protein on graphene surfaces and facilitate potential applications of graphene in biotechnology.

  19. Molecular Dynamics Simulation of TATB-like Explosive

    NASA Astrophysics Data System (ADS)

    Sapozhnikov, Filipp; Dremov, Vladimir; Derbenev, Ilya; Karavaev, Alexey; Soulard, Laurent

    2007-06-01

    A modification of REBO potential has been proposed for the molecular dynamics simulation of a TATB-like condensed explosive whose molecule initially consists of four different atoms. TATB-like means bulk properties of initial state and parameters at CJ point similar to those of real TATB. Parameters of the potential are subdivided into two groups that are responsible for CJ parameters and reaction zone width. The possibility of formation of intermediate detonation products allows variation of reaction zone characteristics without changing CJ parameters. Provided are a number of test MD calculations on the thermodynamic properties of both the original explosive and detonation products, parameters at CJ point, reactions rates and reaction zone width as dependent upon the potential parameters as well as the evaluation of critical diameter. Mechanism of the detonation initiation proper to heterogeneous explosives has been investigated.

  20. Molecular Dynamics Simulation of Tatb-Like Explosive

    NASA Astrophysics Data System (ADS)

    Sapozhnikov, F. A.; Dremov, V. V.; Derbenev, I. V.; Karavaev, A. V.; Soulard, L.

    2007-12-01

    A modification of REBO potential has been proposed for the molecular dynamics simulation of a TATB-like condensed explosive whose molecule initially consists of four different atoms. TATB-like means bulk properties of initial state and parameters at CJ point similar to those of real TATB. Parameters of the potential are subdivided into two groups that are responsible for CJ parameters and reaction zone width. The possibility of formation of intermediate detonation products allows variation of reaction zone characteristics without changing CJ parameters. Provided are a number of test MD calculations on the thermodynamic properties of both the original explosive and detonation products, parameters at CJ point, reactions rates and reaction zone width as dependent upon the potential parameters as well as the evaluation of critical diameter. Mechanism of the detonation initiation proper to heterogeneous explosives has been investigated.

  1. Micellar crystals in solution from molecular dynamics simulations

    SciTech Connect

    Anderson, J.; Lorenz, C.; Travesset, A.

    2008-05-14

    Polymers with both soluble and insoluble blocks typically self-assemble into micelles, which are aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our results show that equilibration of single micelle degrees of freedom and crystal formation occur by polymer transfer between micelles, a process that is described by transition state theory. Near the disordered (or melting) transition, bcc lattices are favored for all triblocks studied. Lattices with fcc ordering are also found but only at lower kinetic temperatures and for triblocks with short hydrophilic blocks. Our results lead to a number of theoretical considerations and suggest a range of implications to experimental systems with a particular emphasis on Pluronic polymers.

  2. 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.

  3. Molecular dynamics simulations of methane hydrate using polarizable force fields

    SciTech Connect

    Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

    2007-03-01

    Molecular dynamics simulations of methane hydrate have been carried out using the AMOEBA and COS/G2 polarizable force fields. Properties examined include the temperature dependence of the lattice constant, the OC and OO radial distribution functions and the vibrational spectra. Both the AMOEBA and COS/G2 models are found to successfully account for the available experimental data, with overall slightly better agreement with experiment being found for the AMOEBA model. Several properties calculated using the AMOEBA and COS/G2 models differ appreciable from the corresponding results obtained previously using the polarizable TIP4P-FQ model. This appears to be due to the inadequacy of the treatment of polarization, especially, the restriction of polarization to in-plane only, in the TIP4P-FQ model.

  4. Molecular dynamics simulation of impurities in nanocrystalline diamond grain boundaries

    SciTech Connect

    Sternberg, M.; Zapol, P.; Frauenheim, T.; Gruen, D. M.; Curtiss, L. A.

    2000-01-12

    Nanocrystalline diamond films grown on Si substrates at 800 C from hydrogen-poor plasmas have a number of highly desirable mechanical and electronic properties. Impurities were found by SIMS measurements to be uniformly distributed throughout the thickness of the films at a level of 10{sup 17}--10{sup 18} cm{sup {minus}3}. It is likely that the impurities are located at the grain boundaries, which play a crucial role in controlling important characteristics of the films, such as electrical conductivity and electron emission. Density-functional based tight-binding (DFTB) molecular dynamics simulations were performed for diamond light-energy high-angle (100) twist grain boundaries with impurities such as N, Si and H.

  5. Molecular dynamics simulation of dislocations in uranium dioxide

    NASA Astrophysics Data System (ADS)

    Fossati, Paul; Van Brutzel, Laurent; Devincre, Benoît

    2013-11-01

    The plasticity of the fluorite structure in UO2 is investigated with molecular dynamics simulation and empirical potential. The stacking fault energies and the dislocation core structures with Burgers vector a2<110> are systematically calculated. All dislocation core structures show a significant increase of the oxygen sub-lattice disorder at temperatures higher than 1500 K. The threshold stress for dislocation glide is found to decrease with increasing temperature but its values is always very high, several GPa at 0 K and several hundred of MPa at 2000 K. A relation between the dislocation mobility dependence with temperature and the increase of the oxygen sub-lattice disorder in the dislocation cores is established.

  6. Measuring kinetic coefficients by molecular dynamics simulation of zone melting

    NASA Astrophysics Data System (ADS)

    Celestini, Franck; Debierre, Jean-Marc

    2002-04-01

    Molecular dynamics simulations are performed to measure the kinetic coefficient at the solid-liquid interface in pure gold. Results are obtained for the (111), (100), and (110) orientations. Both Au(100) and Au(110) are in reasonable agreement with the law proposed for collision-limited growth. For Au(111), stacking fault domains form, as first reported by Burke, Broughton, and Gilmer [J. Chem. Phys. 89, 1030 (1988)]. The consequence on the kinetics of this interface is dramatic: the measured kinetic coefficient is three times smaller than that predicted by collision-limited growth. Finally, crystallization and melting are found to be always asymmetrical and here again the effect is much more pronounced for the (111) orientation.

  7. Molecular dynamics simulations on the melting of gold nanoparticles

    NASA Astrophysics Data System (ADS)

    Qiao, Zhiwei; Feng, Haijun; Zhou, Jian

    2014-01-01

    Molecular dynamics is employed to study the melting of bulk gold and gold nanoparticles. PCFF, Sutton-Chen and COMPASS force fields are adopted to study the melting point of bulk gold and we find out that the Sutton-Chen force field is the most accurate model in predicting the melting point of bulk gold. Consequently, the Sutton-Chen force field is applied to study the melting points of spherical gold nanoparticles with different diameters. Variations of diffusion coefficient, potential energy and translational order parameter with temperature are analyzed. The simulated melting points of gold nanoparticles are between 615∼1115 K, which are much lower than that of bulk gold (1336 K). As the diameter of gold nanoparticle drops, the melting point also descends. The melting mechanism is also analyzed for gold nanoparticles.

  8. 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.

  9. "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. PMID:15641856

  10. Orientation Dependence in Molecular Dynamics Simulations of Shocked Single Crystals

    SciTech Connect

    Germann, Timothy C.; Holian, Brad Lee; Lomdahl, Peter S.; Ravelo, Ramon

    2000-06-05

    We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the <100> direction form intersecting stacking faults by slippage along {l_brace}111{r_brace} close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the <111> case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the <110> direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation. (c) 2000 The American Physical Society.

  11. Gas adsorption and accumulation on hydrophobic surfaces: Molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Luo, Qing-Qun; Yang, Jie-Ming

    2015-09-01

    Molecular dynamics simulations show that the gas dissolved in water can be adsorbed at a hydrophobic interface and accumulates thereon. Initially, a water depletion layer appears on the hydrophobic interface. Gas molecules then enter the depletion layer and form a high-density gas-enriched layer. Finally, the gas-enriched layer accumulates to form a nanobubble. The radian of the nanobubble increases with time until equilibrium is reached. The equilibrium state arises through a Brenner-Lohse dynamic equilibrium mechanism, whereby the diffusive outflux is compensated by an influx near the contact line. Additionally, supersaturated gas also accumulates unsteadily in bulk water, since it can diffuse back into the water and is gradually adsorbed by a solid substrate. Project supported by the National Natural Science Foundation of China (Grant No. 21376161).

  12. Erbium Implantation in Silica Studied by Molecular Dynamics Simulations

    SciTech Connect

    Du, Jincheng; Corrales, Louis R.

    2007-02-01

    Defect formation induced by erbium implantation in silica glass and cristobalite was studied using molecular dynamics simulations employing a partial charge model in combination with the ZBL potential. The results show that the number of displaced atoms generated at the same PKA energy is similar in silica and cristobalite but the number of coordination defects created is much lower in the cristobalite than in silica glass. In both cases, the erbium ion is able to create an optimal coordination environment at the end of the collision cascade. Subsequent thermal annealing causes the relaxation of the silicon oxygen network structure along with a reduction of silicon and oxygen defects. This research is supported by the Divisions of Materials Sciences and Engineering and Chemical Science, Office of Basic Energy Sciences, U.S. Department of Energy. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

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

    PubMed

    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

  14. Quantum molecular dynamics simulations of thermophysical properties of fluid ethane

    NASA Astrophysics Data System (ADS)

    Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping

    2012-12-01

    We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition, that ethane dissociates significantly into molecular and/or atomic hydrogen and some long alkane chains, has been systematically studied by analyzing the optical conductivity spectra, pair correlation functions, electronic density of states, and charge density distribution of fluid ethane.

  15. Clustering effects in ionic polymers: Molecular dynamics simulations

    DOE PAGESBeta

    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

  16. 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.

  17. 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.

  18. 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.

  19. Molecular dynamics simulations of methane hydrate using polarizable force fields

    SciTech Connect

    Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

    2007-06-14

    Molecular dynamics simulations of methane hydrate have been carried out using the polarizable AMOEBA and COS/G2 force fields. Properties calculated include the temperature dependence of the lattice constant, the OC and OO radial distribution functions, and the vibrational spectra. Both the AMOEBA and COS/G2 force fields are found to successfully account for the available experimental data, with overall somewhat better agreement with experiment being found for the AMOEBA model. Comparison is made with previous results obtained using TIP4P and SPC/E effective two-body force fields and the polarizable TIP4P-FQ force field, which allows for in-plane polarization only. Significant differences are found between the properties calculated using the TIP4P-FQ model and those obtained using the other models, indicating an inadequacy of restricting explicit polarization to in-plane onl

  20. Continuum and molecular-dynamics simulation of nanodroplet collisions

    NASA Astrophysics Data System (ADS)

    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 (Kngas=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 (Knliquid=0.01 for D =36 nm ) 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 droplets.

  1. Thermostat artifacts in replica exchange molecular dynamics simulations.

    PubMed

    Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard

    2009-01-01

    We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble. PMID:20046980

  2. Thermostat artifacts in replica exchange molecular dynamics simulations

    PubMed Central

    Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard

    2009-01-01

    We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble. PMID:20046980

  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. 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. PMID:23005226

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

    NASA Astrophysics Data System (ADS)

    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 Di. For the carbon-oxygen system we find that DO for oxygen ions in the solid is much smaller than DC 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.

  6. Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies

    NASA Astrophysics Data System (ADS)

    Oh, Kwang-Im; Choi, Jun-Ho; Lee, Joo-Hyun; Han, Jae-Beom; Lee, Hochan; Cho, Minhaeng

    2008-04-01

    Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9cm-1, respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, β-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.

  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. 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. PMID:26751047

  9. Naratriptan aggregation in lipid bilayers: perspectives from molecular dynamics simulations.

    PubMed

    Wood, Irene; Pickholz, Mónica

    2016-09-01

    In order to understand the interaction between naratriptan and a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC), we carried out molecular dynamics simulations. The simulations were performed considering neutral and protonated ionization states, starting from different initial conditions. At physiological pH, the protonated state of naratriptan is predominant. It is expected that neutral compounds could have larger membrane partition than charged compounds. However, for the specific case of triptans, it is difficult to study neutral species in membranes experimentally, making computer simulations an interesting tool. When the naratriptan molecules were originally placed in water, they partitioned between the bilayer/water interface and water phase, as has been described for similar compounds. From this condition, the drugs displayed low access to the hydrophobic environment, with no significant effects on bilayer organization. The molecules anchored in the interface, due mainly to the barrier function of the polar and oriented lipid heads. On the other hand, when placed inside the bilayer, both neutral and protonated naratriptan showed self-aggregation in the lipid tail environment. In particular, the protonated species exhibited a pore-like structure, dragging water through this environment. Graphical Abstract Different behaviour of Naratriptan and Sumatriptan, when the drugs were originally placed in the lipid core. PMID:27558798

  10. Displacement cascades in metals and ordered alloys. Molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Doan, N. V.; Vascon, R.

    1998-02-01

    The aim of the present Molecular Dynamics (MD) simulations is a better understanding of the mechanisms associated with defect production and atomic mixing occurring in displacement cascades in irradiated metals and alloys. The cascades of energy up to 30 keV were investigated by parallel MD simulations in crystals with a reasonably large size of the simulation box, containing up to 2 millions of atoms. In order to separate the effect of the mass of atoms from the chemical effect on the defect production and the disordering in alloys, cascades were generated in Ni 3Al and NiAl compounds where the Al atoms were artificially given the Ni mass. A series of artificial alloys FeAl, FeSb, FeAu, FeU were also investigated. Large interstitial clusters were found to be very mobile and a glide mechanism was pointed out. A sub-cascade formation mechanism was observed from cascades of energy equal to or higher than 5 keV and related to the quasi-channeling phenomenon.

  11. Large-scale Molecular Dynamics Simulations of Glancing Angle Deposition

    NASA Astrophysics Data System (ADS)

    Hubartt, Bradley; Liu, Xuejing; Amar, Jacques

    2013-03-01

    While a variety of methods have been developed to carry out atomistic simulations of thin-film growth at small deposition angles with respect to the substrate normal, due to the complex morphology as well as the existence of multiple scattering of depositing atoms by the growing thin-film, realistically modeling the deposition process for large deposition angles can be quite challenging. Accordingly, we have developed a computationally efficient method based on the use of a single graphical processing unit (GPU) to carry out molecular dynamics (MD) simulations of the deposition and growth of thin-films via glancing angle deposition. Using this method we have carried out large-scale MD simulations, based on an embedded-atom-method potential, of Cu/Cu(100) growth up to 20 monolayers for deposition angles ranging from 50° to 85° and for both random and fixed azimuthal angles. Our results for the thin-film porosity, roughness, lateral correlation length, and density vs height will be presented and compared with experiments. Results for the dependence of the microstructure, grain-size distribution, surface texture, and defect concentration on deposition angle will also be presented. Supported by NSF DMR-0907399

  12. 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.

  13. Hybrid particle-field molecular dynamics simulation for polyelectrolyte systems.

    PubMed

    Zhu, You-Liang; Lu, Zhong-Yuan; Milano, Giuseppe; Shi, An-Chang; Sun, Zhao-Yan

    2016-04-14

    To achieve simulations on large spatial and temporal scales with high molecular chemical specificity, a hybrid particle-field method was proposed recently. This method is developed by combining molecular dynamics and self-consistent field theory (MD-SCF). The MD-SCF method has been validated by successfully predicting the experimentally observable properties of several systems. Here we propose an efficient scheme for the inclusion of electrostatic interactions in the MD-SCF framework. In this scheme, charged molecules are interacting with the external fields that are self-consistently determined from the charge densities. This method is validated by comparing the structural properties of polyelectrolytes in solution obtained from the MD-SCF and particle-based simulations. Moreover, taking PMMA-b-PEO and LiCF3SO3 as examples, the enhancement of immiscibility between the ion-dissolving block and the inert block by doping lithium salts into the copolymer is examined by using the MD-SCF method. By employing GPU-acceleration, the high performance of the MD-SCF method with explicit treatment of electrostatics facilitates the simulation study of many problems involving polyelectrolytes. PMID:27001709

  14. 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.

  15. 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.

  16. 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

  17. 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. PMID:22653637

  18. Surface Diffusion of Single Polymer Chain Using Molecular Dynamics SIMULATION*

    NASA Astrophysics Data System (ADS)

    Desai, Tapan; Keblinski, Pawel; Kumar, Sanat; Granick, Steve

    2004-05-01

    Results of recent experiments on polymer chains adsorbed from dilute solution at solid-liquid interface show the power scaling law dependence of the chain diffusivity, D, as a function of the degree of polymerization, N, D ˜ N^3/2. By contrast, DNA molecules bound to fluid cationic lipid bilayers follows Rouse dynamics with D ˜ N^1. We used molecular dynamics simulations to gain an understanding of these dissimilar scaling behaviors. Our model systems contain chains comprised of N monomers connected by anharmonic springs described by the finite extendible nonlinear elastic, FENE potential, embedded into a solvent of N=1 monomers. Two types of simulations we performed: (i) the chain is confined to two dimensions, (ii) the three dimensional chain in the solvent is confined between two solids plates. With randomly placed impenetrable obstacles on the surface, the diffusion of 2D chains exhibits, D ˜ N^3/2 behavior, when the chain radius of gyration, Rg, is larger than half the distance between obstacles, and D ˜ N^1 for shorter chains. In the presence of an athermal solvent, the scaling exponent is 0.75 due to hydrodynamic forces, for the two-dimensional system. We will also discuss the nature of dynamic adsorption transition and effects of hydrodynamics forces on chain diffusion for the three-dimensional simulations.

  19. Hemolytic mechanism of dioscin proposed by molecular dynamics simulations.

    PubMed

    Lin, Fu; Wang, Renxiao

    2010-01-01

    Saponins are a class of compounds containing a triterpenoid or steroid core with some attached carbohydrate modules. Many saponins cause hemolysis. However, the hemolytic mechanism of saponins at the molecular level is not yet fully understood. In an attempt to explore this issue, we have studied dioscin-a saponin with high hemolytic activity-through extensive molecular dynamics (MD) simulations. Firstly, all-atom MD simulations of 8 ns duration were conducted to study the stability of the dioscin-cholesterol complex and the cholesterol-cholesterol complex in water and in decane, respectively. MM-GB/SA computations indicate that the dioscin-cholesterol complex is energetically more favorable than the cholesterol-cholesterol complex in a non-polar environment. Next, several coarse-grained MD simulations of 400 ns duration were conducted to directly observe the distribution of multiple dioscin molecules on a DPPC-POPC-PSM-CHOL lipid bilayer. Our results indicate that dioscin can penetrate into the lipid bilayer, accumulate in the lipid raft micro-domain, and then bind cholesterol. This leads to the destabilization of lipid raft and consequent membrane curvature, which may eventually result in the hemolysis of red cells. This possible mechanism of hemolysis can well explain some experimental observations on hemolysis. PMID:19513766

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

    NASA Astrophysics Data System (ADS)

    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.

  1. 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. PMID:22722319

  2. Nonequilibrium radiative hypersonic flow simulation

    NASA Astrophysics Data System (ADS)

    Shang, J. S.; Surzhikov, S. T.

    2012-08-01

    Nearly all the required scientific disciplines for computational hypersonic flow simulation have been developed on the framework of gas kinetic theory. However when high-temperature physical phenomena occur beneath the molecular and atomic scales, the knowledge of quantum physics and quantum chemical-physics becomes essential. Therefore the most challenging topics in computational simulation probably can be identified as the chemical-physical models for a high-temperature gaseous medium. The thermal radiation is also associated with quantum transitions of molecular and electronic states. The radiative energy exchange is characterized by the mechanisms of emission, absorption, and scattering. In developing a simulation capability for nonequilibrium radiation, an efficient numerical procedure is equally important both for solving the radiative transfer equation and for generating the required optical data via the ab-initio approach. In computational simulation, the initial values and boundary conditions are paramount for physical fidelity. Precise information at the material interface of ablating environment requires more than just a balance of the fluxes across the interface but must also consider the boundary deformation. The foundation of this theoretic development shall be built on the eigenvalue structure of the governing equations which can be described by Reynolds' transport theorem. Recent innovations for possible aerospace vehicle performance enhancement via an electromagnetic effect appear to be very attractive. The effectiveness of this mechanism is dependent strongly on the degree of ionization of the flow medium, the consecutive interactions of fluid dynamics and electrodynamics, as well as an externally applied magnetic field. Some verified research results in this area will be highlighted. An assessment of all these most recent advancements in nonequilibrium modeling of chemical kinetics, chemical-physics kinetics, ablation, radiative exchange

  3. 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

  4. Molecular dynamics simulations of heme reorientational motions in myoglobin.

    PubMed Central

    Henry, E R

    1993-01-01

    Molecular dynamics simulations of 2-ns duration were performed on carbonmonoxymyoglobin and deoxymyoglobin in vacuo to study the reorientational dynamics of the heme group. The heme in both simulations undergoes reorientations of approximately 5 degrees amplitude on a subpicosecond time scale, which produce a rapid initial decay in the reorientational correlation function to about 0.99. The heme also experiences infrequent changes in average orientation of approximately 10 degrees amplitude, which lead to a larger slow decay of the reorientational correlation function over a period of hundreds of picoseconds. The simulations have not converged with respect to these infrequent transitions. However, an estimate of the order parameter for rapid internal motions of the heme from those orientations which are sampled by the simulations suggests that the subnanosecond orientational dynamics of the heme accounts for at least 30% of the unresolved initial anisotropy decay observed in the nanosecond time-resolved optical absorption experiments on myoglobin reported by Ansari et al. in a companion paper (Ansari, A., C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton. 1992. Biophys. J. 64:852-868.). A more complete sampling of the accessible heme orientations would most likely increase this fraction further. The simulation of the liganded molecule also suggests that the conformational dynamics of the CO ligand may contribute significantly to discrepancies between the ligand conformation as probed by x-ray diffraction and by infrared-optical photoselection experiments. The protein back-bone explores multiple conformations during the simulations, with the largest structural changes appearing in the E and F helices, which are in contact with the heme. The variations in the heme orientation correlate with the conformational dynamics of the protein on a time scale of hundreds of picoseconds, suggesting that the heme orientation may provide a useful probe of dynamical processes

  5. Validating clustering of molecular dynamics simulations using polymer models

    PubMed Central

    2011-01-01

    Background Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the

  6. 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.

  7. 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.

  8. 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).

  9. Surface identification, meshing and analysis during large molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Dupuy, Laurent M.; Rudd, Robert E.

    2006-03-01

    Techniques are presented for the identification and analysis of surfaces and interfaces in atomistic simulations of solids. Atomistic and other particle-based simulations have no inherent notion of a surface, only atomic positions and interactions. The algorithms we develop here provide an unambiguous means to determine which atoms constitute the surface, and the list of surface atoms and a tessellation (meshing) of the surface are determined simultaneously. The tessellation is then used to calculate various surface integrals such as volume, area and shape (multiple moment). The principle of surface identification and tessellation is closely related to that used in the generation of the r-reduced surface, a step in the visualization of molecular surfaces used in biology. The algorithms have been implemented and demonstrated to run automatically (on the fly) in a large-scale parallel molecular dynamics (MD) code on a supercomputer. We demonstrate the validity of the method in three applications in which the surfaces and interfaces evolve: void surfaces in ductile fracture, the surface morphology due to significant plastic deformation of a nanoscale metal plate, and the interfaces (grain boundaries) and void surfaces in a nanoscale polycrystalline system undergoing ductile failure. The technique is found to be quite robust, even when the topology of the surfaces changes as in the case of void coalescence where two surfaces merge into one. It is found to add negligible computational overhead to an MD code.

  10. Molecular dynamics simulation indicating cold denaturation of β-hairpins

    NASA Astrophysics Data System (ADS)

    Shao, Qiang; Shi, Jiye; Zhu, Weiliang

    2013-02-01

    The folding of a series of β-hairpin structured polypeptides, which share high sequence similarity but differ significantly in structure resistance to temperature decrease, was investigated in the present study using integrated-tempering-sampling molecular dynamics simulations on microsecond time scale. MrH3a is a single mutant (I16A) and MrH4a is a double mutant (Y3L/I16A) of the wild-type polypeptide MrH1. MrH3b and MrH4b have an additional mutation in the turn region (INGK → IDPGK) of MrH3a and MrH4a, respectively. It was observed in the present study that the cold denaturation tendency follows the order of MrH1 > MrH4a > MrH3a, while the folded structures of MrH3b and MrH4b have the enhanced stability and are not subject to cold denaturation. These observations are in good agreement with experimental results of Maynard et al. and Dyer et al. Comparative analysis of simulation results for the 5 polypeptides revealed potential mechanism of β-hairpin cold denaturation. The main determinant of cold denaturation tendency is likely the stability decrease of backbone hydrogen bonds at low temperatures, which in turn is affected by the packing manner of the hydrophobic core cluster of β-hairpin structures.

