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Sample records for lennard-jones lj system

  1. Glass of monatomic Lennard-Jones system at nanoscale

    International Nuclear Information System (INIS)

    Vo Van Hoang

    2010-01-01

    Structure and stability of glass of monatomic Lennard-Jones (LJ) system at nanoscale compared with those of the bulk counterparts have been studied using the classical molecular dynamics (MD) method. Models have been obtained by cooling from the melts. Structure of the systems was analyzed via radial distribution function (RDF), interatomic distances, the Honeycutt-Andersen analysis and coordination number distributions. Surface and core structures of LJ nanoparticles have been analyzed in details. Density dependence and cooling rate effects on structure of the systems have been found and discussed. In addition, size dependence of structure and properties of nanoparticles has been analyzed in detail. Indeed, we found glass formation in monatomic LJ systems; however, their stability is not high. Evolution of structure and thermodynamics of the systems upon cooling from the melts was found. We also discussed annealing-induced crystallization of LJ glass.

  2. Phase diagram of a modified Lennard-Jones system

    International Nuclear Information System (INIS)

    Sakagami, Takahiro; Fuchizaki, Kazuhiro

    2010-01-01

    The well-known Lennard-Jones potential is modified in such a way that it smoothly vanishes at a certain distance. A system whose interparticle interaction is given by such a potential is referred to as a modified Lennard-Jones system, and is served as a standard system describing simple solids and fluids. A phase diagram is determined based on the free energies obtained through thermodynamic integration.

  3. Equilibrium spherically curved two-dimensional Lennard-Jones systems

    NARCIS (Netherlands)

    Voogd, J.M.; Sloot, P.M.A.; van Dantzig, R.

    2005-01-01

    To learn about basic aspects of nano-scale spherical molecular shells during their formation, spherically curved two-dimensional N-particle Lennard-Jones systems are simulated, studying curvature evolution paths at zero-temperature. For many N-values (N < 800) equilibrium configu- rations are traced

  4. Density-scaling exponents and virial potential-energy correlation coefficients for the (2n, n) Lennard-Jones system

    DEFF Research Database (Denmark)

    Friisberg, Ida Marie; Costigliola, Lorenzo; Dyre, Jeppe C.

    2017-01-01

    This paper investigates the relation between the density-scaling exponent γ and the virial potentialenergy coefficient R at several thermodynamic state points in three dimensions for the generalized (2n, n) Lennard-Jones (LJ) system for n = 4, 9, 12, 18, as well as for the standard n = 6 LJ syste...

  5. Freezing and melting line invariants of the Lennard-Jones system

    DEFF Research Database (Denmark)

    Costigliola, Lorenzo; Schrøder, Thomas; Dyre, Jeppe C.

    2016-01-01

    The invariance of several structural and dynamical properties of the Lennard-Jones (LJ) system along the freezing and melting lines is interpreted in terms of isomorph theory. First the freezing/melting lines of the LJ system are shown to be approximated by isomorphs. Then we show...... that the invariants observed along the freezing and melting isomorphs are also observed on other isomorphs in the liquid and crystalline phases. The structure is probed by the radial distribution function and the structure factor and dynamics are probed by the mean-square displacement, the intermediate scattering...... function, and the shear viscosity. Studying these properties with reference to isomorph theory explains why the known single-phase melting criteria hold, e.g., the Hansen–Verlet and the Lindemann criteria, and why the Andrade equation for the viscosity at freezing applies, e.g., for most liquid metals. Our...

  6. Contact angle of sessile drops in Lennard-Jones systems.

    Science.gov (United States)

    Becker, Stefan; Urbassek, Herbert M; Horsch, Martin; Hasse, Hans

    2014-11-18

    Molecular dynamics simulations are used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and dewetting is investigated by varying the solid-fluid dispersive interaction energy. The temperature is varied between the triple point and the critical temperature. A correlation is obtained for the contact angle in dependence of the temperature and the dispersive interaction energy. Size effects are studied by varying the number of fluid particles at otherwise constant conditions, using up to 150,000 particles. For particle numbers below 10,000, a decrease of the contact angle is found. This is attributed to a dependence of the solid-liquid surface tension on the droplet size. A convergence to a constant contact angle is observed for larger system sizes. The influence of the wall model is studied by varying the density of the wall. The effective solid-fluid dispersive interaction energy at a contact angle of θ = 90° is found to be independent of temperature and to decrease linearly with the solid density. A correlation is developed that describes the contact angle as a function of the dispersive interaction, the temperature, and the solid density. The density profile of the sessile drop and the surrounding vapor phase is described by a correlation combining a sigmoidal function and an oscillation term.

  7. Thermodynamic equivalence between the Lennard-Jones and hard-core attractive Yukawa systems

    International Nuclear Information System (INIS)

    Kadiri, Y.; Albaki, R.; Bretonnet, J.L.

    2008-01-01

    The investigation of the thermodynamic properties of the Lennard-Jones (LJ) fluid is made by means of a system of particles interacting with a potential of hard-core plus attractive Yukawa tail (HCY). Due to the similarity between the LJ potential and the HCY potential in its overall form, it is worthwhile seeking to approximate the LJ potential in much the same way that the hard-sphere reference potential has been so used. The study consists in describing the thermodynamics of the LJ fluid in terms of the equivalent HCY system, whose the properties are known accurately, by means of mapping the thermodynamic quantities for the HCY potential parameters. The method is feasible owing to a convenient analytical expression of the Helmholtz free energy from the mean-spherical approximation expanded in power of the inverse temperature. Two different procedures are used to determine the parameters of the HCY potential as a function of the thermodynamic states: one is based on the simultaneous fits of pressure and internal energy of the LJ system and the other uses the concept of collision frequency. The reasonable homogeneity of the results in both procedures of mapping makes that the HCY potential is a very good reference system, whose the proposed theoretical expressions can be used confidently to predict the thermodynamic properties of more realistic potentials

  8. Melting of 2D monatomic solids: Lennard-Jones system

    International Nuclear Information System (INIS)

    Yi, Y.M.; Guo, Z.C.

    1987-09-01

    The Lennard-Jones interaction has been introduced into the Collins mix lattice of 2D liquids. By means of rigorous calculation of the total potential and the free area, the Gibbs functions for 2D liquid and solid have been derived. The melting line obtained from the phase transition equation agrees quite well with the result of recent computer simulation experiments. The obtained reduced temperature of the triple point T* t =0.438 agrees with the data measured in experiments of some inert gas monolayers adsorbed on graphite as well as in computer simulation experiments. (author). 11 refs, 7 figs, 3 tabs

  9. Phase diagram of power law and Lennard-Jones systems: Crystal phases

    International Nuclear Information System (INIS)

    Travesset, Alex

    2014-01-01

    An extensive characterization of the low temperature phase diagram of particles interacting with power law or Lennard-Jones potentials is provided from Lattice Dynamical Theory. For power law systems, only two lattice structures are stable for certain values of the exponent (or softness) (A15, body centered cube (bcc)) and two more (face centered cubic (fcc), hexagonal close packed (hcp)) are always stable. Among them, only the fcc and bcc are equilibrium states. For Lennard-Jones systems, the equilibrium states are either hcp or fcc, with a coexistence curve in pressure and temperature that shows reentrant behavior. The hcp solid never coexists with the liquid. In all cases analyzed, for both power law and Lennard-Jones potentials, the fcc crystal has higher entropy than the hcp. The role of anharmonic terms is thoroughly analyzed and a general thermodynamic integration to account for them is proposed

  10. Atomic size effect on the formation of ionized cluster beam epitaxy in Lennard-Jones systems

    International Nuclear Information System (INIS)

    Hsieh Horngming; Averback, R.S.

    1991-01-01

    Ionized cluster beam deposition is studied by molecular dynamics simulations in which the atomic size of incident cluster atoms is different from the size of substrate atoms. Lennard-Jones interatomic potentials are used for the two-component system. The results provide the morphologies of the overlayers for various atomic sizes and are compared to simulation results of molecular beam epitaxy. (orig.)

  11. Interaction forces between nanoparticles in Lennard-Jones (L-J) solvents

    International Nuclear Information System (INIS)

    Sinha, Indrajit; Mukherjee, Ashim K

    2014-01-01

    Molecular simulations, such as Monte Carlo (MC) and molecular dynamics (MD) have been recently used for understanding the forces between colloidal nanoparticles that determine the dispersion and stability of nanoparticle suspensions. Herein we review the current status of research in the area of nanoparticles immersed in L-J solvents. The first study by Shinto et al. used large smooth spheres to depict nanoparticles in L-J and soft sphere solvents. The nanoparticles were held fixed at a particular interparticle distance and only the solvents were allowed to equilibrate. Both Van-der-waals and solvation forces were computed at different but fixed interparticle separation. Later Qin and Fitchthorn improved on this model by considering the nanoparticles as collection of molecules, thus taking into the account the effect of surface roughness of nanoparticles. Although the inter particle distance was fixed, the rotation of such nanoparticles with respect to each other was also investigated. Recently, in keeping with the experimental situation, we modified this model by allowing the nanoparticles to move and rotate freely. Solvophilic, neutral and solvophobic interactions between the solvent atoms and those that make up the nanoparticles were modelled. While neutral and solvophobic nanoparticles coalesce even at intermediate distances, solvophilic nanoparticles are more stable in solution due to the formation of a solvent shield

  12. Melting in Two-Dimensional Lennard-Jones Systems: Observation of a Metastable Hexatic Phase

    International Nuclear Information System (INIS)

    Chen, K.; Kaplan, T.; Mostoller, M.

    1995-01-01

    Large scale molecular dynamics simulations of two-dimensional melting have been carried out using a recently revised Parrinello-Rahman scheme on massively parallel supercomputers. A metastable state is observed between the solid and liquid phases in Lennard-Jones systems of 36 864 and 102 400 atoms. This intermediate state shows the characteristics of the hexatic phase predicted by the theory of Kosterlitz, Thouless, Halperin, Nelson, and Young

  13. Disordering scaling and generalized nearest-neighbor approach in the thermodynamics of Lennard-Jones systems

    International Nuclear Information System (INIS)

    Vorob'ev, V.S.

    2003-01-01

    We suggest a concept of multiple disordering scaling of the crystalline state. Such a scaling procedure applied to a crystal leads to the liquid and (in low density limit) gas states. This approach provides an explanation to a high value of configuration (common) entropy of liquefied noble gases, which can be deduced from experimental data. We use the generalized nearest-neighbor approach to calculate free energy and pressure of the Lennard-Jones systems after performing this scaling procedure. These thermodynamic functions depend on one parameter characterizing the disordering only. Condensed states of the system (liquid and solid) correspond to small values of this parameter. When this parameter tends to unity, we get an asymptotically exact equation of state for a gas involving the second virial coefficient. A reasonable choice of the values for the disordering parameter (ranging between zero and unity) allows us to find the lines of coexistence between different phase states in the Lennard-Jones systems, which are in a good agreement with the available experimental data

  14. Glass transitions in one-, two-, three-, and four-dimensional binary Lennard-Jones systems

    Energy Technology Data Exchange (ETDEWEB)

    Bruening, Ralf; St-Onge, Denis A; Patterson, Steve [Physics Department, Mount Allison University, Sackville, NB, E4L 1E6 (Canada); Kob, Walter [Laboratoire des Colloides, Verres et Nanomateriaux, UMR5587, Universite Montpellier II and CNRS, 34095 Montpellier Cedex (France)], E-mail: rbruening@mta.ca

    2009-01-21

    We investigate the calorimetric liquid-glass transition by performing simulations of a binary Lennard-Jones mixture in one through four dimensions. Starting at a high temperature, the systems are cooled to T = 0 and heated back to the ergodic liquid state at constant rates. Glass transitions are observed in two, three and four dimensions as a hysteresis between the cooling and heating curves. This hysteresis appears in the energy and pressure diagrams, and the scanning rate dependence of the area and height of the hysteresis can be described using power laws. The one-dimensional system does not experience a glass transition but its specific heat curve resembles the shape of the D{>=}2 results in the supercooled liquid regime above the glass transition. As D increases, the radial distribution functions reflect reduced geometric constraints. Nearest neighbor distances become smaller with increasing D due to interactions between nearest and next-nearest neighbors. Simulation data for the glasses are compared with crystal and melting data obtained with a Lennard-Jones system with only one type of particle and we find that with increasing D crystallization becomes increasingly more difficult.

  15. Phase diagram and universality of the Lennard-Jones gas-liquid system

    KAUST Repository

    Watanabe, Hiroshi

    2012-01-01

    The gas-liquid phase transition of the three-dimensional Lennard-Jones particles system is studied by molecular dynamics simulations. The gas and liquid densities in the coexisting state are determined with high accuracy. The critical point is determined by the block density analysis of the Binder parameter with the aid of the law of rectilinear diameter. From the critical behavior of the gas-liquid coexisting density, the critical exponent of the order parameter is estimated to be β = 0.3285(7). Surface tension is estimated from interface broadening behavior due to capillary waves. From the critical behavior of the surface tension, the critical exponent of the correlation length is estimated to be ν = 0.63(4). The obtained values of β and ν are consistent with those of the Ising universality class. © 2012 American Institute of Physics.

  16. Freezing of Lennard-Jones-type fluids

    International Nuclear Information System (INIS)

    Khrapak, Sergey A.; Chaudhuri, Manis; Morfill, Gregor E.

    2011-01-01

    We put forward an approximate method to locate the fluid-solid (freezing) phase transition in systems of classical particles interacting via a wide range of Lennard-Jones-type potentials. This method is based on the constancy of the properly normalized second derivative of the interaction potential (freezing indicator) along the freezing curve. As demonstrated recently it yields remarkably good agreement with previous numerical simulation studies of the conventional 12-6 Lennard-Jones (LJ) fluid [S.A.Khrapak, M.Chaudhuri, G.E.Morfill, Phys. Rev. B 134, 052101 (2010)]. In this paper, we test this approach using a wide range of the LJ-type potentials, including LJ n-6 and exp-6 models, and find that it remains sufficiently accurate and reliable in reproducing the corresponding freezing curves, down to the triple-point temperatures. One of the possible application of the method--estimation of the freezing conditions in complex (dusty) plasmas with ''tunable'' interactions--is briefly discussed.

  17. Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems

    KAUST Repository

    Watanabe, H.

    2011-08-01

    Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatialdecomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93 GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo. The parallelization efficiency of the largest run, consisting of 4.1 billion particles with 8192 MPI processes, is about 73% relative to that of the smallest run with 128 MPI processes at NIFS, and it is about 66% relative to that of the smallest run with 4 MPI processes at ISSP. The factors causing the parallel overhead are investigated. It is found that fluctuations of the execution time of each process degrade the parallel efficiency. These fluctuations may be due to the interference of the operating system, which is known as OS Jitter.

  18. Dodecagonal order in a two-dimensional Lennard-Jones system

    International Nuclear Information System (INIS)

    Leung, P.W.; Henley, C.L.; Chester, G.V.

    1989-01-01

    We investigate a two-dimensional Lennard-Jones mixture with the interaction parameters chosen so as to favor configurations where the large atoms form squares and equilateral triangles. Many such configurations are possible which by our choice of interactions are nearly degenerate in energy. It is hypothesized that a thermal equilibrium state with 12-fold orientational order exists. Several Monte Carlo simulations were performed to cool the system to a temperature approaching zero. The ordering process was studied by following the evolution of the configurations with temperature. The onset of ordering seemed to be very diffuse in space rather than nucleated at a point. The resulting configurations consist of squares and triangles, except for a few dislocations, and thus have perfect orientational order. We also characterized the deviation from ideal quasiperiodicity in terms of the ''phason strain''; this was analyzed both by fitting a linear relation between the physical space coordinates of the atoms and the corresponding ''perpendicular space'' coordinates, and also by calculating the diffraction peaks. The latter are shifted and broadened, relative to an ideal 12-fold diffraction pattern, as in real quasicrystals

  19. Ab initio study of the atomic motion in liquid metal surfaces: comparison with Lennard-Jones systems

    International Nuclear Information System (INIS)

    Gonzalez, Luis E; Gonzalez, David J

    2006-01-01

    It is established that liquid metals exhibit surface layering at the liquid-vapour interface, while dielectric simple systems, like those interacting through Lennard-Jones potentials, show a monotonic decay from the liquid density to that of the vapour. First principles molecular dynamics simulations of the free liquid surface of several liquid metals (Li, Na, K, Rb, Cs, Mg, Ba, Al, Tl and Si), and the Na 3 K 7 alloy near their triple points have been performed in order to study the atomic motion at the interface, mainly at the outer layer. Comparison with the results of classical molecular dynamics simulations of a Lennard-Jones system shows interesting differences and similarities. The probability distribution function of the time of residence in a layer shows a peak at very short times and a long-lasting tail. The mean residence time in a layer increases when approaching the interfacial region, slightly in the Lennard-Jones system but strongly in the metallic systems. The motion within the layers, parallel to the interface, can be described as diffusion enhanced (strongly in the case of the outermost layer) with respect to the bulk, for both types of systems, despite its reduced dimensionality in metals

  20. Spray flow-network flow transition of binary Lennard-Jones particle system

    KAUST Repository

    Inaoka, Hajime

    2010-07-01

    We simulate gas-liquid flows caused by rapid depressurization using a molecular dynamics model. The model consists of two types of Lennard-Jones particles, which we call liquid particles and gas particles. These two types of particles are distinguished by their mass and strength of interaction: a liquid particle has heavier mass and stronger interaction than a gas particle. By simulations with various initial number densities of these particles, we found that there is a transition from a spray flow to a network flow with an increase of the number density of the liquid particles. At the transition point, the size of the liquid droplets follows a power-law distribution, while it follows an exponential distribution when the number density of the liquid particles is lower than the critical value. The comparison between the transition of the model and that of models of percolation is discussed. The change of the average droplet size with the initial number density of the gas particles is also presented. © 2010 Elsevier B.V. All rights reserved.

  1. Spray flow-network flow transition of binary Lennard-Jones particle system

    KAUST Repository

    Inaoka, Hajime; Yukawa, Satoshi; Ito, Nobuyasu

    2010-01-01

    We simulate gas-liquid flows caused by rapid depressurization using a molecular dynamics model. The model consists of two types of Lennard-Jones particles, which we call liquid particles and gas particles. These two types of particles are distinguished by their mass and strength of interaction: a liquid particle has heavier mass and stronger interaction than a gas particle. By simulations with various initial number densities of these particles, we found that there is a transition from a spray flow to a network flow with an increase of the number density of the liquid particles. At the transition point, the size of the liquid droplets follows a power-law distribution, while it follows an exponential distribution when the number density of the liquid particles is lower than the critical value. The comparison between the transition of the model and that of models of percolation is discussed. The change of the average droplet size with the initial number density of the gas particles is also presented. © 2010 Elsevier B.V. All rights reserved.

  2. Evaporation of Lennard-Jones fluids.

    Science.gov (United States)

    Cheng, Shengfeng; Lechman, Jeremy B; Plimpton, Steven J; Grest, Gary S

    2011-06-14

    Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature T/T(c), where T(c) is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.

  3. Equation of state and Helmholtz free energy for the atomic system of the repulsive Lennard-Jones particles.

    Science.gov (United States)

    Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid

    2017-12-07

    Simple and accurate expressions are presented for the equation of state (EOS) and absolute Helmholtz free energy of a system composed of simple atomic particles interacting through the repulsive Lennard-Jones potential model in the fluid and solid phases. The introduced EOS has 17 and 22 coefficients for fluid and solid phases, respectively, which are regressed to the Monte Carlo (MC) simulation data over the reduced temperature range of 0.6≤T * ≤6.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. The average absolute relative percent deviation in fitting the EOS parameters to the MC data is 0.06 and 0.14 for the fluid and solid phases, respectively. The thermodynamic integration method is used to calculate the free energy using the MC simulation results. The Helmholtz free energy of the ideal gas is employed as the reference state for the fluid phase. For the solid phase, the values of the free energy at the reduced density equivalent to the close-packed of a hard sphere are used as the reference state. To check the validity of the predicted values of the Helmholtz free energy, the Widom particle insertion method and the Einstein crystal technique of Frenkel and Ladd are employed. The results obtained from the MC simulation approaches are well agreed to the EOS results, which show that the proposed model can reliably be utilized in the framework of thermodynamic theories.

  4. Scaling relation and regime map of explosive gas–liquid flow of binary Lennard-Jones particle system

    KAUST Repository

    Inaoka, Hajime

    2012-02-01

    We study explosive gasliquid flows caused by rapid depressurization using a molecular dynamics model of Lennard-Jones particle systems. A unique feature of our model is that it consists of two types of particles: liquid particles, which tend to form liquid droplets, and gas particles, which remain supercritical gaseous states under the depressurization realized by simulations. The system has a pipe-like structure similar to the model of a shock tube. We observed physical quantities and flow regimes in systems with various combinations of initial particle number densities and initial temperatures. It is observed that a physical quantity Q, such as pressure, at position z measured along a pipe-like system at time t follows a scaling relation Q(z,t)=Q(zt) with a scaling function Q(ζ). A similar scaling relation holds for time evolution of flow regimes in a system. These scaling relations lead to a regime map of explosive flows in parameter spaces of local physical quantities. The validity of the scaling relations of physical quantities means that physics of equilibrium systems, such as an equation of state, is applicable to explosive flows in our simulations, though the explosive flows involve highly nonequilibrium processes. In other words, if the breaking of the scaling relations is observed, it means that the explosive flows cannot be fully described by physics of equilibrium systems. We show the possibility of breaking of the scaling relations and discuss its implications in the last section. © 2011 Elsevier B.V. All rights reserved.

  5. Thermal decay of Lennard-Jones clusters

    International Nuclear Information System (INIS)

    Garzon, I.L.; Avalos-Borja, M.

    1989-01-01

    The decay mechanisms of argon clusters have been studied using molecular dynamics simulations and Lennard-Jones potentials. Heating up processes were applied to Ar 13 up to temperatures in the melting region. In this range of temperatures large fluctuations in the mean kinetic energy of the system are present and a sequential evaporation is observed. The thermal decay of these aggregates occurs in a time scale of nanoseconds. (orig.)

  6. Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems

    KAUST Repository

    Watanabe, H.; Suzuki, M.; Ito, N.

    2011-01-01

    simple spatialdecomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute

  7. Cluster fusion algorithm: application to Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2006-01-01

    paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence......We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...

  8. Cluster fusion algorithm: application to Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2008-01-01

    paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence......We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...

  9. Scaling of the dynamics of flexible Lennard-Jones chains

    DEFF Research Database (Denmark)

    Veldhorst, Arno; Dyre, J. C.; Schrøder, Thomas

    2014-01-01

    functions of excess entropy) which has been observed in simulations of both molecular and polymeric systems. Doing molecular dynamics simulations of flexible Lennard-Jones chains (LJC) with rigid bonds, we here provide the first detailed test of the isomorph theory applied to flexible chain molecules. We...

  10. Formation of global energy minimim structures in the growth process of Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Koshelev, Andrey; Shutovich, Andrey

    2003-01-01

    that in this way all known global minimum structures of the Lennard-Jones (LJ) clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic numbers sequence for the clusters of noble gases atoms and compare...

  11. Numerical computations of the Lennard-Jones resonances and ''relative displacements'' of the scattered atomic beams from the system He/LiF(001)

    International Nuclear Information System (INIS)

    Garcia, N.

    1976-01-01

    This paper considers the effect of the attractive part of the interaction potential on the scattering of He atoms from a LiF(001) surface. We calculate, in particular, the Lennard-Jones resonances on the intensities and the phases of the scattered amplitudes, using a square well in the front of a hard corrugated surface model. We show that the amplitudes for incident energies smaller than the depth of the well are dominated by the resonances

  12. Phase behavior of the 38-atom Lennard-Jones cluster

    International Nuclear Information System (INIS)

    Sehgal, Ray M.; Maroudas, Dimitrios; Ford, David M.

    2014-01-01

    We have developed a coarse-grained description of the phase behavior of the isolated 38-atom Lennard-Jones cluster (LJ 38 ). The model captures both the solid-solid polymorphic transitions at low temperatures and the complex cluster breakup and melting transitions at higher temperatures. For this coarse model development, we employ the manifold learning technique of diffusion mapping. The outcome of the diffusion mapping analysis over a broad temperature range indicates that two order parameters are sufficient to describe the cluster's phase behavior; we have chosen two such appropriate order parameters that are metrics of condensation and overall crystallinity. In this well-justified coarse-variable space, we calculate the cluster's free energy landscape (FEL) as a function of temperature, employing Monte Carlo umbrella sampling. These FELs are used to quantify the phase behavior and onsets of phase transitions of the LJ 38 cluster

  13. Effect of Energy Polydispersity on the Nature of Lennard-Jones Liquids

    OpenAIRE

    Ingebrigtsen, Trond S.; Tanaka, Hajime

    2016-01-01

    In the companion paper [T. S. Ingebrigtsen and H. Tanaka, J. Phys. Chem. B 119, 11052 (2015)] the effect of size polydispersity on the nature of Lennard-Jones (LJ) liquids, which represent most molecular liquids without hydrogen bonds, was studied. More specifically, it was shown that even highly size polydisperse LJ liquids are Roskilde-simple (RS) liquids. RS liquids are liquids with strong correlation between constant volume equilibrium fluctuations of virial and potential energy and are s...

  14. Scaling relation and regime map of explosive gas–liquid flow of binary Lennard-Jones particle system

    KAUST Repository

    Inaoka, Hajime; Yukawa, Satoshi; Ito, Nobuyasu

    2012-01-01

    liquid droplets, and gas particles, which remain supercritical gaseous states under the depressurization realized by simulations. The system has a pipe-like structure similar to the model of a shock tube. We observed physical quantities and flow regimes

  15. Effect of dispersive long-range corrections to the pressure tensor: The vapour-liquid interfacial properties of the Lennard-Jones system revisited

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Ruiz, F. J.; Blas, F. J., E-mail: felipe@uhu.es [Departamento de Física Aplicada, Universidad de Huelva, 21071 Huelva (Spain); Centro de Investigación de Física Teórica y Matemática, Universidad de Huelva, 21071 Huelva (Spain); Mendiboure, B. [Laboratoire des Fluides Complexes et leurs Réservoirs, UMR5150, Université de Pau et des Pays de l’Adour, B. P. 1155, Pau Cedex 64014 (France); Moreno-Ventas Bravo, A. I. [Centro de Investigación de Física Teórica y Matemática, Universidad de Huelva, 21071 Huelva (Spain); Departamento de Geología, Facultad de Ciencias Experimentales, Universidad de Huelva, 21071 Huelva (Spain)

    2014-11-14

    We propose an extension of the improved version of the inhomogeneous long-range corrections of Janeček [J. Phys. Chem. B 110, 6264–6269 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] to account for the intermolecular potential energy of spherical, rigid, and flexible molecular systems, to deal with the contributions to the microscopic components of the pressure tensor due to the dispersive long-range corrections. We have performed Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of spherical Lennard-Jones molecules with different cutoff distances, r{sub c} = 2.5, 3, 4, and 5σ. In addition, we have also considered cutoff distances r{sub c} = 2.5 and 3σ in combination with the inhomogeneous long-range corrections proposed in this work. The normal and tangential microscopic components of the pressure tensor are obtained using the mechanical or virial route in combination with the recipe of Irving and Kirkwood, while the macroscopic components are calculated using the Volume Perturbation thermodynamic route proposed by de Miguel and Jackson [J. Chem. Phys. 125, 164109 (2006)]. The vapour-liquid interfacial tension is evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the Test-Area methodology. In addition to the pressure tensor and the surface tension, we also obtain density profiles, coexistence densities, vapour pressure, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the cutoff distance and the long-range corrections on these properties. According to our results, the main effect of increasing the cutoff distance (at fixed temperature) is to sharpen the vapour-liquid interface, to decrease the vapour pressure, and to increase the width of the biphasic coexistence region. As a result, the interfacial

  16. Effect of dispersive long-range corrections to the pressure tensor: The vapour-liquid interfacial properties of the Lennard-Jones system revisited

    International Nuclear Information System (INIS)

    Martínez-Ruiz, F. J.; Blas, F. J.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.

    2014-01-01

    We propose an extension of the improved version of the inhomogeneous long-range corrections of Janeček [J. Phys. Chem. B 110, 6264–6269 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] to account for the intermolecular potential energy of spherical, rigid, and flexible molecular systems, to deal with the contributions to the microscopic components of the pressure tensor due to the dispersive long-range corrections. We have performed Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of spherical Lennard-Jones molecules with different cutoff distances, r c = 2.5, 3, 4, and 5σ. In addition, we have also considered cutoff distances r c = 2.5 and 3σ in combination with the inhomogeneous long-range corrections proposed in this work. The normal and tangential microscopic components of the pressure tensor are obtained using the mechanical or virial route in combination with the recipe of Irving and Kirkwood, while the macroscopic components are calculated using the Volume Perturbation thermodynamic route proposed by de Miguel and Jackson [J. Chem. Phys. 125, 164109 (2006)]. The vapour-liquid interfacial tension is evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the Test-Area methodology. In addition to the pressure tensor and the surface tension, we also obtain density profiles, coexistence densities, vapour pressure, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the cutoff distance and the long-range corrections on these properties. According to our results, the main effect of increasing the cutoff distance (at fixed temperature) is to sharpen the vapour-liquid interface, to decrease the vapour pressure, and to increase the width of the biphasic coexistence region. As a result, the interfacial thickness

  17. Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kadoura, Ahmad, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa; Sun, Shuyu, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa [Computational Transport Phenomena Laboratory, The Earth Sciences and Engineering Department, The Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia); Siripatana, Adil, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa; Hoteit, Ibrahim, E-mail: ibrahim.hoteit@kaust.edu.sa [Earth Fluid Modeling and Predicting Group, The Earth Sciences and Engineering Department, The Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia); Knio, Omar, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa [Uncertainty Quantification Center, The Applied Mathematics and Computational Science Department, The Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia)

    2016-06-07

    In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard-Jones (LJ) particles. The main advantage of such surrogates, once generated, is the capability of accurately computing the needed thermodynamic quantities in a few seconds, thus efficiently replacing the computationally expensive MC molecular simulations. Benefiting from the tremendous computational time reduction, the PC surrogates were used to conduct large-scale optimization in order to propose single-site LJ models for several simple molecules. Experimental data, a set of supercritical isotherms, and part of the two-phase envelope, of several pure components were used for tuning the LJ parameters (ε, σ). Based on the conducted optimization, excellent fit was obtained for different noble gases (Ar, Kr, and Xe) and other small molecules (CH{sub 4}, N{sub 2}, and CO). On the other hand, due to the simplicity of the LJ model used, dramatic deviations between simulation and experimental data were observed, especially in the two-phase region, for more complex molecules such as CO{sub 2} and C{sub 2} H{sub 6}.

  18. Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation

    KAUST Repository

    Kadoura, Ahmad Salim

    2016-06-01

    In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard-Jones (LJ) particles. The main advantage of such surrogates, once generated, is the capability of accurately computing the needed thermodynamic quantities in a few seconds, thus efficiently replacing the computationally expensive MC molecular simulations. Benefiting from the tremendous computational time reduction, the PC surrogates were used to conduct large-scale optimization in order to propose single-site LJ models for several simple molecules. Experimental data, a set of supercritical isotherms, and part of the two-phase envelope, of several pure components were used for tuning the LJ parameters (ε, σ). Based on the conducted optimization, excellent fit was obtained for different noble gases (Ar, Kr, and Xe) and other small molecules (CH4, N2, and CO). On the other hand, due to the simplicity of the LJ model used, dramatic deviations between simulation and experimental data were observed, especially in the two-phase region, for more complex molecules such as CO2 and C2 H6.

  19. Evaporation of Lennard-Jones clusters

    International Nuclear Information System (INIS)

    Roman, C.E.; Garzon, I.L.

    1991-01-01

    Extensive molecular dynamics simulations have been done to study the evaporation of a 13-atom Lennard-Jones cluster. The survival probability and the evaporative lifetime are calculated as a function of the cluster total energy from a classical trajectory analysis. The results are interpreted in terms of the RRK theory of unimolecular dissociation. The calculation of the binding energy of the evaporated species from the evaporation rate and the average kinetic energy release is discussed. (orig.)

  20. Gaussian approximation to single particle correlations at and below the picosecond scale for Lennard-Jones and nanoparticle fluids

    International Nuclear Information System (INIS)

    Van Zon, Ramses; Ashwin, S S; Cohen, E G D

    2008-01-01

    To describe short time (picosecond) and small scale (nanometre) transport in fluids, a Green's function approach was recently developed. This approach relies on an expansion of the distribution of single particle displacements around a Gaussian function, yielding an infinite series of correction terms. Applying a recent theorem (van Zon and Cohen 2006 J. Stat. Phys. 123 1–37) shows that for sufficiently small times the terms in this series become successively smaller, so that truncating the series near or at the Gaussian level might provide a good approximation. In this paper, we derive a theoretical estimate for the time scale at which truncating the series at or near the Gaussian level could be supposed to be accurate for equilibrium nanoscale systems. In order to numerically estimate this time scale, the coefficients for the first few terms in the series are determined in computer simulations for a Lennard-Jones (LJ) fluid, an isotopic LJ mixture and a suspension of a LJ-based model of nanoparticles in a LJ fluid. The results suggest that for LJ fluids an expansion around a Gaussian is accurate at time scales up to a picosecond, while for nanoparticles in suspension (a nanofluid), the characteristic time scale up to which the Gaussian is accurate becomes of the order of 5–10 ps. (invited article)

  1. Phase separation of a Lennard-Jones fluid interacting with a long, condensed polymer chain: implications for the nuclear body formation near chromosomes.

    Science.gov (United States)

    Oh, Inrok; Choi, Saehyun; Jung, YounJoon; Kim, Jun Soo

    2015-08-28

    Phase separation in a biological cell nucleus occurs in a heterogeneous environment filled with a high density of chromatins and thus it is inevitably influenced by interactions with chromatins. As a model system of nuclear body formation in a cell nucleus filled with chromatins, we simulate the phase separation of a low-density Lennard-Jones (LJ) fluid interacting with a long, condensed polymer chain. The influence of the density variation of LJ particles above and below the phase boundary and the role of attractive interactions between LJ particles and polymer segments are investigated at a fixed value of strong self-interaction between LJ particles. For a density of LJ particles above the phase boundary, phase separation occurs and a dense domain of LJ particles forms irrespective of interactions with the condensed polymer chain whereas its localization relative to the polymer chain is determined by the LJ-polymer attraction strength. Especially, in the case of moderately weak attractions, the domain forms separately from the polymer chain and subsequently associates with the polymer chain. When the density is below the phase boundary, however, the formation of a dense domain is possible only when the LJ-polymer attraction is strong enough, for which the domain grows in direct contact with the interacting polymer chain. In this work, different growth behaviors of LJ particles result from the differences in the density of LJ particles and in the LJ-polymer interaction, and this work suggests that the distinct formation of activity-dependent and activity-independent nuclear bodies (NBs) in a cell nucleus may originate from the differences in the concentrations of body-specific NB components and in their interaction with chromatins.

  2. Scaling of the dynamics of flexible Lennard-Jones chains

    DEFF Research Database (Denmark)

    Veldhorst, Arno; Dyre, Jeppe C.; Schrøder, Thomas

    2015-01-01

    The previous paper [A. A. Veldhorst et al., J. Chem. Phys. 141, 054904 (2014)] demonstrated that the isomorph theory explains the scaling properties of a liquid of flexible chains consisting of ten Lennard-Jones particles connected by rigid bonds. We here investigate the same model with harmonic......, dynamics, and the excess entropy are invariant. The Lennard-Jones chain liquid with harmonic bondsdoes have curves in the phase diagram along which the structure and dynamics are invariant. The excess entropy is not invariant on these curves, which we refer to as “pseudoisomorphs.” In particular......, this means that Rosenfeld’s excess-entropy scaling (the dynamics being a function of excess entropy only) does not apply for the Lennard-Jones chain with harmonic bonds...

  3. Molecular dynamics study of the hydration of Lennard-Jones solutes

    International Nuclear Information System (INIS)

    Geiger, A.; Rahman, A.; Stillinger, F.H.

    1979-01-01

    In order to clarify the nature of hydrophobic interactions in water, we have used the molecular dynamics simulation method to study a system comprising two Lennard-Jones solute particles and 214 water molecules. Although the solutes were placed initially in contact, forces in the system drive them slightly apart to permit formation of vertex-sharing solvent ''cages.'' Definite orientational preferences have been observed for water molecules in the first solvation layer around the Lennard-Jones solutes; these preferences are loosely reminiscent of structure in clathrates. Nevertheless, substantial local disorder is obviously present. The dynamical data show that translational and rotational motions of solvation--sheath water molecules are perceptibly slower (by at least 20%) than those in pure bulk water

  4. Fluctuations and thermodynamic response functions in a Lennard-Jones solid

    International Nuclear Information System (INIS)

    Li, M.; Johnson, W.L.

    1992-01-01

    Thermodynamic response functions of a nearest-neighbor Lennard-Jones solid--heat capacity, thermal-expansion coefficient, compressibility, and elastic constants--are calculated directly from fluctuations using molecular-dynamics simulations. The algorithm used is the earlier Parrinello-Rahman molecular dynamics modified to take into account symmetry and rotation invariance of the system under investigation. The convergence is very fast and results are in good agreement with existing Monte Carlo and molecular-dynamics results

  5. Dynamics of an assembly of finite-size Lennard-Jones spheres

    International Nuclear Information System (INIS)

    Singh, P.

    1996-01-01

    The time-averaged Fourier spectra of the number density, velocity, and force fields are obtained numerically for an assembly of spherical particles interacting via the Lennard-Jones potential. The magnitude spectra determine the dominant wave numbers, and the phase difference between the Lennard-Jones force and number density spectra determines the nature of the particle dynamics. The latter is used to show that for every wave number k there is a critical frequency ω c (k), such that when ω c (k) the phase difference is π/2 and when ω approx-gt ω c (k) the phase difference is -π/2. The ratio of the frequency and the wave number at which the phase difference changes sign is used to define an effective sound speed for the particle system. The effective sound speed is shown to be a function of the dimensionless wave number, and is locally minimum at the same dimensionless wave numbers for which the static structure factor is minimum. It is also shown that the dynamical response of the particle system for waves with speeds greater than the effective sound speed is similar to the response of the hyperbolic systems of equations, and for waves with speeds smaller than the effective sound speed the response is similar to the response of the elliptic systems. The convection effects are shown to be of the same order of magnitude as the Lennard-Jones forces, and the change of type of the equations from hyperbolic to elliptic occurs when the magnitude of the convection term is comparable to the magnitude of the Lennard-Jones force term. It is also shown that the change of type cannot occur in a theory where the convection term is neglected. copyright 1996 The American Physical Society

  6. Localized fluidity modes and the topology of the constant-potential-energy hypersurfaces of Lennard-Jones matter

    DEFF Research Database (Denmark)

    Cotterill, Rodney M J; Madsen, J.

    1986-01-01

    Sections of configuration space for Lennard-Jones matter were obtained by probing all the normal-mode energy profiles, following diagonalization of the dynamical matrix for a 240-particle system. For the crystal and sufficiently cold glass, these are single welled, whereas increasing numbers...... of double wells occur as the glass is warmed toward the fluid. This indicates that there might be a fundamental difference between the topologies of the constant-potential-energy hypersurfaces of crystalline and noncrystalline Lennard-Jones matter....

  7. Metastability, spectrum, and eigencurrents of the Lennard-Jones-38 network

    International Nuclear Information System (INIS)

    Cameron, Maria K.

    2014-01-01

    We develop computational tools for spectral analysis of stochastic networks representing energy landscapes of atomic and molecular clusters. Physical meaning and some properties of eigenvalues, left and right eigenvectors, and eigencurrents are discussed. We propose an approach to compute a collection of eigenpairs and corresponding eigencurrents describing the most important relaxation processes taking place in the system on its way to the equilibrium. It is suitable for large and complex stochastic networks where pairwise transition rates, given by the Arrhenius law, vary by orders of magnitude. The proposed methodology is applied to the network representing the Lennard-Jones-38 cluster created by Wales's group. Its energy landscape has a double funnel structure with a deep and narrow face-centered cubic funnel and a shallower and wider icosahedral funnel. However, the complete spectrum of the generator matrix of the Lennard-Jones-38 network has no appreciable spectral gap separating the eigenvalue corresponding to the escape from the icosahedral funnel. We provide a detailed description of the escape process from the icosahedral funnel using the eigencurrent and demonstrate a superexponential growth of the corresponding eigenvalue. The proposed spectral approach is compared to the methodology of the Transition Path Theory. Finally, we discuss whether the Lennard-Jones-38 cluster is metastable from the points of view of a mathematician and a chemical physicist, and make a connection with experimental works

  8. Free energy of the Lennard-Jones solid

    NARCIS (Netherlands)

    Hoef, van der M.A.

    2000-01-01

    We have determined a simple expression for the absolute Helmholtz free energy of the fcc Lennard-Jones solid from molecular dynamics simulations. The pressure and energy data from these simulations have been fitted to a simple functional form (18 parameters) for densities ranging from around

  9. Thermal conductivity of the Lennard-Jones chain fluid model.

    Science.gov (United States)

    Galliero, Guillaume; Boned, Christian

    2009-12-01

    Nonequilibrium molecular dynamics simulations have been performed to estimate, analyze, and correlate the thermal conductivity of a fluid composed of short Lennard-Jones chains (up to 16 segments) over a large range of thermodynamic conditions. It is shown that the dilute gas contribution to the thermal conductivity decreases when the chain length increases for a given temperature. In dense states, simulation results indicate that the residual thermal conductivity of the monomer increases strongly with density, but is weakly dependent on the temperature. Compared to the monomer value, it has been noted that the residual thermal conductivity of the chain was slightly decreasing with its length. Using these results, an empirical relation, including a contribution due to the critical enhancement, is proposed to provide an accurate estimation of the thermal conductivity of the Lennard-Jones chain fluid model (up to 16 segments) over the domain 0.8values of the Lennard-Jones chain fluid model merge on the same "universal" curve when plotted as a function of the excess entropy. Furthermore, it is shown that the reduced configurational thermal conductivity of the Lennard-Jones chain fluid model is approximately proportional to the reduced excess entropy for all fluid states and all chain lengths.

  10. Viscous Growth in Spinodal Decomposition of the Two-component Lennard-Jones Model in Two Dimensions

    DEFF Research Database (Denmark)

    Laradji, M.; Toxvaerd, S.; Mouritsen, Ole G.

    1997-01-01

    The dynamics of phase separation of a two-component Lennard-Jones model in three dimensions is investigated by means of large scale molecular dynamics simulation. A systematic study over a wide range of quench temperatures within the coexistence region shows that the binary system reaches...

  11. Phase diagram of a Lennard-Jones solid

    International Nuclear Information System (INIS)

    Choi, Y.; Ree, T.; Ree, F.H.

    1993-01-01

    A phase diagram of a Lennard-Jones solid at kT/ε≥0.8 is constructed by our recent perturbation theory. It shows the stability of the face-centered-cubic phase except within a small pressure and temperature domain, where the hexagonal-close packed phase may occur. The theory predicts anharmonic contributions to the Helmholtz free energy (important to the crystal stability) in good agreement with Monte Carlo data

  12. Theoretical prediction of crystallization kinetics of a supercooled Lennard-Jones fluid

    Science.gov (United States)

    Gunawardana, K. G. S. H.; Song, Xueyu

    2018-05-01

    The first order curvature correction to the crystal-liquid interfacial free energy is calculated using a theoretical model based on the interfacial excess thermodynamic properties. The correction parameter (δ), which is analogous to the Tolman length at a liquid-vapor interface, is found to be 0.48 ± 0.05 for a Lennard-Jones (LJ) fluid. We show that this curvature correction is crucial in predicting the nucleation barrier when the size of the crystal nucleus is small. The thermodynamic driving force (Δμ) corresponding to available simulated nucleation conditions is also calculated by combining the simulated data with a classical density functional theory. In this paper, we show that the classical nucleation theory is capable of predicting the nucleation barrier with excellent agreement to the simulated results when the curvature correction to the interfacial free energy is accounted for.

  13. A model-adaptivity method for the solution of Lennard-Jones based adhesive contact problems

    Science.gov (United States)

    Ben Dhia, Hachmi; Du, Shuimiao

    2018-05-01

    The surface micro-interaction model of Lennard-Jones (LJ) is used for adhesive contact problems (ACP). To address theoretical and numerical pitfalls of this model, a sequence of partitions of contact models is adaptively constructed to both extend and approximate the LJ model. It is formed by a combination of the LJ model with a sequence of shifted-Signorini (or, alternatively, -Linearized-LJ) models, indexed by a shift parameter field. For each model of this sequence, a weak formulation of the associated local ACP is developed. To track critical localized adhesive areas, a two-step strategy is developed: firstly, a macroscopic frictionless (as first approach) linear-elastic contact problem is solved once to detect contact separation zones. Secondly, at each shift-adaptive iteration, a micro-macro ACP is re-formulated and solved within the multiscale Arlequin framework, with significant reduction of computational costs. Comparison of our results with available analytical and numerical solutions shows the effectiveness of our global strategy.

  14. Crystallisation of a Lennard-Jones fluid by large scale molecular dynamics simulation

    International Nuclear Information System (INIS)

    Snook, I.

    1998-01-01

    Full text: The evolution of the structure of a large system of atoms interacting via a Lennard-Jones pair potential was simulated by the use of the Molecular Dynamics computer simulation technique. The system was initially equilibrated in the one phase region of the phase diagram at a temperature above critical then a temperature quench was performed which placed the system in a region were the single fluid phase was unstable. Quenches to below the triple point temperature gave rise to crystallisation The mechanism and final morphology is shown to depend strongly on the starting conditions e.g. the starting density

  15. Numerical simulation of pool boiling of a Lennard-Jones liquid

    KAUST Repository

    Inaoka, Hajime

    2013-09-01

    We performed a numerical simulation of pool boiling by a molecular dynamics model. In the simulation, a liquid composed of Lennard-Jones particles in a uniform gravitational field is heated by a heat source at the bottom of the system. The model successfully reproduces the change in regimes of boiling from nucleate boiling to film boiling with the increase of the heat source temperature. We present the pool boiling curve by the model, whose general behavior is consistent with those observed in experiments of pool boiling. © 2013 Elsevier B.V. All rights reserved.

  16. Numerical simulation of pool boiling of a Lennard-Jones liquid

    KAUST Repository

    Inaoka, Hajime; Ito, Nobuyasu

    2013-01-01

    We performed a numerical simulation of pool boiling by a molecular dynamics model. In the simulation, a liquid composed of Lennard-Jones particles in a uniform gravitational field is heated by a heat source at the bottom of the system. The model successfully reproduces the change in regimes of boiling from nucleate boiling to film boiling with the increase of the heat source temperature. We present the pool boiling curve by the model, whose general behavior is consistent with those observed in experiments of pool boiling. © 2013 Elsevier B.V. All rights reserved.

  17. Radiation damage in an amorphous Lennard-Jones solid

    International Nuclear Information System (INIS)

    Chaki, T.K.; Li, J.C.M.

    1985-01-01

    A molecular-dynamics simulation of radiation damage in an amorphous Lennard-Jones solid has been undertaken. A three-dimensional structure of 685 atoms with periodic boundary conditions was used. An atom was injected inward from the middle of one surface, and as it lost its energy its velocity and position were recorded. The temperature profile around the injection direction was also calculated. The amorphous structure was examined before and after irradiation by calculating the volume distribution of the Voronoi polyhedra and its time evolution. The production of vacancies and interstitials was observed. The interstitials were found to disappear rapidly, and the vacancies slowly. (author)

  18. Phase Diagram of Kob-Andersen-Type Binary Lennard-Jones Mixtures

    Science.gov (United States)

    Pedersen, Ulf R.; Schrøder, Thomas B.; Dyre, Jeppe C.

    2018-04-01

    The binary Kob-Andersen (KA) Lennard-Jones mixture is the standard model for computational studies of viscous liquids and the glass transition. For very long simulations, the viscous KA system crystallizes, however, by phase separating into a pure A particle phase forming a fcc crystal. We present the thermodynamic phase diagram for KA-type mixtures consisting of up to 50% small (B ) particles showing, in particular, that the melting temperature of the standard KA system at liquid density 1.2 is 1.028(3) in A particle Lennard-Jones units. At large B particle concentrations, the system crystallizes into the CsCl crystal structure. The eutectic corresponding to the fcc and CsCl structures is cutoff in a narrow interval of B particle concentrations around 26% at which the bipyramidal orthorhombic PuBr3 structure is the thermodynamically stable phase. The melting temperature's variation with B particle concentration at two constant pressures, as well as at the constant density 1.2, is estimated from simulations at pressure 10.19 using isomorph theory. Our data demonstrate approximate identity between the melting temperature and the onset temperature below which viscous dynamics appears. Finally, the nature of the solid-liquid interface is briefly discussed.

  19. A Lennard-Jones-like perspective on first order transitions in biological helices

    DEFF Research Database (Denmark)

    Oskolkov, Nikolay N.; Bohr, Jakob

    2013-01-01

    Helical structures with Lennard-Jones self-interactions are studied for optimal conformations. For this purpose, their self-energy is analyzed for extrema with respect to the geometric parameters of the helices. It is found that Lennard-Jones helices exhibit a first order phase transition from...

  20. Water in the presence of inert Lennard-Jones obstacles

    Science.gov (United States)

    Kurtjak, Mario; Urbic, Tomaz

    2014-04-01

    Water confined by the presence of a 'sea' of inert obstacles was examined. In the article, freely mobile two-dimensional Mercedes-Benz (MB) water put to a disordered, but fixed, matrix of Lennard-Jones disks was studied by the Monte Carlo computer simulations. For the MB water molecules in the matrix of Lennard-Jones disks, we explored the structures, hydrogen-bond-network formation and thermodynamics as a function of temperature and size and density of matrix particles. We found that the structure of model water is perturbed by the presence of the obstacles. Density of confined water, which was in equilibrium with the bulk water, was smaller than the density of the bulk water and the temperature dependence of the density of absorbed water did not show the density anomaly in the studied temperature range. The behaviour observed as a consequence of confinement is similar to that of increasing temperature, which can for a matrix lead to a process similar to capillary evaporation. At the same occupancy of space, smaller matrix molecules cause higher destruction effect on the absorbed water molecules than the bigger ones. We have also tested the hypothesis that at low matrix densities the obstacles induce an increased ordering and 'hydrogen bonding' of the MB model molecules, relative to pure fluid, while at high densities the obstacles reduce MB water structuring, as they prevent the fluid to form good 'hydrogen-bonding' networks. However, for the size of matrix molecules similar to that of water, we did not observe this effect.

  1. KAJIAN METODE ANALISA DATA GOAL SEEK (MICROSOFT EXCEL UNTUK PENYELESAIAN PERSAMAAN SCHRÖDINGER DALAM MENENTUKAN KUANTISASI ENERGI DIBAWAH PENGARUH POTENSIAL LENNARD-JONES

    Directory of Open Access Journals (Sweden)

    W. Kurniawan

    2016-11-01

    Full Text Available Penyelesaian persamaan Schrödinger dengan berbagai model potensial sangat penting dilakukan untuk memberikan gambaran perilaku zarah di bawah pengaruh potensial tersebut. Solusinya berupa fungsi gelombang yang memuat informasi penting tentang perilaku gelombang yang ditunjukkan dengan energi terikatnya. Pada penelitian ini kasus yang ingin diteliti adalah model potensial Lennard-Jones dengan menggunakan metode analisa goal seek yang tersedia pada Microsoft excel. Persamaannya dijabarkan dengan metode Euler terlebih dahulu selanjutnya syarat batas ditentukan agar ketelitian hasil diperoleh. Agar perhitungan goal seek  dapat dilakukan maka harus diubah dari besaran fisis menjadi besaran yang tidak berdimensi dimana parameter v menunjukkan keklasikan suatu sistem dan nilai  ε   menunjukkan kuantisasi energi. Hasil yang diperoleh adalah bahwa dengan memasukkan parameter kontrol nilai v tertentu, telah diperoleh beberapa keadaan energi dengan batas zkiri dan zkanan tertentu. Ketika masukan parameter v yang diberikan semakin besar keadaan energinya pun lebih rapat (ditunjukkan energy state yang diperoleh semakin banyak dibandingkan bila masukan v-nya lebih kecil. Penelitian ini bermanfaat untuk menyederhanakan kasus potensial yang lebih rumit, dimana solusinya dapat diperoleh dengan mudah dan konsep kuantisasi energi akibat model potensial L-J dapat dipahami secara utuh. Solution of the Schrödinger equation in various  potential model is very important in order to provide an overview of  behaviour’s particle under influence of potential model. The solution is a wave function that contains important information are shown by energy state. In this research, the investigated is Lennard Jones potential by using Goal Seek analysis which are available in Microsoft Excel. The equation is described by the Euler method and then boundary condition is determined to perecision result which are obtained. It must be changed in terms dimensionless where

  2. The Monte Carlo dynamics of a binary Lennard-Jones glass-forming mixture

    International Nuclear Information System (INIS)

    Berthier, L; Kob, W

    2007-01-01

    We use a standard Monte Carlo algorithm to study the slow dynamics of a binary Lennard-Jones glass-forming mixture at low temperature. We find that the Monte Carlo approach is by far the most efficient way to simulate a stochastic dynamics since the relaxation is about 10 times faster than in Brownian dynamics and about 30 times faster than in stochastic dynamics. Moreover, the average dynamical behaviour of the system is in quantitative agreement with that obtained using Newtonian dynamics, apart from at very short times where thermal vibrations are suppressed. We show, however, that dynamic fluctuations quantified by four-point dynamic susceptibilities do retain a dependence on the microscopic dynamics, as recently predicted theoretically

  3. Shear viscosity of the Lennard-Jones fluid near the triple point: Green-Kubo results

    International Nuclear Information System (INIS)

    Erpenbeck, J.J.

    1988-01-01

    The long-standing disagreement over the shear viscosity coefficient of the Lennard-Jones fluid near the triple point is reexamined through a series of very extensive Monte Carlo molecular-dynamics calculations of this transport coefficient based on the Green-Kubo theory. The stress autocorrelation function is shown to exhibit a slow decay, principally in the kinetic-potential and the potential-potential terms, which is large compared with the kinetic-kinetic long-time tail predicted by simple mode-coupling theory. Nonetheless, the viscosity coefficient, exclusive of any correction for this tail for times greater than are accessible numerically, is found to agree with that of Schoen and Hoheisel (who discounted the existence of such a tail) as well as nonequilibrium molecular-dynamics calculations. The large value of the viscosity coefficient found by Levesque and co-workers for 864 particles is brought into statistical agreement with the present results by a modest, but not unrealistic, increase in its statistical uncertainty. The pressure is found to exhibit an anomalous dependence on the size of the system, but the viscosity as well as the self-diffusion constant appear to be linear in the inverse of the number of particles, within the precision of our calculations. The viscosity coefficient, including a long-time-tail contribution based on the extended mode-coupling theory is (3.796 +- 0.068)σepsilon-c/m)/sup 1/2/ for the Lennard-Jones potential, fitted to a cubic spline, and (3.345 +- 0.068)σepsilon-c/m)/sup 1/2/ for the potential truncated at 2.5σ

  4. Longitudinal and bulk viscosities of Lennard-Jones fluids

    Science.gov (United States)

    Tankeshwar, K.; Pathak, K. N.; Ranganathan, S.

    1996-12-01

    Expressions for the longitudinal and bulk viscosities have been derived using Green Kubo formulae involving the time integral of the longitudinal and bulk stress autocorrelation functions. The time evolution of stress autocorrelation functions are determined using the Mori formalism and a memory function which is obtained from the Mori equation of motion. The memory function is of hyperbolic secant form and involves two parameters which are related to the microscopic sum rules of the respective autocorrelation function. We have derived expressions for the zeroth-, second-and fourth- order sum rules of the longitudinal and bulk stress autocorrelation functions. These involve static correlation functions up to four particles. The final expressions for these have been put in a form suitable for numerical calculations using low- order decoupling approximations. The numerical results have been obtained for the sum rules of longitudinal and bulk stress autocorrelation functions. These have been used to calculate the longitudinal and bulk viscosities and time evolution of the longitudinal stress autocorrelation function of the Lennard-Jones fluids over wide ranges of densities and temperatures. We have compared our results with the available computer simulation data and found reasonable agreement.

