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Sample records for lennard-jones lj system

  1. Gas-solid coexistence of the Lennard-Jones system

    NARCIS (Netherlands)

    van der Hoef, Martin Anton

    2002-01-01

    Recently, the absolute free energies of the Lennard-Jones system at solid–liquid and solid–gas coexistence were computed from Monte Carlo simulations [J. Chem. Phys. 116, 7145 (2002)]. In this note, we show that the values along the sublimation line are in good agreement with the results from an

  2. 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

  3. 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

  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 system...... in two, three, and four dimensions. The state points studied include many low-density states at which the virial potentialenergy correlations are not strong. For these state points we find the roughly linear relation γ ∼= 3n R/d in d dimensions. This result is discussed in light of the approximate...... → 1, a limit that is approached at high densities and/or high temperatures at which the repulsive r−2n term dominates the physics....

  5. 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

  6. Replica exchange molecular simulation of Lennard-Jones particles in a two-dimensional confined system

    Science.gov (United States)

    Doi, Hideo; Yasuoka, Kenji

    2017-05-01

    Confined systems exhibit interesting properties that are applied to the fields of lubrication, adhesion and nanotechnology. The replica exchange molecular simulation method was applied to calculate the phase equilibrium points of Lennard-Jones particles in a two-dimensional confined system. The liquid-solid phase equilibrium points and the solid structure with a dependency of the slit width were determined and the order parameter of the solid structure was analyzed. Such confined systems are shown to be favorable for manipulation of the phase equilibrium points.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. Chemical Potential of a Lennard Jones Fluid

    Directory of Open Access Journals (Sweden)

    Celebonovic, V.

    2010-12-01

    Full Text Available The aim of this paper is to present results of analytical calculation of chemical potential of a Lennard Jones (LJ fluid performed in two ways: by using the thermodynamical formalism and the formalism of statistical mechanics. The integration range is divided into two regions. In the small distance region, which is $rleqsigma$ in the usual notation, the integration range had to be cut off in order to avoid the occurence of divergences. In the large distance region, the calculation is technically simpler. The calculation reported here will be useful in all kinds of studies concerning phase equilibrium in a LJ fluid. Interesting kinds of such systems are the giant planets and the icy satellites in various planetary systems, but also the (so far hypothetical quark stars.

  12. Chemical potential of a Lennard Jones fluid

    Directory of Open Access Journals (Sweden)

    Čelebonović V.

    2010-01-01

    Full Text Available The aim of this paper is to present results of analytical calculation of chemical potential of a Lennard Jones (LJ fluid performed in two ways: by using the thermodynamical formalism and the formalism of statistical mechanics. The integration range is divided into two regions. In the small distance region, which is r ≤ σ in the usual notation, the integration range had to be cut off in order to avoid the occurrence of divergences. In the large distance region, the calculation is technically simpler. The calculation reported here will be useful in all kinds of studies concerning phase equilibrium in a LJ fluid. Interesting kinds of such systems are the giant planets and the icy satellites in various planetary systems, but also the (so far hypothetical quark stars.

  13. 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.

  14. 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.

  15. 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.

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    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...... 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...... 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...

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

    DEFF Research Database (Denmark)

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

    2006-01-01

    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 ...

  18. Size-effects on the surface tension near the critical point: Monte Carlo simulations of the Lennard-Jones fluid

    Science.gov (United States)

    Goujon, Florent; Ghoufi, Aziz; Malfreyt, Patrice

    2018-02-01

    We report Monte Carlo (MC) simulations of the Lennard-Jones (LJ) fluid at the liquid-vapor interface in the critical region. A slab-based tail method is associated with the MC simulations to approach as close as possible the critical point (T∗ = 0.98 TC∗) . We investigate then the impact of system-sizes on the surface tension and coexisting densities by considering very large box dimensions for which the surface tension is independent of system-sizes at low temperatures.

  19. 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

  20. Non-equilibrium surface tension of the vapour-liquid interface of active Lennard-Jones particles

    NARCIS (Netherlands)

    Paliwal, Siddharth; Prymidis, Vasileios; Filion, Laura; Dijkstra, Marjolein

    2017-01-01

    We study a three-dimensional system of self-propelled Brownian particles interacting via the Lennard-Jones potential. Using Brownian dynamics simulations in an elongated simulation box, we investigate the steady states of vapour-liquid phase coexistence of active Lennard-Jones particles with planar

  1. 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...

  2. 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

  3. 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.

  4. Modified Benedict-Webb-Rubin Equation of State for the Modified Lennard-Jones Fluid

    Science.gov (United States)

    Asano, Yuta; Fuchizaki, Kazuhiro

    2014-03-01

    We have proposed a modified Lennard-Jones (mLJ) potential to deal with problems, such as the accurate determination of the melting condition, in which an attractive interaction plays an essential role, but its range need not necessarily extend to infinity. An accurate phase diagram, including the triple and the critical points of the system characterized by the mLJ potential, has been investigated using mainly thermodynamic integration. To predict the thermodynamic behavior of the system, it is further desired to construct the equation of state (EOS) as accurately as possible. The modified Benedict-Webb-Rubin EOS was employed to this end. The 33 parameters involved in the equation were carefully determined in order for the EOS to be compatible with the temperature dependences of the virial coefficients as well as with an extremely large set of thermodynamic data obtained from our own molecular dynamics simulation performed over a wide fluid region. The resultant EOS was found to be not only sufficiently accurate at temperatures up to twenty times as high as the critical-point temperature but also effective in practical use.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    S/T , where ρ is density, T is temperature, and γ S is a material specific scaling exponent) is an approximation to a more general scaling predicted by the isomorph theory. Furthermore, the isomorph theory provides an explanation for Rosenfeld scaling (relaxation times and transport coefficients being...... 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...... confirm the existence of isomorphs, which are curves in the phase diagram along which the dynamics is invariant in the appropriate reduced units. This holds not only for the relaxation times but also for the full time dependence of the dynamics, including chain specific dynamics such as the end...

  6. Mapping the magic numbers in binary Lennard-Jones clusters.

    Science.gov (United States)

    Doye, Jonathan P K; Meyer, Lars

    2005-08-05

    Using a global optimization approach that directly searches for the composition of greatest stability, we have been able to find the particularly stable structures for binary Lennard-Jones clusters with up to 100 atoms for a range of Lennard-Jones parameters. In particular, we have shown that just having atoms of different sizes leads to a remarkable stabilization of polytetrahedral structures, including both polyicosahedral clusters and at larger sizes structures with disclination lines.

  7. 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...... for the clusters of noble gases atoms. Our method serves an efficient alternative to the global optimization techniques based on the Monte-Carlo simulations and it can be applied for the solution of a broad variety of problems in which atomic cluster structure is important....

  8. 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.

  9. 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

  10. 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....

  11. 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.

  12. Origin of line tension for a Lennard-Jones nanodroplet

    NARCIS (Netherlands)

    Weijs, Joost; Weijs, Joost H.; Marchand, Antonin; Andreotti, Bruno; Lohse, Detlef; Snoeijer, Jacobus Hendrikus

    2011-01-01

    The existence and origin of line tension has remained controversial in literature. To address this issue, we compute the shape of Lennard-Jones nanodrops using molecular dynamics and compare them to density functional theory in the approximation of the sharp kink interface. We show that the

  13. Free energy of the Lennard-Jones solid

    NARCIS (Netherlands)

    van der Hoef, Martin Anton

    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

  14. 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

  15. 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...

  16. Solitons in a One-Dimensional Lennard-Jones Lattice

    OpenAIRE

    Yuji, ISHIMORI; Department of Applied Mathematics and Physics Kyoto University

    1982-01-01

    Nonlinear waves in a one-dimensional lattice with (2n, n) Lennard-Jones potential are studied in small-amplitude and long-wavelength approximations. Equations derived are classified into three types according to the value of the force-range parameter n. For n=2 and ≧4, we get the Benjamin-Ono equation and the Korteweg-de Vries equation, respectively.

  17. 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.

  18. Stability limits for the supercooled liquid and superheated crystal of Lennard-Jones particles.

    Science.gov (United States)

    Loscar, Ernesto S; Martin, Daniel A; Grigera, Tomás S

    2017-07-21

    We have studied the limits of stability in the first order liquid-solid phase transition in a Lennard-Jones system by means of the short-time relaxation method and using the bond-orientational order parameter Q 6 . These limits are compared with the melting line. We have paid special attention to the supercooled liquid, comparing our results with the point where the free energy cost of forming a nucleating droplet goes to zero. We also indirectly estimate the dimension associated to the critical nucleus at the spinodal, expected to be fractal according to mean field theories of nucleation.

  19. Origin of line tension for a Lennard-Jones nanodroplet

    Science.gov (United States)

    Weijs, Joost H.; Marchand, Antonin; Andreotti, Bruno; Lohse, Detlef; Snoeijer, Jacco H.

    2011-02-01

    The existence and origin of line tension has remained controversial in literature. To address this issue, we compute the shape of Lennard-Jones nanodrops using molecular dynamics and compare them to density functional theory in the approximation of the sharp kink interface. We show that the deviation from Young's law is very small and would correspond to a typical line tension length scale (defined as line tension divided by surface tension) similar to the molecular size and decreasing with Young's angle. We propose an alternative interpretation based on the geometry of the interface at the molecular scale.

  20. Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations.

    Science.gov (United States)

    Kaukonen, M; Gulans, A; Havu, P; Kauppinen, E

    2012-03-05

    Lennard-Jones (LJ) parameters are derived for classical nonpolarizable force fields for carbon nanotubes (CNTs) and for CNT-water interaction from van der Waals (vdW) enhanced density functional calculations. The new LJ parameters for carbon-carbon interactions are of the same order as those previously used in the literature but differ significantly for CNT-water interactions. This may partially originate from the fact that in addition to pure vdW interactions the polarization and other quantum mechanics effects are embedded into the LJ-potential. Copyright © 2012 Wiley Periodicals, Inc.

  1. 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.

  2. Non-equilibrium surface tension of the vapour-liquid interface of active Lennard-Jones particles

    Science.gov (United States)

    Paliwal, Siddharth; Prymidis, Vasileios; Filion, Laura; Dijkstra, Marjolein

    2017-08-01

    We study a three-dimensional system of self-propelled Brownian particles interacting via the Lennard-Jones potential. Using Brownian dynamics simulations in an elongated simulation box, we investigate the steady states of vapour-liquid phase coexistence of active Lennard-Jones particles with planar interfaces. We measure the normal and tangential components of the pressure tensor along the direction perpendicular to the interface and verify mechanical equilibrium of the two coexisting phases. In addition, we determine the non-equilibrium interfacial tension by integrating the difference of the normal and tangential components of the pressure tensor and show that the surface tension as a function of strength of particle attractions is well fitted by simple power laws. Finally, we measure the interfacial stiffness using capillary wave theory and the equipartition theorem and find a simple linear relation between surface tension and interfacial stiffness with a proportionality constant characterized by an effective temperature.

  3. A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution.

    Science.gov (United States)

    Sumi, Tomonari; Maruyama, Yutaka; Mitsutake, Ayori; Koga, Kenichiro

    2016-06-14

    In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.

  4. More on the melting of Lennard-Jones clusters

    International Nuclear Information System (INIS)

    Garzon, I.L.; Avalos-Borja, M.; Blaisten-Barojas, E.

    1989-01-01

    The melting of 13-atom clusters interacting via Lennard-Jones potentials has been revisited using molecular dynamics coupled to steepest descent quenches. A procedure was devised to account for the fraction of times the global and local minima of the potential energy surface are accessed during a long trajectory. This quantity presents a sigmoid shape. A phenomenological model of melting is given in terms of a correlated walk that maps the short time excursions among the global and local minima in configuration space. Comparison between the simulation results and the theoretical model shows that the melting transition is well described in terms of the temperature changes of the fraction of high energy minima accessed during the cluster trajectory. Cooperativity is clear from the S shape of this quantity, i.e., the access to a local minimum favours the access to other local minima. (orig.)

  5. The self-referential method for linear rigid bodies: application to hard and Lennard-Jones dumbbells.

    Science.gov (United States)

    Sweatman, Martin B; Atamas, Alexander; Leyssale, Jean-Marc

    2009-01-14

    The self-referential (SR) method incorporating thermodynamic integration (TI) [Sweatman et al., J. Chem. Phys. 128, 064102 (2008)] is extended to treat systems of rigid linear bodies. The method is then applied to obtain the canonical ensemble Helmholtz free energy of the alpha-N(2) and plastic face centered cubic phases of systems of hard and Lennard-Jones dumbbells using Monte Carlo simulations. Generally good agreement with reference literature data is obtained, which indicates that the SR-TI method is potentially very general and robust.

  6. 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.

  7. 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.

  8. Premelting, solid-fluid equilibria, and thermodynamic properties in the high density region based on the Lennard-Jones potential

    Science.gov (United States)

    Köster, Andreas; Mausbach, Peter; Vrabec, Jadran

    2017-10-01

    The Lennard-Jones potential is used to study the high density fluid and face centered cubic solid state region, including solid-fluid equilibria. Numerous thermodynamic properties are considered, elucidating the behavior of matter in this poorly studied region. The present molecular simulation results are extensively compared to the latest and most accurate equation of state models for fluid and solid phases. It is shown that current models do not cover the thermodynamics of the system adequately near the solid-fluid phase transition. Furthermore, thermodynamic stability is analyzed, indicating that published solid-fluid coexistence data may not be correct at high temperatures. Particular attention is paid to the premelting zone, a range of states close to the melting line, which is characterized by strong variations of several thermodynamic properties. Because the underlying microscopic mechanisms are not yet fully understood, it is hoped that these data may contribute to the development of a theoretical framework for describing premelting effects.

  9. Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory

    Science.gov (United States)

    Evans, Robert; Stewart, Maria C.; Wilding, Nigel B.

    2017-07-01

    We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory, we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, i.e., in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent ν∥, which controls the parallel correlation length, i.e., the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. Possible reasons for this discrepancy are discussed in the light of fresh insights into the nature of near critical finite-size effects.

  10. Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory.

    Science.gov (United States)

    Evans, Robert; Stewart, Maria C; Wilding, Nigel B

    2017-07-28

    We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory, we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, i.e., in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent ν ∥ , which controls the parallel correlation length, i.e., the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. Possible reasons for this discrepancy are discussed in the light of fresh insights into the nature of near critical finite-size effects.

  11. 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)

  12. Hopping in a supercooled binary Lennard-Jones liquid

    DEFF Research Database (Denmark)

    Schrøder, Thomas; Dyre, Jeppe

    1998-01-01

    A binary Lennard–Jones liquid has been investigated by molecular dynamics at equilibrium supercooled conditions. At the lowest temperature investigated, hopping is present in the system as indicated by a secondary peak in 4r2Gs(r,t), where Gs(r,t) is the van Hove self correlation function......", as often argued, and that the system has a single-peaked distribution of hopping-distances centered around the characteristic intermolecular distance....

  13. Hopping in a supercooled binary Lennard-Jones liquid

    DEFF Research Database (Denmark)

    Schrøder, Thomas; Dyre, Jeppe

    1998-01-01

    A binary Lennard–Jones liquid has been investigated by molecular dynamics at equilibrium supercooled conditions. At the lowest temperature investigated, hopping is present in the system as indicated by a secondary peak in 4r2Gs(r,t), where Gs(r,t) is the van Hove self correlation function...

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. Prediction of vapor-liquid equilibrium and PVTx properties of geological fluid system with SAFT-LJ EOS including multi-polar contribution. Part I: Application to H 2O-CO 2 system

    Science.gov (United States)

    Sun, Rui; Dubessy, Jean

    2010-04-01

    Molecular based equations of state (EOS) are attractive because they can take into account the energetic contribution of the main types of molecular interactions. This study models vapor-liquid equilibrium (VLE) and PVTx properties of the H 2O-CO 2 binary system using a Lennard-Jones (LJ) referenced SAFT (Statistical Associating Fluid Theory) EOS. The improved SAFT-LJ EOS is defined in terms of the residual molar Helmholtz energy, which is a sum of four terms representing the contributions from LJ segment-segment interactions, chain-forming among the LJ segments, short-range associations and long-range multi-polar interactions. CO 2 is modeled as a linear chain molecule with a constant quadrupole moment, and H 2O is modeled as a spherical molecule with four association sites and a dipole moment. The multi-polar contribution to Helmholtz energy, including the dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole contribution for H 2O-CO 2 system, is calculated using the theory of Gubbins and Twu (1978). Six parameters for pure H 2O and four parameters for pure CO 2 are needed in our model. The Van der Waals one-fluid mixing rule is used to calculate the Lennard-Jones energy parameter and volume parameter for the mixture. Two or three binary parameters are needed for CO 2-H 2O mixtures, which are evaluated from phase equilibrium data of the binary system. Comparison with the experimental data shows that our model represents the PVT properties of CO 2 better than other SAFT EOS without a quadrupole contribution. For the CO 2-H 2O system, our model agrees well with the vapor-liquid equilibrium data from 323-623 K. The average relative deviation for CO 2 solubility (expressed in mole fraction) in water is within 6%. Our model can also predict the PVTx properties of CO 2-H 2O mixtures up to 1073 K and 3000 bar. The good performance of this model indicates that: (1) taking account of the multi-polar contribution explicitly improves the agreement of calculated

  19. An equation of state for two-center Lennard-Jones fluids

    Science.gov (United States)

    Mecke, M.; Müller, A.; Winkelmann, J.; Fischer, J.

    1997-05-01

    A new equation of state (EOS) is proposed for the Helmholzt energy F of two-center Lennard-Jones fluids. The EOS is written in the form of a generalized van der Waals equation, F=F H + F A , where F H accounts for the hard-body interaction and F A for the attractive dispersion forces. The equation is constructed on the basis of previously published data sets and results from new extensive computer simulation studies. It correlates pressures and internal energies over a wide fluid range for two-center model fluids with elongations up to 0.67 in reduced units with a high accuracy and shows an excellent description of the vapor-liquid coexistence properties. Comparisons of results from the new EOS with other data sets and recently published VLE from the NpT plus test particle method show very good agreement.

  20. Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential.

    Science.gov (United States)

    Geada, Isidro Lorenzo; Ramezani-Dakhel, Hadi; Jamil, Tariq; Sulpizi, Marialore; Heinz, Hendrik

    2018-02-19

    Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals.

  1. Viscoelastic crack propagation and closing with Lennard-Jones surface forces

    International Nuclear Information System (INIS)

    Greenwood, J A

    2007-01-01

    An analysis of the opening and closing of a crack in a viscoelastic solid has been made assuming a Lennard-Jones law of force acting between the crack faces. The results are compared with those of an earlier analysis in which a simple Dugdale model of the surface forces was assumed. The approximate 'reciprocal rule' between the apparent surface energies for opening and closing cracks is confirmed. At low speeds a linear relation between the apparent surface energy and the crack speed is found. The lengths of the process zone for opening and closing cracks are found to be very similar and so presumably are not responsible for the very different values of the apparent surface energy

  2. Viscoelastic crack propagation and closing with Lennard-Jones surface forces

    Energy Technology Data Exchange (ETDEWEB)

    Greenwood, J A [Department of Engineering, Trumpington Street, Cambridge, CB2 1PZ (United Kingdom)

    2007-03-21

    An analysis of the opening and closing of a crack in a viscoelastic solid has been made assuming a Lennard-Jones law of force acting between the crack faces. The results are compared with those of an earlier analysis in which a simple Dugdale model of the surface forces was assumed. The approximate 'reciprocal rule' between the apparent surface energies for opening and closing cracks is confirmed. At low speeds a linear relation between the apparent surface energy and the crack speed is found. The lengths of the process zone for opening and closing cracks are found to be very similar and so presumably are not responsible for the very different values of the apparent surface energy.

  3. 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.

  4. 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-Jon...

  5. Explicit expressions of self-diffusion coefficient, shear viscosity, and the Stokes-Einstein relation for binary mixtures of Lennard-Jones liquids

    International Nuclear Information System (INIS)

    Ohtori, Norikazu; Ishii, Yoshiki

    2015-01-01

    Explicit expressions of the self-diffusion coefficient, D i , and shear viscosity, η sv , are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m −3 . The scaling equations obtained by multiplying all the single-variable dependences can well express D i and η sv evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for D i can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on D i . The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions

  6. Explicit expressions of self-diffusion coefficient, shear viscosity, and the Stokes-Einstein relation for binary mixtures of Lennard-Jones liquids

    Energy Technology Data Exchange (ETDEWEB)

    Ohtori, Norikazu, E-mail: ohtori@chem.sc.niigata-u.ac.jp [Department of Chemistry, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181 (Japan); Ishii, Yoshiki [Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181 (Japan)

    2015-10-28

    Explicit expressions of the self-diffusion coefficient, D{sub i}, and shear viscosity, η{sub sv}, are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m{sup −3}. The scaling equations obtained by multiplying all the single-variable dependences can well express D{sub i} and η{sub sv} evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for D{sub i} can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on D{sub i}. The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions.

  7. 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

    measured for the clusters of noble gas atoms. Our method serves as an efficient alternative to the global optimization techniques based on the Monte-Carlo simulations and it can be applied for the solutions of a broad variety of problems in which atomic cluster structure is important.......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....... We demonstrate that in this way all known global minima structures of the (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 and compare...

  8. Chemical potential and solid-solid equilibrium of near-spherical Lennard-Jones dumbbell crystal

    International Nuclear Information System (INIS)

    Lee, Sangwon; Kim, Minkyu; Chang, Jaeeon

    2016-01-01

    We studied the orientational order-disorder transition of crystals made up of near-spherical Lennard-Jones dumbbells, of which reduced bond lengths are 0.225, 0.250 and 0.275. Various techniques of Monte Carlo (MC) simulations are used to calculate the chemical potentials of ordered and disordered crystals, and thereby to predict order disorder phase transition. First, we performed NPT MC simulations to determine crystal structure, equilibrium positions and orientations of the molecules. We then calculated the free energies of the crystals using the expanded ensemble MC simulations combined with the Einstein-molecule method and the thermodynamic integration method. The solid-solid phase equilibrium is determined from the free energy profiles of the individual phases by equating the chemical potential. The predictions of phase transition obtained from the conventional NPT MC simulation and the free energy simulation were in excellent agreement with each other, which confirms the validity of the present method of calculating the chemical potential of crystal. In addition, the Gibbs-Duhem integration was performed to obtain a complete coexistence curve between the two crystal phases. Orientational probability distributions of molecular axes were analyzed to find the characteristic behavior of rotational motion of molecule in the crystal. At sufficiently low temperature, flipping rotation of molecule in the ordered crystal is suppressed. In contrast, the flipping rotation occurs at higher temperature close to the transition while orientationally ordered structure is still maintained. In the free energy calculation, such a unique rotational behavior requires to use a suitable form of external rotational potential with proper symmetry number. The present study demonstrates how one can judiciously choose a correct simulation scheme for the calculation of chemical potentials of molecular crystals.

  9. 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

  10. Selection and Validation of Charge and Lennard-Jones Parameters for QM/MM Simulations of Hydrocarbon Interactions with Zeolites.