  11. Molecular dynamics simulations of ionic liquid nanodroplets in electric fields

    NASA Astrophysics Data System (ADS)

    Tiruppathi, Pavithra C.

    2011-12-01

    Ionic liquids are appropriate for the application of electrospray thruster propulsion due to their physical properties such as low volatility and high electrical conductivity. The behavior of ionic liquid droplets and resulting ion and cluster emission in the presence of an electric field impacts the efficiency and thrust of the electrospray thruster. The technique of molecular simulation allows for the study of ionic liquid nanodroplets in atomic detail which is a limitation in mass spectrometric experiments. This thesis discusses the investigation of nanodroplets of the ionic liquid 1-ethyl-3- methylimidaziolium bis(triuoromethylsulfonyl)imide ([Emim+][Tf2n -]) in the presence of an electric field using molecular dynamics simulations. The ratio of the single ions to large clusters emitted from the droplet are observed and compared with experiment. The critical field strength required for ion emission from the droplet agrees with experiment. The critical field strength is also computed as a function of droplet size. The thermal stabilities, structural and dynamical properties are analyzed for the ([Emim +][Tf2n-]) nanodroplets.

  12. Molecular dynamics simulation of complex plasmas: interaction of nonlinear waves

    NASA Astrophysics Data System (ADS)

    Durniak, Celine; Samsonov, Dmitry

    2008-11-01

    Complex plasmas consist of micron sized microspheres immersed into ordinary ion-electron plasmas. They exist in solid, liquid, gaseous states and exhibit a range of dynamic phenomena such as waves, solitons, phase transitions, heat transfer. These phenomena can be modelled in complex plasmas at the microscopic or ``molecular'' scale, which is almost impossible in ordinary solids and liquids. We simulate a monolayer complex plasma consisting of 3000 negatively-charged particles (or grains) with the help of molecular dynamics computer simulations. The equations of grain motion are solved using a 5^th order Runge Kutta method taking into account interaction of every grain with each other via a Yukawa potential. The grains are confined more strongly in the vertical direction than in the horizontal. After seeding the grains randomly the code is run until the equilibrium is reached as the grain kinetics energy reduces due to damping force equal to the neutral friction in the experiments and a monolayer crystal lattice is formed. Then we investigate interactions between nonlinear waves in a monolayer strongly coupled complex plasma moving in three dimensions. Different excitations are applied during a short time symmetrically on both sides of the lattice. Structural properties and nonlinear waves characteristics are examined as the pulses propagate across the complex plasma in opposite directions.

  13. 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.

  14. 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.

  15. 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.

  16. 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. PMID:21500218

  17. Molecular Dynamics Simulation of Thermodynamic Properties in Uranium Dioxide

    SciTech Connect

    Wang, Xiangyu; Wu, Bin; Gao, Fei; Li, Xin; Sun, Xin; Khaleel, Mohammad A.; Akinlalu, Ademola V.; Liu, L.

    2014-03-01

    In the present study, we investigated the thermodynamic properties of uranium dioxide (UO2) by molecular dynamics (MD) simulations. As for solid UO2, the lattice parameter, density, and enthalpy obtained by MD simulations were in good agreement with existing experimental data and previous theoretical predictions. The calculated thermal conductivities matched the experiment results at the midtemperature range but were underestimated at very low and very high temperatures. The calculation results of mean square displacement represented the stability of uranium at all temperatures and the high mobility of oxygen toward 3000 K. By fitting the diffusivity constant of oxygen with the Vogel-Fulcher-Tamman law, we noticed a secondary phase transition near 2006.4 K, which can be identified as a ‘‘strong’’ to ‘‘fragile’’ supercooled liquid or glass phase transition in UO2. By fitting the oxygen diffusion constant with the Arrhenius equation, activation energies of 2.0 and 2.7 eV that we obtained were fairly close to the recommended values of 2.3 to 2.6 eV. Xiangyu Wang, Bin Wu, Fei Gao, Xin Li, Xin Sun, Mohammed A. Khaleel, Ademola V. Akinlalu and Li Liu

  18. 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.

  19. Surface detection, meshing and analysis during large molecular dynamics simulations

    SciTech Connect

    Dupuy, L M; Rudd, R E

    2005-08-01

    New techniques are presented for the detection and analysis of surfaces and interfaces in atomistic simulations of solids. Atomistic and other particle-based simulations have no inherent notion of a surface, only atomic positions and interactions. The algorithms we introduce here provide an unambiguous means to determine which atoms constitute the surface, and the list of surface atoms and a tessellation (meshing) of the surface are determined simultaneously. The algorithms have been implemented and demonstrated to run automatically (on the fly) in a large-scale parallel molecular dynamics (MD) code on a supercomputer. We demonstrate the validity of the method in three applications in which the surfaces and interfaces evolve: void surfaces in ductile fracture, the surface morphology due to significant plastic deformation of a nanoscale metal plate, and the interfaces (grain boundaries) and void surfaces in a nanoscale polycrystalline system undergoing ductile failure. The technique is found to be quite robust, even when the topology of the surfaces changes as in the case of void coalescence where two surfaces merge into one. It is found to add negligible computational overhead to an MD code, and is much less expensive than other techniques such as the solvent-accessible surface.

  20. Post-processing interstitialcy diffusion from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    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.

  1. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations

    PubMed Central

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

    2011-01-01

    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 Public License from http://mdanalysis.googlecode.com. PMID:21500218

  2. 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

  3. Thermomechanical coupling, heat conduction and director rotation in cholesteric liquid crystals studied by molecular dynamics simulation.

    PubMed

    Sarman, Sten; Laaksonen, Aatto

    2013-03-14

    The lack of a centre of inversion in a cholesteric liquid crystal allows linear cross couplings between thermodynamic forces and fluxes that are polar vectors and pseudovectors, respectively. This makes it possible for a temperature gradient parallel to the cholesteric axis to induce a torque that rotates the director, a phenomenon known as the Lehmann effect or thermomechanical coupling. The converse is also possible: a torque applied parallel to the cholesteric axis rotates the director and drives a heat flow. In order to study this phenomenon, nonequilibrium molecular dynamics simulation algorithms and Green-Kubo relations evaluated by equilibrium molecular dynamics simulation have been used to calculate the Leslie coefficient, i.e. the cross coupling coefficient between the temperature gradient and the director angular velocity, for a model system composed of soft prolate ellipsoids of revolution interacting via the Gay-Berne potential augmented by a chiral interaction potential causing the formation of a cholesteric phase. It is found that the Leslie coefficient is two orders of magnitudes smaller than other transport coefficients such as the heat conductivity and the twist viscosity, so that very long simulations are required to evaluate it. The Leslie coefficient decreases with the pitch but it has not been possible to determine the exact functional dependence of this coefficient on the pitch. Since very long simulations have been performed to evaluate the Leslie coefficient, very accurate values have been obtained for the twist viscosity and the heat conductivity as a by-product and it is found that they are very similar to the values of the corresponding quantities in the achiral nematic phase that arises when the pitch goes to infinity. PMID:23223192

  4. Transport properties of 2F <==> F2 in a temperature gradient as studied by molecular dynamics simulations.

    PubMed

    Xu, Jing; Kjelstrup, Signe; Bedeaux, Dick; Simon, Jean-Marc

    2007-02-28

    We calculate transport properties of a reacting mixture of F and F(2) from results of non-equilibrium molecular dynamics simulations. The reaction investigated is controlled by thermal diffusion and is close to local chemical equilibrium. The simulations show that a formulation of the transport problem in terms of classical non-equilibrium thermodynamics theory is sound. The chemical reaction has a large effect on the magnitude and temperature dependence of the thermal conductivity and the interdiffusion coefficient. The increase in the thermal conductivity in the presence of the chemical reaction, can be understood as a response to an imposed temperature gradient, which reduces the entropy production. The heat of transfer for the Soret stationary state was more than 100 kJ mol(-1), meaning that the Dufour and Soret effects are non-negligible in reacting mixtures. This sheds new light on the transport properties of reacting mixtures. PMID:17301887

  5. Towards Microsecond Biological Molecular Dynamics Simulations on Hybrid Processors

    SciTech Connect

    Hampton, Scott S; Agarwal, Pratul K

    2010-01-01

    Biomolecular simulations continue to become an increasingly important component of molecular biochemistry and biophysics investigations. Performance improvements in the simulations based on molecular dynamics (MD) codes are widely desired. This is particularly driven by the rapid growth of biological data due to improvements in experimental techniques. Unfortunately, the factors, which allowed past performance improvements of MD simulations, particularly the increase in microprocessor clock frequencies, are no longer improving. Hence, novel software and hardware solutions are being explored for accelerating the performance of popular MD codes. In this paper, we describe our efforts to port and optimize LAMMPS, a popular MD framework, on hybrid processors: graphical processing units (GPUs) accelerated multi-core processors. Our implementation is based on porting the computationally expensive, non-bonded interaction terms on the GPUs, and overlapping the computation on the CPU and GPUs. This functionality is built on top of message passing interface (MPI) that allows multi-level parallelism to be extracted even at the workstation level with the multi-core CPUs as well as extend the implementation on GPU clusters. The results from a number of typically sized biomolecular systems are provided and analysis is performed on 3 generations of GPUs from NVIDIA. Our implementation allows up to 30-40 ns/day throughput on a single workstation as well as significant speedup over Cray XT5, a high-end supercomputing platform. Moreover, detailed analysis of the implementation indicates that further code optimization and improvements in GPUs will allow {approx}100 ns/day throughput on workstations and inexpensive GPU clusters, putting the widely-desired microsecond simulation time-scale within reach to a large user community.

  6. Homogeneous melting of superheated crystals: Molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Forsblom, Mattias; Grimvall, Göran

    2005-08-01

    The homogeneous melting mechanism in a superheated fcc lattice is studied through molecular dynamics simulations, usually for about 20 000 atoms, with the Ercolessi and Adams interaction that represents aluminum. The periodic boundary conditions for the simulation cell suppress the usual surface-initiated melting at Tm=939K , and the solid-to-liquid transition takes place at the temperature Ts=1.3Tm . By logging the position of each atom at every time step in the simulation, we can follow the melting process in detail at the atomic level. Thermal fluctuations close to Ts create interstitial-vacancy pairs, which occasionally separate into mobile interstitials and almost immobile vacancies. There is an attraction between two interstitials, with a calculated maximum interaction energy of about 0.7eV . When three to four migrating interstitials have come close enough to form a bound aggregate of point defects, and a few thermally created interstitial-vacancy pairs have been added to the aggregate, such a defect configuration usually continues to grow irreversibly to the liquid state. For 20 000 atoms in the simulation cell, the growth process takes about 102τ to be completed, where τ is the period of a typical atomic vibration in the solid phase. This melting mechanism involves fewer atoms in its crucial initial phase than has been suggested in other melting models. The elastic shear moduli c44 and c'=(c11-c12)/2 were calculated as a function of temperature and were shown to be finite at the onset of melting.

  7. Recovering position-dependent diffusion from biased molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez

    2014-02-01

    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.

  8. 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.

  9. Thermodynamics of Writhe in DNA Minicircles from Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Mitchell, Jonathan S.; Harris, Sarah A.

    2013-04-01

    DNA supercoiling plays a role in genetic control by imposing torsional stress. This can induce writhe, which changes the global shape of the DNA. We have used atomistic molecular dynamics simulations to partition the free energy changes driving the writhing and unwrithing transitions in supercoiled minicircle DNA. The calculations show that while writhing is energetically driven, the unwrithing transition occurs because the circular state has a higher configurational entropy than the plectoneme. Writhing improves the van der Waals interactions between stacked bases, but can be suppressed by electrostatic repulsion within the negatively charged backbone strands in low salt conditions where electrostatic screening is poor. The free energy difference between circular and plectonemic DNA is determined by such a delicate balance of opposing thermodynamic terms that any perturbation in the environment, such as a change in salt concentration, can be sufficient to convert between these two states. This switchable behavior provides a mechanism for supercoiled DNA to store and communicate biological information physically as well as chemically.

  10. Molecular dynamics simulation investigations of atomic-scale wear

    NASA Astrophysics Data System (ADS)

    Shao, Yuchong; Falk, Michael

    2013-03-01

    Frictional running-in and material transfer in wear take place at the micro- and nano-scale but the fundamental physics remain poorly understood. Here we intend to investigate wear and running-in phenomena in silicon based materials, which are widely utilized in micro/nano electromechanical systems(MEMS/NEMS). We use an atomic force microscopy (AFM) model composed of a crystalline silicon tip and substrate coated with native oxide layers. Molecular dynamics simulation has been performed over a range of temperatures, external loads and slip rates. Results show that adhesive wear takes place across the interface in an atom-by-atom fashion which remodels the tip leading to a final steady state. We quantify the rate of material transfer as a function of the coverage of non-bridging oxygen (NBO) atoms, which has a pronounced change of the system's tribological and wear behaviors. A constitutive rate and state model is proposed to predict the evolution of frictional strength and wear. This work is supported by the National Science Foundation under Award No. 0926111.

  11. 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.

  12. Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Tao, Peng; Wu, Xiongwu; Brooks, Bernard R.

    2012-10-01

    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. 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. PMID:26574285

  14. 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.

  15. Molecular dynamics simulations of nanometric cutting mechanisms of amorphous alloy

    NASA Astrophysics Data System (ADS)

    Zhu, Peng-Zhe; Qiu, Chen; Fang, Feng-Zhou; Yuan, Dan-Dan; Shen, Xue-Cen

    2014-10-01

    Molecular dynamics simulations are employed to study the nanometric cutting process of Cu50Zr50 amorphous alloy. The effects of cutting depth, cutting speed and tool edge radius on the cutting force, workpiece pile-up and temperature of the cutting region are studied to investigate the mechanisms of the material removal and surface formation in the nanometric cutting process. It is found that the material removal of amorphous alloy workpiece is mainly based on extrusion at the nanoscale instead of shearing at the macroscale. The plastic deformation of amorphous alloy is mainly due to the formation of shear transformation zones during the nanometric cutting process. The results also suggest that bigger cutting depth and cutting speed will lead to larger tangential force and normal force. However, the tool edge radius has a negligible effect on the tangential force although the normal force increases with the increase of tool edge radius. The workpiece pile-up increases with an increase of the cutting depth, but decreases with an increase of the edge radius of the tool. The workpiece pile-up is not significantly affected by the cutting speed. It is also found that larger cutting depth and cutting speed will result in higher temperature in the cutting region of workpiece and the average Newtonian layer temperature of the tool. Tool edge radius has no significant effect on the temperature distribution of the workpiece and the average Newtonian layer temperature of the tool.

  16. Molecular-dynamics simulation of hydrogen diffusion in palladium

    NASA Astrophysics Data System (ADS)

    Li, Yinggang; Wahnström, Göran

    1992-12-01

    Molecular-dynamics simulations for hydrogen diffusion in Pd are performed for a system consisting of 256 Pd atoms and 8 H atoms at the temperature T=623 K. Under these conditions detailed quasielastic-neutron-scattering (QNS) data are available. For the interatomic interactions we use the embedded-atom method (EAM), which incorporates some essential many-body effects in metals. Based on the EAM approach, the wave-vector dependence of the width of the QNS peak is investigated in detail. It is found that a single electronically adiabatic potential-energy surface cannot reproduce the observed wave-vector dependence. After incorporating the coupling of hydrogen atoms to the low-lying electron-hole pair excitations among the conduction electrons, close agreement with the experimental data is obtained. This is a strong indication that one has to go beyond the Born-Oppenheimer approximation in order to characterize correctly the diffusive motion of hydrogen in metals. To reveal the diffusive behavior in more detail, the residence time distribution and the correlation character in diffusion direction are investigated. We found that including the nonadiabatic corrections reduces the probability for the H atoms to move over several lattice sites without getting trapped in between. As a result, the motion of the H atoms becomes more similar to that assumed in the Chudley-Elliott model, which describes well the QNS data for the wave-vector dependence of the width.

  17. Molecular Dynamics Simulations of Glycerol Monooleate Confined between Mica Surfaces.

    PubMed

    Bradley-Shaw, Joshua L; Camp, Philip J; Dowding, Peter J; Lewtas, Ken

    2016-08-01

    The structure and frictional properties of glycerol monooleate (GMO) in organic solvents, with and without water impurity, confined and sheared between two mica surfaces are examined using molecular dynamics simulations. The structure of the fluid is characterized in various ways, and the differences between systems with nonaggregated GMO and with preformed GMO reverse micelles are examined. Preformed reverse micelles are metastable under static conditions in all systems. In n-heptane under shear conditions, with or without water, preformed GMO reverse micelles remain intact and adsorb onto one surface or another, becoming surface micelles. In dry toluene, preformed reverse micelles break apart under shear, while in the presence of water, the reverse micelles survive and become surface micelles. In all systems under static and shear conditions, nonaggregated GMO adsorbs onto both surfaces with roughly equal probability. Added water is strongly associated with the GMO, irrespective of shear or the form of the added GMO. In all cases, with increasing shear rate, the GMO molecules flatten on the surface, and the kinetic friction coefficient increases. Under low-shear conditions, the friction is insensitive to the form of the GMO added, whereas the presence of water is found to lead to a small reduction in friction. Under high-shear conditions, the presence of reverse micelles leads to a significant reduction in friction, whereas the presence of water increases the friction in n-heptane and decreases the friction in toluene. PMID:27429247

  18. Molecular dynamics simulations of ring inversion in RDX

    NASA Astrophysics Data System (ADS)

    Wallis, Eric P.; Thompson, Donald L.

    1993-08-01

    Molecular dynamics simulations, using the finite volume method of Murrell and co-workers [J. Chem. Phys. 94, 3908 (1991)], have been carried out to study conformational changes in hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in isolation and in dense Xe gas. The configurational distributions for RDX in a Xe bath and in the gas-phase are markedly different. The results show that as the solvent concentration increases, the concentration of RDX molecules in the boat conformation increases by a factor of about 4. The rate constant for the chair→boat ring inversion was calculated as a function of the xenon concentration [Xe]. The rate constant obeys Lindemann behavior at low concentrations, i.e., it increases with increasing solvent density. At [Xe]˜6.2 mol dm-3, the rate constant reaches a maximum (Kramer's turnover) and becomes a decreasing function of the solvent concentration. For [Xe] above 16.2 mol dm-3, the rate constant again increases as a function of the solvent density.

  19. 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

  20. 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.

  1. 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.

  2. Atomistic Molecular Dynamics Simulations of the Electrical Double

    NASA Astrophysics Data System (ADS)

    Li, Zifeng; Milner, Scott; Fichthorn, Kristen

    2015-03-01

    The electrical double layer (EDL) near the polymer/water interface plays a key role in the colloidal stability of latex paint. To elucidate the structure of the EDL at the molecular level, we conducted an all-atom molecular dynamics simulations. We studied two representative surface charge groups in latex, the ionic surfactant sodium dodecyl sulfate (SDS) and the grafted short polyelectrolyte charged by dissociated methyl methacrylic acid (MAA) monomers. Our results confirm that the Poisson-Boltzmann theory works well outside the Stern layer. Our calculated electrostatic potential at the Outer Helmholtz Plane (OHP) is close to the zeta potential measured experimentally, which suggests that the potential at the OHP is a good estimate of the zeta potential. We found that the position of the OHP for the MAA polyelectrolyte system extends much further into the aqueous phase than that in the SDS system, resulting in a Stern layer that is twice as thick. This model will allow for future investigations of the interactions of the surface with different surfactants and rheology modifiers, which may serve as a guide to tune the rheology of latex formulations. We thank Dow Chemical Company for financial support.

  3. 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

    2014-11-01

    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. PMID:25244002

  4. Molecular dynamics simulation of VN thin films under indentation

    NASA Astrophysics Data System (ADS)

    Fu, Tao; Peng, Xianghe; Huang, Cheng; Yin, Deqiang; Li, Qibin; Wang, Zhongchang

    2015-12-01

    We investigated with molecular dynamics simulation the mechanical responses of VN (0 0 1) thin films subjected to indentation with a diamond columnar indenter. We calculated the generalized stacking-fault energies as a function of the displacement in the rbond2 1 1 0lbond2 directions on the {0 0 1}, {1 1 0}, and {1 1 1} planes, and analyzed systematically the microstructures and their evolution during the indentation with the centro-symmetry parameters and the slices of the VN films. We found the slips on {1 1 0}rbond2 1 1 0lbond2 of the VN film under indentation at the initial stage. With the increase of indentation depth, slips are also activated on {1 1 1}rbond2 1 1 0lbond2 and {1 0 0}rbond2 0 1 1lbond2 systems. We further found that the slip system is determined by the stacking-fault energy rather than the layer spacing. The indentations with other different parameters were also performed, and the results further prove the validity of the conclusion.

  5. 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. PMID:25704286

  6. 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.

  7. 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. PMID:24588150

  8. Molecular dynamics simulation of paracetamol molecules ordering around glycogen

    NASA Astrophysics Data System (ADS)

    Lim, Wilber; Feng, Yuan Ping; Liu, X. Y.

    2005-05-01

    By the use of classical atomistic molecular dynamics simulations, we demonstrate that paracetamol molecules exist in a highly ordered phase in the presence of a glycogen substrate at 317K whereas the paracetamol fluid exists in an isotropic phase in the absence of the glycogen substrate at the same temperature. This result further validates the studies made on polysaccharide regarding its abilities to promote nucleation of paracetamol via liquid preordering. As little is known regarding liquid ordering induced by a polymeric substrate, we seek to explore the ordering mechanism from an energy perspective. This is accomplished using conformation mappings. Our analysis shows that the conformation space accessible to the paracetamol molecule at 317K in the vicinity of glycogen is smaller than the one in the absence of glycogen. An investigation on the orientation of the dipole moments of the glycogen monomers and paracetamol molecules were carried out as well. From the investigations, we show that dipolar interactions play an important role in the ordering process. These studies bear significance to the understanding of the ordering process as well as the promotion and effective control of the nucleation rate.

  9. Molecular Dynamics Simulations of the Photoactive Protein Nitrile Hydratase

    PubMed Central

    Kubiak, Karina; Nowak, Wieslaw

    2008-01-01

    Nitrile hydratase (NHase) is an enzyme used in the industrial biotechnological production of acrylamide. The active site, which contains nonheme iron or noncorrin cobalt, is buried in the protein core at the interface of two domains, α and β. Hydrogen bonds between βArg-56 and αCys-114 sulfenic acid (αCEA114) are important to maintain the enzymatic activity. The enzyme may be inactivated by endogenous nitric oxide (NO) and activated by absorption of photons of wavelength λ < 630 nm. To explain the photosensitivity and to propose structural determinants of catalytic activity, differences in the dynamics of light-active and dark-inactive forms of NHase were investigated using molecular dynamics (MD) modeling. To this end, a new set of force field parameters for nonstandard NHase active sites have been developed. The dynamics of the photodissociated NO ligand in the enzyme channel was analyzed using the locally enhanced sampling method, as implemented in the MOIL MD package. A series of 1 ns trajectories of NHases shows that the protonation state of the active site affects the dynamics of the catalytic water and NO ligand close to the metal center. MD simulations support the catalytic mechanism in which a water molecule bound to the metal ion directly attacks the nitrile carbon. PMID:18234830

  10. Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers

    PubMed Central

    Leontiadou, Hari; Mark, Alan E.; Marrink, Siewert J.