  5. Vacancy behavior in a compressed fcc Lennard-Jones crystal

    International Nuclear Information System (INIS)

    Beeler, J.R. Jr.

    1981-12-01

    This computer experiment study concerns the determination of the stable vacancy configuration in a compressed fcc Lennard-Jones crystal and the migration of this defect in a compressed crystal. Isotropic and uniaxial compression stress conditions were studied. The isotropic and uniaxial compression magnitudes employed were 0.94 less than or equal to eta less than or equal to 1.5, and 1.0 less than or equal to eta less than or equal to 1.5, respectively. The site-centered vacancy (SCV) was the stable vacancy configuration whenever cubic symmetry was present. This includes all of the isotropic compression cases and the particular uniaxial compression case (eta = √2) that give a bcc structure. In addition, the SCV was the stable configuration for uniaxial compression eta 1.20, the SV-OP is an extended defect and, therefore, a saddle point for SV-OP migration could not be determined. The mechanism for the transformation from the SCV to the SV-OP as the stable form at eta = 1.29 appears to be an alternating sign [101] and/or [011] shear process

  6. Nematic-isotropic transition in some lattice models for rigid cores having semiflexible tails: segmental Lennard-Jones interactions

    International Nuclear Information System (INIS)

    Dowell, F.

    1983-01-01

    Two average-environment simple cubic lattice models: a refined model and a simple model, both having site-site (segmental) pair Lennard-Jones (LJ) interactions: for molecules composed of rigid cores having semiflexible tails are presented. The calculated values of the following properties at the nematic-isotropic transition for rigid rods of varying length are compared with relevant experimental data for PAA (p-azoxyanisole, or 4,4'-dimethoxyazoxybenzene): temperature, core orientational order parameter, nematic density and volume, relative density change, and relative entropy change. The temperature change as a function of volume change at constant order parameter is also discussed. In general, both LJ models give considerably better quantitative agreement with experiment, especially for the temperature and the relative density change, than do the earlier lattice models with hard repulsions, with or without constant segmental pair interaction energies. In most aspects, these LJ models give good quantitative agreement with experiment. These LJ models elucidate the importance of realistic intermolecular potentials, especially the role of soft repulsions, in describing an order-disorder transition between two condensed phases

  7. Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts

    International Nuclear Information System (INIS)

    Chremos, Alexandros; Nikoubashman, Arash; Panagiotopoulos, Athanassios Z.

    2014-01-01

    In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric–isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments

  8. Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts

    Energy Technology Data Exchange (ETDEWEB)

    Chremos, Alexandros, E-mail: achremos@imperial.ac.uk [Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Nikoubashman, Arash, E-mail: arashn@princeton.edu; Panagiotopoulos, Athanassios Z. [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States)

    2014-02-07

    In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric–isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments.

  9. Simulation of depositions of a Lennard-Jones cluster on a crystalline surface

    International Nuclear Information System (INIS)

    Saitoh, Kuniyasu; Hayakawa, Hisao

    2009-01-01

    Depositions of amorphous Lennard-Jones clusters on a crystalline surface are numerically investigated. From the results of the molecular dynamics simulation, we found that the deposited clusters exhibit a transition from multilayered adsorption to monolayered adsorption at a critical incident speed. Employing the energy conservation law, we can explain the behavior of the ratio of the number of atoms adsorbed on the substrate to the cluster size. The boundary shape of the deposited cluster depends strongly on the incident speed, and some unstable modes grow during the spread of the deposited cluster on the substrate. We also discuss the wettability between different Lennard-Jones atoms. (author)

  10. Collision frequency of Lennard-Jones fluids at high densities by equilibrium molecular dynamics simulation

    International Nuclear Information System (INIS)

    Adebayo, G.A.; Anusionwu, B.C.; Njah, A.N.; Adeniran, O.J.; Mathew, B.; Sunmonu, R.S.

    2009-01-01

    Arising from the inability of theoretical calculations to give accurate descriptions of (shear) viscosity in rare gases at high densities, we investigated the likely cause of discrepancy between theory and experiments. Molecular Dynamics simulations were performed to calculate transport coefficients and collision frequency of rare gases at high densities and different temperatures using a Lennard-Jones modelled pair potential. The results, when compared with experiments show an underestimation of the viscosity calculated through the Green-Kubo formalism, but in agreement with some other calculations performed by other groups. In the present work the origin of the underestimation is considered. Analyses of the transport coefficients show a very high collision frequency which suggests an atom may spend much less time in the neighbourhood of the fields of force of another atom and that the distribution in the systems studied adjusts itself to a nearly Maxwellian type which resulted in a locally and temporarily slowly varying temperature. We show that the time spent in the fields of force is so small compared with relaxation time thereby leading to a possible reduction in local velocity auto-correlation between atoms. (author)

  11. A test of the mean density approximation for Lennard-Jones mixtures with large size ratios

    International Nuclear Information System (INIS)

    Ely, J.F.

    1986-01-01

    The mean density approximation for mixture radial distribution functions plays a central role in modern corresponding-states theories. This approximation is reasonably accurate for systems that do not differ widely in size and energy ratios and which are nearly equimolar. As the size ratio increases, however, or if one approaches an infinite dilution of one of the components, the approximation becomes progressively worse, especially for the small molecule pair. In an attempt to better understand and improve this approximation, isothermal molecular dynamics simulations have been performed on a series of Lennard-Jones mixtures. Thermodynamic properties, including the mixture radial distribution functions, have been obtained at seven compositions ranging from 5 to 95 mol%. In all cases the size ratio was fixed at two and three energy ratios were investigated, 22 / 11 =0.5, 1.0, and 1.5. The results of the simulations are compared with the mean density approximation and a modification to integrals evaluated with the mean density approximation is proposed

  12. A perturbed Lennard-Jones chain equation of state for liquid metals

    Energy Technology Data Exchange (ETDEWEB)

    Mousazadeh, M H; Marageh, M Ghanadi [AEOI, JIH Research Laboratory, 11365/8486, Tehran (Iran, Islamic Republic of)

    2006-05-24

    The perturbed Lennard-Jones chain (PLJC) equation of state is formulated based on first-order variational perturbation theory. The model uses two parameters for a monatomic system, segment size, {sigma}, and segment energy, {epsilon}/k. In this work, we employed the PLJC equation to calculate the liquid density of 26 metals, including alkali and alkali earth metals, iron, cobalt, nickel, copper, silver, gold, zinc, cadmium, mercury, aluminium, gallium, indium, thallium, tin, lead, antimony, and bismuth, for which accurate experimental data exist in the literature. The calculations cover a broad range of temperatures ranging from the melting point to close to the critical point and pressures ranging from the vapour-pressure curve up to pressures as high as 2000 bar. The average absolute deviation in the liquid density predicted by the PLJC equation of state in the saturation line compared with experimental data is 1.26%. Also, using the normal melting temperature and liquid density at melting point (T{sub m}, {rho}{sub m}) as input data for the estimation of the equation of state parameters provides a good correlation of liquid density at saturated and compressed pressures.

  13. Comprehensive representation of the Lennard-Jones equation of state based on molecular dynamics simulation data

    Science.gov (United States)

    Pieprzyk, S.; Brańka, A. C.; Maćkowiak, Sz.; Heyes, D. M.

    2018-03-01

    The equation of state (EoS) of the Lennard-Jones fluid is calculated using a new set of molecular dynamics data which extends to higher temperature than in previous studies. The modified Benedict-Webb-Rubin (MBWR) equation, which goes up to ca. T ˜ 6, is reparametrized with new simulation data. A new analytic form for the EoS, which breaks the fluid range into two regions with different analytic forms and goes up to ca. T ≃ 35, is also proposed. The accuracy of the new formulas is at least as good as the MBWR fit and goes to much higher temperature allowing it to now encompass the Amagat line. The fitted formula extends into the high temperature range where the system can be well represented by inverse power potential scaling, which means that our specification of the equation of state covers the entire (ρ, T) plane. Accurate analytic fit formulas for the Boyle, Amagat, and inversion curves are presented. Parametrizations of the extrema loci of the isochoric, CV, and isobaric, CP, heat capacities are given. As found by others, a line maxima of CP terminates in the critical point region, and a line of minima of CP terminates on the freezing line. The line of maxima of CV terminates close to or at the critical point, and a line of minima of CV terminates to the right of the critical point. No evidence for a divergence in CV in the critical region is found.

  14. Enhancement of the droplet nucleation in a dense supersaturated Lennard-Jones vapor

    Energy Technology Data Exchange (ETDEWEB)

    Zhukhovitskii, D. I., E-mail: dmr@ihed.ras.ru [Joint Institute of High Temperatures, Russian Academy of Sciences, Izhorskaya 13, Bd. 2, 125412 Moscow (Russian Federation)

    2016-05-14

    The vapor–liquid nucleation in a dense Lennard-Jones system is studied analytically and numerically. A solution of the nucleation kinetic equations, which includes the elementary processes of condensation/evaporation involving the lightest clusters, is obtained, and the nucleation rate is calculated. Based on the equation of state for the cluster vapor, the pre-exponential factor is obtained. The latter diverges as a spinodal is reached, which results in the nucleation enhancement. The work of critical cluster formation is calculated using the previously developed two-parameter model (TPM) of small clusters. A simple expression for the nucleation rate is deduced and it is shown that the work of cluster formation is reduced for a dense vapor. This results in the nucleation enhancement as well. To verify the TPM, a simulation is performed that mimics a steady-state nucleation experiments in the thermal diffusion cloud chamber. The nucleating vapor with and without a carrier gas is simulated using two different thermostats for the monomers and clusters. The TPM proves to match the simulation results of this work and of other studies.

  15. Liquid-vapour phase behaviour of a polydisperse Lennard-Jones fluid

    International Nuclear Information System (INIS)

    Wilding, Nigel B; Sollich, Peter

    2005-01-01

    We describe a simulation study of the liquid-vapour phase behaviour of a model polydisperse fluid. Particle interactions are given by a Lennard-Jones potential in which polydispersity features both in the particle sizes and the amplitude of their interactions. We address the computational problem of accurately locating the cloud curve for such a system using Monte Carlo simulations within the grand canonical ensemble. The strongly nonlinear variation of the fractional volumes of the phases across the coexistence region precludes naive extrapolation to determine the cloud point density. Instead we propose an improved estimator for the cloud point location and use scaling arguments to predicts its finite-size behaviour. Excellent agreement is found with the simulation results. Application of the method reveals that the measured cloud curve is highly sensitive to the presence of large particles, even when they are extremely rare. This finding is expected to have implications for the reproducibility of experimentally measured phase diagrams in colloids and polymers

  16. RISM theory distribution functions for Lennard--Jones interaction site fluids

    International Nuclear Information System (INIS)

    Johnson, E.; Hazoume, R.P.

    1978-01-01

    Reference interaction site model (RISM) theory distribution functions for Lennard-Jones interaction site fluids are discussed. The comparison with computer simulation results suggests that these distribution functions are as accurate as RISM distribution functions for fused hard sphere molecular fluids

  17. Application of the RISM theory to Lennard-Jones interaction site molecular fluids

    International Nuclear Information System (INIS)

    Johnson, E.; Hazoume, R.P.

    1979-01-01

    It seems that reference interaction site model (RISM) theory atom--atom distribution functions have been obtained directly from the RISM equations only for fused hard sphere molecular fluids. RISM distribution functions for Lennard-Jones interaction site fluids are presented. Results presented suggest that these distribution functions are as accurate as RISM distribution functions for fused hard sphere molecular fluids

  18. Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins

    DEFF Research Database (Denmark)

    D'ovidio, Francesco; Bohr, Henrik; Lindgård, Per-Anker

    2005-01-01

    We study the propagation of solitons along the hydrogen bonds of an alpha helix. Modeling the hydrogen and peptide bonds with Lennard-Jones potentials, we show that the solitons can appear spontaneously and have long lifetimes. Remarkably, even if no explicit solution is known for the Lennard-Jones...... potential, the solitons can be characterized analytically with a good quantitative agreement using formulas for a Toda potential with parameters fitted to the Lennard-Jones potential. We also discuss and show the robustness of the family of periodic solutions called cnoidal waves, corresponding to phonons...

  19. Friction between Two Brownian Particles in a Lennard-Jones Solvent: A Molecular Dynamics Simulation Study

    International Nuclear Information System (INIS)

    Lee, Song Hi

    2010-01-01

    We presented a molecular dynamics (MD) simulation study of friction behavior between two very massive Brownian particles (BPs) oriented along the z axis with BP centers at -R 12 /2 and R 12 /2 in a Lennard-Jones solvent as a function of the inter-particle separation, R 12 . In order to fix the BPs in space an MD simulation method with the mass of the BP as 10 90 g/mol was employed in which the total momentum of the system was conserved. The cross friction coefficients of x- and y-components are nearly insensitive to R 12 but that of z-component varies with R 12 in good accord with the simple hydrodynamic approximation. On the other hand, the self-friction coefficients are estimated as a very small difference from the single particle friction coefficients, ξ 0 , at all inter-particle separations which agrees with the simple hydrodynamic approximation. Consequently ξ (-) xx is nearly independent of R 12 and equal to its asymptotic value of twice the single particle friction coefficient, and the other relative friction, ξ (-) zz , is in good agreement with the simple hydrodynamic approximation. Molecular theory of Brownian motion of a single heavy particle in a fluid had received a considerable attention in earlier years. After molecular dynamics (MD) simulation technique was utilized, this subject has been widely studied by a variety of MD simulation methods. The common issues here were about the long time behavior of the force and velocity autocorrelation functions, the system size dependent friction coefficient of a massive Brownian particle, and test of the Stokes-Einstein law

  20. Collision kernels in the eikonal approximation for Lennard-Jones interaction potential

    International Nuclear Information System (INIS)

    Zielinska, S.

    1985-03-01

    The velocity changing collisions are conveniently described by collisional kernels. These kernels depend on an interaction potential and there is a necessity for evaluating them for realistic interatomic potentials. Using the collision kernels, we are able to investigate the redistribution of atomic population's caused by the laser light and velocity changing collisions. In this paper we present the method of evaluating the collision kernels in the eikonal approximation. We discuss the influence of the potential parameters Rsub(o)sup(i), epsilonsub(o)sup(i) on kernel width for a given atomic state. It turns out that unlike the collision kernel for the hard sphere model of scattering the Lennard-Jones kernel is not so sensitive to changes of Rsub(o)sup(i) as the previous one. Contrary to the general tendency of approximating collisional kernels by the Gaussian curve, kernels for the Lennard-Jones potential do not exhibit such a behaviour. (author)

  1. Stability of relaxed Lennard-Jones models made of 500 to 6000 atoms

    International Nuclear Information System (INIS)

    Raoult, B.; Farges, J.; Feraudy, M.F. de; Torchet, G.

    1989-01-01

    We present a study of the stability of clusters models made of a number N of atoms in the range 500 to 6000 atoms, freely interacting through the Lennard-Jones potential. The potential energy per atom, calculated for relaxed models, shows that stable models belong to an icosahedral sequence when N<1600 and to a decahedral sequence beyond. A coexistence size range of both structures is discussed in connection with experimental results on argon clusters in free jet expansions. (orig.)

  2. Analytic Debye-Grüneisen equation of state for a generalized Lennard-Jones solids

    Institute of Scientific and Technical Information of China (English)

    孙久勋; 吴强; 蔡灵仓; 经福谦

    2003-01-01

    The approximate method to treat the practical quantum anharmonic solids proposed by Hardy,Lacks and Shukla is reformulated with explicit physical meanings.It is shown that the quantum effect is important at low temperature,it can be treated in the harmonic framework; and the anharmonic effect is important at high temperature and tends to zero at low temperature,it can be treated by using a classical approximation.The alternative formulation is easier for various applications,and is applied to a Debye-Gruneisen solid with the generalized Lennard-Jones intermolecular interaction.The expressions for the Debye temperature and Gruneisen parameter as a function of volume are analytically derived.The analytic equation of state is applied to predict the thermodynamic properties of solid xenon at normal-pressure with the nearest-neighbour Lennard-Jones interaction,and is further applied to research the properties of solid xenon and krypton at high pressure by using an all-neighbour Lennard-Jones interaction.The theoretical results are in agreement with the experiments.

  3. An index with improved diagnostic accuracy for the diagnosis of Crohn's disease derived from the Lennard-Jones criteria.

    Science.gov (United States)

    Reinisch, S; Schweiger, K; Pablik, E; Collet-Fenetrier, B; Peyrin-Biroulet, L; Alfaro, I; Panés, J; Moayyedi, P; Reinisch, W

    2016-09-01

    The Lennard-Jones criteria are considered the gold standard for diagnosing Crohn's disease (CD) and include the items granuloma, macroscopic discontinuity, transmural inflammation, fibrosis, lymphoid aggregates and discontinuous inflammation on histology. The criteria have never been subjected to a formal validation process. To develop a validated and improved diagnostic index based on the items of Lennard-Jones criteria. Included were 328 adult patients with long-standing CD (median disease duration 10 years) from three centres and classified as 'established', 'probable' or 'non-CD' by Lennard-Jones criteria at time of diagnosis. Controls were patients with ulcerative colitis (n = 170). The performance of each of the six diagnostic items of Lennard-Jones criteria was modelled by logistic regression and a new index based on stepwise backward selection and cut-offs was developed. The diagnostic value of the new index was analysed by comparing sensitivity, specificity and accuracy vs. Lennard-Jones criteria. By Lennard-Jones criteria 49% (n = 162) of CD patients would have been diagnosed as 'non-CD' at time of diagnosis (sensitivity/specificity/accuracy, 'established' CD: 0.34/0.99/0.67; 'probable' CD: 0.51/0.95/0.73). A new index was derived from granuloma, fibrosis, transmural inflammation and macroscopic discontinuity, but excluded lymphoid aggregates and discontinuous inflammation on histology. Our index provided improved diagnostic accuracy for 'established' and 'probable' CD (sensitivity/specificity/accuracy, 'established' CD: 0.45/1/0.72; 'probable' CD: 0.8/0.85/0.82), including the subgroup isolated colonic CD ('probable' CD, new index: 0.73/0.85/0.79; Lennard-Jones criteria: 0.43/0.95/0.69). We developed an index based on items of Lennard-Jones criteria providing improved diagnostic accuracy for the differential diagnosis between CD and UC. © 2016 John Wiley & Sons Ltd.

  4. Kinetic-contact-driven gigantic energy transfer in a two-dimensional Lennard-Jones fluid confined to a rotating pore

    Science.gov (United States)

    Karbowniczek, Paweł; Chrzanowska, Agnieszka

    2017-11-01

    A two-dimensional Lennard-Jones system in a circular and rotating container has been studied by means of molecular dynamics technique. A nonequilibrium transition to the rotating stage has been detected in a delayed time since an instant switching of the frame rotation. This transition is attributed to the increase of the density at the wall because of the centrifugal force. At the same time the phase transition occurs, the inner system changes its configuration of the solid-state type into the liquid type. Impact of angular frequency and molecular roughness on the transport properties of the nonrotating and rotating systems is analyzed.

  5. Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions.

    Science.gov (United States)

    Fischer, Nina M; van Maaren, Paul J; Ditz, Jonas C; Yildirim, Ahmet; van der Spoel, David

    2015-07-14

    In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http

  6. Cell-model prediction of the melting of a Lennard-Jones solid

    International Nuclear Information System (INIS)

    Holian, B.L.

    1980-01-01

    The classical free energy of the Lennard-Jones 6-12 solid is computed from a single-particle anharmonic cell model with a correction to the entropy given by the classical correlational entropy of quasiharmonic lattice dynamics. The free energy of the fluid is obtained from the Hansen-Ree analytic fit to Monte Carlo equation-of-state calculations. The resulting predictions of the solid-fluid coexistence curves by this corrected cell model of the solid are in excellent agreement with the computer experiments

  7. Third-order WKBJ eigenvalues for Lennard-Jones and Varshni V potentials

    International Nuclear Information System (INIS)

    Kesarwani, R.N.; Varshni, Y.P.

    1978-01-01

    The WKBJ method is applied to the third order for obtaining the eigenvalues for the fifth potential of Varshni, and the relevant integrals are analytically evaluated. Numerical results are obtained for the Lennard-Jones Potential, which is a special case of the Varshni V potential, and are compared to the results of Harrison and Bernstein obtained by a numerical integration of the wave equation. Error estimates are made. It is shown that for diatomic potentials, the Langer correction is not needed if the WKBJ approximation is carried to second and higher orders. (author)

  8. Self-diffusion coefficients of the metastable Lennard-Jones vapor

    International Nuclear Information System (INIS)

    Nie Chu; Zhou Youhua; Marlow, W H; Hassan, Y A

    2008-01-01

    Self-diffusion coefficients of a metastable Lennard-Jones vapor were obtained using the memory function formalism and the frequency moments of the velocity autocorrelation function at reduced temperatures from 0.75 to 1.0. The radial density distribution functions used to evaluate the second, fourth and sixth frequency moments of the velocity autocorrelation function were obtained from the restricted canonical ensemble Monte Carlo simulation (Corti and Debenedetti 1994 Chem. Eng. Sci. 49 2717). The self-diffusion coefficients at reduced temperature 0.75 do not vary monotonically as the density increases, and for the other three temperatures the self-diffusion coefficients vary normally

  9. Self-diffusion coefficients of the metastable Lennard-Jones vapor

    Energy Technology Data Exchange (ETDEWEB)

    Nie Chu; Zhou Youhua [School of Physics and Information Engineering, Jianghan University, Wuhan 430056 (China); Marlow, W H; Hassan, Y A [Department of Nuclear Engineering, Texas A and M University, College Station, TX 77843 (United States)], E-mail: yhzhou@jhun.edu.cn

    2008-10-15

    Self-diffusion coefficients of a metastable Lennard-Jones vapor were obtained using the memory function formalism and the frequency moments of the velocity autocorrelation function at reduced temperatures from 0.75 to 1.0. The radial density distribution functions used to evaluate the second, fourth and sixth frequency moments of the velocity autocorrelation function were obtained from the restricted canonical ensemble Monte Carlo simulation (Corti and Debenedetti 1994 Chem. Eng. Sci. 49 2717). The self-diffusion coefficients at reduced temperature 0.75 do not vary monotonically as the density increases, and for the other three temperatures the self-diffusion coefficients vary normally.

  10. Evidence of hexatic phase formation in two-dimensional Lennard-Jones binary arrays

    International Nuclear Information System (INIS)

    Li, M.; Johnson, W.L.; Goddard, W.A. III

    1996-01-01

    We report evidence of the hexatic phase formation in Lennard-Jones binary substitutional random arrays from isothermal-isobaric molecular-dynamics simulations. The hexatic phase is analogous to those predicted in Kosterlitz-Thouless theory of melting that is characterized by short-range translational order and quasi-long-range orientational order. At the crystal to hexatic phase transition, dislocation pairs are observed to unbind into isolated dislocations. Further disordering of the hexatic phase, however, does not lead to dissociation of dislocations into disclinations. Instead, the dislocations become clustered and form dislocation networks which results in formation of amorphous phases. copyright 1996 The American Physical Society

  11. The potential energy landscape in the Lennard-Jones binary mixture model

    International Nuclear Information System (INIS)

    Sampoli, M; Benassi, P; Eramo, R; Angelani, L; Ruocco, G

    2003-01-01

    The potential energy landscape in the Kob-Andersen Lennard-Jones binary mixture model has been studied carefully from the liquid down to the supercooled regime, from T = 2 down to 0.46. One thousand independent configurations along the time evolution locus have been examined at each temperature investigated. From the starting configuration, we searched for the nearest saddle (or quasi-saddle) and minimum of the potential energy. The vibrational densities of states for the starting and the two derived configurations have been evaluated. Besides the number of negative eigenvalues of the saddles other quantities show some signature of the approach of the dynamical arrest temperature

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

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  13. Nonlinear transport processes and fluid dynamics: Cylindrical Couette flow of Lennard-Jones fluids

    International Nuclear Information System (INIS)

    Khayat, R.E.; Eu, B.C.

    1988-01-01

    In this paper we report on calculations of flow profiles for cylindrical Couette flow of a Lennard-Jones fluid. The flow is subjected to a temperature gradient and thermoviscous effects are taken into consideration. We apply the generalized fluid dynamic equations which are provided by the modified moment method for the Boltzmann equation reported previously. The results of calculations are in good agreement with the Monte Carlo direct simulation method by K. Nanbu [Phys. Fluids 27, 2632 (1984)] for most of Knudsen numbers for which the simulation data are available

  14. A density functional perturbative approach for simple fluids: the structure of a nonuniform Lennard-Jones fluid at interfaces

    International Nuclear Information System (INIS)

    Kim, Soon-Chul; Lee, Song Hi

    2004-01-01

    A density functional perturbation approximation (DFPT), which is based both on the fundamental-measure theory (FMT) to the hard-sphere repulsion and on the weighted-density approximations (WDAs) to the attractive contribution, has been proposed for studying the structural properties of model fluids with an attractive part of the potential. The advantage of the present theory is the simplicity of the calculation of the weight function due to the attractive contribution. It has been applied to predict the equilibrium particle density distributions and adsorption isotherms of Lennard-Jones fluids at interfaces. The theoretical results show that the present theory describes quite well the adsorption isotherms of a Lennard-Jones ethane in a graphite slit pore as well as the equilibrium particle density distributions of a Lennard-Jones fluid near a planar slit pore

  15. A comparison of molecular dynamics and diffuse interface model predictions of Lennard-Jones fluid evaporation

    Energy Technology Data Exchange (ETDEWEB)

    Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)

    2014-12-09

    The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.

  16. Icosahedral binary clusters of glass-forming Lennard-Jones binary alloy

    International Nuclear Information System (INIS)

    Iwamatsu, Masao

    2007-01-01

    It is widely believed that the local icosahedral structure is related to the formation of bulk metallic glasses (BMGs). Specifically the existence of 13-atom icosahedral cluster in undercooled liquid is imagined to play a key role to initiate the glass formation as the seed of amorphous structure or to block the nucleation of regular crystal as the impurity. The existence of 13-atom icosahedral clusters in one-component liquids was predicted more than half a century ago by Frank from his total energy calculation for isolated clusters. In BMG alloys, however, the situation is less clear. In this report, we present the lowest-energy structures of 13-atom Lennard-Jones binary cluster calculated from the modified space-fixed genetic algorithm. We study, in particular, the artificial Lennard-Jones potential designed by Kob and Andersen [W. Kob, H.C. Andersen, Phys. Rev. E 51 (1995) 4626] that is known to form BMG. Curiously, the lowest-energy structures of 13-atom cluster are non-icosahedral for almost all compositions. Our result suggests that the existence of the icosahedral cluster is not a necessary condition but only a sufficient condition for glass formation

  17. Binding energy of large icosahedral and cuboctahedral Lennard-Jones clusters

    International Nuclear Information System (INIS)

    Northby, J.A.; Xie, J.

    1989-01-01

    It is widely believed that the lowest energy configurations for small rare gas clusters have icosahedral symmetry. This contrasts with the bulk crystal structures which have cuboctahedral fcc symmetry. It is of interest to understand the transition between this finite and bulk behavior. To model this transition in rare gas clusters we have undertaken optimization studies within the Lennard-Jones pair potential model. Using a combination of Monte Carlo and Partan Search optimization methods, the lowest energy relaxed structures of Lennard-Jones clusters having icosahedral and cuboctahedral symmetry were found. Studies were performed for complete shell clusters ranging in size from one shell having 13 atoms to 14 shells having 10,179 atoms. It was found that the icosahedral structures are lower in energy than the cuboctahedral structures for cluster sizes having 13 shells or fewer. Additional studies were performed using the more accurate Aziz-Chen [HFD-C] pair potential parameterized for argon. The conclusions appear to be relatively insensitive to the form of the potential. (orig.)

  18. An accurate expression for radial distribution function of the Lennard-Jones fluid

    International Nuclear Information System (INIS)

    Morsali, Ali; Goharshadi, Elaheh K.; Ali Mansoori, G.; Abbaspour, Mohsen

    2005-01-01

    A simple and accurate expression for radial distribution function (RDF) of the Lennard-Jones fluid is presented. The expression explicitly states the RDF as a continuous function of reduced interparticle distance, temperature, and density. It satisfies the limiting conditions of zero density and infinite distance imposed by statistical thermodynamics. The distance dependence of this expression is expressed by an equation which contains 11 adjustable parameters. These parameters are fitted to 353 RDF data, obtained by molecular dynamics calculations, and then expressed as functions of reduced distance, temperature and density. This expression, having a total of 65 constants, reproduces the RDF data with an average root-mean-squared deviation of 0.0152 for the range of state variables of 0.5= * = * = * =ρσ 3 are reduced temperature and density, respectively). The expression predicts the pressure and the internal energy of the Lennard-Jones fluid with an uncertainty that is comparable to that obtained directly from the molecular dynamics simulations

  19. Communication: Studies of the Lennard-Jones fluid in 2, 3, and 4 dimensions highlight the need for a liquid-state 1/d expansion

    International Nuclear Information System (INIS)

    Costigliola, Lorenzo; Schrøder, Thomas B.; Dyre, Jeppe C.

    2016-01-01

    The recent theoretical prediction by Maimbourg and Kurchan [e-print http://arxiv.org/abs/1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2, 3, 4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized by high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly.

  20. Fusion process of Lennard-Jones clusters: global minima and magic numbers formation

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2004-01-01

    We present a new theoretical framework for modeling the fusion process of Lennard–Jones (LJ) clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing paths up to the cluster size of 150 atoms...

  1. The effect of atom mismatch on the fragility of supercooled Lennard-Jones binary mixtures

    International Nuclear Information System (INIS)

    Sun Minhua; Sun Yongli; Wang Aiping; Ma Congxiao; Li Jiayun; Cheng Weidong; Liu Fang

    2006-01-01

    The shear viscosity of the well-known binary Lennard-Jones mixture is simulated under constant temperature and constant volume conditions (NVT) by a molecular-dynamics (MD) method. The effect of atomic size mismatch on the fragility parameter and glass-forming ability is studied. The fragility parameters calculated from shear viscosity data decrease with the increment of the atomic size mismatch. The value of the fragility changes from 168.963 to 22.976 when the mismatch changes from 0.023 to 0.25. It is shown that the fragility parameter is sensitive to the atomic size mismatch. The calculated pair distribution functions and mean square displacements indicate that the glass-forming ability increases with the atomic size mismatch

  2. Dynamics of vacancies in two-dimensional Lennard-Jones crystals

    Science.gov (United States)

    Yao, Zhenwei; Olvera de La Cruz, Monica

    2015-03-01

    Vacancies represent an important class of crystallographic defects, and their behaviors can be strongly coupled with relevant material properties. We report the rich dynamics of vacancies in two-dimensional Lennard-Jones crystals in several thermodynamic states. Specifically, we numerically observe significantly faster diffusion of the 2-point vacancy with two missing particles in comparison with other types of vacancies; it opens the possibility of doping 2-point vacancies into atomic materials to enhance atomic migration. In addition, the resulting dislocations in the healing of a long vacancy suggest the intimate connection between vacancies and topological defects that may provide an extra dimension in the engineering of defects in extensive crystalline materials for desired properties. We thank the financial support from the U.S. Department of Commerce, National Institute of Standards and Technology, the Office of the Director of Defense Research and Engineering (DDR&E) and the Air Force Office of Scientific Research.

  3. Thermal conductivity of the Lennard-Jones fluid: An empirical correlation

    International Nuclear Information System (INIS)

    Bugel, Mathilde; Galliero, Guillaume

    2008-01-01

    In this work, is presented an empirical correlation on the thermal conductivity of the Lennard-Jones fluid based on extensive non-equilibrium molecular dynamics simulations results (103 points). Finite size and cutoff radius effects are investigated and taken into account to develop the correlation. This last, composed of low-density, residual and critical enhancement contributions, is built for a wide range of thermodynamics states, even at the vicinity of the critical point, and yields an average absolute deviation of 1.29% compared to our simulations. In addition, a careful analysis of the different contributions to the microscopic flux is carried out which sheds light on the underlying mechanism of the results. Finally, are discussed the limitations of the proposed model when applied to real simple fluids and mixtures using a standard corresponding states scheme and the van der Waals one-fluid approximation

  4. Crystal phases of a glass-forming Lennard-Jones mixture

    International Nuclear Information System (INIS)

    Fernandez, Julian R.; Harrowell, Peter

    2003-01-01

    We compare the potential energy at zero temperature of a range of crystal structures for a glass-forming binary mixture of Lennard-Jones particles. The lowest-energy ordered state consists of coexisting phases of a single component face centered cubic structure and an equimolar cesium chloride structure. An infinite number of layered crystal structures are identified with energies close to this ground state. We demonstrate that the finite size increase of the energy of the coexisting crystal with incoherent interfaces is sufficient to destabilize this ordered phase in simulations of typical size. Two specific local coordination structures are identified as of possible structural significance in the amorphous state. We observe rapid crystal growth in the equimolar mixture

  5. Simulasi Sifat Fisis Model Molekuler Dinamik Gas Argon dengan Potensial Lennard-Jones

    Directory of Open Access Journals (Sweden)

    Wira Bahari Nurdin

    2014-01-01

    Full Text Available DOWNLOAD PDFTelah  dilakukan  pembuatan  dan  pengujian  suatu  simulasi  tentang  sifat  fisis  gasargon  dengan  menggunakan  dinamika  molekuler  menggunakan  potensial Lennard-Jonesdalam sistem terisolasi (ensemble mikrokanonik. Jumlah molekul, energi total sistem danluas  kotak  simulasi  telah  divariasikan.  Untuk  menghitung  perubahan  posisi  digunakanalgoritma Verlet. Sifat fisis yang ditentukan dalam simulasi adalah temperatur dan energitotal  sistem  untuk  menentukan  adanya  fase  transisi.  Dari  hasil  simulasi,  terdapatkesesuaian antara simulasi dengan gas argon dan tidak diperoleh adanya fase transisi.Kata kunci: Simulasi dinamika molekul, argon, potensial Lennard-Jones, ensemblemikrokanonik, algoritma Verlet

  6. A molecular dynamics study of Lennard-Jones physisorption on W(100)

    International Nuclear Information System (INIS)

    Broughton, J.Q.

    1980-01-01

    The physisorption of Xe on W(100) was modeled by Lennard-Jones pair-wise interaction potentials and the dynamics of coverages ranging from one to four adlayers obtained by molecular dynamics simulation. At 115 K, the first two layers were well-ordered and each adsorbed with c(2 x 2) symmetry. Further adsorption produced a surface similar to that of a distorted Xe(100) face. In accord with the work of Broughton and Woodcock, the top layers of the three- and four-adlayer coverages were rough and had liquid-like diffusion coefficients. The potential energies of all layers other than the first were similar, thus corroborating one of the postulates of BET theory. Generally, the effect of adsorbing a layer was to reduce the entropy of all those beneath. (orig.)

  7. Computation and analysis of the transverse current autocorrelation function, Ct(k,t), for small wave vectors: A molecular-dynamics study for a Lennard-Jones fluid

    Science.gov (United States)

    Vogelsang, R.; Hoheisel, C.

    1987-02-01

    Molecular-dynamics (MD) calculations are reported for three thermodynamic states of a Lennard-Jones fluid. Systems of 2048 particles and 105 integration steps were used. The transverse current autocorrelation function, Ct(k,t), has been determined for wave vectors of the range 0.5viscosities which showed a systematic behavior as a function of k. Extrapolation to the hydrodynamic region at k=0 gave shear viscosity coefficients in good agreement with direct Green-Kubo results obtained in previous work. The two-exponential model fit for the memory function proposed by other authors does not provide a reasonable description of the MD results, as the fit parameters show no systematic wave-vector dependence, although the Ct(k,t) functions are somewhat better fitted. Similarly, the semiempirical interpolation formula for the decay time based on the viscoelastic concept proposed by Akcasu and Daniels fails to reproduce the correct k dependence for the wavelength range investigated herein.

  8. Determination of the friction coefficient via the force autocorrelation function. A molecular dynamics investigation for a dense Lennard-Jones fluid

    International Nuclear Information System (INIS)

    Vogelsang, R.; Hoheisel, C.

    1987-01-01

    For a large region of dense fluid states of a Lennard-Jones system, they have calculated the friction coefficient by the force autocorrelation function of a Brownian-type particle by molecular dynamics (MD). The time integral over the force autocorrelation function showed an interesting behavior and the expected plateau value when the mass of the Brownian particle was chosen to be about a factor of 100 larger than the mass of the fluid particle. Sufficient agreement was found for the friction coefficient calculated by this way and that obtained by calculations of the self-diffusion coefficient using the common relation between these coefficients. Furthermore, a modified friction coefficient was determined by integration of the force autocorrelation function up to the first maximum. This coefficient can successfully be used to derive a reasonable soft part of the friction coefficient necessary for the Rice-Allnatt approximation for the shear velocity and simple liquids

  9. Comparison of Green-Kubo and nonequilibrium calculations of the self-diffusion constant of a Lennard-Jones fluid

    International Nuclear Information System (INIS)

    Erpenbeck, J.J.

    1987-01-01

    We apply the so-called ''synthetic'' nonequilibrium molecular-dynamics method to the calculation of the self-diffusion constant of a Lennard-Jones fluid at a number density of 0.85/σ 3 and a temperature of 1.08 epsilon-c/k/sub B/ (where epsilon-c and σ are the energy and length parameters of the potential and k/sub B/ is the Boltzmann constant). By comparing with the Green-Kubo calculation for the same state of the system and for the same number of particles, N, we find the latter calculation to yield more precise values of the self-diffusion constant for a given number of molecular-dynamics time steps. Even at small values of the diffusion current, a nontrivial time is needed for the nonequilibrium calculation to reach the steady state. For larger values of the driving force, the steady-state flow appears to become unstable and evidence of a secondary flow pattern is presented. The presence of these instabilities acts as a limit to the range of the driving force for which the steady-state method can be applied. With increasing N the range of stable values of the diffusion current density decreases. For the Green-Kubo calculations, the N dependence of the self-diffusion constant is found to be anomalous for N = 108, with the 1/N dependence only exhibited for at least 500 particles. The nonequilibrium results, while approximately independent of N for 108 and 500 particles, are found to have a similar anomalous N dependence when we extend the calculations to 1372 particles, thereby bringing the Green-Kubo and nonequilibrium results into agreement in the large-system limit

  10. Vapour-liquid equilibrium properties for two- and three-dimensional Lennard-Jones fluids from equations of state

    International Nuclear Information System (INIS)

    Mulero, A.; Cuadros, F; Faundez, C.A.

    1999-01-01

    Vapour-liquid equilibrium properties for both three- and two-dimensional Lennard-Jones fluids were obtained using simple cubic-in-density equations of state proposed by the authors. Results were compared with those obtained by other workers from computer simulations and also with results given by other more complex semi-theoretical or semi-empirical equations of state. In the three-dimensional case good agreement is found for all properties and all temperatures. In the two-dimensional case only the coexistence densities were compared, producing good agreement for low temperatures only. The present work is the first to give numerical data for the vapour-liquid equilibrium properties of Lennard-Jones fluids calculated from equations of state. Copyright (1999) CSIRO Australia

  11. Modeling Aggregation Processes of Lennard-Jones particles Via Stochastic Networks

    Science.gov (United States)

    Forman, Yakir; Cameron, Maria

    2017-07-01

    We model an isothermal aggregation process of particles/atoms interacting according to the Lennard-Jones pair potential by mapping the energy landscapes of each cluster size N onto stochastic networks, computing transition probabilities from the network for an N-particle cluster to the one for N+1, and connecting these networks into a single joint network. The attachment rate is a control parameter. The resulting network representing the aggregation of up to 14 particles contains 6427 vertices. It is not only time-irreversible but also reducible. To analyze its transient dynamics, we introduce the sequence of the expected initial and pre-attachment distributions and compute them for a wide range of attachment rates and three values of temperature. As a result, we find the configurations most likely to be observed in the process of aggregation for each cluster size. We examine the attachment process and conduct a structural analysis of the sets of local energy minima for every cluster size. We show that both processes taking place in the network, attachment and relaxation, lead to the dominance of icosahedral packing in small (up to 14 atom) clusters.

  12. Fowler's approximation for the surface tension and surface energy of Lennard-Jones fluids revisited

    International Nuclear Information System (INIS)

    Mulero, A; Galan, C; Cuadros, F

    2003-01-01

    We present a detailed study of the validity of Fowler's approximation for calculating the surface tension and the surface energy of Lennard-Jones fluids. To do so, we consider three different explicit analytical expressions for the radial distribution function (RDF), including one proposed by our research group, together with very accurate expressions for the liquid and vapour densities, also proposed by our group. The calculation of the surface tension from the direct correlation function using both the Percus-Yevick and the hypernetted-chain approximations is also considered. Finally, our results are compared with those obtained by other authors by computer simulations or through relevant theoretical approximations. In particular, we consider the analytical expression proposed by Kalikmanov and Hofmans (1994 J. Phys.: Condens. Matter 6 2207-14) for the surface tension. Our results indicate that the values for the surface energy in Fowler's approximation obtained by other authors are adequate, and can be calculated from the RDF models. For the surface tension, however, the values considered as valid in previous works seem to be incorrect. The correct values can be obtained from our model for the RDF or from the Kalikmanov and Hofmans expression with suitable inputs

  13. Threshold and Lennard-Jones resonances and elastic lifetimes in the scattering of atoms from crystalline surfaces

    International Nuclear Information System (INIS)

    Garcia, N.

    1978-01-01

    The GR method for solving the scattering equations of atoms from a hard corrugated surface is applied on accelerated particles above a hard corrugated surface and a hard corrugated surface with an attractive well. The solutions are given for the Rayleigh hypothesis that under the range of corrugation presented in this paper leads to the exact ones. Threshold resonances are studied observing that the appearance and disappearance of beams must be for a general theory with vertical tangent. The structure of the Lennard-Jones resonances given for the model mentioned above. For the first time it is stressed that Lennard-Jones resonances are not observed in metal surfaces in general, and, accordingly, they are unobserved in compact metallic surfaces. This is correlated with the fact that diffraction has not been observed. Both facts are due to the very weak corrugation of the gas-metal interaction potential. According to our results, the Lennard-Jones resonances in metals present greater difficulties to be observed experimentally. It is also noted that the absence of diffraction in compact metal surfaces is because they are almost plane and not because of the Debye-Waller effect. Finally, the lifetimes of the atoms at the crystal surfaces are calculated. These are larger, the smaller the incident energy and the larger the corrugation. But the lifetimes are particularly large at resonance conditions (10 -11 s). (Auth.)

  14. Liquid-liquid interfacial properties of a symmetrical Lennard-Jones binary mixture

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Ruiz, F. J.; Blas, F. J., E-mail: felipe@uhu.es [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Física Aplicada, Universidad de Huelva, 21007 Huelva (Spain); Moreno-Ventas Bravo, A. I. [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Geología, Universidad de Huelva, 21007 Huelva (Spain)

    2015-09-14

    We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ{sub 11} = σ{sub 22}, with the same dispersive energy between like species, ϵ{sub 11} = ϵ{sub 22}, but different dispersive energies between unlike species low enough to induce phase separation. We use the extensions of the improved version of the inhomogeneous long-range corrections of Janecek [J. Phys. Chem. B 110, 6264 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] and Martínez-Ruiz et al. [J. Chem. Phys. 141, 184701 (2014)], to deal with the interaction energy and microscopic components of the pressure tensor. We perform Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of the symmetrical mixture with different cut-off distances r{sub c} and in combination with the inhomogeneous long-range corrections. The pressure tensor is obtained using the mechanical (virial) and thermodynamic route. The liquid-liquid interfacial tension is also evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the test-area methodology. This allows to check the validity of the recent extensions presented to deal with the contributions due to long-range corrections for intermolecular energy and pressure tensor in the case of binary mixtures that exhibit liquid-liquid immiscibility. In addition to the pressure tensor and the surface tension, we also obtain density profiles and coexistence densities and compositions as functions of pressure, at a given temperature. According to our results, the main effect of increasing the cut-off distance r{sub c} is to sharpen the liquid-liquid interface and to increase the width of the biphasic coexistence region. Particularly interesting is the presence of a relative minimum in the total density profiles of the symmetrical mixture. This minimum is related

  15. Liquid-liquid interfacial properties of a symmetrical Lennard-Jones binary mixture

    International Nuclear Information System (INIS)

    Martínez-Ruiz, F. J.; Blas, F. J.; Moreno-Ventas Bravo, A. I.

    2015-01-01

    We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ 11 = σ 22 , with the same dispersive energy between like species, ϵ 11 = ϵ 22 , but different dispersive energies between unlike species low enough to induce phase separation. We use the extensions of the improved version of the inhomogeneous long-range corrections of Janecek [J. Phys. Chem. B 110, 6264 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] and Martínez-Ruiz et al. [J. Chem. Phys. 141, 184701 (2014)], to deal with the interaction energy and microscopic components of the pressure tensor. We perform Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of the symmetrical mixture with different cut-off distances r c and in combination with the inhomogeneous long-range corrections. The pressure tensor is obtained using the mechanical (virial) and thermodynamic route. The liquid-liquid interfacial tension is also evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the test-area methodology. This allows to check the validity of the recent extensions presented to deal with the contributions due to long-range corrections for intermolecular energy and pressure tensor in the case of binary mixtures that exhibit liquid-liquid immiscibility. In addition to the pressure tensor and the surface tension, we also obtain density profiles and coexistence densities and compositions as functions of pressure, at a given temperature. According to our results, the main effect of increasing the cut-off distance r c is to sharpen the liquid-liquid interface and to increase the width of the biphasic coexistence region. Particularly interesting is the presence of a relative minimum in the total density profiles of the symmetrical mixture. This minimum is related with a desorption of the

  16. Transport coefficients of dense fluids composed of globular molecules. Equilibrium molecular dynamics investigations using more-center Lennard-Jones potentials

    Science.gov (United States)

    Hoheisel, C.

    1988-09-01

    Equilibrium molecular dynamics calculations with constraints have been performed for model liquids SF6 and CF4. The computations were carried out with four- and six-center Lennard-Jones potentials and up to 2×105 integration steps. Shear, bulk viscosity and the thermal conductivity have been calculated with use of Green-Kubo relations in the formulation of ``molecule variables.'' Various thermodynamic states were investigated. For SF6, a detailed comparison with experimental data was possible. For CF4, the MD results could only be compared with experiment for one liquid state. For the latter liquid, a complementary comparison was performed using MD results obtained with a one-center Lennard-Jones potential. A limited test of the particle number dependence of the results is presented. Partial and total correlations functions are shown and discussed with respect to findings obtained for the one-center Lennard-Jones liquid.

  17. Self-consistent phonons revisited. I. The role of thermal versus quantum fluctuations on structural transitions in large Lennard-Jones clusters.

    Science.gov (United States)

    Georgescu, Ionuţ; Mandelshtam, Vladimir A

    2012-10-14

    The theory of self-consistent phonons (SCP) was originally developed to address the anharmonic effects in condensed matter systems. The method seeks a harmonic, temperature-dependent Hamiltonian that provides the "best fit" for the physical Hamiltonian, the "best fit" being defined as the one that optimizes the Helmholtz free energy at a fixed temperature. The present developments provide a scalable O(N) unified framework that accounts for anharmonic effects in a many-body system, when it is probed by either thermal (ℏ → 0) or quantum fluctuations (T → 0). In these important limits, the solution of the nonlinear SCP equations can be reached in a manner that requires only the multiplication of 3N × 3N matrices, with no need of diagonalization. For short range potentials, such as Lennard-Jones, the Hessian, and other related matrices are highly sparse, so that the scaling of the matrix multiplications can be reduced from O(N(3)) to ~O(N). We investigate the role of quantum effects by continuously varying the de-Boer quantum delocalization parameter Λ and report the N-Λ (T = 0), and also the classical N-T (Λ = 0) phase diagrams for sizes up to N ~ 10(4). Our results demonstrate that the harmonic approximation becomes inadequate already for such weakly quantum systems as neon clusters, or for classical systems much below the melting temperatures.

  18. Finite-field evaluation of the Lennard-Jones atom-wall interaction constant C3 for alkali-metal atoms

    International Nuclear Information System (INIS)

    Johnson, W.R.; Dzuba, V.A.; Safronova, U.I.; Safronova, M.S.

    2004-01-01

    A finite-field scaling method is applied to evaluate the Lennard-Jones interaction constant C 3 for alkali-metal atoms. The calculations are based on the relativistic single-double approximation in which single and double excitations of Dirac-Hartree-Fock wave functions are included to all orders in perturbation theory

  19. Dynamical properties and transport coefficients of one-dimensional Lennard-Jones fluids: A molecular dynamics study

    Science.gov (United States)

    Bazhenov, Alexiev M.; Heyes, David M.

    1990-01-01

    The thermodynamics, structure, and transport coefficients, as defined by the Green-Kubo integrals, of the one-dimensional Lennard-Jones fluid are evaluated for a wide range of state points by molecular dynamics computer simulation. These calculations are performed for the first time for thermal conductivity and the viscosity. We observe a transition from hard-rod behavior at low number density to harmonic-spring fluid behavior in the close-packed limit. The self-diffusion coefficient decays with increasing density to a finite limiting value. The thermal conductivity increases with density, tending to ∞ in the close-packed limit. The viscosity in contrast maximizes at intermediate density, tending to zero in the zero density and close-packed limits.

  20. Transport coefficients of liquid CF4 and SF6 computed by molecular dynamics using polycenter Lennard-Jones potentials

    Science.gov (United States)

    Hoheisel, C.

    1989-01-01

    For several liquid states of CF4 and SF4, the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints was chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3×105 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF4, while for SF6 the transport coefficients fall below the experimental ones by about 30%.

  1. Transport coefficients of liquid CF4 and SF6 computed by molecular dynamics using polycenter Lennard-Jones potentials

    International Nuclear Information System (INIS)

    Hoheisel, C.

    1989-01-01

    For several liquid states of CF 4 and SF 6 , the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints were chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3 x 10 5 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF 4 , while for SF 6 the transport coefficients fall below the experimental ones by about 30%

  2. Kapitza thermal conductance at the interface between Lennard-Jones crystals using non-equilibrium molecular dynamics simulations

    International Nuclear Information System (INIS)

    Merabia, Samy; Termentzidis, Konstantinos

    2012-01-01

    We characterize the thermal Kapitza conductance between Lennard-Jones solids using non-equilibrium molecular dynamics simulations. We consider a series of perfect interfaces between mass-mismatched solids. We show that both the acoustic mismatch model (AMM) and the diffuse mismatch model (DMM) fail to predict the interfacial conductance even for large acoustic mismatched solids. This poor agreement may be explained by the use of equilibrium distributions of phonons in the expression of the conductance. On the other hand, we show that an extension of AMM taking into account the out-of-equilibrium phonon distribution on both sides of the interface leads to a good agreement with the simulation results, even for interfaces between almost similar materials. This opens the way to understand interfacial heat transport across real semi-conductors and dielectrics.

  3. Relation between calculated Lennard-Jones potential and thermal stability of Cu-based bulk metallic glasses

    International Nuclear Information System (INIS)

    Lin, T.; Bian, X.F.; Jiang, J.

    2006-01-01

    Two metallic bulk glasses, Cu 60 Zr 30 Ti 10 and Cu 47 Ti 33 Zr 11 Ni 8 Si 1 , with a diameter of 3 mm were prepared by copper mold casting method. Dilatometric measurement was carried out on the two glassy alloys to obtain information about the average nearest-neighbour distance r 0 and the effective depth of pair potential V 0 . By assuming a Lennard-Jones potential, r 0 and V 0 were calculated to be 0.28 nm and 0.16 eV for Cu 60 Zr 30 Ti 10 and 0.27 nm and 0.13 eV for Cu 47 Ti 33 Zr 11 Ni 8 Si 1 , respectively. It was found that the glassy alloy Cu 60 Zr 30 Ti 10 was more stable than Cu 47 Ti 33 Zr 11 Ni 8 Si 1 against heating from both experiment and calculation

  4. Analysis of a Lennard-Jones fcc structure melting to the corresponding frozen liquid: Differences between the bulk and the surface

    International Nuclear Information System (INIS)

    Olivi-Tran, N.; Faivre, A.

    2009-01-01

    We computed a Lennard-Jones frozen liquid with a free surface using classical molecular dynamics. The structure factor curves on the free surface of this sample were calculated for different depths knowing that we have periodic boundary conditions on the other parts of the sample. The resulting structure factor curves show an horizontal shift of their first peak depending on how deep in the sample the curves are computed. We analyze our resulting curves in the light of spatial correlation functions during melting. The conclusion is that the differences between bulk and surface are quite small during melting and that at the end of melting, only the very surface happens to be less dense than the bulk. This result is intrinsic to the shape of the Lennard-Jones potential and does not depend on any other parameter.

  5. Simple approach to approximate predictions of the vapor–liquid equilibrium curve near the critical point and its application to Lennard-Jones fluids

    International Nuclear Information System (INIS)

    Staśkiewicz, B.; Okrasiński, W.

    2012-01-01

    We propose a simple analytical form of the vapor–liquid equilibrium curve near the critical point for Lennard-Jones fluids. Coexistence densities curves and vapor pressure have been determined using the Van der Waals and Dieterici equation of state. In described method the Bernoulli differential equations, critical exponent theory and some type of Maxwell's criterion have been used. Presented approach has not yet been used to determine analytical form of phase curves as done in this Letter. Lennard-Jones fluids have been considered for analysis. Comparison with experimental data is done. The accuracy of the method is described. -- Highlights: ► We propose a new analytical way to determine the VLE curve. ► Simple, mathematically straightforward form of phase curves is presented. ► Comparison with experimental data is discussed. ► The accuracy of the method has been confirmed.

  6. Influence of DC electric field on the Lennard-Jones potential and phonon vibrations of carbon nanotube on catalyst

    International Nuclear Information System (INIS)

    Saeidi, Mohammadreza; Vaezzadeh, Majid; Badakhshan, Farzaneh

    2011-01-01

    Influence of DC electric field on carbon nanotube (CNT) growth in chemical vapor deposition is studied. Investigation of electric field effect in van der Waals interaction shows that increase in DC electric field raises the magnitude of attractive term of the Lennard-Jones potential. By using a theoretical model based on phonon vibrations of CNT on catalyst, it is shown that there is an optimum field for growth. Also it is observed that CNT under optimum electric field is longer than CNT in the absence of field. Finally, the relation between optimum DC electric field and type of catalyst is investigated and for some intervals of electric field, the best catalyst is introduced, which is very useful for experimental researches. -- Research highlights: → Influence of DC electric field on CNT growth in CVD. → Effect of electric field on van der Waals interaction between CNT and its catalyst. → Applying DC electric field increases attractive term of Lennard-Jonespotential. → There is an optimum DC field for CNT growth. → For catalyst with stronger van der Waals interaction, optimum field is smaller.

  7. Fowler's approximation for the surface tension and surface energy of Lennard-Jones fluids revisited

    Energy Technology Data Exchange (ETDEWEB)

    Mulero, A [Departamento de Fisica, Universidad de Extremadura, 06071-Badajoz (Spain); Galan, C [Departamento de Fisica, Universidad de Extremadura, 06071-Badajoz (Spain); Cuadros, F [Departamento de Fisica, Universidad de Extremadura, 06071-Badajoz (Spain)

    2003-04-16

    We present a detailed study of the validity of Fowler's approximation for calculating the surface tension and the surface energy of Lennard-Jones fluids. To do so, we consider three different explicit analytical expressions for the radial distribution function (RDF), including one proposed by our research group, together with very accurate expressions for the liquid and vapour densities, also proposed by our group. The calculation of the surface tension from the direct correlation function using both the Percus-Yevick and the hypernetted-chain approximations is also considered. Finally, our results are compared with those obtained by other authors by computer simulations or through relevant theoretical approximations. In particular, we consider the analytical expression proposed by Kalikmanov and Hofmans (1994 J. Phys.: Condens. Matter 6 2207-14) for the surface tension. Our results indicate that the values for the surface energy in Fowler's approximation obtained by other authors are adequate, and can be calculated from the RDF models. For the surface tension, however, the values considered as valid in previous works seem to be incorrect. The correct values can be obtained from our model for the RDF or from the Kalikmanov and Hofmans expression with suitable inputs.