    Science.gov (United States)

    Zimmerman, Paul M; Head-Gordon, Martin; Bell, Alexis T

    2011-06-14

    Quantum mechanics/molecular mechanics (QM/MM) models are an appealing method for performing zeolite simulations. In QM/MM, a small cluster chosen to encompass the active center is described by QM, while the rest of the zeolite is described by MM. In the present study, we demonstrate that the charges and Lennard-Jones parameters on Si and O must be chosen properly for QM/MM calculations of adsorption energies and activation energies to agree closely with full QM calculations. The selection of parameters for Si and O is based on using the ωB97X-D functional for DFT calculations of the QM region, which is effective in capturing the effects of van der Waals interactions. A comparison of the heats of adsorption for a variety of adsorbates and activation energies for the cracking of propane and butane reveals that energies derived from QM/MM calculation carried out with appropriately selected MM parameters agree to within an rms error of ∼1.5 kcal/mol with QM calculations. To avoid reparametrization for new substrates, Lennard-Jones zeolite parameters are chosen to be compatible with existing CHARMM parameters. Transferability of these parameters is demonstrated by tests utilizing the B3LYP density functional and simulations of MFI and FAU zeolites. Moreover, the computational time for QM/MM calculations is considerably lower than that for QM calculations, and the ratio of computational times decreases rapidly with increasing size of the cluster used to represent the zeolite.

  11. Effect of gold nanoparticles on structure and dynamics of binary Lennard-Jones liquid: Wave-vector space analysis

    Science.gov (United States)

    Separdar, L.; Davatolhagh, S.

    2016-12-01

    Molecular dynamics simulations at constant (N , V , T) are used to study the mutual effects of gold nanoparticles on the structure and dynamics of Kob-Andersen binary Lennard-Jones (BLJ) liquid within the framework of mode coupling theory of dynamic glass transition in the reciprocal space. The results show the 'softening' effect of the gold nanoparticles on the liquid dynamics in terms of (i) reducing the mode coupling crossover temperature Tc with respect to that of the bulk BLJ (i.e. BLJ without nanoparticles), (ii) decreasing the time interval of β-relaxation, and (iii) decreasing the exponent γ characterizing the power-law behavior of the α-relaxation time. This softening effect is explained in terms of the van der Waals attraction between the gold atoms comprising the nanoparticle and the BLJ host atoms, such that adsorption of host atoms onto the nanoparticle surface creates more space or free-volume for the other atoms to diffuse. By the same token interactions of purely excluded-volume-type are expected to result in the opposite effect. It is also noted that, much unlike BLJ host particles, the dynamics of gold nanoparticles is much less dependent on the wave-vector and that it exhibits a nearly exponential behavior in the α-relaxation regime.

  12. Icosahedron-fcc transition size by molecular dynamics simulation of Lennard-Jones clusters at a finite temperature.

    Science.gov (United States)

    Ikeshoji, T; Torchet, G; de Feraudy, M F; Koga, K

    2001-03-01

    We studied finite-temperature ensembles of solid clusters produced by cooling liquid droplets either by evaporation or by a thermostat through a molecular dynamics calculation using the Lennard-Jones potential. The ensembles consist of either single or binary component clusters with 25% of the atoms 8% smaller in diameter than the other 75%. These clusters (380 clusters in total) exhibit various structures in the size range of n=160-2200, where n is the number of atoms in a cluster. For increasing size, the clusters show a gradual transition from icosahedral to a variety of structures: decahedral, face centered cubic, a small amount of hexagonal, and some icosahedral structures. They are asymmetrical or faulted. Electron diffraction patterns calculated with average structure factors of clusters after grouping them into several size regions are very similar to those experimentally observed. The size transition is around n=450 for single component clusters whatever the cooling process, evaporation or thermostat. This size is smaller than the experimental transition size estimated for argon clusters formed in a supersonic expansion. The transition size for binary component clusters is around n=600 for evaporative cooling, and larger for thermostatic cooling. The larger transition size found for the binary component clusters is consistent with the large icosahedral Au-Fe and Au-Cu alloy clusters observed experimentally.

  13. 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.

  14. Vapour-liquid equilibria of two-centre Lennard-Jones fluids from the NpT plus test particle method

    Science.gov (United States)

    Kriebel, Christian; Müller, Andreas; Winkelmann, Jochen; Fischer, Johann

    Vapour-liquid phase equilibria (VLE) are determined from the NpT plus test particle method for two-centre Lennard-Jones fluids of elongations L* = 0·22, 0·3292, 0·505, and 0·67. The resulting vapour pressures as well as the saturated vapour and liquid densities are correlated by simple equations. The thermodynamic consistency of the VLE data is confirmed on the basis of the Clausius-Clapeyron equation. Comparison is made with results from previous simulations, and from perturbation theory.

  15. Monte Carlo simulation of some thermophysical properties of two-centre Lennard-Jones fluids along the vapour-liquid equilibrium curve

    Science.gov (United States)

    Kronome, Gergely; Liszi, Janos; Szalai, Istvan

    The vapour pressures, saturated liquid and vapour densities, enthalpies of vaporization, isobaric, and saturation heat capacities are calculated for ethane and ethylene along their vapour-liquid equilibrium (VLE) curves from Monte Carlo simulations using the extended NpT plus test particle (XNpT + TP) method (Boda, D., Liszi, J., and Szalai, I., 1995, Chem. Phys. Lett. , 235, 140). The substances are modelled by two-centre Lennard-Jones molecules of elongations L * = 0.67 for ethane and L * = 0.74 for ethylene. Simulation results are compared with correlated experimental data. In the case of ethylene new values are required for the model parameters to obtain a good agreement with experimental data along the VLE curve. Our results show that the XNpT + TP method is appropriate for the simulation of caloric properties of molecular fluids along the VLE curve.

  16. 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.

  17. Lennard-Jones fluids in a nanochannel

    NARCIS (Netherlands)

    Hartkamp, Remco; Luding, Stefan; Nuernberg Messe GmbH,

    2010-01-01

    During the past few decades molecular dynamics has been a widely applied tool to simulate fluid confined in micro/nano geometries. What makes interfacial fluids fundamentally different from the bulk fluid is the fact that their density varies considerably over microscopic distances. A class of such

  18. Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

    Science.gov (United States)

    Reif, Maria M.; Hünenberger, Philippe H.

    2011-04-01

    The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [M. A. Kastenholz and P. H. Hünenberger, J. Chem. Phys. 124, 224501 (2006), 10.1529/biophysj.106.083667; M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144103 (2010)], the application of appropriate correction terms permits to obtain methodology-independent results. The corrected values are then exclusively characteristic of the underlying molecular model including in particular the ion-solvent van der Waals interaction parameters, determining the effective ion size and the magnitude of its dispersion interactions. In the present study, the comparison of calculated (corrected) hydration free energies with experimental data (along with the consideration of ionic polarizabilities) is used to calibrate new sets of ion-solvent van der Waals (Lennard-Jones) interaction parameters for the alkali (Li+, Na+, K+, Rb+, Cs+) and halide (F-, Cl-, Br-, I-) ions along with either the SPC or the SPC/E water models. The experimental dataset is defined by conventional single-ion hydration free energies [Tissandier et al., J. Phys. Chem. A 102, 7787 (1998), 10.1021/jp982638r; Fawcett, J. Phys. Chem. B 103, 11181] along with three plausible choices for the (experimentally elusive) value of the absolute (intrinsic) hydration free energy of the proton, namely, Δ G_hyd^{ominus }[H+] = -1100, -1075 or -1050 kJ mol-1, resulting in three sets L, M, and H for the SPC water model and three sets LE, ME, and HE for the SPC/E water model (alternative sets can easily be interpolated to intermediate Δ G_hyd^{ominus }[H+] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective ionic radius entering into the calculation of the correction terms is

  19. 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

  20. LJ Best Audiobooks 2010

    Science.gov (United States)

    Kuzyk, Raya

    2011-01-01

    This article presents a list of the best audiobooks of 2010. Among the past year's most memorable audiobooks, all recipients of starred "Library Journal" reviews, are four "LJ" Best Books, two postapocalyptic trilogy starters, two nonfiction tracts on marriage, a baseball novella, an adult/YA crossover novel, and an Obama biography.

  1. 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 ...

  2. Hierarchical Nanostructures Self-Assembled from a Mixture System Containing Rod-Coil Block Copolymers and Rigid Homopolymers

    Science.gov (United States)

    Li, Yongliang; Jiang, Tao; Lin, Shaoliang; Lin, Jiaping; Cai, Chunhua; Zhu, Xingyu

    2015-05-01

    Self-assembly behavior of a mixture system containing rod-coil block copolymers and rigid homopolymers was investigated by using Brownian dynamics simulations. The morphologies of formed hierarchical self-assemblies were found to be dependent on the Lennard-Jones (LJ) interaction ɛRR between rod blocks, lengths of rod and coil blocks in copolymer, and mixture ratio of block copolymers to homopolymers. As the ɛRR value decreases, the self-assembled structures of mixtures are transformed from an abacus-like structure to a helical structure, to a plain fiber, and finally are broken into unimers. The order parameter of rod blocks was calculated to confirm the structure transition. Through varying the length of rod and coil blocks, the regions of thermodynamic stability of abacus, helix, plain fiber, and unimers were mapped. Moreover, it was discovered that two levels of rod block ordering exist in the helices. The block copolymers are helically wrapped on the homopolymer bundles to form helical string, while the rod blocks are twistingly packed inside the string. In addition, the simulation results are in good agreement with experimental observations. The present work reveals the mechanism behind the formation of helical (experimentally super-helical) structures and may provide useful information for design and preparation of the complex structures.

  3. 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.

  4. Validity of the Rosenfeld relationship: A comparative study of the ...

    Indian Academy of Sciences (India)

    In this paper we explore the validity of the Rosenfeld and the Dzugutov relation for the Lennard- Jones (LJ) system, its repulsive counterpart, the WCA system and a network forming liquid, the NTW model. We find that for all the systems both the relations are valid at high temperature regime with an universalexponent close ...

  5. 77 FR 6945 - Special Conditions: Learjet Inc., Learjet Model LJ-200-1A10; Interaction of Systems and Structures

    Science.gov (United States)

    2012-02-10

    ... adequacy pursuant to Sec. 611 of Public Law 92-574, the ``Noise Control Act of 1972.'' The FAA issues... flight control systems, autopilots, stability augmentation systems, load alleviation systems, and fuel... flight control systems, autopilots, stability augmentation systems, load alleviation systems, fuel...

  6. ;:::,!,lj

    African Journals Online (AJOL)

    containing bisphosphonates including alendronate inhibit prenylation.'" They act directly on the osteoclast by causing apoptosis via Mstl kinase cleavage and the activation of caspases, and these effects can be mimicked by lovastatin and reversed by ...

  7. ;:::,!,lj

    African Journals Online (AJOL)

    has provided many new insights into cellular biology and opened up new and novel therapeutic possibilities. ... to endocrinology and bone mineral metabolism is briefly reviewed. Numerous reviews and articles have been ... prenylation in endocrinology and bone and mineral metabolism are briefly discussed. The potential ...

  8. Equilibrium fluctuations of the Lennard-Jones cluster surface

    Science.gov (United States)

    Zhukhovitskii, D. I.

    2008-11-01

    Spectra of the cluster surface equilibrium fluctuations are treated by decomposition into the bulk and net capillary ones. The bulk fluctuations without capillary ones are simulated by the surface of a cluster truncated by a sphere. The bulk fluctuation spectrum is shown to be generated primarily by the discontinuity in the spatial distribution of cluster internal particles. The net capillary fluctuation slice spectrum is obtained in molecular dynamics simulation by subtraction of the bulk fluctuation spectrum from the total one. This net spectrum is in the best agreement with a theoretical estimation if we assume the intrinsic surface tension to be independent of the wave number. The wave number cutoff is brought in balance with the intrinsic surface tension and excess surface area induced by the capillary fluctuations. It is shown that the ratio of the ordinary surface tension to the intrinsic one can be considered as a universal constant independent of the temperature and cluster size.

  9. 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.

  10. A practical law to predict the appearance sizes of multiply charged rare-gas and molecular clusters

    Science.gov (United States)

    Bonhommeau, David A.

    2017-10-01

    A dimensionless law depending on cluster size N is derived from the Rayleigh limit expressed in reduced Lennard-Jones (LJ) units to predict the critical sizes nc (z) of clusters carrying z positive charges. This relationship provides suitable estimates of nc (z) (z = 2 - 4) for rare-gas clusters, including neon clusters whose predicted critical sizes deviate from experimental expectations by less than 12% for different choices of LJ parameters. An extension to 11 nonpolar and 15 polar molecular clusters, from dimers to aromatic hydrocarbons, is achieved that demonstrates the broad applicability of the formula despite inaccuracies for highly polar systems.

  11. Pressure control in interfacial systems: Atomistic simulations of vapor nucleation

    Science.gov (United States)

    Marchio, S.; Meloni, S.; Giacomello, A.; Valeriani, C.; Casciola, C. M.

    2018-02-01

    A large number of phenomena of scientific and technological interest involve multiple phases and occur at constant pressure of one of the two phases, e.g., the liquid phase in vapor nucleation. It is therefore of great interest to be able to reproduce such conditions in atomistic simulations. Here we study how popular barostats, originally devised for homogeneous systems, behave when applied straightforwardly to heterogeneous systems. We focus on vapor nucleation from a super-heated Lennard-Jones liquid, studied via hybrid restrained Monte Carlo simulations. The results show a departure from the trends predicted for the case of constant liquid pressure, i.e., from the conditions of classical nucleation theory. Artifacts deriving from standard (global) barostats are shown to depend on the size of the simulation box. In particular, for Lennard-Jones liquid systems of 7000 and 13 500 atoms, at conditions typically found in the literature, we have estimated an error of 10-15 kBT on the free-energy barrier, corresponding to an error of 104-106 s-1σ-3 on the nucleation rate. A mechanical (local) barostat is proposed which heals the artifacts for the considered case of vapor nucleation.

  12. 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.

  13. Perturbation theory calculations of model pair potential systems

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Jianwu [Iowa State Univ., Ames, IA (United States)

    2016-01-01

    Helmholtz free energy is one of the most important thermodynamic properties for condensed matter systems. It is closely related to other thermodynamic properties such as chemical potential and compressibility. It is also the starting point for studies of interfacial properties and phase coexistence if free energies of different phases can be obtained. In this thesis, we will use an approach based on the Weeks-Chandler-Anderson (WCA) perturbation theory to calculate the free energy of both solid and liquid phases of Lennard-Jones pair potential systems and the free energy of liquid states of Yukawa pair potentials. Our results indicate that the perturbation theory provides an accurate approach to the free energy calculations of liquid and solid phases based upon comparisons with results from molecular dynamics (MD) and Monte Carlo (MC) simulations.

  14. 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.

  15. Anion inhibition studies of two α-carbonic anhydrases from Lotus japonicus, LjCAA1 and LjCAA2.

    Science.gov (United States)

    Vullo, Daniela; Flemetakis, Emmanouil; Scozzafava, Andrea; Capasso, Clemente; Supuran, Claudiu T

    2014-07-01

    The model organism for the investigation of symbiotic nitrogen fixation in legumes Lotus japonicus encodes two carbonic anhydrases (CAs, EC 4.2.1.1) belonging to the α-class, LjCAA1 and LjCAA2. Here we report the kinetic characterization and inhibition of these two CAs with inorganic and complex anions and other molecules interacting with zinc proteins, such as sulfamide, sulfamic acid, and phenylboronic/arsonic acids. LjCAA1 showed a high catalytic activity for the CO2 hydration reaction, with a k(cat) of 7.4∗10(5) s(-1) and a k(cat)/K(m) of 9.6∗10(7) M(-1) s(-1) and was inhibited in the low micromolar range by N,N-diethyldithiocarbamate, sulfamide, sulfamic acid, phenylboronic/arsonic acid (K(I)s of 4-62 μM). LjCAA2 showed a moderate catalytic activity for the physiologic reaction, with a k(cat) of 4.0∗10(5) s(-1) and a k(cat)/K(m) of 4.9∗10(7) M(-1) s(-1). The same anions mentioned above for the inhibition of LjCAA1 showed the best activity against LjCAA2 (K(I)s of 7-29 μM). Nitrate and nitrite, anions involved in nitrogen fixation, showed lower affinity for the two enzymes, with inhibition constants in the range of 3.7-7.0 mM. Halides and sulfate also behaved in a distinct manner towards the two enzymes investigated here. As LjCAA1/2 participate in the pH regulation processes and CO2 metabolism within the nitrogen-fixing nodules of the plant, our studies may shed some light regarding these complex biochemical processes. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. 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

  17. On the vapor-liquid equilibrium of attractive chain fluids with variable degree of molecular flexibility

    NARCIS (Netherlands)

    Van Westen, T.; Vlugt, T.J.H.; Gross, J.

    2015-01-01

    We study the isotropic (vapor and liquid) phase behavior of attractive chain fluids. Special emphasis is placed on the role of molecular flexibility, which is studied by means of a rod-coil model. Two new equations of state (EoSs) are developed for square-well- (SW) and Lennard-Jones (LJ) chain

  18. From Dimer to Crystal: Calculating the Cohesive Energy of Rare Gas Solids

    Science.gov (United States)

    Halpern, Arthur M.

    2012-01-01

    An upper-level undergraduate project is described in which students perform high-level ab initio computational scans of the potential energy curves for Ne[subscript 2] and Ar[subscript 2] and obtain the respective Lennard-Jones (LJ) potential parameters [sigma] and [epsilon] for the dimers. Using this information, along with the summation of…

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

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 130; Issue 1. Nonpolar solvation ... Frank-Condon type excitation of the solute, previously in equilibrium inRTIL solvent, has been modelled by abruptly changing the Lennard-Jones(LJ) diameter of the solute atoms and thereby disrupting the equilibrium situation.

  20. 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...

  1. Jollrnal of EAEA, VoL lJ, 1996

    African Journals Online (AJOL)

    OICh are also given [4-7). Most of the reference books in the sccood group, however, do not concentrate on electrical-electronic aspects of imtnmeotltioo systems. Besides, the relatively new coocq>ts of intelligent instrumentation and intelligent.

  2. Jollrnal of EAEA, VoL lJ, 1996

    African Journals Online (AJOL)

    course in the Electrical Engineering Department of the Faculty of Technology, Addis Ababa University. A list of ... important senior courses in any electrical engineering. cwTiculum. The coverage of the course, however, ... miaoprocessor fundamentals and communication systems. With reference to the outline of the first ...

  3. Stationary temperature profiles in a liquid nanochannel: comparisons between molecular-dynamics simulation and classical hydrostatics.

    Science.gov (United States)

    Okumura, Hisashi; Heyes, David M

    2006-12-01

    We compare the results of three-dimensional molecular-dynamics (MD) simulations of a Lennard-Jones (LJ) liquid with a hydrostatic (HS) solution of a high temperature liquid channel which is surrounded by a fluid at lower temperature. The maximum temperature gradient, dT/dx , between the two temperature regions ranged from infinity (step function) to dT/dx=0.1 (in the usual LJ units). Because the systems were in stationary-nonequilibrium states with no fluid flow, both MD simulation and the HS solution gave flat profiles for the normal pressure in all temperature-gradient cases. However, the other quantities showed differences between the two methods. The MD-derived density was found to oscillate over the length of ca. 8 LJ particle diameters from the boundary plane in the system with the infinite temperature gradient, while the HS-derived density showed simply a stepwise profile. The MD simulation also showed another anomaly near the boundary in potential energy. We have found systems in which the HS treatment works well and those where the HS approach breaks down, and therefore established the minimum length scale for the HS treatment to be valid. We also compare the kinetic temperature and the configurational temperature in these systems, and show that these can differ in the transition zone between the two temperatures.

  4. Simulation study of nonergodicity transitions: gelation in colloidal systems with short-range attractions.

    Science.gov (United States)

    Puertas, Antonio M; Fuchs, Matthias; Cates, Michael E

    2003-03-01

    Computer simulations were used to study the gel transition occurring in colloidal systems with short-range attractions. A colloid-polymer mixture was modeled and the results were compared with mode coupling theory (MCT) expectations and with the results for other systems (hard-spheres system and Lennard-Jones system). The self-intermediate scattering function and the mean squared displacement were used as the main dynamical quantities. Two different colloid packing fractions have been studied. For the lower packing fraction, alpha-scaling holds and the wave-vector analysis of the correlation function shows that gelation is a regular nonergodicity transition within MCT. The leading mechanism for the novel nonergodicity transition is identified as the bond formation caused by the short-range attraction. The time scale and diffusion coefficient also show qualitatively the expected behavior, although different exponents are found for the power-law divergences of these two quantities. The non-Gaussian parameter was also studied and a very large correction to Gaussian behavior was found. The system with higher colloid packing fraction shows indications of a nearby high-order singularity, causing alpha scaling to fail, but the general expectations for nonergodicity transitions still hold.

  5. 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.

  6. 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......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...... by the Remorin C-terminal region with its coiled-coil domain while the RLK kinase domains transiently interact in vivo and phosphorylate a residue in the N-terminal region of the LjSYMREM1 protein in vitro. These data provide novel insights into the mechanism of this putative molecular scaffold protein...

  7. 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.

  8. 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...

  9. 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)

  10. 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.

  11. Coarse-grained Monte Carlo simulations of non-equilibrium systems.

    Science.gov (United States)

    Liu, Xiao; Crocker, John C; Sinno, Talid

    2013-06-28

    We extend the scope of a recent method for generating coarse-grained lattice Metropolis Monte Carlo simulations [X. Liu, W. D. Seider, and T. Sinno, Phys. Rev. E 86, 026708 (2012); and J. Chem. Phys. 138, 114104 (2013)] from continuous interaction potentials to non-equilibrium situations. The original method has been shown to satisfy detailed balance at the coarse scale and to provide a good representation of various equilibrium properties in both atomic and molecular systems. However, we show here that the original method is inconsistent with non-equilibrium trajectories generated by full-resolution Monte Carlo simulations, which, under certain conditions, have been shown to correspond to Langevin dynamics. The modified coarse-grained method is generated by simultaneously biasing the forward and backward transition probability for every possible move, thereby preserving the detailed balance of the original method. The resulting coarse-grained Monte Carlo simulations are shown to provide trajectories that are consistent with overdamped Langevin (Smoluchowski) dynamics using a sequence of simple non-equilibrium examples. We first consider the purely diffusional spreading of a Gaussian pulse of ideal-gas particles and then include an external potential to study the influence of drift. Finally, we validate the method using a more general situation in which the particles interact via a Lennard-Jones interparticle potential.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. Computer simulation of liquid-vapor coexistence of confined quantum fluids.

    Science.gov (United States)

    Trejos, Víctor M; Gil-Villegas, Alejandro; Martinez, Alejandro

    2013-11-14

    The liquid-vapor coexistence (LV) of bulk and confined quantum fluids has been studied by Monte Carlo computer simulation for particles interacting via a semiclassical effective pair potential Veff(r) = VLJ + VQ, where VLJ is the Lennard-Jones 12-6 potential (LJ) and VQ is the first-order Wigner-Kirkwood (WK-1) quantum potential, that depends on β = 1∕kT and de Boer's quantumness parameter Λ=h/σ√mε, where k and h are the Boltzmann's and Planck's constants, respectively, m is the particle's mass, T is the temperature of the system, and σ and ε are the LJ potential parameters. The non-conformal properties of the system of particles interacting via the effective pair potential Veff(r) are due to Λ, since the LV phase diagram is modified by varying Λ. We found that the WK-1 system gives an accurate description of the LV coexistence for bulk phases of several quantum fluids, obtained by the Gibbs Ensemble Monte Carlo method (GEMC). Confinement effects were introduced using the Canonical Ensemble (NVT) to simulate quantum fluids contained within parallel hard walls separated by a distance Lp, within the range 2σ ≤ Lp ≤ 6σ. The critical temperature of the system is reduced by decreasing Lp and increasing Λ, and the liquid-vapor transition is not longer observed for Lp∕σ < 2, in contrast to what has been observed for the classical system.