    2004-01-01

    Hydrophilic pores are formed in peptide free lipid bilayers under mechanical stress. It has been proposed that the transport of ionic species across such membranes is largely determined by the existence of such meta-stable hydrophilic pores. To study the properties of these structures and understand the mechanism by which pore expansion leads to membrane rupture, a series of molecular dynamics simulations of a dipalmitoylphosphatidylcholine (DPPC) bilayer have been conducted. The system was simulated in two different states; first, as a bilayer containing a meta-stable pore and second, as an equilibrated bilayer without a pore. Surface tension in both cases was applied to study the formation and stability of hydrophilic pores inside the bilayers. It is observed that below a critical threshold tension of ∼38 mN/m the pores are stabilized. The minimum radius at which a pore can be stabilized is 0.7 nm. Based on the critical threshold tension the line tension of the bilayer was estimated to be ∼3 × 10−11 N, in good agreement with experimental measurements. The flux of water molecules through these stabilized pores was analyzed, and the structure and size of the pores characterized. When the lateral pressure exceeds the threshold tension, the pores become unstable and start to expand causing the rupture of the membrane. In the simulations the mechanical threshold tension necessary to cause rupture of the membrane on a nanosecond timescale is much higher in the case of the equilibrated bilayers, as compared with membranes containing preexisting pores. PMID:15041656

  11. 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.

  12. Nucleation Rate Analysis of Methane Hydrate from Molecular Dynamics Simulations

    DOE PAGESBeta

    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)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

  13. 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.

  14. Molecular dynamics simulations of solvated yeast tRNA(Asp).

    PubMed Central

    Auffinger, P; Louise-May, S; Westhof, E

    1999-01-01

    Transfer RNA molecules are involved in a variety of biological processes, implying complex recognition events with proteins and other RNAs. From a structural point of view, tRNAs constitute a reference system for studying RNA folding and architecture. A deeper understanding of their structural and functional properties will derive from our ability to model accurately their dynamical behavior. We present the first dynamical model of a fully neutralized and solvated tRNA molecule over a 500-ps time scale. Starting from the crystallographic structure of yeast tRNA(Asp), the 75-nucleotide molecule was modeled with 8055 water molecules and 74 NH4+ counterions, using the AMBER4.1 program and the particle mesh Ewald (PME) method for the treatment of long-range electrostatic interactions. The calculations led to a dynamically stable model of the tRNA molecule. During the simulation, all secondary and tertiary base pairs are maintained while a certain lability of base triples in the tRNA core is observed. This lability was interpreted as resulting from intrinsic factors associated with the "weaker" hydrogen bonding patterns seen in these base triples and from an altered ionic environment of the tRNA molecule. Calculated thermal factors are used to compare the dynamics of the tRNA in solution and in the crystal. The present molecular dynamics simulation of a complex and highly charged nucleic acid molecule attests to the fact that simulation methods are now able to investigate not only the dynamics of proteins, but also that of large RNA molecules. Thus they also provide a basis for further investigations on the structural and functional effects of chemical and posttranscriptionally modified nucleotides as well as on ionic environmental effects. PMID:9876122

  15. 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.

  16. 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. PMID:26871185

  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. Study of glass transition temperature (Tg) of novel stress-sensitive composites using molecular dynamic simulation

    NASA Astrophysics Data System (ADS)

    Koo, B.; Liu, Y.; Zou, J.; Chattopadhyay, A.; Dai, L. L.

    2014-09-01

    This study investigates the glass transition temperature (Tg) of novel stress-sensitive composites capable of detecting a damage precursor using molecular dynamics (MD) simulations. The molecular structures of a cross-linked epoxy network (which consist of epoxy resin, hardener and stress-sensitive material) have been simulated and experimentally validated. The chemical constituents of the molecular structures are di-glycidyl ether of bisphenol F (DGEBF: epoxy resin), di-ethylene tri-amine (DETA: hardener) and tris-(cinnamoyloxymethyl)-ethane (TCE: stress-sensitive material). The cross-linking degree is varied by manipulating the number of covalent bonds through tuning a cutoff distance between activated DGEBF and DETA during the non-equilibrium MD simulation. A relationship between the cross-linking degree and Tgs has been studied numerically. In order to validate a proposed MD simulation framework, MD-predicted Tgs of materials used in this study have been compared to the experimental results obtained by the differential scanning calorimetry (DSC). Two molecular models have been constructed for comparative study: (i) neat epoxy (epoxy resin with hardener) and (ii) smart polymer (neat epoxy with stress-sensitive material). The predicted Tgs show close agreement with the DSC results.

  19. Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1

    PubMed Central

    Park, Min-Sun

    2015-01-01

    Glucose transporters (GLUTs) provide a pathway for glucose transport across membranes. Human GLUTs are implicated in devastating diseases such as heart disease, hyper- and hypo-glycemia, type 2 diabetes and caner. The human GLUT1 has been recently crystalized in the inward-facing open conformation. However, there is no other structural information for other conformations. The X-ray structures of E. coli Xylose permease (XylE), a glucose transporter homolog, are available in multiple conformations with and without the substrates D-xylose and D-glucose. XylE has high sequence homology to human GLUT1 and key residues in the sugar-binding pocket are conserved. Here we construct a homology model for human GLUT1 based on the available XylE crystal structure in the partially occluded outward-facing conformation. A long unbiased all atom molecular dynamics simulation starting from the model can capture a new fully opened outward-facing conformation. Our investigation of molecular interactions at the interface between the transmembrane (TM) domains and the intracellular helices (ICH) domain in the outward- and inward-facing conformation supports that the ICH domain likely stabilizes the outward-facing conformation in GLUT1. Furthermore, inducing a conformational transition, our simulations manifest a global asymmetric rocker switch motion and detailed molecular interactions between the substrate and residues through the water-filled selective pore along a pathway from the extracellular to the intracellular side. The results presented here are consistent with previously published biochemical, mutagenesis and functional studies. Together, this study shed light on the structure and functional relationships of GLUT1 in multiple conformational states. PMID:25919356

  20. Understanding Miltefosine-Membrane Interactions Using Molecular Dynamics Simulations.

    PubMed

    de Sá, Matheus Malta; Sresht, Vishnu; Rangel-Yagui, Carlota Oliveira; Blankschtein, Daniel

    2015-04-21

    Coarse-grained molecular dynamics simulations are used to calculate the free energies of transfer of miltefosine, an alkylphosphocholine anticancer agent, from water to lipid bilayers to study its mechanism of interaction with biological membranes. We consider bilayers containing lipids with different degrees of unsaturation: dipalmitoylphosphatidylcholine (DPPC, saturated, containing 0%, 10%, and 30% cholesterol), dioleoylphosphatidylcholine (DOPC, diunsaturated), palmitoyloleoylphosphatidylcholine (POPC, monounsaturated), diarachidonoylphosphatidylcholine (DAPC, polyunsaturated), and dilinoleylphosphatidylcholine (DUPC, polyunsaturated). These free energies, calculated using umbrella sampling, were used to compute the partition coefficients (K) of miltefosine between water and the lipid bilayers. The K values for the bilayers relative to that of pure DPPC were found to be 5.3 (DOPC), 7.0 (POPC), 1.0 (DAPC), 2.2 (DUPC), 14.9 (10% cholesterol), and 76.2 (30% cholesterol). Additionally, we calculated the free energy of formation of miltefosine-cholesterol complexes by pulling the surfactant laterally in the DPPC + 30% cholesterol system. The free energy profile that we obtained provides further evidence that miltefosine tends to associate with cholesterol and has a propensity to partition into lipid rafts. We also quantified the kinetics of the transport of miltefosine through the various bilayers by computing permeance values. The highest permeance was observed in DUPC bilayers (2.28 × 10(-2) m/s) and the lowest permeance in the DPPC bilayer with 30% cholesterol (1.10 × 10(-7) m/s). Our simulation results show that miltefosine does indeed interact with lipid rafts, has a higher permeability in polyunsaturated, loosely organized bilayers, and has higher flip-flop rates in specific regions of cellular membranes. PMID:25819781

  1. Metascalable molecular dynamics simulation of nano-mechano-chemistry

    NASA Astrophysics Data System (ADS)

    Shimojo, F.; Kalia, R. K.; Nakano, A.; Nomura, K.; Vashishta, P.

    2008-07-01

    We have developed a metascalable (or 'design once, scale on new architectures') parallel application-development framework for first-principles based simulations of nano-mechano-chemical processes on emerging petaflops architectures based on spatiotemporal data locality principles. The framework consists of (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms, (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these scalable algorithms onto hardware. The EDC-STEP-HCD framework exposes and expresses maximal concurrency and data locality, thereby achieving parallel efficiency as high as 0.99 for 1.59-billion-atom reactive force field molecular dynamics (MD) and 17.7-million-atom (1.56 trillion electronic degrees of freedom) quantum mechanical (QM) MD in the framework of the density functional theory (DFT) on adaptive multigrids, in addition to 201-billion-atom nonreactive MD, on 196 608 IBM BlueGene/L processors. We have also used the framework for automated execution of adaptive hybrid DFT/MD simulation on a grid of six supercomputers in the US and Japan, in which the number of processors changed dynamically on demand and tasks were migrated according to unexpected faults. The paper presents the application of the framework to the study of nanoenergetic materials: (1) combustion of an Al/Fe2O3 thermite and (2) shock initiation and reactive nanojets at a void in an energetic crystal.

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

    PubMed

    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 R_{NP}≅3nm while droplets have initial R_{0}≅42nm. 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 θ_{adv}, self-pinning on entrained NPs occurs; for higher θ_{adv}, 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. PMID:27575186

  3. 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)].

  4. Thermal boundary resistance at Si/Ge interfaces by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Zhan, Tianzhuo; Minamoto, Satoshi; Xu, Yibin; Tanaka, Yoshihisa; Kagawa, Yutaka

    2015-04-01

    In this study, we investigated the temperature dependence and size effect of the thermal boundary resistance at Si/Ge interfaces by non-equilibrium molecular dynamics (MD) simulations using the direct method with the Stillinger-Weber potential. The simulations were performed at four temperatures for two simulation cells of different sizes. The resulting thermal boundary resistance decreased with increasing temperature. The thermal boundary resistance was smaller for the large cell than for the small cell. Furthermore, the MD-predicted values were lower than the diffusion mismatch model (DMM)-predicted values. The phonon density of states (DOS) was calculated for all the cases to examine the underlying nature of the temperature dependence and size effect of thermal boundary resistance. We found that the phonon DOS was modified in the interface regions. The phonon DOS better matched between Si and Ge in the interface region than in the bulk region. Furthermore, in interface Si, the population of low-frequency phonons was found to increase with increasing temperature and cell size. We suggest that the increasing population of low-frequency phonons increased the phonon transmission coefficient at the interface, leading to the temperature dependence and size effect on thermal boundary resistance.

  5. Molecular dynamics simulations of oscillatory Couette flows with slip boundary conditions

    NASA Astrophysics Data System (ADS)

    Priezjev, Nikolai

    2012-11-01

    The effect of interfacial slip on steady-state and time-periodic flows of monatomic liquids is investigated using non-equilibrium molecular dynamics simulations. The simulations were performed in a wide range of oscillation frequencies; namely, when the Stokes boundary layer thickness is smaller than the channel width at the highest frequency, and, on the other hand, at lower frequencies that correspond to quasi-steady flows. It was found that the velocity profiles computed in MD simulations are well described by the continuum solution with the slip length as a fitting parameter that depends on the local shear rate. Interestingly, the shear rate dependence of the slip length obtained in steady-state shear flows is reproduced in oscillatory flows when the slip length is measured as a function of the absolute value of the local shear rate. Finally, for both types of flows, the friction coefficient at the liquid-solid interface correlates well with the structure factor and the contact density of the first fluid layer. Financial support from the National Science Foundation (CBET-1033662) is gratefully acknowledged.

  6. Amorphous silicene-a view from molecular dynamics simulation.

    PubMed

    Van Hoang, Vo; Long, N T

    2016-05-18

    Models of amorphous silicene (a-silicene) containing 10(4) 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 ([Formula: see text] 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 [Formula: see text] direction with the elastic reflection behavior boundary, our models are relevant for a-silicene formed in confinement between two planar simple hard walls. PMID:27071353

  7. Modeling of hydrophilic wafer bonding by molecular dynamics simulations

    SciTech Connect

    Litton, David A.; Garofalini, Stephen H.

    2001-06-01

    The role of moisture in hydrophilic wafer bonding was modeled using molecular dynamics computer simulations of interface formation between amorphous silica surfaces. Three different surface treatments were used in order to determine the effect of moisture on the formation of siloxane (Si{endash}O{endash}Si) bridges across the interface at two temperatures. The three surface conditions that were studied were: (a) wet interfaces containing 1 monolayer of water adsorbed at the interface (based on the room temperature bulk density of water), (b) hydroxylated interfaces with concentrations of 3{endash}5 silanols/nm2 on each surface and no excess water molecules initially in the system, and (c) pristine interfaces that had only Si and O and no water or H present. The surfaces were slowly brought together and siloxane bond formation was monitored. In the pristine interfaces, siloxane bridges formed across the interface by the coalescence of various defect species in each surface. A bimodal distribution of siloxane bond angles formed during the first 2.5 Aa of approach after the first siloxane bond was formed. These bond angles were much lower than and higher than the bulk average, indicating the formation of less stable bonds. The hydroxylated (with no excess water) and wet surfaces showed a more uniform distribution of siloxane bond angles, with no highly reactive small bond angles forming. The presence of water molecules enhanced H-bond formation across the interface, but trapped water molecules inhibited formation of the strong siloxane bridges across the interface. In real systems, high temperatures are required to remove this trapped moisture. {copyright} 2001 American Institute of Physics.

  8. 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

  9. Analyzing machupo virus-receptor binding by molecular dynamics simulations.

    PubMed

    Meyer, Austin G; Sawyer, Sara L; Ellington, Andrew D; Wilke, Claus O

    2014-01-01

    In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein-protein interactions. However, many commonly used methods to predict these effects perform poorly in important test cases. In particular, the effects of multiple mutations, non alanine substitutions, and flexible loops are difficult to predict with available tools and protocols. We present here an existing method applied in a novel way to a new test case; we interrogate affinity differences resulting from mutations in a host-virus protein-protein interface. We use steered molecular dynamics (SMD) to computationally pull the machupo virus (MACV) spike glycoprotein (GP1) away from the human transferrin receptor (hTfR1). We then approximate affinity using the maximum applied force of separation and the area under the force-versus-distance curve. We find, even without the rigor and planning required for free energy calculations, that these quantities can provide novel biophysical insight into the GP1/hTfR1 interaction. First, with no prior knowledge of the system we can differentiate among wild type and mutant complexes. Moreover, we show that this simple SMD scheme correlates well with relative free energy differences computed via free energy perturbation. Second, although the static co-crystal structure shows two large hydrogen-bonding networks in the GP1/hTfR1 interface, our simulations indicate that one of them may not be important for tight binding. Third, one viral site known to be critical for infection may mark an important evolutionary suppressor site for infection-resistant hTfR1 mutants. Finally, our approach provides a framework to compare the effects of multiple mutations, individually and jointly, on protein-protein interactions. PMID:24624315

  10. 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.

  11. 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.

  12. 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.

  13. Replica exchange molecular dynamics simulations of amyloid peptide aggregation

    NASA Astrophysics Data System (ADS)

    Cecchini, M.; Rao, F.; Seeber, M.; Caflisch, A.

    2004-12-01

    The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the β-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides.

  14. Nonequilibrium versus equilibrium molecular dynamics studies of solvation dynamics after photoexcitation of OClO

    NASA Astrophysics Data System (ADS)

    Gunnerson, Kim N.; Brooksby, Craig; Prezhdo, Oleg V.; Reid, Philip J.

    2007-10-01

    The results of our earlier work [C. Brooksby, O. V. Prezhdo, and P. J. Reid, J. Chem. Phys. 119, 9111 (2003)] rationalizing the surprisingly weak solvent dependence of the dynamics following photoexcitation of chlorine dioxide in water, chloroform, and cyclohexane are thoroughly tested. Comparisons are made between equilibrium and nonequilibrium solvent response, equilibrium response in the ground and excited electronic states, as well as the cumulant and direct evaluation of the optical response function. In general, the linear response and cumulant approximations are found to hold, although minor deviations are found with all solvents. The ground state, linear response, and cumulant data show best agreement with experiment, most likely due to the better tested ground-state force field and the robust behavior of the linear response and cumulant approximations. The main conclusion of our earlier work explaining the weak solvent dependence by the domination of the van der Waals interaction component remains intact within the more advanced treatments. However, the molecular origin of this surprising experimental observation is different in water and chloroform compared to cyclohexane.

  15. Molecular dynamics simulation studies of liquid crystalline materials

    NASA Astrophysics Data System (ADS)

    Tian, Pu

    Molecular dynamics (MD) simulation studies of the phase behavior, the response to an applied field of nematic liquid crystalline (LC) materials and interactions of nanoparticles in isotropic mesogenic materials are presented in this work. Molecular models used include the rigid bead-necklace model and soft spherocylinders. Free energy calculations applying thermodynamic integration and the Gibbs-Duhem integration method were used to establish the (T, P) phase diagram of the repulsive bead-necklace model, subsequently the Gibbs-Duhem integration method was further utilized to investigate the influence of attractive interactions on the phase behavior of the bead-necklace model. Analysis of order and thermodynamics of LC phase transitions (Isotropic-Nematic transition and Nematic-Smectic A transition) demonstrate that this simple model can capture the basic physics of liquid crystalline phases, and good agreement with experimental results is obtained. Further addition of chemical details to this multiple interaction sites model is much easier than to the idealized models (Gay-Berne, Spherocylinders) while the computation cost increase with respect to these idealized models is minimal. With a mean field representation of field-molecules interaction, MD simulation studies of the switching behavior of nematic LC, which is the basis of many LC devices, were performed. The switching mechanisms were explained in terms of the compromise between the elastic energy and field-molecules interactions. Qualitative agreement with experiments confirmed the validity of the mean field approximation. Finally, using the standard umbrella sampling technique and MD simulations, the potential of mean force between two nanoparticles in solvent of spherocylinders is calculated. It is found that while dispersed nanoparticles will delay the Isotropic-Nematics transition to higher density (lower temperature), they can induce local ordering fluctuations (within a few molecular lengths of the

  16. Reaction ensemble molecular dynamics: Direct simulation of the dynamic equilibrium properties of chemically reacting mixtures

    NASA Astrophysics Data System (ADS)

    Brennan, John K.; Lísal, Martin; Gubbins, Keith E.; Rice, Betsy M.

    2004-12-01

    A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is formulated upon the reaction ensemble Monte Carlo (RxMC) method, hence the term reaction ensemble molecular dynamics. Thermodynamic and transport properties are calculated in the dynamic cell by using a constant-temperature molecular dynamics simulation method. RxMC forward and reverse reaction steps are performed in the control cell only, while molecular dynamics steps are performed in both the dynamic cell and the control cell. The control cell, which acts as a sink and source reservoir, is maintained at reaction equilibrium conditions via the RxMC algorithm. The reaction ensemble molecular dynamics method is analogous to the grand canonical ensemble molecular dynamics technique, while using some elements of the osmotic molecular dynamics method, and so simulates conditions that directly relate to real, open systems. The accuracy and stability of the method is assessed by considering the ammonia synthesis reaction N2+3H2⇔2NH3 . It is shown to be a viable method for predicting the effects of nonideal environments on the dynamic properties (particularly diffusion) as well as reaction equilibria for chemically reacting mixtures.

  17. 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.

  18. 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)

  19. 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.

  20. Molecular dynamics simulation of electrokinetic flow of an aqueous electrolyte solution in nanochannels

    NASA Astrophysics Data System (ADS)

    Yoshida, Hiroaki; Mizuno, Hideyuki; Kinjo, Tomoyuki; Washizu, Hitoshi; Barrat, Jean-Louis

    2014-06-01

    Electrokinetic flows of an aqueous NaCl solution in nanochannels with negatively charged surfaces are studied using molecular dynamics simulations. The four transport coefficients that characterize the response to weak electric and pressure fields, namely, the coefficients for the electrical current in response to the electric field (Mjj) and the pressure field (Mjm), and those for the mass flow in response to the same fields (Mmj and Mmm), are obtained in the linear regime using a Green-Kubo approach. Nonequilibrium simulations with explicit external fields are also carried out, and the current and mass flows are directly obtained. The two methods exhibit good agreement even for large external field strengths, and Onsager's reciprocal relation (Mjm = Mmj) is numerically confirmed in both approaches. The influence of the surface charge density on the flow is also considered. The values of the transport coefficients are found to be smaller for larger surface charge density, because the counter-ions strongly bound near the channel surface interfere with the charge and mass flows. A reversal of the streaming current and of the reciprocal electro-osmotic flow, with a change of sign of Mmj due to the excess co-ions, takes places for very high surface charge density.

  1. Molecular dynamics simulation of electrokinetic flow of an aqueous electrolyte solution in nanochannels.

    PubMed

    Yoshida, Hiroaki; Mizuno, Hideyuki; Kinjo, Tomoyuki; Washizu, Hitoshi; Barrat, Jean-Louis

    2014-06-01

    Electrokinetic flows of an aqueous NaCl solution in nanochannels with negatively charged surfaces are studied using molecular dynamics simulations. The four transport coefficients that characterize the response to weak electric and pressure fields, namely, the coefficients for the electrical current in response to the electric field (M(jj)) and the pressure field (M(jm)), and those for the mass flow in response to the same fields (M(mj) and M(mm)), are obtained in the linear regime using a Green-Kubo approach. Nonequilibrium simulations with explicit external fields are also carried out, and the current and mass flows are directly obtained. The two methods exhibit good agreement even for large external field strengths, and Onsager's reciprocal relation (M(jm) = M(mj)) is numerically confirmed in both approaches. The influence of the surface charge density on the flow is also considered. The values of the transport coefficients are found to be smaller for larger surface charge density, because the counter-ions strongly bound near the channel surface interfere with the charge and mass flows. A reversal of the streaming current and of the reciprocal electro-osmotic flow, with a change of sign of M(mj) due to the excess co-ions, takes places for very high surface charge density. PMID:24908029

  2. Tight-Binding Molecular Dynamics Simulations of Shock-Compressed Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Kress, J. D.; Bickham, S. R.; Holian, B. L.; Collins, L. A.

    1999-06-01

    We have used tight-binding molecular dynamics to simulate shock waves in liquid hydocarbons. The equations of motion in supercells containing as many as 1024 methane and 576 benzene molecules (8192 and 17,280 valence electrons, respectively) are integrated using an O(N) electronic structure algorithm(S. Goedecker and L. Columbo, Phys. Rev. Lett. 73), 122 (1994); A.F. Voter, J.D. Kress and R.N. Silver, Phys. Rev. B 53, 12733 (1996) implemented on a massively parallel computer. In the non-equilibrium shock compression simulation, uniaxial contracting periodic boundary conditions were employed, with both ends of an elongated supercell moving inward at a constant (piston) velocity. The velocities of the shock waves created in this manner are compared to gas gun experimentsfootnote W. J. Nellis et al., J. Chem. Phys. 75, 3055 (1981). Analysis of the medium between the piston and shock front indicates that methane is decomposed into molecular hydrogen and carbon residue, while shocked benzene forms a mixture of hydrocarbons and molecular hydrogen. The dynamics of these chemical transformations will be discussed.

  3. Molecular dynamics simulation of shock-induced phase transition in Germanium

    NASA Astrophysics Data System (ADS)

    Lane, J. Matthew D.; Thompson, Aidan P.

    2009-06-01

    Results from shock-wave and ramp-wave uniaxial loading of Germanium will be presented. Germanium is known to transition from ambient cubic diamond (cd) phase to the high-pressure body-centered tetragonal (bct) or β-tin phase at pressures between 10 and 12 GPa. Large-scale molecular dynamics (MD) simulations were used to study the phase transition in single-crystal Germanium under uniaxial compression along several different crystal axes. We observed that the transition from the cd phase to the bct phase nucleates through shear banding and advances to relieve uniaxial strain. The macroscopic properties are compared with experimental results for both the Modified Embedded Atom Method (MEAM) and Tersoff potentials. Simulation techniques included standard non-equilibrium MD, as well as alternative computational methods, such as the Continuous Hugoniot Method and homogeneous uniaxial ramp methods. [4pt] This work is supported by the Laboratory Directed Research and Development program at Sandia National Laboratories. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  4. 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.