  8. Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation

    KAUST Repository

    Kadoura, Ahmad Salim; Siripatana, Adil; Sun, Shuyu; Knio, Omar; Hoteit, Ibrahim

    2016-01-01

    In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard

  9. Biocontrol agent Bacillus amyloliquefaciens LJ02 induces systemic resistance against cucurbits powdery mildew.

    Science.gov (United States)

    Li, Yunlong; Gu, Yilin; Li, Juan; Xu, Mingzhu; Wei, Qing; Wang, Yuanhong

    2015-01-01

    Powdery mildew is a fungal disease found in a wide range of plants and can significantly reduce crop yields. Bacterial strain LJ02 is a biocontrol agent (BCA) isolated from a greenhouse in Tianjin, China. In combination of morphological, physiological, biochemical and phylogenetic analyses, strain LJ02 was classified as a new member of Bacillus amyloliquefaciens. Greenhouse trials showed that LJ02 fermentation broth (LJ02FB) can effectively diminish the occurrence of cucurbits powdery mildew. When treated with LJ02FB, cucumber seedlings produced significantly elevated production of superoxide dismutase, peroxidase, polyphenol oxidase and phenylalanine ammonia lyase as compared to that of the control. We further confirmed that the production of free salicylic acid (SA) and expression of one pathogenesis-related (PR) gene PR-1 in cucumber leaves were markedly elevated after treating with LJ02FB, suggesting that SA-mediated defense response was stimulated. Moreover, LJ02FB-treated cucumber leaves could secrete resistance-related substances into rhizosphere that inhibit the germination of fungi spores and the growth of pathogens. Finally, we separated bacterium and its fermented substances to test their respective effects and found that both components have SA-inducing activity and bacterium plays major roles. Altogether, we identified a BCA against powdery mildew and its mode of action by inducing systemic resistance such as SA signaling pathway.

  10. An efficient method for the determination of fourth virial coefficient with Lennard-Jones (12-6) potential and its application

    Energy Technology Data Exchange (ETDEWEB)

    Mamedov, Bahtiyar A. [Department of Physics, Gaziosmanpaşa University, 60250, Tokat (Turkey); Somuncu, Elif; Askerov, Iskender M. [Department of Physics, Giresun University, Giresun (Turkey)

    2016-08-10

    In this work, a new theoretical approach is proposed for calculating fourth virial coefficient with Lennard-Jones potential. The established algorithm can be used to evaluate the thermodynamics properties and the intermolecular interaction potentials of liquids and gases with an improved accuracy. Note that the evaluation of the high-order virial coefficients is very valuable for accurate calculation of thermodynamic parameters. By using the suggested method, the fourth virial coefficient of CH{sub 4}, Ar, C{sub 2}H{sub 6} and SF{sub 6} molecules are evaluated. The calculation results are useful for accurate interpretation of the experimental data and of the determination of related physical properties.

  11. Effect of surface tension on the behavior of adhesive contact based on Lennard-Jones potential law

    Science.gov (United States)

    Zhu, Xinyao; Xu, Wei

    2018-02-01

    The present study explores the effect of surface tension on adhesive contact behavior where the adhesion is interpreted by long-range intermolecular forces. The adhesive contact is analyzed using the equivalent system of a rigid sphere and an elastic half space covered by a membrane with surface tension. The long-range intermolecular forces are modeled with the Lennard‒Jones (L‒J) potential law. The current adhesive contact issue can be represented by a nonlinear integral equation, which can be solved by Newton‒Raphson method. In contrast to previous studies which consider intermolecular forces as short-range, the present study reveals more details of the features of adhesive contact with surface tension, in terms of jump instabilities, pull-off forces, pressure distribution within the contact area, etc. The transition of the pull-off force is not only consistent with previous studies, but also presents some new interesting characteristics in the current situation.

  12. Rare events in many-body systems: reactive paths and reaction constants for structural transitions

    International Nuclear Information System (INIS)

    Picciani, M.

    2012-01-01

    This PhD thesis deals with the study of fundamental physics phenomena, with applications to nuclear materials of interest. We have developed methods for the study of rare events related to thermally activated structural transitions in many body systems. The first method involves the numerical simulation of the probability current associated with reactive paths. After deriving the evolution equations for the probability current, a Diffusion Monte Carlo algorithm is implemented in order to sample this current. This technique, called Transition Current Sampling was applied to the study of structural transitions in a cluster of 38 atoms with Lennard-Jones potential (LJ-38). A second algorithm, called Transition Path Sampling with local Lyapunov bias (LyTPS), was then developed. LyTPS calculates reaction rates at finite temperature by following the transition state theory. A statistical bias based on the maximum local Lyapunov exponents is introduced to accelerate the sampling of reactive trajectories. To extract the value of the equilibrium reaction constants obtained from LyTPS, we use the Multistate Bennett Acceptance Ratio. We again validate this method on the LJ-38 cluster. LyTPS is then used to calculate migration constants for vacancies and divacancies in the α-Iron, and the associated migration entropy. These constants are used as input parameter for codes modeling the kinetic evolution after irradiation (First Passage Kinetic Monte Carlo) to reproduce numerically resistivity recovery experiments in α-Iron. (author) [fr

  13. Density-scaling exponents and virial potential-energy correlation ...

    Indian Academy of Sciences (India)

    This paper investigates the relation between the density-scaling exponent γ and the virial potential energy correlation coefficient R at several thermodynamic state points in three dimensions for the generalized (2n, n) Lennard-Jones (LJ) system for n = 4, 9, 12, 18, as well as for the standard n = 6 LJ system in two,three, and ...

  14. L-J phase in a Cu2.2Mn0.8Al alloy

    Science.gov (United States)

    Jeng, S. C.; Liu, T. F.

    1995-06-01

    A new type of precipitate (designated L-J phase) with two variants was observed within the (DO3 + L21) matrix in a Cu2.2Mn0.8Al alloy. Transmission electron microscopy examinations indicated that the L-J phase has an orthorhombic structure with lattice parameters a = 0.413 nm, b = 0.254 nm and c = 0.728 nm. The orientation relationship between the L-J phase and the matrix is (100)L-J//(011) m , (010)L-J//(111) m and (001)L-J//(211) m . The rotation axis and rotation angle between two variants of the L-J phase are [021] and 90 deg. The L-J phase has never been observed in various Cu-Al, Cu-Mn, and Cu-Al-Mn alloy systems before.

  15. Influence of pressure on the crystallization of systems characterized by different intermolecular attraction

    Science.gov (United States)

    Koperwas, K.; Affouard, F.; Gerges, J.; Valdes, L.-C.; Adrjanowicz, K.; Paluch, M.

    2017-12-01

    In this paper, we examine, in terms of the classical nucleation theory, how the strengthening of the attractive intermolecular interactions influences the crystallization process for systems like Lennard-Jones at different isobaric conditions. For this purpose, we modify the standard Lennard-Jones potential, and as a result, we obtain three different systems characterized by various strengths of attractive potentials occurring between molecules, which are in direct relationship to the physical quantities describing molecules, e.g., its polarizability or dipole moment. Based on performed analysis, we demonstrate that the molecular attraction primarily impacts the thermodynamics of the interface between liquid and crystal. This is reflected in the behavior of nucleation and overall crystallization rates during compression of the system.

  16. The non-separability of ''dielectric'' and ''mechanical'' friction in molecular systems: A simulation study

    International Nuclear Information System (INIS)

    Kumar, P. V.; Maroncelli, M.

    2000-01-01

    Simulations of the time-dependent friction controlling rotational, translational, and vibrational motions of dipolar diatomic solutes in acetonitrile and methanol have been used to examine the nature of ''dielectric'' friction. The way in which electrical interactions increase the friction beyond that present in nonpolar systems is found to be rather different than what is anticipated by most theories of dielectric friction. Long-range electrostatic forces do not simply add an independent contribution to the friction due to short-ranged or ''mechanical'' sources (modeled here in terms of Lennard-Jones forces). Rather, the electrical and Lennard-Jones contributions are found to be strongly anticorrelated and not separable in any useful way. For some purposes, the mechanism by which electrical interactions increase friction is better viewed as a static electrostriction effect: electrical forces cause a subtle increase in atomic density in the solute's first solvation shell, which increases the amplitude of the force fluctuations derived from the Lennard-Jones interactions, i.e., the mechanical friction. However, electrical interactions also modify the dynamics of the friction, typically adding a long-time tail, which significantly increases the integral friction. Both of these effects must be included in a correct description of friction in the presence of polar interactions. (c) 2000 American Institute of Physics

  17. ;:::,!,lj

    African Journals Online (AJOL)

    The potential effect of the ... coenzyme A (HMG-CoA) reductase inhibitors, drugs which have been shown to be .... The Ras family of small GTP-binding proteins act as important ... Defects in this switching mechanism give rise to disease.

  18. 77 FR 6945 - Special Conditions: Learjet Inc., Learjet Model LJ-200-1A10; Interaction of Systems and Structures

    Science.gov (United States)

    2012-02-10

    ...; Interaction of Systems and Structures AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Final... the effects of these systems on structures. The general approach of accounting for the effect of... standards already established for this evaluation. These criteria are only applicable to structures whose...

  19. A Dicarboxylate Transporter, LjALMT4, Mainly Expressed in Nodules of Lotus japonicus.

    Science.gov (United States)

    Takanashi, Kojiro; Sasaki, Takayuki; Kan, Tomohiro; Saida, Yuka; Sugiyama, Akifumi; Yamamoto, Yoko; Yazaki, Kazufumi

    2016-07-01

    Legume plants can establish symbiosis with soil bacteria called rhizobia to obtain nitrogen as a nutrient directly from atmospheric N2 via symbiotic nitrogen fixation. Legumes and rhizobia form nodules, symbiotic organs in which fixed-nitrogen and photosynthetic products are exchanged between rhizobia and plant cells. The photosynthetic products supplied to rhizobia are thought to be dicarboxylates but little is known about the movement of dicarboxylates in the nodules. In terms of dicarboxylate transporters, an aluminum-activated malate transporter (ALMT) family is a strong candidate responsible for the membrane transport of carboxylates in nodules. Among the seven ALMT genes in the Lotus japonicus genome, only one, LjALMT4, shows a high expression in the nodules. LjALMT4 showed transport activity in a Xenopus oocyte system, with LjALMT4 mediating the efflux of dicarboxylates including malate, succinate, and fumarate, but not tricarboxylates such as citrate. LjALMT4 also mediated the influx of several inorganic anions. Organ-specific gene expression analysis showed LjALMT4 mRNA mainly in the parenchyma cells of nodule vascular bundles. These results suggest that LjALMT4 may not be involved in the direct supply of dicarboxylates to rhizobia in infected cells but is responsible for supplying malate as well as several anions necessary for symbiotic nitrogen fixation, via nodule vasculatures.

  20. Recasting a model atomistic glassformer as a system of icosahedra

    Energy Technology Data Exchange (ETDEWEB)

    Pinney, Rhiannon [HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL (United Kingdom); Bristol Centre for Complexity Science, University of Bristol, Bristol BS8 1TS (United Kingdom); Liverpool, Tanniemola B. [School of Mathematics, University of Bristol, Bristol BS8 1TW (United Kingdom); Royall, C. Patrick, E-mail: paddy.royall@bristol.ac.uk [HH Wills Physics Laboratory, Tyndall Avenue, Bristol BS8 1TL (United Kingdom); School of Chemistry, University of Bristol, Cantock Close, Bristol BS8 1TS (United Kingdom); Centre for Nanoscience and Quantum Information, Tyndall Avenue, Bristol BS8 1FD (United Kingdom)

    2015-12-28

    We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics are correlated with the formation of icosahedral structures. Upon cooling, these icosahedra organize into mesoclusters. We recast this glassformer as an effective system of icosahedra which we describe with a population dynamics model. This model we parameterize with data from the temperature regime accessible to molecular dynamics simulations. We then use the model to determine the population of icosahedra in mesoclusters at arbitrary temperature. Using simulation data to incorporate dynamics into the model, we predict relaxation behavior at temperatures inaccessible to conventional approaches. Our model predicts super-Arrhenius dynamics whose relaxation time remains finite for non-zero temperature.

  1. On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems

    Science.gov (United States)

    Junge, Oliver; Kevrekidis, Ioannis G.

    2017-06-01

    We propose to compute approximations to invariant sets in dynamical systems by minimizing an appropriate distance between a suitably selected finite set of points and its image under the dynamics. We demonstrate, through computational experiments, that this approach can successfully converge to approximations of (maximal) invariant sets of arbitrary topology, dimension, and stability, such as, e.g., saddle type invariant sets with complicated dynamics. We further propose to extend this approach by adding a Lennard-Jones type potential term to the objective function, which yields more evenly distributed approximating finite point sets, and illustrate the procedure through corresponding numerical experiments.

  2. Simplicity of condensed matter at its core: generic definition of a Roskilde-simple system.

    Science.gov (United States)

    Schrøder, Thomas B; Dyre, Jeppe C

    2014-11-28

    The isomorph theory is reformulated by defining Roskilde-simple systems by the property that the order of the potential energies of configurations at one density is maintained when these are scaled uniformly to a different density. If the potential energy as a function of all particle coordinates is denoted by U(R), this requirement translates into U(Ra) < U(Rb) ⇒ U(λRa) < U(λRb). Isomorphs remain curves in the thermodynamic phase diagram along which structure, dynamics, and excess entropy are invariant, implying that the phase diagram is effectively one-dimensional with respect to many reduced-unit properties. In contrast to the original formulation of the isomorph theory, however, the density-scaling exponent is not exclusively a function of density and the isochoric heat capacity is not an exact isomorph invariant. A prediction is given for the latter quantity's variation along the isomorphs. Molecular dynamics simulations of the Lennard-Jones and Lennard-Jones Gaussian systems validate the new approach.

  3. Molecular simulation of thermodynamic and transport properties for the H{sub 2}O+NaCl system

    Energy Technology Data Exchange (ETDEWEB)

    Orozco, Gustavo A.; Jiang, Hao; Panagiotopoulos, Athanassios Z., E-mail: azp@princeton.edu [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States); Moultos, Othonas A.; Economou, Ioannis G. [Chemical Engineering Program, Texas A and M University at Qatar, P.O. Box 23874, Doha (Qatar)

    2014-12-21

    Molecular dynamics and Monte Carlo simulations have been carried out to obtain thermodynamic and transport properties of the binary mixture H{sub 2}O+NaCl at temperatures from T = 298 to 473 K. In particular, vapor pressures, liquid densities, viscosities, and vapor-liquid interfacial tensions have been obtained as functions of pressure and salt concentration. Several previously proposed fixed-point-charge models that include either Lennard-Jones (LJ) 12-6 or exponential-6 (Exp6) functional forms to describe non-Coulombic interactions were studied. In particular, for water we used the SPC and SPC/E (LJ) models in their rigid forms, a semiflexible version of the SPC/E (LJ) model, and the Errington-Panagiotopoulos Exp6 model; for NaCl, we used the Smith-Dang and Joung-Cheatham (LJ) parameterizations as well as the Tosi-Fumi (Exp6) model. While none of the model combinations are able to reproduce simultaneously all target properties, vapor pressures are well represented using the SPC plus Joung-Cheathem model combination, and all LJ models do well for the liquid density, with the semiflexible SPC/E plus Joung-Cheatham combination being the most accurate. For viscosities, the combination of rigid SPC/E plus Smith-Dang is the best alternative. For interfacial tensions, the combination of the semiflexible SPC/E plus Smith-Dang or Joung-Cheatham gives the best results. Inclusion of water flexibility improves the mixture densities and interfacial tensions, at the cost of larger deviations for the vapor pressures and viscosities. The Exp6 water plus Tosi-Fumi salt model combination was found to perform poorly for most of the properties of interest, in particular being unable to describe the experimental trend for the vapor pressure as a function of salt concentration.

  4. Solid phase stability of a double-minimum interaction potential system

    International Nuclear Information System (INIS)

    Suematsu, Ayumi; Yoshimori, Akira; Saiki, Masafumi; Matsui, Jun; Odagaki, Takashi

    2014-01-01

    We study phase stability of a system with double-minimum interaction potential in a wide range of parameters by a thermodynamic perturbation theory. The present double-minimum potential is the Lennard-Jones-Gauss potential, which has a Gaussian pocket as well as a standard Lennard-Jones minimum. As a function of the depth and position of the Gaussian pocket in the potential, we determine the coexistence pressure of crystals (fcc and bcc). We show that the fcc crystallizes even at zero pressure when the position of the Gaussian pocket is coincident with the first or third nearest neighbor site of the fcc crystal. The bcc crystal is more stable than the fcc crystal when the position of the Gaussian pocket is coincident with the second nearest neighbor sites of the bcc crystal. The stable crystal structure is determined by the position of the Gaussian pocket. These results show that we can control the stability of the solid phase by tuning the potential function

  5. An EQT-based cDFT approach for a confined Lennard-Jones fluid mixture

    Energy Technology Data Exchange (ETDEWEB)

    Motevaselian, M. H.; Mashayak, S. Y.; Aluru, N. R., E-mail: aluru@illinois.edu [Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)

    2015-09-28

    Empirical potential-based quasi-continuum theory (EQT) provides a route to incorporate atomistic detail into continuum framework such as the Nernst-Planck equation. EQT can also be used to construct a grand potential functional for classical density functional theory (cDFT). The combination of EQT and cDFT provides a simple and fast approach to predict the inhomogeneous density, potential profiles, and thermodynamic properties of confined fluids. We extend the EQT-cDFT approach to confined fluid mixtures and demonstrate it by simulating a mixture of methane and hydrogen inside slit-like channels of graphene. We show that the EQT-cDFT predictions for the structure of the confined fluid mixture compare well with the molecular dynamics simulation results. In addition, our results show that graphene slit nanopores exhibit a selective adsorption of methane over hydrogen.

  6. Molecular dynamics calculation of half-lives for thermal decay of Lennard-Jones clusters

    International Nuclear Information System (INIS)

    Smith, R.W.

    1991-01-01

    Molecular dynamics has been used with a Lenard-Jones (6-12) potential in order to study the decay behavior of neutral Argon clusters containing between 12 and 14 atoms. The clusters were heated to temperatures well above their melting points and then tracked in time via molecular dynamics until evaporation of one or more atoms was observed. In each simulation, the mode of evaporation, energy released during evaporation, and cluster lifetime were recorded. Results from roughly 2000 simulation histories were combined in order to compute statistically significant values of cluster half-lives and decay energies. It was found that cluster half-life decreases with increasing energy and that for a given value of excess energy (defined as E=(E tot -E gnd )/n), the 13 atom cluster is more stable against decay than clusters containing either 12 or 14 atoms. The dominant decay mechanism for all clusters was determined to be single atom emission. (orig.)

  7. Cluster growing process and a sequence of magic numbers

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2003-01-01

    demonstrate that in this way all known global minimum structures of the Lennard-Jones (LJ) clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence for the clusters of noble gas atoms......We present a new theoretical framework for modeling the cluster growing process. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system, and absorbing its energy at each step, we find cluster growing paths up to the cluster sizes of more than 100 atoms. We...

  8. The importance of accurate interaction potentials in the melting of argon nanoclusters

    Science.gov (United States)

    Pahl, E.; Calvo, F.; Schwerdtfeger, P.

    The melting temperatures of argon clusters ArN (N = 13, 55, 147, 309, 561, and 923) and of bulk argon have been obtained from exchange Monte Carlo simulations and are compared using different two-body interaction potentials, namely the standard Lennard-Jones (LJ), Aziz and extended Lennard-Jones (ELJ) potentials. The latter potential has many advantages: while maintaining the computational efficiency of the commonly used LJ potential, it is as accurate as the Aziz potential but the computer time scales more favorably with increasing cluster size. By applying the ELJ form and extrapolating the cluster data to the infinite system, we are able to extract the melting point of argon already in good agreement with experimental measurements. By considering the additional Axilrod-Teller three-body contribution as well, we calculate a melting temperature of T meltELJ = 84.7 K compared to the experimental value of T meltexp = 83.85 K, whereas the LJ potential underestimates the melting point by more than 7 K. Thus melting temperatures within 1 K accuracy are now feasible.

  9. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...

  10. Structure in sheared supercooled liquids: Dynamical rearrangements of an effective system of icosahedra.

    Science.gov (United States)

    Pinney, Rhiannon; Liverpool, Tanniemola B; Royall, C Patrick

    2016-12-21

    We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics are correlated with the formation of particles organized into icosahedra under simple steady state shear. We recast this glassformer as an effective system of icosahedra [Pinney et al., J. Chem. Phys. 143, 244507 (2015)]. From the observed population of icosahedra in each steady state, we obtain an effective temperature which is linearly dependent on the shear rate in the range considered. Upon shear banding, the system separates into a region of high shear rate and a region of low shear rate. The effective temperatures obtained in each case show that the low shear regions correspond to a significantly lower temperature than the high shear regions. Taking a weighted average of the effective temperature of these regions (weight determined by region size) yields an estimate of the effective temperature which compares well with an effective temperature based on the global mesocluster population of the whole system.

  11. Influence of attractions on the static and dynamic properties of simulated single and multichain systems

    International Nuclear Information System (INIS)

    Bishop, M.; Kalos, M.H.; Frisch, H.L.

    1983-01-01

    The influence of the attractive portion of the Lennard-Jones potential on the statics and dynamics of both single chain and multichain systems is investigated by reptation and molecular dynamics simulations. There is no significant effect at a reduced temperature of 10.0. At a temperature of 1.7 the single chain and multichain system at low densities (0.1) indicate that the attractions cause both the chains to be significantly more compact and a slowing of the time autocorrelation functions of the square of the end-to-end distance and radius of gyration. At a moderate density of 0.5, the attractions have almost no effect on the static structure, but they still influence the dynamic properties

  12. The effect of system boundaries on the mean free path for confined gases

    Directory of Open Access Journals (Sweden)

    Sooraj K. Prabha

    2013-10-01

    Full Text Available The mean free path of rarefied gases is accurately determined using Molecular Dynamics simulations. The simulations are carried out on isothermal argon gas (Lennard-Jones fluid over a range of rarefaction levels under various confinements (unbounded gas, parallel reflective wall and explicit solid platinum wall bounded gas in a nanoscale domain. The system is also analyzed independently in constitutive sub-systems to calculate the corresponding local mean free paths. Our studies which predominate in the transition regime substantiate the boundary limiting effect on mean free paths owing to the sharp diminution in molecular free paths near the planar boundaries. These studies provide insight to the transport phenomena of rarefied gases through nanochannels which have established their potential in microscale and nanoscale heat transfer applications.

  13. Theoretical equation of state for classical fluids. I. Test by perturbation theory

    International Nuclear Information System (INIS)

    Gil-Villegas, A.; Chavez, M.; Del Rio, F.

    1993-01-01

    This paper shows how to construct the theoretical equation of state (TEOS) of a classical simple fluid. The theory relies on the mean collisional diameter and range, and maps the thermodynamical properties of the fluid into those of an equivalent square-well (ESW) fluid of appropriate depth ε , diameter σ and range R. It is shown that the ESW has the same pressure as the fluid of interest. Hence the THEOS of any simple fluid takes the form of a SW EOS of the given ε , σ and R. The theory is applied to a Lennard-Jones (LJ) system in a first-order perturbation. The mapping equation have a physical solution for densities where the SW EOS is accurate; the resulting LJ TEOS agrees very well with the results of computer simulations, and compares favorably with the recent TEOS developed by Song and Mason. (Author). 17 refs, 7 figs, 1 tab

  14. Importance of dispersion and electron correlation in ab initio protein folding.

    Science.gov (United States)

    He, Xiao; Fusti-Molnar, Laszlo; Cui, Guanglei; Merz, Kenneth M

    2009-04-16

    Dispersion is well-known to be important in biological systems, but the effect of electron correlation in such systems remains unclear. In order to assess the relationship between the structure of a protein and its electron correlation energy, we employed both full system Hartree-Fock (HF) and second-order Møller-Plesset perturbation (MP2) calculations in conjunction with the Polarizable Continuum Model (PCM) on the native structures of two proteins and their corresponding computer-generated decoy sets. Because of the expense of the MP2 calculation, we have utilized the fragment molecular orbital method (FMO) in this study. We show that the sum of the Hartree-Fock (HF) energy and force field (LJ6)-derived dispersion energy (HF + LJ6) is well correlated with the energies obtained using second-order Møller-Plesset perturbation (MP2) theory. In one of the two examples studied, the correlation energy as well as the empirical dispersive energy term was able to discriminate between native and decoy structures. On the other hand, for the second protein we studied, neither the correlation energy nor dispersion energy showed discrimination capabilities; however, the ab initio MP2 energy and the HF+LJ6 both ranked the native structure correctly. Furthermore, when we randomly scrambled the Lennard-Jones parameters, the correlation between the MP2 energy and the sum of the HF energy and dispersive energy (HF+LJ6) significantly drops, which indicates that the choice of Lennard-Jones parameters is important.

  15. Alternative Hamiltonian for molecular dynamics simulations in the grand canonical ensemble

    International Nuclear Information System (INIS)

    Lo, C.; Palmer, B.

    1995-01-01

    An alternative to the Hamiltonian of Cagin and Pettitt for performing molecular dynamics simulations in the grand canonical ensemble is presented and used as the basis for a new algorithm. The algorithm is tested on the ideal gas and the truncated and shifted Lennard-Jones fluid. Simulations are used to calculate the vapor--liquid coexistence points for the Lennard-Jones system and are found to be in agreement with previous calculations using Gibbs ensemble calculations and with the Nicolas equation of state. Simulations are also performed on the Lennard-Jones solid

  16. Molecular Simulation of the Vapor-Liquid Phase Behavior of Lennard-Jones Mixtures in Porous Solids

    Science.gov (United States)

    2006-09-01

    sur la Catalyse, Centre National de la Recherche Scientifique, Group de Chimie Theorique, 2 Avenue Albert Einstein, 69626 Villeurbanne Cedex, France...and Group de Chimie Theorique, Ecole Normale Superieure de Lyon, 46 Allee d’Italie, 69364 Lyon, Cedex 07, France 14. ABSTRACT We present vapor...Scientifique, Group de Chimie Theorique, 2 Avenue Albert Einstein, 69626 Villeurbanne Cedex, France and Group de Chimie Theorique, Ecole Normale

  17. Lennard-Jones triple-point bulk and shear viscosities. Green-Kubo theory, Hamiltonian mechanics, and nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.; Evans, D.J.; Hickman, R.B.; Ladd, A.J.C.; Ashurst, W.T.; Moran, B.

    1980-01-01

    A new Hamiltonian method for deformation simulations is related to the Green-Kubo fluctuation theory through perturbation theory and linear-response theory. Numerical results for the bulk and shear viscosity coefficients are compared to corresponding Green-Kubo calculations. Both viscosity coefficients depend similarly on frequency, in a way consistent with enhanced ''long-time tails.''

  18. Lennard-Jones fluids in two-dimensional nano-pores. Multi-phase coexistence and fluid structure

    Science.gov (United States)

    Yatsyshin, Petr; Savva, Nikos; Kalliadasis, Serafim

    2014-03-01

    We present a number of fundamental findings on the wetting behaviour of nano-pores. A popular model for fluid confinement is a one-dimensional (1D) slit pore formed by two parallel planar walls and it exhibits capillary condensation (CC): a first-order phase transition from vapour to capillary-liquid (Kelvin shift). Capping such a pore at one end by a third orthogonal wall forms a prototypical two-dimensional (2D) pore. We show that 2D pores possess a wetting temperature such that below this temperature CC remains of first order, above it becomes a continuous phase transition manifested by a slab of capillary-liquid filling the pore from the capping wall. Continuous CC exhibits hysteresis and can be preceded by a first-order capillary prewetting transition. Additionally, liquid drops can form in the corners of the 2D pore (remnant of 2D wedge prewetting). The three fluid phases, vapour, capillary-liquid slab and corner drops, can coexist at the pore triple point. Our model is based on the statistical mechanics of fluids in the density functional formulation. The fluid-fluid and fluid-substrate interactions are dispersive. We analyze in detail the microscopic fluid structure, isotherms and full phase diagrams. Our findings also suggest novel ways to control wetting of nano-pores. We are grateful to the European Research Council via Advanced Grant No. 247031 for support.

  19. Addendum to ''Density fluctuations in liquid rubidium''

    International Nuclear Information System (INIS)

    Haan, S.W.; Mountain, R.D.; Hsu, C.S.; Rahman, A.

    1980-01-01

    We performed molecular-dynamics simulations of liquid rubidium and the Lennard-Jones fluid at several densities and temperatures, and of a system whose pair potential is the repulsive core of the rubidium potential. In all cases, propagating density fluctuations occurred in the rubidiumlike systems at much shorter wavelengths than in the Lennard-Jones system. This indicates that the repulsive part of the pair potential is the dominant factor in determining the relaxation of short-wavelength density fluctuations

  20. Diffusion processes and memory effects

    International Nuclear Information System (INIS)

    Mokshin, Anatolii V; Yulmetyev, Renat M; Haenggi, Peter

    2005-01-01

    We report the results of the numerical estimation of statistical memory effects in diffusion for two various systems: Lennard-Jones fluids and the model of the Brownian particle in a one-dimensional harmonic lattice. We have found the relation between the diffusion coefficient and the non-Markovity parameter, which is linear for the Lennard-Jones systems in liquid state. The relation between the memory measure and the excess entropy is also discussed here

  1. Jollrnal of EAEA, VoL lJ, 1996

    African Journals Online (AJOL)

    (voltage, current, resistance, inductance, capacitance) variation suitable for the signal conditioning system which may be a combination of a bridge circuit, an amplifier, an oscillator and a filter circuit. Signal conversion (analog to digital or digital to analog cooversion) is needed only when digital techniques are necessary.

  2. Boundary layer energies for nonconvex discrete systems

    NARCIS (Netherlands)

    Scardia, L.; Schlömerkemper, A.; Zanini, C.

    2011-01-01

    In this work we consider a one-dimensional chain of atoms which interact through nearest and next-to-nearest neighbour interactions of Lennard-Jones type. We impose Dirichlet boundary conditions and in addition prescribe the deformation of the second and last but one atoms of the chain. This

  3. Translational and rotational diffusion of dilute solid amorphous spherical nanocolloids by molecular dynamics simulation

    Science.gov (United States)

    Heyes, D. M.; Nuevo, M. J.; Morales, J. J.

    Following on from our previous study (Heyes, D. M., Nuevo, M. J, and Morales, J. J., 1996, Molec. Phys., 88, 1503), molecular dynamics simulations have been carried out of translational and rotational diffusion of atomistically rough near-spherical solid Lennard-Jones (LJ) clusters immersed in a Weeks-Chandler-Andersen liquid solvent. A single cluster consisting of up to about 100LJ particles as part of an 8000 atom fluid system was considered in each case. The translational and rotational diffusion coefficients decrease with increasing cluster size and solvent density (roughly in proportion to the molar volume of the solvent). The simulations reveal that for clusters in excess of about 30LJ atoms there is a clear separation of timescales between angular velocity and orientation relaxation which adhere well to the small-step diffusion model encapsulated in Hubbard's relationship. For 100 atom clusters both the StokesEinstein (translation) and Stokes-Einstein-Debye (rotation) equations apply approximately. The small departures from these reference solutions indicate that the translational relaxation experiences a local viscosity in excess of the bulk value (typically by ~ 30%), whereas rotational relaxation experiences a smaller viscosity than the bulk (typically by ~ 30%) reasonably in accord with the Gierer-Wirtz model. Both of these observations are consistent with an observed layering of the liquid molecules next to the cluster observed in our previous study.

  4. A dynamic lattice searching method with rotation operation for optimization of large clusters

    International Nuclear Information System (INIS)

    Wu Xia; Cai Wensheng; Shao Xueguang

    2009-01-01

    Global optimization of large clusters has been a difficult task, though much effort has been paid and many efficient methods have been proposed. During our works, a rotation operation (RO) is designed to realize the structural transformation from decahedra to icosahedra for the optimization of large clusters, by rotating the atoms below the center atom with a definite degree around the fivefold axis. Based on the RO, a development of the previous dynamic lattice searching with constructed core (DLSc), named as DLSc-RO, is presented. With an investigation of the method for the optimization of Lennard-Jones (LJ) clusters, i.e., LJ 500 , LJ 561 , LJ 600 , LJ 665-667 , LJ 670 , LJ 685 , and LJ 923 , Morse clusters, silver clusters by Gupta potential, and aluminum clusters by NP-B potential, it was found that both the global minima with icosahedral and decahedral motifs can be obtained, and the method is proved to be efficient and universal.

  5. New Scenario of Dynamical Heterogeneity in Supercooled Liquid and Glassy States of 2D Monatomic System.

    Science.gov (United States)

    Van Hoang, Vo; Teboul, Victor; Odagaki, Takashi

    2015-12-24

    Via analysis of spatiotemporal arrangements of atoms based on their dynamics in supercooled liquid and glassy states of a 2D monatomic system with a double-well Lennard-Jones-Gauss (LJG) interaction potential, we find a new scenario of dynamical heterogeneity. Atoms with the same or very close mobility have a tendency to aggregate into clusters. The number of atoms with high mobility (and size of their clusters) increases with decreasing temperature passing over a maximum before decreasing down to zero. Position of the peak moves toward a lower temperature if mobility of atoms in clusters is lower together with an enhancement of height of the peak. In contrast, the number of atoms with very low mobility or solidlike atoms (and size of their clusters) has a tendency to increase with decreasing temperature and then it suddenly increases in the vicinity of the glass transition temperature leading to the formation of a glassy state. A sudden increase in the number of strongly correlated solidlike atoms in the vicinity of a glass transition temperature (Tg) may be an origin of a drastical increase in viscosity of the glass-forming systems approaching the glass transition. In fact, we find that the diffusion coefficient decays exponentially with a fraction of solidlike atoms exhibiting a sudden decrease in the vicinity of the glass transition region.

  6. The role of pressure in rubber elasticity.

    Science.gov (United States)

    Bower, A F; Weiner, J H

    2004-06-22

    We describe a series of molecular dynamics computations that reveal an intimate connection at the atomic scale between difference stress (which resists stretches) and pressure (which resists volume changes) in an idealized elastomer, in contrast to the classical theory of rubber elasticity. Our simulations idealize the elastomer as a "pearl necklace," in which the covalent bonds are stiff linear springs, while nonbonded atoms interact through a Lennard-Jones potential with energy epsilon(LJ) and radius sigma(LJ). We calculate the difference stress t(11)-(t(22)+t(33))/2 and mean stress (t(11)+t(22)+t(33))/3 induced by a constant volume extension in the x(1) direction, as a function of temperature T and reduced density rho(*)=Nsigma(IJ) (3)/nu. Here, N is the number of atoms in the simulation cell and nu is the cell volume. Results show that for rho(*)rubber elasticity, which neglects nonbonded interactions. However, data presented by van Krevelen [Properties of Polymers, 3rd ed. (Elsevier, Amsterdam, 1990), p. 79] indicate that rubber at standard conditions corresponds to rho(*)=1.2. For rho(*)>1, the system is entropic for kT/epsilon(LJ)>2, but at lower temperatures the difference stress contains an additional energy component, which increases as rho(*) increases and temperature decreases. Finally, the model exhibits a glass transition for rho(*)=1.2 and kT/epsilon(LJ) approximately 2. The atomic-scale processes responsible for generating stress are explored in detail. Simulations demonstrate that the repulsive portion of the Lennard-Jones potential provides a contribution sigma(nbr)>0 to the difference stress, the attractive portion provides sigma(nba) approximately 0, while the covalent bonds provide sigma(b)nbr)0, and Pi(b)nbr)=-APi(nbr)P(2)(theta(b)), sigma(b)=BPi(b)P(2)(theta(b)), where P(2)(theta(b)) is a measure of the anisotropy of the orientation of the covalent bonds, and A and B are coefficients that depend weakly on rho(*) and temperature. For high

  7. Improved modeling of two-dimensional transitions in dense phases on crystalline surfaces. Krypton-graphite system.

    Science.gov (United States)

    Ustinov, E A

    2015-02-21

    This paper presents a refined technique to describe two-dimensional phase transitions in dense fluids adsorbed on a crystalline surface. Prediction of parameters of 2D liquid-solid equilibrium is known to be an extremely challenging problem, which is mainly due to a small difference in thermodynamic functions of coexisting phases and lack of accuracy of numerical experiments in case of their high density. This is a serious limitation of various attempts to circumvent this problem. To improve this situation, a new methodology based on the kinetic Monte Carlo method was applied. The methodology involves analysis of equilibrium gas-liquid and gas-solid systems undergoing an external potential, which allows gradual shifting parameters of the phase coexistence. The interrelation of the chemical potential and tangential pressure for each system is then treated with the Gibbs-Duhem equation to obtain the point of intersection corresponding to the liquid/solid-solid equilibrium coexistence. The methodology is demonstrated on the krypton-graphite system below and above the 2D critical temperature. Using experimental data on the liquid-solid and the commensurate-incommensurate transitions in the krypton monolayer derived from adsorption isotherms, the Kr-graphite Lennard-Jones parameters have been corrected resulting in a higher periodic potential modulation.

  8. Non-chiral, auxetic system of noncentrosymmetric molecules in two dimensions

    International Nuclear Information System (INIS)

    Wojciechowski, K.W.

    2002-12-01

    A two-dimensional model of tri-atomic molecules (which 'atoms' are distributed on vertices of equilateral triangles, and which are further referred to as cyclic trimers) is solved exactly in the static (zero-temperature) limit for the nearest-neighbor site-site interactions. It is shown that the cyclic trimers (noncentrosymmetric by the definition) can form a mechanically stable and elastically isotropic non-chiral phase of negative Poisson ratio. The properties of the system are illustrated by three examples of the atom-atom interaction potentials: (i) the purely repulsive (n-inverse-power) potential, (ii) the purely attractive (n-power) potential and (iii) the Lennard-Jones-like potential which shows both the repulsive and the attractive part. The analytic form of the dependence of the Poisson ratio on the interatomic potential is obtained. It is shown that the Poisson ratio depends, in a universal way, only on the trimer anisotropy parameter both (1) in the limit of n → ∞ for the cases (i) and (ii), as well as (2) at the zero external pressure for any potential with a doubly differentiable minimum, the case (iii) is an example. (author)

  9. Parametric sensitivity analysis for stochastic molecular systems using information theoretic metrics

    Energy Technology Data Exchange (ETDEWEB)

    Tsourtis, Anastasios, E-mail: tsourtis@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, Crete (Greece); Pantazis, Yannis, E-mail: pantazis@math.umass.edu; Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-70013 Heraklion, Crete (Greece)

    2015-07-07

    In this paper, we present a parametric sensitivity analysis (SA) methodology for continuous time and continuous space Markov processes represented by stochastic differential equations. Particularly, we focus on stochastic molecular dynamics as described by the Langevin equation. The utilized SA method is based on the computation of the information-theoretic (and thermodynamic) quantity of relative entropy rate (RER) and the associated Fisher information matrix (FIM) between path distributions, and it is an extension of the work proposed by Y. Pantazis and M. A. Katsoulakis [J. Chem. Phys. 138, 054115 (2013)]. A major advantage of the pathwise SA method is that both RER and pathwise FIM depend only on averages of the force field; therefore, they are tractable and computable as ergodic averages from a single run of the molecular dynamics simulation both in equilibrium and in non-equilibrium steady state regimes. We validate the performance of the extended SA method to two different molecular stochastic systems, a standard Lennard-Jones fluid and an all-atom methane liquid, and compare the obtained parameter sensitivities with parameter sensitivities on three popular and well-studied observable functions, namely, the radial distribution function, the mean squared displacement, and the pressure. Results show that the RER-based sensitivities are highly correlated with the observable-based sensitivities.

  10. Mechanisms of heterogeneous crystal growth in atomic systems: insights from computer simulations.

    Science.gov (United States)

    Gulam Razul, M S; Hendry, J G; Kusalik, P G

    2005-11-22

    In this paper we analyze the atomic-level structure of solid/liquid interfaces of Lennard-Jones fcc systems. The 001, 011, and 111 faces are examined during steady-state growth and melting of these crystals. The mechanisms of crystallization and melting are explored using averaged configurations generated during these steady-state runs, where subsequent tagging and labeling of particles at the interface provide many insights into the detailed atomic behavior at the freezing and melting interfaces. The interfaces are generally found to be rough and we observe the structure of freezing and melting interfaces to be very similar. Large structural fluctuations with solidlike and liquidlike characteristics are apparent in both the freezing and melting interfaces. The behavior at the interface observed under either growth or melting conditions reflects a competition between ordering and disordering processes. In addition, we observe atom hopping that imparts liquidlike characteristics to the solid side of the interfaces for all three crystal faces. Solid order is observed to extend as rough, three-dimensional protuberances through the interface, particularly for the 001 and 011 faces. We are also able to reconcile our different measures for the interfacial width and address the onset of asymmetry in the growth rates at high rates of crystal growth/melting.

  11. Study of the validity of a combined potential model using the Hybrid Reverse Monte Carlo method in Fluoride glass system

    Directory of Open Access Journals (Sweden)

    M. Kotbi

    2013-03-01

    Full Text Available The choice of appropriate interaction models is among the major disadvantages of conventional methods such as Molecular Dynamics (MD and Monte Carlo (MC simulations. On the other hand, the so-called Reverse Monte Carlo (RMC method, based on experimental data, can be applied without any interatomic and/or intermolecular interactions. The RMC results are accompanied by artificial satellite peaks. To remedy this problem, we use an extension of the RMC algorithm, which introduces an energy penalty term into the acceptance criteria. This method is referred to as the Hybrid Reverse Monte Carlo (HRMC method. The idea of this paper is to test the validity of a combined potential model of coulomb and Lennard-Jones in a Fluoride glass system BaMnMF7 (M = Fe,V using HRMC method. The results show a good agreement between experimental and calculated characteristics, as well as a meaningful improvement in partial pair distribution functions (PDFs. We suggest that this model should be used in calculating the structural properties and in describing the average correlations between components of fluoride glass or a similar system. We also suggest that HRMC could be useful as a tool for testing the interaction potential models, as well as for conventional applications.

  12. An NPT Monte Carlo Molecular Simulation-Based Approach to Investigate Solid-Vapor Equilibrium: Application to Elemental Sulfur-H2S System

    KAUST Repository

    Kadoura, Ahmad Salim

    2013-06-01

    In this work, a method to estimate solid elemental sulfur solubility in pure and gas mixtures using Monte Carlo (MC) molecular simulation is proposed. This method is based on Isobaric-Isothermal (NPT) ensemble and the Widom insertion technique for the gas phase and a continuum model for the solid phase. This method avoids the difficulty of having to deal with high rejection rates that are usually encountered when simulating using Gibbs ensemble. The application of this method is tested with a system made of pure hydrogen sulfide gas (H2S) and solid elemental sulfur. However, this technique may be used for other solid-vapor systems provided the fugacity of the solid phase is known (e.g., through experimental work). Given solid fugacity at the desired pressure and temperature, the mole fraction of the solid dissolved in gas that would be in chemical equilibrium with the solid phase might be obtained. In other words a set of MC molecular simulation experiments is conducted on a single box given the pressure and temperature and for different mole fractions of the solute. The fugacity of the gas mixture is determined using the Widom insertion method and is compared with that predetermined for the solid phase until one finds the mole fraction which achieves the required fugacity. In this work, several examples of MC have been conducted and compared with experimental data. The Lennard-Jones parameters related to the sulfur molecule model (ɛ, σ) have been optimized to achieve better match with the experimental work.

  13. Unexpected finite size effects in interfacial systems: Why bigger is not always better—Increase in uncertainty of surface tension with bulk phase width

    Science.gov (United States)

    Longford, Francis G. J.; Essex, Jonathan W.; Skylaris, Chris-Kriton; Frey, Jeremy G.

    2018-06-01

    We present an unexpected finite size effect affecting interfacial molecular simulations that is proportional to the width-to-surface-area ratio of the bulk phase Ll/A. This finite size effect has a significant impact on the variance of surface tension values calculated using the virial summation method. A theoretical derivation of the origin of the effect is proposed, giving a new insight into the importance of optimising system dimensions in interfacial simulations. We demonstrate the consequences of this finite size effect via a new way to estimate the surface energetic and entropic properties of simulated air-liquid interfaces. Our method is based on macroscopic thermodynamic theory and involves comparing the internal energies of systems with varying dimensions. We present the testing of these methods using simulations of the TIP4P/2005 water forcefield and a Lennard-Jones fluid model of argon. Finally, we provide suggestions of additional situations, in which this finite size effect is expected to be significant, as well as possible ways to avoid its impact.

  14. 77 FR 5990 - Special Conditions: Learjet Inc., Model LJ-200-1A10 Airplane, Pilot-Compartment View Through...

    Science.gov (United States)

    2012-02-07

    ..., and the FAA must issue a finding of regulatory adequacy pursuant to Sec. 611 of Public Law 92-574, the ``Noise Control Act of 1972.'' The FAA issues special conditions, as defined in 14 CFR 11.19, in... novel or unusual design features: The Model LJ-200-1A10 airplane flight deck design incorporates a...

  15. Dynamical phases of attractive particles sliding on a structured surface

    International Nuclear Information System (INIS)

    Hasnain, J; Jungblut, S; Dellago, C

    2015-01-01

    Inspired by experiments on quartz crystal microbalance setups, we study the mobility of a monolayer of Lennard-Jones particles driven over a hexagonal external potential. We pay special attention to the changes in the dynamical phases that arise when the lattice constant of the external substrate potential and the Lennard-Jones interaction are mismatched. We find that if the average particle separation is such that the particles repel each other, or interact harmonically, the qualitative behavior of the system is akin to that of a monolayer of purely repulsive Yukawa particles. On the other hand, if the particles typically attract each other, the ensuing dynamical states are determined entirely by the relative strength of the Lennard-Jones interaction with respect to that of the external potential. (paper)

  16. Anomalous vibrational properties in the continuum limit of glasses

    Science.gov (United States)

    Shimada, Masanari; Mizuno, Hideyuki; Ikeda, Atsushi

    2018-02-01

    The low-temperature thermal properties of glasses are anomalous with respect to those of crystals. These thermal anomalies indicate that the low-frequency vibrational properties of glasses differ from those of crystals. Recent studies revealed that, in the simplest model of glasses, i.e., the harmonic potential system, phonon modes coexist with soft localized modes in the low-frequency (continuum) limit. However, the nature of low-frequency vibrational modes of more realistic models is still controversial. In the present work, we study the Lennard-Jones (LJ) system using large-scale molecular-dynamics (MD) simulation and establish that the vibrational property of the LJ glass converges to coexistence of the phonon modes and the soft localized modes in the continuum limit as in the case of the harmonic potential system. Importantly, we find that the low-frequency vibrations are rather sensitive to the numerical scheme of potential truncation, which is usually implemented in the MD simulation, and this is the reason why contradictory arguments have been reported by previous works. We also discuss the physical origin of this sensitiveness by means of a linear stability analysis.

  17. Equation of state of a hard core fluid with a two-Yukawa tail: toward a simple analytic theory

    International Nuclear Information System (INIS)

    Jedrzejek, C.

    1980-01-01

    Thermodynamic properties of simple fluids are calculated using variational theory for a system of hard-core potential with a two-Yukawa tail. Likewise one Yukawa-tail case the working formulas are analytic. Five parameters of the two Yukawa system are chosen so as to get the best fit to a real argon potential or an ''argon-like'' Lennard-Jones potential. The results are fairly good in light of the extreme simplicity of the method. The discrepancies result from using the variational method and a different shape of Yukawa type potential in comparision to the real argon and Lennard-Jones potentials. (author)

  18. Results of the radiological survey at 4 Branca Court, Lodi, New Jersey (LJ037)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.R.; Crutcher, J.W.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 4 Branca Court, Lodi, New Jersey (LJ037), was conducted during 1985 and 1986. Results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. However, this property is apparently located directly over the old Lodi Brook streambed. This factor in combination with the elevated gamma logs of several auger holes is sufficient to recommend this site for inclusion in the DOE remedial action program. 5 refs., 5 figs., 4 tabs

  19. Results of the radiological survey at 30 Long Valley Road, Lodi, New Jersey (LJ045)

    International Nuclear Information System (INIS)

    Cottrell, W.D.; Floyd, L.M.; Francis, M.W.; Mynatt, J.O.

    1989-11-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 30 Long Valley Road, Lodi, New Jersey (LJ045), was conducted during 1985, 1986, and 1987. Some radionuclide measurements were greater than typical background levels in the northern New Jersey area. However, results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. 5 refs., 10 figs., 3 tabs

  20. Results of the radiological survey at 6 Branca Court, Lodi, New Jersey (LJ041)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.; Crutcher, J.W.

    1989-06-01

    Maywood Chemical works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rate earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 6 Branca Court, Lodi, New Jersey (LJ041), was conducted during 1985 and 1986. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Act program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 6 figs., 3 tabs

  1. Results of the radiological survey at 19 Redstone Lane, Lodi, New Jersey (LJ056)

    International Nuclear Information System (INIS)

    Cottrell, W.D.; Floyd, L.M.; Francis, M.W.; Mynatt, J.O.

    1989-10-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 19 Redstone Lane, Lodi, New Jersey (LJ056), was conducted during 1985 and 1986. Results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions were not significantly different from normal background levels in the northern New Jersey area. 4 refs., 4 figs., 3 tabs

  2. Results of the radiological survey at 62 Trudy Drive, Lodi, New Jersey (LJ080)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 62 Trudy Drive, Lodi, New Jersey (LJ080), was conducted during 1988. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 5 refs., 5 figs., 3 tabs

  3. Results of the radiological survey at 70 State Highway 46, Lodi, New Jersey (LJ094)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-11-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 70 State Highway 46, Lodi, New Jersey (LJ094), was conducted during 1988. 4 refs., 5 figs., 3 tabs

  4. Results of the radiological survey at 72 Sidney Stret, Lodi, New Jersey (LJ067)

    International Nuclear Information System (INIS)

    Foley, R.D.; Carrier, R.F.; Floyd, L.M.; Crutcher, J.W.

    1989-09-01

    Maywood Chemical Works (MCW) of Maywood, New jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residues used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 72 Sidney Street, Lodi, New Jersey (LJ067), was conducted during 1987. Results indicated concentrations of 232 Th slightly in excess of the DOE remedial action criterion for subsurface soil. This finding, coupled with the fact that adjacent properties have been designated by DOE for remedial action, and that the old Lodi Brook streambed is apparently beneath the property, suggests that it be considered for inclusion in the DOE remedial action program. 4 refs., 5 figs., 3 tabs

  5. Results of the radiological survey at 174 Essex Street, Lodi, New Jersey (LJ073)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.; Crutcher, J.W.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 174 Essex Street, Lodi, New Jersey (LJ073), was conducted during 1987. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site

  6. Results of the radiological survey at 160 Essex Street, Lodi, New Jersey (LJ072)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.; Crutcher, J.W.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 160 Essex Street, Lodi, New Jersey (LJ072), was conducted during 1987. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 4 refs., 10 figs., 2 tabs

  7. Results of the radiological survey at 99 Garibaldi Avenue, Lodi, New Jersey (LJ064)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Crutcher, J.W.

    1989-07-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 99 Garibaldi Avenue, Lodi, New Jersey (LJ064), was conducted during 1987. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 4 refs., 8 figs., 3 tabs

  8. Results of the radiological survey at 2 Branca Court, Lodi, New Jersey (LJ036)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.; Crutcher, J.W.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1961 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 2 Branca Court, Lodi, New Jersey (LJ036), was conducted during 1985 and 1986. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site

  9. Results of the radiological survey at 9 Hancock Street, Lodi, New Jersey (LJ028)

    International Nuclear Information System (INIS)

    Cottrell, W.D.; Floyd, L.M.; Francis, M.W.; Mynatt, J.O.

    1989-09-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 9 Hancock Street, Lodi, New Jersey (LJ028), was conducted during 1985 and 1986. Some radionuclide measurements were greater than typical background levels in the northern New Jersey area. However, results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. 5 refs., 6 figs., 3 tabs

  10. Results of the radiological survey at 112 Avenue E, Lodi, New Jersey (LJ082)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residue, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 112 Avenue E, Lodi, New Jersey (LJ082), was conducted during 1988. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 2 figs., 3 tabs

  11. Results of the radiological survey at 108 Avenue E, Lodi, New Jersey (LJ084)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 108 Avenue E, Lodi, New Jersey (LJ084), was conducted during 1988. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 5 refs., 2 figs., 2 tabs

  12. Results of the radiological survey at 106 Columbia Lane, Lodi, New Jersey (LJ063)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Crutcher, J.W.

    1989-07-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 106 Columbia Lane, Lodi, New Jersey (LJ063), was conducted during 1987. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 4 refs., 7 figs., 3 tabs

  13. Results of the radiological survey at 15 John Street, Lodi, New Jersey (LJ087)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-12-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 15 John Street, Lodi, New Jersey (LJ087), was conducted during 1988. 5 refs., 3 figs., 3 tabs

  14. Results of the radiological survey at 32 Long Valley Road, Lodi, New Jersey (LJ046)

    International Nuclear Information System (INIS)

    Cottrell, W.D.; Floyd, L.M.; Francis, M.W.; Mynatt, J.O.

    1989-10-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 32 Long Valley Road, Lodi, New Jersey (LJ046), was conducted during 1985, 1986, and 1987. Some radionuclide measurements were greater than typical background levels in the northern New Jersey area. However, results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. 5 refs., 6 figs., 3 tabs

  15. Results of the radiological survey at 3 Branca Court, Lodi, New Jersey (LJ038)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.

    1989-10-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 3 Branca Court, Lodi, New Jersey (LJ038), was conducted during 1985 and 1986. 4 refs., 4 figs., 3 tabs

  16. Results of the radiological survey at 17 Redstone Lane, Lodi, New Jersey (LJ030)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.; Crutcher, J.W.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 17 Redstone Lane, Lodi, New Jersey (LJ030), was conducted during 1985 and 1986. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 4 refs., 7 figs., 3 tabs

  17. Results of the radiological survey at 10 Long Valley Road, Lodi, New Jersey (LJ055)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.

    1989-11-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 10 Long Valley Road, Lodi, New Jersey (LJ055), was conducted during 1985 and 1986. Results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions were not significantly different from normal background levels in the northern New Jersey area. 4 refs., 5 figs., 3 tabs

  18. Results of the radiological survey at 79 Avenue B, Lodi, New Jersey (LJ091)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 79 Avenue B, Lodi, New Jersey (LJ091), was conducted during 1988. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 5 refs., 2 figs., 2 tabs

  19. Results of the radiological survey at 112 Columbia Lane, Lodi, New Jersey (LJ068)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.

    1989-11-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 112 Columbia Lane, Lodi, New Jersey (LJ068), was conducted during 1987. 4 refs., 6 figs., 3 tabs

  20. Results of the radiological survey at 205 Main Street, Lodi, New Jersey (LJ075)

    International Nuclear Information System (INIS)

    Foley, R.D.; Carrier, R.F.; Floyd, L.M.; Crutcher, J.W.

    1989-08-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 205 Main Street, Lodi, New Jersey (LJ075), was conducted during 1987 and 1988. Results of the survey indicated radioactivity in the range of normal background for the northern New Jersey area. Radiological assessments of soil samples from the site demonstrate no radionuclide concentrations in excess of DOE Formerly Utilized Sites Remedial Action Program criteria. 5 refs., 21 figs., 3 tabs

  1. Results of the radiological survey at 12 Long Valley Road, Lodi, New Jersey (LJ054)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.

    1989-11-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extracting process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 12 Long Valley Road, Lodi, New Jersey (LJ054), was conducted during 1985 and 1986. Results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions were not significantly different from normal background levels in the northern New Jersey area

  2. Results of the radiological survey at 1 Branca Court, Lodi, New Jersey (LJ034)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.

    1989-10-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 1 Branca Court, Lodi, New Jersey (LJ034), was conducted during 1985 and 1986. Results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action program criteria. The radionuclide distributions were not significantly different from normal background levels in the northern New Jersey area. 4 refs., 4 figs., 3 tabs

  3. Results of the radiological survey at 7 Redstone Lane, Lodi, New Jersey (LJ044)

    International Nuclear Information System (INIS)

    Cottrell, W.D.; Floyd, L.M.; Francis, M.W.; Mynatt, J.O.