  20. Computer simulation of liquid-vapor coexistence of confined quantum fluids

    Science.gov (United States)

    Trejos, Víctor M.; Gil-Villegas, Alejandro; Martinez, Alejandro

    2013-11-01

    The liquid-vapor coexistence (LV) of bulk and confined quantum fluids has been studied by Monte Carlo computer simulation for particles interacting via a semiclassical effective pair potential Veff(r) = VLJ + VQ, where VLJ is the Lennard-Jones 12-6 potential (LJ) and VQ is the first-order Wigner-Kirkwood (WK-1) quantum potential, that depends on β = 1/kT and de Boer's quantumness parameter Λ = h/σ √{mɛ }, where k and h are the Boltzmann's and Planck's constants, respectively, m is the particle's mass, T is the temperature of the system, and σ and ɛ are the LJ potential parameters. The non-conformal properties of the system of particles interacting via the effective pair potential Veff(r) are due to Λ, since the LV phase diagram is modified by varying Λ. We found that the WK-1 system gives an accurate description of the LV coexistence for bulk phases of several quantum fluids, obtained by the Gibbs Ensemble Monte Carlo method (GEMC). Confinement effects were introduced using the Canonical Ensemble (NVT) to simulate quantum fluids contained within parallel hard walls separated by a distance Lp, within the range 2σ ⩽ Lp ⩽ 6σ. The critical temperature of the system is reduced by decreasing Lp and increasing Λ, and the liquid-vapor transition is not longer observed for Lp/σ < 2, in contrast to what has been observed for the classical system.

  1. 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 periodic solution found by Simó through S (2). For the LJ system, we calculated the 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.

  2. Effective particle size from molecular dynamics simulations in fluids

    Science.gov (United States)

    Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

    2018-04-01

    We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

  3. Effective particle size from molecular dynamics simulations in fluids

    Science.gov (United States)

    Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

    2017-12-01

    We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

  4. 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

  5. Interlayer interaction and mechanical properties in multi-layer graphene, Boron-Nitride, Aluminum-Nitride and Gallium-Nitride graphene-like structure: A quantum-mechanical DFT study

    Science.gov (United States)

    Ghorbanzadeh Ahangari, Morteza; Fereidoon, A.; Hamed Mashhadzadeh, Amin

    2017-12-01

    In present study, we investigated mechanical, electronic and interlayer properties of mono, bi and 3layer of Boron-Nitride (B-N), Aluminum-Nitride (Al-N) and Gallium-Nitride (Ga-N) graphene sheets and compared these results with results obtained from carbonic graphenes (C-graphenes). For reaching this purpose, first we optimized the geometrical parameters of these graphenes by using density functional theory (DFT) method. Then we calculated Young's modulus of graphene sheet by compressing and then elongating these sheets in small increment. Our results indicates that Young's modulus of graphenes didn't changed obviously by increasing the number of layer sheet. We also found that carbonic graphene has greatest Young's modulus among another mentioned sheets because of smallest equilibrium distance between its elements. Next we modeled the van der Waals interfacial interaction exist between two sheets with classical spring model by using general form of Lennard-Jones (L-J) potential for all of mentioned graphenes. For calculating L-J parameters (ε and σ), the potential energy between layers of mentioned graphene as a function of the separation distance was plotted. Moreover, the density of states (DOS) are calculated to understand the electronic properties of these systems better.

  6. Thermodynamic properties of confined square-well fluids with multiple associating sites

    Science.gov (United States)

    Trejos, Víctor M.; Quintana-H, Jacqueline

    2018-02-01

    In this work, a molecular simulation study of confined hard-spheres particles with square-well (SW) attractive interactions with two and four associating SW sites based on the first-order perturbation form of Wertheim's theory is presented. An extended version of the Gibbs ensemble technique for inhomogeneous fluids [A. Z. Panagiotopoulos, Mol. Phys. 62, 701 (1987)] is used to predict the adsorption density profiles for associating fluids confined between opposite parallel walls. The fluid is confined in four kinds of walls: hard-wall, SW wall, Lennard-Jones (LJ) 12-6 wall potential, and LJ 10-4 wall potential. We analyze the behavior of the confined system for several supercritical temperatures as a function of variation of molecular parameters: potential range λ, bulk densities ρb*, pore width H, cutoff range interaction rc*, and range of the potential and depth of the particle-wall (λw, ɛw*). Additionally, we include predictions for liquid-vapor coexistence of bulk associative particles and how their critical properties are modified by the presence of associative sites in the molecule. The molecular simulation data presented in this work are of prime importance to the development of theoretical approaches for inhomogeneous fluids as classical density functional theory. The simulation results presented here are resourceful for predicting adsorption isotherms of real associating fluids such as water.

  7. 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 o

  8. Predicting the Function of 4-Coumarate:CoA Ligase (LJ4CL1 in Lonicera japonica

    Directory of Open Access Journals (Sweden)

    Yuan Yuan

    2014-02-01

    Full Text Available 4-Coumarate:CoA ligases (4CLs are a group of essential enzymes involved in the pathway of phenylpropanoid-derived compound metabolisms; however it is still difficult to identify orthologs and paralogs of these important enzymes just based on sequence similarity of the conserved domains. Using sequence data of 20 plant species from the public databases and sequences from Lonicera japonica, we define 1252 adenosine monophosphate (AMP-dependent synthetase/ligase sequences and classify them into three phylogenetic clades. 4CLs are in one of the four subgroups, according to their partitioning, with known proteins characterized in A. thaliana and Oryza sativa. We also defined 184 non-redundant sequences that encode proteins containing the GEICIRG motif and the taxonomic distribution of these GEICIRG-containing proteins suggests unique catalytic activities in plants. We further analyzed their transcription levels in L. japonica and L. japonica. var. chinensis flowers and chose the highest expressed genes representing the subgroups for structure and binding site predictions. Coupled with liquid chromatography-mass spectrometry (LC-MS analysis of the L. japonica flowers, the structural study on putative substrate binding amino acid residues, ferulate, and 4-coumaric acid of the conserved binding-site of LJ4CL1 leads to a conclusion that this highly expressed protein group in the flowers may process 4-coumarate that represents 90% of the known phenylpropanoid-derived compounds. The activity of purified crude LJ4CL1 protein was analyzed using 4-coumarate as template and high activity indicating that 4-coumarate is one of the substrates of LJ4CL1.

  9. 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 ...

  10. Effect of electrostatic interactions on lubrication in polymeric and biological systems

    Science.gov (United States)

    Carrillo, Jan-Michael

    2012-02-01

    Many connective tissues, such as cartilage demonstrate excellent lubrication and wear characteristics. Cartilages in mammalian joints can withstand pressures of the order of ten atmospheres and have remarkably low friction coefficient in the range of 0.001-0.03. The surface of the cartilage is covered with bottle-brush-like polyelectrolyte layer consisting of glycoproteins. This brush layer, which faces a similar layer on the opposing cartilage, is sheared as two surfaces slide passing each other during joint motion. We have performed molecular dynamics simulations of charged and neutral bottle-brush macromolecules tethered to substrates to understand the role of the electrostatic and hydrodynamic coupling between brush layers on the lubricating properties in biological and polymeric systems. Glycoprotein layers were modeled as two opposing layers of highly charged bottle-brush macromolecules composed of Lennard-Jones particles grafted to a substrate. Simulations have shown that charged bottle-brush systems have lower friction under shear and weaker dependence of the disjoining pressure on substrate separation than neutral bottle-brush systems. This was explained by formation of lubricating layer with excess of counterions located in the middle between brush-bearing surfaces. In overlapping brush layers the disjoining pressure between brush-bearing surfaces is controlled by the bottle-brush bending rigidity. Under shear, the main deformation mode of the charged bottle-brush layers is associated with the bottle-brush backbone deformation resulting in backbone deformation ratio and shear viscosity being universal functions of the Weissenberg number. In the case of neutral bottle-brush systems there is coupling between backbone and side chain deformation. This violates universality in backbone deformation ratio and manifests itself in shear viscosity dependence on the shear rate. The shear viscosity as a function of the shear rate for the neutral bottle-brush systems

  11. Formation of Surface Nanobubbles and the Universality of Their Contact Angles: A Molecular Dynamics Approach

    NARCIS (Netherlands)

    Weijs, Joost; Snoeijer, Jacobus Hendrikus; Lohse, Detlef

    2012-01-01

    We study surface nanobubbles using molecular dynamics simulation of ternary (gas, liquid, solid) systems of Lennard-Jones fluids. They form for a sufficiently low gas solubility in the liquid, i.e., for a large relative gas concentration. For a strong enough gas-solid attraction, the surface

  12. 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

  13. 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

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

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2016-01-01

    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...

  15. Use of polydispersity index as control parameter to study melting ...

    Indian Academy of Sciences (India)

    Use of polydispersity index as control parameter to study melting/freezing of Lennard-Jones system: Comparison among predictions of bifurcation theory with Lindemann criterion, inherent structure analysis and Hansen-Verlet rule. SARMISTHA SARKARa,b, RAJIB BISWASa, PARTHA PRATIM RAYb and BIMAN BAGCHIa, ...

  16. 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.

  17. 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.

  18. Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

    Science.gov (United States)

    Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

    Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiency has been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume.

  19. Thermodynamics of confined gallium clusters.

    Science.gov (United States)

    Chandrachud, Prachi

    2015-11-11

    We report the results of ab initio molecular dynamics simulations of Ga13 and Ga17 clusters confined inside carbon nanotubes with different diameters. The cluster-tube interaction is simulated by the Lennard-Jones (LJ) potential. We discuss the geometries, the nature of the bonding and the thermodynamics under confinement. The geometries as well as the isomer spectra of both the clusters are significantly affected. The degree of confinement decides the dimensionality of the clusters. We observe that a number of low-energy isomers appear under moderate confinement while some isomers seen in the free space disappear. Our finite-temperature simulations bring out interesting aspects, namely that the heat capacity curve is flat, even though the ground state is symmetric. Such a flat nature indicates that the phase change is continuous. This effect is due to the restricted phase space available to the system. These observations are supported by the mean square displacement of individual atoms, which are significantly smaller than in free space. The nature of the bonding is found to be approximately jellium-like. Finally we note the relevance of the work to the problem of single file diffusion for the case of the highest confinement.

  20. 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.

  1. 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.

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

    OpenAIRE

    Cabral,V.F.; Pinto,R.R.C.; Tavares,F.W.; Castier,M.

    2001-01-01

    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 rule...

  3. L.J. Erasmus

    African Journals Online (AJOL)

    Scand. Supp\\. 25, 9. MILLER, E.L. & 0RSKOV, E.R., 1986. Degradabilityof protein and its prediction. Bulletin of the International. Dairy Federation No. 196/1986. Brussels, Belgium. NRC, 1985. Ruminant nitrogen usage. US National Academy of Science, Washington, DC. ROHR, 1987. Present situation of the modern protein.

  4. lJ

    African Journals Online (AJOL)

    1974-06-15

    Jun 15, 1974 ... congenital cataracts, macular degeneration and tapeto- retinal degeneration. ... especially important in the diagnosis of tapetoretinal degeneration. Macular degeneration may be noted, or the cherry-red spot in Tay-Sachs disease. Optokinetic ... Persistence of a particular abnormality necessitates treatment.

  5. 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

  6. A detailed investigation on the global minimum structures of mixed rare-gas clusters: geometry, energetics, and site occupancy.

    Science.gov (United States)

    Marques, Jorge M C; Pereira, Francisco B

    2013-03-05

    We performed a global minimum search of mixed rare-gas clusters by applying an evolutionary algorithm (EA), which was recently proposed for binary atomic systems (Marques and Pereira, Chem. Phys. Lett. 2010, 485, 211). Before being applied to the potentials used in this work, the EA was further tested against results previously reported for the Ar(N)Xe(38-N) clusters and several new putative global minima were discovered. We employed either simple Lennard-Jones (LJ) potentials or more realistic functions to describe pair interactions in Ar(N)Kr(38-N), Ar(N)Xe(38-N), and Kr(N)Xe(38-N) clusters. The long-range tail of the pair-potentials shows some influence on the energetic features and shape of the structure of clusters. In turn, core-shell type structures are mostly observed for global minima of the binary rare-gas clusters, for both accurate and LJ potentials. However, the long-range tail of the potential may have influence on the type of atoms that segregate on the surface or form the core of the cluster. While relevant differences for the preferential site occupancy occur between the two potentials for Ar(N)Kr(38-N) (for N > 21), the type of atoms that segregate on the surface for Ar(N)Xe(38-N) and Kr(N)Xe(38-N) clusters is unaffected by the accuracy of the long-range part of the interaction in almost all cases. Moreover, the global minimum search for model-potentials in binary systems reveals that the surface-site occupancy is mainly determined by the combination of two parameters: the size ratio of the two types of particles forming the cluster and the minimum-energy ratio corresponding to the pair-interactions between unlike atoms. Copyright © 2012 Wiley Periodicals, Inc.

  7. Molecular Force Field Development for Aqueous Electrolytes: 1. Incorporating Appropriate Experimental Data and the Inadequacy of Simple Electrolyte Force Fields Based on Lennard-Jones and Point Charge Interactions with Lorentz-Berthelot Rules

    Czech Academy of Sciences Publication Activity Database

    Moučka, F.; Nezbeda, Ivo; Smith, W. R.

    2013-01-01

    Roč. 9, č. 11 (2013), s. 5076-5085 ISSN 1549-9618 Grant - others:GA MŠMT(CZ) LH12019; NSERCC(CA) OGP1041; UJEP(CZ) GAP208/12/0105 Institutional support: RVO:67985858 Keywords : sodium-chloride * ionic hydration * free-energy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.310, year: 2013

  8. 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.

  9. 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

    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...... 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...... 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...

  10. Isomorph invariance of the structure and dynamics of classical crystals

    DEFF Research Database (Denmark)

    Albrechtsen, Dan; Olsen, Andreas Elmerdahl; Pedersen, Ulf Rørbæk

    2014-01-01

    This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework......, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics...... of a defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnström binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles...

  11. BIO 300, a nanosuspension of genistein, mitigates pneumonitis/fibrosis following high-dose radiation exposure in the C57L/J murine model.

    Science.gov (United States)

    Jackson, Isabel L; Zodda, Andrew; Gurung, Ganga; Pavlovic, Radmila; Kaytor, Michael D; Kuskowski, Michael A; Vujaskovic, Zeljko

    2017-12-01

    BIO 300 nanosuspension (Humanetics Corporation) is being developed as a medical countermeasure (MCM) for the mitigation of the delayed effects of acute radiation exposure, specifically pneumonitis and fibrosis of the lung. The objective of this study was to determine the best dose and treatment duration of BIO 300 to mitigate lung injury and improve the likelihood for survival in C57L/J mice exposed to whole thorax lung irradiation (WTLI). Age- and sex-matched C57L/J mice received a single dose of 11.0 or 12.5 Gy WTLI. BIO 300 (200 or 400 mg·kg -1 , oral gavage) was administered daily starting 24 h post-exposure for a duration of 2, 4, 6 or, in some cases, 10 weeks. Non-treated controls were included for comparison in both sexes. Animals were observed daily for signs of major morbidity. Respiratory function was assessed biweekly. Lungs were collected, weighed and paraffin embedded for histological evaluation post mortem. BIO 300 administered at an oral dose of 400 mg·kg -1 for 4 to 6 weeks starting 24 h post-WTLI reduced morbidity associated with WTLI. The improvement in survival correlated with reduced respiratory frequency and enhanced pause. The irradiated lungs of mice treated with BIO 300 (400 mg·kg -1 ) for 4 to 6 weeks displayed less morphological damage and airway loss due to oedema, congestion and fibrotic scarring than the untreated, irradiated controls. BIO 300 is a promising MCM candidate to mitigate pneumonitis/fibrosis when administered daily for 4-6 weeks starting 24 h post-exposure. © 2017 The British Pharmacological Society.

  12. 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

  13. 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

  14. Generalized Lyapunov exponents of the random harmonic oscillator: Cumulant expansion approach

    Science.gov (United States)

    Vallejos, Raúl O.; Anteneodo, Celia

    2012-02-01

    The cumulant expansion is used to estimate generalized Lyapunov exponents of the random-frequency harmonic oscillator. Three stochastic processes are considered: Gaussian white noise, Ornstein-Uhlenbeck, and Poisson shot noise. In some cases, nontrivial numerical difficulties arise. These are mostly solved by implementing an appropriate importance-sampling Monte Carlo scheme. We analyze the relation between random-frequency oscillators and many-particle systems with pairwise interactions like the Lennard-Jones gas.

  15. 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

  16. Molecular dynamics as a foundation for flux prediction through nanoporous membranes: A vectorized, constraint-free approach to conservative simulations

    Science.gov (United States)

    Inman, Matthew Clay

    A novel, open-cathode direct methanol fuel cell (DMFC ) has been designed and built by researchers at the University of North Florida and University of Florida. Foremost among the advances of this system over previous DMFC architectures is a passive water recovery system which allows product water to replenish that consumed at the anode. This is enabled by a specially-designed water pathway combined with a liquid barrier layer (LBL ). The LBL membrane is positioned between the cathode catalyst layer and the cathode gas diffusion layer, and must exhibit high permeability and low diffusive resistance to both oxygen and water vapor, bulk hydrophobicity to hold back the product liquid water, and must remain electrically conductive. Maintaining water balance at optimum operating temperatures is problematic with the current LBL design, forcing the system to run at lower temperatures decreasing the overall system efficiency. This research presents a novel approach to nanoporous membrane design whereby flux of a given species is determined based upon the molecular properties of said species and those of the diffusing medium, the pore geometry, and the membrane thickness. A molecular dynamics (MD ) model is developed for tracking Knudsen regime flows of a Lennard-Jones (LJ ) fluid through an atomistic pore structure, hundreds of thousands of wall collision simulations are performed on the University of Florida HiPerGator supercomputer, and the generated trajectory information is used to develop number density and axial velocity profiles for use in a rigorous approach to total flux calculation absent in previously attempted MD models. Results are compared to other published approaches and diffusion data available in the literature. The impact of this study on various applications of membrane design is discussed and additional simulations and model improvements are outlined for future consideration.

  17. Nanoscale colloids in a freely adsorbing polymer solution: a Monte Carlo simulation study.

    Science.gov (United States)

    Marla, Krishna Tej; Meredith, J Carson

    2004-02-17

    A key issue in nanoscale materials and chemical processing is the need for thermodynamic and kinetic models covering colloid-polymer systems over the mesoscopic length scale (approximately 1-100 nm). We have applied Monte Carlo simulations to attractive nanoscale colloid-polymer mixtures toward developing a molecular basis for models of these complex systems. The expanded ensemble Monte Carlo simulation method is applied to calculate colloid chemical potentials (micro(c)) and polymer adsorption (gamma) in the presence of freely adsorbing Lennard-Jones (LJ) homopolymers (surface modifiers). gamma and micro(c) are studied as a function of nanoparticle diameter (sigma(c)), modifier chain length (n) and concentration, and colloid-polymer attractive strength over 0.3 attractive regime, nanocolloid chemical potential decreases and adsorbed amount increases as sigma(c), or n is increased. The scaling of gamma with n from the simulations agrees with the theory of Aubouy and Raphael (Macromolecules 1998, 31, 4357) in the extreme limits of Rg/sigma(c). When Rg/sigma(c) is large, the "colloid" approaches a molecular size and interacts only locally with a few polymer segments and gamma approximately n. When Rg/sigma(c) is small, the system approaches the conventional colloid-polymer size regime where multiple chains interact with a single particle, and gamma approximately sigma(c)2, independent of n. In contrast, adsorption in the mesoscopic range of Rg/sigma(c) investigated here is represented well by a power law gamma approximately n(p), with 0 attractive strength. Likewise, the chemical potential from our results is fitted well with micro(c) approximately n(q)sigma(c)3, where the cubic term results from the sigma(c) dependence of particle surface area (approximately sigma(c)2) and LJ attractive magnitude (approximately sigma(c)). The q-exponent for micro(c) (micro(c) approximately n(q)) varies with composition and LJ attractive strength but is always very close to the power

  18. 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

  19. 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.

  20. Coding coarse grained polymer model for LAMMPS and its application to polymer crystallization

    Science.gov (United States)

    Luo, Chuanfu; Sommer, Jens-Uwe

    2009-08-01

    We present a patch code for LAMMPS to implement a coarse grained (CG) model of poly(vinyl alcohol) (PVA). LAMMPS is a powerful molecular dynamics (MD) simulator developed at Sandia National Laboratories. Our patch code implements tabulated angular potential and Lennard-Jones-9-6 (LJ96) style interaction for PVA. Benefited from the excellent parallel efficiency of LAMMPS, our patch code is suitable for large-scale simulations. This CG-PVA code is used to study polymer crystallization, which is a long-standing unsolved problem in polymer physics. By using parallel computing, cooling and heating processes for long chains are simulated. The results show that chain-folded structures resembling the lamellae of polymer crystals are formed during the cooling process. The evolution of the static structure factor during the crystallization transition indicates that long-range density order appears before local crystalline packing. This is consistent with some experimental observations by small/wide angle X-ray scattering (SAXS/WAXS). During the heating process, it is found that the crystalline regions are still growing until they are fully melted, which can be confirmed by the evolution both of the static structure factor and average stem length formed by the chains. This two-stage behavior indicates that melting of polymer crystals is far from thermodynamic equilibrium. Our results concur with various experiments. It is the first time that such growth/reorganization behavior is clearly observed by MD simulations. Our code can be easily used to model other type of polymers by providing a file containing the tabulated angle potential data and a set of appropriate parameters. Program summaryProgram title: lammps-cgpva Catalogue identifier: AEDE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU's GPL No. of lines in distributed program

  1. 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

  2. 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.

  3. New Aspects of Collective Phenomena at Nanoscales in Quantum Plasmas

    Science.gov (United States)

    Shukla, P. K.; Eliasson, B.

    We present two novel collective effects is quantum plasmas. First, we discuss novel attractive force between ions that are shielded by the degenerate electrons in quantum plasmas. Here we show that the electric potential around an isolated ion has a hard core negative part that resembles the Lennard-Jones (LJ)-type potential. Second, we present theory for stimulated scattering instabilities of electromagnetic waves off quantum plasma modes. Our studies are based on the quantum hydrodynamical description of degenerate electrons that are greatly influenced by electromagnetic and quantum forces. The relevance of our investigation to bringing ions closer for fusion in high-energy solid density plasmas at atomic dimensions, and for producing coherent short wavelength radiation in the x-ray regime at nanoscales are discussed.