  5. 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. PMID:26641107

  6. Molecular dynamics simulation of shock induced ejection on fused silica surface

    SciTech Connect

    Su, Rui; Xiang, Meizhen; Jiang, Shengli; Chen, Jun; Wei, Han

    2014-05-21

    Shock response and surface ejection behaviors of fused silica are studied by using non-equilibrium molecular dynamics combining with the Tersoff potential. First, bulk structure and Hugoniot curves of fused silica are calculated and compared with experimental results. Then, the dynamical process of surface ejection behavior is simulated under different loading velocities ranging from 3.5 to 5.0 km∕s, corresponding to shock wave velocities from 7.1 to 8.8 km∕s. The local atomistic shear strain parameter is used to describe the local plastic deformation under conditions of shock compression or releasing. Our result shows that the shear strain is localized in the bottom area of groove under the shock compression. Surface ejection is observed when the loading velocity exceeds 4.0 km∕s. Meanwhile, the temperature of the micro-jet is ∼5574.7 K, which is close to experiment measurement. Several kinds of structural defects including non-bridging oxygen are found in the bulk area of the sample after ejection.

  7. Molecular dynamics simulations of thermal transport in porous nanotube network structures

    NASA Astrophysics Data System (ADS)

    Varshney, Vikas; Roy, Ajit K.; Froudakis, George; Farmer, Barry L.

    2011-09-01

    Carbon nanotube based 3D nanostructures have shown a lot of promise towards designing next generation of multi-functional systems, such as nano-electronic devices. Motivated by their recent successful experimental synthesis as well as characterization, and realizing that thermal dissipation is an important concern in proposed devices because of ever-increasing power density, we have investigated the phononic thermal transport behavior in 3D porous nanotube network structures using reverse non-equilibrium molecular dynamics simulations. Based on our study, the length scale associated with the distance between nanotube junctions emerges as the most dominating parameter that governs phonon scattering (hence the characteristic mean free path) and the heat flow in these nanostructures at molecular length scales. However, because of their spatial inhomogeneity, we show that the aerial density of carbon nanotubes (normal to heat flow) is also of critical importance in determining their system-level thermal conductivity. Based on our findings, we postulate that both parameters should be considered while designing nano-devices where thermal management is relevant.

  8. Molecular dynamics simulation overcoming the finite size effects of thermal conductivity of bulk silicon and silicon nanowires

    NASA Astrophysics Data System (ADS)

    Hou, Chaofeng; Xu, Ji; Ge, Wei; Li, Jinghai

    2016-05-01

    Nonequilibrium molecular dynamics simulation has been a powerful tool for studying the thermophysical properties of bulk silicon and silicon nanowires. Nevertheless, usually limited by the capacity and capability of computational resources, the traditional longitudinal and transverse simulation sizes are evidently restricted in a narrow range much less than the experimental scales, which seriously hinders the exploration of the thermal properties. In this research, based on a powerful and efficient molecular dynamics (MD) simulation method, the computation of thermal conductivity beyond the known Casimir size limits is realized. The longitudinal dimensions of the simulations significantly exceed the micrometer scale. More importantly, the lateral characteristic sizes are much larger than 10 nanometers, explicitly comparable with the silicon nanowires fabricated and measured experimentally, whereas the traditional simulation size is several nanometers. The powerful virtual experimental measurement provided in our simulations achieves the direct prediction of the thermal conductivity of bulk silicon and real-scale silicon nanowires, and delineates the complete longitudinal size dependence of their thermal conductivities, especially at the elusive mesoscopic scale. Furthermore, the presented measurement paves an exciting and promising way to explore in depth the thermophysical properties of other bulk covalent solids and their low-dimensional structures, such as nanowires and nanosheets.

  9. 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.

  10. An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Tsuchida, Eiji

    2016-08-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.

  11. Simulation of screw dislocation motion in iron by molecular dynamics simulations.

    PubMed

    Domain, Christophe; Monnet, Ghiath

    2005-11-18

    Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine the activation energy of the double kink mechanism from MD simulations. It is shown that the differences between experimental and simulation conditions lead to a significant difference in activation energy. These differences are explained, and the method developed provides the link between MD and mesoscopic simulations. PMID:16384158

  12. Molecular dynamics simulation of surface segregation, diffusion and reaction phenomena in equiatomic Ni-Al systems

    NASA Astrophysics Data System (ADS)

    Evteev, A. V.; Levchenko, E. V.; Belova, I. V.; Murch, G. E.

    2012-12-01

    The molecular dynamics method is used to provide fundamental insights into surface segregation, bulk diffusion and alloying reaction phenomena in equiatomic Ni-Al systems. This knowledge can serve as a guide for the search and development of economic routes for controlling microstructure and properties of the intermetallic compound NiAl. This paper gives an overview of recent molecular dynamics simulations in the area along with other theoretical calculations and experimental measurements.

  13. 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

  14. Semi-grand canonical molecular dynamics simulation of bovine pancreatic trypsin inhibitor

    NASA Astrophysics Data System (ADS)

    Lynch, Gillian C.; Pettitt, B. Montgomery

    2000-08-01

    In the quest to understand both the structural and thermodynamic facets of biomolecular-solvent systems semi-grand canonical ensemble molecular dynamics simulations of a protein in solution are performed. In these simulations only the water molecules in the system are allowed to fluctuate; the final number of water molecules is determined by the chemical potential. An unbiased sampling technique is used for the insertion/deletion procedure of the water molecules thereby providing a benchmark grand ensemble simulation of the hydration structure of proteins. Three different chemical potential simulations were carried out offering a direct route to thermodynamic information from a molecular dynamics simulation.

  15. Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method.

    PubMed

    Cheluvaraja, Srinath; Meirovitch, Hagai

    2006-07-14

    Hypothetical scanning (HS) is a method for calculating the absolute entropy S and free energy F from a sample generated by any simulation technique. With this approach each sample configuration is reconstructed with the help of transition probabilities (TPs) and their product leads to the configuration's probability, hence to the entropy. Recently a new way for calculating the TPs by Monte Carlo (MC) simulations has been suggested, where all system interactions are taken into account. Therefore, this method--called HSMC--is in principle exact where the only approximation is due to insufficient sampling. HSMC has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks on a lattice, and peptides. Because molecular dynamics (MD) is considered to be significantly more efficient than MC for a compact polymer chain, in this paper HSMC is extended to MD simulations as applied to peptides. Like before, we study decaglycine in vacuum but for the first time also a peptide with side chains, (Val)(2)(Gly)(6)(Val)(2). The transition from MC to MD requires implementing essential changes in the reconstruction process of HSMD. Results are calculated for three microstates, helix, extended, and hairpin. HSMD leads to very stable differences in entropy TDeltaS between these microstates with small errors of 0.1-0.2 kcal/mol (T=100 K) for a wide range of calculation parameters with extremely high efficiency. Various aspects of HSMD and plans for future work are discussed. PMID:16848609

  16. 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.

  17. 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.

  18. Virtual reality visualization of parallel molecular dynamics simulation

    SciTech Connect

    Disz, T.; Papka, M.; Stevens, R.; Pellegrino, M.; Taylor, V.

    1995-12-31

    When performing communications mapping experiments for massively parallel processors, it is important to be able to visualize the mappings and resulting communications. In a molecular dynamics model, visualization of the atom to atom interaction and the processor mappings provides insight into the effectiveness of the communications algorithms. The basic quantities available for visualization in a model of this type are the number of molecules per unit volume, the mass, and velocity of each molecule. The computational information available for visualization is the atom to atom interaction within each time step, the atom to processor mapping, and the energy resealing events. We use the CAVE (CAVE Automatic Virtual Environment) to provide interactive, immersive visualization experiences.

  19. 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.

  20. 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. PMID:27078486

  1. Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane.

    PubMed Central

    Bernèche, S; Nina, M; Roux, B

    1998-01-01

    Molecular dynamics trajectories of melittin in an explicit dimyristoyl phosphatidylcholine (DMPC) bilayer are generated to study the details of lipid-protein interactions at the microscopic level. Melittin, a small amphipathic peptide found in bee venom, is known to have a pronounced effect on the lysis of membranes. The peptide is initially set parallel to the membrane-solution interfacial region in an alpha-helical conformation with unprotonated N-terminus. Solid-state nuclear magnetic resonance (NMR) and polarized attenuated total internal reflectance Fourier transform infrared (PATIR-FTIR) properties of melittin are calculated from the trajectory to characterize the orientation of the peptide relative to the bilayer. The residue Lys7 located in the hydrophobic moiety of the helix and residues Lys23, Arg24, Gln25, and Gln26 at the C-terminus hydrophilic form hydrogen bonds with water molecules and with the ester carbonyl groups of the lipids, suggesting their important contribution to the stability of the helix in the bilayer. Lipid acyl chains are closely packed around melittin, contributing to the stable association with the membrane. Calculated density profiles and order parameters of the lipid acyl chains averaged over the molecular dynamics trajectory indicate that melittin has effects on both layers of the membrane. The presence of melittin in the upper layer causes a local thinning of the bilayer that favors the penetration of water through the lower layer. The energetic factors involved in the association of melittin at the membrane surface are characterized using an implicit mean-field model in which the membrane and the surrounding solvent are represented as structureless continuum dielectric material. The results obtained by solving the Poisson-Bolztmann equation numerically are in qualitative agreement with the detailed dynamics. The influence of the protonation state of the N-terminus of melittin is examined. After 600 ps, the N-terminus of melittin

  2. The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations.

    PubMed

    Borštnik, Urban; Miller, Benjamin T; Brooks, Bernard R; Janežič, Dušanka

    2011-11-15

    Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used. PMID:21793007

  3. The temperature dependence of the heat conductivity of a liquid crystal studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Sarman, Sten; Laaksonen, Aatto

    2010-01-01

    The temperature dependence of the heat conductivity has been obtained for a liquid crystal model based on the Gay-Berne fluid, from the isotropic phase at high temperatures through the nematic phase to the smectic A phase at low temperatures. The ratio of the parallel and the perpendicular components of the heat conductivity is about 2.5:1 in the nematic phase, which is similar to that of real systems. Both Green-Kubo methods and nonequilibrium molecular dynamics methods have been applied and the results agree within in a relative error of a couple of percent, but the latter method is much more efficient.

  4. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    SciTech Connect

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D. Kühn, Oliver

    2015-06-28

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  5. Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

    PubMed Central

    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. PMID:26539292

  6. Hypercrosslinked polystyrene networks: An atomistic molecular dynamics simulation combined with a mapping/reverse mapping procedure

    SciTech Connect

    Lazutin, A. A.; Glagolev, M. K.; Vasilevskaya, V. V.; Khokhlov, A. R.

    2014-04-07

    An algorithm involving classical molecular dynamics simulations with mapping and reverse mapping procedure is here suggested to simulate the crosslinking of the polystyrene dissolved in dichloroethane by monochlorodimethyl ether. The algorithm comprises consecutive stages: molecular dynamics atomistic simulation of a polystyrene solution, the mapping of atomistic structure onto coarse-grained model, the crosslink formation, the reverse mapping, and finally relaxation of the structure dissolved in dichloroethane and in dry state. The calculated values of the specific volume and the elastic modulus are in reasonable quantitative correspondence with experimental data.

  7. Thermal Conductivity of Single-Walled Carbon Nanotube with Internal Heat Source Studied by Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Li, Yuan-Wei; Cao, Bing-Yang

    2013-12-01

    The thermal conductivity of (5, 5) single-walled carbon nanotubes (SWNTs) with an internal heat source is investigated by using nonequilibrium molecular dynamics (NEMD) simulation incorporating uniform heat source and heat source-and-sink schemes. Compared with SWNTs without an internal heat source, i.e., by a fixed-temperature difference scheme, the thermal conductivity of SWNTs with an internal heat source is much lower, by as much as half in some cases, though it still increases with an increase of the tube length. Based on the theory of phonon dynamics, a function called the phonon free path distribution is defined to develop a simple one-dimensional heat conduction model considering an internal heat source, which can explain diffusive-ballistic heat transport in carbon nanotubes well.

  8. Surface 3D nanostructuring by tightly focused laser pulse: simulations by Lagrangian code and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Inogamov, Nail A.; Zhakhovsky, Vasily V.

    2016-02-01

    There are many important applications in which the ultrashort diffraction-limited and therefore tightly focused laser pulses irradiates metal films mounted on dielectric substrate. Here we present the detailed picture of laser peeling and 3D structure formation of the thin (relative to a depth of a heat affected zone in the bulk targets) gold films on glass substrate. The underlying physics of such diffraction-limited laser peeling was not well understood previously. Our approach is based on a physical model which takes into consideration the new calculations of the two-temperature (2T) equation of state (2T EoS) and the two-temperature transport coefficients together with the coupling parameter between electron and ion subsystems. The usage of the 2T EoS and the kinetic coefficients is required because absorption of an ultrashort pulse with duration of 10-1000 fs excites electron subsystem of metal and transfers substance into the 2T state with hot electrons (typical electron temperatures 1-3 eV) and much colder ions. It is shown that formation of submicrometer-sized 3D structures is a result of the electron-ion energy transfer, melting, and delamination of film from substrate under combined action of electron and ion pressures, capillary deceleration of the delaminated liquid metal or semiconductor, and ultrafast freezing of molten material. We found that the freezing is going in non-equilibrium regime with strongly overcooled liquid phase. In this case the Stefan approximation is non-applicable because the solidification front speed is limited by the diffusion rate of atoms in the molten material. To solve the problem we have developed the 2T Lagrangian code including all this reach physics in. We also used the high-performance combined Monte- Carlo and molecular dynamics code for simulation of surface 3D nanostructuring at later times after completion of electron-ion relaxation.

  9. Determination of the crystal-melt interface kinetic coefficient from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Monk, J.; Yang, Y.; Mendelev, M. I.; Asta, M.; Hoyt, J. J.; Sun, D. Y.

    2010-01-01

    The generation and dissipation of latent heat at the moving solid-liquid boundary during non-equilibrium molecular dynamics (MD) simulations of crystallization can lead to significant underestimations of the interface mobility. In this work we examine the heat flow problem in detail for an embedded atom description of pure Ni and offer strategies to obtain an accurate value of the kinetic coefficient, μ. For free-solidification simulations in which the entire system is thermostated using a Nose-Hoover or velocity rescaling algorithm a non-uniform temperature profile is observed and a peak in the temperature is found at the interface position. It is shown that if the actual interface temperature, rather than the thermostat set point temperature, is used to compute the kinetic coefficient then μ is approximately a factor of 2 larger than previous estimates. In addition, we introduce a layered thermostat method in which several sub-regions, aligned normal to the crystallization direction, are indepently thermostated to a desired undercooling. We show that as the number of thermostats increases (i.e., as the width of each independently thermostated layer decreases) the kinetic coefficient converges to a value consistent with that obtained using a single thermostat and the calculated interface temperature. Also, the kinetic coefficient was determined from an analysis of the equilibrium fluctuations of the solid-liquid interface position. We demonstrate that the kinetic coefficient obtained from the relaxation times of the fluctuation spectrum is equivalent to the two values obtained from free-solidification simulations provided a simple correction is made for the contribution of heat flow controlled interface motion. Finally, a one-dimensional phase field model that captures the effect of thermostats has been developed. The mesoscale model reproduces qualitatively the results from MD simulations and thus allows for an a priori estimate of the accuracy of a kinetic

  10. Molecular dynamics simulation of alkali borate glass using coordination dependent potential

    SciTech Connect

    Park, B.; Cormack, A.N.

    1997-12-31

    The structure of sodium borate glass was investigated by molecular dynamics simulation using coordination dependent potential model. The simulated alkali borate glass consists of basic units, BO{sub 3} triangle, BO{sub 4} tetrahedra and structural groups such as boroxol ring and triborate units. The coordination of boron is converted from 3 to 4 by adding alkali oxide.

  11. Vapor-liquid equilibrium of ethanol by molecular dynamics simulation and Voronoi tessellation.

    PubMed

    Fern, Jared T; Keffer, David J; Steele, William V

    2007-11-22

    Explicit atom simulations of ethanol were performed by molecular dynamics using the OPLS-AA potential. The phase densities were determined self-consistently by comparing the distribution of Voronoi volumes from two-phase and single-phase simulations. This is the first demonstration of the use of Voronoi tessellation in two-phase molecular dynamics simulation of polyatomic fluids. This technique removes all arbitrary determination of the phase diagram by using single-phase simulations to self-consistently validate the probability distribution of Voronoi volumes of the liquid and vapor phases extracted from the two-phase molecular dynamics simulations. Properties from the two phase simulations include critical temperature, critical density, critical pressure, phase diagram, surface tension, and molecule orientation at the interface. The simulations were performed from 375 to 472 K. Also investigated were the vapor pressure and hydrogen bonding along the two phase envelope. The phase envelope agrees extremely well with literature values from GEMC at lower temperatures. The combined use of two-phase molecular dynamics simulation and Voronoi tessellation allows us to extend the phase diagram toward the critical point. PMID:17973521

  12. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles.

    PubMed

    Shaytan, Alexey K; Armeev, Grigoriy A; Goncearenco, Alexander; Zhurkin, Victor B; Landsman, David; Panchenko, Anna R

    2016-06-01

    We present here raw trajectories of molecular dynamics simulations for nucleosome with linker DNA strands as well as minimalistic nucleosome core particle model. The simulations were done in explicit solvent using CHARMM36 force field. We used this data in the research article Shaytan et al., 2016 [1]. The trajectory files are supplemented by TCL scripts providing advanced visualization capabilities. PMID:27222871

  13. Computer simulations of cyclic and acyclic cholinergic agonists: conformational search and molecular dynamics simulations.

    PubMed Central

    McGroddy, K A; Brady, J W; Oswald, R E

    1994-01-01

    Molecular dynamics simulations have been performed on aqueous solutions of two chemically similar nicotinic cholinergic agonists in order to compare their structural and dynamical differences. The cyclic 1,1-dimethyl-4-acetylpiperazinium iodide (HPIP) molecule was previously shown to be a strong agonist for nicotinic acetylcholine receptors (McGroddy et al., 1993), while the acyclic N,N,N,N'-tetramethyl-N'-acetylethylenediamine iodide (HTED) derivative is much less potent. These differences were expected to arise from differences in the solution structures and internal dynamics of the two molecules. HPIP was originally thought to be relatively rigid; however, molecular dynamics simulations suggest that the acetyl portion of the molecule undergoes significant ring dynamics on a psec timescale. The less constrained HTED molecule is relatively rigid, with only one transition observed about any of the major dihedrals in four 100 psec simulations, each started from a different conformation. The average structures obtained from the simulations are very similar to the starting minimized structure in each case, except for the HTED simulation where a single rotation about the N-C-C-N(+) backbone occurred. In each case, HTED had three to five more water molecules in its primary solvation shell than HPIP, indicating that differences in the energetics of desolvation before binding may partially explain the increased potency of HPIP as compared to HTED. Images FIGURE 1 FIGURE 2 PMID:8161685

  14. Ab initio based force field and molecular dynamics simulations of crystalline TATB.

    PubMed

    Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E

    2004-04-15

    An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608

  15. Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture

    SciTech Connect

    Feng, Wei; Xu, Luting; Li, Xin-Qi; Fang, Weihai; Yan, YiJing

    2014-07-15

    Mixed-quantum-classical molecular dynamics simulation implies an effective quantum measurement on the electronic states by the classical motion of atoms. Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods.

  16. Molecular Dynamics Simulations of Chemical Reactions for Use in Education

    ERIC Educational Resources Information Center

    Qian Xie; Tinker, Robert

    2006-01-01

    One of the simulation engines of an open-source program called the Molecular Workbench, which can simulate thermodynamics of chemical reactions, is described. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations…

  17. Phonon transport in molecular dynamics simulations: Formulation and thermal conductivity prediction

    NASA Astrophysics Data System (ADS)

    McGaughey, Alan J. H.

    Atomic-level thermal transport is explored using lattice dynamics theory and molecular dynamics (MD) simulations. Due to the classical nature of the simulations and the small system sizes considered, a formulation different than the standard quantum-particle based approach is required. This is addressed by using real and phonon space analysis techniques to develop links between the atomic structure of dielectric materials and their thermal conductivities. Crystalline, liquid, and amorphous Lennard-Jones phases, and silica-based crystals (including zeolites) are considered. In predicting the thermal conductivity using the Green-Kubo method (a real space approach), two thermal transport mechanisms are identified. The first is temperature independent, related to short length and time scales, and governed by the atomic coordination. The second is temperature dependent, related to long length and time scales, and typically dominates the thermal transport. In the zeolites, the presence of cage structures, and disorder and anisotropy at sub-unit cell length scales, are found to inhibit the second mechanism, resulting in room temperature thermal conductivities of order 1 W/m-K, an order of magnitude less than that of quartz. The thermal conductivity of the Lennard-Jones crystal is also predicted with the Boltzmann transport equation under the single mode relaxation time approximation. Results from the simulations are used to specify all of the parameters in this phonon space model. Due to the inherent anharmonic nature of the simulations, the inclusion of anharmonic effects is straightforward. By comparing the predictions to those from the Greek-Kubo method, the quantitative validity of this model is established. Prior work required simplifying assumptions and the fitting of the results to experimental data, leading to a masking of the underlying physics. Using unsteady, steady non-equilibrium, and equilibrium simulations, three-phonon interactions are observed. Little

  18. Nanoscale heat transport via electrons and phonons by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lin, Keng-Hua

    Nanoscale heat transport has become a crucial research topic due to the growing importance of nanotechnology for manufacturing, energy conversion, medicine and electronics. Thermal transport properties at the nanoscale are distinct from the macroscopic ones since the sizes of nanoscale features, such as free surfaces and interfaces, are comparable to the wavelengths and mean free paths of the heat carriers (electrons and phonons), and lead to changes in thermal transport properties. Therefore, understanding how the nanoscale features and energy exchange between the heat carriers affect thermal transport characteristics are the goals of this research. Molecular dynamics (MD) is applied in this research to understand the details of nanoscale heat transport. The advantage of MD is that the size effect, anharmonicity, atomistic structure, and non-equilibrium behavior of the system can all be captured since the dynamics of atoms are described explicitly in MD. However, MD neglects the thermal role of electrons and therefore it is unable to describe heat transport in metal or metal-semiconductor systems accurately. To address this limitation of MD, we develop a method to simulate electronic heat transport by implementing electronic degrees of freedom to MD. In this research, nanoscale heat transport in semiconductor, metal, and metal-semiconductor systems is studied. Size effects on phonon thermal transport in SiGe superlattice thin films and nanowires are studied by MD. We find that, opposite to the macroscopic trend, superlattice thin films can achieve lower thermal conductivity than nanowires at small scales due to the change of phonon nature caused by adjusting the superlattice periodic length and specimen length. Effects of size and electron-phonon coupling rate on thermal conductivity and thermal interface resistivity in Al and model metal-semiconductor systems are studied by MD with electronic degrees of freedom. The results show that increasing the specimen

  19. Molecular Dynamics Simulations from SNL's Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)

    DOE Data Explorer

    Plimpton, Steve; Thompson, Aidan; Crozier, Paul

    LAMMPS (http://lammps.sandia.gov/index.html) stands for Large-scale Atomic/Molecular Massively Parallel Simulator and is a code that can be used to model atoms or, as the LAMMPS website says, as a parallel particle simulator at the atomic, meso, or continuum scale. This Sandia-based website provides a long list of animations from large simulations. These were created using different visualization packages to read LAMMPS output, and each one provides the name of the PI and a brief description of the work done or visualization package used. See also the static images produced from simulations at http://lammps.sandia.gov/pictures.html The foundation paper for LAMMPS is: S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995), but the website also lists other papers describing contributions to LAMMPS over the years.

  20. Interactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    Schroeder, Daniel V.

    2015-03-01

    Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.

  1. Spotting the difference in molecular dynamics simulations of biomolecules.

    PubMed

    Sakuraba, Shun; Kono, Hidetoshi

    2016-08-21

    Comparing two trajectories from molecular simulations conducted under different conditions is not a trivial task. In this study, we apply a method called Linear Discriminant Analysis with ITERative procedure (LDA-ITER) to compare two molecular simulation results by finding the appropriate projection vectors. Because LDA-ITER attempts to determine a projection such that the projections of the two trajectories do not overlap, the comparison does not suffer from a strong anisotropy, which is an issue in protein dynamics. LDA-ITER is applied to two test cases: the T4 lysozyme protein simulation with or without a point mutation and the allosteric protein PDZ2 domain of hPTP1E with or without a ligand. The projection determined by the method agrees with the experimental data and previous simulations. The proposed procedure, which complements existing methods, is a versatile analytical method that is specialized to find the "difference" between two trajectories. PMID:27544096

  2. A fast recursive algorithm for molecular dynamics simulation

    NASA Technical Reports Server (NTRS)

    Jain, A.; Vaidehi, N.; Rodriguez, G.