    1989-10-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclides analyses. The survey of this site, 7 Redstone Lane, Lodi, New Jersey (LJ044), was conducted during 1985 and 1986. Some radionuclide measurements were greater than typical background levels in the northern New Jersey area. However, results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. 5 refs., 4 figs., 3 tabs

  4. Results of the radiological survey at 24 Long Valley Road, Lodi, New Jersey (LJ048)

    International Nuclear Information System (INIS)

    Cottrell, W.D.; Floyd, L.M.; Francis, M.W.; Mynatt, J.O.

    1989-08-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monozite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 24 Long Valley Road, Lodi, New Jersey (LJ048), was conducted during 1985 and 1986. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 4 refs., 8 figs., 3 tabs

  5. Results of the radiological survey at 113 Avenue E, Lodi, New Jersey (LJ081)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 113 Avenue E, Lodi, New Jersey (LJ081), was conducted during 1988. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 5 refs, 2 figs., 3 tabs

  6. Results of the radiological survey at 4 Hancock Street, Lodi, New Jersey (LJ060)

    International Nuclear Information System (INIS)

    Foley, R.D.; Carier, R.F.; Floyd, L.M.; Crutcher, J.W.

    1989-09-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 4 Hancock Street, Lodi, New Jersey (LJ060), was conducted during 1985 and 1986. Gamma logging results found during this survey and during a previous survey conducted by Bechtel National, Incorporated, strongly indicated radionuclide concentrations in subsurface soil in excess of DOE remedial action criteria. This finding, coupled with the fact that adjacent properties have been found to be contaminated and that Lodi Brook apparently flows under the property, suggests that it be considered for inclusion in the DOE remedial action program. 5 refs., 4 figs., 4 tabs

  7. Results of the radiological survey at 80 Industrial Road, Lodi, New Jersey (LJ061)

    International Nuclear Information System (INIS)

    Foley, R.D.; Carrier, R.F.; Floyd, L.M.; Crutcher, J.W.

    1989-07-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 80 Industrial Road, Lodi, New Jersey (LJ061), was conducted during 1985 and 1986. Results of the survey demonstrated radionuclide concentrations in excess of DOE remedial action criteria, primarily from the 232 Th decay chain, with some contamination from 226 Ra. The radionuclide distributions are typical of the type of material originating from the MCW site. 5 refs., 11 figs., 3 tabs

  8. Results of the radiological survey at 90 C Avenue, Lodi, New Jersey (LJ079)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducted an investigative radiological survey during 1988 at 90 C Avenue, Lodi, New Jersey (LJ079), one of the properties in the vicinity of the MCW site. The survey included a gamma radiation scan of the surface and at one meter above the surface, as well as radionuclide sampling of surface and subsurface soil. The survey objective was to determine whether this site was contaminated with radioactive residues derived from MCW, principally 232 Th. Results of the survey demonstrated radionuclide concentrations in excess of DOE remedial action criteria, primarily from the 232 Th decay chain, with some contamination from 226 Ra. The radionuclide distributions are typical of the type of material originating from the MCW site. 5 refs., 3 figs., 3 tabs

  9. Results of the radiological survey at 28 Long Valley Road, Lodi, New Jersey (LJ047)

    International Nuclear Information System (INIS)

    Cottrell, W.D.; Floyd, L.M.; Francis, M.W.; Mynatt, J.O.

    1989-10-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 28 Long Valley Road, Lodi, New Jersey (LJ047), was conducted during 1985, 1986, 1987. Some radionuclide measurements were greater than typical background levels in the northern New Jersey area. However, results of the Survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. 5 refs., 8 figs., 3 tabs

  10. Results of the radiological survey at 14 Long Valley Road, Lodi, New Jersey (LJ070)

    International Nuclear Information System (INIS)

    Foley, R.D.; Carrier, R.F.

    1989-12-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 14 Long Valley Road, Lodi New Jersey (LJ070), was conducted during 1987. Survey measurements indicate that the property contained radioactive contamination primarily from the 232 Th decay chain. The radionuclide distributions are typical of the type of material originating from processing operations at the MCW. 5 refs., 5 figs., 3 tabs

  11. Results of the radiological survey at 10 Hancock Street, Lodi, New Jersey (LJ031)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.; Crutcher, J.W.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling from radionuclide analyses. The survey of this site, 10 Hancock Street, Lodi, New Jersey (LJ031), was conducted during 1985 and 1986. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 4 refs., 4 figs., 3 tabs

  12. Results of the radiological survey at 6 Hancock Street, Lodi, New Jersey (LJ033)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.; Crutcher, J.W.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth, earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 6 Hancock Street, Lodi, New Jersey (LJ033), was conducted during 1985 and 1986. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site

  13. Results of the radiological survey at 7 Hancock Street, Lodi, New Jersey (LJ027)

    International Nuclear Information System (INIS)

    Cottrell, W.D.; Floyd, L.M.; Francis, M.W.; Mynatt, J.O.

    1989-09-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. AT the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 7 Hancock Street, Lodi, New Jersey (LJ027), was conducted during 1985 and 1986. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 5 refs., 5 figs., 3 tabs

  14. Results of the radiological survey at 48 Long Valley Road, Lodi, New Jersey (LJ085)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-11-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 48 Long Valley Road, Lodi, New Jersey (LJ085), was conducted during 1988. 5 refs., 6 figs., 3 tabs

  15. Results of the radiological survey at 105 Garibaldi Avenue, Lodi, New Jersey (LJ065)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.

    1989-11-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 105 Garibaldi Avenue, Lodi, New Jersey (LJ065), was conducted during 1987. 4 refs., 4 figs., 3 tabs

  16. Results of the radiological survey at 104 Avenue E, Lodi, New Jersey (LJ086)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-12-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 104 Avenue E, Lodi, New Jersey (LJ086), was conducted during 1988. 5 refs., 2 figs., 3 tabs

  17. The anti-tumor effects of the recombinant toxin protein rLj-RGD3 from Lampetra japonica on pancreatic carcinoma Panc-1 cells in nude mice.

    Science.gov (United States)

    Wang, Yue; Zheng, Yuanyuan; Tu, Zuoyu; Dai, Yongguo; Xu, Hong; Lv, Li; Wang, Jihong

    2017-02-01

    Recombinant Lampetra japonica RGD peptide (rLj-RGD3) is a soluble toxin protein with three RGD (Arg-Gly-Asp) motifs and a molecular weight of 13.5kDa. The aim of this study was to investigate the effects and mechanisms of rLj-RGD3 on tumor growth and survival in pancreatic carcinoma Panc-1 cell-bearing mice. A Panc-1 human pancreatic carcinoma-bearing nude mouse model was successfully generated, and the animals were treated with different doses of rLj-RGD3 for 3 weeks. The volume and weight of the subcutaneous tumors, the survival of the nude mice, histopathological changes, the intratumoral MVD, the number of apoptotic Panc-1 cells, and apoptosis-related proteins and gene expressions were determined. rLj-RGD3 significantly decreased the tumor volumes and weights, and the maximum tumor volume and weight IR values were 53.2% (pPanc-1-bearing nude mice treated with rLj-RGD3 was increased by 56.3% (pPanc-1 cells in a nude mouse model, implying that rLj-RGD3 may serve as a potent clinical therapeutic agent for human pancreatic carcinoma. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Results of the radiological survey at 9 Redstone Lane, Lodi, New Jersey (LJ069)

    International Nuclear Information System (INIS)

    Foley, R.D.; Carrier, R.F.

    1989-07-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process waste and residues associated with the production and refining of thorium and thorium compounds from monozite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Areas residents used the sandlike waste from this thorium extraction process mixed with teas and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigate radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 9 Redstone Lane, Lodi, New Jersey (LJ069), was conducted during 1987. Measurements at the private property located at 9 Redstone Lane indicate slightly elevated gamma exposure rates in association with cinder-like material observed in logging holes. These elevated levels result from naturally occurring radioactivity present in such substances as ashes and cinders. They are not related to the deposit of residues from processing operations at the MCW site. All other radiological findings conform to the guidelines established by the DOE for the Maywood, New Jersey, area remedial action plan. 4 refs., 3 figs., 3 tabs

  19. Study of structure and spectroscopy of water–hydroxide ion clusters ...

    Indian Academy of Sciences (India)

    Experimen- talists are interested in determining the bonding,1–18 structure and spectroscopy of these systems and the- oreticians have contributed to the logical explanation of experimental findings. There are different types of systems ranging from atomic clusters, especially noble gas clusters (modelled by Lennard Jones ...

  20. Webbaserad pedagogisk meritportfölj - från idé till verklighet

    Directory of Open Access Journals (Sweden)

    Jakob Johansson

    2011-03-01

    åväl sökanden som bedömare. Det finns behov av redovisning av pedagogiska meriter även för andra ändamål än vid tjänstetillsättningar. Många medarbetare (som inte avser att söka akademisk tjänst gör betydande insatser i undervisningen exempelvis i form av administration, föreläsningar, seminarieledning samt klinisk handledning, och dessa prestationer bör användas som underlag för exempelvis planeringssamtal, löneförhandlingar och kompetensutveckling. Många finner det svårt att redovisa dessa undervisningsinsatser. Orsaken till detta är sannolikt delvis bristen på tradition att bokföra pedagogiskt arbetet (i kontrast till vetenskapligt arbete, men också bristen på ett användarvänligt verktyg för bokföring. Detta var startskottet för ett projekt som syftade till att framställa en personlig webbaserad pedagogisk meritportfölj som skulle kunna överbrygga det praktiska bekymret och ge medarbetarna ett smidigt verktyg för dokumentation av och reflektion runt pedagogiska meriter. Detta samtidigt som det skulle vara acceptabelt som instrument för sökande av akademisk tjänst genom att bygga på Uppsala universitets pedagogiska program och riktlinjer för meritvärdering. Denna artikel beskriver processen från idé till färdig webbaserad pedagogisk meritportfölj för vetenskapsområdet för medicin och farmaci vid Uppsala universitet. Även om det sannolikt existerar liknande webb-verktyg för bokföring av pedagogiska meriter så är detta oss veterligen det första verktyg i sitt slag som framställts och beskrivits. Syftet med artikeln är att sprida kunskap om både konceptet och arbetsprocessen för att underlätta spridning till andra fakulteter och lärosäten.

  1. Molecular beam scattering experiments with polar molecules. 1. Differential elastic scattering of H2+NH3 and H2+H2O

    International Nuclear Information System (INIS)

    Bickes, R.W. Jr.; Scoles, G.; Smith, K.M.

    1974-01-01

    Differential elastic scattering cross sections with well resolved quantum oscillations have been measuremed for the systems H 2 +NH 3 and H 2 +H 2 O. Assuming a spherically symmetric interaction the data show that a simple spherical potential (i.e. Lennard-Jones) does not properly describe the scattering

  2. Gas Enrichment at Liquid-Wall Interfaces

    NARCIS (Netherlands)

    Dammer, S.M.; Lohse, Detlef

    2006-01-01

    Molecular dynamics simulations of Lennard-Jones systems are performed to study the effects of dissolved gas on liquid-wall and liquid-gas interfaces. Gas enrichment at walls, which for hydrophobic walls can exceed more than 2 orders of magnitude when compared to the gas density in the bulk liquid,

  3. Density scaling and quasiuniversality of flow-event statistics for athermal plastic flows

    NARCIS (Netherlands)

    Lerner, E.; Bailey, N.P.; Dyre, J.C.

    2014-01-01

    Athermal steady-state plastic flows were simulated for the Kob-Andersen binary Lennard-Jones system and its repulsive version in which the sign of the attractive terms is changed to a plus. Properties evaluated include the distributions of energy drops, stress drops, and strain intervals between the

  4. Calculation of Liquid Water-Hydrate-Methane Vapor Phase Equilibria from Molecular Simulations

    DEFF Research Database (Denmark)

    Jensen, Lars; Thomsen, Kaj; von Solms, Nicolas

    2010-01-01

    using the TIP4P/ice potential and a united-atom Lennard-Jones potential. respectively. The equilibrium calculation method for this system has three components, (i) thermodynamic integration from a supercritical ideal gas to obtain the fluid-phase chemical potentials. (ii) calculation of the chemical...

  5. 1D momentum-conserving systems: the conundrum of anomalous versus normal heat transport

    Science.gov (United States)

    Li, Yunyun; Liu, Sha; Li, Nianbei; Hänggi, Peter; Li, Baowen

    2015-04-01

    asymptotic free part (Lennard-Jones model). We compare our findings with recent predictions obtained from nonlinear fluctuating hydrodynamics theory.

  6. Nonlinear Dynamics and Chaos of Microcantilever-Based TM-AFMs with Squeeze Film Damping Effects

    Directory of Open Access Journals (Sweden)

    Jie-Yu Chen

    2009-05-01

    Full Text Available In Atomic force microscope (AFM examination of a vibrating microcantilever, the nonlinear tip-sample interaction would greatly influence the dynamics of the cantilever. In this paper, the nonlinear dynamics and chaos of a tip-sample dynamic system being run in the tapping mode (TM were investigated by considering the effects of hydrodynamic loading and squeeze film damping. The microcantilever was modeled as a spring-mass-damping system and the interaction between the tip and the sample was described by the Lennard-Jones (LJ potential. The fundamental frequency and quality factor were calculated from the transient oscillations of the microcantilever vibrating in air. Numerical simulations were carried out to study the coupled nonlinear dynamic system using the bifurcation diagram, Poincaré maps, largest Lyapunov exponent, phase portraits and time histories. Results indicated the occurrence of periodic and chaotic motions and provided a comprehensive understanding of the hydrodynamic loading of microcantilevers. It was demonstrated that the coupled dynamic system will experience complex nonlinear oscillation as the system parameters change and the effect of squeeze film damping is not negligible on the micro-scale.

  7. Morse index for figure-eight choreographies of the planar equal mass three-body problem

    Science.gov (United States)

    Fukuda, Hiroshi; Fujiwara, Toshiaki; Ozaki, Hiroshi

    2018-04-01

    We report on numerical calculations of the Morse index for figure-eight choreographic solutions to a system of three identical bodies in a plane interacting through the homogeneous potential, -1/r a , or through the Lennard-Jones-type (LJ) potential, 1/r12 - 1/r6 , where r is a distance between the bodies. The Morse index is a number of independent variational functions giving negative second variation S (2) of action functional S. We calculated three kinds of Morse indices, N, N c and N e, in the domain of the periodic, the choreographic and the figure-eight choreographic function, respectively. For the homogeneous system, we obtain N  =  4 for 0 ≤slant a index for the solution tending to the figure-eight solution of the a  =  6 homogeneous system for the period T \\to ∞ . We obtain N, N c and N e as monotonically increasing functions of T from T \\to ∞ , which start with N=N_c=N_e=0 , jump at the smallest T by 1, and reach N  =  12, N_c=4 , and N_e=1 for T \\to ∞ in the other branch.

  8. An Analytical Model for Adsorption and Diffusion of Atoms/Ions on Graphene Surface

    Directory of Open Access Journals (Sweden)

    Yan-Zi Yu

    2015-01-01

    Full Text Available Theoretical investigations are made on adsorption and diffusion of atoms/ions on graphene surface based on an analytical continuous model. An atom/ion interacts with every carbon atom of graphene through a pairwise potential which can be approximated by the Lennard-Jones (L-J potential. Using the Fourier expansion of the interaction potential, the total interaction energy between the adsorption atom/ion and a monolayer graphene is derived. The energy-distance relationships in the normal and lateral directions for varied atoms/ions, including gold atom (Au, platinum atom (Pt, manganese ion (Mn2+, sodium ion (Na1+, and lithium-ion (Li1+, on monolayer graphene surface are analyzed. The equilibrium position and binding energy of the atoms/ions at three particular adsorption sites (hollow, bridge, and top are calculated, and the adsorption stability is discussed. The results show that H-site is the most stable adsorption site, which is in agreement with the results of other literatures. What is more, the periodic interaction energy and interaction forces of lithium-ion diffusing along specific paths on graphene surface are also obtained and analyzed. The minimum energy barrier for diffusion is calculated. The possible applications of present study include drug delivery system (DDS, atomic scale friction, rechargeable lithium-ion graphene battery, and energy storage in carbon materials.

  9. Mechanics of single-walled carbon nanotubes inside open single-walled carbon nanocones

    International Nuclear Information System (INIS)

    Ansari, R.; Hosseinzadeh, M.

    2013-01-01

    This study investigates the mechanical characteristics of single-walled carbon nanotubes (CNTs) inside open single-walled carbon nanocones (CNCs). New semi-analytical expressions are presented to evaluate van der Waals (vdW) interactions between CNTs and open CNCs. Continuum approximation, along with the the Lennard-Jones (LJ) potential function, is used in this study. The effects of geometrical parameters on alterations in vdW potential energy and the interaction force are extensively examined for the concentric CNT-open CNC configuration. The CNT is assumed to enter the nanocone either through the small end or the wide end of the cone. The preferred position of the CNT with respect to the nanocone axis is fully investigated for various geometrical parameters. The optimum nanotube radius minimizing the total potential energy of the concentric configuration is determined for different radii of the small end of the cone. The examined configuration generates asymmetric oscillation; thus, the system constitutes a nano-oscillator.

  10. Hemoglobin LjGlb1-1 is involved in nodulation and regulates the level of nitric oxide in the Lotus japonicus-Mesorhizobium loti symbiosis.

    Science.gov (United States)

    Fukudome, Mitsutaka; Calvo-Begueria, Laura; Kado, Tomohiro; Osuki, Ken-Ichi; Rubio, Maria Carmen; Murakami, Ei-Ichi; Nagata, Maki; Kucho, Ken-Ichi; Sandal, Niels; Stougaard, Jens; Becana, Manuel; Uchiumi, Toshiki

    2016-09-01

    Leghemoglobins transport and deliver O2 to the symbiosomes inside legume nodules and are essential for nitrogen fixation. However, the roles of other hemoglobins (Hbs) in the rhizobia-legume symbiosis are unclear. Several Lotus japonicus mutants affecting LjGlb1-1, a non-symbiotic class 1 Hb, have been used to study the function of this protein in symbiosis. Two TILLING alleles with single amino acid substitutions (A102V and E127K) and a LORE1 null allele with a retrotransposon insertion in the 5'-untranslated region (96642) were selected for phenotyping nodulation. Plants of all three mutant lines showed a decrease in long infection threads and nodules, and an increase in incipient infection threads. About 4h after inoculation, the roots of mutant plants exhibited a greater transient accumulation of nitric oxide (NO) than did the wild-type roots; nevertheless, in vitro NO dioxygenase activities of the wild-type, A102V, and E127K proteins were similar, suggesting that the mutated proteins are not fully functional in vivo The expression of LjGlb1-1, but not of the other class 1 Hb of L. japonicus (LjGlb1-2), was affected during infection of wild-type roots, further supporting a specific role for LjGlb1-1. In conclusion, the LjGlb1-1 mutants reveal that this protein is required during rhizobial infection and regulates NO levels. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  11. Phase equilibria of binary mixtures by molecular simulation and cubic equations of state

    Directory of Open Access Journals (Sweden)

    Cabral V.F.

    2001-01-01

    Full Text Available Molecular simulation data were used to study the performance of equations of state (EoS and combining rules usually employed in thermodynamic property calculations. The Monte Carlo method and the Gibbs ensemble technique were used for determining composition and densities of vapor and liquid phases in equilibrium for binary mixtures of Lennard-Jones fluids. Simulation results are compared to data in the literature and to those calculated by the t-PR-LJ EoS. The use of adequate combining rules has been shown to be very important for the satisfactory representation of molecular simulation data.

  12. Free energy evaluation in polymer translocation via Jarzynski equality

    Energy Technology Data Exchange (ETDEWEB)

    Mondaini, Felipe, E-mail: fmondaini@if.ufrj.br [Centro Federal de Educação Tecnológica Celso Suckow da Fonseca, Petrópolis, 25.620-003, RJ (Brazil); Moriconi, L., E-mail: moriconi@if.ufrj.br [Instituto de Física, Universidade Federal do Rio de Janeiro, C.P. 68528, 21945-970, Rio de Janeiro, RJ (Brazil)

    2014-05-01

    We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.

  13. Free energy evaluation in polymer translocation via Jarzynski equality

    International Nuclear Information System (INIS)

    Mondaini, Felipe; Moriconi, L.

    2014-01-01

    We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.

  14. Results of the radiological survey at Kennedy Park, Money and Sidney Streets, Lodi, New Jersey (LJ062)

    International Nuclear Information System (INIS)

    Foley, R.D.; Cottrell, W.D.; Floyd, L.M.

    1989-07-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, Kennedy Park, Money and Sidney Streets, Lodi, New Jersey (LJ062), was conducted during 1986 and 1987. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 4 refs., 4 figs., 3 tabs

  15. Results of the radiological survey at Interstate 80, North Right of Way at Lodi Brook, Lodi, New Jersey (LJ077)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-06-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and oil sampling for radionuclide analyses. The survey of this site, on the North Right of Way of Interstate 80 at Lodi Brook, Lodi, New Jersey (LJ077), was conducted during 1988. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 5 refs., 3 figs., 3 tabs

  16. Results of the radiological survey at the property at Main Street and Highway 46, Lodi, New Jersey (LJ074)

    International Nuclear Information System (INIS)

    Foley, R.D.; Carrier, R.F.; Floyd, L.M.; Crutcher, J.W.

    1989-09-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurements of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site located at the intersection of Main Street and Highway 46, Lodi, New Jersey (LJ074), was conducted during 1987. While some radiological measurements taken at the vacant lot at the intersection of Main Street and Highway 46 were greater than background levels typically encountered in the northern New Jersey area, no radiation levels nor radionuclide concentrations exceeded the applicable DOE criteria. The survey results demonstrate that the radiological condition of this property conforms to DOE guidelines for remedial action. 4 refs., 5 figs., 3 tabs

  17. Results of the radiological survey at the Napp Chemical Company, 199 Main Street, Lodi, New Jersey (LJ076)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Carrier, R.F.

    1989-11-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, the Napp Chemical Company, 199 Main Street, Lodi, New Jersey (LJ076), was conducted during 1987. Results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions were not significantly different from normal background levels in the northern New Jersey area. 4 refs., 8 figs., 3 tabs

  18. Towards the Irving-Kirkwood limit of the mechanical stress tensor

    Science.gov (United States)

    Smith, E. R.; Heyes, D. M.; Dini, D.

    2017-06-01

    The probability density functions (PDFs) of the local measure of pressure as a function of the sampling volume are computed for a model Lennard-Jones (LJ) fluid using the Method of Planes (MOP) and Volume Averaging (VA) techniques. This builds on the study of Heyes, Dini, and Smith [J. Chem. Phys. 145, 104504 (2016)] which only considered the VA method for larger subvolumes. The focus here is typically on much smaller subvolumes than considered previously, which tend to the Irving-Kirkwood limit where the pressure tensor is defined at a point. The PDFs from the MOP and VA routes are compared for cubic subvolumes, V =ℓ3. Using very high grid-resolution and box-counting analysis, we also show that any measurement of pressure in a molecular system will fail to exactly capture the molecular configuration. This suggests that it is impossible to obtain the pressure in the Irving-Kirkwood limit using the commonly employed grid based averaging techniques. More importantly, below ℓ ≈3 in LJ reduced units, the PDFs depart from Gaussian statistics, and for ℓ =1.0 , a double peaked PDF is observed in the MOP but not VA pressure distributions. This departure from a Gaussian shape means that the average pressure is not the most representative or common value to arise. In addition to contributing to our understanding of local pressure formulas, this work shows a clear lower limit on the validity of simply taking the average value when coarse graining pressure from molecular (and colloidal) systems.

  19. Phase-coexistence simulations of fluid mixtures by the Markov Chain Monte Carlo method using single-particle models

    KAUST Repository

    Li, Jun

    2013-09-01

    We present a single-particle Lennard-Jones (L-J) model for CO2 and N2. Simplified L-J models for other small polyatomic molecules can be obtained following the methodology described herein. The phase-coexistence diagrams of single-component systems computed using the proposed single-particle models for CO2 and N2 agree well with experimental data over a wide range of temperatures. These diagrams are computed using the Markov Chain Monte Carlo method based on the Gibbs-NVT ensemble. This good agreement validates the proposed simplified models. That is, with properly selected parameters, the single-particle models have similar accuracy in predicting gas-phase properties as more complex, state-of-the-art molecular models. To further test these single-particle models, three binary mixtures of CH4, CO2 and N2 are studied using a Gibbs-NPT ensemble. These results are compared against experimental data over a wide range of pressures. The single-particle model has similar accuracy in the gas phase as traditional models although its deviation in the liquid phase is greater. Since the single-particle model reduces the particle number and avoids the time-consuming Ewald summation used to evaluate Coulomb interactions, the proposed model improves the computational efficiency significantly, particularly in the case of high liquid density where the acceptance rate of the particle-swap trial move increases. We compare, at constant temperature and pressure, the Gibbs-NPT and Gibbs-NVT ensembles to analyze their performance differences and results consistency. As theoretically predicted, the agreement between the simulations implies that Gibbs-NVT can be used to validate Gibbs-NPT predictions when experimental data is not available. © 2013 Elsevier Inc.

  20. Temporal disconnectivity of the energy landscape in glassy systems

    Science.gov (United States)

    Lempesis, Nikolaos; Boulougouris, Georgios C.; Theodorou, Doros N.

    2013-03-01

    An alternative graphical representation of the potential energy landscape (PEL) has been developed and applied to a binary Lennard-Jones glassy system, providing insight into the unique topology of the system's potential energy hypersurface. With the help of this representation one is able to monitor the different explored basins of the PEL, as well as how - and mainly when - subsets of basins communicate with each other via transitions in such a way that details of the prior temporal history have been erased, i.e., local equilibration between the basins in each subset has been achieved. In this way, apart from detailed information about the structure of the PEL, the system's temporal evolution on the PEL is described. In order to gather all necessary information about the identities of two or more basins that are connected with each other, we consider two different approaches. The first one is based on consideration of the time needed for two basins to mutually equilibrate their populations according to the transition rate between them, in the absence of any effect induced by the rest of the landscape. The second approach is based on an analytical solution of the master equation that explicitly takes into account the entire explored landscape. It is shown that both approaches lead to the same result concerning the topology of the PEL and dynamical evolution on it. Moreover, a "temporal disconnectivity graph" is introduced to represent a lumped system stemming from the initial one. The lumped system is obtained via a specially designed algorithm [N. Lempesis, D. G. Tsalikis, G. C. Boulougouris, and D. N. Theodorou, J. Chem. Phys. 135, 204507 (2011), 10.1063/1.3663207]. The temporal disconnectivity graph provides useful information about both the lumped and the initial systems, including the definition of "metabasins" as collections of basins that communicate with each other via transitions that are fast relative to the observation time. Finally, the two examined

  1. lJ

    African Journals Online (AJOL)

    1974-06-15

    Jun 15, 1974 ... a particular abnormality necessitates treatment. Strabismus is diagnosed ... Paralysis of movement of the extra-ocular muscles may indicate involvement ... such as pigmentary dystrophy, vessel attenuation more marked in the ...

  2. More Appropriate Information Systems and Services for the Social Scientist: Time to Put Our Findings to Work. A review of: Line, Maurice B. “The Information Uses and Needs of Social Scientists: An Overview of INFROSS.” Aslib Proceedings 23.8 (1971: 412‐34. Rpt. in Lines of Thought: Selected Papers. Ed. L.J. Anthony. London: Bingley, 1988. 45‐66.

    Directory of Open Access Journals (Sweden)

    R. Laval Hunsucker

    2007-12-01

    Full Text Available Objective – The study reported in this article was conceived in order to answer a question of very large scope: What are the information systems and services requirements of social scientists? Inherent in this question was the correlative question: How do social scientists tend to use such systems and services, and what resources and information access approaches do they by choice employ? The choice for such an approach was well‐considered, given that 1 there were at the time almost no research results available in this area; 2 the investigators feared that approaches developed earlier for the natural sciences and technology would be uncritically adopted for the social sciences as well; and 3 “the social science information system was developing anyway, and if it was to develop in appropriate ways, some guidance had to be provided quickly” (412. The Investigation into Information Requirements of the Social Sciences (INFROSS project team believed that there was “no point” (412 in embarking first on a series of more narrowly focused studies. The express intention was to derive findings that would be usable “for the improvement of information systems, or for the design of new ones” (414. For more on the project's conceptual underpinnings, see Line’s “Information Requirements.” Design – Exploratory study employing both quantitative and qualitative approaches over a period of three and a half years, beginning in the autumn of 1967.Setting – The whole of the United Kingdom. The project was funded by that country’s Office for Scientific and Technical Information (OSTI, which had been established in 1965.Subjects – Almost 1,100 randomly selected academic social science researchers, plus a substantial number of government socialscience researchers and social science “practitioners” (“college of education lecturers, schoolteachers, and individuals in social work and welfare” [413]. For the purposes of the study, the

  3. A method of integration of atomistic simulations and continuum mechanics by collecting of dynamical systems with dimensional reduction

    International Nuclear Information System (INIS)

    Kaczmarek, J.

    2002-01-01

    Elementary processes responsible for phenomena in material are frequently related to scale close to atomic one. Therefore atomistic simulations are important for material sciences. On the other hand continuum mechanics is widely applied in mechanics of materials. It seems inevitable that both methods will gradually integrate. A multiscale method of integration of these approaches called collection of dynamical systems with dimensional reduction is introduced in this work. The dimensional reduction procedure realizes transition between various scale models from an elementary dynamical system (EDS) to a reduced dynamical system (RDS). Mappings which transform variables and forces, skeletal dynamical system (SDS) and a set of approximation and identification methods are main components of this procedure. The skeletal dynamical system is a set of dynamical systems parameterized by some constants and has variables related to the dimensionally reduced model. These constants are identified with the aid of solutions of the elementary dynamical system. As a result we obtain a dimensionally reduced dynamical system which describes phenomena in an averaged way in comparison with the EDS. Concept of integration of atomistic simulations with continuum mechanics consists in using a dynamical system describing evolution of atoms as an elementary dynamical system. Then, we introduce a continuum skeletal dynamical system within the dimensional reduction procedure. In order to construct such a system we have to modify a continuum mechanics formulation to some degree. Namely, we formalize scale of averaging for continuum theory and as a result we consider continuum with finite-dimensional fields only. Then, realization of dimensional reduction is possible. A numerical example of realization of the dimensional reduction procedure is shown. We consider a one dimensional chain of atoms interacting by Lennard-Jones potential. Evolution of this system is described by an elementary

  4. Detailed balance method for chemical potential determination in Monte Carlo and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Fay, P.J.; Ray, J.R.; Wolf, R.J.

    1994-01-01

    We present a new, nondestructive, method for determining chemical potentials in Monte Carlo and molecular dynamics simulations. The method estimates a value for the chemical potential such that one has a balance between fictitious successful creation and destruction trials in which the Monte Carlo method is used to determine success or failure of the creation/destruction attempts; we thus call the method a detailed balance method. The method allows one to obtain estimates of the chemical potential for a given species in any closed ensemble simulation; the closed ensemble is paired with a ''natural'' open ensemble for the purpose of obtaining creation and destruction probabilities. We present results for the Lennard-Jones system and also for an embedded atom model of liquid palladium, and compare to previous results in the literature for these two systems. We are able to obtain an accurate estimate of the chemical potential for the Lennard-Jones system at higher densities than reported in the literature

  5. Isomorph invariance of Couette shear flows simulated by the SLLOD equations of motion

    DEFF Research Database (Denmark)

    Separdar, Leila; Bailey, Nicholas; Schrøder, Thomas

    2013-01-01

    fluctuations of virial and potential energy. Such systems have good isomorphs (curves in the thermodynamic phase diagram along which structural, dynamical, and some thermodynamic quantities are invariant when expressed in reduced units). The SLLOD equations of motion were used to simulate Couette shear flows......Non-equilibrium molecular dynamics simulations were performed to study the thermodynamic, structural, and dynamical properties of the single-component Lennard-Jones and the Kob-Andersen binary Lennard-Jones liquids. Both systems are known to have strong correlations between equilibrium thermal...... of the two systems. We show analytically that these equations are isomorph invariant provided the reduced strain rate is fixed along the isomorph. Since isomorph invariance is generally only approximate, a range of strain rates were simulated to test for the predicted invariance, covering both the linear...

  6. Analysis of two potential long-distance signaling molecules, LjCLE-RS1/2 and jasmonic acid, in a hypernodulating mutant too much love.

    Science.gov (United States)

    Magori, Shimpei; Kawaguchi, Masayoshi

    2010-04-01

    Legume plants tightly control the number and development of root nodules. This is partly regulated by a long-distance signaling known as auto-regulation of nodulation (AON). AON signaling involves at least two potential long-distance signals: root-derived signal and shoot-derived signal. However, their molecular characteristics and the mode of action remain unclear. In our recent study, we isolated a novel Lotus japonicus hypernodulating mutant too much love (tml). Based on several grafting experiments, we concluded that its causative gene TML functions as a receptor of the shoot-derived signal. This finding prompted us to ask how the candidates of the long-distance signal molecules, LjCLE-RS1/2 and jasmonic acid (JA), are affected in tml mutants. Expression analysis revealed that rapid induction of LjCLE-RS1/2 upon rhizobial inoculation is still intact in tml, supporting that TML plays a role in reception of the shoot-derived signal but not in generation of the root-derived signal. Furthermore, physiological analysis showed that JA, a candidate of the shoot-derived signal, can suppress tml hypernodulation. Therefore, contrary to the previous report, JA might not be a component of AON signaling.

  7. Statistical mechanical calculations of molecular pair correlation functions and scattering intensities

    International Nuclear Information System (INIS)

    Bertagnolli, H.

    1978-01-01

    For the case of special molecular models representing the acetonitrile molecule the expansion coefficients of the molecular par distribution function are calculated by use of pertubation theory. These results are used to get theoretical access to scattering intensities in the frame of several approximations. The first model describes the molecule by three hard spheres and uses a hard sphere liquid as reference. In the second cast the calculations are based on an anisotropic Lennard-Jones potential by application of a model of overlapping ellipsoids and by use of a Lennard-Jones liquid as a reference system. In the third model dipolar attractive forces are taken into account with an anisotropic hard-sphere liquid as a reference. In the third model dipolar attractive forces are taken into account with an anisotropic hard-sphere liquid as a reference. Finally all the calculations with different intermolecular potentials are compared with neutron scattering experiments. (orig.) 891 HK [de

  8. On the equivalence of continuum and lattice models for fluids

    International Nuclear Information System (INIS)

    Panagiotopoulos, Athanassios Z.

    2000-01-01

    It was demonstrated that finely discretized lattice models for fluids with particles interacting via Lennard-Jones or exponential-6 potentials have essentially identical thermodynamic and structural properties to their continuum counterparts. Grand canonical histogram reweighting Monte Carlo calculations were performed for systems with repulsion exponents between 11 and 22. Critical parameters were determined from mixed-field finite-size scaling methods. Numerical equivalence of lattice and continuous space models, within simulation uncertainties, was observed for lattices with ratio of particle diameter σ to grid spacing of 10. The lattice model calculations were more efficient computationally by factors between 10 and 20. It was also shown that Lennard-Jones and exponential-6 based models with identical critical properties can be constructed by appropriate choice of the repulsion exponent. (c) 2000 American Institute of Physics

  9. Impact of wall potential on the fluid-wall interaction in a cylindrical capillary and a generalized Kelvin equation

    International Nuclear Information System (INIS)

    Jakubov, T.S.; Mainwaring, D.E.

    2006-01-01

    In the present work a generalized Kelvin equation for a fluid confined in thick-walled cylindrical capillary is developed. This has been accomplished by including the potential energy function for interaction between a solid wall of a capillary and a confined fluid into the Kelvin equation. Using the Lennard-Jones 12-6 potential, an explicit form of the potential energy functions as expressed by hypergeometrical functions have been derived-firstly, for the interaction between a solid wall and a test atom placed at an arbitrary point in a long open-end capillary, and thereafter for the body-body interaction between the solid wall and a confined Lennard-Jones fluid. Further, this generalized Kelvin equation has been applied to detailed description hysteresis phenomena in such capillaries. All numerical calculations have been carried out for the model argon-graphite system at 90 K

  10. Kinetic energy of solid and liquid para-hydrogen: a path integral Monte Carlo simulation

    International Nuclear Information System (INIS)

    Zoppi, M.; Neumann, M.

    1992-01-01

    The translational (center of mass) kinetic energy of solid and liquid para-hydrogen have been recently measured by means of Deep Inelastic Neutron Scattering. We have evaluated the same quantity, in similar thermodynamic conditions, by means of Path Integral Monte Carlo computer simulation, modelling the system as composed of a set of spherical molecules interacting through a pairwise additive Lennard-Jones potential. In spite of the crude approximations on the interaction potential, the agreement is excellent. The pressure was also computed by means of the same simulations. This quantity, compared with the equation of state for solid para-hydrogen given by Driessen and Silvera, gives an agreement of a lesser quality and a negative value for the liquid state. We attribute this discrepancy to the limitations of the Lennard-Jones potential. (orig.)

  11. Microcanonical Monte Carlo approach for computing melting curves by atomistic simulations

    OpenAIRE

    Davis, Sergio; Gutiérrez, Gonzalo

    2017-01-01

    We report microcanonical Monte Carlo simulations of melting and superheating of a generic, Lennard-Jones system starting from the crystalline phase. The isochoric curve, the melting temperature $T_m$ and the critical superheating temperature $T_{LS}$ obtained are in close agreement (well within the microcanonical temperature fluctuations) with standard molecular dynamics one-phase and two-phase methods. These results validate the use of microcanonical Monte Carlo to compute melting points, a ...

  12. Molecular dynamics simulations of the penetration lengths: application within the fluctuation theory for diffusion coefficients

    DEFF Research Database (Denmark)

    Galliero, Guillaume; Medvedev, Oleg; Shapiro, Alexander

    2005-01-01

    A 322 (2004) 151). In the current study, a fast molecular dynamics scheme has been developed to determine the values of the penetration lengths in Lennard-Jones binary systems. Results deduced from computations provide a new insight into the concept of penetration lengths. It is shown for four different...... fluctuation theory and molecular dynamics scheme exhibit consistent trends and average deviations from experimental data around 10-20%. (c) 2004 Elsevier B.V. All rights reserved....

  13. First order phase transition of expanding matter and its fragmentation

    International Nuclear Information System (INIS)

    Chikazumi, Shinpei; Iwamoto, Akira

    2002-01-01

    Using an expanding matter model with a Lennard-Jones potential, the instability of the expanding system is investigated. The pressure, the temperature, and the density fluctuations are calculated as functions of density during the time evolution of the expanding matter, which are compared to the coexistence curve calculated by the Gibbs ensemble. The expanding matter undergoes the first order phase transition in the limit of the quasistatic expansion. The resultant fragment mass distributions are also investigated. (author)

  14. Molecular dynamics simulation of a chemical reaction

    International Nuclear Information System (INIS)

    Gorecki, J.; Gryko, J.

    1988-06-01

    Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs

  15. Properties of water along the liquid-vapor coexistence curve via molecular dynamics simulations using the polarizable TIP4P-QDP-LJ water model.

    Science.gov (United States)

    Bauer, Brad A; Patel, Sandeep

    2009-08-28

    We present an extension of the TIP4P-QDP model, TIP4P-QDP-LJ, that is designed to couple changes in repulsive and dispersive nonbond interactions to changes in polarizability. Polarizability is intimately related to the dispersion component of classical force field models of interactions, and we explore the effect of incorporating this connection explicitly on properties along the liquid-vapor coexistence curve of pure water. Parametrized to reproduce condensed-phase liquid water properties at 298 K, the TIP4P-QDP-LJ model predicts density, enthalpy of vaporization, self-diffusion constant, and the dielectric constant at ambient conditions to about the same accuracy as TIP4P-QDP but shows remarkable improvement in reproducing the liquid-vapor coexistence curve. TIP4P-QDP-LJ predicts critical constants of T(c)=623 K, rho(c)=0.351 g/cm(3), and P(c)=250.9 atm, which are in good agreement with experimental values of T(c)=647.1 K, rho(c)=0.322 g/cm(3), and P(c)=218 atm, respectively. Applying a scaling factor correction (obtained by fitting the experimental vapor-liquid equilibrium data to the law of rectilinear diameters using a three-term Wegner expansion) the model predicts critical constants (T(c)=631 K and rho(c)=0.308 g/cm(3)). Dependence of enthalpy of vaporization, self-diffusion constant, surface tension, and dielectric constant on temperature are shown to reproduce experimental trends. We also explore the interfacial potential drop across the liquid-vapor interface for the temperatures studied. The interfacial potential demonstrates little temperature dependence at lower temperatures (300-450 K) and significantly enhanced (exponential) dependence at elevated temperatures. Terms arising from the decomposition of the interfacial potential into dipole and quadrupole contributions are shown to monotonically approach zero as the temperature approaches the critical temperature. Results of this study suggest that self-consistently treating the coupling of phase

  16. rLj-RGD3, a Novel Recombinant Toxin Protein from Lampetra japonica, Protects against Cerebral Reperfusion Injury Following Middle Cerebral Artery Occlusion Involving the Integrin-PI3K/Akt Pathway in Rats.

    Directory of Open Access Journals (Sweden)

    Qian Lu

    Full Text Available The RGD-toxin protein Lj-RGD3 is a naturally occurring 118 amino acid peptide that can be obtained from the salivary gland of the Lampetra japonica fish. This unique peptide contains 3 RGD (Arg-Gly-Asp motifs in its primary structure. Lj-RGD3 is available in recombinant form (rLj-RGD3 and can be produced in large quantities using DNA recombination techniques. The pharmacology of the three RGD motif-containing peptides has not been studied. This study investigated the protective effects of rLj-RGD3, a novel polypeptide, against ischemia/reperfusion-induced damage to the brain caused by middle cerebral artery occlusion (MCAO in a rat stroke model. We also explored the mechanism by which rLj-RGD3 acts by measuring protein and mRNA expression levels, with an emphasis on the FAK and integrin-PI3K/Akt anti-apoptosis pathways.rLj-RGD3 was obtained from the buccal secretions of Lampetra japonica using gene recombination technology. Sprague Dawley (SD rats were randomly divided into the following seven groups: a sham group; a vehicle-treated (VT group; 100.0 μg·kg-1, 50.0 μg·kg-1 and 25.0 μg·kg-1 dose rLj-RGD3 groups; and two positive controls, including 1.5 mg·kg-1 Edaravone (ED and 100.0 μg·kg-1 Eptifibatide (EP. MCAO was induced using a model consisting of 2 h of ischemia and 24 h of reperfusion. Behavioral changes were observed in the normal and operation groups after focal cerebral ischemia/reperfusion was applied. In addition, behavioral scores were evaluated at 4 and 24 h after reperfusion. Brain infarct volumes were determined based on 2,3,5-triphenyltetrazolium chloride (TTC staining. Pathological changes in brain tissues were observed using hematoxylin and eosin (H&E staining. Moreover, neuronal apoptosis was detected using terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick-end labeling (TUNEL assays. We determined the expression levels of focal adhesion kinase (FAK, phosphatidyl inositol 3-kinase (PI3K, protein kinase B

  17. Molecular dynamics study of vacancy-like defects in a model glass : static behaviour

    Science.gov (United States)

    Delaye, J. M.; Limoge, Y.

    1993-10-01

    The possibility of defining vacancy-like defects in a Lennard-Jones glass is searched for in a systematic manner. Considering different relaxation levels of the same system, as well as different external pressures, we use a Molecular Dynamics simulation method, to study at constant volume or external pressure, the relaxation of a “piece” of glass, after the sudden removal of an atom. Three typical kinds of behaviour can be observed: the persistence of the empty volume left by the missing atom, its migration by clearly identifiable atomic jumps and the dissipation “on the spot”. A careful analysis of the probabilities of these three kinds of behaviour shows that a meaningful definition of vacancy-like defects can be given in a Lennard-Jones glass. Dans cet article, nous nous penchons de façon systématique sur la possibilité de définir des défauts de type lacunaire dans un verre de Lennard-Jones, à différents niveaux de relaxation et de pression, par une méthode de simulation numérique en dynamique moléculaire à volume ou à pression constants. Le défaut est créé en supprimant un atome et en suivant la réponse du système. Nous observons trois comportements typiques : la persistance sur place du “trou” laissé par l'atome supprimé, sa migration par des sauts atomiques clairement identifiés et enfin sa dissipation sur place. Une analyse détaillée de ces trois comportements montre qu'il est possible dans un verre de Lennard-Jones de définir des défauts de type lacunaire.

  18. Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids

    Science.gov (United States)

    Pádua, Agílio A. H.

    2017-05-01

    One important development in interaction potential models, or atomistic force fields, for molecular simulation is the inclusion of explicit polarisation, which represents the induction effects of charged or polar molecules on polarisable electron clouds. Polarisation can be included through fluctuating charges, induced multipoles, or Drude dipoles. This work uses Drude dipoles and is focused on room-temperature ionic liquids, for which fixed-charge models predict too slow dynamics. The aim of this study is to devise a strategy to adapt existing non-polarisable force fields upon addition of polarisation, because induction was already contained to an extent, implicitly, due to parametrisation against empirical data. Therefore, a fraction of the van der Waals interaction energy should be subtracted so that the Lennard-Jones terms only account for dispersion and the Drude dipoles for induction. Symmetry-adapted perturbation theory is used to resolve the dispersion and induction terms in dimers and to calculate scaling factors to reduce the Lennard-Jones terms from the non-polarisable model. Simply adding Drude dipoles to an existing fixed-charge model already improves the prediction of transport properties, increasing diffusion coefficients, and lowering the viscosity. Scaling down the Lennard-Jones terms leads to still faster dynamics and densities that match experiment extremely well. The concept developed here improves the overall prediction of density and transport properties and can be adapted to other models and systems. In terms of microscopic structure of the ionic liquids, the inclusion of polarisation and the down-scaling of Lennard-Jones terms affect only slightly the ordering of the first shell of counterions, leading to small decreases in coordination numbers. Remarkably, the effect of polarisation is major beyond first neighbours, significantly weakening spatial correlations, a structural effect that is certainly related to the faster dynamics of

  19. A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties

    Science.gov (United States)

    Fu, Chia-Chun; Kulkarni, Pandurang M.; Scott Shell, M.; Gary Leal, L.

    2012-10-01

    Coarse-graining (CG) techniques have recently attracted great interest for providing descriptions at a mesoscopic level of resolution that preserve fluid thermodynamic and transport behaviors with a reduced number of degrees of freedom and hence less computational effort. One fundamental question arises: how well and to what extent can a "bottom-up" developed mesoscale model recover the physical properties of a molecular scale system? To answer this question, we explore systematically the properties of a CG model that is developed to represent an intermediate mesoscale model between the atomistic and continuum scales. This CG model aims to reduce the computational cost relative to a full atomistic simulation, and we assess to what extent it is possible to preserve both the thermodynamic and transport properties of an underlying reference all-atom Lennard-Jones (LJ) system. In this paper, only the thermodynamic properties are considered in detail. The transport properties will be examined in subsequent work. To coarse-grain, we first use the iterative Boltzmann inversion (IBI) to determine a CG potential for a (1-ϕ)N mesoscale particle system, where ϕ is the degree of coarse-graining, so as to reproduce the radial distribution function (RDF) of an N atomic particle system. Even though the uniqueness theorem guarantees a one to one relationship between the RDF and an effective pairwise potential, we find that RDFs are insensitive to the long-range part of the IBI-determined potentials, which provides some significant flexibility in further matching other properties. We then propose a reformulation of IBI as a robust minimization procedure that enables simultaneous matching of the RDF and the fluid pressure. We find that this new method mainly changes the attractive tail region of the CG potentials, and it improves the isothermal compressibility relative to pure IBI. We also find that there are optimal interaction cutoff lengths for the CG system, as a function of

  20. Approaches to Learning or Levels of Processing: What Did Marton and Säljö (1976a) Really Say? the Legacy of the Work of the Göteborg Group in the 1970s

    Science.gov (United States)

    Richardson, John T.

    2015-01-01

    Marton and Säljö ("Br J Educ Psychol" 46:4-11, 1976a) described deep-level and surface-level processing in experiments in which students read and recalled academic texts. They did not discuss whether levels of processing had any counterparts in students' everyday studies. However, their article is often credited as the source of the…

  1. On the equilibrium contact angle of sessile liquid drops from molecular dynamics simulations.

    Science.gov (United States)

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

    2018-04-28

    We present a new methodology to estimate the contact angles of sessile drops from molecular simulations by using the Gaussian convolution method of Willard and Chandler [J. Phys. Chem. B 114, 1954-1958 (2010)] to calculate the coarse-grained density from atomic coordinates. The iso-density contour with average coarse-grained density value equal to half of the bulk liquid density is identified as the average liquid-vapor (LV) interface. Angles between the unit normal vectors to the average LV interface and unit normal vector to the solid surface, as a function of the distance normal to the solid surface, are calculated. The cosines of these angles are extrapolated to the three-phase contact line to estimate the sessile drop contact angle. The proposed methodology, which is relatively easy to implement, is systematically applied to three systems: (i) a Lennard-Jones (LJ) drop on a featureless LJ 9-3 surface; (ii) an SPC/E water drop on a featureless LJ 9-3 surface; and (iii) an SPC/E water drop on a graphite surface. The sessile drop contact angles estimated with our methodology for the first two systems are shown to be in good agreement with the angles predicted from Young's equation. The interfacial tensions required for this equation are computed by employing the test-area perturbation method for the corresponding planar interfaces. Our findings suggest that the widely adopted spherical-cap approximation should be used with caution, as it could take a long time for a sessile drop to relax to a spherical shape, of the order of 100 ns, especially for water molecules initiated in a lattice configuration on a solid surface. But even though a water drop can take a long time to reach the spherical shape, we find that the contact angle is well established much faster and the drop evolves toward the spherical shape following a constant-contact-angle relaxation dynamics. Making use of this observation, our methodology allows a good estimation of the sessile drop contact

  2. Continuum modeling investigation of gigahertz oscillators based on a C60 fullerene inside cyclic peptide nanotubes

    Science.gov (United States)

    Sadeghi, F.; Ansari, R.; Darvizeh, M.

    2016-02-01

    Research concerning the fabrication of nano-oscillators with operating frequency in the gigahertz (GHz) range has become a focal point in recent years. In this paper, a new type of GHz oscillators is introduced based on a C60 fullerene inside a cyclic peptide nanotube (CPN). To study the dynamic behavior of such nano-oscillators, using the continuum approximation in conjunction with the 6-12 Lennard-Jones (LJ) potential function, analytical expressions are derived to determine the van der Waals (vdW) potential energy and interaction force between the two interacting molecules. Employing Newton's second law, the equation of motion is solved numerically to arrive at the telescopic oscillatory motion of a C60 fullerene inside CPNs. It is shown that the fullerene molecule exhibits different kinds of oscillation inside peptide nanotubes which are sensitive to the system parameters. Furthermore, for the precise evaluation of the oscillation frequency, a novel semi-analytical expression is proposed based on the conservation of the mechanical energy principle. Numerical results are presented to comprehensively study the effects of the number of peptide units and initial conditions (initial separation distance and velocity) on the oscillatory behavior of C60 -CPN oscillators. It is found out that for peptide nanotubes comprised of one unit, the maximum achievable frequency is obtained when the inner core oscillates with respect to its preferred positions located outside the tube, while for other numbers of peptide units, such frequency is obtained when the inner core oscillates with respect to the preferred positions situated in the space between the two first or the two last units. It is further found out that four peptide units are sufficient to obtain the optimal frequency.

  3. Light hydrogen isotopes in the single - walled carbon nano tube

    International Nuclear Information System (INIS)

    Khugaev, A.V.; Sultanov, R.A.; Guster, D.

    2007-01-01

    Full text: Progress of our understanding of the molecular hydrogen behavior in the nano tube interior open an intriguing possibility for the applications of these knowledge's to the solution of the hydrogen storage problem and light isotopes gas selectivity. That can strongly change the situation at the energy production in the world and completely change our civil life. These investigations underline the influence of the quantum effects on the properties of molecular hydrogen in the nano tube interior and it leads to the pure quantum-mechanical reformulation of the problem for the hydrogen behavior inside carbon nano tube as a problem of molecular quantum system behavior in the external field induced by the regular nano tube surface. In the present paper the molecular hydrogen behavior in the carbon nano tube was considered in the simple quantum mechanical manner. The main attention was paid to the investigation of the quantum sieving selectivity in the dependence of nano tube composition, radius and symmetry properties. For the interaction potential between hydrogen and nano tube surface was taken some phenomenological LJ(12,6) - (Lennard - Jones) potential and the external field induced by the nano tube in its interior is considered as a simple sum over the all nano tube carbon atoms. Influence of the structure of rotation (vibration) spectrum of the energy levels of diatomic molecules, such as H 2 , HD and D 2 on the final results and finite size of the nano tube along the axis of symmetry, its boundary effects is discussed in details. Thermal oscillations of nano tube surface were considered separately in the dependence of the temperature gradient along of the axis of symmetry

  4. Results of the radiological survey at the Firemen's Memorial Park and Fire Hall No. 2, Garibaldi Avenue and Kennedy Drive, Lodi, New Jersey (LJ066)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.; Crutcher, J.W.

    1989-08-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of the gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, the Firemen's Memorial Park and Fire Hall number sign 2, Garibaldi Avenue and Kennedy Drive, Lodi, New Jersey (LJ066) was conducted during 1987. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 4 refs., 10 figs., 3 tabs

  5. Results of the radiological survey of the Saddle River's East Bank, from State Highway 46 to the River's confluence with Lodi Brook, Lodi, New Jersey (LJ083)

    International Nuclear Information System (INIS)

    Foley, R.D.; Floyd, L.M.

    1989-11-01

    Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, the Saddle River's East Bank, from State Highway 46 to the River's Confluence with Lodi Brook, Lodi, New Jersey (LJ083), was conducted during 1988. Results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions were not significantly different from normal background levels in the northern New Jersey area. 4 refs., 2 figs., 3 tabs

  6. Structural behavior of supercritical fluids under confinement

    Science.gov (United States)

    Ghosh, Kanka; Krishnamurthy, C. V.

    2018-01-01

    The existence of the Frenkel line in the supercritical regime of a Lennard-Jones (LJ) fluid shown through molecular dynamics (MD) simulations initially and later corroborated by experiments on argon opens up possibilities of understanding the structure and dynamics of supercritical fluids in general and of the Frenkel line in particular. The location of the Frenkel line, which demarcates two distinct physical states, liquidlike and gaslike within the supercritical regime, has been established through MD simulations of the velocity autocorrelation (VACF) and radial distribution function (RDF). We, in this article, explore the changes in the structural features of supercritical LJ fluid under partial confinement using atomistic walls. The study is carried out across the Frenkel line through a series of MD simulations considering a set of thermodynamics states in the supercritical regime (P =5000 bar, 240 K ≤T ≤1500 K ) of argon well above the critical point. Confinement is partial, with atomistic walls located normal to z and extending to "infinity" along the x and y directions. In the "liquidlike" regime of the supercritical phase, particles are found to be distributed in distinct layers along the z axis with layer spacing less than one atomic diameter and the lateral RDF showing amorphous-like structure for specific spacings (packing frustration) and non-amorphous-like structure for other spacings. Increasing the rigidity of the atomistic walls is found to lead to stronger layering and increased structural order. For confinement with reflective walls, layers are found to form with one atomic diameter spacing and the lateral RDF showing close-packed structure for the smaller confinements. Translational order parameter and excess entropy assessment confirms the ordering taking place for atomistic wall and reflective wall confinements. In the "gaslike" regime of the supercritical phase, particle distribution along the spacing and the lateral RDF exhibit features

  7. JCZS: An Intermolecular Potential Database for Performing Accurate Detonation and Expansion Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Baer, M.R.; Hobbs, M.L.; McGee, B.C.