  4. Transport properties of water molecules confined between hydroxyapaptite surfaces: A Molecular dynamics simulation approach

    Science.gov (United States)

    Prakash, Muthuramalingam; Lemaire, Thibault; Di Tommaso, Devis; de Leeuw, Nora; Lewerenz, Marius; Caruel, Matthieu; Naili, Salah

    2017-10-01

    Water diffusion in the vicinity of hydroxyapatite (HAP) crystals is a key issue to describe biomineralization process. In this study, a configuration of parallel HAP platelets mimicking bone nanopores is proposed to characterize the nanoscopic transport properties of water molecules at HAP-water surface and interfaces using various potential models such as combination of the Core-Shell (CS) model, Lennard-Jones (LJ) potentials with SPC or SPC/E water models. When comparing all these potentials models, it appears that the core-shell potential for HAP together with the SPC/E water model more accurately predicts the diffusion properties of water near HAP surface. Moreover, we have been able to put into relief the possibility of observing hydroxyl (OH-) ion dissociation that modifies the water structure near the HAP surface.

  5. On the vapor-liquid equilibrium of attractive chain fluids with variable degree of molecular flexibility

    Science.gov (United States)

    van Westen, Thijs; Vlugt, Thijs J. H.; Gross, Joachim

    2015-06-01

    We study the isotropic (vapor and liquid) phase behavior of attractive chain fluids. Special emphasis is placed on the role of molecular flexibility, which is studied by means of a rod-coil model. Two new equations of state (EoSs) are developed for square-well- (SW) and Lennard-Jones (LJ) chain fluids. The EoSs are developed by applying the perturbation theory of Barker and Henderson (BH) to a reference fluid of hard chain molecules. The novelty of the approach is based on (1) the use of a recently developed hard-chain reference EoS that explicitly incorporates the effects of molecular flexibility, (2) the use of recent molecular simulation data for the radial distribution function of hard-chain fluids, and (3) a newly developed effective segment size, which effectively accounts for the soft repulsion between segments of LJ chains. It is shown that the effective segment size needs to be temperature-, density-, and chain-length dependent. To obtain a simplified analytical EoS, the perturbation terms are fitted by polynomials in density (SW and LJ), chain length (SW and LJ), and temperature (only for LJ). It is shown that the equations of state result in an accurate description of molecular simulation data for vapor-liquid equilibria (VLE) and isotherms of fully flexible SW- and LJ chain fluids and their mixtures. To evaluate the performance of the equations of state in describing the effects of molecular flexibility on VLE, we present new Monte Carlo simulation results for the VLE of rigid linear- and partially flexible SW- and LJ chain fluids. For SW chains, the developed EoS is in a good agreement with simulation results. For increased rigidity of the chains, both theory and simulations predict an increase of the VL density difference and a slight increase of the VL critical temperature. For LJ chains, the EoS proves incapable of reproducing part of these trends.

  6. Optimization of long range potential interaction parameters in ion mobility spectrometry

    Science.gov (United States)

    Wu, Tianyang; Derrick, Joseph; Nahin, Minal; Chen, Xi; Larriba-Andaluz, Carlos

    2018-02-01

    The problem of optimizing Lennard-Jones (L-J) potential parameters to perform collision cross section (CCS) calculations in ion mobility spectrometry has been undertaken. The experimental CCS of 16 small organic molecules containing carbon, hydrogen, oxygen, nitrogen, and fluoride in N2 was compared to numerical calculations using Density Functional Theory (DFT). CCS calculations were performed using the momentum transfer algorithm IMoS and a 4-6-12 potential without incorporating the ion-quadrupole potential. A ceteris paribus optimization method was used to optimize the intercept σ and potential well-depth ɛ for the given atoms. This method yields important information that otherwise would remain concealed. Results show that the optimized L-J parameters are not necessarily unique with intercept and well-depth following an exponential relation at an existing line of minimums. Similarly, the method shows that some molecules containing atoms of interest may be ill-conditioned candidates to perform optimizations of the L-J parameters. The final calculated CCSs for the chosen parameters differ 1% on average from their experimental counterparts. This result conveys the notion that DFT calculations can indeed be used as potential candidates for CCS calculations and that effects, such as the ion-quadrupole potential or diffuse scattering, can be embedded into the L-J parameters without loss of accuracy but with a large increase in computational efficiency.

  7. 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

  8. What Is a Simple Liquid?

    Science.gov (United States)

    Ingebrigtsen, Trond S.; Schrøder, Thomas B.; Dyre, Jeppe C.

    2012-01-01

    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 characterized in three quite

  9. 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.

  10. The effect of production system and management practices on the ...

    African Journals Online (AJOL)

    The effect of production system and management practices on the environmental impact, quality and safety of milk and dairy products. LJ Erasmus, EC Webb. Abstract. There is an increasing trend to label milk and dairy products according to production system, absence of certain feed additives and non-use of specific ...

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. An Oxygen-Sensing Two-Component System in the Burkholderia cepacia Complex Regulates Biofilm, Intracellular Invasion, and Pathogenicity.

    Directory of Open Access Journals (Sweden)

    Matthew M Schaefers

    2017-01-01

    Full Text Available Burkholderia dolosa is a member of the Burkholderia cepacia complex (BCC, which is a group of bacteria that cause chronic lung infection in patients with cystic fibrosis (CF and can be associated with outbreaks carrying high morbidity and mortality. While investigating the genomic diversity of B. dolosa strains collected from an outbreak among CF patients, we previously identified fixL as a gene showing signs of strong positive selection. This gene has homology to fixL of the rhizobial FixL/FixJ two-component system. The goals of this study were to determine the functions of FixLJ and their role in virulence in B. dolosa. We generated a fixLJ deletion mutant and complemented controls in B. dolosa strain AU0158. Using a fixK-lacZ reporter we found that FixLJ was activated in low oxygen in multiple BCC species. In a murine pneumonia model, the B. dolosa fixLJ deletion mutant was cleared faster from the lungs and spleen than wild-type B. dolosa strain AU0158 at 7 days post infection. Interestingly, the fixLJ deletion mutant made more biofilm, albeit with altered structure, but was less motile than strain AU0158. Using RNA-seq with in vitro grown bacteria, we found ~11% of the genome was differentially expressed in the fixLJ deletion mutant relative to strain AU0158. Multiple flagella-associated genes were down-regulated in the fixLJ deletion mutant, so we also evaluated virulence of a fliC deletion mutant, which lacks a flagellum. We saw no difference in the ability of the fliC deletion mutant to persist in the murine model relative to strain AU0158, suggesting factors other than flagella caused the phenotype of decreased persistence. We found the fixLJ deletion mutant to be less invasive in human lung epithelial and macrophage-like cells. In conclusion, B. dolosa fixLJ is a global regulator that controls biofilm formation, motility, intracellular invasion/persistence, and virulence.

  16. 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.

  17. Equilibrium properties in the thermodynamic limit from small-sized molecular dynamics simulations

    Science.gov (United States)

    Cortes-Huerto, Robinson; Kremer, Kurt; Potestio, Raffaello

    We present an accurate and efficient method to obtain equilibrium thermodynamic properties of bulk systems from small-sized molecular dynamics simulations by introducing finite size effects into integral equations of statistical mechanics. We validate the method by calculating thermodynamic properties of prototypical complex mixtures such as the activity coefficients of aqueous urea mixtures and the Kirkwood-Buff integrals of Lennard-Jones fluids. Moreover, our results demonstrate how to identify simulation conditions under which computer simulations reach the thermodynamic limit. Alexander von Humboldt Foundation.

  18. 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...

  19. 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....

  20. Fluctuations and Linear Response in Supercooled Liquids

    DEFF Research Database (Denmark)

    Nielsen, Johannes K.

    Fluctuation dissipation theorems are derived for thermodynamic properties like frequency dependent specific heat and compressibility. First the case where a systems dynamics are restricted by constant volume and energy is considered. The dynamic linear response to a heat pulse and a volume change...... of the theory in the field of supercooled liquids are showed. First the full frequency dependent thermodynamic response matrix is extracted from simulations of a binary Lennard Jones liquid. Secondly some simple stochastic models of supercooled liquids are analysed in the framework of linear thermodynamic...

  1. Comparison of Hard-Core and Soft-Core Potentials for Modelling Flocking in Free Space

    OpenAIRE

    Smith, J. A; Martin, A. M

    2009-01-01

    An investigation into the properties of a two dimensional (2D+1) system of self propelled particles (known as boids) in free space is conducted using a Lagrangian Individual-Based Model. A potential, associated with each boid is specified and a Lagrangian is subsequently derived in order to obtain the equations of motion for each particle in the flock. The Morse potential and the Lennard-Jones potential, both well understood in atomic and molecular physics, are specified. In contrast to the o...

  2. On the potential energy landscape of supercooled liquids and glasses

    DEFF Research Database (Denmark)

    Rodney, D.; Schrøder, Thomas

    2011-01-01

    The activation-relaxation technique (ART), a saddle-point search method, is applied to determine the potential energy landscape around supercooled and glassy configurations of a three-dimensional binary Lennard-Jones system. We show a strong relation between the distribution of activation energies...... of transitions undergone by the same supercooled liquid during a time trajectory simulated by molecular dynamics. We find that ART is biased towards more heterogeneous transitions with higher activation energies and more broken bonds than the MD simulation....

  3. 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...... binary liquid mixtures of non-polar components that computed penetration lengths, for various temperatures and compositions, are consistent with those deduced from experiments in the framework of the formalism of the fluctuation theory. Moreover, the mutual diffusion coefficients obtained from a coupled...

  4. From elementary steps to structural relaxation: a continuous-time random-walk analysis of a supercooled liquid.

    Science.gov (United States)

    Rubner, Oliver; Heuer, Andreas

    2008-07-01

    We show that the dynamics of supercooled liquids, analyzed from computer simulations of the binary mixture Lennard-Jones system, can be described in terms of a continuous-time random walk (CTRW). The required discretization comes from mapping the dynamics on transitions between metabasins. This yields a quantitative link between the elementary step and the full structural relaxation. The analysis involves a verification of the CTRW conditions as well as a quantitative test of the predictions. The wave-vector dependence of the relaxation time and the degree of nonexponentiality can be expressed in terms of the first moments of the waiting time distribution.

  5. BACTEC MGIT 960 system for screening of Mycobacterium ...

    African Journals Online (AJOL)

    Jane

    2011-10-17

    Oct 17, 2011 ... 1Department of Bacterial Diagnostic Products, Veterinary Serum and Vaccine Research Institute, Abbassia, Cairo, .... Type of lesions. MGIT. L.J. 960. Figure 1. Comparison of the recovery rates of mycobacteria from slaughtered tuberculin positive cows by. BACTEC MGIT 960 TM system and conventional ...

  6. Alien plants as mediators of ecosystem services and disservices in urban systems: a global review

    CSIR Research Space (South Africa)

    Potgieter, LJ

    2017-12-01

    Full Text Available , vol. 19(12): 3571-3588 Alien plants as mediators of ecosystem services and disservices in urban systems: a global review Potgieter LJ Gaertner M Kueffer C Livingstone SW O’Farrell PJ Richardson DM ABSTRACT: Urban areas have unique...

  7. 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.

  8. 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.

  9. 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.

  10. Pramana – Journal of Physics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    We have carried out Monte Carlo simulations in Gibbs ensemble for two-and three-dimensional double Yukawa fluid. We have compared liquid–vapour equilibrium curve with that of Lennard-Jones, when parameters occurring in double Yukawa potential are chosen to fit Lennard-Jones potential. The results are in good ...

  11. Equation of state of matter irradiated by short laser pulse and geometry of spalled cupola

    Science.gov (United States)

    Petrov, Yu. V.; Zhakhovskii, V. V.; Inogamov, N. A.; Ashitkov, S. I.; Khokhlov, V. A.; Upadhyay, A. K.; Agranat, M. B.; Anisimov, S. I.; Nishihara, K.; Rethfeld, B.; Urbassek, H. M.

    2008-05-01

    The motion of both Lennard-Jones solids and metals induced by ultrashort laser irradiation near the ablation threshold is investigated by molecular dynamics simulation. The universality of the ablation threshold fluence with respect to the cohesion energy of solids irradiated by femtosecond laser pulses is demonstrated for Lennard-Jones solid and metals simulated by many-body EAM potentials.

  12. Vapour–liquid equilibria of the two-and three-dimensional ...

    Indian Academy of Sciences (India)

    We have carried out Monte Carlo simulations in Gibbs ensemble for two-and three-dimensional double Yukawa fluid. We have compared liquid–vapour equilibrium curve with that of Lennard-Jones, when parameters occurring in double Yukawa potential are chosen to fit Lennard-Jones potential. The results are in good ...

  13. The impact range for smooth wall–liquid interactions in nanoconfined liquids

    DEFF Research Database (Denmark)

    Ingebrigtsen, Trond; Dyre, J. C.

    2014-01-01

    decade. Inspired by these observations, we present results from molecular dynamics computer simulations of four nanoconfined liquids (the single-component Lennard-Jones liquid, the Kob–Andersen binary Lennard-Jones mixture, an asymmetric dumbbell model, and the Dzugutov liquid) demonstrating also...

  14. Development of the knowledge-based and empirical combined scoring algorithm (KECSA) to score protein-ligand interactions.

    Science.gov (United States)

    Zheng, Zheng; Merz, Kenneth M

    2013-05-24

    We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the Protein Databank (PDB). Forty-nine (49) types of atomic pairwise interactions were derived using this method, which we call the knowledge-based and empirical combined scoring algorithm (KECSA). Two validation benchmarks were introduced to test the performance of KECSA. The first validation benchmark included two test sets that address the training set and enthalpy/entropy of KECSA. The second validation benchmark suite included two large-scale and five small-scale test sets, to compare the reproducibility of KECSA, with respect to two empirical score functions previously developed in our laboratory (LISA and LISA+), as well as to other well-known scoring methods. Validation results illustrate that KECSA shows improved performance in all test sets when compared with other scoring methods, especially in its ability to minimize the root mean square error (RMSE). LISA and LISA+ displayed similar performance using the correlation coefficient and Kendall τ as the metric of quality for some of the small test sets. Further pathways for improvement are discussed for which would allow KECSA to be more sensitive to subtle changes in ligand structure.

  15. Microscopic structure of the hydrogen-xenon mixture

    Science.gov (United States)

    Senesi, R.; Nardone, M.; Ricci, F. P.; Ricci, M. A.; Soper, A. K.

    1997-09-01

    We report a neutron-diffraction study of the microscopic structure of the H2-Xe binary mixture in the Xe-rich phase, xXe=0.78, at T=283 K and P=170 bars, i.e., in the vicinity of the second-type gas-gas demixing surface. The site-site distribution functions are extracted employing the H-D isotopic substitution technique. We report also molecular-dynamics simulations for a mixture of equivalent Lennard-Jones (LJ) atoms. The experimental results are compared with previous ones obtained for the He-Xe and Ne-Xe mixtures, which show a first- and a second-type gas-gas transition, respectively. The general picture already suggested by the other two mixtures agrees also with the present results, although in this case the center-center distribution functions H2-H2 and H2-Xe are clearly modulated by the Xe-Xe correlations. In particular the features found in the distribution functions of the mixture suggest that the LJ potential model is not able to reproduce at a satisfactory level the H2-H2 and the H2-Xe correlation functions and that a (XeH4) chemical complex is present.

  16. Adsorption of ethylene on graphitized thermal carbon black and in slit pores: a computer simulation study.

    Science.gov (United States)

    Do, D D; Do, H D

    2004-08-17

    In this paper, we studied vapor-liquid equilibria (VLE) and adsorption of ethylene on graphitized thermal carbon black and in slit pores whose walls are composed of graphene layers. Simple models of a one-center Lennard-Jones (LJ) potential and a two-center united atom (UA)-LJ potential are investigated to study the impact of the choice of potential models in the description of VLE and adsorption behavior. Here, we used a Monte Carlo simulation method with grand canonical Monte Carlo (GCMC) and Gibbs ensemble Monte Carlo ensembles. The one-center potential model cannot describe adequately the VLE over the practical range of temperature from the triple point to the critical point. On the other hand, the two-center potential model (Wick et al. J. Phys. Chem. B 2000, 104, 8008-8016) performs well in the description of VLE (saturated vapor and liquid densities and vapor pressure) over the wide range of temperature. This UA-LJ model is then used in the study of adsorption of ethylene on graphitized thermal carbon black and in slit pores. Agreement between the GCMC simulation results and the experimental data on graphitized thermal carbon black for moderate temperatures is excellent, demonstrating that the potential of the GCMC method and the proper choice of potential model are essential to investigate adsorption. For slit pores of various sizes, we have found that the behavior of ethylene exhibits a number of features that are not manifested in the study of spherical LJ particles. In particular, the singlet density distribution versus distance across the pore and the angle between the molecular axis and the z direction provide rich information about the way molecules arrange themselves when the pore width is varied. Such an arrangement has been found to be very sensitive to the pore width.

  17. Thermal conductivity of simple liquids: temperature and packing-fraction dependence.

    Science.gov (United States)

    Ohtori, Norikazu; Ishii, Yoshiki; Togawa, Yoshinori; Oono, Takuya; Takase, Keiichi

    2014-02-01

    The thermal conductivity of rare gases in liquid and dense fluid states has been evaluated using molecular dynamics simulation with the Lennard-Jones (LJ) potentials and the Green-Kubo (GK) formula. All the calculated thermal conductivities are in very good agreement with experimental results for a wide range of temperature and density. Special attention was paid to temperature and packing-fraction dependence which is nontrivial from dimensional analysis on the LJ potentials and the GK formula. First, the temperature dependence of T(1/4) was determined from the calculations at constant densities. Secondly, in order to obtain the dependence on packing fraction from that on number density separately, a scaling method of particle and/or cell size was introduced. The number density dependence of (N/V)(2/3) which is expected from the dimensional analysis of the GK formulas was confirmed and the packing-fraction dependence of η(3/2) was determined by using the scaling method. It turned out that the summarized functional form of m(-1/2)(N/V)(2/3)η(3/2)T(1/4) can well express both the calculated and experimental thermal conductivities for Ar, Kr, and Xe, where m is the atomic mass. The scaling method has also been applied to molten NaCl and KCl so that it has been found that the thermal conductivity has the packing-fraction dependence of η(2/3) which is much weaker than that of the simple LJ liquids.

  18. Thermodynamic properties of non-conformal soft-sphere fluids with effective hard-sphere diameters.

    Science.gov (United States)

    Rodríguez-López, Tonalli; del Río, Fernando

    2012-01-28

    In this work we study a set of soft-sphere systems characterised by a well-defined variation of their softness. These systems represent an extension of the repulsive Lennard-Jones potential widely used in statistical mechanics of fluids. This type of soft spheres is of interest because they represent quite accurately the effective intermolecular repulsion in fluid substances and also because they exhibit interesting properties. The thermodynamics of the soft-sphere fluids is obtained via an effective hard-sphere diameter approach that leads to a compact and accurate equation of state. The virial coefficients of soft spheres are shown to follow quite simple relationships that are incorporated into the equation of state. The approach followed exhibits the rescaling of the density that produces a unique equation for all systems and temperatures. The scaling is carried through to the level of the structure of the fluids.

  19. Multilayer approximation for a confined fluid in a slit pore

    Directory of Open Access Journals (Sweden)

    V. A. Kuz

    2010-02-01

    Full Text Available A simple Lennard-Jones fluid confined in a slit nanopore with hard walls is studied on the basis of a multilayer structured model. Each layer is homogeneous and parallel to the walls of the pore. The Helmholtz energy of this system is constructed following van der Waals-like approximations, with the advantage that the model geometry permits to obtain analytical expressions for the integrals involved. Being the multilayer system in thermodynamic equilibrium, a system of non-linear equations is obtained for the densities and widths of the layers. A numerical solution of the equations gives the density profile and the longitudinal pressures. The results are compared with Monte Carlo simulations and with experimental data for Nitrogen, showing very good agreement.Received: 23 December 2009, Accepted: 24 February 2010; Edited by: D. A. Stariolo; DOI: 10.4279/PIP.020002

  20. Anomalous diffusion and diffusion anomaly in confined Janus dumbbells.

    Science.gov (United States)

    B Krott, Leandro; Gavazzoni, Cristina; Bordin, José Rafael

    2016-12-28

    Self-assembly and dynamical properties of Janus nanoparticles have been studied by molecular dynamic simulations. The nanoparticles are modeled as dimers and they are confined between two flat parallel plates to simulate a thin film. One monomer from the dumbbells interacts by a standard Lennard-Jones potential and the other by a two-length scales shoulder potential, typically used for anomalous fluids. Here, we study the effects of removing the Brownian effects, typical from colloidal systems immersed in aqueous solution, and consider a molecular system, without the drag force and the random collisions from the Brownian motion. Self-assembly and diffusion anomaly are preserved in relation to the Brownian system. Additionally, a superdiffusive regime associated to a collective reorientation in a highly structured phase is observed. Diffusion anomaly and anomalous diffusion are explained in the two length scale framework.

  1. Anomalous diffusion and diffusion anomaly in confined Janus dumbbells

    Science.gov (United States)

    Krott, Leandro B.; Gavazzoni, Cristina; Bordin, José Rafael

    2016-12-01

    Self-assembly and dynamical properties of Janus nanoparticles have been studied by molecular dynamic simulations. The nanoparticles are modeled as dimers and they are confined between two flat parallel plates to simulate a thin film. One monomer from the dumbbells interacts by a standard Lennard-Jones potential and the other by a two-length scales shoulder potential, typically used for anomalous fluids. Here, we study the effects of removing the Brownian effects, typical from colloidal systems immersed in aqueous solution, and consider a molecular system, without the drag force and the random collisions from the Brownian motion. Self-assembly and diffusion anomaly are preserved in relation to the Brownian system. Additionally, a superdiffusive regime associated to a collective reorientation in a highly structured phase is observed. Diffusion anomaly and anomalous diffusion are explained in the two length scale framework.

  2. 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

  3. 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).

  4. Stability of surface nanobubbles

    Science.gov (United States)

    Maheshwari, Shantanu; van der Hoef, Martin; Zhang, Xuehua; Lohse, Detlef

    2015-11-01

    We have studied the stability and dissolution of surface nanobubbles on the chemical heterogenous surface by performing Molecular Dynamics (MD) simulations of binary mixture consists of Lennard-Jones (LJ) particles. Recently our group has derived the exact expression for equilibrium contact angle of surface nanobubbles as a function of oversaturation of the gas concentration in bulk liquid and the lateral length of bubble. It has been showed that the contact line pinning and the oversaturation of gas concentration in bulk liquid is crucial in the stability of surface nanobubbles. Our simulations showed that how pinning of the three-phase contact line on the chemical heterogenous surface lead to the stability of the nanobubble. We have calculated the equilibrium contact angle by varying the gas concentration in bulk liquid and the lateral length of the bubble. Our results showed that the equilibrium contact angle follows the expression derived analytically by our group. We have also studied the bubble dissolution dynamics and showed the ''stick-jump'' mechanism which was also observed experimentally in case of dissolution of nanodrops.

  5. 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.

  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. 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.

  8. 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)

  9. 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.

  10. 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

  11. 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.