    1993-01-01

    The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.

  3. Generalized Langevin models of molecular dynamics simulations with applications to ion channels

    NASA Astrophysics Data System (ADS)

    Gordon, Dan; Krishnamurthy, Vikram; Chung, Shin-Ho

    2009-10-01

    We present a new methodology, which combines molecular dynamics and stochastic dynamics, for modeling the permeation of ions across biological ion channels. Using molecular dynamics, a free energy profile is determined for the ion(s) in the channel, and the distribution of random and frictional forces is measured over discrete segments of the ion channel. The parameters thus determined are used in stochastic dynamics simulations based on the nonlinear generalized Langevin equation. We first provide the theoretical basis of this procedure, which we refer to as "distributional molecular dynamics," and detail the methods for estimating the parameters from molecular dynamics to be used in stochastic dynamics. We test the technique by applying it to study the dynamics of ion permeation across the gramicidin pore. Given the known difficulty in modeling the conduction of ions in gramicidin using classical molecular dynamics, there is a degree of uncertainty regarding the validity of the MD-derived potential of mean force (PMF) for gramicidin. Using our techniques and systematically changing the PMF, we are able to reverse engineer a modified PMF which gives a current-voltage curve closely matching experimental results.

  4. Free energy calculations from adaptive molecular dynamics simulations with adiabatic reweighting

    NASA Astrophysics Data System (ADS)

    Cao, Lingling; Stoltz, Gabriel; Lelièvre, Tony; Marinica, Mihai-Cosmin; Athènes, Manuel

    2014-03-01

    We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled configurations. We apply the algorithm to a structural transition in a cluster and to the migration of a crystalline defect along a reaction coordinate. Compared to standard adaptive molecular dynamics, we observe an acceleration of convergence. With the aid of the algorithm, it is also possible to iteratively construct the free energy along the reaction coordinate without having to differentiate the gradient of the reaction coordinate or any biasing potential.

  5. 27ps DFT Molecular Dynamics Simulation of a-maltose: A Reduced Basis Set Study.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as alpha-maltose, requiring up to three or more weeks on a fast 16-processor computer to obtain just 5ps of constant energy dynamics. In a recent publication [1] forces for dynamics were generated from B3LY...

  6. Epitaxial growth simulation employing a combined molecular dynamics and Monte Carlo approach

    SciTech Connect

    Grein, C.H.; Benedek, R.; Rubia, T. de la

    1995-07-01

    The epitaxial growth of Ge on Si(OO1) is simulated by employing a hybrid approach based on molecular dynamics to describe the initial kinetic behavior of deposited adatoms and Monte Carlo displacements to account for subsequent equilibration. This method is well suited to describe initial nucleation and growth. Stillinger-Weber potentials are employed to describe interatomic interactions.

  7. Molecular dynamics simulations of shallow nitrogen and silicon implantation into diamond

    NASA Astrophysics Data System (ADS)

    Lehtinen, Ossi; Naydenov, Boris; Börner, Pia; Melentjevic, Kristina; Müller, Christoph; McGuinness, Liam Paul; Pezzagna, Sebastien; Meijer, Jan; Kaiser, Ute; Jelezko, Fedor

    2016-01-01

    A solid understanding of the implantation process of N and Si ions into diamond is needed for the controlled creation of shallow color centers for quantum computing, simulation, and sensing applications. Here, molecular dynamics simulations of the shallow implantation of N and Si ions into diamond is simulated at 100-5000 eV kinetic energies and different angles of incidence. We find that ion channeling is an important effect with an onset energy depending on the crystal orientation. Consequently, the molecular dynamics simulations produce improved predictions as compared to standard Monte Carlo simulations. When implanting in a channeling direction, the spatial distribution of the channeled ions becomes markedly narrow, allowing a higher degree of control over the location of the nitrogen vacancy (NV-) centers. A contamination layer on the ion entry surface reduces the fraction of channeled ions. A comparison to an experimentally determined depth profile based on a NMR signal from protons yields a quantitative agreement, validating the simulation approach.

  8. Elucidation of GB1 Protein Unfolding Mechanism via a Long-timescale Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Sumaryada, T.; Hati, J.; Wahyudi, S. T.; Malau, N. D.; Sawitri, K. N.

    2016-01-01

    This study investigates the unfolding mechanism of 1GB1 protein at various simulation temperatures using a long-timescale molecular dynamics simulation. Analysis of structural parameters of molecular dynamics simulation have indicated that the unfolding process of GB1 protein has started at 95 ns for 475 K simulation, and at 745 ps for 500 K simulation. The unfolding process in this simulation exhibit the feature of hydrophobic core collapse model, in which the beta-hairpin destruction precedes the a-helix to coil transition. The unfolding was started with the increasing flexibility of the beta-sheets and hydrophobic core region, continued with beta-hairpins destruction, and ended with a-helix to coil and turn transition. The final structures of GB1 protein after unfolding, suggest an unfinished denaturation of protein as seen from the small remains of α-helix structure.

  9. Melittin Aggregation in Aqueous Solutions: Insight from Molecular Dynamics Simulations.

    PubMed

    Liao, Chenyi; Esai Selvan, Myvizhi; Zhao, Jun; Slimovitch, Jonathan L; Schneebeli, Severin T; Shelley, Mee; Shelley, John C; Li, Jianing

    2015-08-20

    Melittin is a natural peptide that aggregates in aqueous solutions with paradigmatic monomer-to-tetramer and coil-to-helix transitions. Since little is known about the molecular mechanisms of melittin aggregation in solution, we simulated its self-aggregation process under various conditions. After confirming the stability of a melittin tetramer in solution, we observed—for the first time in atomistic detail—that four separated melittin monomers aggregate into a tetramer. Our simulated dependence of melittin aggregation on peptide concentration, temperature, and ionic strength is in good agreement with prior experiments. We propose that melittin mainly self-aggregates via a mechanism involving the sequential addition of monomers, which is supported by both qualitative and quantitative evidence obtained from unbiased and metadynamics simulations. Moreover, by combining computer simulations and a theory of the electrical double layer, we provide evidence to suggest why melittin aggregation in solution likely stops at the tetramer, rather than forming higher-order oligomers. Overall, our study not only explains prior experimental results at the molecular level but also provides quantitative mechanistic information that may guide the engineering of melittin for higher efficacy and safety. PMID:26208115

  10. An Undergraduate Laboratory Activity on Molecular Dynamics Simulations

    ERIC Educational Resources Information Center

    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…

  11. Simulation of the 2-dimensional Drude’s model using molecular dynamics method

    SciTech Connect

    Naa, Christian Fredy; Amin, Aisyah; Ramli,; Suprijadi,; Djamal, Mitra; Wahyoedi, Seramika Ari; Viridi, Sparisoma

    2015-04-16

    In this paper, we reported the results of the simulation of the electronic conduction in solids. The simulation is based on the Drude’s models by applying molecular dynamics (MD) method, which uses the fifth-order predictor-corrector algorithm. A formula of the electrical conductivity as a function of lattice length and ion diameter τ(L, d) cand be obtained empirically based on the simulation results.

  12. Carbon atom, dimer and trimer chemistry on diamond surfaces from molecular dynamics simulations

    SciTech Connect

    Valone, S.M.

    1995-07-01

    Spectroscopic studies of various atmospheres appearing in diamond film synthesis suggest evidence for carbon atoms, dimers, or trimers. Molecular dynamics simulations with the Brenner hydrocarbon potential are being used to investigate the elementary reactions of these species on a hydrogen-terminated diamond (111) surface. In principle these types of simulations can be extended to simulations of growth morphologies, in the 1-2 monolayer regime presently.

  13. Molecular dynamics simulation strategies for protein-micelle complexes.

    PubMed

    Cheng, Xi; Kim, Jin-Kyoung; Kim, Yangmee; Bowie, James U; Im, Wonpil

    2016-07-01

    The structure and stability of membrane proteins can vary widely in different detergents and this variability has great practical consequences for working with membrane proteins. Nevertheless, the mechanisms that operate to alter the behavior of proteins in micelles are poorly understood and not predictable. Atomic simulations could provide considerable insight into these mechanisms. Building protein-micelle complexes for simulation is fraught with uncertainty, however, in part because it is often unknown how many detergent molecules are present in the complex. Here, we describe several convenient ways to employ Micelle Builder in CHARMM-GUI to rapidly construct protein-micelle complexes and performed simulations of the isolated voltage-sensor domain of voltage-dependent potassium-selective channel and an antimicrobial peptide papiliocin with varying numbers of detergents. We found that once the detergent number exceeds a threshold, protein-detergent interactions change very little and remain very consistent with experimental observations. Our results provide a platform for future studies of the interplays between protein structure and detergent properties at the atomic level. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26679426

  14. Growth of bi- and tri-layered graphene on silicon carbide substrate via molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    Molecular dynamics (MD) simulation with simulated annealing method is used to study the growth process of bi- and tri-layered graphene on a 6H-SiC (0001) substrate via molecular dynamics simulation. Tersoff-Albe-Erhart (TEA) potential is used to describe the inter-atomic interactions among the atoms in the system. The formation temperature, averaged carbon-carbon bond length, pair correlation function, binding energy and the distance between the graphene formed and the SiC substrate are quantified. The growth mechanism, graphitization of graphene on the SiC substrate and characteristics of the surface morphology of the graphene sheet obtained in our MD simulation compare well to that observed in epitaxially grown graphene experiments and other simulation works.

  15. Growth of bi- and tri-layered graphene on silicon carbide substrate via molecular dynamics simulation

    SciTech Connect

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

    2015-04-24

    Molecular dynamics (MD) simulation with simulated annealing method is used to study the growth process of bi- and tri-layered graphene on a 6H-SiC (0001) substrate via molecular dynamics simulation. Tersoff-Albe-Erhart (TEA) potential is used to describe the inter-atomic interactions among the atoms in the system. The formation temperature, averaged carbon-carbon bond length, pair correlation function, binding energy and the distance between the graphene formed and the SiC substrate are quantified. The growth mechanism, graphitization of graphene on the SiC substrate and characteristics of the surface morphology of the graphene sheet obtained in our MD simulation compare well to that observed in epitaxially grown graphene experiments and other simulation works.

  16. Ewald artifacts in liquid state molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Smith, Paul E.; Pettitt, B. Montgomery

    1996-09-01

    An investigation into the effects of the anisotropic nature of the Ewald potential for the treatment of long range electrostatic interactions in liquid solutions has been performed. The rotational potential energy surface for two simple charge distributions, and a small protein, have been studied under conditions typically implemented in current biomolecular simulations. A transition between hindered and free rotation is observed which can be modeled quantitatively for simple charge distributions. For most systems in aqueous solution, the transition involves an energy change well below kBT. It is argued that, for solvents with a reasonably high relative permittivity, Ewald artifacts will be small and in many cases may be safely ignored.

  17. Molecular dynamics simulation of nitric oxide in myoglobin

    USGS Publications Warehouse

    Lee, Myung Won; Meuwly, Markus

    2012-01-01

    The infrared (IR) spectroscopy and ligand migration of photodissociated nitric oxide (NO) in and around the active sites in myoglobin (Mb) are investigated. A distributed multipolar model for open-shell systems is developed and used, which allows one to realistically describe the charge distribution around the diatomic probe molecule. The IR spectra were computed from the trajectories for two conformational substates at various temperatures. The lines are narrow (width of 3–7 cm–1 at 20–100 K), in agreement with the experimental observations where they have widths of 4–5 cm–1 at 4 K. It is found that within one conformational substate (B or C) the splitting of the spectrum can be correctly described compared with recent experiments. Similar to photodissociated CO in Mb, additional substates exist for NO in Mb, which are separated by barriers below 1 kcal/mol. Contrary to full quantum mechanical calculations, however, the force field and mixed QM/MM simulations do not correctly describe the relative shifts between the B- and C-states relative to gas-phase NO. Free energy simulations establish that NO preferably localizes in the distal site and the barrier for migration to the neighboring Xe4 pocket is ΔGB→C = 1.7–2.0 kcal/mol. The reverse barrier is ΔGB←C = 0.7 kcal/mol, which agrees well with the experimental value of 0.7 kcal/mol, estimated from kinetic data.

  18. Striped gold nanoparticles: New insights from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Velachi, Vasumathi; Bhandary, Debdip; Singh, Jayant K.; Cordeiro, M. Natália D. S.

    2016-06-01

    Recent simulations have improved our knowledge of the molecular-level structure and hydration properties of mixed self-assembled monolayers (SAMs) with equal and unequal alkyl thiols at three different arrangements, namely, random, patchy, and Janus. In our previous work [V. Vasumathi et al., J. Phys. Chem. C 119, 3199-3209 (2015)], we showed that the bending of longer thiols over shorter ones clearly depends on the thiols' arrangements and chemical nature of their terminal groups. In addition, such a thiol bending revealed to have a strong impact on the structural and hydration properties of SAMs coated on gold nanoparticles (AuNPs). In this paper, we extend our previous atomistic simulation study to investigate the bending of longer thiols by increasing the stripe thickness of mixed SAMs of equal and unequal lengths coated on AuNPs. We study also the effect of stripe thickness on the structural morphology and hydration of the coated SAMs. Our results show that the structural and hydration properties of SAMs are affected by the stripe thickness for mixtures of alkyl thiols with unequal chain length but not for equal length. Hence, the stability of the stripe configuration depends on the alkyl's chain length, the length difference between the thiol mixtures, and solvent properties.

  19. Molecular dynamics simulation of amorphization in forsterite by cosmic rays

    SciTech Connect

    Devanathan, Ram; Durham, Philip; Du, Jincheng; Corrales, Louis R.; Bringa, Eduardo M.

    2007-02-16

    We have examined cosmic ray interactions with silicate dust grains by simulating a thermal spike in a 1.25 million atom forsterite (Mg2SiO4) crystal with periodic boundaries. Spikes were generated by giving a kinetic energy of 1 or 2 eV to every atom within a cylinder of radius 1.73 nm along the [001] direction. An amorphous track of radius ~3 nm was produced for the 2 eV/atom case, but practically no amorphization was produced for 1 eV/atom because of effective dynamic annealing. Chemical segregation was not observed in the track. These results agree with recent experimental studies of ion irradiation effects in silicates, and indicate that cosmic rays can cause the amorphization of interstellar dust.

  20. Calibrating elastic parameters from molecular dynamics simulations of capsid proteins

    NASA Astrophysics Data System (ADS)

    Hicks, Stephen; Henley, Christopher

    2008-03-01

    Virus capsids are modeled with elastic network models in which a handful of parameters determine transitions in assembly [1] and morphology [2]. We introduce an approach to compute these parameters from the microscopic structure of the proteins involved. We consider each protein as one or a few rigid bodies with very general interactions, which we parameterize by fitting the simulated equilibrium fluctuations (relative translations and rotations) of a pair of proteins (or fragments) to a 6-dimensional Gaussian. We can then compose these generalized springs into the global capsid structure to determine the continuum elastic parameters. We demonstrate our approach on HIV capsid protein and compare our results with the observed lattice structure (from cryo-EM [3] and AFM indentation studies). [1] R. Zandi et al, PNAS 101 (2004) 15556. [2] J. Lidmar, L. Mirny, and D. R. Nelson, PRE 68 (2003) 051910. [3] B. K. Ganser-Pornillos et al, Cell 131 (2007) 70.

  1. Introduction to the quantum trajectory method and to Fermi molecular dynamics

    NASA Astrophysics Data System (ADS)

    La Gattuta, K. J.

    2003-06-01

    The quantum trajectory method (QTM) will be introduced, and an approximation to the QTM known as Fermi molecular dynamics (FMD) will be described. Results of simulations based on FMD will be mentioned for specific nonequilibrium systems dominated by Coulomb interactions.

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

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  3. An extended-Lagrangian scheme for charge equilibration in reactive molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Nomura, Ken-ichi; Small, Patrick E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2015-07-01

    Reactive molecular dynamics (RMD) simulations describe chemical reactions at orders-of-magnitude faster computing speed compared with quantum molecular dynamics (QMD) simulations. A major computational bottleneck of RMD is charge-equilibration (QEq) calculation to describe charge transfer between atoms. Here, we eliminate the speed-limiting iterative minimization of the Coulombic energy in QEq calculation by adapting an extended-Lagrangian scheme that was recently proposed in the context of QMD simulations, Souvatzis and Niklasson (2014). The resulting XRMD simulation code drastically improves energy conservation compared with our previous RMD code, Nomura et al. (2008), while substantially reducing the time-to-solution. The XRMD code has been implemented on parallel computers based on spatial decomposition, achieving a weak-scaling parallel efficiency of 0.977 on 786,432 IBM Blue Gene/Q cores for a 67.6 billion-atom system.

  4. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations.

    PubMed

    Hardy, David J; Wolff, Matthew A; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D

    2016-03-21

    The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle-mesh Ewald method falls short. PMID:27004867

  5. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Hardy, David J.; Wolff, Matthew A.; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D.

    2016-03-01

    The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle-mesh Ewald method falls short.

  6. Molecular Dynamics Simulations of Phosphatidylinositol Bisphosphate (PIP2)

    NASA Astrophysics Data System (ADS)

    Slochower, David; Janmey, Paul

    2012-02-01

    We are interested in the dynamics of membranes containing the highly charged phospholipid phosphatidylinositol bisphosphate (PIP2 or PtdInsP2). We performed a geometry optimization at the Hartree-Fock 6-31+G* level of theory to determine the biological conformation of the phospholipid headgroup in the presence of water and partial charge distribution. The angle between the headgroup and the acyl chains that form an anchor in the membrane is 94 ^o, indicating that the inositol ring may lie flat along the surface of the inner plasma membrane. Next, we employed hybrid quantum mechanics/molecular mechanics simulations to investigate the protonation state of PIP2 and its interactions with physiological divalent cations such as magnesium and calcium. Based on preliminary data, we propose that the binding of magnesium to PIP2 is mediated by a water molecule that is absent when calcium binds. These results may explain the ability of calcium to induce the formation of PIP2 clusters and phase separation from other phospholipids.

  7. Dry and Wet Molecular Dynamics Simulations of Nafion® Polymer Electrolyte Fuel Cell Membrane

    NASA Astrophysics Data System (ADS)

    Yana, Janchai; Lee, Vannajan Sanghiran; Nimmanpipug, Piyarat; Dokmaisrijan, Supaporn; Aukkaravittayapun, Suparerk; Vilaithong, Thirapat

    The interactions between the hydronium ions and the waters in Nafion® polyelectrolyte membrane are relevant in the proton transfer process of fuel cell. To investigate a role of water in the proton transfer mechanism, molecular dynamic simulations have been performed for models of Nafion® side chains cluster with the water molecules and the hydronium ions comparing with dry system. After simulations, the trajectories were analyzed in term of intermolecular distances, potential energy, and radial distribution function.

  8. Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation

    SciTech Connect

    Petridis, Loukas; Pingali, Sai Venkatesh; Urban, Volker; Heller, William T; O'Neill, Hugh Michael; Foston, Marcus B; Ragauskas, Arthur J; Smith, Jeremy C

    2011-01-01

    Lignin, a major polymeric component of plant cell walls, forms aggregates in vivo and poses a barrier to cellulosic ethanol production. Here, neutron scattering experiments and molecular dynamics simulations reveal that lignin aggregates are characterized by a surface fractal dimension that is invariant under change of scale from 1 1000 A. The simulations also reveal extensive water penetration of the aggregates and heterogeneous chain dynamics corresponding to a rigid core with a fluid surface.

  9. Molecular Dynamics Simulations for Neutrino Scattering in Heterogeneous High Dense Media

    SciTech Connect

    Caballero, O. L.

    2008-03-13

    The dynamics of core-collapse supernovae is sensitive to neutrino scattering. Using molecular dynamics simulations, we calculated ion static structure factors and neutrino mean free paths. We simulated the stellar medium as composed in one case by single ion specie, and in the other by a mixture of ions. For the heterogeneous plasma we used two different models and systematically found the neutrino mean free path is shorter for an ion mixture.

  10. Study of Fracture in SiC by Parallel Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Chatterjee, A.; Omeltchenko, A.; Kalia, R. K.; Vashishta, P.

    1997-03-01

    Large scale molecular-dynamics simulations are performed on parallel architectures to investigate dynamic fracture in SiC. The simulations are based on an empirical bond-order potential proposed by Tersoff.(J. Tersoff, Phys. Rev. B 39), 5566(1989) (M. Tang and S. Yip, Phys. Rev. B 52), 15150(1995) Results will be presented for crack-front morphology, crack-tip speed, and the effect of strain rate on dynamic fracture.

  11. A Molecular Dynamics Simulation of Phase Transitions: Thermodynamics and Transport Coefficients

    NASA Astrophysics Data System (ADS)

    Uno, Toshiaki; Sogo, Kiyoshi

    2015-03-01

    Molecular dynamics simulations are performed by using the Nosé-Poincaré thermostat for N = 103 particles system. A new finite range potential function with both attractive and repulsive forces is employed to investigate the phase transitions covering three phases of gas, liquid and solid. Besides the thermodynamic properties, transport coefficients such as diffusion constant, shear and bulk viscosities and thermal conductivity are computed from simulation data. A phase diagram is constructed by locating the phase boundaries from these quantities.

  12. Linear Viscoelastic Response of PBX-9501 Binder using Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Davande, Hemali

    2005-03-01

    Quantum-chemistry based force fields for Estane, bis-dinitropropyl formal (BDNPF) and bis dinitropropyl acetal (BDNPA) plasticizer have been developed, validated and utilized in atomistic molecular dynamics (MD) simulations of a model PBX-9501 binder. The viscoelastic response of unentangled binder melt using MD simulations was studied. These results were then used in prediction of linear viscoelastic response of an entangled melt using theoretical models for viscoelastic response of block copolymers and compared with experiments.

  13. Solvation of fullerene in a course grained water: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Patawane, Sanwardhini; Pant, Shashank; Choudhury, Niharendu

    2015-06-01

    We present a detailed molecular dynamics simulation investigation on hydration of C60 fullerene in a coarse-grained water-like solvent. Based on our recent study (J. Chem. Phys. 2013), which has demonstrated the capability of a coarse-grained, core-soft model of water to describe water-like anomalies, we report here the applicability of this model to describe hydration characteristic of C60 fullerenes. Molecular dynamics simulation has been performed in NVE ensemble and structural characteristics of water around C60 fullerene have been analyzed by calculating C60-water radial distribution function. The computational economy and simplicity of the coarse-grained model will allow us to investigate self-assembly processes that require simulations of a much larger system over a longer period of time.

  14. Investigation of crack tip dislocation emission in aluminum using multiscale molecular dynamics simulation and continuum modeling

    NASA Astrophysics Data System (ADS)

    Yamakov, V. I.; Warner, D. H.; Zamora, R. J.; Saether, E.; Curtin, W. A.; Glaessgen, E. H.

    2014-04-01

    This work investigates the dislocation nucleation processes that occur at the tip of a crack in aluminum under a broad range of crystallographic orientations and temperatures. A concurrent multiscale molecular dynamics - continuum simulation framework is employed. The results are then interpreted using a Peierls continuum model that uses finite temperature material properties derived from molecular dynamics simulation. Under ramped loading, partial dislocation nucleation at the crack tip is found to lead to both full dislocation emission and twinning, depending upon the orientation, temperature, and magnitude of the applied load in the simulation. The origins of the dependencies are made apparent by the Peierls continuum model. The continuum model suggests that in many instances dislocation nucleation from the crack tip can be considered to be a strain rate independent process, yet still temperature dependent through the temperature dependence of the stacking fault energies and elastic constants.

  15. Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.

    SciTech Connect

    Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael; Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl

    2011-09-01

    Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.

  16. Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations.

    PubMed

    Hedger, George; Sansom, Mark S P

    2016-10-01

    Lipid molecules are able to selectively interact with specific sites on integral membrane proteins, and modulate their structure and function. Identification and characterization of these sites are of importance for our understanding of the molecular basis of membrane protein function and stability, and may facilitate the design of lipid-like drug molecules. Molecular dynamics simulations provide a powerful tool for the identification of these sites, complementing advances in membrane protein structural biology and biophysics. We describe recent notable biomolecular simulation studies which have identified lipid interaction sites on a range of different membrane proteins. The sites identified in these simulation studies agree well with those identified by complementary experimental techniques. This demonstrates the power of the molecular dynamics approach in the prediction and characterization of lipid interaction sites on integral membrane proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26946244

  17. Theoretical studies of amorphous silicon and hydrogenated amorphous silicon with molecular dynamics simulations

    SciTech Connect

    Kwon, I.