    1998-11-03

    Exponential-13,6 (EXP-13,6) potential pammeters for 750 gases composed of 48 elements were determined and assembled in a database, referred to as the JCZS database, for use with the Jacobs Cowperthwaite Zwisler equation of state (JCZ3-EOS)~l) The EXP- 13,6 force constants were obtained by using literature values of Lennard-Jones (LJ) potential functions, by using corresponding states (CS) theory, by matching pure liquid shock Hugoniot data, and by using molecular volume to determine the approach radii with the well depth estimated from high-pressure isen- tropes. The JCZS database was used to accurately predict detonation velocity, pressure, and temperature for 50 dif- 3 Accurate predictions were also ferent explosives with initial densities ranging from 0.25 glcm3 to 1.97 g/cm . obtained for pure liquid shock Hugoniots, static properties of nitrogen, and gas detonations at high initial pressures.

  8. Classical square-plus-triangle well fluid

    International Nuclear Information System (INIS)

    Boghdadi, M.

    1984-01-01

    A simplified model for the intermolecular-potential function which consists of a hard core and a square-plus-triangle well is proposed. The square width is taken to be lambda 1 -1 and the triangle width is lambda 2 -lambda 1 , where the diameter of the molecules is assumed to be epsilon. Under the restriction that the area under the potential well should be equal to 0.5epsilon, which has its own reason, it is shown that the appropriate choice of lambda 1 and lambda 2 that best mimics the Lennard-Jones (LJ) cut-off results is 1.15 and 1.85 respectively. With this choice for lambda 1 and lambda 2 , the proposed model is effective and satisfactory

  9. What Is a Simple Liquid?

    Directory of Open Access Journals (Sweden)

    Trond S. Ingebrigtsen

    2012-03-01

    Full Text Available This paper is an attempt to identify the real essence of simplicity of liquids in John Locke’s understanding of the term. Simple liquids are traditionally defined as many-body systems of classical particles interacting via radially symmetric pair potentials. We suggest that a simple liquid should be defined instead by the property of having strong correlations between virial and potential-energy equilibrium fluctuations in the NVT ensemble. There is considerable overlap between the two definitions, but also some notable differences. For instance, in the new definition simplicity is not a direct property of the intermolecular potential because a liquid is usually only strongly correlating in part of its phase diagram. Moreover, not all simple liquids are atomic (i.e., with radially symmetric pair potentials and not all atomic liquids are simple. The main part of the paper motivates the new definition of liquid simplicity by presenting evidence that a liquid is strongly correlating if and only if its intermolecular interactions may be ignored beyond the first coordination shell (FCS. This is demonstrated by NVT simulations of the structure and dynamics of several atomic and three molecular model liquids with a shifted-forces cutoff placed at the first minimum of the radial distribution function. The liquids studied are inverse power-law systems (r^{-n} pair potentials with n=18,6,4, Lennard-Jones (LJ models (the standard LJ model, two generalized Kob-Andersen binary LJ mixtures, and the Wahnstrom binary LJ mixture, the Buckingham model, the Dzugutov model, the LJ Gaussian model, the Gaussian core model, the Hansen-McDonald molten salt model, the Lewis-Wahnstrom ortho-terphenyl model, the asymmetric dumbbell model, and the single-point charge water model. The final part of the paper summarizes properties of strongly correlating liquids, emphasizing that these are simpler than liquids in general. Simple liquids, as defined here, may be

  10. Long-range interaction of anisotropic systems

    KAUST Repository

    Zhang, Junyi

    2015-02-01

    The first-order electrostatic interaction energy between two far-apart anisotropic atoms depends not only on the distance between them but also on their relative orientation, according to Rayleigh-Schrödinger perturbation theory. Using the first-order interaction energy and the continuum model, we study the long-range interaction between a pair of parallel pristine graphene sheets at zero temperature. The asymptotic form of the obtained potential density, &epsi:(D) &prop: ?D ?3 ?O(D?4), is consistent with the random phase approximation and Lifshitz theory. Accordingly, neglectance of the anisotropy, especially the nonzero first-order interaction energy, is the reason why the widely used Lennard-Jones potential approach and dispersion corrections in density functional theory give a wrong asymptotic form ε(D) &prop: ?D?4. © EPLA, 2015.

  11. Long-range interaction of anisotropic systems

    KAUST Repository

    Zhang, Junyi; Schwingenschlö gl, Udo

    2015-01-01

    The first-order electrostatic interaction energy between two far-apart anisotropic atoms depends not only on the distance between them but also on their relative orientation, according to Rayleigh-Schrödinger perturbation theory. Using the first-order interaction energy and the continuum model, we study the long-range interaction between a pair of parallel pristine graphene sheets at zero temperature. The asymptotic form of the obtained potential density, &epsi:(D) &prop: ?D ?3 ?O(D?4), is consistent with the random phase approximation and Lifshitz theory. Accordingly, neglectance of the anisotropy, especially the nonzero first-order interaction energy, is the reason why the widely used Lennard-Jones potential approach and dispersion corrections in density functional theory give a wrong asymptotic form ε(D) &prop: ?D?4. © EPLA, 2015.

  12. Crustal thermal state and origin of silicic magma in Iceland: the case of Torfajökull, Ljósufjöll and Snæfellsjökull volcanoes

    Science.gov (United States)

    Martin, E.; Sigmarsson, O.

    2007-05-01

    Pleistocene and Holocene peralkaline rhyolites from Torfajökull (South Iceland Volcanic Zone) and Ljósufjöll central volcanoes and trachytes from Snæfellsjökull (Snæfellsnes Volcanic Zone) allow the assessment of the mechanism for silicic magma genesis as a function of geographical location and crustal geothermal gradient. The low δ18O (2.4‰) and low Sr concentration (12.2 ppm) measured in Torfajökull rhyolites are best explained by partial melting of hydrated metabasaltic crust followed by major fractionation of feldspar. In contrast, very high 87Sr/86Sr (0.70473) and low Ba (8.7 ppm) and Sr (1.2 ppm) concentrations measured in Ljósufjöll silicic lavas are best explained by fractional crystallisation and subsequent 87Rb decay. Snæfellsjökull trachytes are also generated by fractional crystallisation, with less than 10% crustal assimilation, as inferred from their δ18O. The fact that silicic magmas within, or close to, the rift zone are principally generated by crustal melting whereas those from off-rift zones are better explained by fractional crystallisation clearly illustrates the controlling influence of the thermal state of the crust on silicic magma genesis in Iceland.

  13. Communication: Simple liquids' high-density viscosity

    Science.gov (United States)

    Costigliola, Lorenzo; Pedersen, Ulf R.; Heyes, David M.; Schrøder, Thomas B.; Dyre, Jeppe C.

    2018-02-01

    This paper argues that the viscosity of simple fluids at densities above that of the triple point is a specific function of temperature relative to the freezing temperature at the density in question. The proposed viscosity expression, which is arrived at in part by reference to the isomorph theory of systems with hidden scale invariance, describes computer simulations of the Lennard-Jones system as well as argon and methane experimental data and simulation results for an effective-pair-potential model of liquid sodium.

  14. Effect of pairwise additivity on finite-temperature behavior of classical ideal gas

    Science.gov (United States)

    Shekaari, Ashkan; Jafari, Mahmoud

    2018-05-01

    Finite-temperature molecular dynamics simulations have been applied to inquire into the effect of pairwise additivity on the behavior of classical ideal gas within the temperature range of T = 250-4000 K via applying a variety of pair potentials and then examining the temperature dependence of a number of thermodynamical properties. Examining the compressibility factor reveals the most deviation from ideal-gas behavior for the Lennard-Jones system mainly due to the presence of both the attractive and repulsive terms. The systems with either attractive or repulsive intermolecular potentials are found to present no resemblance to real gases, but the most similarity to the ideal one as temperature rises.

  15. Chemical potential calculations in dense liquids using metadynamics

    Science.gov (United States)

    Perego, C.; Giberti, F.; Parrinello, M.

    2016-10-01

    The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to insert an extra particle in the system. In dense systems this method fails since the insertion probability is very low. In this paper we show that in a homogeneous fluid the insertion probability can be increased using metadynamics. We test our method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain efficiently converged results even when Widom's method fails.

  16. Communication: Simple liquids' high-density viscosity.

    Science.gov (United States)

    Costigliola, Lorenzo; Pedersen, Ulf R; Heyes, David M; Schrøder, Thomas B; Dyre, Jeppe C

    2018-02-28

    This paper argues that the viscosity of simple fluids at densities above that of the triple point is a specific function of temperature relative to the freezing temperature at the density in question. The proposed viscosity expression, which is arrived at in part by reference to the isomorph theory of systems with hidden scale invariance, describes computer simulations of the Lennard-Jones system as well as argon and methane experimental data and simulation results for an effective-pair-potential model of liquid sodium.

  17. Identifying Structural Flow Defects in Disordered Solids Using Machine-Learning Methods

    Science.gov (United States)

    Cubuk, E. D.; Schoenholz, S. S.; Rieser, J. M.; Malone, B. D.; Rottler, J.; Durian, D. J.; Kaxiras, E.; Liu, A. J.

    2015-03-01

    We use machine-learning methods on local structure to identify flow defects—or particles susceptible to rearrangement—in jammed and glassy systems. We apply this method successfully to two very different systems: a two-dimensional experimental realization of a granular pillar under compression and a Lennard-Jones glass in both two and three dimensions above and below its glass transition temperature. We also identify characteristics of flow defects that differentiate them from the rest of the sample. Our results show it is possible to discern subtle structural features responsible for heterogeneous dynamics observed across a broad range of disordered materials.

  18. Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling.

    Science.gov (United States)

    Fačkovec, B; Vanden-Eijnden, E; Wales, D J

    2015-07-28

    A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.

  19. Chaotic dynamics in dense fluids

    International Nuclear Information System (INIS)

    Posch, H.A.; Hoover, W.G.

    1987-09-01

    We present calculations of the full spectra of Lyapunov exponents for 8- and 32-particle systems with periodic boundary conditions and interacting with the repulsive part of a Lennard-Jones potential both in equilibrium and nonequilibrium steady states. Lyapunov characteristic exponents λ/sub n/ describe the mean exponential rates of divergence and convergence of neighbouring trajectories in phase-space. They are useful in characterizing the stochastic properties of a dynamical system. A new algorithm for their calculation is presented which incorporates ideas from control theory and constraint nonequilibrium molecular dynamics. 4 refs., 1 fig

  20. Algebraic relaxation of a time correlation function

    International Nuclear Information System (INIS)

    Srivastava, S.; Kumar, C.N.; Tankeshwar, K.

    2004-06-01

    A second order non-linear differential equation obtained from Mori's integro- differential equation is shown to transform to another form which provides algebraic decay to a time correlation function. Involved parameters in algebraic formula are related to exact properties of the corresponding correlation function. The model has been used to study a sol-gel system which is known, experimentally, to exhibit a power law decay to stress auto-correlation function. The expression obtained for the viscosity shows a logarithmic divergence at some critical value of the parameter. Some features of the model have also been tested using available information about Lennard-Jones fluids. (author)

  1. Solitons on H bonds in proteins

    DEFF Research Database (Denmark)

    d'Ovidio, F.; Bohr, H.G.; Lindgård, Per-Anker

    2003-01-01

    system shows that the solitons are spontaneously created and are stable and moving along the helix axis. A perturbation on one of the three H-bond lines forms solitons on the other H bonds as well. The robust solitary wave may explain very long-lived modes in the frequency range of 100 cm(-1) which...... are found in recent x-ray laser experiments. The dynamics parameters of the Toda lattice are in accordance with the usual Lennard-Jones parameters used for realistic H-bond potentials in proteins....

  2. Nucleation and droplet growth from supersaturated vapor at temperatures below the triple point temperature

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2016-01-01

    temperature Ttr.p. crystallizes via a liquid droplet is an example of Ostwald's step rule. The homogeneous nucleation in the supersaturated gas is not to a crystal, but to a liquid-like critical nucleus. We have for the first time performed constant energy (NVE) Molecular Dynamics (MD) of homogeneous...... nucleation without the use of a thermostat. The simulations of homogeneous nucleation in a Lennard-Jones system from supersaturated vapor at temperatures below Ttr.p. reveals that the nucleation to a liquid-like critical nucleus is initiated by a small cold cluster [S. Toxvaerd, J. Chem. Phys. \\textbf{143...

  3. Estimating the density-scaling exponent of a monatomic liquid from its pair potential

    DEFF Research Database (Denmark)

    Bøhling, Lasse; Bailey, Nicholas; Schrøder, Thomas

    2014-01-01

    This paper investigates two conjectures for calculating the density dependence of the density-scaling exponent γ of a single-component, pair-potential liquid with strong virial potential-energy correlations. The first conjecture gives an analytical expression for γ directly in terms of the pair...... potential. The second conjecture is a refined version of this involving the most likely nearest-neighbor distance determined from the pair-correlation function. The conjectures are tested by simulations of three systems, one of which is the standard Lennard-Jones liquid. While both expressions give...

  4. Role of attractive forces in determining the equilibrium structure and dynamics of simple liquids

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2015-01-01

    Molecular Dynamics simulations of a Lennard-Jones system with different range of attraction show that the attractive forces modify the radial distribution of the particles. For condensed liquids only, the forces within the the first coordination shell (FCS) are important, but for gases and moderate...... condensed fluids, even the attractive forces outside the FCS play a role. The changes in the distribution caused by neglecting the attractive forces, lead to a too high pressure. The weak long-range attractions damp the dynamics and the diffusion of the particles in gas-, super critical fluid- and in liquid...

  5. Cluster structures influenced by interaction with a surface.

    Science.gov (United States)

    Witt, Christopher; Dieterich, Johannes M; Hartke, Bernd

    2018-05-30

    Clusters on surfaces are vitally important for nanotechnological applications. Clearly, cluster-surface interactions heavily influence the preferred cluster structures, compared to clusters in vacuum. Nevertheless, systematic explorations and an in-depth understanding of these interactions and how they determine the cluster structures are still lacking. Here we present an extension of our well-established non-deterministic global optimization package OGOLEM from isolated clusters to clusters on surfaces. Applying this approach to intentionally simple Lennard-Jones test systems, we produce a first systematic exploration that relates changes in cluster-surface interactions to resulting changes in adsorbed cluster structures.

  6. Capillary condensation in pores with rough walls: a density functional approach.

    Science.gov (United States)

    Bryk, P; Rzysko, W; Malijevsky, Al; Sokołowski, S

    2007-09-01

    The effect of surface roughness of slit-like pore walls on the capillary condensation of a spherical particles and short chains is studied. The gas molecules interact with the substrate by a Lennard-Jones (9,3) potential. The rough layer at each pore wall has a variable thickness and density and consists of a disordered quenched matrix of spherical particles. The system is described in the framework of a density functional approach and using computer simulations. The contribution due to attractive van der Waals interactions between adsorbate molecules is described by using first-order mean spherical approximation and mean-field approximation.

  7. Modulation of capillary condensation by trace component

    Directory of Open Access Journals (Sweden)

    Shiqi Zhou

    2011-06-01

    Full Text Available Impact of trace component on capillary condensation (CC is investigated systematically using a classical density functional theory. It is discovered that (i presence of the trace component makes the CC to occur at much lower condensation pressure than when its absence; (ii Lennard-Jones potential parameters like size parameter and energy parameter of the trace component, and its concentration in the bulk adsorption system, show their effects the most remarkably within a particular range beyond which the effects eventually become insignificant. The present discoveries have implications in low pressure storage of gases, separation and enrichment of low concentration component, and easy control of CC transition, etc.

  8. Similarity Laws for the Lines of Ideal Free Energy and Chemical Potential in Supercritical Fluids.

    Science.gov (United States)

    Apfelbaum, E M; Vorob'ev, V S

    2017-09-21

    We have found the curves on the density-temperature plane, along which the values of free energy and chemical potential correspond to ideal gas quantities. At first, we have applied the van der Waals equation to construct them and to derive their equations. Then we have shown that the same lines for real substances (Ar, N 2 , CH 4 , SF 6 , H 2 , H 2 O) and for the model Lennard-Jones system constructed on the basis of the measurements data and calculations are well matched with the derived equations. The validity and deviations from the obtained similarity laws are discussed.

  9. Experimental studies of the NaRb ground-state potential up to the v''=76 level

    International Nuclear Information System (INIS)

    Docenko, O.; Nikolayeva, O.; Tamanis, M.; Ferber, R.; Pazyuk, E.A.; Stolyarov, A.V.

    2002-01-01

    Laser induced fluorescence spectra of the C 1 Σ + -X 1 Σ + system of 23 Na 85 Rb and 23 Na 87 Rb have allowed vibrational levels of the electronic ground state up to v '' =76, spanning 99.85% of the potential well to be observed. The ground-state term values have been fitted to a Dunham polynomial expansion, and also to a direct modified Lennard-Jones (MLJ) potential. The analytical MLJ construction allowed us to match previous measured term values for v '' ≤30 with long-range behavior of the potential through the intermediate internuclear distance region covered by the present investigation

  10. Calculations on isotope separation by laser induced photodissociation of polyatomic molecules. Progress report, February 1, 1977--June 30, 1978

    International Nuclear Information System (INIS)

    Lamb, W.E. Jr.

    1978-07-01

    The molecule SF 6 is treated as a classical dynamical system obeying Newton's laws of motion. This report describes how the current SF 6 potential is determined. The initial approach is described in terms of a pair of Lennard--Jones potential functions with arbitrary coefficients. A method for determining the potential constants is developed. The SF 6 spectrum was reproduced by including three-body forces. By specifying certain parameters such as the 1/r 6 F-F constant and the total dissociation energy of the molecule, a satisfactory global potential was obtained. The laser-molecule interaction energy was developed

  11. Density scaling and quasiuniversality of flow-event statistics for athermal plastic flows

    DEFF Research Database (Denmark)

    Lerner, Edan; Bailey, Nicholas; Dyre, J. C.

    2014-01-01

    Athermal steady-state plastic flows were simulated for the Kob-Andersen binary Lennard-Jones system and its repulsive version in which the sign of the attractive terms is changed to a plus. Properties evaluated include the distributions of energy drops, stress drops, and strain intervals between...... the flow events. We show that simulations at a single density in conjunction with an equilibrium-liquid simulation at the same density allow one to predict the plastic flow-event statistics at other densities. This is done by applying the recently established “hidden scale invariance” of simple liquids...

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  13. A strategy to find minimal energy nanocluster structures.

    Science.gov (United States)

    Rogan, José; Varas, Alejandro; Valdivia, Juan Alejandro; Kiwi, Miguel

    2013-11-05

    An unbiased strategy to search for the global and local minimal energy structures of free standing nanoclusters is presented. Our objectives are twofold: to find a diverse set of low lying local minima, as well as the global minimum. To do so, we use massively the fast inertial relaxation engine algorithm as an efficient local minimizer. This procedure turns out to be quite efficient to reach the global minimum, and also most of the local minima. We test the method with the Lennard-Jones (LJ) potential, for which an abundant literature does exist, and obtain novel results, which include a new local minimum for LJ13 , 10 new local minima for LJ14 , and thousands of new local minima for 15≤N≤65. Insights on how to choose the initial configurations, analyzing the effectiveness of the method in reaching low-energy structures, including the global minimum, are developed as a function of the number of atoms of the cluster. Also, a novel characterization of the potential energy surface, analyzing properties of the local minima basins, is provided. The procedure constitutes a promising tool to generate a diverse set of cluster conformations, both two- and three-dimensional, that can be used as an input for refinement by means of ab initio methods. Copyright © 2013 Wiley Periodicals, Inc.

  14. The role of binary and many-centre molecular interactions in spin crossover in the solid state. Part II. Non-ideality parameters defined via binary molecular potentials

    International Nuclear Information System (INIS)

    Koudriavtsev, A.B.; Linert, W.

    2005-01-01

    Parameters of the formalism [1-6] describing spin crossover in the solid state have been defined via molecular potentials in model systems of neutral and ionic complexes. In the first instance Lennard-Jones and electric dipole-dipole potentials have been used whereas in ionic systems Lennard-Jones and electric point-charge potentials have been used. Electric dipole-dipole interaction of neutral complexes brings about a positive excess energy controlled by the difference of electric dipole moments of HS and LS molecules. Differences of the order of Δμ = 1-2D cause an abrupt spin crossover in systems with T 1/2 = 100-150K. Magnetic coupling contributes both to the excess energy and excess entropy, however the overall effect is equivalent to a modest positive excess energy. Ionic systems in the absence of specific interactions are characterized by very small excess energies corresponding to practically linear van't Hoff plots. Detectable positive and negative excess energies in these systems may arise from interactions of ligands belonging to neighbouring complexes. The HOMO-LUMO overlap in HS-LS pairs can bring about a nontrivial variation of the shape of transition curves. Examples of regression analysis of experimental transition curves in terms of molecular potentials are given. (author)

  15. Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations

    Science.gov (United States)

    Yuhara, Daisuke; Brumby, Paul E.; Wu, David T.; Sum, Amadeu K.; Yasuoka, Kenji

    2018-05-01

    To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

  16. Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations.

    Science.gov (United States)

    Yuhara, Daisuke; Brumby, Paul E; Wu, David T; Sum, Amadeu K; Yasuoka, Kenji

    2018-05-14

    To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

  17. Spatial updating grand canonical Monte Carlo algorithms for fluid simulation: generalization to continuous potentials and parallel implementation.

    Science.gov (United States)

    O'Keeffe, C J; Ren, Ruichao; Orkoulas, G

    2007-11-21

    Spatial updating grand canonical Monte Carlo algorithms are generalizations of random and sequential updating algorithms for lattice systems to continuum fluid models. The elementary steps, insertions or removals, are constructed by generating points in space either at random (random updating) or in a prescribed order (sequential updating). These algorithms have previously been developed only for systems of impenetrable spheres for which no particle overlap occurs. In this work, spatial updating grand canonical algorithms are generalized to continuous, soft-core potentials to account for overlapping configurations. Results on two- and three-dimensional Lennard-Jones fluids indicate that spatial updating grand canonical algorithms, both random and sequential, converge faster than standard grand canonical algorithms. Spatial algorithms based on sequential updating not only exhibit the fastest convergence but also are ideal for parallel implementation due to the absence of strict detailed balance and the nature of the updating that minimizes interprocessor communication. Parallel simulation results for three-dimensional Lennard-Jones fluids show a substantial reduction of simulation time for systems of moderate and large size. The efficiency improvement by parallel processing through domain decomposition is always in addition to the efficiency improvement by sequential updating.

  18. Ablation by ultrashort laser pulses: Atomistic and thermodynamic analysis of the processes at the ablation threshold

    International Nuclear Information System (INIS)

    Upadhyay, Arun K.; Inogamov, Nail A.; Rethfeld, Baerbel; Urbassek, Herbert M.

    2008-01-01

    Ultrafast laser irradiation of solids may ablate material off the surface. We study this process for thin films using molecular-dynamics simulation and thermodynamic analysis. Both metals and Lennard-Jones (LJ) materials are studied. We find that despite the large difference in thermodynamical properties between these two classes of materials--e.g., for aluminum versus LJ the ratio T c /T tr of critical to triple-point temperature differs by more than a factor of 4--the values of the ablation threshold energy E abl normalized to the cohesion energy, ε abl =E abl /E coh , are surprisingly universal: all are near 0.3 with ±30% scattering. The difference in the ratio T c /T tr means that for metals the melting threshold ε m is low, ε m abl , while for LJ it is high, ε m >ε abl . This thermodynamical consideration gives a simple explanation for the difference between metals and LJ. It explains why despite the universality in ε abl , metals thermomechanically ablate always from the liquid state. This is opposite to LJ materials, which (near threshold) ablate from the solid state. Furthermore, we find that immediately below the ablation threshold, the formation of large voids (cavitation) in the irradiated material leads to a strong temporary expansion on a very slow time scale. This feature is easily distinguished from the acoustic oscillations governing the material response at smaller intensities, on the one hand, and the ablation occurring at larger intensities, on the other hand. This finding allows us to explain the puzzle of huge surface excursions found in experiments at near-threshold laser irradiation

  19. Effect of temperature dependence of the Langmuir constant molecular pair potentials on gas hydrates formation mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Mokhtari, B.; Enayati, M. [Iranian Offshore Oil Co., Tehran (Iran, Islamic Republic of); Heidaryan, E. [Islamic Azad Univ., Tehran (Iran, Islamic Republic of). Masjidosolayman Branch

    2008-07-01

    Theoretical methods show that crystalline hydrates can form from single-phase systems consisting of both vapor water with gaseous hydrate former and liquid water with dissolved hydrate former. Two phase systems consist of both liquid water with gaseous hydrate former and with liquid hydrate former on the surface. This paper presented a Langmuir constant related model for the prediction of equilibrium pressures and cage occupancies of pure component hydrates. Intermolecular potentials were fit to quantum mechanical energies to obtain the Langmuir constants, which differed from the procedure utilized with the vdWP model. The paper described the experimental method and model calculations. This included the Fugacity model and Van der Waals and Platteeuw model. The paper also discussed pair potential of non-spherical molecules, including the multicentre (site-site) potential; Gaussian overlap potential; Lennard-Jones potential; and Kihara generalized pair potential. It was concluded that fraction of occupied cavities is a function of pair potentials between hard core and empty hydrate lattice. These pair potentials could be calculated from some model as Kihara cell potential, Gaussian potential, Lennard-Jones potential and multicentre pair potential. 49 refs., 3 figs.

  20. Accelerating Monte Carlo molecular simulations by reweighting and reconstructing Markov chains: Extrapolation of canonical ensemble averages and second derivatives to different temperature and density conditions

    KAUST Repository

    Kadoura, Ahmad Salim

    2014-08-01

    Accurate determination of thermodynamic properties of petroleum reservoir fluids is of great interest to many applications, especially in petroleum engineering and chemical engineering. Molecular simulation has many appealing features, especially its requirement of fewer tuned parameters but yet better predicting capability; however it is well known that molecular simulation is very CPU expensive, as compared to equation of state approaches. We have recently introduced an efficient thermodynamically consistent technique to regenerate rapidly Monte Carlo Markov Chains (MCMCs) at different thermodynamic conditions from the existing data points that have been pre-computed with expensive classical simulation. This technique can speed up the simulation more than a million times, making the regenerated molecular simulation almost as fast as equation of state approaches. In this paper, this technique is first briefly reviewed and then numerically investigated in its capability of predicting ensemble averages of primary quantities at different neighboring thermodynamic conditions to the original simulated MCMCs. Moreover, this extrapolation technique is extended to predict second derivative properties (e.g. heat capacity and fluid compressibility). The method works by reweighting and reconstructing generated MCMCs in canonical ensemble for Lennard-Jones particles. In this paper, system\\'s potential energy, pressure, isochoric heat capacity and isothermal compressibility along isochors, isotherms and paths of changing temperature and density from the original simulated points were extrapolated. Finally, an optimized set of Lennard-Jones parameters (ε, σ) for single site models were proposed for methane, nitrogen and carbon monoxide. © 2014 Elsevier Inc.

  1. Combination Rules for Morse-Based van der Waals Force Fields.

    Science.gov (United States)

    Yang, Li; Sun, Lei; Deng, Wei-Qiao

    2018-02-15

    In traditional force fields (FFs), van der Waals interactions have been usually described by the Lennard-Jones potentials. Conventional combination rules for the parameters of van der Waals (VDW) cross-termed interactions were developed for the Lennard-Jones based FFs. Here, we report that the Morse potentials were a better function to describe VDW interactions calculated by highly precise quantum mechanics methods. A new set of combination rules was developed for Morse-based FFs, in which VDW interactions were described by Morse potentials. The new set of combination rules has been verified by comparing the second virial coefficients of 11 noble gas mixtures. For all of the mixed binaries considered in this work, the combination rules work very well and are superior to all three other existing sets of combination rules reported in the literature. We further used the Morse-based FF by using the combination rules to simulate the adsorption isotherms of CH 4 at 298 K in four covalent-organic frameworks (COFs). The overall agreement is great, which supports the further applications of this new set of combination rules in more realistic simulation systems.

  2. Evolution of short range order in Ar: Liquid to glass and solid transitions-A computational study

    Science.gov (United States)

    Shor, Stanislav; Yahel, Eyal; Makov, Guy

    2018-04-01

    The evolution of the short range order (SRO) as a function of temperature in a Lennard-Jones model liquid with Ar parameters was determined and juxtaposed with thermodynamic and kinetic properties obtained as the liquid was cooled (heated) and transformed between crystalline solid or glassy states and an undercooled liquid. The Lennard-Jones system was studied by non-equilibrium molecular dynamics simulations of large supercells (approximately 20000 atoms) rapidly cooled or heated at selected quenching rates and at constant pressure. The liquid to solid transition was identified by discontinuities in the atomic volume and molar enthalpy; the glass transition temperature range was identified from the temperature dependence of the self-diffusion. The SRO was studied within the quasi-crystalline model (QCM) framework and compared with the Steinhardt bond order parameters. Within the QCM it was found that the SRO evolves from a bcc-like order in the liquid through a bct-like short range order (c/a=1.2) in the supercooled liquid which persists into the glass and finally to a fcc-like ordering in the crystalline solid. The variation of the SRO that results from the QCM compares well with that obtained with Steinhardt's bond order parameters. The hypothesis of icosahedral order in liquids and glasses is not supported by our results.

  3. Divergence of activity expansions: Is it actually a problem?

    Science.gov (United States)

    Ushcats, M. V.; Bulavin, L. A.; Sysoev, V. M.; Ushcats, S. Yu.

    2017-12-01

    For realistic interaction models, which include both molecular attraction and repulsion (e.g., Lennard-Jones, modified Lennard-Jones, Morse, and square-well potentials), the asymptotic behavior of the virial expansions for pressure and density in powers of activity has been studied taking power terms of high orders into account on the basis of the known finite-order irreducible integrals as well as the recent approximations of infinite irreducible series. Even in the divergence region (at subcritical temperatures), this behavior stays thermodynamically adequate (in contrast to the behavior of the virial equation of state with the same set of irreducible integrals) and corresponds to the beginning of the first-order phase transition: the divergence yields the jump (discontinuity) in density at constant pressure and chemical potential. In general, it provides a statistical explanation of the condensation phenomenon, but for liquid or solid states, the physically proper description (which can turn the infinite discontinuity into a finite jump of density) still needs further study of high-order cluster integrals and, especially, their real dependence on the system volume (density).

  4. Accelerating Monte Carlo molecular simulations by reweighting and reconstructing Markov chains: Extrapolation of canonical ensemble averages and second derivatives to different temperature and density conditions

    Energy Technology Data Exchange (ETDEWEB)

    Kadoura, Ahmad; Sun, Shuyu, E-mail: shuyu.sun@kaust.edu.sa; Salama, Amgad

    2014-08-01

    Accurate determination of thermodynamic properties of petroleum reservoir fluids is of great interest to many applications, especially in petroleum engineering and chemical engineering. Molecular simulation has many appealing features, especially its requirement of fewer tuned parameters but yet better predicting capability; however it is well known that molecular simulation is very CPU expensive, as compared to equation of state approaches. We have recently introduced an efficient thermodynamically consistent technique to regenerate rapidly Monte Carlo Markov Chains (MCMCs) at different thermodynamic conditions from the existing data points that have been pre-computed with expensive classical simulation. This technique can speed up the simulation more than a million times, making the regenerated molecular simulation almost as fast as equation of state approaches. In this paper, this technique is first briefly reviewed and then numerically investigated in its capability of predicting ensemble averages of primary quantities at different neighboring thermodynamic conditions to the original simulated MCMCs. Moreover, this extrapolation technique is extended to predict second derivative properties (e.g. heat capacity and fluid compressibility). The method works by reweighting and reconstructing generated MCMCs in canonical ensemble for Lennard-Jones particles. In this paper, system's potential energy, pressure, isochoric heat capacity and isothermal compressibility along isochors, isotherms and paths of changing temperature and density from the original simulated points were extrapolated. Finally, an optimized set of Lennard-Jones parameters (ε, σ) for single site models were proposed for methane, nitrogen and carbon monoxide.

  5. Instantaneous, parameter-free methods to define a solute’s hydration shell

    International Nuclear Information System (INIS)

    Chatterjee, Anupam; Higham, Jonathan; Henchman, Richard H.

    2015-01-01

    A range of methods are presented to calculate a solute’s hydration shell from computer simulations of dilute solutions of monatomic ions and noble gas atoms. The methods are designed to be parameter-free and instantaneous so as to make them more general, accurate, and consequently applicable to disordered systems. One method is a modified nearest-neighbor method, another considers solute-water Lennard-Jones overlap followed by hydrogen-bond rearrangement, while three methods compare various combinations of water-solute and water-water forces. The methods are tested on a series of monatomic ions and solutes and compared with the values from cutoffs in the radial distribution function, the nearest-neighbor distribution functions, and the strongest-acceptor hydrogen bond definition for anions. The Lennard-Jones overlap method and one of the force-comparison methods are found to give a hydration shell for cations which is in reasonable agreement with that using a cutoff in the radial distribution function. Further modifications would be required, though, to make them capture the neighboring water molecules of noble-gas solutes if these weakly interacting molecules are considered to constitute the hydration shell

  6. Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering.

    Science.gov (United States)

    Slepoy, A; Peters, M D; Thompson, A P

    2007-11-30

    Molecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time-consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force-field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters. The methodology was tested using a nontrivial problem with a well-defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard-Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard-Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. Copyright (c) 2007 Wiley Periodicals, Inc.

  7. Molar excess volumes of liquid hydrogen and neon mixtures from path integral simulation

    International Nuclear Information System (INIS)

    Challa, S.R.; Johnson, J.K.

    1999-01-01

    Volumetric properties of liquid mixtures of neon and hydrogen have been calculated using path integral hybrid Monte Carlo simulations. Realistic potentials have been used for the three interactions involved. Molar volumes and excess volumes of these mixtures have been evaluated for various compositions at 29 and 31.14 K, and 30 atm. Significant quantum effects are observed in molar volumes. Quantum simulations agree well with experimental molar volumes. Calculated excess volumes agree qualitatively with experimental values. However, contrary to the existing understanding that large positive deviations from ideal mixtures are caused due to quantum effects in Ne - H 2 mixtures, both classical as well as quantum simulations predict the large positive deviations from ideal mixtures. Further investigations using two other Ne - H 2 potentials of Lennard - Jones (LJ) type show that excess volumes are very sensitive to the cross-interaction potential. We conclude that the cross-interaction potential employed in our simulations is accurate for volumetric properties. This potential is more repulsive compared to the two LJ potentials tested, which have been obtained by two different combining rules. This repulsion and a comparatively lower potential well depth can explain the positive deviations from ideal mixing. copyright 1999 American Institute of Physics

  8. Comparisons of perturbation and integral equation theories for the angular pair correlation function in molecular fluids

    International Nuclear Information System (INIS)

    Murad, S.; Gubbins, K.E.; Gray, C.G.

    1983-01-01

    We compare several recently proposed theories for the angular pair correlation function g(rω 1 ω 2 ), including first- and second-order perturbation theory (the u-expansion), a Pade approximant to this series, first-order f-expansion, the single superchain, generalized mean field, linearized hypernetted chain, and quadratic hypernetted chain approximations. Numerical results from these theories are compared with available computer simulation data for four model fluids whose intermolecular pair potential is of the form u 0 +usub(a), where u 0 is a hard-sphere of Lennard-Jones model, while usub(a) is a dipole-dipole or quadrupole-quadrupole interaction; we refer to these model fluids as HS+μμ, HS+QQ, LJ+μμ, and LJ+QQ. Properties studied include the angular pair correlation function and its spherical harmonic components, the thermodynamic properties, and the angular correlation parameters G 1 and G 2 that are related to the dielectric and Kerr constants. The second-order perturbation theory is superior to the integral equation theories for the thermodynamic harmonics of g(rω 1 ω 2 ) and for the thermodynamic properties themselves at moderate multipole strengths. For other harmonics and properties, the integral equation theories are better, with the quadratic hypernetted chain approximation being the best overall. (orig.)

  9. Excipient-assisted vinpocetine nanoparticles: experiments and molecular dynamic simulations.

    Science.gov (United States)

    Li, Cai-Xia; Wang, Hao-Bo; Oppong, Daniel; Wang, Jie-Xin; Chen, Jian-Feng; Le, Yuan

    2014-11-03

    Hydrophilic excipients can be used to increase the solubility and bioavailability of poorly soluble drugs. In this work, the conventional water-soluble pharmaceutical excipients hydroxypropylmethylcellulose (HPMC), polyvinylpyrrolidone (PVP), and lactose (LAC) were used as solid supports to prevent drug nanoparticles from aggregation and enhance drug dissolution. Excipient-assisted vinpocetine (VIN) nanoparticles were prepared by reactive precipitation. The analysis results indicated that HPMC was a suitable excipient to prepare VIN nanoparticles. VIN/HPMC nanoparticles had a mean size of 130 nm within a narrow distribution. The dissolution rate of VIN nanoparticles was significantly faster than those of a physical mixture of VIN/HPMC and raw VIN. VIN/HPMC nanoparticles had a higher dissolution profile than VIN/PVP and VIN/LAC nanoparticles. Besides, molecular dynamics (MD) simulation was applied to investigate the molecular interactions between VIN and excipients. The calculated results revealed that VIN interacted with excipients by Coulomb and Lennard-Jones (LJ) interactions. Few hydrogen bonds were formed between VIN and excipients. The HPMC affording smaller particle size may be a result of the stronger interactions between VIN and HPMC (mainly LJ interaction) and the property of HPMC. These characteristics may greatly influence the adsorption behavior and may be the crucial parameter for the better performance of HPMC.

  10. Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

    International Nuclear Information System (INIS)

    Zhou Shiqi

    2005-01-01

    A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.

  11. Use of bactec 460 TB system in the diagnosis of tuberculosis

    Directory of Open Access Journals (Sweden)

    Rodrigues C

    2007-01-01

    Full Text Available Purpose : To evaluate, the efficacy of BACTEC 460 TB system for the diagnosis of tuberculosis in a tertiary care hospital in Mumbai, India. Methods : We compared 12,726 clinical specimens using BACTEC 460 TB system and conventional method for detection of Mycobacterium tuberculosis over a period of six years. Result: The overall recovery rate was 39% by BACTEC technique and 29% using Lowenstein-Jensen (LJ medium. An average detection time for B actec0 460 TB system was found to be 13.3 days and 15.3 days as against 31.2 days and 35.3 days by LJ method for respiratory and nonrespiratory specimens respectively. The average reporting time for drug susceptibility results ranged from 6-10 days for the BACTEC 460 TB system. Conclusions: The BACTEC system is a good system for level II laboratories, especially in the diagnosis of extrapulmonary and smear negative tuberculosis.

  12. Evaluation of Uniform Cost Accounting System to Fully Capture Depot Level Repair Costs.

    Science.gov (United States)

    1985-12-01

    RD-RI65 522 EVALUATION OF UNIFORM COST ACCOUNTING SYSTEM TO FULLY i/I CAPTURE DEPOT LEVEL REPAIR COSTS (U) NAVAL POSTGRADUATE SCHOOL MONTEREY CA D R...8217.LECTE B ,- THESIS EVALUATION OF UNIFORM COST ACCOUNTING SYSTEM 0TO FULLY CAPTURE DEPOT LEVEL REPAIR COSTS Jby __jDavid Richmond O’Brien lj,,, December...Include Security Classification) EVALUATION OF UNIFORM COST ACCOUNTING SYSTEM TO FULLY CAPTURE DEPOT LEVEL REPAIR COSTS 12 PERSONAL AUTHOR(S) O’Brien- David

  13. Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins.

    Science.gov (United States)

    Harris, Robert C; Pettitt, B Montgomery

    2016-03-02

    The idea that a 'hydrophobic energy' drives protein folding, aggregation, and binding by favoring the sequestration of bulky residues from water into the protein interior is widespread. The solvation free energies (ΔGsolv) of small nonpolar solutes increase with surface area (A), and the free energies of creating macroscopic cavities in water increase linearly with A. These observations seem to imply that there is a hydrophobic component (ΔGhyd) of ΔGsolv that increases linearly with A, and this assumption is widely used in implicit solvent models. However, some explicit-solvent molecular dynamics studies appear to contradict these ideas. For example, one definition (ΔG(LJ)) of ΔGhyd is that it is the free energy of turning on the Lennard-Jones (LJ) interactions between the solute and solvent. However, ΔG(LJ) decreases with A for alanine and glycine peptides. Here we argue that these apparent contradictions can be reconciled by defining ΔGhyd to be a near hard core insertion energy (ΔGrep), as in the partitioning proposed by Weeks, Chandler, and Andersen. However, recent results have shown that ΔGrep is not a simple function of geometric properties of the molecule, such as A and the molecular volume, and that the free energy of turning on the attractive part of the LJ potential cannot be computed from first-order perturbation theory for proteins. The theories that have been developed from these assumptions to predict ΔGhyd are therefore inadequate for proteins.

  14. Evaporation of liquid droplets of nano- and micro-meter size as a function of molecular mass and intermolecular interactions: experiments and molecular dynamics simulations.

    Science.gov (United States)

    Hołyst, Robert; Litniewski, Marek; Jakubczyk, Daniel

    2017-09-13

    Transport of heat to the surface of a liquid is a limiting step in the evaporation of liquids into an inert gas. Molecular dynamics (MD) simulations of a two component Lennard-Jones (LJ) fluid revealed two modes of energy transport from a vapour to an interface of an evaporating droplet of liquid. Heat is transported according to the equation of temperature diffusion, far from the droplet of radius R. The heat flux, in this region, is proportional to temperature gradient and heat conductivity in the vapour. However at some distance from the interface, Aλ, (where λ is the mean free path in the gas), the temperature has a discontinuity and heat is transported ballistically i.e. by direct individual collisions of gas molecules with the interface. This ballistic transport reduces the heat flux (and consequently the mass flux) by the factor R/(R + Aλ) in comparison to the flux obtained from temperature diffusion. Thus it slows down the evaporation of droplets of sizes R ∼ Aλ and smaller (practically for sizes from 10 3 nm down to 1 nm). We analyzed parameter A as a function of interactions between molecules and their masses. The rescaled parameter, A(k B T b /ε 11 ) 1/2 , is a linear function of the ratio of the molecular mass of the liquid molecules to the molecular mass of the gas molecules, m 1 /m 2 (for a series of chemically similar compounds). Here ε 11 is the interaction parameter between molecules in the liquid (proportional to the enthalpy of evaporation) and T b is the temperature of the gas in the bulk. We tested the predictions of MD simulations in experiments performed on droplets of ethylene glycol, diethylene glycol, triethylene glycol and tetraethylene glycol. They were suspended in an electrodynamic trap and evaporated into dry nitrogen gas. A changes from ∼1 (for ethylene glycol) to approximately 10 (for tetraethylene glycol) and has the same dependence on molecular parameters as obtained for the LJ fluid in MD simulations. The value of x = A

  15. A perspective on the interfacial properties of nanoscopic liquid drops

    International Nuclear Information System (INIS)

    Malijevský, Alexandr; Jackson, George

    2012-01-01

    century by Gibbs and then promoted by Tolman) with a microscopic DFT treatment allows for a direct and unambiguous description of the interfacial properties of drops of arbitrary size; DFT provides all of the bulk and surface characteristics of the system that are required to uniquely define its thermodynamic properties. In this vein, we propose a non-local mean-field DFT for Lennard-Jones (LJ) fluids to examine drops of varying size. A comparison of the predictions of our DFT with recent simulation data based on a second-order fluctuation analysis (Sampayo et al 2010 J. Chem. Phys. 132 141101) reveals the consistency of the two treatments. This observation highlights the significance of fluctuation effects in small drops, which give rise to additional entropic (thermal non-mechanical) contributions, in contrast to what one observes in the case of planar interfaces which are governed by the laws of mechanical equilibrium. A small negative Tolman length (which is found to be about a tenth of the molecular diameter) and a non-monotonic behaviour of the surface tension with the drop radius are predicted for the LJ fluid. Finally, the limits of the validity of the Tolman approach, the effect of the range of the intermolecular potential, and the behaviour of bubbles are briefly discussed.

  16. Thermal conductivity at the nanoscale: A molecular dynamics study

    Science.gov (United States)

    Lyver, John W., IV

    With the growing use of nanotechnology and nanodevices in many fields of engineering and science, a need for understanding the thermal properties of such devices has increased. The ability for nanomaterials to conduct heat is highly dependent on the purity of the material, internal boundaries due to material changes and the structure of the material itself. Experimentally measuring the heat transport at the nanoscale is extremely difficult and can only be done as a macro output from the device. Computational methods such as various Monte Carlo (MC) and molecular dynamics (MD) techniques for studying the contribution of atomic vibrations associated with heat transport properties are very useful. The Green--Kubo method in conjunction with Fourier's law for calculating the thermal conductivity, kappa, has been used in this study and has shown promise as one approach well adapted for understanding nanosystems. Investigations were made of the thermal conductivity using noble gases, modeled with Lennard-Jones (LJ) interactions, in solid face-centered cubic (FCC) structures. MC and MD simulations were done to study homogeneous monatomic and binary materials as well as slabs of these materials possessing internal boundaries. Additionally, MD simulations were done on silicon carbide nanowires, nanotubes, and nanofilaments using a potential containing two-body and three-body terms. The results of the MC and MD simulations were matched against available experimental and other simulations and showed that both methods can accurately simulate real materials in a fraction of the time and effort. The results of the study show that in compositionally disordered materials the selection of atomic components by their mass, hard-core atomic diameter, well depth, and relative concentration can change the kappa by as much as an order of magnitude. It was found that a 60% increase in mass produces a 25% decrease in kappa. A 50% increase in interatomic strength produces a 25% increase in

  17. Evaluation of BacT/Alert 3D Liquid Culture System for Recovery of Mycobacteria from Clinical Specimens Using Sodium Dodecyl (Lauryl) Sulfate-NaOH Decontamination

    Science.gov (United States)

    Carricajo, A.; Fonsale, N.; Vautrin, A. C.; Aubert, G.

    2001-01-01

    A total of 52 mycobacterial isolates were recovered from 1,197 clinical specimens decontaminated by a sodium dodecyl (lauryl) sulfate (SDS)-NaOH protocol. Of these, 94% were recovered with the BacT/Alert 3D system (Organon Teknika, Durham, N.C.) and 79% were recovered on Löwenstein-Jensen (LJ) medium. Mean times to detection of organisms of the Mycobacterium tuberculosis complex (n = 47) were 22.8 days with LJ medium and 16.2 days with the system. The BacT/Alert 3D system is a rapid and efficient detection system which can be used with an SDS-NaOH decontamination procedure. PMID:11574623

  18. Monte Carlo simulation of continuous-space crystal growth

    International Nuclear Information System (INIS)

    Dodson, B.W.; Taylor, P.A.

    1986-01-01

    We describe a method, based on Monte Carlo techniques, of simulating the atomic growth of crystals without the discrete lattice space assumed by conventional Monte Carlo growth simulations. Since no lattice space is assumed, problems involving epitaxial growth, heteroepitaxy, phonon-driven mechanisms, surface reconstruction, and many other phenomena incompatible with the lattice-space approximation can be studied. Also, use of the Monte Carlo method circumvents to some extent the extreme limitations on simulated timescale inherent in crystal-growth techniques which might be proposed using molecular dynamics. The implementation of the new method is illustrated by studying the growth of strained-layer superlattice (SLS) interfaces in two-dimensional Lennard-Jones atomic systems. Despite the extreme simplicity of such systems, the qualitative features of SLS growth seen here are similar to those observed experimentally in real semiconductor systems

  19. Statistical mechanics of addition polymerisation. Calculations of the expectation and variance of the average atmosphere in growing self avoiding walks

    Science.gov (United States)

    Taniya, Abraham; Deepthi, Murali; Padmanabhan, Alapat

    2018-06-01

    Recent calculations on the change in radial dimensions of reacting (growing) polyethylene in the gas phase experiencing Lennard Jones and Kihara type potentials revealed that a single reacting polyethylene molecule does not experience polymer collapse. This implies that a transition that is the converse of what happens when molten polyethylene crystallizes, i.e. it transforms from random coil like structure to folded rigid rod type structure, occurs. The predicted behaviour of growing polyethylene was explained by treating the head of the growing polymer chain as myopic whereas as the whole chain (i.e. when under equilibrium conditions) being treated as having normal vision, i.e. the growing chain does not see the attractive part of the LJ or Kihara Potentials. In this paper we provide further proof for this argument in two ways. Firstly we carry forward the exact enumeration calculations on growing self avoiding walks reported in that paper to larger values of number of steps by using Monte Carlo type calculations. We thereby assign physical significance to the connective constant of self avoiding walks, which until now was treated as a purely abstract mathematical entity. Secondly since a reacting polymer molecule that grows by addition polymerisation sees only one step ahead at a time, we extend this calculation by estimating the average atmosphere for molecules, with repulsive potential only (growing self avoiding walks in two dimensions), that look at two, three, four, five ...steps ahead. Our calculation shows that the arguments used in the previous work are correct.

  20. Dimers in nucleating vapors

    Science.gov (United States)

    Lushnikov, A. A.; Kulmala, M.

    1998-09-01

    The dimer stage of nucleation may affect considerably the rate of the nucleation process at high supersaturation of the nucleating vapor. Assuming that the dimer formation limits the nucleation rate, the kinetics of the particle formation-growth process is studied starting with the definition of dimers as bound states of two associating molecules. The partition function of dimer states is calculated by summing the Boltzmann factor over all classical bound states, and the equilibrium population of dimers is found for two types of intermolecular forces: the Lennard-Jones (LJ) and rectangular well+hard core (RW) potentials. The principle of detailed balance is used for calculating the evaporation rate of dimers. The kinetics of the particle formation-growth process is then investigated under the assumption that the trimers are stable with respect to evaporation and that the condensation rate is a power function of the particle mass. If the power exponent λ=n/(n+1) (n is a non-negative integer), the kinetics of the process is described by a finite set of moments of particle mass distribution. When the characteristic time of the particle formation by nucleation is much shorter than that of the condensational growth, n+2 universal functions of a nondimensional time define the kinetic process. These functions are calculated for λ=2/3 (gas-to-particle conversion in the free molecular regime) and λ=1/2 (formation of islands on surfaces).

  1. Monte Carlo Molecular Simulation with Isobaric-Isothermal and Gibbs-NPT Ensembles

    KAUST Repository

    Du, Shouhong

    2012-01-01

    This thesis presents Monte Carlo methods for simulations of phase behaviors of Lennard-Jones fluids. The isobaric-isothermal (NPT) ensemble and Gibbs-NPT ensemble are introduced in detail. NPT ensemble is employed to determine the phase diagram of pure component. The reduced simulation results are verified by comparison with the equation of state by by Johnson et al. and results with L-J parameters of methane agree considerably with the experiment measurements. We adopt the blocking method for variance estimation and error analysis of the simulation results. The relationship between variance and number of Monte Carlo cycles, error propagation and Random Number Generator performance are also investigated. We review the Gibbs-NPT ensemble employed for phase equilibrium of binary mixture. The phase equilibrium is achieved by performing three types of trial move: particle displacement, volume rearrangement and particle transfer. The simulation models and the simulation details are introduced. The simulation results of phase coexistence for methane and ethane are reported with comparison of the experimental data. Good agreement is found for a wide range of pressures. The contribution of this thesis work lies in the study of the error analysis with respect to the Monte Carlo cycles and number of particles in some interesting aspects.

  2. The existence of a plastic phase and a solid-liquid dynamical bistability region in small fullerene cluster (C60)7: molecular dynamics simulation

    International Nuclear Information System (INIS)

    Piatek, A; Dawid, A; Gburski, Z

    2006-01-01

    We have simulated (by the molecular dymanics (MD) method) the dynamics of fullerenes (C 60 ) in an extremely small cluster composed of only as many as seven C 60 molecules. The interaction is taken to be the full 60-site pairwise additive Lennard-Jones (LJ) potential which generates both translational and anisotropic rotational motions of each molecule. Our atomically detailed MD simulations discover the plastic phase (no translations but active reorientations of fullerenes) at low energies (temperatures) of the (C 60 ) 7 cluster. We provide the in-depth evidence of the dynamical solid-liquid bistability region in the investigated cluster. Moreover, we confirm the existence of the liquid phase in (C 60 ) 7 , the finding of Gallego et al (1999 Phys. Rev. Lett. 83 5258) obtained earlier on the basis of Girifalco's model, which assumes single-site only and spherically symmetrical interaction between C 60 molecules. We have calculated the translational and angular velocity autocorrelation functions and estimated the diffusion coefficient of fullerene in the liquid phase

  3. Monte Carlo Molecular Simulation with Isobaric-Isothermal and Gibbs-NPT Ensembles

    KAUST Repository

    Du, Shouhong

    2012-05-01

    This thesis presents Monte Carlo methods for simulations of phase behaviors of Lennard-Jones fluids. The isobaric-isothermal (NPT) ensemble and Gibbs-NPT ensemble are introduced in detail. NPT ensemble is employed to determine the phase diagram of pure component. The reduced simulation results are verified by comparison with the equation of state by by Johnson et al. and results with L-J parameters of methane agree considerably with the experiment measurements. We adopt the blocking method for variance estimation and error analysis of the simulation results. The relationship between variance and number of Monte Carlo cycles, error propagation and Random Number Generator performance are also investigated. We review the Gibbs-NPT ensemble employed for phase equilibrium of binary mixture. The phase equilibrium is achieved by performing three types of trial move: particle displacement, volume rearrangement and particle transfer. The simulation models and the simulation details are introduced. The simulation results of phase coexistence for methane and ethane are reported with comparison of the experimental data. Good agreement is found for a wide range of pressures. The contribution of this thesis work lies in the study of the error analysis with respect to the Monte Carlo cycles and number of particles in some interesting aspects.

  4. Laser-irradiated thermodynamic behaviors of spallation and recombination at solid-state interface

    International Nuclear Information System (INIS)

    Lai, H.-Y.; Huang, P.-H.

    2008-01-01

    A microscopic insight of interfacial spallation and recombination behaviors at multilayer thin-film interface induced by incident femtosecond pulsed laser is presented in this paper. Such two different aforementioned behaviors are investigated via the thermodynamic trajectories obtained by using standard Lennard-Jones (L-J) molecular dynamics (MD) simulation. Based on the simulation results, the interfacial damages of multilayer thin film are dominated by a critical threshold that induces an extraordinary expansive dynamics and phase transitions leading to the structural softened and tensile spallation at interface. The critical damage threshold is evaluated at around 8.5 J/m 2 which governs the possible occurrence of two different regimes, i.e. interfacial spallaiton and recombination. In interfacial damage region, quasi-isothermal thermodynamic trajectories can be observed after the interfacial spallation occurs. Moreover, the result of thermodynamic trajectories analyses indicates that, the relaxation of pressure wave may cause the over-heated interfacial zone to reduce volumetric density, thus leading to structural softness and even weaken interfacial structural strength. The crucial effect leading to the phenomenon of low tension spallation is identified

  5. Study of structural and transport properties of argon, krypton, and their binary mixtures at different temperatures.

    Science.gov (United States)

    Ghimire, Sunil; Adhikari, Narayan Prasad

    2017-03-01

    Molecular dynamics simulation of argon, krypton, and their binary mixtures were performed at different temperatures and constant pressure (P = 1.013 bar) using GROMACS - Groningen Machine for Chemical Simulations. The gases are modeled by Lennard-Jones pair potential, with parameters taken from the literature. The study of radial distribution functions (RDFs) shows a single peak which indicates that there is no packing effect in gaseous state for argon, krypton, and their binary mixtures. The self-diffusion coefficients of argon and krypton is determined by using mean-square displacement(MSD) method and the mutual diffusion coefficients of binary mixtures are determined using Darken's relation. The values of simulated diffusion coefficients are compared with their corresponding theoretical values, numerical estimation, and experimental data. A good agreement between these sets of data is found. The diffusion coefficients obey Arrhenius behavior to a good extent for both pure components and binary mixtures. The values of simulated diffusion coefficient are used to estimate viscosities and thermal conductivities which agree with theoretical values, numerical estimation, and experimental data within 10 %. These results support that the LJ potential is sufficient for description of molecular interactions in argon and krypton.

  6. Interaction potentials and their effect on crystal nucleation and symmetry

    International Nuclear Information System (INIS)

    Hsu, C.S.; Rahman, A.