  12. The differential interference in collisional quantum interference on rotational energy transfer

    International Nuclear Information System (INIS)

    Yang Xin; Wang Weili

    2012-01-01

    The collisional quantum interference (CQI) on rotational energy transfer was observed in the experiment of the static cell, and the integral interference angles were measured. To obtain more accurate information, the experiment in the molecular beam should be taken, from which the differential interference angle can be obtained. Based on the first-Born approximation of time-dependent perturbation theory, the theoretical model of CQI is developed in an atom-diatom collision system in the condition of the molecular beam. The model has taken into account the Lennard-Jones interaction potentials and 'straight-line' trajectory approximation. The effect factors that the interference angle depend on are investigated. The changing tendencies of the differential interference angle with the impact parameter, velocity, and collision partner are discussed. This theoretical model is important to understand or perform the experiment in the molecular beam. (authors)

  13. Shape matters: The case for Ellipsoids and Ellipsoidal Water

    Science.gov (United States)

    Tillack, Andreas F.; Robinson, Bruce H.

    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 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 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. ).

  14. 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.

  15. Effect of the ordering potential on the structure of liquid alloys

    Directory of Open Access Journals (Sweden)

    Grosdidier B.

    2011-05-01

    Full Text Available The concept of “ordering or alloying potential” (J. Hafneri: from Hamiltonians to phase diagrams: Springer Berlin 1987 and R. N. Singh and F. Sommerii Rep. Prog. Phys. 60 (1997 57–150 enables the understanding of the different kind of alloys: hetero-coordinated one’s leading to compounds, homocoordinated ones leading to miscibility gap systems and substitutional alloys. The ordering potential is based on the comparison of identical atom interionic potentials (V11 and V22 and different atom interionic potential (V12 It allows the description of the demixing properties of some alloys. In order to understand the concepts, we developed our calculations by using a Lennard-Jones potential, the atomic structure being calculated by molecular dynamics simulation. We obtained surprising and unexpected results putting in evidence the time of simulation and the strength of the ordering potential.

  16. 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.

  17. 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.)

  18. 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

  19. 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...

  20. Comparing crystal-melt interfacial free energies through homogeneous nucleation rates

    International Nuclear Information System (INIS)

    Bai Xianming; Li Mo

    2008-01-01

    In this work, we compared several available crystal-melt interfacial free energies via homogeneous nucleation rates in a pure Lennard-Jones model system using both model fitting and numerical methods. We examined the homogeneous nucleation temperature obtained from the classical nucleation theory using the available interfacial free energies from three different methods as inputs, i.e. the free energy integration method, the interface fluctuation method and the classical nucleation theory based method. We found that the critical temperature obtained by using the interfacial free energy calculated recently (Bai and Li 2006 J. Chem. Phys. 124 124707) is in better agreement with that obtained from spontaneous crystallization in an independent molecular dynamics simulation. The discrepancies among the interface energies are discussed in light of these results

  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. 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)

  3. Broadening and shift of the inter-combination spectral line of Cd 326.1 nm perturbed by Kr

    Energy Technology Data Exchange (ETDEWEB)

    Roston, G D [Physics Department, Faculty of Science, Alexandria University, PO Box 21511, Alexandria (Egypt); Ghatass, Z F, E-mail: dr.gamal_daniel@yahoo.co [Department of Environmental Studies, Institute of Graduate Studies and Research, Alexandria University, 163 Horrya Avenue, PO 832, Shatby, Alexandria (Egypt)

    2010-07-15

    The line center of the Cd inter-combination spectral line at 326.1 nm (5{sup 1}S{sub 0}-5{sup 3}P{sub 1}) perturbed by Kr has been investigated using a high-resolution scanning Fabry-Perot interferometer. The van der Waals and Lennard-Jones potentials for a Cd-Kr system have been calculated using the Coulomb approximation. The values of the pressure broadening ({beta}) and shift ({delta}) coefficients for the studied line at a temperature of 468 K, density of cadmium N=4.02x10{sup 12} cm{sup -3} and Kr gas pressure ranging from 3 to 95 Torr have been obtained and compared with published theoretical and experimental values.

  4. 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

  5. Atomistic modeling of interfacial interaction between polyvinyl chloride and polypropylene with Boron-Nitride monolayer sheet: A density functional theory study

    Science.gov (United States)

    Hamed Mashhadzadeh, A.; Fereidoon, A.; Ghorbanzadeh Ahangari, M.

    2017-11-01

    In present work, we performed Density Functional Theory calculation (DFT) to prepare polypropylene (PP) and polyvinyl chloride (PVC) nanocomposite. For mentioned purpose, we chose Boron-Nitride graphene (BN-graphene) sheet as nano reinforcement. Next, we calculated adsorbed energy between these two polymeric matrixes with BN-monolayer sheet. Our DFT results demonstrated that interaction energy between PP/BN-graphene and PVC/BN-graphene are equal, approximately, because in mentioned two nanocomposite systems, polymer matrix approached to nano reinforcement from hydrogen atom in optimized structure. Then, the adsorbed energy and equilibrium distance between mentioned polymeric matrixes and BN-graphene sheet in nanocomposite with increasing the number of polymer monomers onto surface of BN-graphene were calculated. Finally, we modeled van der Waals interfacial interaction between polymer matrixes and nano reinforcement with linear classical spring by using lennard-jones parameters.

  6. 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.

  7. Using the k-d Tree Data Structure to Accelerate Monte Carlo Simulations.

    Science.gov (United States)

    Chen, Qile P; Xue, Bai; Siepmann, J Ilja

    2017-04-11

    The k-d tree data structure is implemented in a Monte Carlo (MC) molecular simulation program to accelerate the range search for particles or interaction sites within the cutoff distance when Lennard-Jones and Coulomb interactions are computed. MC simulations are performed for different molecules in various ensembles to assess the efficiency enhancements due to the k-d tree data structure. It is found that the use of k-d trees accelerates significantly simulations for Lennard-Jones particles in the NVT and NVT-Gibbs ensembles and for n-butane and 2,4,6,8,10,12,14,16,18,20,22-undecamethylpentacosane represented by the TraPPE-UA force field in the NpT ensemble. Simulations for TraPPE-UA ethanol in the NpT ensemble and for the rigid TIP4P water model in the Gibbs ensemble gain slightly in efficiency with the k-d tree, whereas simulations for TIP4P water in the NpT ensemble do not benefit from the use of the k-d tree. The speed-up can be attributed to the reduction in the number of distance calculations in the range search from scaling as [Formula: see text] to [Formula: see text]. In addition, these tests suggest that the efficiency gain from the use of the k-d tree data structure depends on the flexibility of the molecular model (requiring configurational-bias MC moves to sample changes in conformation), on the ensemble (with open ensembles requiring special MC moves to aid particle transfers), and on the number of interaction sites per molecule (with compact multisite models not seeing an efficiency gain). Overall, the use of the k-d tree data structure can substantially enhance MC simulation efficiency for a variety of systems, and it will enable simulations for larger system sizes in the future.

  8. Pramana – Journal of Physics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    dimensional spatial inhomogeneity is parallel to the direction of propagation. pp 269-279 Research Articles. Structures and autocorrelation functions of liquid Al and Mg modelled via Lennard-Jones potential from molecular dynamics simulation.

  9. 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 ...

  10. 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.

  11. A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water.

    Science.gov (United States)

    Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul

    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.

  12. 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.

  13. 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

  14. 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.

  15. 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…

  16. Non-Local Propagation of Correlations in Quantum Systems with Long-Range Interactions

    Science.gov (United States)

    2014-07-10

    quantum system: an ab initio study of the dynamics of the highly excited states of 1D lattice hard-core bosons. Phys. Rev. Lett. 98, 050405 (2007). 13...power-law couplings Jkl< jk2 lj2a (a. 0) in 1D, choosing k0 right in themiddle of i and jwill generally give the tightest bound. Multi- hop processes...where Hi~ X p hip Hj~ X q hjq We can expand the time-evolution operator to obtain Ai tð Þ~Aizih Hi,Ai½ { t2 2! Hi, Hi,Ai½ ½ z . . . ~Aizit X p1 hip1,Ai

  17. Simulation of Liquid and Supercritical Hydrogen Sulfide and of Alkali Ions in the Pure and Aqueous Liquid.

    Science.gov (United States)

    Orabi, Esam A; Lamoureux, Guillaume

    2014-08-12

    A polarizable model for hydrogen sulfide (H2S) is optimized based on the experimental properties of the monomer and of the bulk liquid. The model is characterized by rigid SH bonds but flexible HSH angle and the polarizability is based on the Drude oscillator model. Bonded parameters and atomic charges are based on the experimental properties of the gaseous monomer. Atomic Lennard-Jones (LJ) parameters are adjusted based on the density of H2S around the critical point (in the temperature range 363-393 K and pressure range 8.023-10.013 MPa). The model gives binding energies for H2S dimers, trimers, and tetramers in good agreement with ab initio MP2(full)/6-311++G(d,p) results. It shows a liquid structure in very good agreement with neutron diffraction data. The model also gives density, self-diffusion coefficient, heat of vaporization, and dielectric constant of liquid hydrogen sulfide at the normal boiling point in good agreement with experimental data. In addition, the model is transferable to high temperature and pressure conditions, as evidenced from simulations up to 542.2 K and 40 MPa. The model is used in combination with the SWM4-NDP water model, with LJ parameters between the S and O atoms adjusted to reproduce the experimental hydration free energy of H2S. Simulations suggest that, in its first solvation shell, a single H2O molecule is solvated by 10 H2S molecules while a single H2S molecule is solvated by 20.5 H2O molecules. Pair-specific LJ parameters between alkali ions (Li(+), Na(+), K(+), Rb(+), Cs(+)) and the S atom are adjusted to reproduce ab initio binding energies of the ion-H2S pairs at the CCSD(T) level. Simulations based on these parameters show that alkali ions have higher coordination numbers and lower solvation free energies in liquid H2S than in liquid water or liquid ammonia. The model is also used to investigate the preferential solvation of the ions in aqueous solutions with a 10% H2S mole fraction. Results show that the ions are

  18. 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

  19. 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

  20. 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.

  1. Thermodynamic scaling and corresponding states for the self-diffusion coefficient of non-conformal soft-sphere fluids.

    Science.gov (United States)

    Rodríguez-López, Tonalli; Moreno-Razo, J Antonio; del Río, Fernando

    2013-03-21

    In this work, we explore transport properties of a special type of repulsive spheres that exhibit remarkable scaling of their thermodynamic properties. In order to accomplish that we propose a new way to derive and express effective hard-sphere diameters for transport properties of simple fluids. The procedure relies on mapping the system's transport properties, in the low density limit, to the hard-sphere fluid. We have chosen a set of soft-sphere systems characterised by a well-defined variation of their softness. These systems represent an extension of the repulsive Lennard-Jones potential widely used in statistical mechanics of fluids and are an accurate representation of the effective repulsive potentials of real systems. The self-diffusion coefficient of the soft-sphere fluids is obtained by equilibrium molecular dynamics. The soft-sphere collision integrals of different systems are shown to follow quite simple relationships between each other. These collision integrals are incorporated, through the definition of the effective hard-sphere diameter, in the resulting equation for the self-diffusion coefficient. The approach followed exhibits a density rescaling that leads to a single master curve for all systems and temperatures. The scaling is carried through to the level of the mean-squared displacement.

  2. Assessing the accuracy of integral equation theories for nano-sized hydrophobic solutes in water

    Science.gov (United States)

    Fujita, Takatoshi; Yamamoto, Takeshi

    2017-07-01

    Integral equation theories provide an efficient route for computing the solvation free energy (SFE) of molecular systems in water. The accuracy of those theories is usually tested against small molecules via comparison of SFE with reference data. However, tests against larger molecules in the nanometer regime are scarce in literature despite recent applications to such systems. Here, we thus study the accuracy and validity of a commonly used integral equation theory, namely, a three-dimensional reference interaction site model (3D-RISM), by considering the following problems: (1) solvation of a small to large Lennard-Jones particle, (2) binding of planar hydrophobic systems with varying size and hydrophobicity, and (3) self-assembly of amphiphilic molecules into a nanocapsule. The energy representation method is also utilized for comparison. The results show that the 3D-RISM method works successfully for small molecules, while the accuracy degrades systematically with system size and hydrophobicity. The size-dependent error in SFE does not cancel adequately between two solute configurations, resulting in a substantial error in the free energy difference. It is also shown that the free energy profiles for hydrophobic association exhibit a fictitious high-energy barrier, suggesting that care must be taken for studying such systems. The numerical difficulties observed above are discussed based on the relation between hypernetted-chain approximation, classical density functional theory with quadratic expansion, and the size-dependent error arising from the cavity region of the system.

  3. 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

    2018-03-01

    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.

  4. 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.

  5. 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.

  6. 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].

  7. Surface tension of mixtures of molecular fluids: Comparison between the experimental and theoretical study of CH{sub 4} + Kr, Kr + NO, and CH{sub 4} + NO

    Energy Technology Data Exchange (ETDEWEB)

    Calado, J.C.G.; Saramago, B.J.V. [Instituto Superior Tecnico, Lisbon (Portugal). Centro de Quimica Estrutural; Santos Mendonca, A.F.S. dos; Soares, V.A.M. [Univ. de Lisboa, Lisbon (Portugal). Centro de Ciencia e Tecnologia de Materiais

    1997-01-01

    The authors report a study of the surface tension of three binary liquid mixtures of molecular fluids. A microscopic mean field theory (MFT) has been used to calculate the theoretical results enabling the comparison with the experimental data. The mean field theory has been successfully used in the prediction of the surface properties of simple systems composed by quasi-spherical molecules. In the present study the MFT was able to reproduce the essential features of the interfacial properties of the systems CH{sub 4} + Kr, Kr + NO and CH{sub 4} + NO. The pure components were modeled by Lennard-Jones potentials with a set of intermolecular parameters taken from the literature for Kr and calculated from the fitting of the energy parameters to the surface tension, for CH{sub 4} and NO. In the case of the mixtures, it was found that reasonable agreement with experiment can only be obtained by allowing deviations from the Lorentz-Berthelot combining rules. For the CH{sub 4} + Kr system the authors used the binary energy parameter {xi} obtained through a fitting to the bulk properties; for the Kr + NO and CH{sub 4} + NO systems the binary parameter was adjusted to the interfacial properties.

  8. Surface Tension of Mixtures of Molecular Fluids: Comparison between the Experimental and Theoretical Study of CH4 + Kr, Kr + NO, and CH4 + NO

    Science.gov (United States)

    Calado; Mendonca; Saramago; Soares

    1997-01-01

    We report a study of the surface tension of three binary liquid mixtures of molecular fluids. A microscopic mean field theory (MFT) has been used to calculate the theoretical results enabling the comparison with the experimental data. The mean field theory has been successfully used in the prediction of the surface properties of simple systems composed by quasi-spherical molecules. In the present study the MFT was able to reproduce the essential features of the interfacial properties of the systems CH4 + Kr, Kr + NO and CH4 + NO. The pure components were modeled by Lennard-Jones potentials with a set of intermolecular parameters taken from the literature for Kr and calculated from the fitting of the energy parameters (epsilon) to the surface tension, for CH4 and NO. In the case of the mixtures, it was found that reasonable agreement with experiment can only be obtained by allowing deviations from the Lorentz-Berthelot combining rules. For the CH4 + Kr system we used the binary energy parameter xi obtained through a fitting to the bulk properties; for the Kr + NO and CH4 + NO systems the binary parameter was adjusted to the interfacial properties.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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)

  15. 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.

  16. Collective behavior of penetrable self-propelled rods in two dimensions

    Science.gov (United States)

    Abkenar, Masoud; Marx, Kristian; Auth, Thorsten; Gompper, Gerhard

    2013-12-01

    Collective behavior of self-propelled particles is observed on a microscale for swimmers such as sperm and bacteria as well as for protein filaments in motility assays. The properties of such systems depend both on their dimensionality and the interactions between their particles. We introduce a model for self-propelled rods in two dimensions that interact via a separation-shifted Lennard-Jones potential. Due to the finite potential barrier, the rods are able to cross. This model allows us to efficiently simulate systems of self-propelled rods that effectively move in two dimensions but can occasionally escape to the third dimension in order to pass each other. Our quasi-two-dimensional self-propelled particles describe a class of active systems that encompasses microswimmers close to a wall and filaments propelled on a substrate. Using Monte Carlo simulations, we first determine the isotropic-nematic transition for passive rods. Using Brownian dynamics simulations, we characterize cluster formation of self-propelled rods as a function of propulsion strength, noise, and energy barrier. Contrary to rods with an infinite potential barrier, an increase of the propulsion strength does not only favor alignment but also effectively decreases the potential barrier that prevents crossing of rods. We thus find a clustering window with a maximum cluster size at medium propulsion strengths.

  17. 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

  18. Memory versus irreversibility in the thermal densification of amorphous glasses

    Science.gov (United States)

    Ovadyahu, Z.

    2017-06-01

    We report on dynamic effects associated with thermally annealing amorphous indium-oxide films. In this process, the resistance of a given sample may decrease by several orders of magnitude at room temperatures, while its amorphous structure is preserved. The main effect of the process is densification, i.e., increased system density. The study includes the evolution of the system resistivity during and after the thermal treatment, the changes in the conductance noise, and the accompanying changes in the optical properties. The sample resistance is used to monitor the system dynamics during the annealing period as well as the relaxation that ensues after its termination. These reveal slow processes that fit well with a stretched-exponential law, a behavior that is commonly observed in structural glasses. There is an intriguing similarity between these effects and those obtained in high-pressure densification experiments. Both protocols exhibit the "slow spring-back" effect, a familiar response of memory foams. A heuristic picture based on a modified Lennard-Jones potential for the effective interparticle interaction is argued to qualitatively account for these densification-rarefaction phenomena in amorphous materials, whether affected by thermal treatment or by application of high pressure.

  19. A study of τ , the critical exponent of nuclear fragmentation

    International Nuclear Information System (INIS)

    Cardenas, R.; Lopez, J.A.; Barranon, A.; Dorso, C.O.

    2001-01-01

    Full text: When nuclei break into pieces, fragments with different sizes mass and charge numbers, are generated. Using the Fisher droplet model this fragmentation process can be characterized as a second order phase transitions of the excited nuclear matter. For breakups occurring near the critical point, the mass distribution should obeys a power law of the form ∼ A - τ , with τ being a critical exponent, apparently universal to processes at different scales with values within 2 ≤ τ ≤3. In this work we study the behavior of this exponent considering four different models. In summary the findings are as follows. Using percolation theory for a cubic system with 216 sites, a value of τ = 2.3 was obtained. A spherical system, also yielded a value of τ = 2.3. The third model, consisting of two 74-particle colliding nuclei interacting via a Lennard-Jones potential, also produced fragments with a power law distribution of τ = 2.3. Finally, studying a series of collisions of 147-particle nuclei using a more realistic potential (Pandharipande), a τ = 1.92 was obtained. This last result, however, can be expected for breakups not occurring near the critical point. Further refinements of this last study are in progress. JAL acknowledges support from the National Science Foundation, through grant PHY-96-00038. (Author)

  20. 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

  1. From lime to silica and alumina: systematic modeling of cement clinkers using a general force-field.

    Science.gov (United States)

    Freitas, A A; Santos, R L; Colaço, R; Bayão Horta, R; Canongia Lopes, J N

    2015-07-28

    Thirteen different cement-clinker crystalline phases present in the lime-silica-alumina system have been systematically modeled using a simple and general force field. This constitutes a new type of approach towards the study of lime-silica-alumina systems, where the simpler and more transferable Lennard-Jones potential was used instead of the more traditional Buckingham potential. The results were validated using experimental density and structural data. The elastic properties were also considered. Six amorphous phases (corresponding to calcium/silicon ratios corresponding to belite, rankinite, wollastonite and alumina-doped amorphous wollastonite with 5%, 10% and 15% alumina content) were also studied using molecular dynamics simulations. The obtained MD trajectories were used to characterize the different crystalline and amorphous phases in terms of the corresponding radial distribution functions, aggregate analyses and connectivity among silica groups. These studies allowed a direct comparison between the crystalline and amorphous phases and revealed how the structure of the silica network was modified in the amorphous materials or by the inclusion of other structural units such as alumina. The knowledge at an atomistic level of such modifications is paramount for the formulation of new cement-clinker phases.

  2. 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.

  3. Interface structure and mechanics between graphene and metal substrates: a first-principles study

    International Nuclear Information System (INIS)

    Xu Zhiping; Buehler, Markus J

    2010-01-01

    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.

  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. 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.

  6. Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator.

    Science.gov (United States)

    Lin, Fang-Yu; MacKerell, Alexander D

    2018-02-13

    The quality of the force field is crucial to ensure the accuracy of simulations used in molecular modeling, including computer-aided drug design (CADD). To perform more accurate modeling and simulations of halogenated molecules, in this study the polarizable force field based on the classical Drude oscillator model was extended to both aliphatic and aromatic systems using halogenated ethane and benzene model compounds for the halogens F, Cl, Br, and I. The force field parameters were optimized targeting quantum mechanical dipole moments, water interactions, and molecular polarizabilities as well as experimental observables, including enthalpies of vaporization, molecular volumes, hydration free energies, and dielectric constants. The developed halogenated polarizable force field is capable of reproducing QM relative energies and geometries of both halogen bonds and halogen-hydrogen bond donor interactions at an unprecedented level due to the inclusion of a virtual particle and anisotropic atomic polarizability on the halogen and, notably, the inclusion of Lennard-Jones parameters on the halogen Drude particle. The model was validated on the basis of its ability to accurately reproduce pure solvent properties for halogenated naphthalenes and alkanes, including species analogous to those used as refrigerants. Accordingly, it is anticipated that the model will be applicable for the study of halogenated derivatives in CADD as well as in other chemical and biophysical studies.

  7. Classical Fractals and Quantum Chaos in Ultracold Dipolar Collisions.

    Science.gov (United States)

    Yang, B C; Pérez-Ríos, Jesús; Robicheaux, F

    2017-04-14

    We examine a dipolar-gas model to address fundamental issues regarding the correspondence between classical chaos and quantum observations in ultracold dipolar collisions. The theoretical model consists of a short-range Lennard-Jones potential well with an anisotropic, long-range dipole-dipole interaction between two atoms. Both the classical and quantum dynamics are explored for the same Hamiltonian of the system. The classical chaotic scattering is revealed by the fractals developed in the scattering function (defined as the final atom separation as a function of initial conditions), while the quantum chaotic features lead to the repulsion of the eigenphases from the corresponding quantum S matrix. The nearest-eigenphase-spacing statistics have an intermediate behavior between the Poisson and the Wigner-Dyson distributions. The character of the distribution can be controlled by changing an effective Planck constant or the dipole moment. The degree of quantum chaos shows a good correspondence with the overall average of the classical scattering function. The results presented here also provide helpful insights for understanding the role of the inherent dipole-dipole interaction in the currently ongoing experiments on ultracold collisions of highly magnetic atoms.

  8. 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)

  9. 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.

  10. Molecular dynamics simulations of shock waves in hydroxyl-terminated polybutadiene melts: Mechanical and structural responses

    Energy Technology Data Exchange (ETDEWEB)

    Fröhlich, Markus G., E-mail: FroehlichM@missouri.edu, E-mail: ThompsonDon@missouri.edu; Sewell, Thomas D., E-mail: SewellT@missouri.edu; Thompson, Donald L., E-mail: FroehlichM@missouri.edu, E-mail: ThompsonDon@missouri.edu [Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211-7600 (United States)

    2014-01-14

    The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s{sup −1}, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ∼0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.