    1991-12-20

    Amorphous silicon (a-Si) and hydrogenated amorphous silicon (a-Si:H) have been studied with molecular dynamics simulations. The structural, vibrational, and electronic properties of these materials have been studied with computer-generated structural models and compare well with experimental observations. The stability of a-si and a-Si:H have been studied with the aim of understanding microscopic mechanisms underlying light-induced degradation in a-Si:H (the Staebler-Wronski effect). With a view to understanding thin film growth processes, a-Si films have been generated with molecular dynamics simulations by simulating the deposition of Si-clusters on a Si(111) substrate. A new two- and three-body interatomic potential for Si-H interactions has been developed. The structural properties of a-Si:H networks are in good agreement with experimental measurements. The presence of H atoms reduces strain and disorder relative to networks without H.

  18. Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

    DOE PAGESBeta

    Gordiz, Kiarash; Singh, David J.; Henry, Asegun

    2015-01-29

    In this report we compare time sampling and ensemble averaging as two different methods available for phase space sampling. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium molecular dynamics. We introduce two different schemes for the ensemble averaging approach, and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical molecular dynamics, the ensemble generation approaches may find their greatest utility in computationally expensive simulations such asmore » first principles molecular dynamics. For such simulations, where each time step is costly, time sampling can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each ensemble is independent. For this reason, particularly when using massively parallel architectures, ensemble sampling can result in much shorter simulation times and exhibits similar overall computational effort.« less

  19. Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

    SciTech Connect

    Gordiz, Kiarash; Singh, David J.; Henry, Asegun

    2015-01-29

    In this report we compare time sampling and ensemble averaging as two different methods available for phase space sampling. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium molecular dynamics. We introduce two different schemes for the ensemble averaging approach, and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical molecular dynamics, the ensemble generation approaches may find their greatest utility in computationally expensive simulations such as first principles molecular dynamics. For such simulations, where each time step is costly, time sampling can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each ensemble is independent. For this reason, particularly when using massively parallel architectures, ensemble sampling can result in much shorter simulation times and exhibits similar overall computational effort.

  20. Structure-function studies of DNA damage using AB INITIO quantum mechanics and molecular dynamics simulation

    SciTech Connect

    Miller, J.; Miaskiewicz, K.; Osman, R.

    1993-12-01

    Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.

  1. The Effect of Water on the Work of Adhesion at Epoxy Interfaces by Molecular Dynamics Simulation

    NASA Technical Reports Server (NTRS)

    Hinkley, J.A.; Frankland, S.J.V.; Clancy, T.C.

    2009-01-01

    Molecular dynamics simulation can be used to explore the detailed effects of chemistry on properties of materials. In this paper, two different epoxies found in aerospace resins are modeled using molecular dynamics. The first material, an amine-cured tetrafunctional epoxy, represents a composite matrix resin, while the second represents a 177 C-cured adhesive. Surface energies are derived for both epoxies and the work of adhesion values calculated for the epoxy/epoxy interfaces agree with experiment. Adding water -- to simulate the effect of moisture exposure -- reduced the work of adhesion in one case, and increased it in the other. To explore the difference, the various energy terms that make up the net work of adhesion were compared and the location of the added water was examined.

  2. Temperature Dependence of NMR Parameters Calculated from Path Integral Molecular Dynamics Simulations.

    PubMed

    Dračínský, Martin; Bouř, Petr; Hodgkinson, Paul

    2016-03-01

    The influence of temperature on NMR chemical shifts and quadrupolar couplings in model molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory (DFT) calculations of shielding and electric field gradient (EFG) tensors. An approach based on convoluting calculated shielding or EFG tensor components with probability distributions of selected bond distances and valence angles obtained from DFT-PIMD simulations at several temperatures is used to calculate the temperature effects. The probability distributions obtained from the quantum PIMD simulations, which includes nuclear quantum effects, are significantly broader and less temperature dependent than those obtained with conventional DFT molecular dynamics or with 1D scans through the potential energy surface. Predicted NMR observables for the model systems were in excellent agreement with experimental data. PMID:26857802

  3. Classical Magnetic Dipole Moments for the Simulation of Vibrational Circular Dichroism by ab Initio Molecular Dynamics.

    PubMed

    Thomas, Martin; Kirchner, Barbara

    2016-02-01

    We present a new approach for calculating vibrational circular dichroism spectra by ab initio molecular dynamics. In the context of molecular dynamics, these spectra are given by the Fourier transform of the cross-correlation function of magnetic dipole moment and electric dipole moment. We obtain the magnetic dipole moment from the electric current density according to the classical definition. The electric current density is computed by solving a partial differential equation derived from the continuity equation and the condition that eddy currents should be absent. In combination with a radical Voronoi tessellation, this yields an individual magnetic dipole moment for each molecule in a bulk phase simulation. Using the chiral alcohol 2-butanol as an example, we show that experimental spectra are reproduced very well. Our approach requires knowing only the electron density in each simulation step, and it is not restricted to any particular electronic structure method. PMID:26771403

  4. Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

    DOE PAGESBeta

    Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; Huang, Patrick; Lightstone, Felice C.

    2015-10-22

    Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholinemore » catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.« less

  5. Temperature dependence of protein-hydration hydrodynamics by molecular dynamics simulations.

    PubMed

    Lau, Edmond Y; Krishnan, V V

    2007-10-01

    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. PMID:17720293

  6. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

    SciTech Connect

    Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S

    2014-10-16

    The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

  7. Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

    SciTech Connect

    Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; Huang, Patrick; Lightstone, Felice C.

    2015-10-22

    Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholine catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.

  8. Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

    NASA Technical Reports Server (NTRS)

    Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

  9. Self Diffusion in Nano Filled Polymer Melts: a Molecular Dynamics Simulation Study

    NASA Astrophysics Data System (ADS)

    Desai, Tapan; Keblinski, Pawel

    2003-03-01

    SELF DIFFUSION IN NANO FILLED POLYMER MELTS: A MOLECULAR DYNAMICS SIMULATION STUDY* T. G. Desai,P. Keblinski, Material Science and Engineering Department, Rensselaer Polytechnic Institute, Troy, NY. Using molecular dynamics simulations, we studied the dynamics of the polymeric systems containing immobile and analytically smooth spherical nanoparticles. Each chain consisted of N monomers connected by an anharmonic springs described by the finite extendible nonlinear elastic, FENE potential. The system comprises of 3nanoparticles and the rest by freely rotating but not overlapping chains. The longest chain studied has a Radius of gyration equal to particle size radius and comparable to inter-particle distance. There is no effect on the structural characteristics such as Radius of gyration or end to end distance due to the nanoparticles. Diffusion of polymeric chains is not affected by the presence of either attractive or repulsive nanoparticles. In all cases Rouse dynamics is observed for short chains with a crossover to reptation dynamics for longer chains.

  10. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

    PubMed

    Kirmizialtin, Serdal; Hennelly, Scott P; Schug, Alexander; Onuchic, Jose N; Sanbonmatsu, Karissa Y

    2015-01-01

    Integration and calibration of molecular dynamics simulations with experimental data remain a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2'-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the force field according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. PMID:25726467

  11. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT

    PubMed Central

    Kirmizialtin, Serdal; Hennelly, Scott P.; Schug, Alexander; Onuchic, Jose N.; Sanbonmatsu, Karissa Y.

    2016-01-01

    Integration and calibration of molecular dynamics simulations with experimental data remains a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2’-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the forcefield according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. PMID:25726467

  12. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

    PubMed

    Šponer, Jiří; Banáš, Pavel; Jurečka, Petr; Zgarbová, Marie; Kührová, Petra; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, Michal

    2014-05-15

    We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation. PMID:26270382

  13. Lipid-converter, a framework for lipid manipulations in molecular dynamics simulations

    PubMed Central

    Larsson, Per; Kasson, Peter M.

    2014-01-01

    Construction of lipid membrane and membrane protein systems for molecular dynamics simulations can be a challenging process. In addition, there are few available tools to extend existing studies by repeating simulations using other force fields and lipid compositions. To facilitate this, we introduce lipidconverter, a modular Python framework for exchanging force fields and lipid composition in coordinate files obtained from simulations. Force fields and lipids are specified by simple text files, making it easy to introduce support for additional force fields and lipids. The converter produces simulation input files that can be used for structural relaxation of the new membranes. PMID:25081234

  14. A Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices

    PubMed Central

    Hall, Benjamin A; Halim, Khairul Abd; Buyan, Amanda; Emmanouil, Beatrice; Sansom, Mark S P

    2016-01-01

    The interactions of transmembrane (TM) α-helices with the phospholipid membrane and with one another are central to understanding the structure and stability of integral membrane proteins. These interactions may be analysed via coarse-grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analysis of TM helix interactions, large (N ca. 100) ensembles of CGMD simulations are needed. To facilitate the running and analysis of such ensembles of simulations we have developed Sidekick, an automated pipeline software for performing high throughput CGMD simulations of α-helical peptides in lipid bilayer membranes. Through an end-to-end approach, which takes as input a helix sequence and outputs analytical metrics derived from CGMD simulations, we are able to predict the orientation and likelihood of insertion into a lipid bilayer of a given helix of family of helix sequences. We illustrate this software via analysis of insertion into a membrane of short hydrophobic TM helices containing a single cationic arginine residue positioned at different positions along the length of the helix. From analysis of these ensembles of simulations we estimate apparent energy barriers to insertion which are comparable to experimentally determined values. In a second application we use CGMD simulations to examine self-assembly of dimers of TM helices from the ErbB1 receptor tyrosine kinase, and analyse the numbers of simulation repeats necessary to obtain convergence of simple descriptors of the mode of packing of the two helices within a dimer. Our approach offers proof-of-principle platform for the further employment of automation in large ensemble CGMD simulations of membrane proteins. PMID:26580541

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

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

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

  16. Large-scale molecular dynamics simulations of dislocation intersection in copper

    PubMed

    Zhou; Preston; Lomdahl; Beazley

    1998-03-01

    The results of massively parallel three-dimensional molecular dynamics simulations of the perpendicular intersection of extended dislocations in copper are reported. The intersection process, which involves three of the four possible 111 glide planes in the face-centered cubic lattice, begins with junction formation, followed by unzipping, partial dislocation bowing, cutting, and, finally, unit jog formation. The investigation provides insights into this complex atomistic process, which is currently not accessible to experimental investigation. PMID:9488649

  17. Dispersion curves from short-time molecular dynamics simulation. 1. Diatomic chain results

    SciTech Connect

    Noid, D.W.; Broocks, B.T.; Gray, S.K.; Marple, S.L.

    1988-06-16

    The multiple signal classification method (MUSIC) for frequency estimation is used to compute the frequency dispersion curves of a diatomic chain from the time-dependent structure factor. In this paper, the authors demonstrate that MUSIC can accurately determine the frequencies from very short time trajectories. MUSIC is also used to show how the frequencies can vary in time, i.e., along a trajectory. The method is ideally suited for analyzing molecular dynamics simulations of large systems.

  18. Molecular Dynamics Simulations of the Time Evolution of Irradiation Induced Defects

    SciTech Connect

    Sopu, Daniel; Girtu, Mihai A.

    2007-04-23

    We present here molecular dynamics simulations of collision cascades in various metals irradiated with ions having the initial kinetic energy of 500 eV. We find that although during the collision cascade some regions of the sample become amorphous, after the thermal spike, the crystal starts to recrystallize. The multiple vacancy clusters tend to break into smaller fragments and to migrate towards the surface, leaving behind only a small number of defects.

  19. A Linked-Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor

    DOE PAGESBeta

    Yang, L. H.; Brooks III, E. D.; Belak, J.

    1992-01-01

    A molecular dynamics algorithm for performing large-scale simulations using the Parallel C Preprocessor (PCP) programming paradigm on the BBN TC2000, a massively parallel computer, is discussed. The algorithm uses a linked-cell data structure to obtain the near neighbors of each atom as time evoles. Each processor is assigned to a geometric domain containing many subcells and the storage for that domain is private to the processor. Within this scheme, the interdomain (i.e., interprocessor) communication is minimized.

  20. Anion pairs in room temperature ionic liquids predicted by molecular dynamics simulation, verified by spectroscopic characterization

    SciTech Connect

    Schwenzer, Birgit; Kerisit, Sebastien N.; Vijayakumar, M.

    2014-01-01

    Molecular-level spectroscopic analyses of an aprotic and a protic room-temperature ionic liquid, BMIM OTf and BMIM HSO4, respectively, have been carried out with the aim of verifying molecular dynamics simulations that predict anion pair formation in these fluid structures. Fourier-transform infrared spectroscopy, Raman spectroscopy and nuclear magnetic resonance spectroscopy of various nuclei support the theoretically-determined average molecular arrangements.

  1. Grand canonical ensemble molecular dynamics simulations: Reformulation of extended system dynamics approaches

    NASA Astrophysics Data System (ADS)

    Lynch, Gillian C.; Pettitt, B. Montgomery

    1997-11-01

    The extended system Hamiltonian for carrying out grand canonical ensemble molecular dynamics simulations is reformulated. This new Hamiltonian includes a generalized treatment of the reference state partition function of the total chemical potential that reproduces the ideal gas behavior and various previous partitionings of ideal and excess terms. Initial calculations are performed on a system of Lennard-Jones particles near the triple point and on liquid water at room temperature.

  2. Anharmonic infrared and Raman spectra in Car-Parrinello molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pagliai, Marco; Cavazzoni, Carlo; Cardini, Gianni; Erbacci, Giovanni; Parrinello, Michele; Schettino, Vincenzo

    2008-06-01

    The infrared and Raman spectra of naphthalene crystal with inclusion of anharmonic effects have been calculated by adopting the generalized variational density functional perturbation theory in the framework of Car-Parrinello molecular dynamics simulations. The computational approach has been generalized for cells of arbitrary shape. The intermolecular interactions have been analyzed with and without the van der Waals corrections, showing the importance of such interactions in the naphthalene crystal to reproduce the structural, dynamical, and spectroscopic properties.

  3. Crystalline and liquid Si3 N4 characterization by first-principles molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mauri, Aurelio; Celino, Massimo; Castellani, Niccoló; Erbetta, Davide

    2011-05-01

    Silicon nitride (Si3 N4) has a wide range of engineering applications where its mechanical and electronic properties can be effectively exploited. In particular, in the microelectronics field, the amorphous silicon nitride films are widely used as charge storage layer in metal-alumina-nitrideoxide nonvolatile memory devices. Atomic structure of amorphous silicon nitride is characterized by an high concentration of traps that control the electric behavior of the final device by the trappingde-trapping mechanism of the electrical charge occurring in its traps. In order to have a deep understanding of the material properties and, in particular, the nature of the electrical active traps a detailed numerical characterization of the crystalline and liquid phases is mandatory. For these reasons first-principles molecular dynamics simulations are extensively employed to simulate the crystalline Si3 N4 in its crystalline and liquid phases. Good agreement with experimental results is obtained in terms of density and formation entalpy. Detailed characterization of c-Si3 N4 electronic properties is performed in terms of band structure and band gap. Then constant temperature and constant volume first-principles molecular dynamics is used to disorder a stoichiometric sample of Si3 N4 . Extensive molecular dynamics simulations are performed to obtain a reliable liquid sample whose atomic structure does not depend on the starting atomic configuration. Detailed characterization of the atomic structure is achieved in terms of radial distribution functions and total structure factor.

  4. Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations

    PubMed Central

    Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

    2015-01-01

    Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic. PMID:26177039

  5. Ab initio molecular dynamics simulation of proton hopping in a model polymer membrane.

    PubMed

    Devanathan, Ram; Idupulapati, Nagesh; Baer, Marcel D; Mundy, Christopher J; Dupuis, Michel

    2013-12-27

    We report the results of ab initio molecular dynamics simulations of a model Nafion polymer membrane initially equilibrated using classical molecular dynamics simulations. We studied three hydration levels (λ) of 3, 9, and 15 H2O/SO3(-) corresponding to dry, hydrated, and saturated fuel cell membrane, respectively. The barrier for proton transfer from the SO3(-)-H3O(+) contact ion pair to a solvent-separated ion pair decreased from 2.3 kcal/mol for λ = 3 to 0.8 kcal/mol for λ = 15. The barrier for proton transfer between two water molecules was in the range from 0.7 to 0.8 kcal/mol for the λ values studied. The number of proton shuttling events between a pair of water molecules is an order of magnitude more than the number of proton hops across three distinct water molecules. The proton diffusion coefficient at λ = 15 is about 0.9 × 10(-5) cm(2)/s, which is in good agreement with experiment and our previous quantum hopping molecular dynamics simulations. PMID:24320080

  6. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    PubMed

    Koldsø, Heidi; Autzen, Henriette Elisabeth; Grouleff, Julie; Schiøtt, Birgit

    2013-01-01

    The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design. PMID:23776432

  7. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

    PubMed

    Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-10-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754

  8. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

    PubMed Central

    Dijkstra, Maurits J. J.; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-01-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754

  9. Ligand Induced Conformational Changes of the Human Serotonin Transporter Revealed by Molecular Dynamics Simulations

    PubMed Central

    Grouleff, Julie; Schiøtt, Birgit

    2013-01-01

    The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design. PMID:23776432

  10. Molecular dynamics simulations of creatine kinase and adenine nucleotide translocase in mitochondrial membrane patch.

    PubMed

    Karo, Jaanus; Peterson, Pearu; Vendelin, Marko

    2012-03-01

    Interaction between mitochondrial creatine kinase (MtCK) and adenine nucleotide translocase (ANT) can play an important role in determining energy transfer pathways in the cell. Although the functional coupling between MtCK and ANT has been demonstrated, the precise mechanism of the coupling is not clear. To study the details of the coupling, we turned to molecular dynamics simulations. We introduce a new coarse-grained molecular dynamics model of a patch of the mitochondrial inner membrane containing a transmembrane ANT and an MtCK above the membrane. The membrane model consists of three major types of lipids (phosphatidylcholine, phosphatidylethanolamine, and cardiolipin) in a roughly 2:1:1 molar ratio. A thermodynamics-based coarse-grained force field, termed MARTINI, has been used together with the GROMACS molecular dynamics package for all simulated systems in this work. Several physical properties of the system are reproduced by the model and are in agreement with known data. This includes membrane thickness, dimension of the proteins, and diffusion constants. We have studied the binding of MtCK to the membrane and demonstrated the effect of cardiolipin on the stabilization of the binding. In addition, our simulations predict which part of the MtCK protein sequence interacts with the membrane. Taken together, the model has been verified by dynamical and structural data and can be used as the basis for further studies. PMID:22241474

  11. Chain dynamics in a hexadecane melt as seen by neutron scattering and identified by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Morhenn, Humphrey; Busch, Sebastian; Unruh, Tobias

    2012-09-01

    Different local and global chain dynamics in a C16H34 melt could be revealed by resolution resolved time-of-flight quasielastic neutron scattering and complementary molecular dynamics simulations. Thereby it has been demonstrated that the measured intermediate scattering functions can validate the simulated data on the pico- to nanosecond timescale. Remarkably the shape of the experimentally measured intermediate scattering functions can be reproduced excellently by molecular dynamics simulations. It was found that although the extracted apparent activation energy corresponds to the long-range diffusion value, the molecular dynamics in this time range are mainly due to local bond rotations and the rotation of entire molecules.

  12. Seeking new mutation clues from Bacillus licheniformis amylase by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lu, Tao

    2009-07-01

    Amylase is one of the most important industrial enzymes in the world. Researchers have been searching for a highly thermal stable mutant for many years, but most focus on point mutations of one or few nitrogenous bases. According to this molecular dynamic simulation of amylase from Bacillus licheniformis (BLA), the deletion of some nitrogenous bases would be more efficacious than point mutations. The simulation reveals strong fluctuation of the BLA structure at optimum temperature. The fluctuation of the outer domains of BLA is stronger than that of the core domain. Molecular simulation provides a clue to design thermal stable amylases through deletion mutations in the outer domain.

  13. Molecular Dynamics Simulation of Defect Production in Collision Cascades in Zircon

    SciTech Connect

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

    2005-01-01

    Defect production in collision cascades in zircon has been examined by molecular dynamics simulations using a partial charge model combined with the Ziegler-Biersack-Littmark potential. U, Zr, Si and O recoils with energies ranging from 250 eV to 5 keV were simulated in the NVE ensemble. To obtain good statistics, 5-10 cascades in randomly chosen directions were simulated for each ion and energy. The damage consists of mainly Si and O Frenkel pairs, a smaller number of Zr Frenkel pairs, and Zr on Si antisite defects. Defect production, interstitial clustering, ion beam mixing and Si-O-Si polymerization increase with PKA mass and energy.

  14. Coarse-grain molecular dynamics simulations of diblock copolymer surfactants interacting with a lipid bilayer

    NASA Astrophysics Data System (ADS)

    Srinivas, Goundla; Klein, Michael L.

    2004-01-01

    The interaction of surfactant diblock poly(ethylene oxide)-poly(ethylethylene) copolymers (PEO-PEE) with a lipid bilayer of dimyristoylphosphatidylcholine has been studied by means of coarse-grain molecular dynamics simulations. The effect of the surfactants on the lipid bilayer was studied over a wide range of diblock copolymer concentrations. The simulations show that the hydrophilic PEO chains adopt different structures at low and high concentrations. In particular, the computed density profiles reveal that the PEO chains extend over a longer range from the bilayer surface, with increasing copolymer concentration. The simulated density profiles are in agreement with the scaling law predictions.

  15. Low energy and low fluence helium implantations in tungsten: Molecular dynamics simulations and experiments

    NASA Astrophysics Data System (ADS)

    Pentecoste, L.; Brault, P.; Thomann, A.-L.; Desgardin, P.; Lecas, T.; Belhabib, T.; Barthe, M.-F.; Sauvage, T.

    2016-03-01

    300 eV Helium implantation process into tungsten at 300 K has been studied with molecular dynamic simulations (MD). Predicted retention doses were compared to that obtained from experiments performed in equivalent conditions. A saturation phenomenon of the helium retention was evidenced for a number of impinging He atoms and a retention dose similar in both, experiments and simulations. From MD simulations it is learnt that observed Helium diffusion, formation and coalescence of clusters are the phenomena leading to the flaking of the substrate. These processes could explain the saturation of the Helium retention observed experimentally at low energies.

  16. Lithium(I) in liquid ammonia: A quantum mechanical charge field (QMCF) molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Prasetyo, Niko; Canaval, Lorenz R.; Wijaya, Karna; Armunanto, Ria

    2015-01-01

    The solvation of Li(I) in liquid ammonia has been investigated by an ab initio quantum mechanical charge-field molecular dynamics (QMCF-MD) simulation. Being the first simulation of a metal cation in liquid ammonia employing this methodology, the work yields a wide range of accurate structural and dynamical data. Li(I) is tetrahedrally coordinated by four ammonia molecules in the first solvation shell at a distance of 2.075 Å. Two ligand exchange attempts have been observed within 12 ps of simulation time. The second solvation shell shows a more labile structure with numerous successful exchanges. The results are in excellent agreement with experiments.

  17. Molecular dynamics simulations of soliton-like structures in a dusty plasma medium

    SciTech Connect

    Tiwari, Sanat Kumar Das, Amita; Sen, Abhijit; Kaw, Predhiman

    2015-03-15

    The existence and evolution of soliton-like structures in a dusty plasma medium are investigated in a first principles approach using molecular dynamic (MD) simulations of particles interacting via a Yukawa potential. These localized structures are found to exist in both weakly and strongly coupled regimes with their structures becoming sharper as the correlation effects between the dust particles get stronger. A surprising result, compared to fluid simulations, is the existence of rarefactive soliton-like structures in our non-dissipative system, a feature that arises from the charge conjugation symmetry property of the Yukawa fluid. Our simulation findings closely resemble many diverse experimental results reported in the past.

  18. Molecular dynamics simulations of an apoliprotein A I derived peptide in explicit water

    NASA Astrophysics Data System (ADS)

    Stavrakoudis, Athanassios

    2008-08-01

    Molecular dynamics simulations have been performed for the 104-117 α-helical fragment of apoliprotein A-I using the CHARMM22 force field and the N AMD simulation engine. Simulation (50 ns in explicit water) resulted in significant appearance of π-helix conformation, which was totally diminished when the CMAP correction of the CHARMM force field was applied. This is consistent with other similar studies which suggest that the observation of π-helix in peptide conformation was force field biased rather actually existed. This study suggests that the 104-117 fragment of apoliprotein A-I has a stable α-helical conformation in water.