    1979-01-01

    Molecular dynamics technique has been used to study the effect of the interaction potential on crystal nucleation and the symmetry of the nucleated phase. Four systems, namely rubidium, Lennard-Jones, rubidium-truncated, and Lennard-Jones-truncated, have been studied each at reduced density 0.95. Two types of calculations were performed. Firstly, starting from a liquid state, each system was quenched rapidly to a reduced temperature of approx.0.1. The nucleation process for these systems was monitored by studying the time dependence of temperature and the pair correlation function, and the resulting crystalline structure analyzed using among other properties the Voronoi polyhedra. Only in the case of rubidium was a b.c.c. structure nucleated. In the other three cases we obtained a f.c.c. ordering. Secondly, we have studied the effect of changing the interaction potential in a system which has already achieved an ordered state under the action of some other potential. After establishing a b.c.c. structure in a rubidium system, the change in the symmetry of the system was studied when the pair potential was modified to one of the other three forms. The results from both types of calculations are consistent: the rubidium potential leads to a b.c.c. structure while the other three potentials give an f.c.c. structure. Metastable disordered structures were not obtained in any of the calculations. However, the time elapse between the moment when the system is quick-quenched and the moment when nucleation occurs appears to depend upon the potential of interaction

  7. Diffusion in Coulomb crystals.

    Science.gov (United States)

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

    2011-07-01

    Diffusion in Coulomb crystals can be important for the structure of neutron star crusts. We determine diffusion constants D from molecular dynamics simulations. We find that D for Coulomb crystals with relatively soft-core 1/r interactions may be larger than D for Lennard-Jones or other solids with harder-core interactions. Diffusion, for simulations of nearly perfect body-centered-cubic lattices, involves the exchange of ions in ringlike configurations. Here ions "hop" in unison without the formation of long lived vacancies. Diffusion, for imperfect crystals, involves the motion of defects. Finally, we find that diffusion, for an amorphous system rapidly quenched from Coulomb parameter Γ=175 to Coulomb parameters up to Γ=1750, is fast enough that the system starts to crystalize during long simulation runs. These results strongly suggest that Coulomb solids in cold white dwarf stars, and the crust of neutron stars, will be crystalline and not amorphous.

  8. Isoviscosity lines and the liquid-glass transition in simple liquids.

    Science.gov (United States)

    Fomin, Yu D; Brazhkin, V V; Ryzhov, V N

    2012-07-01

    This article presents the study of the generic behavior of viscosity of liquids based on some simple theoretical models, the soft-spheres and Lennard-Jones systems. The use of these simple models allows us to investigate in detail the viscosity behavior in a wide range of temperatures and pressures including the high-temperature-high-pressure limits. Based on the simulation results, we discuss the shape of isoviscosity lines and analyze the glass transition at high temperatures and high pressures. Despite the fact that the viscosity drastically increases in the limit of high temperatures and high pressures along the melting line, the relaxation time rapidly decreases in this region, and the system becomes further from the glass transition.

  9. Molecular Dynamics Simulation for the Mechanical Properties of CNT/Polymer Nanocomposites

    International Nuclear Information System (INIS)

    Yang, Seung Hwa; Cho, Maeg Hyo

    2007-01-01

    In order to obtain mechanical properties of CNT/Polymer nano-composites, molecular dynamics simulation is performed. Overall system was modeled as a flexible unit cell in which carbon nanotubes are embedded into a polyethylene matrix for N σ T ensemble simulation. COMPASS force field was chosen to describe inter and intra molecular potential and bulk effect was achieved via periodic boundary conditions. In CNT-polymer interface, only Lennard-Jones non-bond potential was considered. Using Parrinello-Rahman fluctuation method, mechanical properties of orthotropic nano-composites under various temperatures were successfully obtained. Also, we investigated thermal behavior of the short CNT reinforced nanocomposites system with predicting glass transition temperature

  10. Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model

    Science.gov (United States)

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-03-01

    A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg-Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard-Jones fluid in the region close to the liquid-vapor critical point. The procedure is general and can be adapted to other coarse-grained models.

  11. Molecular Dynamics Simulations of a Linear Nanomotor Driven by Thermophoretic Forces

    DEFF Research Database (Denmark)

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

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

  12. The structure of the solid-liquid interface: atomic size effect; La structure de l'interface solide-liquide: effet de taille atomique

    Energy Technology Data Exchange (ETDEWEB)

    Geysermans, P.; Pontikis, V. [Centre National de la Recherche Scientifique (CNRS), 94 - Vitry-sur-Seine (France). Centre d' Etudes de Chimie Metallurgique

    2002-09-01

    The atomic structure of the solid-liquid heterophase interface was investigated by using molecular dynamics. Two kinds of systems were studied; the first one was crystalline copper with (100) and (111) surface terminations in contact with liquid aluminium, while in the second one the interface was modelled by two systems in contact made of Lennard-Jones particles with different size ({sigma}) and energy ({epsilon}) parameters. We found that at the interface the liquid was layered whatever the crystallographic orientation of the surface. The layering of the liquid is still preserved when the ratio of particles sites ({chi}={sigma}{sub 1}/{sigma}{sub 2}) changes while an epitaxial relationship is always found between the crystal and the first liquid layer. The average density of the latter is closely related to the {chi} value. (authors)

  13. Probing heterogeneous dynamics from spatial density correlation in glass-forming liquids.

    Science.gov (United States)

    Li, Yan-Wei; Zhu, You-Liang; Sun, Zhao-Yan

    2016-12-01

    We numerically investigate the connection between spatial density correlation and dynamical heterogeneity in glass-forming liquids. We demonstrate that the cluster size defined by the spatial aggregation of densely packed particles (DPPs) can better capture the difference between the dynamics of the Lennard-Jones glass model and the Weeks-Chandler-Andersen truncation model than the commonly used pair correlation functions. More interestingly, we compare the mobility of DPPs and loosely packed particles, and we find that high local density correlates well with slow dynamics in systems with relatively hard repulsive interactions but links to mobile ones in the system with soft repulsive interactions at one relaxation time scale. Our results show clear evidence that the above model dependence behavior stems from the hopping motion of DPPs at the end of the caging stage due to the compressive nature of soft repulsive spheres, which activates the dynamics of DPPs in the α relaxation stage.

  14. Dislocations and melting in two and three dimensions

    DEFF Research Database (Denmark)

    Tallon, Jeffery L.

    1980-01-01

    included, the model system may jump discontinuously from a volume below the dislocation transition to a volume above the disclination transition so that both transitions are virtual and are hidden in the first-order discontinuity. A reinterpretation of the recent molecular-dynamics simulation of two-dimensional......Comments are presented on the recent theories of two-dimensional melting which envisage melting as proceeding via two second-order transitions comprising dislocation dipole dissociation followed by disclination dipole dissociation. It is suggested that if the configurational entropy is properly...... melting of Frenkel and McTague, reveals that such is the case for a Lennard-Jones system. There may be no fundamental difference between two-and three-dimensional melting. ©1980 The American Physical Society...

  15. The structure of the solid-liquid interface: atomic size effect

    International Nuclear Information System (INIS)

    Geysermans, P.; Pontikis, V.

    2002-01-01

    The atomic structure of the solid-liquid heterophase interface was investigated by using molecular dynamics. Two kinds of systems were studied; the first one was crystalline copper with (100) and (111) surface terminations in contact with liquid aluminium, while in the second one the interface was modelled by two systems in contact made of Lennard-Jones particles with different size (σ) and energy (ε) parameters. We found that at the interface the liquid was layered whatever the crystallographic orientation of the surface. The layering of the liquid is still preserved when the ratio of particles sites (χ=σ 1 /σ 2 ) changes while an epitaxial relationship is always found between the crystal and the first liquid layer. The average density of the latter is closely related to the χ value. (authors)

  16. NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface

    DEFF Research Database (Denmark)

    Ingebrigtsen, Trond; Toxværd, Søren; Heilmann, Ole

    2011-01-01

    that ensures potential-energy and step-length conservation; center-of-mass drift is also eliminated. Analytical arguments confirmed by simulations demonstrate that the modified NVU algorithm is absolutely stable. Finally, we present simulations showing that the NVU algorithm and the standard leap-frog NVE......An algorithm is derived for computer simulation of geodesics on the constant-potential-energy hypersurface of a system of N classical particles. First, a basic time-reversible geodesic algorithm is derived by discretizing the geodesic stationarity condition and implementing the constant......-potential-energy constraint via standard Lagrangian multipliers. The basic NVU algorithm is tested by single-precision computer simulations of the Lennard-Jones liquid. Excellent numerical stability is obtained if the force cutoff is smoothed and the two initial configurations have identical potential energy within machine...

  17. Molecular dynamics investigation of tracer diffusion in a simple liquid

    International Nuclear Information System (INIS)

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

    1991-05-01

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

  18. Local elastic properties of nano-confined fluids: A density functional study

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Zongli, E-mail: zongli_sun@163.com [Science and Technology College, North China Electric Power University, Baoding 071051 (China); Kang, Yanshuang [College of Science, Agriculture University of Hebei, Baoding 071001 (China)

    2014-05-01

    The understanding of mechanical properties of confined fluids is essential for modeling and manipulating of nano-scaled systems. Unlike the uniform phase, the confined fluids usually display different features in structure and related properties. Due to the presence of the confining geometry, the density profile and many physical and chemical properties may be position-dependent. The aim of our research is to derive an expression for the local elastic property by using the classical elastic theory. Both the bulk and shear moduli are expressed as functional of density of particle. The theoretical result derived is applied to the Lennard-Jones fluids confined in nano-cavity. Comparison of our numerical result and the simulation result is made and qualitative agreement is observed. Further, influence of bulk density, temperature and external potential on moduli is calculated and the physical mechanism is analyzed. Relationship between contact modulus and the interfacial tension is also calculated. Their opposite trend with temperature is observed.

  19. Low-temperature behaviour of the Kob-Andersen binary mixture

    International Nuclear Information System (INIS)

    Ashwin S S; Sastry, Srikanth

    2003-01-01

    The dynamical behaviours of glass-forming liquids have been analysed extensively via computer simulations of model liquids, among which the Kob-Andersen binary Lennard-Jones mixture has been a widely studied system. Typically, studies of this model have been restricted to temperatures above the mode coupling temperature. Preliminary results concerning the dynamics of the Kob-Andersen binary mixture are presented at temperatures that extend below the mode coupling temperature, along with properties of the local energy minima sampled. These results show that a crossover in the dynamics occurs alongside changes in the properties of the inherent structures sampled. Furthermore, a crossover is observed from non-Arrhenius behaviour of the diffusivity above the mode coupling temperature to Arrhenius behaviour at lower temperatures

  20. Coronene molecules in helium clusters: Quantum and classical studies of energies and configurations

    Energy Technology Data Exchange (ETDEWEB)

    Rodríguez-Cantano, Rocío; Pérez de Tudela, Ricardo; Bartolomei, Massimiliano; Hernández, Marta I.; Campos-Martínez, José; González-Lezana, Tomás, E-mail: t.gonzalez.lezana@csic.es; Villarreal, Pablo [Instituto de Física Fundamental, IFF-CSIC, Serrano 123, 28006 Madrid (Spain); Hernández-Rojas, Javier; Bretón, José [Departamento de Física and IUdEA, Universidad de La Laguna, 38205 Tenerife (Spain)

    2015-12-14

    Coronene-doped helium clusters have been studied by means of classical and quantum mechanical (QM) methods using a recently developed He–C{sub 24}H{sub 12} global potential based on the use of optimized atom-bond improved Lennard-Jones functions. Equilibrium energies and geometries at global and local minima for systems with up to 69 He atoms were calculated by means of an evolutive algorithm and a basin-hopping approach and compared with results from path integral Monte Carlo (PIMC) calculations at 2 K. A detailed analysis performed for the smallest sizes shows that the precise localization of the He atoms forming the first solvation layer over the molecular substrate is affected by differences between relative potential minima. The comparison of the PIMC results with the predictions from the classical approaches and with diffusion Monte Carlo results allows to examine the importance of both the QM and thermal effects.

  1. A variational approach to nucleation simulation.

    Science.gov (United States)

    Piaggi, Pablo M; Valsson, Omar; Parrinello, Michele

    2016-12-22

    We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the liquid phase. The large free energy barriers to transition make the time scale of this process impossible to study by ordinary molecular dynamics simulations. Therefore we use a recently developed enhanced sampling method [Valsson and Parrinello, Phys. Rev. Lett.113, 090601 (2014)] based on the variational determination of a bias potential. We differ from previous applications of this method in that the bias is constructed on the basis of the physical model provided by the classical theory of nucleation. We examine the technical problems associated with this approach. Our results are very satisfactory and will pave the way for calculating the nucleation rates in many systems.

  2. Cumulative distribution functions associated with bubble-nucleation processes in cavitation

    KAUST Repository

    Watanabe, Hiroshi

    2010-11-15

    Bubble-nucleation processes of a Lennard-Jones liquid are studied by molecular dynamics simulations. Waiting time, which is the lifetime of a superheated liquid, is determined for several system sizes, and the apparent finite-size effect of the nucleation rate is observed. From the cumulative distribution function of the nucleation events, the bubble-nucleation process is found to be not a simple Poisson process but a Poisson process with an additional relaxation time. The parameters of the exponential distribution associated with the process are determined by taking the relaxation time into account, and the apparent finite-size effect is removed. These results imply that the use of the arithmetic mean of the waiting time until a bubble grows to the critical size leads to an incorrect estimation of the nucleation rate. © 2010 The American Physical Society.

  3. Application of a non-integer Bessel uniform approximation to inelastic molecular collisions

    International Nuclear Information System (INIS)

    Connor, J.N.L.; Mayne, H.R.

    1979-01-01

    A non-integer Bessel uniform approximation has been used to calculate transition probabilities for collinear atom-oscillator collisions. The collision systems used are a harmonic oscillator interacting via a Lennard-Jones potential and a Morse oscillator interacting via an exponential potential. Both classically allowed and classically forbidden transitions have been treated. The order of the Bessel function is chosen by a physical argument that makes use of information contained in the final-action initial-angle plot. Limitations of this procedure are discussed. It is shown that the non-integer Bessel approximation is accurate for elastic 0 → 0 collisions at high collision energies, where the integer Bessel approximation is inaccurate or inapplicable. (author)

  4. Classically exact surface diffusion constants at arbitrary temperature

    International Nuclear Information System (INIS)

    Voter, A.F.; Cohen, J.M.

    1989-01-01

    An expression is presented for computing the classical diffusion constant of a point defect (e.g., an adatom) in an infinite lattice of binding sites at arbitrary temperature. The transition state theory diffusion constant is simply multiplied by a dynamical correction factor that is computed from short-time classical trajectories initiated at the site boundaries. The time scale limitations of direct molecular dynamics are thus avoided in the low- and middle-temperature regimes. The expression results from taking the time derivative of the particle mean-square displacement in the lattice-discretized coordinate system. Applications are presented for surface diffusion on fcc(100) and fcc(111) Lennard-Jones crystal faces

  5. Shape matters: The case for Ellipsoids and Ellipsoidal Water

    Energy Technology Data Exchange (ETDEWEB)

    Tillack, Andreas F. [ORNL; Robinson, Bruce H. [University of Washington, Seattle

    2017-11-01

    We describe the shape potentials used for the van der Waals interactions between soft-ellipsoids used to coarse-grain molecular moieties in our Metropolis Monte-Carlo simulation software. The morphologies resulting from different expressions for these van der Waals interaction potentials are discussed for the case of a prolate spheroid system with a strong dipole at the ellipsoid center. We also show that the calculation of ellipsoids is, at worst, only about fivefold more expensive computationally when compared to a simple Lennard- Jones sphere. Finally, as an application of the ellipsoidal shape we parametrize water from the original SPC water model and observe – just through the difference in shape alone – a significant improvement of the O-O radial distribution function when compared to experimental data.

  6. Interaction energy for a fullerene encapsulated in a carbon nanotorus

    Science.gov (United States)

    Sarapat, Pakhapoom; Baowan, Duangkamon; Hill, James M.

    2018-06-01

    The interaction energy of a fullerene symmetrically situated inside a carbon nanotorus is studied. For these non-bonded molecules, the main interaction originates from the van der Waals energy which is modelled by the 6-12 Lennard-Jones potential. Upon utilising the continuum approximation which assumes that there are infinitely many atoms that are uniformly distributed over the surfaces of the molecules, the total interaction energy between the two structures is obtained as a surface integral over the spherical and the toroidal surfaces. This analytical energy is employed to determine the most stable configuration of the torus encapsulating the fullerene. The results show that a torus with major radius around 20-22 Å and minor radius greater than 6.31 Å gives rise to the most stable arrangement. This study will pave the way for future developments in biomolecules design and drug delivery system.

  7. Permeation, diffusion and dissolution of hydrogen isotopes, methane and inert gases through/in a tetrafluoroethylene film

    International Nuclear Information System (INIS)

    Matsuyama, M.; Miyake, H.; Ashida, K.; Watanabe, K.

    1982-01-01

    Tetrafluoroethylene (TFE) is widely used for conventional tritium handling systems such as vacuum seals, tubing and so on. We measured the permeation of the three hydrogen isotopes, methane and the inert gases through a TFE film at room temperature by means of the time-lag method in order to establish the physicochemical properties which determine the solubility and diffusivity of those gases. It was found that the diffusion constant of the inert gases changed exponentially with the heat of vaporization and the solubility was an exponential function of the Lennard-Jones force constant of the gases. On the other hand, hydrogen isotopes and methane deviated from these relations. It is concluded that chemical interactions between the solute and the solvent play an important role for the dissolution and the diffusion of these gases in TFE. (orig.)

  8. Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models

    DEFF Research Database (Denmark)

    Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob

    2018-01-01

    embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdWTS) scheme aimed......Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable...... at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdWTSexpression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We...

  9. Density functional study of the pressure tensor for inhomogeneous Lennard—Jones fluids

    International Nuclear Information System (INIS)

    Sun Zong-Li; Liu Zhi-Cheng; Kang Yan-Shuang; Ma Heng-Xin; Kang Yan-Mei

    2012-01-01

    Based on classical density functional theory, an expression of the pressure tensor for inhomogeneous fluids is presented. This takes into account greater correlation between particles, especially for systems that are geometrically confined or involve an interface. The density and pressure components of Lennard-Jones fluids confined in hard and softened nano-cavities are calculated. A comparison between the results of this work and IK expression suggests that the agreement depends on temperature. The interfacial tension for hard sphere fluids agrees well with the Monte Carlo result when the bulk density is not too large. The results of the solid-fluid interfacial tension for Lennard—Jones fluids demonstrate that different types of external potentials modulate the interfacial tension in different manners. (condensed matter: structural, mechanical, and thermal properties)

  10. Empirical potential for molecular simulation of graphene nanoplatelets

    Science.gov (United States)

    Bourque, Alexander J.; Rutledge, Gregory C.

    2018-04-01

    A new empirical potential for layered graphitic materials is reported. Interatomic interactions within a single graphene sheet are modeled using a Stillinger-Weber potential. Interatomic interactions between atoms in different sheets of graphene in the nanoplatelet are modeled using a Lennard-Jones interaction potential. The potential is validated by comparing molecular dynamics simulations of tensile deformation with the reported elastic constants for graphite. The graphite is found to fracture into graphene nanoplatelets when subjected to ˜15% tensile strain normal to the basal surface of the graphene stack, with an ultimate stress of 2.0 GPa and toughness of 0.33 GPa. This force field is useful to model molecular interactions in an important class of composite systems comprising 2D materials like graphene and multi-layer graphene nanoplatelets.

  11. Atomistic simulation of processes in Ni-base alloys with account for local relaxations

    International Nuclear Information System (INIS)

    Bursik, Jiri

    2007-01-01

    Ordering in Ni-base superalloys is the crucial process controlling the development of the characteristic two-phase microstructure and subsequently the mechanical properties. Systems containing up to six alloying elements typical of advanced Ni-based superalloys are modelled in this work using a Monte Carlo approach with phenomenological Lennard-Jones pair potentials and interactions up to the third coordination sphere. Three-dimensional crystal block is used with over 10 5 atoms. Molecular dynamics approach is used to relax local atomic positions in course of ordering processes under applied stress. The importance of taking into account both relaxation of modelled block dimensions and relaxation of local atomic positions is discussed

  12. Local elastic properties of nano-confined fluids: A density functional study

    International Nuclear Information System (INIS)

    Sun, Zongli; Kang, Yanshuang

    2014-01-01

    The understanding of mechanical properties of confined fluids is essential for modeling and manipulating of nano-scaled systems. Unlike the uniform phase, the confined fluids usually display different features in structure and related properties. Due to the presence of the confining geometry, the density profile and many physical and chemical properties may be position-dependent. The aim of our research is to derive an expression for the local elastic property by using the classical elastic theory. Both the bulk and shear moduli are expressed as functional of density of particle. The theoretical result derived is applied to the Lennard-Jones fluids confined in nano-cavity. Comparison of our numerical result and the simulation result is made and qualitative agreement is observed. Further, influence of bulk density, temperature and external potential on moduli is calculated and the physical mechanism is analyzed. Relationship between contact modulus and the interfacial tension is also calculated. Their opposite trend with temperature is observed.

  13. Response functions for crystals and surfaces, with applications to surface scattering

    International Nuclear Information System (INIS)

    Barker, J.A.; Steele, W.A.

    1978-01-01

    A general solution of the equations of forced motion of a harmonic crystal or other vibrating system with arbitrary time-dependent forces acting on the atoms is given. The solution is given in terms of dynamical 'response functions', for which expressions in terms of the normal mode frequencies and eigenvectors (polarization vectors) are given. Numerical calculations of the response functions are described for (111) and (100) surfaces of face-centered cubic crystals interacting with Lennard-Jones 6-12 potentials, and the qualitative features of the surface and bulk response functions are discussed. The use of these functions in problems of atomic scattering from surface is outlined, and convenient parametrized forms for this application are given. (Auth.)

  14. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics

    Science.gov (United States)

    Yin, Jian; Fenley, Andrew T.; Henriksen, Niel M.; Gilson, Michael K.

    2015-01-01

    Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by non-optimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery. PMID:26181208

  15. Adhesive contact: from atomistic model to continuum model

    International Nuclear Information System (INIS)

    Fan Kang-Qi; Jia Jian-Yuan; Zhu Ying-Min; Zhang Xiu-Yan

    2011-01-01

    Two types of Lennard-Jones potential are widely used in modeling adhesive contacts. However, the relationships between the parameters of the two types of Lennard-Jones potential are not well defined. This paper employs a self-consistent method to derive the Lennard-Jones surface force law from the interatomic Lennard-Jones potential with emphasis on the relationships between the parameters. The effect of using correct parameters in the adhesion models is demonstrated in single sphere-flat contact via continuum models and an atomistic model. Furthermore, the adhesion hysteresis behaviour is investigated, and the S-shaped force-distance relation is revealed by the atomistic model. It shows that the adhesion hysteresis loop is generated by the jump-to-contact and jump-off-contact, which are illustrated by the S-shaped force-distance curve. (atomic and molecular physics)

  16. A free energy study of the liquid-liquid phase transition of the Jagla ...

    Indian Academy of Sciences (India)

    Appendix” preliminary free energy surface calculations for select parameterizations of the generalized family of Jagla potentials spanning from the original (anomalous,water-like) Jagla model to the Lennard-Jones model. These calculations ...

  17. The Voronoi volume and molecular representation of molar volume: equilibrium simple fluids.

    Science.gov (United States)

    Hunjan, Jagtar Singh; Eu, Byung Chan

    2010-04-07

    The Voronoi volume of simple fluids was previously made use of in connection with volume transport phenomena in nonequilibrium simple fluids. To investigate volume transport phenomena, it is important to develop a method to compute the Voronoi volume of fluids in nonequilibrium. In this work, as a first step to this goal, we investigate the equilibrium limit of the nonequilibrium Voronoi volume together with its attendant related molar (molal) and specific volumes. It is proved that the equilibrium Voronoi volume is equivalent to the molar (molal) volume. The latter, in turn, is proved equivalent to the specific volume. This chain of equivalences provides an alternative procedure of computing the equilibrium Voronoi volume from the molar volume/specific volume. We also show approximate methods of computing the Voronoi and molar volumes from the information on the pair correlation function. These methods may be employed for their quick estimation, but also provide some aspects of the fluid structure and its relation to the Voronoi volume. The Voronoi volume obtained from computer simulations is fitted to a function of temperature and pressure in the region above the triple point but below the critical point. Since the fitting function is given in terms of reduced variables for the Lennard-Jones (LJ) model and the kindred volumes (i.e., specific and molar volumes) are in essence equivalent to the equation of state, the formula obtained is a reduced equation state for simple fluids obeying the LJ model potential in the range of temperature and pressure examined and hence can be used for other simple fluids.

  18. Accelerating Monte Carlo Molecular Simulations Using Novel Extrapolation Schemes Combined with Fast Database Generation on Massively Parallel Machines

    KAUST Repository

    Amir, Sahar Z.

    2013-05-01

    We introduce an efficient thermodynamically consistent technique to extrapolate and interpolate normalized Canonical NVT ensemble averages like pressure and energy for Lennard-Jones (L-J) fluids. Preliminary results show promising applicability in oil and gas modeling, where accurate determination of thermodynamic properties in reservoirs is challenging. The thermodynamic interpolation and thermodynamic extrapolation schemes predict ensemble averages at different thermodynamic conditions from expensively simulated data points. The methods reweight and reconstruct previously generated database values of Markov chains at neighboring temperature and density conditions. To investigate the efficiency of these methods, two databases corresponding to different combinations of normalized density and temperature are generated. One contains 175 Markov chains with 10,000,000 MC cycles each and the other contains 3000 Markov chains with 61,000,000 MC cycles each. For such massive database creation, two algorithms to parallelize the computations have been investigated. The accuracy of the thermodynamic extrapolation scheme is investigated with respect to classical interpolation and extrapolation. Finally, thermodynamic interpolation benefiting from four neighboring Markov chains points is implemented and compared with previous schemes. The thermodynamic interpolation scheme using knowledge from the four neighboring points proves to be more accurate than the thermodynamic extrapolation from the closest point only, while both thermodynamic extrapolation and thermodynamic interpolation are more accurate than the classical interpolation and extrapolation. The investigated extrapolation scheme has great potential in oil and gas reservoir modeling.That is, such a scheme has the potential to speed up the MCMC thermodynamic computation to be comparable with conventional Equation of State approaches in efficiency. In particular, this makes it applicable to large-scale optimization of L-J

  19. A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

    Energy Technology Data Exchange (ETDEWEB)

    Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

    2016-03-21

    The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a “first-principles” DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

  20. Numerical Investigation of the Thermal Conductivity of Graphite Nanofibers

    Science.gov (United States)

    Hakak Khadem, Masoud

    The thermal conductivity of graphite nano-fibers (GNFs) with different styles is predicted computationally. GNFs are formed as basal planes of graphene stacked based on the catalytic configuration. The large GNF thermal conductivity relative to a base phase change material (PCM) may lead to improved PCM performance when embedded with GNFs. Three different types of GNFs are modeled: platelet, ribbon, and herringbone. Molecular dynamics (MD) simulations are used in this study as a means to predict the thermal conductivity tensor based on atomic behavior. The in-house MD code, Molecular Dynamics in Arbitrary Geometries (MDAG), was updated with the features required to create the predictions. To model both interlayer van-der Waals and intralayer covalent bonding of carbon atoms in GNFs, a combination of the optimized Tersoff potential function for atoms within the layers and a pairwise Lennard-Jones (LJ) potential function to model the interactions between the layers was used. Tests of energy conservation in the NVE ensemble have been performed to validate the employed potential model. Nose-Hoover, Andersen, and Berendsen thermostats were also incorporated into MDAG to enable MD simulations in NVT ensembles, where the volume, number of atoms, and temperature of the system are conserved. Equilibrium MD with Green-Kubo (GK) relations was then employed to extract the thermal conductivity tensor for symmetric GNFs (platelet and ribbon). The thermal conductivity of solid argon at different temperatures was calculated and compared to other studies to validate the GK implementation. Different heat current formulations, as a result of using the three-body Tersoff potential, were considered and the discrepancy in the calculated thermal conductivity values of graphene using each formula was resolved by employing a novel comparative technique that identifies the most accurate formulation. The effect of stacking configuration on the thermal conductivity of platelet and ribbon GNFs

  1. The molecular dynamic simulation on impact and friction characters of nanofluids with many nanoparticles system

    Directory of Open Access Journals (Sweden)

    Bai Minli

    2011-01-01

    Full Text Available Abstract Impact and friction model of nanofluid for molecular dynamics simulation was built which consists of two Cu plates and Cu-Ar nanofluid. The Cu-Ar nanofluid model consisted of eight spherical copper nanoparticles with each particle diameter of 4 nm and argon atoms as base liquid. The Lennard-Jones potential function was adopted to deal with the interactions between atoms. Thus motion states and interaction of nanoparticles at different time through impact and friction process could be obtained and friction mechanism of nanofluids could be analyzed. In the friction process, nanoparticles showed motions of rotation and translation, but effected by the interactions of nanoparticles, the rotation of nanoparticles was trapped during the compression process. In this process, agglomeration of nanoparticles was very apparent, with the pressure increasing, the phenomenon became more prominent. The reunited nanoparticles would provide supporting efforts for the whole channel, and in the meantime reduced the contact between two friction surfaces, therefore, strengthened lubrication and decreased friction. In the condition of overlarge positive pressure, the nanoparticles would be crashed and formed particles on atomic level and strayed in base liquid.

  2. Design Guidelines and Criteria for User/Operator Transactions with Battlefield Automated Systems. Volume III-A. Human Factors Analyses of User/ Operator Transactions with TACFIRE - The Tactical Fire Direction System

    Science.gov (United States)

    1981-02-01

    7. Reseaarch Product 81-26 - DESIGN GUIDELINES AND CRITERIA FOR USER/ I;. I’OPERATOR TRANSACTIONS WITH BATTLEFIELD AUTOMIATED SYSTEMS I’ /HVtAN...FACTORS XWLYSES :’F K~R/ OPERATOR TRANSACTIONS WTHT TACFIRE - THE TACTICAL FIRE DiRECTION SY2T3EM A HUMAN FACTORS TECHNICAL AREA L~h~h K L-J 1’ U~~i~ ll...Battlefield Auto- Inter : Oct 1979-Feb 1981 mated Systems Volume III-A: Human Factors 4t C/ Analyses of User/Operator Transactions with 6. PERFORMING

  3. CalCOFI Larvae Counts, Scientific Names LJ to MA

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Fish larvae counts and standardized counts for larvae captured in CalCOFI icthyoplankton nets (primarily vertical [Calvet or Pairovet], oblique [bongo or ring nets],...

  4. LJ Best of 2009 Business Books: 32 Titles

    Science.gov (United States)

    Cords, Sarah Statz

    2010-01-01

    It should come as no surprise that a large share of this year's business books focus squarely on the 2008-09 financial crisis and security-backed mortgage implosion. Investing books followed the trend as either alarmist titles advocating selling stocks, or books urging readers to take advantage of this time to buy undervalued investments. An…

  5. Steven MacCall: Winner of LJ's 2010 Teaching Award

    Science.gov (United States)

    Berry, John N., III

    2010-01-01

    This article profiles Steven L. MacCall, winner of "Library Journal's" 2010 Teaching Award. An associate professor at the School of Library and Information Studies (SLIS) at the University of Alabama, Tuscaloosa, MacCall was nominated by Kathie Popadin, known as "Kpop" to the members of her cohort in the online MLIS program at SLIS. Sixteen of…

  6. More appropriate information systems and services for the social scientist: time to put our findings to work

    OpenAIRE

    Hunsucker, R.L.

    2007-01-01

    A review of: Line, Maurice B. "The Information Uses and Needs of Social Scientists: An Overview of INFROSS." Aslib Proceedings 23.8 (1971): 412-34. Rpt. in Lines of Thought: Selected Papers. Ed. L.J. Anthony. London: Bingley, 1988. 45-66. Objective - The study reported in this article was conceived in order to answer a question of very large scope: What are the information systems and services requirements of social scientists? Inherent in this question was the correlative question: How do so...

  7. Thermodynamic scaling of α-relaxation time and viscosity stems from the Johari-Goldstein β-relaxation or the primitive relaxation of the coupling model.

    Science.gov (United States)

    Ngai, K L; Habasaki, J; Prevosto, D; Capaccioli, S; Paluch, Marian

    2012-07-21

    By now it is well established that the structural α-relaxation time, τ(α), of non-associated small molecular and polymeric glass-formers obey thermodynamic scaling. In other words, τ(α) is a function Φ of the product variable, ρ(γ)/T, where ρ is the density and T the temperature. The constant γ as well as the function, τ(α) = Φ(ρ(γ)/T), is material dependent. Actually this dependence of τ(α) on ρ(γ)/T originates from the dependence on the same product variable of the Johari-Goldstein β-relaxation time, τ(β), or the primitive relaxation time, τ(0), of the coupling model. To support this assertion, we give evidences from various sources itemized as follows. (1) The invariance of the relation between τ(α) and τ(β) or τ(0) to widely different combinations of pressure and temperature. (2) Experimental dielectric and viscosity data of glass-forming van der Waals liquids and polymer. (3) Molecular dynamics simulations of binary Lennard-Jones (LJ) models, the Lewis-Wahnström model of ortho-terphenyl, 1,4 polybutadiene, a room temperature ionic liquid, 1-ethyl-3-methylimidazolium nitrate, and a molten salt 2Ca(NO(3))(2)·3KNO(3) (CKN). (4) Both diffusivity and structural relaxation time, as well as the breakdown of Stokes-Einstein relation in CKN obey thermodynamic scaling by ρ(γ)/T with the same γ. (5) In polymers, the chain normal mode relaxation time, τ(N), is another function of ρ(γ)/T with the same γ as segmental relaxation time τ(α). (6) While the data of τ(α) from simulations for the full LJ binary mixture obey very well the thermodynamic scaling, it is strongly violated when the LJ interaction potential is truncated beyond typical inter-particle distance, although in both cases the repulsive pair potentials coincide for some distances.

  8. Structure and stability of small Li2 +(X2Σ+ g )-Xen (n = 1-6) clusters

    Science.gov (United States)

    Saidi, Sameh; Ghanmi, Chedli; Berriche, Hamid

    2014-04-01

    We have studied the structure and stability of the Li2 +(X2Σ+ g )Xe n ( n = 1-6) clusters for special symmetry groups. The potential energy surfaces of these clusters, are described using an accurate ab initio approach based on non-empirical pseudopotential, parameterized l-dependent polarization potential and analytic potential forms for the Li+Xe and Xe-Xe interactions. The pseudopotential technique has reduced the number of active electrons of Li2 +(X2Σ+ g )-Xe n ( n = 1-6) clusters to only one electron, the Li valence electron. The core-core interactions for Li+Xe are included using accurate CCSD(T) potential fitted using the analytical form of Tang and Toennies. For the Xe-Xe potential interactions we have used the analytical form of Lennard Jones (LJ6 - 12). The potential energy surfaces of the Li2 +(X2Σ+ g )Xe n ( n = 1-6) clusters are performed for a fixed distance of the Li2 +(X2Σ+ g ) alkali dimer, its equilibrium distance. They are used to extract information on the stability of the Li2 +(X2Σ+ g Xe n ( n = 1-6) clusters. For each n, the stability of the different isomers is examined by comparing their potential energy surfaces. Moreover, we have determined the quantum energies ( D 0), the zero-point-energies (ZPE) and the ZPE%. To our best knowledge, there are neither experimental nor theoretical works realized for the Li2 +(X2Σ+ g Xe n ( n = 1-6) clusters, our results are presented for the first time.

  9. Highly efficient molecular simulation methods for evaluation of thermodynamic properties of crystalline phases

    Science.gov (United States)

    Moustafa, Sabry Gad Al-Hak Mohammad

    shown to vary slowly with system-size. This allow us to get the FE in the thermodynamic limit by extrapolating the one isomer results to infinity and correct for that by the effect from considering proton-disorder measured at a small system. These techniques are applied to empty hydrates (of types: SI, SII, and SH) to estimate their thermodynamic stability. For conditions where the harmonic model fails, performing MS is needed to estimate rigorously the full (harmonic plus anharmonic) quantity. Although several MS methods are available for that purpose, they do not benefit from the harmonic nature of crystals---which represents the main contribution and is cheap to compute. In other words, those "conventional" methods always "start from scratch" even at states where anharmonic part is negligible. In this work, we develop very efficient MS methods that leverage information, on-the-fly, from the harmonic behavior of configurations such that the anharmonic contributions are directly measured. The approach is named harmonically-mapped averaging (HMA) for the rest of this thesis. Since the major contribution of thermodynamic properties comes from the harmonic nature of crystal, the fluctuations in the anharmonic quantities is to be small; hence, uncertainty associated with the HMA method is small. The HMA method is given in a general formulation such that it can handle properties related to both first- and second-derivatives of free energy. The HMA approach is first applied to Lennard-Jones (LJ) model. First- and second-derivatives of FE with respect to temperature and volume yield the following properties: energy, pressure, isochoric heat capacity, bulk modulus, and thermal pressure coefficient. A considerable improvement in the efficiency of measuring those properties is observed even at melting conditions where anharmonicity is non-negligible. First-derivative properties are computed with 100 to 10,000 times less computational effort, while speedup for the second

  10. Accurate and precise determination of critical properties from Gibbs ensemble Monte Carlo simulations

    International Nuclear Information System (INIS)

    Dinpajooh, Mohammadhasan; Bai, Peng; Allan, Douglas A.; Siepmann, J. Ilja

    2015-01-01

    Since the seminal paper by Panagiotopoulos [Mol. Phys. 61, 813 (1997)], the Gibbs ensemble Monte Carlo (GEMC) method has been the most popular particle-based simulation approach for the computation of vapor–liquid phase equilibria. However, the validity of GEMC simulations in the near-critical region has been questioned because rigorous finite-size scaling approaches cannot be applied to simulations with fluctuating volume. Valleau [Mol. Simul. 29, 627 (2003)] has argued that GEMC simulations would lead to a spurious overestimation of the critical temperature. More recently, Patel et al. [J. Chem. Phys. 134, 024101 (2011)] opined that the use of analytical tail corrections would be problematic in the near-critical region. To address these issues, we perform extensive GEMC simulations for Lennard-Jones particles in the near-critical region varying the system size, the overall system density, and the cutoff distance. For a system with N = 5500 particles, potential truncation at 8σ and analytical tail corrections, an extrapolation of GEMC simulation data at temperatures in the range from 1.27 to 1.305 yields T c = 1.3128 ± 0.0016, ρ c = 0.316 ± 0.004, and p c = 0.1274 ± 0.0013 in excellent agreement with the thermodynamic limit determined by Potoff and Panagiotopoulos [J. Chem. Phys. 109, 10914 (1998)] using grand canonical Monte Carlo simulations and finite-size scaling. Critical properties estimated using GEMC simulations with different overall system densities (0.296 ≤ ρ t ≤ 0.336) agree to within the statistical uncertainties. For simulations with tail corrections, data obtained using r cut = 3.5σ yield T c and p c that are higher by 0.2% and 1.4% than simulations with r cut = 5 and 8σ but still with overlapping 95% confidence intervals. In contrast, GEMC simulations with a truncated and shifted potential show that r cut = 8σ is insufficient to obtain accurate results. Additional GEMC simulations for hard-core square-well particles with various

  11. Comparative molecular simulation study of low and high density polymer glasses: A competition between attractive and repulsive interactions

    Science.gov (United States)

    Singh, Jalim; Jose, Prasanth

    Results of molecular dynamics simulations of a system of Kremer and Grest linear polymer melts are presented at moderate and high number density. A detailed study of molecular pair distribution function shows that potential of mean force between the molecules has form of Gaussian with an attractive tail at number density ρ = 0.85 (in Lennard-Jones units), which is due to the dominating attractive interactions from temperature T = 0.7. This system shows gelation assisted glass transition, which is interpreted from peaks of molecular structure factor at small wave-numbers. At low temperature, this system phase separate to form dense domains whose local density is high; these domains show many dynamical features of glass transition in monomer and molecular level of relaxation indicating glass transition is assisted by gelation in this system. In the same system, at ρ = 1.0, repulsive interactions dominate, structure does not change even at low temperatures; the system exhibits dynamic heterogeneity and known to undergo glass transition. In this work, we compare and contrast the structure and dynamics of the system near its glass transition. Also, we computed correlation length of systems from the peak value of four-point structural dynamic susceptibility. HPC facility at IIT Mandi.

  12. A Four-Site Molecular Model for Simulations of Liquid Methanol and Water-Methanol Mixtures: MeOH-4P.

    Science.gov (United States)

    Martínez-Jiménez, Manuel; Saint-Martin, Humberto

    2018-04-17

    In this work, we present a new four-site potential for methanol, MeOH-4P, fitted to reproduce the dielectric constant ε, the surface tension γ s , and the liquid density ρ of the pure liquid at T = 298.15 K and p = 1 bar. The partial charges on each site were taken from the OPLS/2016 model with the only difference of putting the negative charge on the fourth site ( M) instead of on the O atom, as done in four-site water models. The original Lennard-Jones (LJ) parameters of OPLS/2016 for the methyl moiety (Me) were modified for the fitting of ρ and γ s , whereas the parameters of the TIP4P-FB water model were used for the O atom without change. Taking into account the energetic cost of the enhanced dipole relative to the isolated molecule, the results from simulations with this model showed good agreement with experiments for ρ, α p , κ T , C p , and Δ H v- l . Also, the temperature dependence of γ s and ε is satisfactory in the interval between 260 and 360 K, and the critical point description is similar to that of OPLS/2016. It is shown that orientational correlations, described by the Kirkwood factor G k , play a prominent role in the appropriate description of dielectric constants in existing models; unfortunately, the enhancement of the dipole moment produced a low diffusion coefficient D MeOH ; thus, a compromise was required between a good reproduction of ε and an acceptable D MeOH . The use of a fourth site resulted in a significant improvement for water-methanol mixtures described with TIP4P-FB and MeOH-4P, respectively, but required the modification of the LJ geometric combination rule to allow a good description of the methanol molar-fraction dependence of ρ, ε, and methanol (water) diffusion coefficients D MeOH ( D H 2 O ) and excess volume of mixing Δ V mix in the entire range of composition. The resulting free energy of hydration Δ G hyd shows excellent agreement with experiments in the interval between 280 and 360 K.

  13. Low pressure broadening and shift of the 540.06 nm line of neon

    International Nuclear Information System (INIS)

    Bielski, A.; Dokurno, W.; Szudy, J.; Wolnikowski, J.

    1980-01-01

    The collision broadening and shift of the 540.06 nm line of neon emitted from a low pressure glow discharge in pure neon and a neon-helium mixture have been measured. The values of the broadening and shift coefficients were determined and compared with the results of calculations based on the Lindholm-Foley impact theory assuming a Lennard-Jones potential. The results for pure neon demonstrate the inadequacy of the Lennard-Jones potential for the Ne-Ne interaction. (orig.)

  14. Calculation of thermal-diffusion coefficients from plane-wave fluctuations in the heat energy density

    International Nuclear Information System (INIS)

    Palmer, B.J.

    1994-01-01

    A method to calculate the thermal diffusivity D T from spontaneous fluctuations in the local heat energy density is presented. Calculations of the thermal diffusivity are performed for the Lennard-Jones fluid, carbon dioxide, and water. The results for the Lennard-Jones fluid are in agreement with calculations of the thermal conductivity using Green-Kubo relations and nonequilibrium molecular-dynamics techniques. The results for carbon dioxide and water give thermal diffusivities within a factor of 2 of the experimental values

  15. Laser Photochemistry.

    Science.gov (United States)

    1981-07-01

    inverted by the first, i.e., at the moment of time t = T, such that i = (2n+)lT, where 0 is the Rabi frequency (Oraevski et al., 1976). . classical... anisotropic molecule present. CW HeNe, Ar+ and Kr+ lasers are used, and the filter method is necessary because of time-scales lo8 - 10ll Hz. Some general...e.g., truncated harmonic oscillator, square well, spherically symmetric Morse or Lennard-Jones, anisotropic (angle-dependent) Morse or Lennard-Jones

  16. Parallel continuous simulated tempering and its applications in large-scale molecular simulations

    Energy Technology Data Exchange (ETDEWEB)

    Zang, Tianwu; Yu, Linglin; Zhang, Chong [Applied Physics Program and Department of Bioengineering, Rice University, Houston, Texas 77005 (United States); Ma, Jianpeng, E-mail: jpma@bcm.tmc.edu [Applied Physics Program and Department of Bioengineering, Rice University, Houston, Texas 77005 (United States); Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, Texas 77030 (United States)

    2014-07-28

    In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); C. Zhang and J. Ma, J. Chem. Phys. 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2–3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard-Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent.

  17. Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures.

    Science.gov (United States)

    Bishop, Kevin P; Roy, Pierre-Nicholas

    2018-03-14

    Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

  18. Geometric integrator for simulations in the canonical ensemble

    Energy Technology Data Exchange (ETDEWEB)

    Tapias, Diego, E-mail: diego.tapias@nucleares.unam.mx [Departamento de Física, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510 (Mexico); Sanders, David P., E-mail: dpsanders@ciencias.unam.mx [Departamento de Física, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510 (Mexico); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Bravetti, Alessandro, E-mail: alessandro.bravetti@iimas.unam.mx [Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510 (Mexico)

    2016-08-28

    We introduce a geometric integrator for molecular dynamics simulations of physical systems in the canonical ensemble that preserves the invariant distribution in equations arising from the density dynamics algorithm, with any possible type of thermostat. Our integrator thus constitutes a unified framework that allows the study and comparison of different thermostats and of their influence on the equilibrium and non-equilibrium (thermo-)dynamic properties of a system. To show the validity and the generality of the integrator, we implement it with a second-order, time-reversible method and apply it to the simulation of a Lennard-Jones system with three different thermostats, obtaining good conservation of the geometrical properties and recovering the expected thermodynamic results. Moreover, to show the advantage of our geometric integrator over a non-geometric one, we compare the results with those obtained by using the non-geometric Gear integrator, which is frequently used to perform simulations in the canonical ensemble. The non-geometric integrator induces a drift in the invariant quantity, while our integrator has no such drift, thus ensuring that the system is effectively sampling the correct ensemble.

  19. Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

    International Nuclear Information System (INIS)

    Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten

    2017-01-01

    Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

  20. Geometric integrator for simulations in the canonical ensemble

    International Nuclear Information System (INIS)

    Tapias, Diego; Sanders, David P.; Bravetti, Alessandro

    2016-01-01

    We introduce a geometric integrator for molecular dynamics simulations of physical systems in the canonical ensemble that preserves the invariant distribution in equations arising from the density dynamics algorithm, with any possible type of thermostat. Our integrator thus constitutes a unified framework that allows the study and comparison of different thermostats and of their influence on the equilibrium and non-equilibrium (thermo-)dynamic properties of a system. To show the validity and the generality of the integrator, we implement it with a second-order, time-reversible method and apply it to the simulation of a Lennard-Jones system with three different thermostats, obtaining good conservation of the geometrical properties and recovering the expected thermodynamic results. Moreover, to show the advantage of our geometric integrator over a non-geometric one, we compare the results with those obtained by using the non-geometric Gear integrator, which is frequently used to perform simulations in the canonical ensemble. The non-geometric integrator induces a drift in the invariant quantity, while our integrator has no such drift, thus ensuring that the system is effectively sampling the correct ensemble.

  1. Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

    Science.gov (United States)

    Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten

    2017-11-01

    Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

  2. GPU-accelerated Gibbs ensemble Monte Carlo simulations of Lennard-Jonesium

    Science.gov (United States)

    Mick, Jason; Hailat, Eyad; Russo, Vincent; Rushaidat, Kamel; Schwiebert, Loren; Potoff, Jeffrey

    2013-12-01

    This work describes an implementation of canonical and Gibbs ensemble Monte Carlo simulations on graphics processing units (GPUs). The pair-wise energy calculations, which consume the majority of the computational effort, are parallelized using the energetic decomposition algorithm. While energetic decomposition is relatively inefficient for traditional CPU-bound codes, the algorithm is ideally suited to the architecture of the GPU. The performance of the CPU and GPU codes are assessed for a variety of CPU and GPU combinations for systems containing between 512 and 131,072 particles. For a system of 131,072 particles, the GPU-enabled canonical and Gibbs ensemble codes were 10.3 and 29.1 times faster (GTX 480 GPU vs. i5-2500K CPU), respectively, than an optimized serial CPU-bound code. Due to overhead from memory transfers from system RAM to the GPU, the CPU code was slightly faster than the GPU code for simulations containing less than 600 particles. The critical temperature Tc∗=1.312(2) and density ρc∗=0.316(3) were determined for the tail corrected Lennard-Jones potential from simulations of 10,000 particle systems, and found to be in exact agreement with prior mixed field finite-size scaling calculations [J.J. Potoff, A.Z. Panagiotopoulos, J. Chem. Phys. 109 (1998) 10914].

  3. Local free energies for the coarse-graining of adsorption phenomena: The interacting pair approximation

    Science.gov (United States)

    Pazzona, Federico G.; Pireddu, Giovanni; Gabrieli, Andrea; Pintus, Alberto M.; Demontis, Pierfranco

    2018-05-01

    We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely accepted approach, in which the contributions to the free energy given by the molecules located in two neighboring pores are estimated through Monte Carlo simulations where the two pores are kept separated from the rest of the system, leads to inaccurate results at high sorbate densities. In the coarse-graining strategy that we propose, which is based on the Bethe-Peierls approximation, density-independent interaction terms are instead computed according to local effective potentials that take into account the correlations between the pore pair and its surroundings by means of mean-field correction terms without the need for simulating the pore pair separately. Use of the interaction parameters obtained this way allows the coarse-grained system to reproduce more closely the equilibrium properties of the original one. Results are shown for lattice-gases where the local free energy can be computed exactly and for a system of Lennard-Jones particles under the effect of a static confining field.

  4. Algorithms for GPU-based molecular dynamics simulations of complex fluids: Applications to water, mixtures, and liquid crystals.

    Science.gov (United States)

    Kazachenko, Sergey; Giovinazzo, Mark; Hall, Kyle Wm; Cann, Natalie M

    2015-09-15

    A custom code for molecular dynamics simulations has been designed to run on CUDA-enabled NVIDIA graphics processing units (GPUs). The double-precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse-grained and atomistic models, holonomic constraints, Nosé-Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard-Jones and Gay-Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n-hexane/2-propanol mixture; and a liquid crystal mesogen, 2-(4-butyloxyphenyl)-5-octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33-119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69-287 fold improvement and three GPUs yield a 101-377 fold speedup. © 2015 Wiley Periodicals, Inc.

  5. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.

    1979-01-01

    Over the last fifteen years computer modeling of liquids and solids has become a useful method of understanding the structural and dynamical correlations in these systems. Some characteristics of the method are presented with an example from work on homogeneous nucleation in monoatomic liquids; the interaction potential determines the structure: a Lennard--Jones system nucleates a close packed structure while an alkali metal potential nucleates a bcc packing. In the study of ionic systems like CaF 2 the Coulomb interaction together with the short range repulsion is enough to produce a satisfactory model for the motion of F - ions in CaF 2 at approx. 1600 0 K. Analysis of this motion shows that F - ions reside at their fluorite sites for about 6 x 10 -12 s and that the diffusion is mainly due to F - jumps in the 100 direction. The motion can be analyzed in terms of the generation and annihilation of anti-Frenkel pairs. The temperature dependence of the F - diffusion constant at two different densities has also been calculated. The computer model does not correspond with experiment in this regard

  6. Contribution to diffusion mechanism study in amorphous metallic alloys

    International Nuclear Information System (INIS)

    Delaye, Jean-Marc

    1993-01-01

    This work is dedicated to the study of the vacancy diffusion mechanism in mono-elementary and binary amorphous Lennard-Jones systems, by a molecular dynamics method. The first chapter is a review of the preceding works performed before the beginning of this thesis, the method of simulation is described in the second chapter. We showed in the following chapters that the vacancies, introduced by the removal of one atom, remain stable on a large percentage of sites, especially in the binary system. By calculating some thermodynamical values, formation and migration enthalpies and entropies, we showed that the vacancy mechanism is magnified in a disordered system, as compared to a crystal of the same composition, and therefore can explain the magnitudes of the experimental diffusion coefficients. In parallel, to measure diffusion coefficients, we have settled an experimental method based on the evolution of the resistivity of a multilayer sample during interdiffusion, a gold-silver multilayer in our case (chapter six). By measurements under pressure, the activation volume is determined and our results agree well with the preceding ones. (author) [fr

  7. Equilibrium and non equilibrium in fragmentation

    International Nuclear Information System (INIS)

    Dorso, C.O.; Chernomoretz, A.; Lopez, J.A.

    2001-01-01

    Full text: In this communication we present recent results regarding the interplay of equilibrium and non equilibrium in the process of fragmentation of excited finite Lennard Jones drops. Because the general features of such a potential resemble the ones of the nuclear interaction (fact that is reinforced by the similarity between the EOS of both systems) these studies are not only relevant from a fundamental point of view but also shed light on the problem of nuclear multifragmentation. We focus on the microscopic analysis of the state of the fragmenting system at fragmentation time. We show that the Caloric Curve (i e. the functional relationship between the temperature of the system and the excitation energy) is of the type rise plateau with no vapor branch. The usual rise plateau rise pattern is only recovered when equilibrium is artificially imposed. This result puts a serious question on the validity of the freeze out hypothesis. This feature is independent of the dimensionality or excitation mechanism. Moreover we explore the behavior of magnitudes which can help us determine the degree of the assumed phase transition. It is found that no clear cut criteria is presently available. (Author)

  8. Yield point of metallic glass

    International Nuclear Information System (INIS)

    Shimizu, Futoshi; Ogata, Shigenobu; Li, Ju

    2006-01-01

    Shear bands form in most bulk metallic glasses (BMGs) within a narrow range of uniaxial strain ε y ≅ 2%. We propose this critical condition corresponds to embryonic shear band (ESB) propagation, not its nucleation. To propagate an ESB, the far-field shear stress τ ∞ ∼ Eε y /2 must exceed the quasi-steady-state glue traction τ glue of shear-alienated glass until the glass transition temperature is approached internally due to frictional heating, at which point ESB matures as a runaway shear crack. The incubation length scale l inc necessary for this maturation is estimated to be ∼10 2 nm for Zr-based BMGs, below which sample size-scale shear localization does not happen. In shear-alienated glass, the last resistance against localized shearing comes from extremely fast downhill dissipative dynamics of timescale comparable to atomic vibrations, allowing molecular dynamics (MD) simulations to capture this recovery process which governs τ glue . We model four metallic glasses: a binary Lennard-Jones system, two binary embedded atom potential systems and a quinternary embedded atom system. Despite vast differences in the structure and interatomic interactions, the four MD calculations give ε y predictions of 2.4%, 2.1%, 2.6% and 2.9%, respectively

  9. Capillary condensation hysteresis in overlapping spherical pores: a Monte Carlo simulation study.

    Science.gov (United States)

    Gor, Gennady Yu; Rasmussen, Christopher J; Neimark, Alexander V

    2012-08-21

    The mechanisms of hysteretic phase transformations in fluids confined to porous bodies depend on the size and shape of pores, as well as their connectivity. We present a Monte Carlo simulation study of capillary condensation and evaporation cycles in the course of Lennard-Jones fluid adsorption in the system of overlapping spherical pores. This model system mimics pore shape and connectivity in some mesoporous materials obtained by templating cubic surfactant mesophases or colloidal crystals. We show different mechanisms of capillary hysteresis depending on the size of the window between the pores. For the system with a small window, the hysteresis cycle is similar to that in a single spherical pore: capillary condensation takes place upon achieving the limit of stability of adsorption film and evaporation is triggered by cavitation. When the window is large enough, the capillary condensation shifts to a pressure higher than that of the isolated pore, and the possibility for the equilibrium mechanism of desorption is revealed. These finding may have important implications for practical problems of assessment of the pore size distributions in mesoporous materials with cagelike pore networks.

  10. Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

    Science.gov (United States)

    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.

  11. Pressure effects on martensitic transformation under quenching process in a molecular dynamics model of NiAl alloy

    International Nuclear Information System (INIS)

    Kazanc, S.; Ozgen, S.; Adiguzel, O.