  11. 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.

  12. Molecular Dynamics Simulation of Coarse-Grain Model of Silicon Functionalized Graphene

    Directory of Open Access Journals (Sweden)

    Hui Zhixin

    2015-01-01

    Full Text Available The electronic transport, the storage capacity and the service life of the anode material for lithium ion batteries will be reduced seriously in the event of the material layering or cracking, so the anode material must have strong mechanical reliability. Firstly, in view of the traditional molecular dynamics (MD limited by the geometric scales of the model of Silicon functionalized graphenen (SFG as lithium ion batteries anode material, some full atomic models of SFG were established using Tersoff potential and Lennard-Jones potential, and used to calculate the modulus and the adhesion properties. What’s more, the assertion of mechanical equilibrium condition and energy conservation between full atomic and coarse-grain models through elastic strain energy were enforced to arrive at model parameters. The model of SFG coarse-grain bead-spring elements and its system energy function were obtained via full atomic simulations. Finally, the validity of the SFG coarse-grain model was verified by comparing the tensile property of coarse-grain model with full atoms model.

  13. 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

  14. Cigarette smoking and quality of life in patients with inflammatory bowel disease. South Limburg IBD Study Group.

    Science.gov (United States)

    Russel, M G; Nieman, F H; Bergers, J M; Stockbrügger, R W

    1996-11-01

    Smoking has been reported as influencing disease activity in inflammatory bowel disease. The aim of our study was to elucidate the relationship between smoking and aspects of disease-specific quality of life in inflammatory bowel disease. Cross-sectional study. In 1105 prevalent patients with inflammatory bowel disease, diagnosed according to the criteria of Lennard-Jones and Truelove and Witts, disease-specific quality of life was investigated using the Inflammatory Bowel Disease Questionnaire (IBDQ). In Crohn's disease, smoking females reported a lower quality of life than non-smoking females (all four dimensions of the IBDQ). Using an explanatory model of relationships between the four dimensions for the analysis, it became evident that smoking is associated with more bowel symptoms in young Crohn's disease females, with more emotional dysfunction in all Crohn's disease females, and with more systemic symptoms in all three diagnostic groups with marked bowel symptoms. Moderately smoking male ulcerative colitis patients reported fewer bowel complaints compared with non-smoking male ulcerative colitis patients. There is a relationship between smoking and disease-specific quality of life in both ulcerative colitis and Crohn's disease. The hypothesis is presented that a part of the observed differences in the studied quality of life dimensions with respect to age, sex and disease group are related to concomitant oral contraceptive use.

  15. Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

    Energy Technology Data Exchange (ETDEWEB)

    Kamberaj, Hiqmet, E-mail: hkamberaj@ibu.edu.mk [Department of Computer Engineering, International Balkan University, Tashko Karadza 11A, Skopje (Macedonia, The Former Yugoslav Republic of)

    2015-09-28

    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.

  16. Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence.

    Science.gov (United States)

    Kamberaj, Hiqmet

    2015-09-28

    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.

  17. 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.

  18. Vibrations and thermal conductivity in inorganic and polymeric glasses.

    Science.gov (United States)

    Shenogin, Sergei; Bodapati, Arun; Keblinski, Pawel

    2006-03-01

    The mechanism of thermal transport in amorphous materials was studied by means of vibrational mode analysis and classical nonequilibrium molecular dynamics (MD) simulations. We studied four different model systems of (a) Lennard-Jones glass, (b) bead-spring model of an amorphous polymer, (c) amorphous silicon with Stillinger-Weber potential; and (d) all-atom model of glassy polystyrene with PCFF-type force field. For all structures we evaluated thermal conductivity from the harmonic theory of disordered solids [P.B.Allen, and J.L.Feldman, Phys.Rev.B 48, 12581 (1993)] and from direct MD simulations. We found that for all models but polystyrene, the harmonic theory accurately predicts thermal conductivity. By contrast, in the case of polystyrene, only ˜1/2 of thermal conductivity can be explained within the harmonic approximation. Consequently, a major part of the transport has to be attributed to anharmonic coupling between vibrational modes. The reasons for the failure of harmonic theory of disordered solids to model amorphous glassy polymers will be discussed.

  19. Thermodynamics of Aβ16-21 dissociation from a fibril: Enthalpy, entropy, and volumetric properties.

    Science.gov (United States)

    Rao Jampani, Srinivasa; Mahmoudinobar, Farbod; Su, Zhaoqian; Dias, Cristiano L

    2015-11-01

    Here, we provide insights into the thermodynamic properties of A β16-21 dissociation from an amyloid fibril using all-atom molecular dynamics simulations in explicit water. An umbrella sampling protocol is used to compute potentials of mean force (PMF) as a function of the distance ξ between centers-of-mass of the A β16-21 peptide and the preformed fibril at nine temperatures. Changes in the enthalpy and the entropic energy are determined from the temperature dependence of these PMF(s) and the average volume of the simulation box is computed as a function of ξ. We find that the PMF at 310 K is dominated by enthalpy while the entropic energy does not change significantly during dissociation. The volume of the system decreases during dissociation. Moreover, the magnitude of this volume change also decreases with increasing temperature. By defining dock and lock states using the solvent accessible surface area (SASA), we find that the behavior of the electrostatic energy is different in these two states. It increases (unfavorable) and decreases (favorable) during dissociation in lock and dock states, respectively, while the energy due to Lennard-Jones interactions increases continuously in these states. Our simulations also highlight the importance of hydrophobic interactions in accounting for the stability of A β16-21. © 2015 Wiley Periodicals, Inc.

  20. 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.

  1. 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.

  2. Classical Trajectory Study of Collision Energy Transfer between Ne and C2H2 on a Full Dimensional Accurate Potential Energy Surface.

    Science.gov (United States)

    Liu, Yang; Huang, Yin; Ma, Jianyi; Li, Jun

    2018-02-15

    Collision energy transfer plays an important role in gas phase reaction kinetics and relaxation of excited molecules. However, empirical treatments are generally adopted for the collisional energy transfer in the master equation based approach. In this work, classical trajectory approach is employed to investigate the collision energy transfer dynamics in the C 2 H 2 -Ne system. The entire potential energy surface is described as the sum of the C 2 H 2 potential and interaction potential between C 2 H 2 and Ne. It is highlighted that both parts of the entire potential are highly accurate. In particular, the interaction potential is fit to ∼41 300 configurations determined at the level of CCSD(T)-F12a/cc-pCVTZ-F12 with the counterpoise correction. Collision energy transfer dynamics are then carried out on this benchmark potential and the widely used Lennard-Jones and Buckingham interaction potentials. Energy transfers and related probability densities at different collisional energies are reported and discussed.

  3. 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)

  4. 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)

  5. Simple expression for the dependence of the nanodrop contact angle on liquid-solid interactions and temperature

    Science.gov (United States)

    Berim, Gersh O.; Ruckenstein, Eli

    2009-01-01

    The density distributions and contact angles of nanodrops on smooth solid surfaces are calculated on the basis of a nonlocal density functional theory in wide ranges of temperature and parameters of the Lennard-Jones potentials representing the fluid-fluid and fluid-solid interactions. A simple linear dependence of the contact angle on the fluid-solid energy parameter ɛfs was found for various temperatures, hard core fluid-solid parameters σfs, and average fluid density of the system. A simple expression is suggested which represents all the above results in a unified form that relates the contact angle θ to the parameters of the interaction potentials and temperature. The most intriguing feature was that for each considered σfs there is a value ɛfs0 of ɛfs for which the contact angle θ=θ0 can be considered independent of temperature and of σfs. It is shown that ɛfs=ɛfs0 divides the materials for which θ increases from those for which θ decreases with increasing temperature. The results obtained for the dependence of the contact angle on the parameters of the model are in qualitative agreement with known molecular dynamics results.

  6. 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.

  7. Molecular docking using the molecular lipophilicity potential as hydrophobic descriptor: impact on GOLD docking performance.

    Science.gov (United States)

    Nurisso, Alessandra; Bravo, Juan; Carrupt, Pierre-Alain; Daina, Antoine

    2012-05-25

    GOLD is a molecular docking software widely used in drug design. In the initial steps of docking, it creates a list of hydrophobic fitting points inside protein cavities that steer the positioning of ligand hydrophobic moieties. These points are generated based on the Lennard-Jones potential between a carbon probe and each atom of the residues delimitating the binding site. To thoroughly describe hydrophobic regions in protein pockets and properly guide ligand hydrophobic moieties toward favorable areas, an in-house tool, the MLP filter, was developed and herein applied. This strategy only retains GOLD hydrophobic fitting points that match the rigorous definition of hydrophobicity given by the molecular lipophilicity potential (MLP), a molecular interaction field that relies on an atomic fragmental system based on 1-octanol/water experimental partition coefficients (log P(oct)). MLP computations in the binding sites of crystallographic protein structures revealed that a significant number of points considered hydrophobic by GOLD were actually polar according to the MLP definition of hydrophobicity. To examine the impact of this new tool, ligand-protein complexes from the Astex Diverse Set and the PDB bind core database were redocked with and without the use of the MLP filter. Reliable docking results were obtained by using the MLP filter that increased the quality of docking in nonpolar cavities and outperformed the standard GOLD docking approach.

  8. 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

  9. Molecular Dynamics: from basic techniques to applications (A Molecular Dynamics Primer)

    Science.gov (United States)

    Hernández, E. R.

    2008-11-01

    It is now 50 years since the first papers describing the use of Molecular Dynamics (MD) were published by Alder and Wainright, and since then, together with Monte Carlo (MC) techniques, MD has become an essential tool in the theoretical study of materials properties at finite temperatures. In its early days, MD was used in combination with simple yet general models, such as hard spheres or Lennard-Jones models of liquids, systems which, though simple, were nevertheless not amenable to an analytical statistical mechanical treatment. Nowadays, however, MD is most frequently used in combination with rather sophisticated models, ranging all the way between empirical force fields to first-principles methods, with the aim of describing as accurately as possible any given material. From a computational aid in statistical mechanics and many-body physics, MD has evolved to become a widely used tool in physical chemistry, condensed matter physics, biology, geology and materials science. The aim of this course is to describe the basic algorithms of MD, and to provide attendees with the necessary theoretical background in order to enable them to use MD simulations in their research work. Also, examples of the use of MD in different scientific disciplines will be provided, with the aim of illustrating the the many possibilities and the wide spread use of MD simulation techniques in scientific research today.

  10. 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.

  11. Empirical intermolecular potential from depolarized interaction-induced light scattering spectra for tetrafluoromethane

    Science.gov (United States)

    Kader, Mohamed Sayed Abdel

    2002-07-01

    Depolarized interaction-induced light scattering spectra of tetrafluoromethane in the frequency range 2-150 cm-1 at 294.5 K and 0.91 mol/l with the interaction pressure virial coefficient and viscosity have been used for deriving the empirical multiparameter Morse-Morse-Morse-Spline-van der Waals (M3SV), Lennard-Jones, Kihara, and exp-6 intermolecular potentials. The line shape at relatively low frequencies is determined largely by the effect of bound and free transitions. At intermediate frequencies it is sensitive to both the attractive part of the potential and the short-range part of the polarizability anisotropy. The high frequency wings are discussed in terms of the collision-induced rotational Raman effect and estimates for the dipole-quadrupole and dipole-octopole polarizabilities A and E, respectively, are obtained. Absolute zeroth and second moments have been measured and compared with theoretical calculations using these models of the intermolecular potentials. The results show that M3SV is the most accurate potential yet reported for this system.

  12. 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.

  13. Influence of contact-line curvature on the evaporation of nanodroplets from solid substrates.

    Science.gov (United States)

    Zhang, Jianguo; Leroy, Frédéric; Müller-Plathe, Florian

    2014-07-25

    The effect of the three-phase contact-line curvature on the evaporation mechanism of nanoscopic droplets from smooth and chemically homogenous substrates is studied by molecular dynamics simulations. Spherical droplets, whose three-phase contact line is curved, and cylindrical droplets, whose contact radius is infinite, are compared. It is found that the evaporation of cylindrical droplets takes place at constant contact angle, while spherical droplets evaporate by simultaneous reduction of their contact area and their contact angle. This is independent of the substrate-liquid interaction strength. The dependence of the evaporation mechanism on the contact-line curvature can be rationalized with the help of the concept of a contact-line tension, and the evaporation simulations of the spherical droplets are used to extract the line tension on each surface. The corresponding values for the Lennard-Jones systems studied here are of the order of 10(-11)N, which is in a good agreement with previous theoretical and experimental estimates. With this order of magnitude, the line tension is expected to have an effect on the contact angle of spherical droplets only, when their diameter is less than about 100 nm. The observed difference in evaporation mechanism is interpreted as a manifestation of the line tension whose existence has been controversial.

  14. 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.

  15. Molecular Dynamics Simulation of Spinodal Decomposition in Three-Dimensional Binary Fluids

    DEFF Research Database (Denmark)

    Laradji, Mohamed; Toxvaerd, Søren; Mouritsen, Ole G.

    1996-01-01

    Using large-scale molecular dynamics simulations of a two-component Lennard-Jones model in three dimensions, we show that the late-time dynamics of spinodal decomposition in concentrated binary fluids reaches a viscous scaling regime with a growth exponent n = 1, in agreement with experiments...

  16. Optmizied random phase approximation for the phase diagram of C ...

    African Journals Online (AJOL)

    Our perturbation/variational approach for the Helmholtz free energy of the C60 molecules is based on the Lennard-Jones intermolecular interaction. We observe that higher accuracy is obtainable by treating all the grid points within the exclusion hole of the pair distribution function as independent variables. Our numerical ...

  17. 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.

  18. 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.

  19. 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....

  20. 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.

  1. G A Adebayo

    Indian Academy of Sciences (India)

    Structures and autocorrelation functions of liquid Al and Mg modelled via Lennard-Jones potential from molecular dynamics simulation ... Collision frequency of Lennard–Jones fluids at high densities by equilibrium molecular dynamics simulation ... Adhesion energy, surface traction and surface tension in liquid xenon.

  2. Application of the cluster variation method to ordering in an interstitital solid solution

    DEFF Research Database (Denmark)

    Pekelharing, Marjon I.; Böttger, Amarante; Somers, Marcel A. J.

    1999-01-01

    The tetrahedron approximation of the cluster variation method (CVM) was applied to describe the ordering on the fcc interstitial sublattice of gamma-Fe[N] and gamma'-Fe4N1-x. A Lennard-Jones potential was used to describe the dominantly strain-induced interactions, caused by misfitting of the N a...

  3. A Computational Study of Rare Gas Clusters: Stepping Stones to the Solid State

    Science.gov (United States)

    Glendening, Eric D.; Halpern, Arthur M.

    2012-01-01

    An upper-level undergraduate or beginning graduate project is described in which students obtain the Lennard-Jones 6-12 potential parameters for Ne[subscript 2] and Ar[subscript 2] from ab initio calculations and use the results to express pairwise interactions between the atoms in clusters containing up to N = 60 atoms. The students use simulated…

  4. Line Tension and Wettability of Nanodrops on Curved Surfaces

    NARCIS (Netherlands)

    Maheshwari, Shantanu; van der Hoef, Martin Anton; Lohse, Detlef

    2016-01-01

    In this work we study the formation of nanodrops on curved surfaces (both convex and concave) by means of molecular dynamics simulations, where the particles interact via a Lennard-Jones potential. We find that the contact angle is not affected by the curvature of the substrate, in agreement with

  5. Feasibility of a single-parameter description of equilibrium viscous liquid dynamics

    DEFF Research Database (Denmark)

    Pedersen, Ulf Rørbæk; Christensen, Tage Emil; Schrøder, Thomas

    2008-01-01

    -Andersen binary Lennard-Jones mixture as well as for an asymmetric dumbbell model liquid, a single-parameter description works quite well. This is confirmed by time-domain results where it is found that energy and pressure fluctuations are strongly correlated on the alpha time scale in the constant...

  6. 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

  7. 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.)

  8. "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…

  9. 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…

  10. LJ van der Veen et S. Bodinga-bwa-Bodinga. Gedandedi sa Geviya

    African Journals Online (AJOL)

    rbr

    intitulé Gedandedi sa Geviya/Dictionnaire Geviya–Français (en abrégé DGF dans les reste de l'article) a été ... de l'accession du Gabon à la souveraineté internationale (Nyangone Assam et. Mavoungou 2000 ... du dictionnaire, la macro- et microstructure du DGF, et le traitement lexicographique des termes de spécialité. 1.

  11. 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

  12. 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

  13. 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.

  14. Correlations in the low-density Fermi gas: Fermi-liquid state, dimerization, and Bardeen-Cooper-Schrieffer pairing

    Science.gov (United States)

    Fan, H. H.; Krotscheck, E.; Lichtenegger, T.; Mateo, D.; Zillich, R. E.

    2015-08-01

    We present ground-state calculations for low-density Fermi gases described by two model interactions, an attractive square-well potential and a Lennard-Jones potential, of varying strength. We use the optimized Fermi-hypernetted chain integral equation method, which has been proved to provide, in the density regimes of interest here, an accuracy of better than 1%. We first examine the low-density expansion of the energy and compare it with the exact answer of H. Huang and C. N. Yang [Phys. Rev. 105, 767 (1957), 10.1103/PhysRev.105.767]. It is shown that a locally correlated wave function of the Jastrow-Feenberg type does not recover the quadratic term in the expansion of the energy in powers of a0kF , where a0 is the vacuum s -wave scattering length and kF the Fermi wave number. The problem is cured by adding second-order perturbation corrections in a correlated basis. Going to higher densities and/or more strongly coupled systems, we encounter an instability of the normal state of the system which is characterized by a divergence of the in-medium scattering length. We interpret this divergence as a phonon-exchange-driven dimerization of the system, similar to what occurs at zero density when the vacuum scattering length a0 diverges. We then study, in the stable regime, the superfluid gap and its dependence on the density and the interaction strength. We identify two corrections to low-density expansions: One is medium corrections to the pairing interaction, and the other is finite-range corrections. We show that the most important finite-range corrections are a direct manifestation of the many-body nature of the system.

  15. 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.

  16. systems

    Directory of Open Access Journals (Sweden)

    Patrick L. Brockett

    1978-01-01

    Full Text Available Suppose S={{Xnj,   j=1,2,…,kn}} is an infinitesimal system of random variables whose centered sums converge in law to a (necessarily infinitely divisible distribution with Levy representation determined by the triple (γ,σ2,M. If {Yj,   j=1,2,…} are independent indentically distributed random variables independent of S, then the system S′={{YjXnj,j=1,2,…,kn}} is obtained by randomizing the scale parameters in S according to the distribution of Y1. We give sufficient conditions on the distribution of Y in terms of an index of convergence of S, to insure that centered sums from S′ be convergent. If such sums converge to a distribution determined by (γ′,(σ′2,Λ, then the exact relationship between (γ,σ2,M and (γ′,(σ′2,Λ is established. Also investigated is when limit distributions from S and S′ are of the same type, and conditions insuring products of random variables belong to the domain of attraction of a stable law.

  17. 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.

  18. 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

  19. 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.

  20. Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures.

    Science.gov (United States)

    Chatzieleftheriou, Stavros; Adendorff, Matthew R; Lagaros, Nikos D

    2016-10-24

    The potential energy of molecules and nanostructures is commonly calculated in the molecular mechanics formalism by superimposing bonded and nonbonded atomic energy terms, i.e. bonds between two atoms, bond angles involving three atoms, dihedral angles involving four atoms, nonbonded terms expressing the Coulomb and Lennard-Jones interactions, etc. In this work a new, generalized numerical simulation is presented for studying the mechanical behavior of three-dimensional nanostructures at the atomic scale. The energy gradient and Hessian matrix of such assemblies are usually computed numerically; a potential energy finite element model is proposed herein where these two components are expressed analytically. In particular, generalized finite elements are developed that express the interactions among atoms in a manner equivalent to that invoked in simulations performed based on the molecular dynamics method. Thus, the global tangent stiffness matrix for any nanostructure is formed as an assembly of the generalized finite elements and is directly equivalent to the Hessian matrix of the potential energy. The advantages of the proposed model are identified in terms of both accuracy and computational efficiency. In the case of popular force fields (e.g., CHARMM), the computation of the Hessian matrix by implementing the proposed method is of the same order as that of the gradient. This analysis can be used to minimize the potential energy of molecular systems under nodal loads in order to derive constitutive laws for molecular systems where the entropy and solvent effects are neglected and can be approximated as solids, such as double stranded DNA nanostructures. In this context, the sequence dependent stretch modulus for some typical base pairs step is calculated.

  1. 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.

  2. Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains.

    Science.gov (United States)

    Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A

    2011-05-19

    A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. © 2011 American Chemical Society

  3. Determining force field parameters using a physically based equation of state.

    Science.gov (United States)

    van Westen, Thijs; Vlugt, Thijs J H; Gross, Joachim

    2011-06-23

    Force field parameters used in classical molecular simulations can be estimated from quantum mechanical calculations or spectroscopic measurements. This especially applies to bonded interactions such as bond-stretching, bond-bending, and torsional interactions. However, it is difficult and computational expensive to obtain accurate parameters describing the nonbonded van der Waals interactions from quantum mechanics. In many studies, these parameters are adjusted to reproduce experimental data, such as vapor-liquid equilibria (VLE) data. Adjusting these force field parameters to VLE data is currently a cumbersome and computationally expensive task. The reason is that the result of a calculation of the vapor-liquid equilibria depends on the van der Waals interactions of all atom types in the system, therefore requiring many time-consuming iterations. In this work, we use an analytical equation of state, the perturbed chain statistical associating fluid theory (PC-SAFT), to predict the results of molecular simulations for VLE. The analytical PC-SAFT equation of state is used to approximate the objective function f(p) as a function of the array of force field parameters p. The objective function is here for example defined as the deviations of vapor pressure, enthalpy of vaporization and liquid density data, with respect to experimental data. The parameters are optimized using the analytical PC-SAFT equation of state, which is orders of magnitude quicker to calculate than molecular simulation. The solution is an excellent approximation of the real objective function, so that the resulting method requires only very few molecular simulation runs to converge. The method is here illustrated by optimizing transferable Lennard-Jones parameters for the n-alkane series. Optimizing four force field parameters p = (ε(CH(2))(CH(2)), ε(CH(3))(CH(3)), σ(CH(2))(CH(2)), σ(CH(3))(CH(3))) we obtain excellent agreement of coexisting densities, vapor pressure and caloric properties

  4. Local pressure components and interfacial tensions of a liquid film in the vicinity of a solid surface with a nanometer-scale slit pore obtained by the perturbative method.