  19. Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

    SciTech Connect

    Kimminau, G; Nagler, B; Higginbotham, A; Murphy, W; Park, N; Hawreliak, J; Kadau, K; Germann, T C; Bringa, E M; Kalantar, D; Lorenzana, H; Remington, B; Wark, J

    2008-06-19

    Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

  20. Discotic columnar liquid crystal studied in the bulk and nanoconfined states by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Busselez, Rémi; Cerclier, Carole V.; Ndao, Makha; Ghoufi, Aziz; Lefort, Ronan; Morineau, Denis

    2014-10-01

    A prototypical Gay Berne discotic liquid crystal was studied by means of molecular dynamics simulations both in the bulk state and under confinement in a nanoporous channel. The phase behavior of the confined system strongly differs from its bulk counterpart: the bulk isotropic-to-columnar transition is replaced by a continuous ordering from a paranematic to a columnar phase. Moreover, a new transition is observed at a lower temperature in the confined state, which corresponds to a reorganization of the intercolumnar order. It reflects the competing effects of pore surface interaction and genuine hexagonal packing of the columns. The translational molecular dynamics in the different phases has been thoroughly studied and discussed in terms of collective relaxation modes, non-Gaussian behavior, and hopping processes.

  1. Discotic columnar liquid crystal studied in the bulk and nanoconfined states by molecular dynamics simulation.

    PubMed

    Busselez, Rémi; Cerclier, Carole V; Ndao, Makha; Ghoufi, Aziz; Lefort, Ronan; Morineau, Denis

    2014-10-01

    A prototypical Gay Berne discotic liquid crystal was studied by means of molecular dynamics simulations both in the bulk state and under confinement in a nanoporous channel. The phase behavior of the confined system strongly differs from its bulk counterpart: the bulk isotropic-to-columnar transition is replaced by a continuous ordering from a paranematic to a columnar phase. Moreover, a new transition is observed at a lower temperature in the confined state, which corresponds to a reorganization of the intercolumnar order. It reflects the competing effects of pore surface interaction and genuine hexagonal packing of the columns. The translational molecular dynamics in the different phases has been thoroughly studied and discussed in terms of collective relaxation modes, non-Gaussian behavior, and hopping processes. PMID:25296832

  2. An Allosteric Mechanism Inferred from Molecular Dynamics Simulations on Phospholamban Pentamer in Lipid Membranes

    PubMed Central

    Lian, Peng; Wei, Dong-Qing; Wang, Jing-Fang; Chou, Kuo-Chen

    2011-01-01

    Phospholamban functions as a regulator of Ca2+ concentration of cardiac muscle cells by triggering the bioactivity of sarcoplasmic reticulum Ca2+-ATPase. In order to understand its dynamic mechanism in the environment of bilayer surroundings, we performed long time-scale molecular dynamic simulations based on the high-resolution NMR structure of phospholamban pentamer. It was observed from the molecular dynamics trajectory analyses that the conformational transitions between the “bellflower” and “pinwheel” modes were detected for phospholamban. Particularly, the two modes became quite similar to each other after phospholamban was phosphorylated at Ser16. Based on these findings, an allosteric mechanism was proposed to elucidate the dynamic process of phospholamban interacting with Ca2+-ATPase. PMID:21525996

  3. Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

    NASA Astrophysics Data System (ADS)

    Tringe, J. W.; Ileri, N.; Levie, H. W.; Stroeve, P.; Ustach, V.; Faller, R.; Renaud, P.

    2015-08-01

    We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.

  4. Quantum molecular dynamics simulation of shock-wave experiments in aluminum

    SciTech Connect

    Minakov, D. V.; Khishchenko, K. V.; Fortov, V. E.; Levashov, P. R.

    2014-06-14

    We present quantum molecular dynamics calculations of principal, porous, and double shock Hugoniots, release isentropes, and sound velocity behind the shock front for aluminum. A comprehensive analysis of available shock-wave data is performed; the agreement and discrepancies of simulation results with measurements are discussed. Special attention is paid to the melting region of aluminum along the principal Hugoniot; the boundaries of the melting zone are estimated using the self-diffusion coefficient. Also, we make a comparison with a high-quality multiphase equation of state for aluminum. Independent semiempirical and first-principle models are very close to each other in caloric variables (pressure, density, particle velocity, etc.) but the equation of state gives higher temperature on the principal Hugoniot and release isentropes than ab initio calculations. Thus, the quantum molecular dynamics method can be used for calibration of semiempirical equations of state in case of lack of experimental data.

  5. Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation

    NASA Technical Reports Server (NTRS)

    Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.

    2007-01-01

    The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.

  6. MDSLB: A new static load balancing method for parallel molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wu, Yun-Long; Xu, Xin-Hai; Yang, Xue-Jun; Zou, Shun; Ren, Xiao-Guang

    2014-02-01

    Large-scale parallelization of molecular dynamics simulations is facing challenges which seriously affect the simulation efficiency, among which the load imbalance problem is the most critical. In this paper, we propose, a new molecular dynamics static load balancing method (MDSLB). By analyzing the characteristics of the short-range force of molecular dynamics programs running in parallel, we divide the short-range force into three kinds of force models, and then package the computations of each force model into many tiny computational units called “cell loads”, which provide the basic data structures for our load balancing method. In MDSLB, the spatial region is separated into sub-regions called “local domains”, and the cell loads of each local domain are allocated to every processor in turn. Compared with the dynamic load balancing method, MDSLB can guarantee load balance by executing the algorithm only once at program startup without migrating the loads dynamically. We implement MDSLB in OpenFOAM software and test it on TianHe-1A supercomputer with 16 to 512 processors. Experimental results show that MDSLB can save 34%-64% time for the load imbalanced cases.

  7. Study of silicon crystal surface formation based on molecular dynamics simulation results

    NASA Astrophysics Data System (ADS)

    Barinovs, G.; Sabanskis, A.; Muiznieks, A.

    2014-04-01

    The equilibrium shape of <110>-oriented single crystal silicon nanowire, 8 nm in cross-section, was found from molecular dynamics simulations using LAMMPS molecular dynamics package. The calculated shape agrees well to the shape predicted from experimental observations of nanocavities in silicon crystals. By parametrization of the shape and scaling to a known value of {111} surface energy, Wulff form for solid-vapor interface was obtained. The Wulff form for solid-liquid interface was constructed using the same model of the shape as for the solid-vapor interface. The parameters describing solid-liquid interface shape were found using values of surface energies in low-index directions known from published molecular dynamics simulations. Using an experimental value of the liquid-vapor interface energy for silicon and graphical solution of Herring's equation, we constructed angular diagram showing relative equilibrium orientation of solid-liquid, liquid-vapor and solid-vapor interfaces at the triple phase line. The diagram gives quantitative predictions about growth angles for different growth directions and formation of facets on the solid-liquid and solid-vapor interfaces. The diagram can be used to describe growth ridges appearing on the crystal surface grown from a melt. Qualitative comparison to the ridges of a Float zone silicon crystal cone is given.

  8. Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

    NASA Astrophysics Data System (ADS)

    Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy; Jacobs, Donald; Cai, Wei

    2013-07-01

    This paper extends the image charge solvation model (ICSM) [Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, W. Cai, An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions, J. Chem. Phys. 131 (2009) 154103], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated.

  9. Molecular dynamics of tryptophan in ribonuclease-T1. I. Simulation strategies and fluorescence anisotropy decay.

    PubMed Central

    Axelsen, P H; Haydock, C; Prendergast, F G

    1988-01-01

    Molecular dynamics simulations of Ribonuclease-T1 (RNAse-T1) were performed using x-ray crystal coordinates for the enzyme and various simulation strategies. From each of the simulations, a predicted fluorescence anisotropy decay for the single-tryptophan residue was derived and compared with experimental values for the limiting anisotropy of this protein. Simulations conducted in vacuo demonstrated large displacements among some of the residues adjacent to the tryptophan side chain. As a consequence, the ring system rotates relatively unhindered through an angle far in excess of that implied by experimental data. In contrast, the explicit simulation of solvent within a stochastic boundary led to excellent agreement between simulation and experiment. In the case of RNAse-T1, the experimentally-determined limiting anisotropy is useful as a criterion of simulation accuracy in the vicinity of the tryptophan side chain. PMID:3145038

  10. Liquid-Liquid Phase Transformation in Silicon: Evidence from First-Principles Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Jakse, N.; Pasturel, A.

    2007-11-01

    We report results of first principles molecular dynamics simulations that confirm early speculations on the presence of liquid-liquid phase transition in undercooled silicon. However, we find that structural and electronic properties of both low-density liquid (LDL) and high-density liquid (HDL) phases are quite different from those obtained by empirical calculations, the difference being more pronounced for the HDL phase. The discrepancy between quantum and classical simulations is attributed to the inability of empirical potentials to describe changes in chemical bonds induced by density and temperature variations.

  11. Single-asperity contributions to multi-asperity wear simulated with molecular dynamics

    NASA Astrophysics Data System (ADS)

    Eder, S. J.; Cihak-Bayr, U.; Bianchi, D.

    2016-03-01

    We use a molecular dynamics approach to simulate the wear of a rough ferrite surface due to multiple hard, abrasive particles under variation of normal pressure, grinding direction, and particle geometry. By employing a clustering algorithm that incorporates some knowledge about the grinding process such as the main grinding direction, we can break down the total wear volume into contributions from the individual abrasive particles in a time-resolved fashion. The resulting analysis of the simulated grinding process allows statements on wear particle generation, distribution, and stability depending on the initial topography, the grinding angle, the normal pressure, as well as the abrasive shape and orientation with respect to the surface.

  12. An Assessment of Molecular Dynamic Force Fields for Silica for Use in Simulating Laser Damage Mitigation

    SciTech Connect

    Soules, T F; Gilmer, G H; Matthews, M J; Stolken, J S; Feit, M D

    2010-10-21

    We compare force fields (FF's) that have been used in molecular dynamic (MD) simulations of silica in order to assess their applicability for use in simulating IR-laser damage mitigation. Although pairwise FF?s obtained by fitting quantum mechanical calculations such as the BKS and CHIK potentials have been shown to reproduce many of the properties of silica including the stability of silica polymorphs and the densification of the liquid, we show that melting temperatures and fictive temperatures are much too high. Softer empirical force fields give liquid and glass properties at experimental temperatures but may not predict all properties important to laser mitigation experiments.

  13. Molecular dynamic simulation for nanometric cutting of single-crystal face-centered cubic metals

    PubMed Central

    2014-01-01

    In this work, molecular dynamics simulations are performed to investigate the influence of material properties on the nanometric cutting of single crystal copper and aluminum with a diamond cutting tool. The atomic interactions in the two metallic materials are modeled by two sets of embedded atom method (EAM) potential parameters. Simulation results show that although the plastic deformation of the two materials is achieved by dislocation activities, the deformation behavior and related physical phenomena, such as the machining forces, machined surface quality, and chip morphology, are significantly different for different materials. Furthermore, the influence of material properties on the nanometric cutting has a strong dependence on the operating temperature. PMID:25426007

  14. Deformation behavior of bulk and nanostructured metallic glasses studied via molecular dynamics simulations

    SciTech Connect

    Sopu, D.; Ritter, Y.; Albe, K.; Gleiter, H.

    2011-03-01

    In this study, we characterize the mechanical properties of Cu{sub 64}Zr{sub 36} nanoglasses under tensile load by means of large-scale molecular dynamics simulations and compare the deformation behavior to the case of a homogeneous bulk glass. The simulations reveal that interfaces act as precursors for the formation of multiple shear bands. In contrast, a bulk metallic glass under uniaxial tension shows inhomogeneous plastic flow confined in one dominant shear band. The results suggest that controlling the microstructure of a nanoglass can pave the way for tuning the mechanical properties of glassy materials.

  15. Evaporative cooling of microscopic water droplets in vacuo: Molecular dynamics simulations and kinetic gas theory.

    PubMed

    Schlesinger, Daniel; Sellberg, Jonas A; Nilsson, Anders; Pettersson, Lars G M

    2016-03-28

    In the present study, we investigate the process of evaporative cooling of nanometer-sized droplets in vacuum using molecular dynamics simulations with the TIP4P/2005 water model. The results are compared to the temperature evolution calculated from the Knudsen theory of evaporation which is derived from kinetic gas theory. The calculated and simulation results are found to be in very good agreement for an evaporation coefficient equal to unity. Our results are of interest to experiments utilizing droplet dispensers as well as to cloud micro-physics. PMID:27036456

  16. Evaporative cooling of microscopic water droplets in vacuo: Molecular dynamics simulations and kinetic gas theory

    NASA Astrophysics Data System (ADS)

    Schlesinger, Daniel; Sellberg, Jonas A.; Nilsson, Anders; Pettersson, Lars G. M.

    2016-03-01

    In the present study, we investigate the process of evaporative cooling of nanometer-sized droplets in vacuum using molecular dynamics simulations with the TIP4P/2005 water model. The results are compared to the temperature evolution calculated from the Knudsen theory of evaporation which is derived from kinetic gas theory. The calculated and simulation results are found to be in very good agreement for an evaporation coefficient equal to unity. Our results are of interest to experiments utilizing droplet dispensers as well as to cloud micro-physics.

  17. Classical molecular dynamics simulations of hypervelocity nanoparticle impacts on amorphous silica

    SciTech Connect

    Samela, Juha; Nordlund, Kai

    2010-02-01

    We have investigated the transition from the atomistic to the macroscopic impact mechanism by simulating large Argon cluster impacts on amorphous silica. The transition occurs at cluster sizes less than 50 000 atoms at hypervelocity regime (22 km/s). After that, the crater volume increases linearly with the cluster size opposite to the nonlinear scaling typical of small cluster impacts. The simulations demonstrate that the molecular dynamics method can be used to explore atomistic mechanisms that lead to damage formation in small particle impacts, for example, in impacts of micrometeorites on spacecraft.

  18. Evaporative cooling of microscopic water droplets in vacuo: Molecular dynamics simulations and kinetic gas theory

    DOE PAGESBeta

    Schlesinger, Daniel; Sellberg, Jonas A.; Nilsson, Anders; Pettersson, Lars G. M.

    2016-03-22

    In the present study, we investigate the process of evaporative cooling of nanometer-sized droplets in vacuum using molecular dynamics simulations with the TIP4P/2005 water model. The results are compared to the temperature evolution calculated from the Knudsen theory of evaporation which is derived from kinetic gas theory. The calculated and simulation results are found to be in very good agreement for an evaporation coefficient equal to unity. Lastly, our results are of interest to experiments utilizing droplet dispensers as well as to cloud micro-physics.

  19. Molecular dynamics simulation of Ga penetration along grain boundaries in Al: a dislocation climb mechanism.

    PubMed

    Nam, Ho-Seok; Srolovitz, David J

    2007-07-13

    Many systems where a liquid metal is in contact with a polycrystalline solid exhibit deep liquid grooves where the grain boundary meets the solid-liquid interface. For example, liquid Ga quickly penetrates deep into grain boundaries in Al, leading to intergranular fracture under very small stresses. We report on a series of molecular dynamics simulations of liquid Ga in contact with an Al bicrystal. We identify the mechanism for liquid metal embrittlement, develop a new model for it, and show that is in excellent agreement with both simulation and experimental data. PMID:17678231

  20. Deposition of an energetic Al cluster on Si(111) substrate: a molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Li, He; Zongning, Xia; Hao, Zhang; Jiayou, Feng; Yunwen, Lu

    1998-11-01

    A molecular dynamics simulation on the deposition of an energetic Al cluster on Si(111) substrate was studied. We employed the Stillinger-Weber three-body potential to simulate the Si substrate and the Born-Mayer-Higgins potential to compute the interactions between cluster and substrate. For one impacting Al cluster, the migration distance of the cluster atoms and the deposition morphology were investigated under different substrate temperatures, impacting cluster energies and cluster sizes. It can be found that diffusion distance increases with the increasing substrate temperature, cluster energy and cluster size; moreover the deposition morphologies also change under similar conditions.

  1. Molecular dynamic simulation for nanometric cutting of single-crystal face-centered cubic metals.

    PubMed

    Huang, Yanhua; Zong, Wenjun

    2014-01-01

    In this work, molecular dynamics simulations are performed to investigate the influence of material properties on the nanometric cutting of single crystal copper and aluminum with a diamond cutting tool. The atomic interactions in the two metallic materials are modeled by two sets of embedded atom method (EAM) potential parameters. Simulation results show that although the plastic deformation of the two materials is achieved by dislocation activities, the deformation behavior and related physical phenomena, such as the machining forces, machined surface quality, and chip morphology, are significantly different for different materials. Furthermore, the influence of material properties on the nanometric cutting has a strong dependence on the operating temperature. PMID:25426007

  2. Molecular Dynamics Simulation of Palmitate Ester Self-Assembly with Diclofenac

    PubMed Central

    Karjiban, Roghayeh Abedi; Basri, Mahiran; Rahman, Mohd Basyaruddin Abdul; Salleh, Abu Bakar

    2012-01-01

    Palm oil-based esters (POEs) are unsaturated and non-ionic esters with a great potential to act as chemical penetration enhancers and drug carriers for transdermal drug nano-delivery. A ratio of palmitate ester and nonionic Tween80 with and without diclofenac acid was chosen from an experimentally determined phase diagram. Molecular dynamics simulations were performed for selected compositions over a period of 15 ns. Both micelles showed a prolate-like shape, while adding the drug produced a more compact micellar structure. Our results proposed that the drug could behave as a co-surfactant in our simulated model. PMID:22949816

  3. Molecular dynamics simulation of palmitate ester self-assembly with diclofenac.

    PubMed

    Karjiban, Roghayeh Abedi; Basri, Mahiran; Rahman, Mohd Basyaruddin Abdul; Salleh, Abu Bakar

    2012-01-01

    Palm oil-based esters (POEs) are unsaturated and non-ionic esters with a great potential to act as chemical penetration enhancers and drug carriers for transdermal drug nano-delivery. A ratio of palmitate ester and nonionic Tween80 with and without diclofenac acid was chosen from an experimentally determined phase diagram. Molecular dynamics simulations were performed for selected compositions over a period of 15 ns. Both micelles showed a prolate-like shape, while adding the drug produced a more compact micellar structure. Our results proposed that the drug could behave as a co-surfactant in our simulated model. PMID:22949816

  4. Parallel implementation of three-dimensional molecular dynamic simulation for laser-cluster interaction

    SciTech Connect

    Holkundkar, Amol R.

    2013-11-15

    The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of the experiments reported in the literature. Scaling laws for the computational time is established by varying the number of processor cores and number of macroparticles used. The capabilities of the code are highlighted by implementing various diagnostic tools. To study the dynamics of the laser-cluster interactions, the executable version of the code is available from the author.

  5. Molecular dynamics simulations of turbostratic dry and hydrated montmorillonite with intercalated carbon dioxide.

    PubMed

    Myshakin, Evgeniy M; Makaremi, Meysam; Romanov, Vyacheslav N; Jordan, Kenneth D; Guthrie, George D

    2014-09-01

    Molecular dynamics simulations using classical force fields were carried out to study energetic and structural properties of rotationally disordered clay mineral-water-CO2 systems at pressure and temperature relevant to geological carbon storage. The simulations show that turbostratic stacking of hydrated Na- and Ca-montmorillonite and hydrated montmorillonite with intercalated carbon dioxide is an energetically demanding process accompanied by an increase in the interlayer spacing. On the other hand, rotational disordering of dry or nearly dry smectite systems can be energetically favorable. The distributions of interlayer species are calculated as a function of the rotational angle between adjacent clay layers. PMID:24745358

  6. Thermal Decomposition of the Solid Phase of Nitromethane: Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Chang, Jing; Lian, Peng; Wei, Dong-Qing; Chen, Xiang-Rong; Zhang, Qing-Ming; Gong, Zi-Zheng

    2010-10-01

    The Car-Parrinello molecular dynamics simulations were employed to investigate thermal decomposition of the solid nitromethane. It is found that it undergoes chemical decomposition at about 2200 K under ambient pressure. The initiation of reactions involves both proton transfer and commonly known C-N bond cleavage. About 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2, and CNCNC. It represents the first complete simulation of solid-phase explosive reactions reported to date, which is of far-reaching implication for design and development of new energetic materials.

  7. Dielectric relaxation of ethylene carbonate and propylene carbonate from molecular dynamics simulations

    SciTech Connect

    Chaudhari, Mangesh I.; You, Xinli; Pratt, Lawrence R.; Rempe, Susan B.

    2015-11-24

    Ethylene carbonate (EC) and propylene carbonate (PC) are widely used solvents in lithium (Li)-ion batteries and supercapacitors. Ion dissolution and diffusion in those media are correlated with solvent dielectric responses. Here, we use all-atom molecular dynamics simulations of the pure solvents to calculate dielectric constants and relaxation times, and molecular mobilities. The computed results are compared with limited available experiments to assist more exhaustive studies of these important characteristics. As a result, the observed agreement is encouraging and provides guidance for further validation of force-field simulation models for EC and PC solvents.

  8. Molecular dynamics simulation of a binary mixture near the lower critical point

    NASA Astrophysics Data System (ADS)

    Pousaneh, Faezeh; Edholm, Olle; Maciołek, Anna

    2016-07-01

    2,6-lutidine molecules mix with water at high and low temperatures but in a wide intermediate temperature range a 2,6-lutidine/water mixture exhibits a miscibility gap. We constructed and validated an atomistic model for 2,6-lutidine and performed molecular dynamics simulations of 2,6-lutidine/water mixture at different temperatures. We determined the part of demixing curve with the lower critical point. The lower critical point extracted from our data is located close to the experimental one. The estimates for critical exponents obtained from our simulations are in a good agreement with the values corresponding to the 3D Ising universality class.

  9. Classical molecular dynamics simulations of hypervelocity nanoparticle impacts on amorphous silica

    NASA Astrophysics Data System (ADS)

    Samela, Juha; Nordlund, Kai

    2010-02-01

    We have investigated the transition from the atomistic to the macroscopic impact mechanism by simulating large Argon cluster impacts on amorphous silica. The transition occurs at cluster sizes less than 50000 atoms at hypervelocity regime (22 km/s). After that, the crater volume increases linearly with the cluster size opposite to the nonlinear scaling typical of small cluster impacts. The simulations demonstrate that the molecular dynamics method can be used to explore atomistic mechanisms that lead to damage formation in small particle impacts, for example, in impacts of micrometeorites on spacecraft.

  10. Temperature-dependent mechanical properties of single-layer molybdenum disulphide: Molecular dynamics nanoindentation simulations

    NASA Astrophysics Data System (ADS)

    Zhao, Junhua; Jiang, Jin-Wu; Rabczuk, Timon

    2013-12-01

    The temperature-dependent mechanical properties of single-layer molybdenum disulphide (MoS2) are obtained using molecular dynamics (MD) nanoindentation simulations. The Young's moduli, maximum load stress, and maximum loading strain decrease with increasing temperature from 4.2 K to 500 K. The obtained Young's moduli are in good agreement with those using our MD uniaxial tension simulations and the available experimental results. The tendency of maximum loading strain with different temperature is opposite with that of metal materials due to the short range Stillinger-Weber potentials in MoS2. Furthermore, the indenter tip radius and fitting strain effect on the mechanical properties are also discussed.

  11. Molecular dynamics simulation of vapour-liquid nucleation of water with constant energy

    NASA Astrophysics Data System (ADS)

    Duška, Michal; Němec, Tomáš; Hrubý, Jan; Vinš, Václav; Planková, Barbora

    2015-05-01

    The paper describes molecular dynamics study of nucleation of water in NVE ensemble. The numerical simulation was performed with the DL_POLY. The metastable steam consisting of 10976 water molecules with TIP4P/2005 potential was driven on the desired energy level by a simulation at constant temperature, and then the nucleation at constant energy was studied for several tens of nanoseconds, which was sufficient for clusters to evolve at hundred molecules size. The results were compared with the previously published results and the classical nucleation theory predictions.