    2003-01-01

    The solid-solid phase transitions in NiAl alloys occur by the temperature changes and application of a pressure on the system. Both types of transitions are called martensitic transformation and have displacive and thermoelastic characters. Pressure effects on thermoelastic transformation in Ni 62.5 Al 37.5 alloy model have been studied by means of molecular dynamics method proposed by Parrinello-Rahman. Interaction forces between atoms in the model system were calculated by Lennard-Jones potential energy function. Thermodynamics and structural analysis of the martensitic transformations under hydrostatic pressure during the quenching processes have been performed. The simulation runs have been carried out in different hydrostatic pressures changing from zero to 40.65 GPa during the quenching process of the model alloy. At the zero and nonzero pressures, the system with B2-type ordered structure undergoes the product phase with L1 0 -type ordered structure by Bain distortion in the first step of martensitic transformation under the quenching process. The increase in hydrostatic pressure causes decrease in the formation time of the product phase, and twin-like lattice distortion is observed in low temperature L1 0 phase

  12. Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

    Science.gov (United States)

    Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

    2018-03-13

    Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

  13. The energetics and structure of nickel clusters: Size dependence

    International Nuclear Information System (INIS)

    Cleveland, C.L.; Landman, U.

    1991-01-01

    The energetics of nickel clusters over a broad size range are explored within the context of the many-body potentials obtained via the embedded atom method. Unconstrained local minimum energy configurations are found for single crystal clusters consisting of various truncations of the cube or octahedron, with and without (110) faces, as well as some monotwinnings of these. We also examine multitwinned structures such as icosahedra and various truncations of the decahedron, such as those of Ino and Marks. These clusters range in size from 142 to over 5000 atoms. As in most such previous studies, such as those on Lennard-Jones systems, we find that icosahedral clusters are favored for the smallest cluster sizes and that Marks' decahedra are favored for intermediate sizes (all our atomic systems larger than about 2300 atoms). Of course very large clusters will be single crystal face-centered-cubic (fcc) polyhedra: the onset of optimally stable single-crystal nickel clusters is estimated to occur at 17 000 atoms. We find, via comparisons to results obtained via atomistic calculations, that simple macroscopic expressions using accurate surface, strain, and twinning energies can usefully predict energy differences between different structures even for clusters of much smaller size than expected. These expressions can be used to assess the relative energetic merits of various structural motifs and their dependence on cluster size

  14. Constant pressure and temperature discrete-time Langevin molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Grønbech-Jensen, Niels [Department of Mechanical and Aerospace Engineering, University of California, Davis, California 95616 (United States); Department of Mathematics, University of California, Davis, California 95616 (United States); Farago, Oded [Department of Biomedical Engineering, Ben Gurion University of the Negev, Be' er Sheva 84105 (Israel); Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Be' er Sheva 84105 (Israel)

    2014-11-21

    We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are built on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems—a one-dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three-dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb and Dünweg [J. Chem. Phys. 111, 4453 (1999)], show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation.

  15. Interfacial layering and capillary roughness in immiscible liquids.

    Science.gov (United States)

    Geysermans, P; Pontikis, V

    2010-08-21

    The capillary roughness and the atomic density profiles of extended interfaces between immiscible liquids are determined as a function of the interface area by using molecular dynamics and Lennard-Jones (12-6) potentials. We found that with increasing area, the interface roughness diverges logarithmically, thus fitting the theoretical mean-field prediction. In systems small enough for the interfacial roughness not to blur the structural details, atomic density profiles across the fluid interface are layered with correlation length in the range of molecular correlations in liquids. On increasing the system size, the amplitude of the thermally excited position fluctuations of the interface increases, thus causing layering to rapidly vanish, if density profiles are computed without special care. In this work, we present and validate a simple method, operating in the direct space, for extracting from molecular dynamics trajectories the "intrinsic" structure of a fluid interface that is the local density profile of the interface cleaned from capillary wave effects. Estimated values of interfacial properties such as the tension, the intrinsic width, and the lower wavelength limit of position fluctuations are in agreement with results collected from the literature.

  16. Clustering and phase behaviour of attractive active particles with hydrodynamics.

    Science.gov (United States)

    Navarro, Ricard Matas; Fielding, Suzanne M

    2015-10-14

    We simulate clustering, phase separation and hexatic ordering in a monolayered suspension of active squirming disks subject to an attractive Lennard-Jones-like pairwise interaction potential, taking hydrodynamic interactions between the particles fully into account. By comparing the hydrodynamic case with counterpart simulations for passive and active Brownian particles, we elucidate the relative roles of self-propulsion, interparticle attraction, and hydrodynamic interactions in determining clustering and phase behaviour. Even in the presence of an attractive potential, we find that hydrodynamic interactions strongly suppress the motility induced phase separation that might a priori have been expected in a highly active suspension. Instead, we find only a weak tendency for the particles to form stringlike clusters in this regime. At lower activities we demonstrate phase behaviour that is broadly equivalent to that of the counterpart passive system at low temperatures, characterized by regimes of gas-liquid, gas-solid and liquid-solid phase coexistence. In this way, we suggest that a dimensionless quantity representing the level of activity relative to the strength of attraction plays the role of something like an effective non-equilibrium temperature, counterpart to the (dimensionless) true thermodynamic temperature in the passive system. However there are also some important differences from the equilibrium case, most notably with regards the degree of hexatic ordering, which we discuss carefully.

  17. Speeding up Monte Carlo molecular simulation by a non-conservative early rejection scheme

    KAUST Repository

    Kadoura, Ahmad Salim

    2015-04-23

    Monte Carlo (MC) molecular simulation describes fluid systems with rich information, and it is capable of predicting many fluid properties of engineering interest. In general, it is more accurate and representative than equations of state. On the other hand, it requires much more computational effort and simulation time. For that purpose, several techniques have been developed in order to speed up MC molecular simulations while preserving their precision. In particular, early rejection schemes are capable of reducing computational cost by reaching the rejection decision for the undesired MC trials at an earlier stage in comparison to the conventional scheme. In a recent work, we have introduced a ‘conservative’ early rejection scheme as a method to accelerate MC simulations while producing exactly the same results as the conventional algorithm. In this paper, we introduce a ‘non-conservative’ early rejection scheme, which is much faster than the conservative scheme, yet it preserves the precision of the method. The proposed scheme is tested for systems of structureless Lennard-Jones particles in both canonical and NVT-Gibbs ensembles. Numerical experiments were conducted at several thermodynamic conditions for different number of particles. Results show that at certain thermodynamic conditions, the non-conservative method is capable of doubling the speed of the MC molecular simulations in both canonical and NVT-Gibbs ensembles. © 2015 Taylor & Francis

  18. Simple relationship between the virial-route hypernetted-chain and the compressibility-route Percus-Yevick values of the fourth virial coefficient.

    Science.gov (United States)

    Santos, Andrés; Manzano, Gema

    2010-04-14

    As is well known, approximate integral equations for liquids, such as the hypernetted chain (HNC) and Percus-Yevick (PY) theories, are in general thermodynamically inconsistent in the sense that the macroscopic properties obtained from the spatial correlation functions depend on the route followed. In particular, the values of the fourth virial coefficient B(4) predicted by the HNC and PY approximations via the virial route differ from those obtained via the compressibility route. Despite this, it is shown in this paper that the value of B(4) obtained from the virial route in the HNC theory is exactly three halves the value obtained from the compressibility route in the PY theory, irrespective of the interaction potential (whether isotropic or not), the number of components, and the dimensionality of the system. This simple relationship is confirmed in one-component systems by analytical results for the one-dimensional penetrable-square-well model and the three-dimensional penetrable-sphere model, as well as by numerical results for the one-dimensional Lennard-Jones model, the one-dimensional Gaussian core model, and the three-dimensional square-well model.

  19. Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass.

    Science.gov (United States)

    Snyder, James A; Abramyan, Tigran; Yancey, Jeremy A; Thyparambil, Aby A; Wei, Yang; Stuart, Steven J; Latour, Robert A

    2012-12-01

    Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5-9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.

  20. Fast-forward Langevin dynamics with momentum flips

    Science.gov (United States)

    Hijazi, Mahdi; Wilkins, David M.; Ceriotti, Michele

    2018-05-01

    Stochastic thermostats based on the Langevin equation, in which a system is coupled to an external heat bath, are popular methods for temperature control in molecular dynamics simulations due to their ergodicity and their ease of implementation. Traditionally, these thermostats suffer from sluggish behavior in the limit of high friction, unlike thermostats of the Nosé-Hoover family whose performance degrades more gently in the strong coupling regime. We propose a simple and easy-to-implement modification to the integration scheme of the Langevin algorithm that addresses the fundamental source of the overdamped behavior of high-friction Langevin dynamics: if the action of the thermostat causes the momentum of a particle to change direction, it is flipped back. This fast-forward Langevin equation preserves the momentum distribution and so guarantees the correct equilibrium sampling. It mimics the quadratic behavior of Nosé-Hoover thermostats and displays similarly good performance in the strong coupling limit. We test the efficiency of this scheme by applying it to a 1-dimensional harmonic oscillator, as well as to water and Lennard-Jones polymers. The sampling efficiency of the fast-forward Langevin equation thermostat, measured by the correlation time of relevant system variables, is at least as good as the traditional Langevin thermostat, and in the overdamped regime, the fast-forward thermostat performs much better, improving the efficiency by an order of magnitude at the highest frictions we considered.

  1. Fluids in micropores. V. Effects of thermal motion in the walls of a slit-micropore

    International Nuclear Information System (INIS)

    Diestler, D.J.; Schoen, M.

    1996-01-01

    Previous articles in this series have concerned the prototypal slit-pore with rigid walls, in which a Lennard-Jones (12,6) monatomic film is constrained between two plane-parallel walls comprising like atoms fixed in the face-centered-cubic (fcc) (100) configuration. The behavior of molecularly thin films in the rigid-wall prototype is governed by the template effect, whereby solid films can form epitaxially when the walls are properly aligned in the lateral directions. In this article the influence of thermal motion of the wall atoms on the template effect is investigated. The walls are treated as Einstein solids, the atoms moving independently in harmonic potentials centered on rigidly fixed equilibrium positions in the fcc (100) configuration. The force constant f c is a measure of the stiffness of the walls, the rigid-wall limit being f c =∞. Formal thermodynamic and statistical mechanical analyses of the system are carried out. The results of grand canonical ensemble Monte Carlo simulations indicate that for values of f c characteristic of a soft (e.g., noble-gas) crystal dynamic coupling between wall and film has a substantial influence on such equilibrium properties as normal stress (load) and interfacial tensions. In general, the softer the walls (i.e., the smaller the value of f c ), the weaker the template effect and hence the softer and more disordered the confined film. copyright 1996 American Institute of Physics

  2. Stokes-Einstein relation for pure simple fluids

    Science.gov (United States)

    Cappelezzo, M.; Capellari, C. A.; Pezzin, S. H.; Coelho, L. A. F.

    2007-06-01

    The authors employed the equilibrium molecular dynamics technique to calculate the self-diffusion coefficient and the shear viscosity for simple fluids that obey the Lennard-Jones 6-12 potential in order to investigate the validity of the Stokes-Einstein (SE) relation for pure simple fluids. They performed calculations in a broad range of density and temperature in order to test the SE relation. The main goal of this work is to exactly calculate the constant, here denominated by α, present in the SE relation. Also, a modified SE relation where a fluid density is raised to a power in the usual expression is compared to the classical expression. According to the authors' simulations slip boundary conditions (α=4) can be satisfied in some state points. An intermediate value of α =5 was found in some regions of the phase diagram confirming the mode coupling theory. In addition depending on the phase diagram point and the definition of hydrodynamics radius, stick boundary condition (α=6) can be reproduced. The authors investigated the role of the hydrodynamic radius in the SE relation using three different definitions. The authors also present calculations for α in a hard-sphere system showing that the slip boundary conditions hold at very high density. They discuss possible explanations for their results and the role of the hydrodynamic radius for different definitions in the SE relation.

  3. Computer simulation of liquid crystals

    International Nuclear Information System (INIS)

    McBride, C.

    1999-01-01

    Molecular dynamics simulation performed on modern computer workstations provides a powerful tool for the investigation of the static and dynamic characteristics of liquid crystal phases. In this thesis molecular dynamics computer simulations have been performed for two model systems. Simulations of 4,4'-di-n-pentyl-bibicyclo[2.2.2]octane demonstrate the growth of a structurally ordered phase directly from an isotropic fluid. This is the first time that this has been achieved for an atomistic model. The results demonstrate a strong coupling between orientational ordering and molecular shape, but indicate that the coupling between molecular conformational changes and molecular reorientation is relatively weak. Simulations have also been performed for a hybrid Gay-Berne/Lennard-Jones model resulting in thermodynamically stable nematic and smectic phases. Frank elastic constants have been calculated for the nematic phase formed by the hybrid model through analysis of the fluctuations of the nematic director, giving results comparable with those found experimentally. Work presented in this thesis also describes the parameterization of the torsional potential of a fragment of a dimethyl siloxane polymer chain, disiloxane diol (HOMe 2 Si) 2 O, using ab initio quantum mechanical calculations. (author)

  4. Collision of hydrogen molecules interacting with two grapheme sheets

    Directory of Open Access Journals (Sweden)

    Malivuk-Gak Dragana

    2017-01-01

    Full Text Available It have been performed the computational experiments with two hydrogen molecules and two graphene sheets. Hydrogen - hydrogen and hydrogen - carbon interactions are described by Lennard - Jones potential. Equations of motion of the wave packet centre are solved numerically. The initial molecule velocity was determined by temperature and collisions occur in central point between two sheets. The molecules after collision stay near or get far away of graphene sheets. Then one can find what temperatures, graphene sheet sizes and their distances are favourable for hydrogen storage. It is found that quantum corrections of the molecule classical trajectories are not significant here. Those investigations of possibility of hydrogen storage by physisorption are of interest for improvement of the fuel cell systems. The main disadvantages of computational experiments are: (1 it cannot compute with very large number of C atoms, (2 it is assumed that carbon atoms are placed always in their equilibrium positions and (3 the changes of wave packet width are not considered.

  5. Homogeneous SPC/E water nucleation in large molecular dynamics simulations.

    Science.gov (United States)

    Angélil, Raymond; Diemand, Jürg; Tanaka, Kyoko K; Tanaka, Hidekazu

    2015-08-14

    We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to ∼ 4 ⋅ 10(6) molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to ∼ 10(19) cm(-3) s(-1), helping close the gap between experimentally measured rates ∼ 10(17) cm(-3) s(-1). We are also able to precisely measure size distributions, sticking efficiencies, cluster temperatures, and cluster internal densities. We introduce a new functional form to implement the Yasuoka-Matsumoto nucleation rate measurement technique (threshold method). Comparison to nucleation models shows that classical nucleation theory over-estimates nucleation rates by a few orders of magnitude. The semi-phenomenological nucleation model does better, under-predicting rates by at worst a factor of 24. Unlike what has been observed in Lennard-Jones simulations, post-critical clusters have temperatures consistent with the run average temperature. Also, we observe that post-critical clusters have densities very slightly higher, ∼ 5%, than bulk liquid. We re-calibrate a Hale-type J vs. S scaling relation using both experimental and simulation data, finding remarkable consistency in over 30 orders of magnitude in the nucleation rate range and 180 K in the temperature range.

  6. Deviation from equilibrium conditions in molecular dynamic simulations of homogeneous nucleation.

    Science.gov (United States)

    Halonen, Roope; Zapadinsky, Evgeni; Vehkamäki, Hanna

    2018-04-28

    We present a comparison between Monte Carlo (MC) results for homogeneous vapour-liquid nucleation of Lennard-Jones clusters and previously published values from molecular dynamics (MD) simulations. Both the MC and MD methods sample real cluster configuration distributions. In the MD simulations, the extent of the temperature fluctuation is usually controlled with an artificial thermostat rather than with more realistic carrier gas. In this study, not only a primarily velocity scaling thermostat is considered, but also Nosé-Hoover, Berendsen, and stochastic Langevin thermostat methods are covered. The nucleation rates based on a kinetic scheme and the canonical MC calculation serve as a point of reference since they by definition describe an equilibrated system. The studied temperature range is from T = 0.3 to 0.65 ϵ/k. The kinetic scheme reproduces well the isothermal nucleation rates obtained by Wedekind et al. [J. Chem. Phys. 127, 064501 (2007)] using MD simulations with carrier gas. The nucleation rates obtained by artificially thermostatted MD simulations are consistently lower than the reference nucleation rates based on MC calculations. The discrepancy increases up to several orders of magnitude when the density of the nucleating vapour decreases. At low temperatures, the difference to the MC-based reference nucleation rates in some cases exceeds the maximal nonisothermal effect predicted by classical theory of Feder et al. [Adv. Phys. 15, 111 (1966)].

  7. The interpretation of polycrystalline coherent inelastic neutron scattering from aluminium

    Science.gov (United States)

    Roach, Daniel L.; Ross, D. Keith; Gale, Julian D.; Taylor, Jon W.

    2013-01-01

    A new approach to the interpretation and analysis of coherent inelastic neutron scattering from polycrystals (poly-CINS) is presented. This article describes a simulation of the one-phonon coherent inelastic scattering from a lattice model of an arbitrary crystal system. The one-phonon component is characterized by sharp features, determined, for example, by boundaries of the (Q, ω) regions where one-phonon scattering is allowed. These features may be identified with the same features apparent in the measured total coherent inelastic cross section, the other components of which (multiphonon or multiple scattering) show no sharp features. The parameters of the model can then be relaxed to improve the fit between model and experiment. This method is of particular interest where no single crystals are available. To test the approach, the poly-CINS has been measured for polycrystalline aluminium using the MARI spectrometer (ISIS), because both lattice dynamical models and measured dispersion curves are available for this material. The models used include a simple Lennard-Jones model fitted to the elastic constants of this material plus a number of embedded atom method force fields. The agreement obtained suggests that the method demonstrated should be effective in developing models for other materials where single-crystal dispersion curves are not available. PMID:24282332

  8. Thermodynamical modeling of nuclear glasses: coexistence of amorphous phases

    International Nuclear Information System (INIS)

    Adjanor, G.

    2007-11-01

    Investigating the stability of borosilicate glasses used in the nuclear industry with respect to phase separation requires to estimate the Gibbs free energies of the various phases appearing in the material. In simulation, using current computational resources, a direct state-sampling of a glassy system with respect to its ensemble statistics is not ergodic and the estimated ensemble averages are not reliable. Our approach consists in generating, at a given cooling rate, a series of quenches, or paths connecting states of the liquid to states of the glass, and then in taking into account the probability to generate the paths leading to the different glassy states in ensembles averages. In this way, we introduce a path ensemble formalism and calculate a Landau free energy associated to a glassy meta-basin. This method was validated by accurately mapping the free energy landscape of a 38-atom glassy cluster. We then applied this approach to the calculation of the Gibbs free energies of binary amorphous Lennard-Jones alloys, and checked the correlation between the observed tendencies to order or to phase separate and the computed Gibbs free energies. We finally computed the driving force to phase separation in a simplified three-oxide nuclear glass modeled by a Born-Mayer-Huggins potential that includes a three-body term, and we compared the estimated quantities to the available experimental data. (author)

  9. The 1-ethyl-3-methylimidazolium bis(trifluoro-methylsulfonyl)-imide ionic liquid nanodroplets on solid surfaces and in electric field: A molecular dynamics simulation study

    Science.gov (United States)

    Dong, Dengpan; Vatamanu, Jenel P.; Wei, Xiaoyu; Bedrov, Dmitry

    2018-05-01

    Atomistic molecular dynamics simulations were conducted to study the wetting states of 1-ethyl-3-methylimidazolium bis(trifluoro-methylsulfonyl)-imide ionic liquid (IL) nanodroplets on surfaces with different strengths of van der Waals (VDW) interactions and in the presence of an electric field. By adjusting the depth of Lennard-Jones potential, the van der Waals interaction between the solid surface and ionic liquid was systematically varied. The shape of the droplets was analyzed to extract the corresponding contact angle utilized to characterize wetting states of the nanodroplets. The explored range of surface-IL interactions allowed contact angles ranging from complete IL spreading on the surface to poor wettability. The effect of the external electrical field was explored by adding point charges to the surface atoms. Systems with two charge densities (±0.002 e/atom and ±0.004 e/atom) that correspond to 1.36 V/nm and 2.72 V/nm electric fields were investigated. Asymmetrical wetting states were observed for both cases. At 1.36 V/nm electric field, contributions of IL-surface VDW interactions and Coulombic interactions to the wetting state were competitive. At 2.72 V/nm field, electrostatic interactions dominate the interaction between the nanodroplet and surface, leading to enhanced wettability on all surfaces.

  10. The free energy of the metastable supersaturated vapor via restricted ensemble simulations. III. An extension to the Corti and Debenedetti subcell constraint algorithm

    International Nuclear Information System (INIS)

    Nie, Chu; Geng, Jun; Marlow, William H.

    2016-01-01

    In order to improve the sampling of restricted microstates in our previous work [C. Nie, J. Geng, and W. H. Marlow, J. Chem. Phys. 127, 154505 (2007); 128, 234310 (2008)] and quantitatively predict thermal properties of supersaturated vapors, an extension is made to the Corti and Debenedetti subcell constraint algorithm [D. S. Corti and P. Debenedetti, Chem. Eng. Sci. 49, 2717 (1994)], which restricts the maximum allowed local density at any point in a simulation box. The maximum allowed local density at a point in a simulation box is defined by the maximum number of particles N m allowed to appear inside a sphere of radius R, with this point as the center of the sphere. Both N m and R serve as extra thermodynamic variables for maintaining a certain degree of spatial homogeneity in a supersaturated system. In a restricted canonical ensemble, at a given temperature and an overall density, series of local minima on the Helmholtz free energy surface F(N m , R) are found subject to different (N m , R) pairs. The true equilibrium metastable state is identified through the analysis of the formation free energies of Stillinger clusters of various sizes obtained from these restricted states. The simulation results of a supersaturated Lennard-Jones vapor at reduced temperature 0.7 including the vapor pressure isotherm, formation free energies of critical nuclei, and chemical potential differences are presented and analyzed. In addition, with slight modifications, the current algorithm can be applied to computing thermal properties of superheated liquids.

  11. Monte Carlo Studies of Phase Separation in Compressible 2-dim Ising Models

    Science.gov (United States)

    Mitchell, S. J.; Landau, D. P.

    2006-03-01

    Using high resolution Monte Carlo simulations, we study time-dependent domain growth in compressible 2-dim ferromagnetic (s=1/2) Ising models with continuous spin positions and spin-exchange moves [1]. Spins interact with slightly modified Lennard-Jones potentials, and we consider a model with no lattice mismatch and one with 4% mismatch. For comparison, we repeat calculations for the rigid Ising model [2]. For all models, large systems (512^2) and long times (10^ 6 MCS) are examined over multiple runs, and the growth exponent is measured in the asymptotic scaling regime. For the rigid model and the compressible model with no lattice mismatch, the growth exponent is consistent with the theoretically expected value of 1/3 [1] for Model B type growth. However, we find that non-zero lattice mismatch has a significant and unexpected effect on the growth behavior.Supported by the NSF.[1] D.P. Landau and K. Binder, A Guide to Monte Carlo Simulations in Statistical Physics, second ed. (Cambridge University Press, New York, 2005).[2] J. Amar, F. Sullivan, and R.D. Mountain, Phys. Rev. B 37, 196 (1988).

  12. Non-chiral, molecular model of negative Poisson ratio in two dimensions

    International Nuclear Information System (INIS)

    Wojciechowski, K W

    2003-01-01

    A two-dimensional model of tri-atomic molecules (in which 'atoms' are distributed on vertices of equilateral triangles, and which are further referred to as cyclic trimers) is solved exactly in the static (zero-temperature) limit for the nearest-neighbour site-site interactions. It is shown that the cyclic trimers form a mechanically stable and elastically isotropic non-chiral phase of negative Poisson ratio. The properties of the system are illustrated by three examples of atom-atom interaction potentials: (i) the purely repulsive (n-inverse-power) potential, (ii) the purely attractive (n-power) potential and (iii) the Lennard-Jones potential which shows both the repulsive and the attractive part. The analytic form of the dependence of the Poisson ratio on the interatomic potential is obtained. It is shown that the Poisson ratio depends, in a universal way, only on the trimer anisotropy parameter both (1) in the limit of n → ∞ for cases (i) and (ii), as well as (2) at the zero external pressure for any potential with a doubly differentiable minimum, case (iii) is an example

  13. How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory.

    Science.gov (United States)

    Mondal, Jagannath; Halverson, Duncan; Li, Isaac T S; Stirnemann, Guillaume; Walker, Gilbert C; Berne, Bruce J

    2015-07-28

    It is currently the consensus belief that protective osmolytes such as trimethylamine N-oxide (TMAO) favor protein folding by being excluded from the vicinity of a protein, whereas denaturing osmolytes such as urea lead to protein unfolding by strongly binding to the surface. Despite there being consensus on how TMAO and urea affect proteins as a whole, very little is known as to their effects on the individual mechanisms responsible for protein structure formation, especially hydrophobic association. In the present study, we use single-molecule atomic force microscopy and molecular dynamics simulations to investigate the effects of TMAO and urea on the unfolding of the hydrophobic homopolymer polystyrene. Incorporated with interfacial energy measurements, our results show that TMAO and urea act on polystyrene as a protectant and a denaturant, respectively, while complying with Tanford-Wyman preferential binding theory. We provide a molecular explanation suggesting that TMAO molecules have a greater thermodynamic binding affinity with the collapsed conformation of polystyrene than with the extended conformation, while the reverse is true for urea molecules. Results presented here from both experiment and simulation are in line with earlier predictions on a model Lennard-Jones polymer while also demonstrating the distinction in the mechanism of osmolyte action between protein and hydrophobic polymer. This marks, to our knowledge, the first experimental observation of TMAO-induced hydrophobic collapse in a ternary aqueous system.

  14. Molecular dynamics study on the structure I clathrate-hydrate of methane + ethane mixture

    International Nuclear Information System (INIS)

    Erfan-Niya, Hamid; Modarress, Hamid; Zaminpayma, Esmaeil

    2011-01-01

    Molecular dynamics (MD) simulations are used to study the structure I stability of methane + ethane clathrate-hydrates at temperatures 273, 275 and 277 K. NVT- and NPT-ensembles are utilized in MD simulation, and each consists of 3 x 3 x 3 replica unit cells containing 46 water molecules which are considered as the host molecules and up to eight methane + ethane molecules considered as the guest molecules. In MD simulations for host-host interactions, the potential model used was a type of simple point charge (SPC) model, and for guest-guest and host-guest interactions the potential used was Lennard-Jones model. In the process of MD simulation, achieving equilibrium of the studied system was recognized by stability in calculated pressure for NVT-ensemble and volume for NPT-ensemble. To understand the characteristic configurations of the structure I hydrate, the radial distribution functions (RDFs) of host-host, host-guest and guest-guest molecules as well as other properties including kinetic energy, potential energy and total energy were calculated. The results show that guest molecules interaction with host molecules cannot decompose the hydrate structure, and these results are consistent with most previous experimental and theoretical investigations that methane + ethane mixtures form structure I hydrates over the entire mixture composition range.

  15. Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

    International Nuclear Information System (INIS)

    Ng, T Y; Yeak, S H; Liew, K M

    2008-01-01

    A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods

  16. Employing multi-GPU power for molecular dynamics simulation: an extension of GALAMOST

    Science.gov (United States)

    Zhu, You-Liang; Pan, Deng; Li, Zhan-Wei; Liu, Hong; Qian, Hu-Jun; Zhao, Yang; Lu, Zhong-Yuan; Sun, Zhao-Yan

    2018-04-01

    We describe the algorithm of employing multi-GPU power on the basis of Message Passing Interface (MPI) domain decomposition in a molecular dynamics code, GALAMOST, which is designed for the coarse-grained simulation of soft matters. The code of multi-GPU version is developed based on our previous single-GPU version. In multi-GPU runs, one GPU takes charge of one domain and runs single-GPU code path. The communication between neighbouring domains takes a similar algorithm of CPU-based code of LAMMPS, but is optimised specifically for GPUs. We employ a memory-saving design which can enlarge maximum system size at the same device condition. An optimisation algorithm is employed to prolong the update period of neighbour list. We demonstrate good performance of multi-GPU runs on the simulation of Lennard-Jones liquid, dissipative particle dynamics liquid, polymer and nanoparticle composite, and two-patch particles on workstation. A good scaling of many nodes on cluster for two-patch particles is presented.

  17. Statistical mechanics of Roskilde liquids: configurational adiabats, specific heat contours, and density dependence of the scaling exponent.

    Science.gov (United States)

    Bailey, Nicholas P; Bøhling, Lasse; Veldhorst, Arno A; Schrøder, Thomas B; Dyre, Jeppe C

    2013-11-14

    We derive exact results for the rate of change of thermodynamic quantities, in particular, the configurational specific heat at constant volume, CV, along configurational adiabats (curves of constant excess entropy Sex). Such curves are designated isomorphs for so-called Roskilde liquids, in view of the invariance of various structural and dynamical quantities along them. The slope of the isomorphs in a double logarithmic representation of the density-temperature phase diagram, γ, can be interpreted as one third of an effective inverse power-law potential exponent. We show that in liquids where γ increases (decreases) with density, the contours of CV have smaller (larger) slope than configurational adiabats. We clarify also the connection between γ and the pair potential. A fluctuation formula for the slope of the CV-contours is derived. The theoretical results are supported with data from computer simulations of two systems, the Lennard-Jones fluid, and the Girifalco fluid. The sign of dγ∕dρ is thus a third key parameter in characterizing Roskilde liquids, after γ and the virial-potential energy correlation coefficient R. To go beyond isomorph theory we compare invariance of a dynamical quantity, the self-diffusion coefficient, along adiabats and CV-contours, finding it more invariant along adiabats.

  18. LAMMPS strong scaling performance optimization on Blue Gene/Q

    Energy Technology Data Exchange (ETDEWEB)

    Coffman, Paul; Jiang, Wei; Romero, Nichols A.

    2014-11-12

    LAMMPS "Large-scale Atomic/Molecular Massively Parallel Simulator" is an open-source molecular dynamics package from Sandia National Laboratories. Significant performance improvements in strong-scaling and time-to-solution for this application on IBM's Blue Gene/Q have been achieved through computational optimizations of the OpenMP versions of the short-range Lennard-Jones term of the CHARMM force field and the long-range Coulombic interaction implemented with the PPPM (particle-particle-particle mesh) algorithm, enhanced by runtime parameter settings controlling thread utilization. Additionally, MPI communication performance improvements were made to the PPPM calculation by re-engineering the parallel 3D FFT to use MPICH collectives instead of point-to-point. Performance testing was done using an 8.4-million atom simulation scaling up to 16 racks on the Mira system at Argonne Leadership Computing Facility (ALCF). Speedups resulting from this effort were in some cases over 2x.

  19. 369 TFlop/s molecular dynamics simulations on the Roadrunner general-purpose heterogeneous supercomputer

    Energy Technology Data Exchange (ETDEWEB)

    Swaminarayan, Sriram [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; Kadau, Kai [Los Alamos National Laboratory; Fossum, Gordon C [IBM CORPORATION

    2008-01-01

    The authors present timing and performance numbers for a short-range parallel molecular dynamics (MD) code, SPaSM, that has been rewritten for the heterogeneous Roadrunner supercomputer. Each Roadrunner compute node consists of two AMD Opteron dual-core microprocessors and four PowerXCell 8i enhanced Cell microprocessors, so that there are four MPI ranks per node, each with one Opteron and one Cell. The interatomic forces are computed on the Cells (each with one PPU and eight SPU cores), while the Opterons are used to direct inter-rank communication and perform I/O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard-Jones pair potential benchmark reached a peak of 369 Tflop/s double-precision floating-point performance on the full Roadrunner system (27.7% of peak), corresponding to 124 MFlop/Watt/s at a price of approximately 3.69 MFlops/dollar. They demonstrate an initial target application, the jetting and ejection of material from a shocked surface.

  20. Frequency-dependent hydrodynamic interaction between two solid spheres

    Science.gov (United States)

    Jung, Gerhard; Schmid, Friederike

    2017-12-01

    Hydrodynamic interactions play an important role in many areas of soft matter science. In simulations with implicit solvent, various techniques such as Brownian or Stokesian dynamics explicitly include hydrodynamic interactions a posteriori by using hydrodynamic diffusion tensors derived from the Stokes equation. However, this equation assumes the interaction to be instantaneous which is an idealized approximation and only valid on long time scales. In the present paper, we go one step further and analyze the time-dependence of hydrodynamic interactions between finite-sized particles in a compressible fluid on the basis of the linearized Navier-Stokes equation. The theoretical results show that at high frequencies, the compressibility of the fluid has a significant impact on the frequency-dependent pair interactions. The predictions of hydrodynamic theory are compared to molecular dynamics simulations of two nanocolloids in a Lennard-Jones fluid. For this system, we reconstruct memory functions by extending the inverse Volterra technique. The simulation data agree very well with the theory, therefore, the theory can be used to implement dynamically consistent hydrodynamic interactions in the increasingly popular field of non-Markovian modeling.

  1. Crystallization in Two Dimensions and a Discrete Gauss-Bonnet Theorem

    Science.gov (United States)

    De Luca, L.; Friesecke, G.

    2018-02-01

    We show that the emerging field of discrete differential geometry can be usefully brought to bear on crystallization problems. In particular, we give a simplified proof of the Heitmann-Radin crystallization theorem (Heitmann and Radin in J Stat Phys 22(3):281-287, 1980), which concerns a system of N identical atoms in two dimensions interacting via the idealized pair potential V(r)=+∞ if r1. This is done by endowing the bond graph of a general particle configuration with a suitable notion of discrete curvature, and appealing to a discrete Gauss-Bonnet theorem (Knill in Elem Math 67:1-7, 2012) which, as its continuous cousins, relates the sum/integral of the curvature to topological invariants. This leads to an exact geometric decomposition of the Heitmann-Radin energy into (i) a combinatorial bulk term, (ii) a combinatorial perimeter, (iii) a multiple of the Euler characteristic, and (iv) a natural topological energy contribution due to defects. An analogous exact geometric decomposition is also established for soft potentials such as the Lennard-Jones potential V(r)=r^{-6}-2r^{-12}, where two additional contributions arise, (v) elastic energy and (vi) energy due to non-bonded interactions.

  2. Fragmentation of suddenly heated liquids in ICF reactors. Revision 1

    International Nuclear Information System (INIS)

    Blink, J.A.; Hoover, W.G.

    1985-01-01

    Fragmentation of free liquids in Inertial Confinement Fusion reactors could determine the upper bound on reactor pulse rate because increased surface area will enhance the cooling and condensation of coolant ablated by the fusion x rays. Relaxation from the suddenly (neutron) heated state will move a liquid into the negative pressure region under the liquid-vapor P-V dome. The resulting expansion in a diverging geometry will hydrodynamically force the liquid to fragment, with vapor then forming from the new surfaces to fill the cavities. An energy minimization model is used to determine the fragment size that produces the least amount of non-fragment-center-of-mass energy; i.e., the sum of the surface and dilational kinetic energies. This model predicts fragmentation dependence on original system size and amount of isochoric heating as well as liquid density, Grueneisen parameter, surface tension, and sound speed. A two dimensional molecular dynamics code was developed to test the model at a microscopic scale for the Lennard-Jones fluid with its two adjustable constants chosen to represent lithium

  3. Direct numerical simulations of agglomeration of circular colloidal particles in two-dimensional shear flow

    International Nuclear Information System (INIS)

    Choi, Young Joon; Djilali, Ned

    2016-01-01

    Colloidal agglomeration of nanoparticles in shear flow is investigated by solving the fluid-particle and particle-particle interactions in a 2D system. We use an extended finite element method in which the dynamics of the particles is solved in a fully coupled manner with the flow, allowing an accurate description of the fluid-particle interfaces without the need of boundary-fitted meshes or of empirical correlations to account for the hydrodynamic interactions between the particles. Adaptive local mesh refinement using a grid deformation method is incorporated with the fluid-structure interaction algorithm, and the particle-particle interaction at the microscopic level is modeled using the Lennard-Jones potential. Motivated by the process used in fabricating fuel cell catalysts from a colloidal ink, the model is applied to investigate agglomeration of colloidal particles under external shear flow in a sliding bi-periodic Lees-Edwards frame with varying shear rates and particle fraction ratios. Both external shear and particle fraction are found to have a crucial impact on the structure formation of colloidal particles in a suspension. Segregation intensity and graph theory are used to analyze the underlying agglomeration patterns and structures, and three agglomeration regimes are identified

  4. Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

    International Nuclear Information System (INIS)

    Kamberaj, Hiqmet

    2015-01-01

    In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4,  5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias

  5. Formation of graphene on BN substrate by vapor deposition method and size effects on its structure

    Science.gov (United States)

    Giang, Nguyen Hoang; Hanh, Tran Thi Thu; Ngoc, Le Nhu; Nga, Nguyen To; Van Hoang, Vo

    2018-04-01

    We report MD simulation of the growth of graphene by the vapor deposition on a two-dimensional hBN substrate. The systems (containing carbon vapor and hBN substrate) are relaxed at high temperature (1500 K), and then it is cooled down to room one (300 K). Carbon atoms interact with the substrate via the Lennard-Jones potential while the interaction between carbon atoms is computed via the Tersoff potential. Depending on the size of the model, different crystalline honeycomb structures have been found. Structural properties of the graphene obtained at 300 K are studied by analyzing radial distribution functions (RDFs), coordination numbers, ring statistics, interatomic distances, bond-angle distributions and 2D visualization of atomic configurations. We find that the models containing various numbers of atoms have a honeycomb structure. Besides, differences in structural properties of graphene formed by the vapor deposition on the substrate and free standing one are found. Moreover, the size effect on the structure is significant.

  6. Dynamic Simulation of Random Packing of Polydispersive Fine Particles

    Science.gov (United States)

    Ferraz, Carlos Handrey Araujo; Marques, Samuel Apolinário

    2018-02-01

    In this paper, we perform molecular dynamic (MD) simulations to study the two-dimensional packing process of both monosized and random size particles with radii ranging from 1.0 to 7.0 μm. The initial positions as well as the radii of five thousand fine particles were defined inside a rectangular box by using a random number generator. Both the translational and rotational movements of each particle were considered in the simulations. In order to deal with interacting fine particles, we take into account both the contact forces and the long-range dispersive forces. We account for normal and static/sliding tangential friction forces between particles and between particle and wall by means of a linear model approach, while the long-range dispersive forces are computed by using a Lennard-Jones-like potential. The packing processes were studied assuming different long-range interaction strengths. We carry out statistical calculations of the different quantities studied such as packing density, mean coordination number, kinetic energy, and radial distribution function as the system evolves over time. We find that the long-range dispersive forces can strongly influence the packing process dynamics as they might form large particle clusters, depending on the intensity of the long-range interaction strength.

  7. Thermodynamical modeling of nuclear glasses: coexistence of amorphous phases; Modelisation thermodynamique des verres nucleaires: coexistence entre phases amorphes

    Energy Technology Data Exchange (ETDEWEB)

    Adjanor, G

    2007-11-15

    Investigating the stability of borosilicate glasses used in the nuclear industry with respect to phase separation requires to estimate the Gibbs free energies of the various phases appearing in the material. In simulation, using current computational resources, a direct state-sampling of a glassy system with respect to its ensemble statistics is not ergodic and the estimated ensemble averages are not reliable. Our approach consists in generating, at a given cooling rate, a series of quenches, or paths connecting states of the liquid to states of the glass, and then in taking into account the probability to generate the paths leading to the different glassy states in ensembles averages. In this way, we introduce a path ensemble formalism and calculate a Landau free energy associated to a glassy meta-basin. This method was validated by accurately mapping the free energy landscape of a 38-atom glassy cluster. We then applied this approach to the calculation of the Gibbs free energies of binary amorphous Lennard-Jones alloys, and checked the correlation between the observed tendencies to order or to phase separate and the computed Gibbs free energies. We finally computed the driving force to phase separation in a simplified three-oxide nuclear glass modeled by a Born-Mayer-Huggins potential that includes a three-body term, and we compared the estimated quantities to the available experimental data. (author)

  8. Sensitivity of ion-induced sputtering to the radial distribution of energy transfers: A molecular dynamics study

    International Nuclear Information System (INIS)

    Mookerjee, S.; Khan, S. A.; Roy, A.; Beuve, M.; Toulemonde, M.

    2008-01-01

    Using different models for the deposition of energy on the lattice and a classical molecular dynamics approach to the subsequent transport, we evaluate how the details of the energy deposition model influence sputtering yield from a Lennard-Jones target irradiated with a MeV/u ion beam. Two energy deposition models are considered: a uniform, instantaneous deposition into a cylinder of fixed radius around the projectile ion track, used in earlier molecular dynamics and fluid dynamics simulations of sputtering yields; and an energy deposition distributed in time and space based on the formalism developed in the thermal spike model. The dependence of the sputtering yield on the total energy deposited on the target atoms is very sensitive to the energy deposition model. To clarify the origin of this strong dependence, we explore the role of the radial expansion of the electronic system prior to the transfer of its energy to the lattice. The results imply that observables such as the sputtering yield may be used as signatures of the fast electron-lattice energy transfer in the electronic energy-loss regime, and indicate the need for more experimental and theoretical investigations of these processes

  9. A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces.

    Science.gov (United States)

    Schneider, Julian; Ciacchi, Lucio Colombi

    2011-02-08

    The behavior of titanium implants in physiological environments is governed by the thin oxide layer that forms spontaneously on the metal surface and mediates the interactions with adsorbate molecules. In order to study the adsorption of biomolecules on titanium in a realistic fashion, we first build up a model of an oxidized Ti surface in contact with liquid water by means of extensive first-principles molecular dynamics simulations. Taking the obtained structure as reference, we then develop a classical potential to model the Ti/TiOx/water interface. This is based on the mapping with Coulomb and Lennard-Jones potentials of the adsorption energy landscape of single water and ammonia molecules on the rutile TiO2(110) surface. The interactions with arbitrary organic molecules are obtained via standard combination rules to established biomolecular force fields. The transferability of our potential to the case of organic molecules adsorbing on the oxidized Ti surface is checked by comparing the classical potential energy surfaces of representative systems to quantum mechanical results at the level of density functional theory. Moreover, we calculate the heat of immersion of the TiO2 rutile surface and the detachment force of a single tyrosine residue from steered molecular dynamics simulations, finding good agreement with experimental reference data in both cases. As a first application, we study the adsorption behavior of the Arg-Gly-Asp (RGD) peptide on the oxidized titanium surface, focusing particularly on the calculation of the free energy of desorption.

  10. Extension of Kirkwood-Buff theory to the canonical ensemble

    Science.gov (United States)

    Rogers, David M.

    2018-02-01

    Kirkwood-Buff (KB) integrals are notoriously difficult to converge from a canonical simulation because they require estimating the grand-canonical radial distribution. The same essential difficulty is encountered when attempting to estimate the direct correlation function of Ornstein-Zernike theory by inverting the pair correlation functions. We present a new theory that applies to the entire, finite, simulation volume, so that no cutoff issues arise at all. The theory gives the direct correlation function for closed systems, while smoothness of the direct correlation function in reciprocal space allows calculating canonical KB integrals via a well-posed extrapolation to the origin. The present analysis method represents an improvement over previous work because it makes use of the entire simulation volume and its convergence can be accelerated using known properties of the direct correlation function. Using known interaction energy functions can make this extrapolation near perfect accuracy in the low-density case. Because finite size effects are stronger in the canonical than in the grand-canonical ensemble, we state ensemble correction formulas for the chemical potential and the KB coefficients. The new theory is illustrated with both analytical and simulation results on the 1D Ising model and a supercritical Lennard-Jones fluid. For the latter, the finite-size corrections are shown to be small.

  11. A conservative and a hybrid early rejection schemes for accelerating Monte Carlo molecular simulation

    KAUST Repository

    Kadoura, Ahmad Salim

    2014-03-17

    Molecular simulation could provide detailed description of fluid systems when compared to experimental techniques. They can also replace equations of state; however, molecular simulation usually costs considerable computational efforts. Several techniques have been developed to overcome such high computational costs. In this paper, two early rejection schemes, a conservative and a hybrid one, are introduced. In these two methods, undesired configurations generated by the Monte Carlo trials are rejected earlier than it would when using conventional algorithms. The methods are tested for structureless single-component Lennard-Jones particles in both canonical and NVT-Gibbs ensembles. The computational time reduction for both ensembles is observed at a wide range of thermodynamic conditions. Results show that computational time savings are directly proportional to the rejection rate of Monte Carlo trials. The proposed conservative scheme has shown to be successful in saving up to 40% of the computational time in the canonical ensemble and up to 30% in the NVT-Gibbs ensemble when compared to standard algorithms. In addition, it preserves the exact Markov chains produced by the Metropolis scheme. Further enhancement for NVT-Gibbs ensemble is achieved by combining this technique with the bond formation early rejection one. The hybrid method achieves more than 50% saving of the central processing unit (CPU) time.

  12. Interface structure and mechanics between graphene and metal substrates: a first-principles study

    Science.gov (United States)

    Xu, Zhiping; Buehler, Markus J.

    2010-12-01

    Graphene is a fascinating material not only for technological applications, but also as a test bed for fundamental insights into condensed matter physics due to its unique two-dimensional structure. One of the most intriguing issues is the understanding of the properties of graphene and various substrate materials. In particular, the interfaces between graphene and metal substrates are of critical importance in applications of graphene in integrated electronics, as thermal materials, and in electromechanical devices. Here we investigate the structure and mechanical interactions at a graphene-metal interface through density functional theory (DFT)-based calculations. We focus on copper (111) and nickel (111) surfaces adhered to a monolayer of graphene, and find that their cohesive energy, strength and electronic structure correlate directly with their atomic geometry. Due to the strong coupling between open d-orbitals, the nickel-graphene interface has a much stronger cohesive energy with graphene than copper. We also find that the interface cohesive energy profile features a well-and-shoulder shape that cannot be captured by simple pair-wise models such as the Lennard-Jones potential. Our results provide a detailed understanding of the interfacial properties of graphene-metal systems, and help to predict the performance of graphene-based nanoelectronics and nanocomposites. The availability of structural and energetic data of graphene-metal interfaces could also be useful for the development of empirical force fields for molecular dynamics simulations.

  13. Solvent density inhomogeneities and solvation free energies in supercritical diatomic fluids: a density functional approach.

    Science.gov (United States)

    Husowitz, B; Talanquer, V

    2007-02-07

    Density functional theory is used to explore the solvation properties of a spherical solute immersed in a supercritical diatomic fluid. The solute is modeled as a hard core Yukawa particle surrounded by a diatomic Lennard-Jones fluid represented by two fused tangent spheres using an interaction site approximation. The authors' approach is particularly suitable for thoroughly exploring the effect of different interaction parameters, such as solute-solvent interaction strength and range, solvent-solvent long-range interactions, and particle size, on the local solvent structure and the solvation free energy under supercritical conditions. Their results indicate that the behavior of the local coordination number in homonuclear diatomic fluids follows trends similar to those reported in previous studies for monatomic fluids. The local density augmentation is particularly sensitive to changes in solute size and is affected to a lesser degree by variations in the solute-solvent interaction strength and range. The associated solvation free energies exhibit a nonmonotonous behavior as a function of density for systems with weak solute-solvent interactions. The authors' results suggest that solute-solvent interaction anisotropies have a major influence on the nature and extent of local solvent density inhomogeneities and on the value of the solvation free energies in supercritical solutions of heteronuclear molecules.

  14. Exploring Lightning Jump Characteristics

    Science.gov (United States)

    Chronis, Themis; Carey, Larry D.; Schultz, Christopher J.; Schultz, Elise; Calhoun, Kristin; Goodman, Steven J.

    2014-01-01

    This study is concerned with the characteristics of storms exhibiting an abrupt temporal increase in the total lightning flash rate (i.e., lightning jump, LJ). An automated storm tracking method is used to identify storm "clusters" and total lightning activity from three different lightning detection systems over Oklahoma, northern Alabama and Washington, D.C. On average and for different employed thresholds, the clusters that encompass at least one LJ (LJ1) last longer, relate to higher Maximum Expected Size of Hail, Vertical Integrated Liquid and lightning flash rates (area-normalized) than the clusters that did not exhibit any LJ (LJ0). The respective mean values for LJ1 (LJ0) clusters are 80 min (35 min), 14 mm (8 mm), 25 kg per square meter (18 kg per square meter) and 0.05 flash per min per square kilometer (0.01 flash per min per square kilometer). Furthermore, the LJ1 clusters are also characterized by slower decaying autocorrelation functions, a result that implies a less "random" behavior in the temporal flash rate evolution. In addition, the temporal occurrence of the last LJ provides an estimate of the time remaining to the storm's dissipation. Depending of the LJ strength (i.e., varying thresholds), these values typically range between 20-60 min, with stronger jumps indicating more time until storm decay. This study's results support the hypothesis that the LJ is a proxy for the storm's kinematic and microphysical state rather than a coincidental value.

  15. Contact angle dependence on the fluid-wall dispersive energy

    NARCIS (Netherlands)

    Horsch, M.; Heitzig, M.; Dan, C.M.; Harting, J.D.R.; Hasse, H.; Vrabec, J.

    2010-01-01

    Menisci of the truncated and shifted Lennard-Jones fluid between parallel planar walls are investigated by molecular dynamics simulation. Thereby, the characteristic energy of the unlike dispersive interaction between fluid molecules and wall atoms is systematically varied to determine its influence

  16. Elastic properties of surfactant monolayers at liquid-liquid interfaces: A molecular dynamics study

    DEFF Research Database (Denmark)

    Laradji, Mohamed; Mouritsen, Ole G.

    2000-01-01

    Using a simple molecular model based on the Lennard-Jones potential, we systematically study the elastic properties of liquid-liquid interfaces containing surfactant molecules by means of extensive and large-scale molecular dynamics simulations. The main elastic constants of the interface, corres...

  17. Some aspects of equations of state

    International Nuclear Information System (INIS)

    Frisch, H.L.

    1979-02-01

    Some elementary properties of the equation of state of molecules repulsing each other as point centers of force are developed briefly. An inequality for the Lennard--Jones gas is presented. The scaled particle theory equation of state of hard spheres is also reviewed briefly. Means of possibly applying these concepts to represent thermodynamic data on model detonating gases are suggested

  18. Role of the first coordination shell in determining the equilibrium structure and dynamics of simple liquids

    DEFF Research Database (Denmark)

    Toxværd, Søren; Dyre, J. C.

    2011-01-01

    . Lett. 103, 170601 (2009);10.1103/PhysRevLett.103.170601 J. Chem. Phys. 134, 214503 (2011)10.1063/1.3592709] . We present simulations of the standard Lennard-Jones liquid at several condensed-fluid state points, including a fairly low density state and a very high density state, as well as simulations...

  19. Switching Between the NVT and NpT Ensembles Using the Reweighting and Reconstruction Scheme

    KAUST Repository

    Kadoura, Ahmad Salim; Salama, Amgad; Sun, Shuyu

    2015-01-01

    thermodynamic conditions from a single MC Markov chain. The latter scheme, was first developed to extrapolate quantities in NV T ensemble for struc- tureless Lennard-Jones particles. However, it is evident that for most real life applications the NpT ensemble

  20. Validity of the Rosenfeld relationship: A comparative study of the ...

    Indian Academy of Sciences (India)

    ATREYEE BANERJEE

    we find that the NTW model has mixed characteristics of simple liquids and ionic melts. Our study further ... and the value of the Rosenfeld exponents are differ- ent from that found for ..... Lennard-Jones chains J. Chem. Phys. 129 164904. 4.

  1. Stochasticity thresholds in the Fermi-Pasta-Ulam model

    International Nuclear Information System (INIS)

    Callegari, B.; Galgani, L.; Milan Univ.

    1979-01-01

    The authors consider the celebrated model of Fermi, Pasta and Ulam and give a numerical estimate for its thresholds of stochasticity, thus determining a critical energy as a function of the frequency of the corresponding oscillators. The results turn out to be qualitatively similar to those already obtained for a chain of particles with nearest-neighbour Lennard-Jones interaction potential. (author)

  2. Stochasticity thresholds in the Fermi-Pasta-Ulam model

    Energy Technology Data Exchange (ETDEWEB)

    Callegari, B [Ferrara Univ. (Italy). Ist. di Matematica; Carotta, M C; Ferrario, C [Ferrara Univ. (Italy). Ist. di Fisica; Lo Vecchio, G [Ferrara Univ. (Italy). Ist. di Fisica; Gruppo Nazionale di Struttura della Materia, Ferrara (Italy)); Galgani, L [Milan Univ. (Italy). Ist. di Fisica; Milan Univ. (Italy). Ist. di Matematica)

    1979-12-11

    The authors consider the celebrated model of Fermi, Pasta and Ulam and give a numerical estimate for its thresholds of stochasticity, thus determining a critical energy as a function of the frequency of the corresponding oscillators. The results turn out to be qualitatively similar to those already obtained for a chain of particles with nearest-neighbour Lennard-Jones interaction potential.

  3. Pramana – Journal of Physics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics. O akinlade. Articles written in Pramana – Journal of Physics. Volume 64 Issue 2 February 2005 pp 269-279 Research Articles. Structures and autocorrelation functions of liquid Al and Mg modelled via Lennard-Jones potential from molecular dynamics simulation.

  4. Growing correlation length on cooling below the onset of caging in a simulated glass-forming liquid

    DEFF Research Database (Denmark)

    Lačević, N.; Starr, F. W.; Schrøder, Thomas

    2002-01-01

    We present a calculation of a fourth-order, time-dependent density correlation function that measures higher-order spatiotemporal correlations of the density of a liquid. From molecular dynamics simulations of a glass-forming Lennard-Jones liquid, we find that the characteristic length scale...... of the dynamics of the liquid in the alpha-relaxation regime....

  5. G A Adebayo

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics. G A Adebayo. Articles written in Pramana – Journal of Physics. Volume 64 Issue 2 February 2005 pp 269-279 Research Articles. Structures and autocorrelation functions of liquid Al and Mg modelled via Lennard-Jones potential from molecular dynamics simulation.

  6. Pramana – Journal of Physics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics. L A Hussain. Articles written in Pramana – Journal of Physics. Volume 64 Issue 2 February 2005 pp 269-279 Research Articles. Structures and autocorrelation functions of liquid Al and Mg modelled via Lennard-Jones potential from molecular dynamics simulation.

  7. Calculation of partial enthalpies in argon-krypton mixtures by NPT molecular dynamics

    NARCIS (Netherlands)

    Sindzingre, P.; Massobrio, C.; Ciccotti, G.; Frenkel, D.

    1989-01-01

    In an earlier paper, we have indicated how, by using a particle-insertion technique, partial molar enthalpies and related quantities can be evaluated from simulations on a single state point. In the present paper we apply this method to a Lennard-Jones argon-krypton mixture. For this particular

  8. HNC variational calculations of boson matter

    International Nuclear Information System (INIS)

    Lantto, L.J.; Jackson, A.D.; Siemens, P.J.

    1977-01-01

    A simple and reliable numerical technique is given for determining the two-body distribution function which minimizes the HNC energy of boson matter. Numerical results are presented for the neutron matter homework problem and the 4 He Lennard-Jones potential. The resulting distribution function is found to have proper asymptotic behaviour and yields reasonable binding energies. (Auth.)