    Science.gov (United States)

    Fujiwara, K; Shibahara, M

    2015-03-07

    A classical molecular dynamics simulation was conducted for a liquid-solid interfacial system with a nanometer-scale slit pore in order to reveal local thermodynamic states: local pressure components and interfacial tensions of a liquid film in the vicinity of the slit. The simulation also examined the transition mechanism between the two states of the liquid film: (a) liquid film on the slit and (b) liquid film in the slit, based on the local thermodynamic quantities from a molecular point of view. An instantaneous expression of the local pressure components and interfacial tensions, which is based on a volume perturbation, was presented to investigate time-dependent phenomena in molecular dynamics simulations. The interactions between the particles were described by the 12-6 Lennard-Jones potential, and effects of the fluid-solid interaction intensity on the local pressure components and interfacial tensions of the fluid in the vicinity of the slit were examined in detail by the presented perturbative method. The results revealed that the local pressure components tangential to the solid surface in the vicinity of the 1st fluid layer from the solid surface are different in a two dimensional plane, and the difference became pronounced in the vicinity of the corner of the slit, for cases where the fluid-solid interaction intensities are relatively strong. The results for the local interfacial tensions of the fluid inside the slit suggested that the local interfacial tensions in the vicinity of the 2nd and 3rd layers of the solid atoms from the entrance of the slit act as a trigger for the transition between the two states under the influence of a varying fluid-solid interaction.

  5. 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.

  6. 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.

  7. Scaling of viscous dynamics in simple liquids

    DEFF Research Database (Denmark)

    Bøhling, Lasse; Ingebrigtsen, Trond; Grzybowski, A.

    2012-01-01

    Supercooled liquids are characterized by relaxation times that increase dramatically by cooling or compression. From a single assumption follows a scaling law according to which the relaxation time is a function of h(ρ) over temperature, where ρ is the density and the function h(ρ) depends...... on the liquid in question. This scaling is demonstrated to work well for simulations of the Kob–Andersen binary Lennard-Jones mixture and two molecular models, as well as for the experimental results for two van der Waals liquids, dibutyl phthalate and decahydroisoquinoline. The often used power-law density...... scaling, h(ρ)∝ργ, is an approximation to the more general form of scaling discussed here. A thermodynamic derivation was previously given for an explicit expression for h(ρ) for liquids of particles interacting via the generalized Lennard-Jones potential. Here a statistical mechanics derivation is given...

  8. 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....

  9. 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

  10. 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.

  11. 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.

  12. Modeling of Hydraulic Fracturing on the Basis of the Particle Method

    Science.gov (United States)

    Berezhnoi, D. V.; Gabsalikova, N. F.; Izotov, V. G.; Miheev, V. V.

    2018-01-01

    A technique of calculating the deformation of the soil environment when it interacts with a liquid on the basis of the particle method a is realized. To describe the behavior of the solid and liquid phases of the soil, a classical two-parameter Lennard-Jones interaction potential and its modified version proposed by the authors were chosen. The model problem of deformation and partial destruction of a soil massif under strong pressure from the liquid pumped into it is solved. Analysis of the results shows that the use of the modified Lennard-Jones potential for describing the solid phase of the soil environment makes it possible to describe the process of formation of cracks in the soil during hydraulic fracturing of the formation.

  13. Blood Clotting Inspired Polymer Physics

    Science.gov (United States)

    Sing, Charles Edward

    The blood clotting process is one of the human body's masterpieces in targeted molecular manipulation, as it requires the activation of the clotting cascade at a specific place and a specific time. Recent research in the biological sciences have discovered that one of the protein molecules involved in the initial stages of the clotting response, von Willebrand Factor (vWF), exhibits counterintuitive and technologically useful properties that are driven in part by the physical environment in the bloodstream at the site of a wound. In this thesis, we take inspiration from initial observations of the vWF in experiments, and aim to describe the behaviors observed in this process within the context of polymer physics. By understanding these physical principles, we hope to harness nature's ability to both direct molecules in both spatial and conformational coordinates. This thesis is presented in three complementary sections. After an initial introduction describing the systems of interest, we first describe the behavior of collapsed Lennard-Jones polymers in the presence of an infinite medium. It has been shown that simple bead-spring homopolymer models describe vWF quite well in vitro. We build upon this previous work to first describe the behavior of a collapsed homopolymer in an elongational fluid flow. Through a nucleation-protrusion mechanism, scaling relationships can be developed to provide a clear picture of a first-order globule-stretch transition and its ramifications in dilute-solution rheology. The implications of this behavior and its relation to the current literature provides qualitative explanations for the physiological process of vasoconstriction. In an effort to generalize these observations, we present an entire theory on the behavior of polymer globules under influence of any local fluid flow. Finally, we investigate the internal dynamics of these globules by probing their pulling response in an analogous fashion to force spectroscopy. We elucidate

  14. How reliable is the HMSA integral equation for the pair structure of supercooled and amorphous mixtures?

    International Nuclear Information System (INIS)

    Kaddour, F.O.; Pastore, G.

    1993-07-01

    Accurate Molecular Dynamics calculations on highly asymmetric Lennard-Jones mixtures have been performed to check in rather extreme cases the ability of the self-consistent HMSA integral equation to predict the pair correlations in supercooled and glassy mixtures. We find that, in the supercooled region, the HMSA is a reasonable approximation for the structural properties and thermodynamics properties, but systematic deviations from MD data appear when the glass transition is approached. (author). 12 refs, 4 figs, 1 tab

  15. 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.

  16. 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.

  17. 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…

  18. 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.

  19. Intermolecular interactions and the thermodynamic properties of supercritical fluids.

    Science.gov (United States)

    Yigzawe, Tesfaye M; Sadus, Richard J

    2013-05-21

    The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of β = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids.

  20. Molecular simulation of adsorption and transport diffusion of model fluids in carbon nanotubes

    Science.gov (United States)

    Düren, Tina; Keil, Frerich J.; Seaton, Nigel A.

    Grand canonical Monte Carlo (GCMC) and dual-control-volume grand canonical molecular dynamics (DCV-GCMD) simulations were carried out with Lennard-Jones model fluids in carbon nanotubes, with the objective of investigating the effect of varying molecular properties on adsorption and diffusion. The influence of the molecular weight, and the Lennard Jones parameters σ (a measure of the molecule size) and ɛ (a measure of the interaction strength) on adsorption isotherms, fluxes, and transport diffusivities was studied. For these simulations, the properties of component 1 in the mixture were held constant and one of the properties of component 2 was changed systematically. Furthermore, the validity of Graham's law, which relates the fluxes of two counter diffusing species to their molecular weight, was investigated on a molecular level. Graham's law is fulfilled for the whole range of molecular weights and Lennard-Jones parameters σ investigated. However, large deviations were observed for large values of ɛ2. Here, the interaction of the two components in the mixture becomes so strong that component 1 is dragged along by component 2.

  1. 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.

  2. The Enigmatic Nature of the Israeli Legal System

    African Journals Online (AJOL)

    RV

    of New London.5 A third party transfer occurs when the state expropriates property. *. Bradley Virgill ... Rubenfield 1993 Yale LJ 1077-1163 advocates an extreme version of this narrow interpretation of the public use ... O'Connor stated that "[t]he [Supreme] Court long ago rejected any literal requirement that condemned ...

  3. Quantum transport in one-dimensional systems via a master ...

    Indian Academy of Sciences (India)

    1Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, C.P. 62132,. Cuernavaca, Morelos, Mexico. 2Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana,. Jadranska 19, SI-1000 Ljubljana, Slovenia. E-mail: marko.znidaric@fmf.uni-lj.si. Abstract. We discuss recent findings ...

  4. Molecular Force Fields for Aqueous Electrolytes: SPC/E-Compatible Charged LJ Sphere Models and Their Limitations

    Czech Academy of Sciences Publication Activity Database

    Moučka, F.; Nezbeda, Ivo; Smith, W. R.

    2013-01-01

    Roč. 138, č. 15 (2013), s. 154102 ISSN 0021-9606 Grant - others:GA MŠMT(CZ) LH12019; GA ČR(CZ) GAP208/12/0105; NSERCC(CA) OGP1041 Institutional support: RVO:67985858 Keywords : free-energy * computer- simulation * water Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.122, year: 2013

  5. (I lJ.6 - 55 Department of B iochemistr~. Lni,erstl) of.fos. Jos

    African Journals Online (AJOL)

    BSN

    used. The rats were random!) distributed into four groups (A-D• (3 rats per group) and kept in mctabol ic cages. The rats were allowed to stabi I ize on tht normal laborat01") feed for three cla)s thereafter. staned for 2-t hours before feeding \\\\it.i the experimental diets as follows: Group A \\\\Cre fed diet I. Group B \\\\ere fed diet 2.

  6. Results of the radiological verification survey of the partial remediation at 90 Avenue C, Lodi, New Jersey (LJ079V)

    International Nuclear Information System (INIS)

    Foley, R.D.; Johnson, C.A.

    1994-02-01

    The property at 90 Avenue C, Lodi, New Jersey is one of the vicinity properties of the former Maywood Chemical Works, Maywood, New Jersey designated for remedial action by the US Department of Energy (DOE). In July 1991, Bechtel National, Inc. performed a partial remedial action on this property. At the request of DOE, a team from Oak Ridge National Laboratory conducted an independent radiological verification survey in July, 1991 at this site. The purpose of the verification survey was to ensure the effectiveness of remedial actions performed within FUSRAP and to confirm the site's compliance with DOE guidelines. The radiological survey included surface gamma scans indoors and outdoors, ground-level beta-gamma measurements, and systematic and biased soil and material sampling. Results of the verification survey demonstrated that all radiological measurements on the portions of the property that had been remediated were within DOE guidelines. However, there still remains a portion of the property to be remediated that is not covered by this verification survey

  7. 78 FR 65235 - Special Conditions: Learjet Inc., Model LJ-200-1A10 Airplane; Crashworthiness, Emergency Landing...

    Science.gov (United States)

    2013-10-31

    ... the state of technology envisioned in the airworthiness standards for transport category airplanes... (425) 227-1320. SUPPLEMENTARY INFORMATION: Comments Invited We invite interested people to take part in... assessment is largely dependent on the similarities and differences between the new type design and...

  8. L.J. van der Veen et S. Bodinga-bwa-Bodinga. Gedandedi sa Geviya/ Dictionnaire Geviya?Fran?ais

    Directory of Open Access Journals (Sweden)

    P.A. Mavoungou

    2011-10-01

    Full Text Available La parution aux ?ditions Peeters de l'ouvrage de r?f?rence lexicographique intitul? Gedandedi sa Geviya/Dictionnaire Geviya?Fran?ais (en abr?g? DGF dans les reste de l'article a ?t? accueilli avec joie et fiert? aussi bien par les locuteurs geviya1 en particulier que par les Gabonais en g?n?ral. Ce dictionnaire, r?sultat d'une longue et fructueuse collaboration scientifique entre Lolke van der Veen et S?bastien Bodinga-bwa-Bodinga, marque le d?but d'une nouvelle ?re dans la r?daction des dictionnaires au Gabon. En effet, la majorit? des ouvrages de r?f?rence lexicographique disponibles dans les langues gabonaises sont des dictionnaires bilingues r?dig?s par les missionnaires catholiques et protestants ou par les administrateurs coloniaux dans la p?riode allant de 1800 ? 1960, date de l'accession du Gabon ? la souverainet? internationale (Nyangone Assam et Mavoungou 2000, Mavoungou 2001.

  9. An Operational Analysis of System Calibration.

    Science.gov (United States)

    1984-09-01

    CONCLUSION The purpose of this thesis has been to show that mathe - matical models, augmented by a computer simulation program, can provide useful ways of...34VC-H LLi > CL )- 0 r-~1LL Li 0-~iC Li .Ci-O " IL HA - .U-LJi~C~ .i .---Z 00 UCJ CU CLIL . L L 4.H CC - HHt EIfH’! Z -+F- -- =LjC~r 4f4 - U Li LiJ i- F

  10. Hyperkalemic periodic paralysis

    Science.gov (United States)

    ... Rott K, Rudel R, Lehmann-Horn F. Muscle channelopathies: myotonias and periodic paralyses. In: Darras BT, Jones ... Elsevier; 2015:chap 38. Kerchner GA, Ptacek LJ. Channelopathies: episodic and electrical disorders of nervous system. In: ...

  11. Cost effective system for monitoring of fish migration with a camera

    Science.gov (United States)

    Sečnik, Matej; Brilly, Mitja; Vidmar, Andrej

    2016-04-01

    Within the European LIFE project Ljubljanica connects (LIFE10 NAT/SI/000142) we have developed a cost-effective solution for the monitoring of fish migration through the fish passes with the underwater camera. In the fish pass at Ambrožev trg and in the fish pass near the Fužine castle we installed a video camera called "Fishcam" to be able to monitor the migration of fish through the fish passes and success of its reconstruction. Live stream from fishcams installed in the fishpassesis available on our project website (http://ksh.fgg.uni-lj.si/ljubljanicaconnects/ang/12_camera). The system for the fish monitoring is made from two parts. First is the waterproof box for the computer with charger and the second part is the camera itself. We used a high sensitive Sony analogue camera. The advantage of this camera is that it has very good sensitivity in low light conditions, so it can take good quality pictures even at night with a minimum additional lighting. For the night recording we use additional IR reflector to illuminate passing fishes. The camera is connected to an 8-inch tablet PC. We decided to use a tablet PC because it is quite small, cheap, it is relatively fast and has a low power consumption. On the computer we use software which has advanced motion detection capabilities, so we can also detect the small fishes. When the fish is detected by a software, its photograph is automatically saved to local hard drive and for backup also on Google drive. The system for monitoring of fish migration has turned out to work very well. From the beginning of monitoring in June 2015 to end of the year there were more than 100.000 photographs produced. The first analysis of them was already prepared estimating fish species and their frequency in passing the fish pass.

  12. Two putative-aquaporin genes are differentially expressed during arbuscular mycorrhizal symbiosis in Lotus japonicus

    Directory of Open Access Journals (Sweden)

    Giovannetti Marco

    2012-10-01

    Full Text Available Abstract Background Arbuscular mycorrhizas (AM are widespread symbioses that provide great advantages to the plant, improving its nutritional status and allowing the fungus to complete its life cycle. Nevertheless, molecular mechanisms that lead to the development of AM symbiosis are not yet fully deciphered. Here, we have focused on two putative aquaporin genes, LjNIP1 and LjXIP1, which resulted to be upregulated in a transcriptomic analysis performed on mycorrhizal roots of Lotus japonicus. Results A phylogenetic analysis has shown that the two putative aquaporins belong to different functional families: NIPs and XIPs. Transcriptomic experiments have shown the independence of their expression from their nutritional status but also a close correlation with mycorrhizal and rhizobial interaction. Further transcript quantification has revealed a good correlation between the expression of one of them, LjNIP1, and LjPT4, the phosphate transporter which is considered a marker gene for mycorrhizal functionality. By using laser microdissection, we have demonstrated that one of the two genes, LjNIP1, is expressed exclusively in arbuscule-containing cells. LjNIP1, in agreement with its putative role as an aquaporin, is capable of transferring water when expressed in yeast protoplasts. Confocal analysis have demonstrated that eGFP-LjNIP1, under its endogenous promoter, accumulates in the inner membrane system of arbusculated cells. Conclusions Overall, the results have shown different functionality and expression specificity of two mycorrhiza-inducible aquaporins in L. japonicus. One of them, LjNIP1 can be considered a novel molecular marker of mycorrhizal status at different developmental stages of the arbuscule. At the same time, LjXIP1 results to be the first XIP family aquaporin to be transcriptionally regulated during symbiosis.

  13. Molecular interactions and thermal transport in ionic liquids with carbon nanomaterials.

    Science.gov (United States)

    França, João M P; Nieto de Castro, Carlos A; Pádua, Agílio A H

    2017-07-05

    We used molecular dynamics simulation to study the effect of suspended carbon nanomaterials, nanotubes and graphene sheets, on the thermal conductivity of ionic liquids, an issue related to understanding the properties of nanofluids. One important aspect that we developed is an atomistic model of the interactions between the organic ions and carbon nanomaterials, so we did not rely on existing force fields for small organic molecules or assume simple combining rules to describe the interactions at the liquid/material interface. Instead, we used quantum calculations with a density functional suitable for non-covalent interactions to parameterize an interaction model, including van der Waals terms and also atomic partial charges on the materials. We fitted a n-m interaction potential function with n values of 9 or 10 and m values between 5 and 8, so a 12-6 Lennard-Jones function would not fit the quantum calculations. For the atoms of ionic liquids and carbon nanomaterials interacting among themselves, we adopted existing models from the literature. We studied the imidazolium ionic liquids [C 4 C 1 im][SCN], [C 4 C 1 im][N(CN) 2 ], [C 4 C 1 im][C(CN) 3 ] and [C 4 C 1 im][(CF 3 SO 2 ) 2 N]. Attraction is stronger for cations (than for anions) above and below the π-system of the nanomaterials, whereas anions show stronger attraction for the hydrogenated edges. The ordering of ions around and inside (7,7) and (10,10) single-walled nanotubes, and near a stack of graphene sheets, was analysed in terms of density distribution functions. We verified that anions are found, as well as cations, in the first interfacial layer interacting with the materials, which is surprising given the interaction potential surfaces. The thermal conductivity of the ionic liquids and of composite systems containing one nanotube or one graphene stack in suspension was calculated using non-equilibrium molecular dynamics. Thermal conductivity was calculated along the axis of the nanotube and

  14. Quantum population and entanglement evolution in photosynthetic process

    Science.gov (United States)

    Zhu, Jing

    Applications of the concepts of quantum information theory are usually related to the powerful and counter-intuitive quantum mechanical effects of superposition, interference and entanglement. In this thesis, I examine the role of coherence and entanglement in complex chemical systems. The research has focused mainly on two related projects: The first project is developing a theoretical model to explain the recent ultrafast experiments on excitonic migration in photosynthetic complexes that show long-lived coherence of the order of hundreds of femtoseconds and the second project developing the Grover algorithm for global optimization of complex systems. The first part can be divided into two sections. The first section is investigating the theoretical frame about the transfer of electronic excitation energy through the Fenna-Matthews-Olson (FMO) pigment-protein complex. The new developed modified scaled hierarchical equation of motion (HEOM) approach is employed for simulating the open quantum system. The second section is investigating the evolution of entanglement in the FMO complex based on the simulation result via scaled HEOM approach. We examine the role of multipartite entanglement in the FMO complex by direct computation of the convex roof optimization for a number of different measures, including pairwise, triplet, quadruple and quintuple sites entanglement. Our results support the hypothesis that multipartite entanglement is maximum primary along the two distinct electronic energy transfer pathways. The second part of this thesis can be separated into two sections. The first section demonstrated that a modified Grover's quantum algorithm can be applied to real problems of finding a global minimum using modest numbers of quantum bits. Calculations of the global minimum of simple test functions and Lennard-Jones clusters have been carried out on a quantum computer simulator using a modified Grover's algorithm. The second section is implementing the basic

  15. More appropriate information systems and services for the social scientist: time to put our findings to work

    NARCIS (Netherlands)

    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

  16. Simulation of self-assembled nanopatterns in binary alloys on the fcc(111) surface

    Energy Technology Data Exchange (ETDEWEB)

    Weber, Sebastian

    2008-07-01

    In this PhD thesis, we study the heteroepitaxial crystal growth by means of Monte Carlo simulations. Of particular interest in this work is the influence of the lattice mismatch of the adsorbates relative to the substrate on surface structures. In the framework of an off-lattice model, we consider one monolayer of adsorbate and investigate the emerging nanopatterns in equilibrium and their formation during growth. In chapter 1, a brief introduction is given, which describes the role of computer simulations in the field of the physics of condensed matter. Chapter 2 is devoted to some technical basics of experimental methods of molecular beam epitaxy and the theoretical description. Before a model for the simulation can be designed, it is necessary to make some considerations of the single processes which occur during epitaxial growth. For that purpose we look at an experimental setup and extract the main microscopic processes. Afterwards a brief overview of different theoretical concepts describing that physical procedures is given. In chapter 3, the model used in the simulations is presented. The aim is to investigate the growth of an fcc crystal in the [111] direction. In order to keep the simulation times within a feasible limit a simple pair potential, the Lennard-Jones potential, with continuous particle positions is used, which are necessary to describe effects resulting from the atomic mismatch in the crystal. Furthermore the detailed algorithm is introduced which is based on the idea to calculate the barrier of each diffusion event and to use the barriers in a rejection-free method. Chapter 4 is attended to the simulation of equilibrium. The influence of different parameters on the emerging structures in the first monolayer upon the surface, which is completely covered with two adsorbate materials, is studied. Especially the competition between binding energy and strain leads to very interesting pattern formations like islands or stripes. In chapter 5 the

  17. Fitting Vibrational Energy Parameters to Falloff Experiments: CH3 + CH3 + He (0.6-2 Torr 200-298 K)

    Science.gov (United States)

    Tardy, Dwight C.; Cody, Regina J.; Payne, Walter A.; Thorn, R. Peyton; Nesbitt, Fred L.; Iannone, Mark A.; Stief, Louis J.; Vondrak, Richard R. (Technical Monitor)

    2001-01-01

    There are many reported experiments and theoretical calculations for the combination of methyl free radicals diluted in a non-reactive 'deactivator. At high pressure the ethane (C2H6) combination product is the sole product; with decreasing pressure the chemically activated C2H6 will decompose. The falloff in the observed rate coefficient is the result of the competition between collisional stabilization of the chemically activated CA and unimolecular decomposition. The dependence of the rate coefficient on pressure, temperature and collision properties is complex and can not be calculated from first principles. The understanding of this system is not only of fundamental importance but is relevant to the recent detection of methyl free radicals in the atmospheres of Saturn - and Neptune. The temperatures of these outer planet atmospheres are in the 140-200 K region with total pressures (predominately H2 and He) less than 0.2 Torr. Experimentally determined rate coefficients have been reported for this reaction at T = 296-906 K and T = 200-408 K mostly with argon as the deactivator. At T = 200 K only the high pressure rate coefficient has been determined. Complete falloff curves over a wide temperature range (200-1600 K) with a variety of weak collider models used to simulate argon as the deactivator have also been reported by Klippenstein and Harding (KH). More recently we have reported the experimental rate coefficients in the falloff region with helium as the deactivator at 200 and 298 K. In this paper we have used the calculated falloff curves reported by KH for argon to determine the average energy transferred per collision for helium in our recently reported experiments. Collision rates were converted using Lennard Jones parameters; the temperature dependence of this conversion factor is noted. The helium experiments were consistent with a down of approximately 100 cm (exp-1); the temperature dependence was slight. The magnitude of down and its temperature

  18. Particle rearrangement and softening contributions to the nonlinear mechanical response of glasses

    Science.gov (United States)

    Fan, Meng; Zhang, Kai; Schroers, Jan; Shattuck, Mark D.; O'Hern, Corey S.