  12. Dislocation mechanism of void growth at twin boundary of nanotwinned nickel based on molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Yanqiu; Jiang, Shuyong; Zhu, Xiaoming; Zhao, Yanan

    2016-08-01

    Molecular dynamics simulation was performed to investigate dislocation mechanism of void growth at twin boundary (TB) of nanotwinned nickel. Simulation results show that the deformation of nanotwinned nickel containing a void at TB is dominated by the slip involving both leading and trailing partials, where the trailing partials are the dissociation products of stair-rod dislocations formed by the leading partials. The growth of a void at TB is attributed to the successive emission of the leading partials followed by trailing partials as well as the escape of these partial dislocations from the void surface.

  13. Molecular dynamics simulations of the liquid/vapor interface of SPC/E water

    SciTech Connect

    Taylor, R.S.; Dang, L,X.; Garrett, B.C.

    1996-07-11

    Molecular dynamics computer simulations have been used to explore the structural and dynamical properties of water`s liquid/vapor interface using the simple extended point charge (SPC/E) model. Comparisons to the existing experimental and simulation data suggest that the SPC/E potential energy function provides a semiquantitative description of this interface. The orientation of H{sub 2}O molecules at the interface is found to be bimodal in nature. The self-diffusion constant of water is calculated to be larger at the surface than in the bulk. 46 refs., 10 figs., 1 tab.

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

    NASA Astrophysics Data System (ADS)

    Shekhar, Adarsh

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

  15. i-PI: A Python interface for ab initio path integral molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

    2014-03-01

    Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic

  16. Folding simulations of gramicidin A into the β-helix conformations: Simulated annealing molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Mori, Takaharu; Okamoto, Yuko

    2009-10-01

    Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the β6.3-helix, to act as a cation-selective ion channel in the natural conditions. In order to investigate the intrinsic ability of the gramicidin A monomer to form secondary structures, we performed the folding simulation of gramicidin A using a simulated annealing molecular dynamics (MD) method in vacuum mimicking the low-dielectric, homogeneous membrane environment. The initial conformation was a fully extended one. From the 200 different MD runs, we obtained a right-handed β4.4-helix as the lowest-potential-energy structure, and left-handed β4.4-helix, right-handed and left-handed β6.3-helix as local-minimum energy states. These results are in accord with those of the experiments of gramicidin A in homogeneous organic solvent. Our simulations showed a slight right-hand sense in the lower-energy conformations and a quite β-sheet-forming tendency throughout almost the entire sequence. In order to examine the stability of the obtained right-handed β6.3-helix and β4.4-helix structures in more realistic membrane environment, we have also performed all-atom MD simulations in explicit water, ion, and lipid molecules, starting from these β-helix structures. The results suggested that β6.3-helix is more stable than β4.4-helix in the inhomogeneous, explicit membrane environment, where the pore water and the hydrogen bonds between Trp side-chains and lipid-head groups have a role to further stabilize the β6.3-helix conformation.

  17. Folding simulations of gramicidin A into the beta-helix conformations: Simulated annealing molecular dynamics study.

    PubMed

    Mori, Takaharu; Okamoto, Yuko

    2009-10-28

    Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the beta(6.3)-helix, to act as a cation-selective ion channel in the natural conditions. In order to investigate the intrinsic ability of the gramicidin A monomer to form secondary structures, we performed the folding simulation of gramicidin A using a simulated annealing molecular dynamics (MD) method in vacuum mimicking the low-dielectric, homogeneous membrane environment. The initial conformation was a fully extended one. From the 200 different MD runs, we obtained a right-handed beta(4.4)-helix as the lowest-potential-energy structure, and left-handed beta(4.4)-helix, right-handed and left-handed beta(6.3)-helix as local-minimum energy states. These results are in accord with those of the experiments of gramicidin A in homogeneous organic solvent. Our simulations showed a slight right-hand sense in the lower-energy conformations and a quite beta-sheet-forming tendency throughout almost the entire sequence. In order to examine the stability of the obtained right-handed beta(6.3)-helix and beta(4.4)-helix structures in more realistic membrane environment, we have also performed all-atom MD simulations in explicit water, ion, and lipid molecules, starting from these beta-helix structures. The results suggested that beta(6.3)-helix is more stable than beta(4.4)-helix in the inhomogeneous, explicit membrane environment, where the pore water and the hydrogen bonds between Trp side-chains and lipid-head groups have a role to further stabilize the beta(6.3)-helix conformation. PMID:19894978

  18. Atomistic hybrid DSMC/NEMD method for nonequilibrium multiscale simulations

    SciTech Connect

    Gu Kai; Watkins, Charles B. Koplik, Joel

    2010-03-01

    A multiscale hybrid method for coupling the direct simulation Monte Carlo (DSMC) method to the nonequilibrium molecular dynamics (NEMD) method is introduced. The method addresses Knudsen layer type gas flows within a few mean free paths of an interface or about an object with dimensions of the order of a few mean free paths. It employs the NEMD method to resolve nanoscale phenomena closest to the interface along with coupled DSMC simulation of the remainder of the Knudsen layer. The hybrid DSMC/NEMD method is a particle based algorithm without a buffer zone. It incorporates a new, modified generalized soft sphere (MGSS) molecular collision model to improve the poor computational efficiency of the traditional generalized soft sphere GSS model and to achieve DSMC compatibility with Lennard-Jones NEMD molecular interactions. An equilibrium gas, a Fourier thermal flow, and an oscillatory Couette flow, are simulated to validate the method. The method shows good agreement with Maxwell-Boltzmann theory for the equilibrium system, Chapman-Enskog theory for Fourier flow, and pure DSMC simulations for oscillatory Couette flow. Speedup in CPU time of the hybrid solver is benchmarked against a pure NEMD solver baseline for different system sizes and solver domain partitions. Finally, the hybrid method is applied to investigate interaction of argon gas with solid surface molecules in a parametric study of the influence of wetting effects and solid molecular mass on energy transfer and thermal accommodation coefficients. It is determined that wetting effect strength and solid molecular mass have a significant impact on the energy transfer between gas and solid phases and thermal accommodation coefficient.

  19. Molecular dynamics simulation of effective thermal conductivity and study of enhanced thermal transport mechanism in nanofluids

    NASA Astrophysics Data System (ADS)

    Sarkar, Suranjan; Selvam, R. Panneer

    2007-10-01

    Nanofluids have been proposed as a route for surpassing the performance of currently available heat transfer liquids in the near future. In this study an equilibrium molecular dynamics simulation was used to model a nanofluid system. The thermal conductivity of the base fluid and nanofluid was computed using the Green-Kubo method for various volume fractions of nanoparticle loadings. This study showed the ability of molecular dynamics to predict the enhanced thermal conductivity of nanofluids. Through molecular dynamics calculation of mean square displacements for liquid phase in base fluid and for liquid and solid phases in nanofluid, this study tried to investigate the mechanisms involved in thermal transport of nanofluids at the atomic level. The result showed that the thermal transport enhancement of nanofluids was mostly due to the increased movement of liquid atoms in the presence of nanoparticle. Diffusion coefficients were also calculated for base fluid and nanofluids. Similarity of enhancement in thermal conductivity and diffusion coefficient for nanofluids indicates similar transport process for mass and heat.

  20. Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain

    PubMed Central

    Freddolino, Peter L.; Liu, Feng; Gruebele, Martin; Schulten, Klaus

    2008-01-01

    All-atom molecular dynamics (MD) simulations of protein folding allow analysis of the folding process at an unprecedented level of detail. Unfortunately, such simulations have not yet reached their full potential both due to difficulties in sufficiently sampling the microsecond timescales needed for folding, and because the force field used may yield neither the correct dynamical sequence of events nor the folded structure. The ongoing study of protein folding through computational methods thus requires both improvements in the performance of molecular dynamics programs to make longer timescales accessible, and testing of force fields in the context of folding simulations. We report a ten-microsecond simulation of an incipient downhill-folding WW domain mutant along with measurement of a molecular time and activated folding time of 1.5 microseconds and 13.3 microseconds, respectively. The protein simulated in explicit solvent exhibits several metastable states with incorrect topology and does not assume the native state during the present simulations. PMID:18339748

  1. Triplet correlation functions in the Lennard-Jones fluid: Tests against molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    McNeil, William J.; Madden, William G.; Haymet, A. D. J.; Rice, Stuart A.

    1983-01-01

    A recent theory of Haymet, Rice, and Madden (HRM) for the pair and triplet correlation functions is tested at liquid state densities against new molecular dynamics results for the Lennard-Jones (12,6) fluid. The HRM integral equation, based on the Born-Green equation and a topological reduction of the diagrammatic expansion of the triplet correlation function, has been solved for a high temperature state (T*=2.74, ρ*=0.80) and is found to give triplet correlation functions in good agreement with the molecular dynamics results. For a lower-temperature state (T*=0.73, ρ*=0.85), where numerical difficulties have thus far frustrated attempts to obtain a self-consistent solution of the HRM integral equation, direct tests of the HRM closure are made using molecular dynamics pair correlation functions to evaluate the diagrams. Although some striking qualitative features of the triplet correlations are correctly described by the HRM closure for this low-temperature state, the HRM approach is not in quantitative agreement with the molecular dynamics results. Test calculations indicate that the principle source of these errors is the neglect of important higher-order diagrams for the triplet correlation function. A reorganization of the diagrammatic series is suggested which may identify the most important of these neglected diagrams. Additional computer simulation results are also reported for the purely repulsive Weeks-Chandler-Andersen (WCA) ``reference'' fluid and for the underlying hard sphere fluid. The similarity of the pair structures of these fluids, noted by WCA, is also found to hold with high accuracy for the triplet structures. It is suggested that these similarities may be exploited in applying the methods of HRM to the hard sphere fluid.

  2. Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition.

    SciTech Connect

    Weksberg, Tiffany E; Lynch, Gillian C; Krause, Kurt; Pettitt, Bernard M

    2007-05-01

    The crystal structure of the oxidized Trichomonas vaginalis ferredoxin (Tvfd) showed a unique crevice that exposed the redox center. Here we have examined the dynamics and solvation of the active site of Tvfd using molecular dynamics simulations of both the reduced and oxidized states. The oxidized simulation stays true to the crystal form with a heavy atom root mean-squared deviation of 2Å. However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the exceptionally fast electron transfer rate between Tvfd and the drug metronidazole is due to the increased access of the antibiotic to the redox center of the protein and not due to the reduction potential.

  3. Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition

    SciTech Connect

    Weksberg, Tiffany E; Lynch, Gillian C; Krause, Kurt; Pettitt, Bernard M

    2007-05-01

    The crystal structure of the oxidized Trichomonas vaginalis ferredoxin (Tvfd) showed a unique crevice that exposed the redox center. Here we have examined the dynamics and solvation of the active site of Tvfd using molecular dynamics simulations of both the reduced and oxidized states. The oxidized simulation stays true to the crystal form with a heavy atom root mean-squared deviation of 2Å . However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the exceptionally fast electron transfer rate between Tvfd and the drug metronidazole is due to the increased access of the antibiotic to the redox center of the protein and not due to the reduction potential.

  4. Molecular Dynamics and Monte Carlo simulations in the microcanonical ensemble: Quantitative comparison and reweighting techniques.

    PubMed

    Schierz, Philipp; Zierenberg, Johannes; Janke, Wolfhard

    2015-10-01

    Molecular Dynamics (MD) and Monte Carlo (MC) simulations are the most popular simulation techniques for many-particle systems. Although they are often applied to similar systems, it is unclear to which extent one has to expect quantitative agreement of the two simulation techniques. In this work, we present a quantitative comparison of MD and MC simulations in the microcanonical ensemble. For three test examples, we study first- and second-order phase transitions with a focus on liquid-gas like transitions. We present MD analysis techniques to compensate for conservation law effects due to linear and angular momentum conservation. Additionally, we apply the weighted histogram analysis method to microcanonical histograms reweighted from MD simulations. By this means, we are able to estimate the density of states from many microcanonical simulations at various total energies. This further allows us to compute estimates of canonical expectation values. PMID:26450299

  5. Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition

    PubMed Central

    Weksberg, Tiffany E.; Lynch, Gillian C.; Krause, Kurt L.; Pettitt, B. Montgomery

    2007-01-01

    The crystal structure of the oxidized Trichomonas vaginalis ferredoxin (Tvfd) showed a unique crevice that exposed the redox center. Here we have examined the dynamics and solvation of the active site of Tvfd using molecular dynamics simulations of both the reduced and oxidized states. The oxidized simulation stays true to the crystal form with a heavy atom root mean-squared deviation of 2 Å. However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the exceptionally fast electron transfer rate between Tvfd and the drug metronidazole is due to the increased access of the antibiotic to the redox center of the protein and not due to the reduction potential. PMID:17325017

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

    PubMed

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

    2016-06-22

    The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments. PMID:27228560

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

    PubMed Central

    2016-01-01

    The nucleation of crystals in liquids is one of nature’s most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments. PMID:27228560

  8. Molecular-dynamics simulations of crosslinking and confinement effects on structure, segmental mobility and mechanics of filled elastomers

    NASA Astrophysics Data System (ADS)

    Davris, Theodoros; Lyulin, Alexey V.

    2016-05-01

    The significant drop of the storage modulus under uniaxial deformation (Payne effect) restrains the performance of the elastomer-based composites and the development of possible new applications. In this paper molecular-dynamics (MD) computer simulations using LAMMPS MD package have been performed to study the mechanical properties of a coarse-grained model of this family of nanocomposite materials. Our goal is to provide simulational insights into the viscoelastic properties of filled elastomers, and try to connect the macroscopic mechanics with composite microstructure, the strength of the polymer-filler interactions and the polymer mobility at different scales. To this end we simulate random copolymer films capped between two infinite solid (filler aggregate) walls. We systematically vary the strength of the polymer-substrate adhesion interactions, degree of polymer confinement (film thickness), polymer crosslinking density, and study their influence on the equilibrium and non-equilibrium structure, segmental dynamics, and the mechanical properties of the simulated systems. The glass-transition temperature increases once the mesh size became smaller than the chain radius of gyration; otherwise it remained invariant to mesh-size variations. This increase in the glass-transition temperature was accompanied by a monotonic slowing-down of segmental dynamics on all studied length scales. This observation is attributed to the correspondingly decreased width of the bulk density layer that was obtained in films whose thickness was larger than the end-to-end distance of the bulk polymer chains. To test this hypothesis additional simulations were performed in which the crystalline walls were replaced with amorphous or rough walls.

  9. Mass accommodation of water: bridging the gap between molecular dynamics simulations and kinetic condensation models.

    PubMed

    Julin, Jan; Shiraiwa, Manabu; Miles, Rachael E H; Reid, Jonathan P; Pöschl, Ulrich; Riipinen, Ilona

    2013-01-17

    The condensational growth of submicrometer aerosol particles to climate relevant sizes is sensitive to their ability to accommodate vapor molecules, which is described by the mass accommodation coefficient. However, the underlying processes are not yet fully understood. We have simulated the mass accommodation and evaporation processes of water using molecular dynamics, and the results are compared to the condensation equations derived from the kinetic gas theory to shed light on the compatibility of the two. Molecular dynamics simulations were performed for a planar TIP4P-Ew water surface at four temperatures in the range 268-300 K as well as two droplets, with radii of 1.92 and 4.14 nm at T = 273.15 K. The evaporation flux from molecular dynamics was found to be in good qualitative agreement with that predicted by the simple kinetic condensation equations. Water droplet growth was also modeled with the kinetic multilayer model KM-GAP of Shiraiwa et al. [Atmos. Chem. Phys. 2012, 12, 2777]. It was found that, due to the fast transport across the interface, the growth of a pure water droplet is controlled by gas phase diffusion. These facts indicate that the simple kinetic treatment is sufficient in describing pure water condensation and evaporation. The droplet size was found to have minimal effect on the value of the mass accommodation coefficient. The mass accommodation coefficient was found to be unity (within 0.004) for all studied surfaces, which is in agreement with previous simulation work. Additionally, the simulated evaporation fluxes imply that the evaporation coefficient is also unity. Comparing the evaporation rates of the mass accommodation and evaporation simulations indicated that the high collision flux, corresponding to high supersaturation, present in typical molecular dynamics mass accommodation simulations can under certain conditions lead to an increase in the evaporation rate. Consequently, in such situations the mass accommodation coefficient

  10. Mass Accommodation of Water: Bridging the Gap Between Molecular Dynamics Simulations and Kinetic Condensation Models

    PubMed Central

    2012-01-01

    The condensational growth of submicrometer aerosol particles to climate relevant sizes is sensitive to their ability to accommodate vapor molecules, which is described by the mass accommodation coefficient. However, the underlying processes are not yet fully understood. We have simulated the mass accommodation and evaporation processes of water using molecular dynamics, and the results are compared to the condensation equations derived from the kinetic gas theory to shed light on the compatibility of the two. Molecular dynamics simulations were performed for a planar TIP4P-Ew water surface at four temperatures in the range 268–300 K as well as two droplets, with radii of 1.92 and 4.14 nm at T = 273.15 K. The evaporation flux from molecular dynamics was found to be in good qualitative agreement with that predicted by the simple kinetic condensation equations. Water droplet growth was also modeled with the kinetic multilayer model KM-GAP of Shiraiwa et al. [Atmos. Chem. Phys.2012, 117, 2777]. It was found that, due to the fast transport across the interface, the growth of a pure water droplet is controlled by gas phase diffusion. These facts indicate that the simple kinetic treatment is sufficient in describing pure water condensation and evaporation. The droplet size was found to have minimal effect on the value of the mass accommodation coefficient. The mass accommodation coefficient was found to be unity (within 0.004) for all studied surfaces, which is in agreement with previous simulation work. Additionally, the simulated evaporation fluxes imply that the evaporation coefficient is also unity. Comparing the evaporation rates of the mass accommodation and evaporation simulations indicated that the high collision flux, corresponding to high supersaturation, present in typical molecular dynamics mass accommodation simulations can under certain conditions lead to an increase in the evaporation rate. Consequently, in such situations the mass accommodation

  11. Molecular-dynamics simulations of stress relaxation in metals and polymers

    NASA Astrophysics Data System (ADS)

    Blonski, Slawomir; Brostow, Witold; Kubát, Josef

    1994-03-01

    Molecular-dynamics simulations of stress relaxation have been performed for models of metals and polymers. A method that employs coupling between the simulation cell and an applied stress as well as an external thermal bath has been used. Two-dimensional models of the materials are defined with interactions described by the Lennard-Jones (Mie 6-12) and harmonic potentials. A special method is employed to generate chains in dense polymeric systems. In agreement with experiments, simulated stress-relaxation curves are similar for metals and polymers. At the same time, there exists an essential difference in the stress-strain behavior of the two kinds of simulated materials. During the relaxation, trajectories of the particles in different materials display a common feature: There exist domains in which movement of the particles is highly correlated. Thus, the simulation results support the cooperative theory of stress relaxation.

  12. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    PubMed Central

    2016-01-01

    Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. PMID:27118886

  13. Transport properties of carbon dioxide and ammonia in water - ethylene glycol mixtures from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Iskrenova, Eugeniya; Patnaik, Soumya S.

    2015-03-01

    The endothermic decomposition of ammonium carbamate has been proposed as a novel heat sink mechanism for aircraft thermal management (Johnson et al. SAE Technical Paper 2012-01-2190, 2012, doi:10.4271/2012-01-2190]). The products of this decomposition are carbon dioxide and ammonia which need to be efficiently removed in order to better control the decomposition reaction. Molecular dynamics simulations can provide insight into the transport properties of carbon dioxide and ammonia in the carrier fluid. In this work, an extensive set of molecular dynamics simulations was performed to better quantify the concentration dependence of solubility and diffusivity of carbon dioxide and ammonia in water, ethylene glycol, and their mixtures at standard temperature and pressure and at elevated temperature. The simulation results confirm the experimental observations that ammonia is more soluble than carbon dioxide in either water or ethylene glycol and that both carbon dioxide and ammonia are more soluble in ethylene glycol than in water. The simulations of water - ethylene glycol mixtures show that increasing the molar fraction of ethylene glycol leads to increased solubility of carbon dioxide and ammonia in the mixture. The authors gratefully acknowledge the DoD High Performance Computing Centers for computational resources.

  14. On Achieving Experimental Accuracy from Molecular Dynamics Simulations of Flexible Molecules: Aqueous Glycerol

    PubMed Central

    Yongye, Austin B.; Foley, B. Lachele; Woods, Robert J.

    2014-01-01

    The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueous phase via a 1 μs conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replica exchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. The MD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment of solvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar 3JHH coupling constants that were comparable to those from the much longer traditional MD simulation. The 3JHH coupling constants computed from the MD methods were in excellent agreement with those observed experimentally. Despite the agreement between the computed and the experimental J-values, there were variations between the rotamer populations computed directly from the MD data and those derived from the experimental NMR data. The experimentally derived populations were determined utilizing limiting J-values from an analysis of NMR data from substituted ethane molecules and may not be completely appropriate for application in more complex molecules, such as glycerol. Here, new limiting J-values have been derived via a combined MD and quantum mechanical approach and were used to decompose the experimental 3JHH coupling constants into population distributions for the glycerol RIS. PMID:18311953

  15. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

    PubMed

    Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

    2016-07-01

    This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26766517

  16. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity

    PubMed Central

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations. PMID:26075210

  17. Exploration of the chlorpyrifos escape pathway from acylpeptide hydrolases using steered molecular dynamics simulations.

    PubMed

    Wang, Dongmei; Jin, Hanyong; Wang, Junling; Guan, Shanshan; Zhang, Zuoming; Han, Weiwei

    2016-04-01

    Acylpeptide hydrolases (APH) catalyze the removal of an N-acylated amino acid from blocked peptides. APH is significantly more sensitive than acetylcholinesterase, a target of Alzheimer's disease, to inhibition by organophosphorus (OP) compounds. Thus, OP compounds can be used as a tool to probe the physiological functions of APH. Here, we report the results of a computational study of molecular dynamics simulations of APH bound to the OP compounds and an exploration of the chlorpyrifos escape pathway using steered molecular dynamics (SMD) simulations. In addition, we apply SMD simulations to identify potential escape routes of chlorpyrifos from hydrolase hydrophobic cavities in the APH-inhibitor complex. Two previously proposed APH pathways were reliably identified by CAVER 3.0, with the estimated relative importance of P1 > P2 for its size. We identify the major pathway, P2, using SMD simulations, and Arg526, Glu88, Gly86, and Asn65 are identified as important residues for the ligand leaving via P2. These results may help in the design of APH-targeting drugs with improved efficacy, as well as in understanding APH selectivity of the inhibitor binding in the prolyl oligopeptidase family. PMID:26155973

  18. Molecular Dynamics Simulations of Aldol Condensation Catalyzed by Alkylamine-Functionalized Crystalline Silica Surfaces.

    PubMed

    Kim, Ki Chul; Moschetta, Eric G; Jones, Christopher W; Jang, Seung Soon

    2016-06-22

    Molecular dynamics simulations are performed to investigate the cooperatively catalyzed aldol condensation between acetone and 4-nitrobenzaldehyde on alkylamine (or alkylenamine)-grafted silica surfaces, focusing on the mechanism of the catalytic activation of the acetone and 4-nitrobenzaldehyde by the acidic surface silanols followed by the nucleophilic attack of the basic amine functional group toward the activated reactant. From the analysis of the correlations between the catalytically active acid-base sites and reactants, it is concluded that the catalytic cooperativity of the acid-base pair can be affected by two factors: (1) the competition between the silanol and the amine (or enamine) to form a hydrogen bond with a reactant and (2) the flexibility of the alkylamine (or alkylenamine) backbone. Increasing the flexibility of the alkylamine facilitates the nucleophilic attack of the amine on the reactants. From the molecular dynamics simulations, it is found that C3 propylamine and C4 butylamine linkers exhibit the highest probability of reaction, which is consistent with the experimental observation that the activity of the aldol reaction on mesoporous silica depends on the length of alkylamine grafted on the silica surface. This simulation work serves as a pioneering study demonstrating how the molecular simulation approach can be successfully employed to investigate the cooperative catalytic activity of such bifunctional acid-base catalysts. PMID:27238580

  19. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations

    PubMed Central

    Hertig, Samuel

    2016-01-01

    Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein’s constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery—the fact that the two sites involved influence one another in a symmetrical manner—can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest. PMID:27285999

  20. The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

    PubMed

    Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

    2016-09-01

    Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. PMID:27235585