  9. Non-hard sphere thermodynamic perturbation theory.

    Science.gov (United States)

    Zhou, Shiqi

    2011-08-21

    A non-hard sphere (HS) perturbation scheme, recently advanced by the present author, is elaborated for several technical matters, which are key mathematical details for implementation of the non-HS perturbation scheme in a coupling parameter expansion (CPE) thermodynamic perturbation framework. NVT-Monte Carlo simulation is carried out for a generalized Lennard-Jones (LJ) 2n-n potential to obtain routine thermodynamic quantities such as excess internal energy, pressure, excess chemical potential, excess Helmholtz free energy, and excess constant volume heat capacity. Then, these new simulation data, and available simulation data in literatures about a hard core attractive Yukawa fluid and a Sutherland fluid, are used to test the non-HS CPE 3rd-order thermodynamic perturbation theory (TPT) and give a comparison between the non-HS CPE 3rd-order TPT and other theoretical approaches. It is indicated that the non-HS CPE 3rd-order TPT is superior to other traditional TPT such as van der Waals/HS (vdW/HS), perturbation theory 2 (PT2)/HS, and vdW/Yukawa (vdW/Y) theory or analytical equation of state such as mean spherical approximation (MSA)-equation of state and is at least comparable to several currently the most accurate Ornstein-Zernike integral equation theories. It is discovered that three technical issues, i.e., opening up new bridge function approximation for the reference potential, choosing proper reference potential, and/or using proper thermodynamic route for calculation of f(ex-ref), chiefly decide the quality of the non-HS CPE TPT. Considering that the non-HS perturbation scheme applies for a wide variety of model fluids, and its implementation in the CPE thermodynamic perturbation framework is amenable to high-order truncation, the non-HS CPE 3rd-order or higher order TPT will be more promising once the above-mentioned three technological advances are established. © 2011 American Institute of Physics

  10. Hepatorenal syndrome

    Science.gov (United States)

    ... 2016:chap 153. Nevah MI, Fallon MB. Hepatic encephalopathy, hepatorenal syndrome, hepatopulmonary syndrome, and other systemic complications of liver disease. In: Feldman M, Friedman LS, Brandt LJ, ...

  11. Systems

    International Nuclear Information System (INIS)

    Anon.

    1980-01-01

    Papers in this session describe the concept of mined geologic disposal system and methods for ensuring that the system, when developed, will meet all technical requirements. Also presented in the session are analyses of system parameters, such as cost and nuclear criticality potential, as well as a technical analysis of a requirement that the system permit retrieval of the waste for some period of time. The final paper discusses studies under way to investigate technical alternatives or complements to the mined geologic disposal system. Titles of the presented papers are: (1) Waste Isolation System; (2) Waste Isolation Economics; (3) BWIP Technical Baseline; (4) Criticality Considerations in Geologic Disposal of High-Level Waste; (5) Retrieving Nuclear Wastes from Repository; (6) NWTS Programs for the Evaluation of Technical Alternatives or Complements to Mined Geologic Repositories - Purpose and Objectives

  12. systems

    Directory of Open Access Journals (Sweden)

    Alexander Leonessa

    2000-01-01

    Full Text Available A nonlinear robust control-system design framework predicated on a hierarchical switching controller architecture parameterized over a set of moving nominal system equilibria is developed. Specifically, using equilibria-dependent Lyapunov functions, a hierarchical nonlinear robust control strategy is developed that robustly stabilizes a given nonlinear system over a prescribed range of system uncertainty by robustly stabilizing a collection of nonlinear controlled uncertain subsystems. The robust switching nonlinear controller architecture is designed based on a generalized (lower semicontinuous Lyapunov function obtained by minimizing a potential function over a given switching set induced by the parameterized nominal system equilibria. The proposed framework robustly stabilizes a compact positively invariant set of a given nonlinear uncertain dynamical system with structured parametric uncertainty. Finally, the efficacy of the proposed approach is demonstrated on a jet engine propulsion control problem with uncertain pressure-flow map data.

  13. Functional domain analysis of the Remorin protein LjSYMREM1 in Lotus japonicus

    DEFF Research Database (Denmark)

    Tóth, Katalin; Stratil, Thomas F; Madsen, Esben B

    2012-01-01

    In legumes rhizobial infection during root nodule symbiosis (RNS) is controlled by a conserved set of receptor proteins and downstream components. MtSYMREM1, a protein of the Remorin family in Medicago truncatula, was shown to interact with at least three receptor-like kinases (RLKs) that are ess...

  14. Radiological survey results at 1 Shady Lane, Lodi, New Jersey (LJ095)

    International Nuclear Information System (INIS)

    Foley, R.D.; Johnson, C.A.

    1995-07-01

    The US Department of Energy (DOE) conducted remedial action at the Stepan property in Maywood, New Jersey and several vicinity properties in Lodi, New Jersey as part of the Formerly Utilized Sites Remedial Action Program (FUSRAP). These properties are in the vicinity of the DOE-owned Maywood Interim Storage Site (MISS), adjacent to the former Maywood Chemical Works facility. The property at One Shady Lane, Lodi, New Jersey was not one of these vicinity properties but was surveyed by DOE at the request of the owner. At the request of DOE, a team from Oak Ridge National Laboratory conducted a radiological survey at this property. The purpose of the survey, conducted in November 1994, was to confirm whether remedial actions were to be performed on the property in order to be in compliance with the identified Guidelines. The radiological survey included surface gamma scans and gamma readings at 1 meter, and the collection of soil samples for radionuclide analysis. Results of the survey demonstrated that all radiological measurements on the property at One Shady Lane, Lodi, New Jersey, were comparable to background levels in the area, and well within the limits prescribed by DOE radiological guidelines. Based on the results of the radiological survey data, this property does not meet guidelines for inclusion under FUSRAP

  15. "LJ" Report "Anaheim, ALA 2008": Amid the Fantasy, Doses of Reality

    Science.gov (United States)

    Blumenstein, Lynn; Berry, John; Fialkoff, Francine; Fox, Bette-Lee; Hadro, Josh; Horrocks, Norman; Oder, Norman; Roncevic, Mirela

    2008-01-01

    If the resort city of Anaheim, California, home of Disneyland and its "imagineers," marked a departure from the urban reality of the typical American Library Association (ALA) annual conference, it was impossible, at this 2008 meeting, to avoid urgent library issues. How do libraries maintain their value and cultural presence as users…

  16. Shifting with the Paradigm: LJ's Picks & Pans for ALA in Disneyland

    Science.gov (United States)

    Berry, John N., III

    2008-01-01

    The feelings of librarians planning for the American Library Association (ALA) conference at Disneyland (aka Anaheim, California, June 26-July 2) range from moderate pleasure to dread. Some remember the joys and difficulties of Orlando, especially the exorbitant cab fares and mediocre restaurants. Others quail at screaming kids and tourists in…

  17. Semiflexible polymers confined in a slit pore with attractive walls: two-dimensional liquid crystalline order versus capillary nematization.

    Science.gov (United States)

    Milchev, Andrey; Egorov, Sergei A; Binder, Kurt

    2017-03-01

    Semiflexible polymers under good solvent conditions interacting with attractive planar surfaces are investigated by Molecular Dynamics (MD) simulations and classical Density Functional Theory (DFT). A bead-spring type potential complemented by a bending potential is used, allowing variation of chain stiffness from completely flexible coils to rod-like polymers whose persistence length by far exceeds their contour length. Solvent is only implicitly included, monomer-monomer interactions being purely repulsive, while two types of attractive wall-monomer interactions are considered: (i) a strongly attractive Mie-type potential, appropriate for a strictly structureless wall, and (ii) a corrugated wall formed by Lennard-Jones particles arranged on a square lattice. It is found that in dilute solutions the former case leads to the formation of a strongly adsorbed surface layer, and the profile of density and orientational order in the z-direction perpendicular to the wall is predicted by DFT in nice agreement with MD. While for very low bulk densities a Kosterlitz-Thouless type transition from the isotropic phase to a phase with power-law decay of nematic correlations is suggested to occur in the strongly adsorbed layer, for larger densities a smectic-C phase in the surface layer is detected. No "capillary nematization" effect at higher bulk densities is found in this system, unlike systems with repulsive walls. This finding is attributed to the reduction of the bulk density (in the center of the slit pore) due to polymer adsorption on the attractive wall, for a system studied in the canonical ensemble. Consequently in a system with two attractive walls nematic order in the slit pore can occur only at a higher density than for a bulk system.

  18. Ionic diffusion through confined geometries: from Langevin equations to partial differential equations

    International Nuclear Information System (INIS)

    Nadler, Boaz; Schuss, Zeev; Singer, Amit; Eisenberg, R S

    2004-01-01

    Ionic diffusion through and near small domains is of considerable importance in molecular biophysics in applications such as permeation through protein channels and diffusion near the charged active sites of macromolecules. The motion of the ions in these settings depends on the specific nanoscale geometry and charge distribution in and near the domain, so standard continuum type approaches have obvious limitations. The standard machinery of equilibrium statistical mechanics includes microscopic details, but is also not applicable, because these systems are usually not in equilibrium due to concentration gradients and to the presence of an external applied potential, which drive a non-vanishing stationary current through the system. We present a stochastic molecular model for the diffusive motion of interacting particles in an external field of force and a derivation of effective partial differential equations and their boundary conditions that describe the stationary non-equilibrium system. The interactions can include electrostatic, Lennard-Jones and other pairwise forces. The analysis yields a new type of Poisson-Nernst-Planck equations, that involves conditional and unconditional charge densities and potentials. The conditional charge densities are the non-equilibrium analogues of the well studied pair correlation functions of equilibrium statistical physics. Our proposed theory is an extension of equilibrium statistical mechanics of simple fluids to stationary non-equilibrium problems. The proposed system of equations differs from the standard Poisson-Nernst-Planck system in two important aspects. First, the force term depends on conditional densities and thus on the finite size of ions, and second, it contains the dielectric boundary force on a discrete ion near dielectric interfaces. Recently, various authors have shown that both of these terms are important for diffusion through confined geometries in the context of ion channels

  19. Molecular dynamics studies of transport properties and equation of state of supercritical fluids

    Science.gov (United States)

    Nwobi, Obika C.

    Many chemical propulsion systems operate with one or more of the reactants above the critical point in order to enhance their performance. Most of the computational fluid dynamics (CFD) methods used to predict these flows require accurate information on the transport properties and equation of state at these supercritical conditions. This work involves the determination of transport coefficients and equation of state of supercritical fluids by equilibrium molecular dynamics (MD) simulations on parallel computers using the Green-Kubo formulae and the virial equation of state, respectively. MD involves the solution of equations of motion of a system of molecules that interact with each other through an intermolecular potential. Provided that an accurate potential can be found for the system of interest, MD can be used regardless of the phase and thermodynamic conditions of the substances involved. The MD program uses the effective Lennard-Jones potential, with system sizes of 1000-1200 molecules and, simulations of 2,000,000 time-steps for computing transport coefficients and 200,000 time-steps for pressures. The computer code also uses linked cell lists for efficient sorting of molecules, periodic boundary conditions, and a modified velocity Verlet algorithm for particle displacement. Particle decomposition is used for distributing the molecules to different processors of a parallel computer. Simulations have been carried out on pure argon, nitrogen, oxygen and ethylene at various supercritical conditions, with self-diffusion coefficients, shear viscosity coefficients, thermal conductivity coefficients and pressures computed for most of the conditions. Results compare well with experimental and the National Institute of Standards and Technology (NIST) values. The results show that the number of molecules and the potential cut-off radius have no significant effect on the computed coefficients, while long-time integration is necessary for accurate determination of the

  20. Free energy study of H2O, N2O5, SO2, and O3 gas sorption by water droplets/slabs

    Science.gov (United States)

    Li, Wentao; Pak, Chi Yuen; Tse, Ying-Lung Steve

    2018-04-01

    Understanding gas sorption by water in the atmosphere is an active research area because the gases can significantly alter the radiation and chemical properties of the atmosphere. We attempt to elucidate the molecular details of the gas sorption of water and three common atmospheric gases (N2O5, SO2, and O3) by water droplets/slabs in molecular dynamics simulations. The system size effects are investigated, and we show that the calculated solvation free energy decreases linearly as a function of the reciprocal of the number of water molecules from 1/215 to 1/1000 in both the slab and the droplet systems. By analyzing the infinitely large system size limit by extrapolation, we find that all our droplet results are more accurate than the slab results when compared to the experimental values. We also show how the choice of restraints in umbrella sampling can affect the sampling efficiency for the droplet systems. The free energy changes were decomposed into the energetic ΔU and entropic -TΔS contributions to reveal the molecular details of the gas sorption processes. By further decomposing ΔU into Lennard-Jones and Coulombic interactions, we observe that the ΔU trends are primarily determined by local effects due to the size of the gas molecule, charge distribution, and solvation structure around the gas molecule. Moreover, we find that there is a strong correlation between the change in the entropic contribution and the mean residence time of water, which is spatially nonlocal and related to the mobility of water.

  1. SYSTEM

    Directory of Open Access Journals (Sweden)

    K. Swarnalatha

    2013-01-01

    Full Text Available Risk analysis of urban aquatic systems due to heavy metals turns significant due to their peculiar properties viz. persis tence, non-degradab ility, toxicity, and accumulation. Akkulam Veli (AV, an urba n tropical lake in south India is subjected to various environmental stresses due to multiple waste discharge, sand mining, developmental activities, tour ism related activitie s etc. Hence, a comprehensive approach is adopted for risk assessment using modified degree of contamination factor, toxicity units based on numerical sediment quality guidelines (SQGs, and potentialecological risk indices. The study revealed the presence of toxic metals such as Cr, C d, Pb and As and the lake is rated under ‘low ecological risk’ category.

  2. Simulations of cold nuclear matter at sub-saturation densities

    Energy Technology Data Exchange (ETDEWEB)

    Giménez Molinelli, P.A., E-mail: pagm@df.uba.ar [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA, CONICET, Ciudad Universitaria, Buenos Aires 1428 (Argentina); Nichols, J.I. [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA, CONICET, Ciudad Universitaria, Buenos Aires 1428 (Argentina); López, J.A. [Department of Physics, University of Texas at El Paso, El Paso, TX 79968 (United States); Dorso, C.O. [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA, CONICET, Ciudad Universitaria, Buenos Aires 1428 (Argentina)

    2014-03-01

    Ideal nuclear matter is expected to undergo a first order phase transition at the thermodynamic limit. At such phase transitions the size of density fluctuations (bubbles or droplets) scale with the size of the system. This means that simulations of nuclear matter at sub-saturation densities will inexorably suffer from what is vaguely referred to as “finite size effects”. It is usually thought that these finite size effects can be diminished by imposing periodic boundary conditions and making the system large enough, but as we show in this work, that is actually not the case at sub-saturation densities. In this paper we analyze the equilibrium configurations of molecular dynamics simulations of a classical model for symmetric ideal (uncharged) nuclear matter at sub-saturation densities and low temperatures, where phase coexistence is expected at the thermodynamic limit. We show that the most stable configurations in this density range are almost completely determined by artificial aspects of the simulations (i.e. boundary conditions) and can be predicted analytically by surface minimization. This result is very general and is shown to hold true for several well known semi-classical models of nuclear interaction and even for a simple Lennard-Jones potential. Also, in the limit of very large systems, when “small size” effects can be neglected, those equilibrium configurations seem to be restricted to a few structures reminiscent to the “Pasta Phases” expected in Neutron Star matter, but arising from a completely different origin: In Neutron Star matter, the non-homogeneous structures arise from a competition between nuclear and Coulomb interactions while for ideal nuclear matter they emerge from finite (yet not “small”) size effects. The role of periodic boundary conditions and finite size effects in Neutron Star matter simulations are reexamined.

  3. Local yield stress statistics in model amorphous solids

    Science.gov (United States)

    Barbot, Armand; Lerbinger, Matthias; Hernandez-Garcia, Anier; García-García, Reinaldo; Falk, Michael L.; Vandembroucq, Damien; Patinet, Sylvain

    2018-03-01

    We develop and extend a method presented by Patinet, Vandembroucq, and Falk [Phys. Rev. Lett. 117, 045501 (2016), 10.1103/PhysRevLett.117.045501] to compute the local yield stresses at the atomic scale in model two-dimensional Lennard-Jones glasses produced via differing quench protocols. This technique allows us to sample the plastic rearrangements in a nonperturbative manner for different loading directions on a well-controlled length scale. Plastic activity upon shearing correlates strongly with the locations of low yield stresses in the quenched states. This correlation is higher in more structurally relaxed systems. The distribution of local yield stresses is also shown to strongly depend on the quench protocol: the more relaxed the glass, the higher the local plastic thresholds. Analysis of the magnitude of local plastic relaxations reveals that stress drops follow exponential distributions, justifying the hypothesis of an average characteristic amplitude often conjectured in mesoscopic or continuum models. The amplitude of the local plastic rearrangements increases on average with the yield stress, regardless of the system preparation. The local yield stress varies with the shear orientation tested and strongly correlates with the plastic rearrangement locations when the system is sheared correspondingly. It is thus argued that plastic rearrangements are the consequence of shear transformation zones encoded in the glass structure that possess weak slip planes along different orientations. Finally, we justify the length scale employed in this work and extract the yield threshold statistics as a function of the size of the probing zones. This method makes it possible to derive physically grounded models of plasticity for amorphous materials by directly revealing the relevant details of the shear transformation zones that mediate this process.

  4. Towards understanding the structure and capacitance of electrical double layer in ionic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Fedorov, Maxim V. [Max Planck Institute for Mathematics in the Sciences, D 04103 Leipzig (Germany); Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Kornyshev, Alexei A. [Department of Chemistry, Faculty of Natural Sciences, Imperial College London, SW7 2AZ London (United Kingdom)

    2008-10-01

    In order to understand basic principles of the double layer formation in room temperature ionic liquids, we have performed Molecular Dynamic simulations for a simplified system: dense assembly of charged Lennard-Jones spheres between charged walls. For simplicity, in this first investigation we have considered the cations and anions of the same size. We have calculated the corresponding values of the double layer capacitance as a function of the electrode potential and compared the results with existing theories. We have found that the capacitance curve does not follow the U-shape of the Gouy-Chapman theory, but has a bell-shape in agreement with the mean-field theory that takes into account the effect of limited maximum packing of ions. The wings of capacitance decrease inversely proportional to the square root of the electrode potential, as prescribed by the mean-field theory and the charge conservation law at large electrode polarizations. We have found, however, that the mean-field theory does not quantitatively reproduce the simulation results at small electrode potentials, having detected their remarkable overscreening effects (ionic correlations). The plots for the distributions of ions near the electrode at different electrode charges show that for the considered system, unlike it is often assumed, the double layer is not one layer thick. The overscreening effects, dominating near the potential of zero charge (p.z.c.), are suppressed by the high electrode polarizations, following the onset of the so-called 'lattice saturation effect'. The maximum of the capacitance coincides with the p.z.c., but it is true only for this 'symmetric' system. If sizes of cations and anions are different the maximum will be shifted away from the p.z.c., and generally the shape of the capacitance curve could be more complicated. (author)

  5. MaMiCo: Software design for parallel molecular-continuum flow simulations

    KAUST Repository

    Neumann, Philipp

    2015-11-19

    The macro-micro-coupling tool (MaMiCo) was developed to ease the development of and modularize molecular-continuum simulations, retaining sequential and parallel performance. We demonstrate the functionality and performance of MaMiCo by coupling the spatially adaptive Lattice Boltzmann framework waLBerla with four molecular dynamics (MD) codes: the light-weight Lennard-Jones-based implementation SimpleMD, the node-level optimized software ls1 mardyn, and the community codes ESPResSo and LAMMPS. We detail interface implementations to connect each solver with MaMiCo. The coupling for each waLBerla-MD setup is validated in three-dimensional channel flow simulations which are solved by means of a state-based coupling method. We provide sequential and strong scaling measurements for the four molecular-continuum simulations. The overhead of MaMiCo is found to come at 10%-20% of the total (MD) runtime. The measurements further show that scalability of the hybrid simulations is reached on up to 500 Intel SandyBridge, and more than 1000 AMD Bulldozer compute cores. Program summary: Program title: MaMiCo. Catalogue identifier: AEYW_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEYW_v1_0.html Program obtainable from: CPC Program Library, Queen\\'s University, Belfast, N. Ireland. Licensing provisions: BSD License. No. of lines in distributed program, including test data, etc.: 67905. No. of bytes in distributed program, including test data, etc.: 1757334. Distribution format: tar.gz. Programming language: C, C++II. Computer: Standard PCs, compute clusters. Operating system: Unix/Linux. RAM: Test cases consume ca. 30-50 MB. Classification: 7.7. External routines: Scons (http:www.scons.org), ESPResSo, LAMMPS, ls1 mardyn, waLBerla. Nature of problem: Coupled molecular-continuum simulation for multi-resolution fluid dynamics: parts of the domain are resolved by molecular dynamics whereas large parts are covered by a CFD solver, e.g. a lattice Boltzmann automaton

  6. Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors.

    Science.gov (United States)

    Su, Pin-Chih; Johnson, Michael E

    2016-04-05

    Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the parahalogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme. © 2015 Wiley Periodicals, Inc.

  7. Stochastic characteristics and Second Law violations of atomic fluids in Couette flow

    Science.gov (United States)

    Raghavan, Bharath V.; Karimi, Pouyan; Ostoja-Starzewski, Martin

    2018-04-01

    Using Non-equilibrium Molecular Dynamics (NEMD) simulations, we study the statistical properties of an atomic fluid undergoing planar Couette flow, in which particles interact via a Lennard-Jones potential. We draw a connection between local density contrast and temporal fluctuations in the shear stress, which arise naturally through the equivalence between the dissipation function and entropy production according to the fluctuation theorem. We focus on the shear stress and the spatio-temporal density fluctuations and study the autocorrelations and spectral densities of the shear stress. The bispectral density of the shear stress is used to measure the degree of departure from a Gaussian model and the degree of nonlinearity induced in the system owing to the applied strain rate. More evidence is provided by the probability density function of the shear stress. We use the Information Theory to account for the departure from Gaussian statistics and to develop a more general probability distribution function that captures this broad range of effects. By accounting for negative shear stress increments, we show how this distribution preserves the violations of the Second Law of Thermodynamics observed in planar Couette flow of atomic fluids, and also how it captures the non-Gaussian nature of the system by allowing for non-zero higher moments. We also demonstrate how the temperature affects the band-width of the shear-stress and how the density affects its Power Spectral Density, thus determining the conditions under which the shear-stress acts is a narrow-band or wide-band random process. We show that changes in the statistical characteristics of the parameters of interest occur at a critical strain rate at which an ordering transition occurs in the fluid causing shear thinning and affecting its stability. A critical strain rate of this kind is also predicted by the Loose-Hess stability criterion.

  8. Elasticity of frictionless particles near jamming.

    Science.gov (United States)

    Karimi, Kamran; Maloney, Craig E

    2015-08-01

    We study the linear elastic response of harmonic disk packings near jamming via three types of probes: (i) point forcing, (ii) constrained homogeneous deformation of subregions of large systems, and (iii) unconstrained deformation of the full system subject to periodic boundary conditions. For the point forcing, our results indicate that the transverse component of the response is governed by a lengthscale ξT, which scales with the confining pressure, p, as ξT∼p-0.25, while the longitudinal component is governed by ξL, which scales as ξL∼p-0.4. The former scaling is precisely the transverse lengthscale, which has been invoked to explain the structure of normal modes near the density of states anomaly in sphere packings, while the latter is much closer to the rigidity length, l*∼p-0.5, which has been invoked to describe the jamming scenario. For the case of constrained homogeneous deformation, we find that μ(R), the value of the shear modulus measured in boxes of size R, gives a value much higher than the continuum result for small boxes and recedes to its continuum limit only for boxes bigger than a characteristic length, which scales like p-0.5, precisely the same way as l*. Finally, for the case of unconstrained homogeneous deformation, we find displacement fields with power spectra, which are consistent with independent, uncorrelated Eshelby transformations. The transverse sector is amazingly invariant with respect to p and very similar to what is seen in Lennard-Jones glasses. The longitudinal piece, however, is sensitive to p. It develops a plateau at long wavelength, the start of which occurs at a length that grows in the p→0 limit. Strikingly, the same behavior is observed both for applied shear and dilation.

  9. Structures of simple liquids in contact with nanosculptured surfaces.

    Science.gov (United States)

    Singh, Swarn Lata; Schimmele, Lothar; Dietrich, S

    2015-03-01

    We present a density functional study of Lennard-Jones liquids in contact with a nanocorrugated wall. The corresponding substrate potential is taken to exhibit a repulsive hard core and a Van der Waals attraction. The corrugation is modeled by a periodic array of square nanopits. We have used the modified Rosenfeld density functional in order to study the interfacial structure of these liquids which with respect to their thermodynamic bulk state are considered to be deep inside their liquid phase. We find that already considerably below the packing fraction of bulk freezing of these liquids, inside the nanopits a three-dimensional-like density localization sets in. If the sizes of the pits are commensurate with the packing requirements, we observe high-density spots separated from each other in all spatial directions by liquid of comparatively very low density. The number, shape, size, and density of these high-density spots depend sensitively on the depth and width of the pits. Outside the pits, only layering is observed; above the pit openings these layers are distorted with the distortion reaching up to a few molecular diameters. We discuss quantitatively how this density localization is affected by the geometrical features of the pits and how it evolves upon increasing the bulk packing fraction. Our results are transferable to colloidal systems and pit dimensions corresponding to several diameters of the colloidal particles. For such systems the predicted unfolding of these structural changes can be studied experimentally on much larger length scales and more directly (e.g., optically) than for molecular fluids which typically call for sophisticated x-ray scattering.

  10. Ion association in concentrated NaCl brines from ambient to supercritical conditions: results from classical molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Collings Matthew D

    2002-11-01

    Full Text Available Highly concentrated NaCl brines are important geothermal fluids; chloride complexation of metals in such brines increases the solubility of minerals and plays a fundamental role in the genesis of hydrothermal ore deposits. There is experimental evidence that the molecular nature of the NaCl–water system changes over the pressure–temperature range of the Earth's crust. A transition of concentrated NaCl–H2O brines to a "hydrous molten salt" at high P and T has been argued to stabilize an aqueous fluid phase in the deep crust. In this work, we have done molecular dynamic simulations using classical potentials to determine the nature of concentrated (0.5–16 m NaCl–water mixtures under ambient (25°C, 1 bar, hydrothermal (325°C, 1 kbar and deep crustal (625°C, 15 kbar conditions. We used the well-established SPCE model for water together with the Smith and Dang Lennard-Jones potentials for the ions (J. Chem. Phys., 1994, 100, 3757. With increasing temperature at 1 kbar, the dielectric constant of water decreases to give extensive ion-association and the formation of polyatomic (NanClmn-m clusters in addition to simple NaCl ion pairs. Large polyatomic (NanClmn-m clusters resemble what would be expected in a hydrous NaCl melt in which water and NaCl were completely miscible. Although ion association decreases with pressure, temperatures of 625°C are not enough to overcome pressures of 15 kbar; consequently, there is still enhanced Na–Cl association in brines under deep crustal conditions.

  11. Do the contact angle and line tension of surface-attached droplets depend on the radius of curvature?

    Science.gov (United States)

    Das, Subir K; Egorov, Sergei A; Virnau, Peter; Winter, David; Binder, Kurt

    2018-06-27

    Results from Monte Carlo simulations of wall-attached droplets in the three-dimensional Ising lattice gas model and in a symmetric binary Lennard-Jones fluid, confined by antisymmetric walls, are analyzed, with the aim to estimate the dependence of the contact angle [Formula: see text] on the droplet radius [Formula: see text] of curvature. Sphere-cap shape of the wall-attached droplets is assumed throughout. An approach, based purely on 'thermodynamic' observables, e.g. chemical potential, excess density due to the droplet, etc, is used, to avoid ambiguities in the decision which particles belong (or do not belong, respectively) to the droplet. It is found that the results are compatible with a variation [Formula: see text], [Formula: see text] being the contact angle in the thermodynamic limit ([Formula: see text]). The possibility to use such results to estimate the excess free energy related to the contact line of the droplet, namely the line tension, at the wall, is discussed. Various problems that hamper this approach and were not fully recognized in previous attempts to extract the line tension are identified. It is also found that the dependence of wall tensions on the difference of chemical potential of the droplet from that at the bulk coexistence provides effectively a change of the contact angle of similar magnitude. The simulation approach yields precise estimates for the excess density due to wall-attached droplets and the corresponding free energy excess, relative to a system without a droplet at the same chemical potential. It is shown that this information suffices to estimate nucleation barriers, not affected by ambiguities on droplet shape, contact angle and line tension.

  12. Thermal transpiration: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    T, Joe Francis [Computational Nanotechnology Laboratory, School of Nano Science and Technology, National Institute of Technology Calicut, Kozhikode (India); Sathian, Sarith P. [Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai (India)

    2014-12-09

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  13. The effect of substrate on thermodynamic and kinetic anisotropies in atomic thin films.

    Science.gov (United States)

    Haji-Akbari, Amir; Debenedetti, Pablo G

    2014-07-14

    Glasses have a wide range of technological applications. The recent discovery of ultrastable glasses that are obtained by depositing the vapor of a glass-forming liquid onto the surface of a cold substrate has sparked renewed interest in the effects of confinements on physicochemical properties of liquids and glasses. Here, we use molecular dynamics simulations to study the effect of substrate on thin films of a model glass-forming liquid, the Kob-Andersen binary Lennard-Jones system, and compute profiles of several thermodynamic and kinetic properties across the film. We observe that the substrate can induce large oscillations in profiles of thermodynamic properties such as density, composition, and stress, and we establish a correlation between the oscillations in total density and the oscillations in normal stress. We also demonstrate that the kinetic properties of an atomic film can be readily tuned by changing the strength of interactions between the substrate and the liquid. Most notably, we show that a weakly attractive substrate can induce the emergence of a highly mobile region in its vicinity. In this highly mobile region, structural relaxation is several times faster than in the bulk, and the exploration of the potential energy landscape is also more efficient. In the subsurface region near a strongly attractive substrate, however, the dynamics is decelerated and the sampling of the potential energy landscape becomes less efficient than the bulk. We explain these two distinct behaviors by establishing a correlation between the oscillations in kinetic properties and the oscillations in lateral stress. Our findings offer interesting opportunities for designing better substrates for the vapor deposition process or developing alternative procedures for situations where vapor deposition is not feasible.

  14. The effect of substrate on thermodynamic and kinetic anisotropies in atomic thin films

    Energy Technology Data Exchange (ETDEWEB)

    Haji-Akbari, Amir; Debenedetti, Pablo G., E-mail: pdebene@exchange.princeton.edu [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States)

    2014-07-14

    Glasses have a wide range of technological applications. The recent discovery of ultrastable glasses that are obtained by depositing the vapor of a glass-forming liquid onto the surface of a cold substrate has sparked renewed interest in the effects of confinements on physicochemical properties of liquids and glasses. Here, we use molecular dynamics simulations to study the effect of substrate on thin films of a model glass-forming liquid, the Kob-Andersen binary Lennard-Jones system, and compute profiles of several thermodynamic and kinetic properties across the film. We observe that the substrate can induce large oscillations in profiles of thermodynamic properties such as density, composition, and stress, and we establish a correlation between the oscillations in total density and the oscillations in normal stress. We also demonstrate that the kinetic properties of an atomic film can be readily tuned by changing the strength of interactions between the substrate and the liquid. Most notably, we show that a weakly attractive substrate can induce the emergence of a highly mobile region in its vicinity. In this highly mobile region, structural relaxation is several times faster than in the bulk, and the exploration of the potential energy landscape is also more efficient. In the subsurface region near a strongly attractive substrate, however, the dynamics is decelerated and the sampling of the potential energy landscape becomes less efficient than the bulk. We explain these two distinct behaviors by establishing a correlation between the oscillations in kinetic properties and the oscillations in lateral stress. Our findings offer interesting opportunities for designing better substrates for the vapor deposition process or developing alternative procedures for situations where vapor deposition is not feasible.

  15. Does an electronic continuum correction improve effective short-range ion-ion interactions in aqueous solution?

    Science.gov (United States)

    Bruce, Ellen E.; van der Vegt, Nico F. A.

    2018-06-01

    Non-polarizable force fields for hydrated ions not always accurately describe short-range ion-ion interactions, frequently leading to artificial ion clustering in bulk aqueous solutions. This can be avoided by adjusting the nonbonded anion-cation or cation-water Lennard-Jones parameters. This approach has been successfully applied to different systems, but the parameterization is demanding owing to the necessity of separate investigations of each ion pair. Alternatively, polarization effects may effectively be accounted for using the electronic continuum correction (ECC) of Leontyev et al. [J. Chem. Phys. 119, 8024 (2003)], which involves scaling the ionic charges with the inverse square-root of the water high-frequency dielectric permittivity. ECC has proven to perform well for monovalent salts as well as for divalent salts in water. Its performance, however, for multivalent salts with higher valency remains unexplored. The present work illustrates the applicability of the ECC model to trivalent K3PO4 and divalent K2HPO4 in water. We demonstrate that the ECC models, without additional tuning of force field parameters, provide an accurate description of water-mediated interactions between salt ions. This results in predictions of the osmotic coefficients of aqueous K3PO4 and K2HPO4 solutions in good agreement with experimental data. Analysis of ion pairing thermodynamics in terms of contact ion pair (CIP), solvent-separated ion pair, and double solvent-separated ion pair contributions shows that potassium-phosphate CIP formation is stronger with trivalent than with divalent phosphate ions.

  16. The effect of substrate on thermodynamic and kinetic anisotropies in atomic thin films

    International Nuclear Information System (INIS)

    Haji-Akbari, Amir; Debenedetti, Pablo G.

    2014-01-01

    Glasses have a wide range of technological applications. The recent discovery of ultrastable glasses that are obtained by depositing the vapor of a glass-forming liquid onto the surface of a cold substrate has sparked renewed interest in the effects of confinements on physicochemical properties of liquids and glasses. Here, we use molecular dynamics simulations to study the effect of substrate on thin films of a model glass-forming liquid, the Kob-Andersen binary Lennard-Jones system, and compute profiles of several thermodynamic and kinetic properties across the film. We observe that the substrate can induce large oscillations in profiles of thermodynamic properties such as density, composition, and stress, and we establish a correlation between the oscillations in total density and the oscillations in normal stress. We also demonstrate that the kinetic properties of an atomic film can be readily tuned by changing the strength of interactions between the substrate and the liquid. Most notably, we show that a weakly attractive substrate can induce the emergence of a highly mobile region in its vicinity. In this highly mobile region, structural relaxation is several times faster than in the bulk, and the exploration of the potential energy landscape is also more efficient. In the subsurface region near a strongly attractive substrate, however, the dynamics is decelerated and the sampling of the potential energy landscape becomes less efficient than the bulk. We explain these two distinct behaviors by establishing a correlation between the oscillations in kinetic properties and the oscillations in lateral stress. Our findings offer interesting opportunities for designing better substrates for the vapor deposition process or developing alternative procedures for situations where vapor deposition is not feasible

  17. Stable isotope enrichment by thermal diffusion

    International Nuclear Information System (INIS)

    Vasaru, Gheorghe

    2003-01-01

    Thermal diffusion (TD) in both gaseous and liquid phase has been the subject of extensive experimental and theoretical investigations, especially after the invention by K. Clusius and G. Dickel of the thermal diffusion column, sixty years ago. This paper gives a brief overview of the most important applications and developments of this transport phenomenon for enrichment of 13 C and of some noble gases isotopes in our institute. The results of calculations of the transport coefficients H and K for a concentric tube type TD column, operated with methane as process gas, are presented. Static separation factor at equilibrium vs gas pressure has been calculated for various molecular models. The experimental separation factors for different gas pressure were found to be consistent with those calculated for the inverse power repulsion model and the Lennard-Jones model. The most important characteristics of a seven-stage cascade consisting of 19 TD columns of concentric tube type are given. This system has been constructed and successfully operated at a temperature of 673 K and produces an enrichment of methane of natural isotopic 13 C abundance, up to the concentration of 25% 13 CH 4 . Enrichment of the noble gases isotopes implies: - a . Enrichment of 20 Ne and 22 Ne in a eight-stage cascade consisting of 8 TD columns; - b. enrichment of 46 Ar in a seven-stage cascade consisting of TD columns and finally; - c. enrichment of 78 Kr and 86 Kr in a fifteen-stage cascade, consisting of 35 TD columns. For all these installations we have adopted TD columns of hot wire type (4 m in length), operated at a temperature of 1073 K. (author)

  18. Photodissociation dynamics of CH3C(O)SH in argon matrix: A QM/MM nonadiabatic dynamics simulation

    Science.gov (United States)

    Xia, Shu-Hua; Liu, Xiang-Yang; Fang, Qiu; Cui, Ganglong

    2015-11-01

    In this work, we have first employed the combined quantum mechanics/molecular mechanics (QM/MM) method to study the photodissociation mechanism of thioacetic acid CH3C(O)SH in the S1, T1, and S0 states in argon matrix. CH3C(O)SH is treated quantum mechanically using the complete active space self-consistent field and complete active space second-order perturbation theory methods; argon matrix is described classically using Lennard-Jones potentials. We find that the C-S bond fission is predominant due to its small barriers of ca. 3.0 and 1.0 kcal/mol in the S1 and T1 states. It completely suppresses the nearby C—C bond fission. After the bond fission, the S1 radical pair of CH3CO and SH can decay to the S0 and T1 states via internal conversion and intersystem crossing, respectively. In the S0 state, the radical pair can either recombine to form CH3C(O)SH or proceed to form molecular products of CH2CO and H2S. We have further employed our recently developed QM/MM generalized trajectory-based surface-hopping method to simulate the photodissociation dynamics of CH3C(O)SH. In 1 ps dynamics simulation, 56% trajectories stay at the Franck-Condon region; the S1 C—S bond fission takes place in the remaining 44% trajectories. Among all nonadiabatic transitions, the S1 → S0 internal conversion is major (55%) but the S1 → T1 intersystem crossing is still comparable and cannot be ignored, which accounts for 28%. Finally, we have found a radical channel generating the molecular products of CH2CO and H2S, which is complementary to the concerted molecular channel. The present work sets the stage for simulating photodissociation dynamics of similar thio-carbonyl systems in matrix.

  19. Excess entropy scaling for the segmental and global dynamics of polyethylene melts.

    Science.gov (United States)

    Voyiatzis, Evangelos; Müller-Plathe, Florian; Böhm, Michael C

    2014-11-28

    The range of validity of the Rosenfeld and Dzugutov excess entropy scaling laws is analyzed for unentangled linear polyethylene chains. We consider two segmental dynamical quantities, i.e. the bond and the torsional relaxation times, and two global ones, i.e. the chain diffusion coefficient and the viscosity. The excess entropy is approximated by either a series expansion of the entropy in terms of the pair correlation function or by an equation of state for polymers developed in the context of the self associating fluid theory. For the whole range of temperatures and chain lengths considered, the two estimates of the excess entropy are linearly correlated. The scaled bond and torsional relaxation times fall into a master curve irrespective of the chain length and the employed scaling scheme. Both quantities depend non-linearly on the excess entropy. For a fixed chain length, the reduced diffusion coefficient and viscosity scale linearly with the excess entropy. An empirical reduction to a chain length-independent master curve is accessible for both dynamic quantities. The Dzugutov scheme predicts an increased value of the scaled diffusion coefficient with increasing chain length which contrasts physical expectations. The origin of this trend can be traced back to the density dependence of the scaling factors. This finding has not been observed previously for Lennard-Jones chain systems (Macromolecules, 2013, 46, 8710-8723). Thus, it limits the applicability of the Dzugutov approach to polymers. In connection with diffusion coefficients and viscosities, the Rosenfeld scaling law appears to be of higher quality than the Dzugutov approach. An empirical excess entropy scaling is also proposed which leads to a chain length-independent correlation. It is expected to be valid for polymers in the Rouse regime.

  20. Estimated Viscosities and Thermal Conductivities of Gases at High Temperatures

    Science.gov (United States)

    Svehla, Roger A.

    1962-01-01

    Viscosities and thermal conductivities, suitable for heat-transfer calculations, were estimated for about 200 gases in the ground state from 100 to 5000 K and 1-atmosphere pressure. Free radicals were included, but excited states and ions were not. Calculations for the transport coefficients were based upon the Lennard-Jones (12-6) potential for all gases. This potential was selected because: (1) It is one of the most realistic models available and (2) intermolecular force constants can be estimated from physical properties or by other techniques when experimental data are not available; such methods for estimating force constants are not as readily available for other potentials. When experimental viscosity data were available, they were used to obtain the force constants; otherwise the constants were estimated. These constants were then used to calculate both the viscosities and thermal conductivities tabulated in this report. For thermal conductivities of polyatomic gases an Eucken-type correction was made to correct for exchange between internal and translational energies. Though this correction may be rather poor at low temperatures, it becomes more satisfactory with increasing temperature. It was not possible to obtain force constants from experimental thermal conductivity data except for the inert atoms, because most conductivity data are available at low temperatures only (200 to 400 K), the temperature range where the Eucken correction is probably most in error. However, if the same set of force constants is used for both viscosity and thermal conductivity, there is a large degree of cancellation of error when these properties are used in heat-transfer equations such as the Dittus-Boelter equation. It is therefore concluded that the properties tabulated in this report are suitable for heat-transfer calculations of gaseous systems.

  1. Pinning of the Contact Line during Evaporation on Heterogeneous Surfaces: Slowdown or Temporary Immobilization? Insights from a Nanoscale Study.

    Science.gov (United States)

    Zhang, Jianguo; Müller-Plathe, Florian; Leroy, Frédéric

    2015-07-14

    The question of the effect of surface heterogeneities on the evaporation of liquid droplets from solid surfaces is addressed through nonequilibrium molecular dynamics simulations. The mechanism behind contact line pinning which is still unclear is discussed in detail on the nanoscale. Model systems with the Lennard-Jones interaction potential were employed to study the evaporation of nanometer-sized cylindrical droplets from a flat surface. The heterogeneity of the surface was modeled through alternating stripes of equal width but two chemical types. The first type leads to a contact angle of 67°, and the other leads to a contact angle of 115°. The stripe width was varied between 2 and 20 liquid-particle diameters. On the surface with the narrowest stripes, evaporation occurred at constant contact angle as if the surface was homogeneous, with a value of the contact angle as predicted by the regular Cassie-Baxter equation. When the width was increased, the contact angle oscillated during evaporation between two boundaries whose values depend on the stripe width. The evaporation behavior was thus found to be a direct signature of the typical size of the surface heterogeneity domains. The contact angle both at equilibrium and during evaporation could be predicted from a local Cassie-Baxter equation in which the surface composition within a distance of seven fluid-particle diameters around the contact line was considered, confirming the local nature of the interactions that drive the wetting behavior of droplets. More importantly, we propose a nanoscale explanation of pinning during evaporation. Pinning should be interpreted as a drastic slowdown of the contact line dynamics rather than a complete immobilization of it during a transition between two contact angle boundaries.

  2. Linking Action Learning and Inter-Organisational Learning: The Learning Journey Approach

    Science.gov (United States)

    Schumacher, Thomas

    2015-01-01

    The article presents and illustrates the learning journey (LJ)--a new management development approach to inter-organisational learning based on observation, reflection and problem-solving. The LJ involves managers from different organisations and applies key concepts of action learning and systemic organisational development. Made up of…

  3. Group leaders optimization algorithm

    Science.gov (United States)

    Daskin, Anmer; Kais, Sabre

    2011-03-01

    We present a new global optimization algorithm in which the influence of the leaders in social groups is used as an inspiration for the evolutionary technique which is designed into a group architecture. To demonstrate the efficiency of the method, a standard suite of single and multi-dimensional optimization functions along with the energies and the geometric structures of Lennard-Jones clusters are given as well as the application of the algorithm on quantum circuit design problems. We show that as an improvement over previous methods, the algorithm scales as N 2.5 for the Lennard-Jones clusters of N-particles. In addition, an efficient circuit design is shown for a two-qubit Grover search algorithm which is a quantum algorithm providing quadratic speedup over the classical counterpart.

  4. NVU dynamics. II. Comparing to four other dynamics

    DEFF Research Database (Denmark)

    Ingebrigtsen, Trond; Toxværd, Søren; Schrøder, Thomas

    2011-01-01

    -potential-energy hypersurface. Here, simulations of NVU dynamics are compared to results for four other dynamics, both deterministic and stochastic. First, NVU dynamics is compared to the standard energy-conserving Newtonian NVE dynamics by simulations of the Kob-Andersen binary Lennard-Jones liquid, its WCA version (i.......e., with cut-off's at the pair potential minima), and the Lennard-Jones Gaussian liquid. We find identical results for all quantities probed: radial distribution functions, incoherent intermediate scattering functions, and mean-square displacement as function of time. Arguments are presented...... on the constant-potential-energy hypersurface, and to Nos-Hoover NVT dynamics. If time is scaled for the two stochastic dynamics to make single-particle diffusion constants identical to that of NVE dynamics, the simulations show that all five dynamics are equivalent at low temperatures except at short times....

  5. Graphene on Cu(111) at the nonzero temperatures: Molecular dynamic simulation

    Science.gov (United States)

    Sidorenkov, A. V.; Kolesnikov, S. V.; Saletsky, A. M.

    2017-11-01

    We present results of molecular dynamic simulation of continuous graphene monolayer on Cu(111). In this paper, we investigate the dependencies of the average binding energy and the average binding distance on the temperature. The interaction between carbon and copper atoms was described by Lennard-Jones potential. It is shown that the binding energy practically remains constant in a wide range of temperatures 0-800 K. However, in the same temperature range, the binding distance of graphene on Cu(111) surface has a linear dependence on temperature. The dependence of the linear thermal expansion coefficient of the binding distance on Lennard-Jones parameters has been calculated. We suggest a simple theoretical model to explain this dependence qualitatively.

  6. Dislocation-like Structures in a Simulated Liquid

    DEFF Research Database (Denmark)

    Cotterill, Rodney M J

    1979-01-01

    The free-volume distribution in a simulated Lennard-Jones liquid is heterogeneous. Chains of holes, appearing as segments rather than a continuous network, have lifetimes that are brief compared with the mean vibration period of the atoms. Larger isolated holes persist for longer times. If the ch......The free-volume distribution in a simulated Lennard-Jones liquid is heterogeneous. Chains of holes, appearing as segments rather than a continuous network, have lifetimes that are brief compared with the mean vibration period of the atoms. Larger isolated holes persist for longer times....... If the chains are interpreted as dislocation cores, the observed dislocation density is 1.0×1014 cm-2, but the actual density is probably higher....

  7. Phononless soliton waves as early forerunners of crystalline material fracture

    International Nuclear Information System (INIS)

    Dubovskij, O.A.; Orlov, A.V.

    2007-01-01

    Phononless soliton waves of compression are shown to generate at a critical tension of crystals featuring real Lennard-Jones potential of interatomic interaction just before their fracture. A new method of nonlinear micro dynamics was applied to define the initial atomic displacements at high excitation energies. A solution is found that corresponds to a soliton wave running before the front of fracture. In a bounded crystal, the soliton being reflected from the crystal boundary passes the front of fracture and deforms while moving in the opposite direction. The amplitude and spectral characteristics of that type of soliton waves in crystals with a modified Lennard-Jones potential have been investigated. An approximate analytical solution was found for the soliton waves [ru

  8. Shear-induced phase changes in mixtures

    International Nuclear Information System (INIS)

    Romig, K.D.; Hanley, H.J.M.

    1986-01-01

    A thermodynamic theory to account for the behavior of liquid mixtures exposed to a shear is developed. One consequence of the theory is that shear-induced phase changes are predicted. The theory is based on a thermodynamics that includes specifically the shear rate in the formalism and is applied to mixtures by a straightforward modification of the corresponding states, conformalsolution approach. The approach is general but is used here for a mixture of Lennard-Jones particles with a Lennard-Jones equation of state as a reference fluid. The results are discussed in the context of the Scott and Van Konynenberg phase classification. It is shown that the influence of a shear does affect substantially the type of the phase behavior. Results from the model mixture are equated loosely with those from real polymeric liquids

  9. Molecular dynamic simulation of Copper and Platinum nanoparticles Poiseuille flow in a nanochannels

    Science.gov (United States)

    Toghraie, Davood; Mokhtari, Majid; Afrand, Masoud

    2016-10-01

    In this paper, simulation of Poiseuille flow within nanochannel containing Copper and Platinum particles has been performed using molecular dynamic (MD). In this simulation LAMMPS code is used to simulate three-dimensional Poiseuille flow. The atomic interaction is governed by the modified Lennard-Jones potential. To study the wall effects on the surface tension and density profile, we placed two solid walls, one at the bottom boundary and the other at the top boundary. For solid-liquid interactions, the modified Lennard-Jones potential function was used. Velocity profiles and distribution of temperature and density have been obtained, and agglutination of nanoparticles has been discussed. It has also shown that with more particles, less time is required for the particles to fuse or agglutinate. Also, we can conclude that the agglutination time in nanochannel with Copper particles is faster that in Platinum nanoparticles. Finally, it is demonstrated that using nanoparticles raises thermal conduction in the channel.

  10. Equilibrium properties of dense hydrogen isotope gases based on the theory of simple fluids.

    Science.gov (United States)

    Kowalczyk, Piotr; MacElroy, J M D

    2006-08-03

    We present a new method for the prediction of the equilibrium properties of dense gases containing hydrogen isotopes. The proposed approach combines the Feynman-Hibbs effective potential method and a deconvolution scheme introduced by Weeks et al. The resulting equations of state and the chemical potentials as functions of pressure for each of the hydrogen isotope gases depend on a single set of Lennard-Jones parameters. In addition to its simplicity, the proposed method with optimized Lennard-Jones potential parameters accurately describes the equilibrium properties of hydrogen isotope fluids in the regime of moderate temperatures and pressures. The present approach should find applications in the nonlocal density functional theory of inhomogeneous quantum fluids and should also be of particular relevance to hydrogen (clean energy) storage and to the separation of quantum isotopes by novel nanomaterials.

  11. Evaluation of MGIT 960 System for the Second-Line Drugs Susceptibility Testing of Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Hyejin Kim

    2013-01-01

    Full Text Available Many laboratories validate DST of the second-line drugs by BACTEC MGIT 960 system. The objective of this study is to evaluate the critical concentration and perform DST for the 2nd line drugs. We evaluated 193 clinical strains of M. tuberculosis isolated from patients in South Korea. Testing the critical concentration of six second-line drugs was performed by MGIT 960 and compared with L-J proportion method. The critical concentration was determined to establish the most one that gave the difference between drug resistance and susceptibility in MGIT960 system. Good agreement of the following concentrations was found: Concordance was 95% for 0.5 μg/mL of moxifloxacin; 93.6%, 1.0 μg/mL of levofloxacin; 97.5%, 2.5 μg/mL of kanamycin; 90.6%, 2.5 μg/mL of capreomycin; 86.2%, 5.0 μg/mL of ethionamide; and 90.8%, 2.0 μg/mL of ρ-aminosalicylic acid. The critical concentrations of the four drugs, moxifloxacin, levofloxacin, kanamycin, and capreomycin, were concordant and reliable for testing 2nd line drug resistance. Further study of ethionamide and ρ-aminosalicylic acid is required.

  12. Effective diameters and corresponding states of fluids

    Science.gov (United States)

    Del Río, Fernando

    Effective hard-sphere diameters of fluids with purely repulsive interactions are derived from a generalized corresponding-states principle of Leland, Rowlinson and coworkers. Various alternative definitions are discussed and related. Virial expansions of the effective diameters and their corresponding volumes are obtained and compared with results of perturbation theory. Applications are made to inverse-power potentials, the repulsive part of the Lennard-Jones potential and hard spherocylinders and dumbells.

  13. Cluster pair correlation function of simple fluids: energetic connectivity criteria

    OpenAIRE

    Pugnaloni, Luis A.; Zarragoicoechea, Guillermo J.; Vericat, Fernando

    2006-01-01

    We consider the clustering of Lennard-Jones particles by using an energetic connectivity criterion proposed long ago by T.L. Hill [J. Chem. Phys. 32, 617 (1955)] for the bond between pairs of particles. The criterion establishes that two particles are bonded (directly connected) if their relative kinetic energy is less than minus their relative potential energy. Thus, in general, it depends on the direction as well as on the magnitude of the velocities and positions of the particles. An integ...

  14. SIMPLE FLUID IN AN ATTRACTIVE, DISORDERED POLYDISPERSE MATRIX

    Directory of Open Access Journals (Sweden)

    T.Patsahan

    2004-01-01

    Full Text Available The extension of the replica Ornstein-Zernike (ROZ equations is applied to the study of the structural properties of a Lennard-Jones fluid confined in an attractive polydisperse disordered matrix. The ROZ equations in combination with the orthogonal polynomial expansions for the correlation functions are used. The radial distribution functions are calculated for the adsorbed fluid at different temperatures. The effect of matrix polydispersity on the excess internal energy is considered in our study as well.

  15. Effects of Surface Structure and of Embedded-Atom Pair Functionals on Adatom Diffusion on FCC Metallic Surfaces

    Science.gov (United States)

    1992-11-01

    is more compact relative to that in the [001] direction. Detailed MD studies (De Lorenzi, Jacucci, and Pontikis 1982), using Lennard-Jones...Jacucci, and Pontikis 1982) have shown that the predominance of the adatom exchange mechanism results in nearly isotropic diffusion which is further...G., G. Jacucci, and V. Pontikis . Surface Science, vol. 116, p. 391, 1982. Doll, J. D., and A. F. Voter. Ann. Rev. Phys. Chem., vol. 38, p. 413, 1987

  16. The second virial coefficients of some halogenated ethanes

    Science.gov (United States)

    Kohler, Friedrich; van Nhu, Nguyen

    The second virial coefficients of 1,1-difluoroethane, 1,1,1-trifluoroethane, 1,1,1,2-tetrafluoroethane and 1-chloro-1,1-difluoroethane have been calculated on the basis of two-centre-Lennard-Jones + superimposed dipole model potentials and compared with experimental results. These can be explained taking into account the reduced dipole moments and the angle between dipole moment and molecular axis.

  17. Condensation and Evaporation Transitions in Deep Capillary Grooves

    OpenAIRE

    Malijevský, A. (Alexandr); Parry, A.O.

    2014-01-01

    We study the order of capillary condensation and evaporation transitions of a simple fluid adsorbed in a deep capillary groove using a fundamental measure density functional theory (DFT). The walls of the capillary interact with the fluid particles via long-ranged, dispersion, forces while the fluid-fluid interaction is modelled as a truncated Lennard-Jones-like potential. We find that below the wetting temperature $T_w$ condensation is first-order and evaporation is continuous with the metas...

  18. Adsorption of metal atoms at a buckled graphene grain boundary using model potentials

    International Nuclear Information System (INIS)

    Helgee, Edit E.; Isacsson, Andreas

    2016-01-01

    Two model potentials have been evaluated with regard to their ability to model adsorption of single metal atoms on a buckled graphene grain boundary. One of the potentials is a Lennard-Jones potential parametrized for gold and carbon, while the other is a bond-order potential parametrized for the interaction between carbon and platinum. Metals are expected to adsorb more strongly to grain boundaries than to pristine graphene due to their enhanced adsorption at point defects resembling those that constitute the grain boundary. Of the two potentials considered here, only the bond-order potential reproduces this behavior and predicts the energy of the adsorbate to be about 0.8 eV lower at the grain boundary than on pristine graphene. The Lennard-Jones potential predicts no significant difference in energy between adsorbates at the boundary and on pristine graphene. These results indicate that the Lennard-Jones potential is not suitable for studies of metal adsorption on defects in graphene, and that bond-order potentials are preferable

  19. Phase transitions of quadrupolar fluids

    International Nuclear Information System (INIS)

    OShea, S.F.; Dubey, G.S.; Rasaiah, J.C.

    1997-01-01

    Gibbs ensemble simulations are reported for Lennard-Jones particles with embedded quadrupoles of strength Q * =Q/(εσ 5 ) 1/2 =2.0 where ε and σ are the Lennard-Jones parameters. Calculations revealing the effect of the dispersive forces on the liquid endash vapor coexistence were carried out by scaling the attractive r -6 term in the Lennard-Jones pair potential by a factor λ ranging from 0 to 1. Liquid endash vapor coexistence is observed for all values of λ including λ=0 for Q * =2.0, unlike the corresponding dipolar fluid studied by van Leeuwen and Smit et al. [Phys. Rev. Lett. 71, 3991 (1993)] which showed no phase transition below λ=0.35 when the reduced dipole moment μ * =2.0. The simulation data are analyzed to estimate the critical properties of the quadrupolar fluid and their dependence on the strength λ of the dispersive force. The critical temperature and pressure show a clear quadratic dependence on λ, while the density is less confidently identified as being linear in λ. The compressibility is roughly linear in λ. copyright 1997 American Institute of Physics

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

    Science.gov (United States)

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

    2011-04-28

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