    2017-09-01

    Amorphous materials such as metallic, polymeric, and colloidal glasses exhibit complex preparation-dependent mechanical response to applied shear. In particular, glassy solids yield, with a mechanical response that transitions from elastic to plastic, with increasing shear strain. We perform numerical simulations to investigate the mechanical response of binary Lennard-Jones glasses undergoing athermal, quasistatic pure shear as a function of the cooling rate R used to prepare them. The ensemble-averaged stress versus strain curve 〈σ (γ )〉 resembles the spatial average in the large size limit, which appears smooth and displays a putative elastic regime at small strains, a yielding-related peak in stress at intermediate strain, and a plastic flow regime at large strains. In contrast, for each glass configuration in the ensemble, the stress-strain curve σ (γ ) consists of many short nearly linear segments that are punctuated by particle-rearrangement-induced rapid stress drops. To explain the nonlinearity of 〈σ (γ )〉 , we quantify the shape of the small stress-strain segments and the frequency and size of the stress drops in each glass configuration. We decompose the stress loss [i.e., the deviation in the slope of 〈σ (γ )〉 from that at 〈σ (0 )〉 ] into the loss from particle rearrangements and the loss from softening [i.e., the reduction of the slopes of the linear segments in σ (γ ) ], and then compare the two contributions as a function of R and γ . For the current studies, the rearrangement-induced stress loss is larger than the softening-induced stress loss, however, softening stress losses increase with decreasing cooling rate. We also characterize the structure of the potential energy landscape along the strain direction for glasses prepared with different R , and observe a dramatic change of the properties of the landscape near the yielding transition. We then show that the rearrangement-induced energy loss per strain can serve as

  19. Pyrazine in supercritical xenon: local number density defined by experiment and calculation.

    Science.gov (United States)

    Hrnjez, Bruce J; Kabarriti, Abdo; Dach, Benjamin I; Buldyrev, Sergey V; Asherie, Neer; Natanov, Georgiy R; Balderman, Joshua

    2008-12-04

    Toward our goal of using supercritical fluids to study solvent effects in physical and chemical phenomena, we develop a method to spatially define the solvent local number density at the solute in the highly compressible regime of a supercritical fluid. Experimentally, the red shift of the pyrazine n-pi* electronic transition was measured at high dilution in supercritical xenon as a function of pressure from 0 to approximately 24 MPa at two temperatures: one (293.2 K) close to the critical temperature and the other (333.2 K) remote. Computationally, several representative stationary points were located on the potential surfaces for pyrazine and 1, 2, 3, and 4 xenons at the MP2/6-311++G(d,p)/aug-cc-pVTZ-PP level. The vertical n-pi* ((1)B(3u)) transition energies were computed for these geometries using a TDDFT/B3LYP/DGDZVP method. The combination of experiment and quantum chemical computation allows prediction of supercritical xenon bulk densities at which the pyrazine primary solvation shell contains an average of 1, 2, 3, and 4 xenon molecules. These density predictions were achieved by graphical superposition of calculated shifts on the experimental shift versus density curves for 293.2 and 333.2 K. Predicted bulk densities are 0.50, 0.91, 1.85, and 2.50 g cm(-3) for average pyrazine primary solvation shell occupancy by 1, 2, 3, and 4 xenons at 293.2 K. Predicted bulk densities are 0.65, 1.20, 1.85, and 2.50 g cm(-3) for average pyrazine primary solvation shell occupancy by 1, 2, 3, and 4 xenons at 333.2 K. These predictions were evaluated with classical Lennard-Jones molecular dynamics simulations designed to replicate experimental conditions at the two temperatures. The average xenon number within 5.0 A of the pyrazine center-of-mass at the predicted densities is 1.3, 2.1, 3.0, and 4.0 at both simulation temperatures. Our three-component method-absorbance measurement, quantum chemical prediction, and evaluation of prediction with classical molecular dynamics

  20. The Evolution of the Information Systems Manager.

    Science.gov (United States)

    1982-12-01

    Print. it is no lonqer in publication . In fact Harrell did not use the oriainal edition of the survey, he and his associates used a revised edition with a...rshp.12910 Vol. 26, No. 1, 1.7 3, pp. 127-34. 16. Edwards, A.., " Manual for th Edwards Personal Prefererence Schedule," The Pschological orp, N.Y...December, 1982 L~j Thesis Advisor: ,John Senger Approved for Public Release; Distribution Unlimited Au (i secume~v cLiaincaea o This PSEE 1Pm as

  1. Lie algebra symmetries and quantum phase transitions in nuclei

    Indian Academy of Sciences (India)

    2014-04-05

    Apr 5, 2014 ... li and S+(2) = ∑q j=1 b† lj. · b† lj . For the combined system, the pair creation operator S+ = S+(1) − S+(2) and annihilation operator is S− = (S+)†. Note that S+S− is related to the quadratic Casimir invariant of SO(n1 + n2) in a simple manner. Now, N-boson coherent state can be written as [19]. |N,α 〉 = 1. √.

  2. Identification and Expression Analysis of Medicago truncatula Isopentenyl Transferase Genes (IPTs Involved in Local and Systemic Control of Nodulation

    Directory of Open Access Journals (Sweden)

    Mahboobeh Azarakhsh

    2018-03-01

    Full Text Available Cytokinins are essential for legume plants to establish a nitrogen-fixing symbiosis with rhizobia. Recently, the expression level of cytokinin biosynthesis IPTs (ISOPENTENYLTRANSFERASES genes was shown to be increased in response to rhizobial inoculation in Lotus japonicus, Medicago truncatula and Pisum sativum. In addition to its well-established positive role in nodule primordium initiation in root cortex, cytokinin negatively regulates infection processes in the epidermis. Moreover, it was reported that shoot-derived cytokinin inhibits the subsequent nodule formation through AON (autoregulation of nodulation pathway. In L. japonicus, LjIPT3 gene was shown to be activated in the shoot phloem via the components of AON system, negatively affecting nodulation. However, in M. truncatula, the detailed analysis of MtIPTs expression, both in roots and shoots, in response to nodulation has not been performed yet, and the link between IPTs and AON has not been studied so far. In this study, we performed an extensive analysis of MtIPTs expression levels in different organs, focusing on the possible role of MtIPTs in nodule development. MtIPTs expression dynamics in inoculated roots suggest that besides its early established role in the nodule primordia development, cytokinin may be also important for later stages of nodulation. According to expression analysis, MtIPT3, MtIPT4, and MtIPT5 are activated in the shoots in response to inoculation. Among these genes, MtIPT3 is the only one the induction of which was not observed in leaves of the sunn-3 mutant defective in CLV1-like kinase, the key component of AON, suggesting that MtIPT3 is activated in the shoots in an AON-dependent manner. Taken together, our findings suggest that MtIPTs are involved in the nodule development at different stages, both locally in inoculated roots and systemically in shoots, where their expression can be activated in an AON-dependent manner.

  3. Thermal motion in proteins: Large effects on the time-averaged interaction energies

    Energy Technology Data Exchange (ETDEWEB)

    Goethe, Martin, E-mail: martingoethe@ub.edu; Rubi, J. Miguel [Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona (Spain); Fita, Ignacio [Institut de Biologia Molecular de Barcelona, Baldiri Reixac 10, 08028 Barcelona (Spain)

    2016-03-15

    As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

  4. Exponential and Bessel fitting methods for the numerical solution of the Schroedinger equation

    International Nuclear Information System (INIS)

    Raptis, A.D.; Cash, J.R.

    1987-01-01

    A new method is developed for the numerical integration of the one dimensional radial Schroedinger equation. This method involves using different integration formulae in different parts of the range of integration rather than using the same integration formula throughout. Two new integration formulae are derived, one which integrates Bessel and Neumann functions exactly and another which exactly integrates certain exponential functions. It is shown that, for large r, these new formulae are much more accurate than standard integration methods for the Schroedinger equation. The benefit of using this new approach is demonstrated by considering some numerical examples based on the Lennard-Jones potential. (orig.)

  5. A new shared-memory programming paradigm for molecular dynamics simulations on the Intel Paragon

    Energy Technology Data Exchange (ETDEWEB)

    D`Azevedo, E.F.; Romine, C.H.

    1994-12-01

    This report describes the use of shared memory emulation with DOLIB (Distributed Object Library) to simplify parallel programming on the Intel Paragon. A molecular dynamics application is used as an example to illustrate the use of the DOLIB shared memory library. SOTON-PAR, a parallel molecular dynamics code with explicit message-passing using a Lennard-Jones 6-12 potential, is rewritten using DOLIB primitives. The resulting code has no explicit message primitives and resembles a serial code. The new code can perform dynamic load balancing and achieves better performance than the original parallel code with explicit message-passing.

  6. Isomorphs in the phase diagram of a model liquid without inverse power law repulsion

    DEFF Research Database (Denmark)

    Veldhorst, Arnold Adriaan; Bøhling, Lasse; Dyre, J. C.

    2012-01-01

    scattering function are calculated. The results are shown to reflect a hidden scale invariance; despite its exponential repulsion the Buckingham potential is well approximated by an inverse power-law plus a linear term in the region of the first peak of the radial distribution function. As a consequence...... the dynamics of the viscous Buckingham liquid is mimicked by a corresponding model with purely repulsive inverse-power-law interactions. The results presented here closely resemble earlier results for Lennard-Jones type liquids, demonstrating that the existence of strong correlations and isomorphs does...... not depend critically on the mathematical form of the repulsion being an inverse power law....

  7. Ideal and defective vertex configurations in the planar octagonal quasilattice

    Science.gov (United States)

    Baake, M.; Joseph, D.

    1990-11-01

    The well-known two-dimensional octagonal quasilattice is realized by means of dualization and Klotz construction. We discuss the geometric properties and the extended symmetry of the pattern. The concept of geometric defects is introduced, and an elastic energy measure ΔE is presented that allows a simple sequencing of the forbidden vertices. After a sketchy comparison with Lennard-Jones calculations, some thermodynamic consequences of ΔE are discussed. It turns out that the specific heat should show a significant increase in comparison with the crystallographic case.

  8. Variation along liquid isomorphs of the driving force for crystallization

    DEFF Research Database (Denmark)

    Pedersen, Ulf Rørbæk; Adrjanowicz, Karolina; Niss, Kristine

    2017-01-01

    at a reference temperature. More general analysis allows interpretation of experimental data for molecular liquids such as dimethyl phthalate and indomethacin, and suggests that the isomorph scaling exponent γ in these cases is an increasing function of density, although this cannot be seen in measurements......We investigate the variation of the driving force for crystallization of a supercooled liquid along isomorphs, curves along which structure and dynamics are invariant. The variation is weak, and can be predicted accurately for the Lennard-Jones fluid using a recently developed formalism and data...

  9. Transport properties of N2 gas at cryogenic temperatures. [computation of viscosity and thermal conductivity

    Science.gov (United States)

    Pearson, W. E.

    1974-01-01

    The viscosity and thermal conductivity of nitrogen gas for the temperature range 5 K - 135 K have been computed from the second Chapman-Enskog approximation. Quantum effects, which become appreciable at the lower temperatures, are included by utilizing collision integrals based on quantum theory. A Lennard-Jones (12-6) potential was assumed. The computations yield viscosities about 20 percent lower than those predicted for the high end of this temperature range by the method of corresponding states, but the agreement is excellent when the computed values are compared with existing experimental data.

  10. Partial structure factors and orientational correlations in liquid HI

    International Nuclear Information System (INIS)

    Andreani, C.; Nardone, M.; Ricci, F.P.

    1993-01-01

    The three atomic partial structure factors of orthobaric liquid HI at 253 K derived from neutron diffraction experiments are presented. The analysis of these structure factors and of the corresponding pair distribution functions indicates that the molecular center of mass distribution function is essentially that of a monoatomic Lennard-Jones fluid and that the anisotropic part of the intermolecular potential is able to build up orientational correlations between molecular axes without however giving rise to well defined correlations between the intermolecular axis and the molecular axis. These findings are consistent with an anisotropic part of the intermolecular potential due essentially to electric multipoles. (authors). 4 figs., 4 refs

  11. Nanolayering around and thermal resistivity of the water-hexagonal boron nitride interface

    Science.gov (United States)

    Akıner, Tolga; Mason, Jeremy K.; Ertürk, Hakan

    2017-07-01

    The water-hexagonal boron nitride interface was investigated by molecular dynamics simulations. Since the properties of the interface change significantly with the interatomic potential, a new method for calibrating the solid-liquid interatomic potential is proposed based on the experimental energy of the interface. The result is markedly different from that given by Lorentz-Berthelot mixing for the Lennard-Jones parameters commonly used in the literature. Specifically, the extent of nanolayering and interfacial thermal resistivity is measured for several interatomic potentials, and the one calibrated by the proposed method gives the least thermal resistivity.

  12. A new shared-memory programming paradigm for molecular dynamics simulations on the Intel Paragon

    International Nuclear Information System (INIS)

    D'Azevedo, E.F.; Romine, C.H.

    1994-12-01

    This report describes the use of shared memory emulation with DOLIB (Distributed Object Library) to simplify parallel programming on the Intel Paragon. A molecular dynamics application is used as an example to illustrate the use of the DOLIB shared memory library. SOTON-PAR, a parallel molecular dynamics code with explicit message-passing using a Lennard-Jones 6-12 potential, is rewritten using DOLIB primitives. The resulting code has no explicit message primitives and resembles a serial code. The new code can perform dynamic load balancing and achieves better performance than the original parallel code with explicit message-passing

  13. Size dependence of the contact angle of a nanodrop in a nanocavity: Density functional theory considerations

    Science.gov (United States)

    Berim, Gersh O.; Ruckenstein, Eli

    2011-02-01

    The dependence of the contact angles of nanodrops of Lennard-Jones type fluids in nanocavities on their sizes are calculated using a nonlocal density functional theory in a canonical ensemble. Cavities of various radii and depths, various temperatures, as well as various values of the energy parameter of the fluid-solid interactions were considered. It is argued that this dependence might affect strongly, for instance, the rate of heterogeneous nucleation on rough surfaces, which is usually calculated under the assumption of constant contact angle.

  14. Strong pressure-energy correlations in van der Waals liquids

    DEFF Research Database (Denmark)

    Pedersen, Ulf Rørbæk; Bailey, Nicholas; Schrøder, Thomas

    2008-01-01

    in the crystal and glass phases reflect an effective inverse power-law repulsive potential dominating fluctuations, even at zero and slightly negative pressure. In experimental data for supercritical argon, the correlations are found to be approximately 96%. Consequences for viscous liquid dynamics are discussed.......Strong correlations between equilibrium fluctuations of the configurational parts of pressure and energy are found in computer simulations of the Lennard-Jones liquid and other simple liquids, but not for hydrogen-bonding liquids such as methanol and water. The correlations that are present also...

  15. Note: Nonpolar solute partial molar volume response to attractive interactions with water.

    Science.gov (United States)

    Williams, Steven M; Ashbaugh, Henry S

    2014-01-07

    The impact of attractive interactions on the partial molar volumes of methane-like solutes in water is characterized using molecular simulations. Attractions account for a significant 20% volume drop between a repulsive Weeks-Chandler-Andersen and full Lennard-Jones description of methane interactions. The response of the volume to interaction perturbations is characterized by linear fits to our simulations and a rigorous statistical thermodynamic expression for the derivative of the volume to increasing attractions. While a weak non-linear response is observed, an average effective slope accurately captures the volume decrease. This response, however, is anticipated to become more non-linear with increasing solute size.

  16. Effect of pressure on the structure and lattice dynamics of fullerene crystal C60

    International Nuclear Information System (INIS)

    Prilutski, Yu.I.; Shapovalov, G.G.

    1997-01-01

    The low-temperature orientationally ordered crystalline phase of fullerene C 60 was investigated in dependence on the external pressure. An assumption was made that the energy of the lattice includes two contributions: a Lennard-Jones (12-6) potential and electrostatic interaction. The vibrational spectrum of C 60 crystal was calculated using the atom-atom potential method. The frequencies of intermolecular modes as functions of external pressure were studied. The sound velocities, elastic constants and bulk modulus are calculated. The dependence of sound velocities in fullerene crystal C 60 on the external pressure is investigated. The results obtained are in good agreement with the available experimental data. (orig.)

  17. Modeling New Adsorbents for Ethylene/Ethane Separations by Adsorption via {Pi}-Complexation

    Energy Technology Data Exchange (ETDEWEB)

    Blas, F. J.; Vega, L. F.; Gubbins, K. E.

    1998-01-01

    The adsorption of olefins and paraffins in a novel model porous adsorbent is studied by means of molecular simulations. The adsorbents are synthesized by effective dispersion of CuCI on substrates with hydrocarbon-phobic surfaces, such as {gamma}-A1{sub 2}O{sub 3}. The Cu(I) cations are able to undergo {pi}-complexation with olefin molecules. Ethane and ethylene are studied as adsorbents, and the molecules are modeled as having two Lennard-Jones sites. Ethylene molecules have two additional associating square-well sites placed in the line perpendicular to the symmetry axis of the molecules in order to reproduce the {pi}-complexation.

  18. NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface

    DEFF Research Database (Denmark)

    Ingebrigtsen, Trond; Toxværd, Søren; Heilmann, Ole

    2011-01-01

    -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...... precision. Nevertheless, just as for NVE algorithms, stabilizers are needed for very long runs in order to compensate for the accumulation of numerical errors that eventually lead to “entropic drift” of the potential energy towards higher values. A modification of the basic NVU algorithm is introduced...

  19. Computer simulation of the thermal pressure in solids and the equation of state

    International Nuclear Information System (INIS)

    Welch, D.O.; Dienes, G.J.; Paskin, A.

    1976-01-01

    The equation of state of solids was investigated with molecular dynamics techniques by obtaining the pressure as a function of temperature over a wide range of compressions. Data were obtained for fcc crystals with Lennard--Jones interactions and for bcc crystals with Morse interactions. The results were analyzed in terms of the Mie--Gruneisen equation of state. The Gruneisen constant at zero temperature is found to be essentially that obtained from the volume dependence of the mean-squared lattice vibration frequency, and its temperature dependence can be approximated well with a self-consistent cell model. Calculated results are compared with experimental data for argon along the melting line

  20. Um modelo para a superfície líquida no estudo da dinâmica do espalhamento de Xe e Ne pelo esqualano

    Directory of Open Access Journals (Sweden)

    Leal Alexandre S.

    2004-01-01

    Full Text Available In this work we present a theoretical model to investigate the scattering of Xe and Ne by a liquid squalane surface. The liquid surface is modeled as a grid of harmonic oscillators with frequencies adjusted to experimental vibration as frequencies of the liquid squalane and the atom-surface interaction potential is modeled by a Lennard-Jones function. The three dimensional description of the dynamics of the process which occurs at the gas-liquid interface is obtained by the classical trajectory method. The general characteristics of the dynamics of the scattering process are in good agreement with experimental data.

  1. [Evaluation of blood agar medium for the growth of mycobacteria].

    Science.gov (United States)

    Coban, Ahmet Yılmaz; Akgüneş, Alper; Durupınar, Belma

    2011-10-01

    This study was aimed to evaluate the performance of blood agar for the growth of mycobacteria from clinical specimens sent to Mycobacteriology Laboratory of Samsun Chest Diseases Hospital. One hundred fifty six clinical specimens including 123 sputum, 28 bronchoalveolar lavage (BAL) and 5 pleural fluid specimens were inoculated in Löwenstein-Jensen (LJ), BACTEC MGIT 960 system (Becton Dickinson, USA) and blood agar following decontamination process. The specimens were also simultaneously examined for the presence of acid-fast bacilli (AFB). Thirty five mycobacteria strains (33 Mycobacterium tuberculosis and 2 atypical mycobacteria) grew in blood agar, 38 (36 M.tuberculosis and 2 atypical mycobacteria) in LJ media and 46 (44 M.tuberculosis and 2 atypical mycobacteria) in BACTEC MGIT 960 system. Among 29 AFB negative specimens, 20 revealed growth in both blood agar and LJ medium and 27 in MGIT system. AFB positive 20 samples yielded growth in 15 samples in blood agar, 18 in LJ medium and 19 in MGIT system. Among the total of 156 samples, contamination was observed in 15 (9.6%) samples in blood agar, 16 (10.2%) in LJ medium and 18 (11.5%) in MGIT system. Growth time was 5-35 days (mean 18 ± 7.4), 11-35 days (mean 19 ± 5.9) and 5-15 days (mean 10 ± 2.4) for blood agar, LJ medium and BACTEC MGIT 960 system, respectively. The three samples which revealed contamination in BACTEC MGIT 960 system, grew successfully in both blood agar and LJ medium without contamination. In one sample, growth was observed only in LJ medium but neither in blood agar nor BACTEC MGIT 960 system. However, in another sample, growth was observed only in blood agar while no growth was detected in LJ or BACTEC MGIT 960 system. Six samples yielded mycobacteria only in BACTEC MGIT 960 system. These results indicated that simultaneous use of one liquid and one solid medium to grow mycobacteria from the clinical samples seemed to be complementary. Blood agar was a promising choice since it was found

  2. Influence of the Periodic Boundary Conditions on the Fluid Structure and on the Thermodynamic Properties Computed from the Molecular Simulations Influence des conditions périodiques sur la structure et sur les propriétés thermodynamiques calculées à partir des simulations moléculaires

    Directory of Open Access Journals (Sweden)

    Janeček J.

    2013-03-01

    Full Text Available The components of pair distribution function in different directions with respect to the coordinate system defined by the simulation box are determined for Lennard-Jones fluid simulated using the Monte Carlo technique in cubic boxes of various size. The approach of Pratt and Haan is employed to analyze the distortion of isotropic fluid structure due to the periodic boundary conditions and qualitative agreement is found between the theoretical and simulated course of particular angular components of distribution function. The relation between the anisotropy of correlation functions and the system size dependency of residual energy and compressibility factor is analyzed. The finite size effects become significantly pronounced in systems with size lower than 5 particle diameters, especially if the length of the box-edge is equal to a non-integer multiple of molecular diameter. With increasing temperature the implicit finite size effects on fluid structure as well as on the thermodynamic properties become less important. The primary cause of the structure deformation lies in the short-range interparticle correlations and the long-range interactions are not important; therefore, the implicit finite size effects influence all kinds of atomistic simulations, including those using the interactions of finite range and in the molecular dynamics simulations. However, at present the simulated systems are usually of sufficiently large size and ignoring the implicit finite size does not lead to serious problems, except for the determination of surface properties using the inhomogeneous simulations which are more sensitive to the lateral dimension of simulation box. Nous avons déterminé les contributions directionnelles de la fonction de distribution par paire du fluide de Lennard-Jones, par simulation moléculaire de Monte Carlo dans des boîtes cubiques de différentes tailles. L’approche de Pratt et Haan est utilisée pour analyser la distorsion de la

  3. Modeling a calixarene-crown-6 and its alkali complexes by means of a hybrid quantum mechanical/molecular mechanical method

    International Nuclear Information System (INIS)

    Lamare, V.; Golebiowski, J.; Ruiz-Lopez, M.F.; Martins-Costa, M.; Millot, C.

    2000-01-01

    Calixarene-crown-6s in 1,3-alternate conformation are compounds currently investigated for their ability to selectively extract traces of cesium from acidic or strong salinity aqueous solutions. Studies based on molecular modeling were undertaken on these systems to understand their behavior regarding cesium and other alkali cations, in particular sodium. In this work, a recently developed molecular modeling approach was used to investigate calixarene BC6 and its alkali complexes. The whole calixarene ligand is treated by the semiempirical AM1 quantum method (QM) whereas the cation and solvent are treated by a conventional force field (MM). The total energy of the system is the sum of the QM and MM sub-system contributions plus the QM/MM interaction energy. The latter includes the electrostatic interaction between QM charges (nuclei + electrons) and MM sites, and the non-electrostatic QM/MM van der Weals term, usually expressed by a Lennard-Jones potential. In the QM/MM method, van der Waals interactions between the QM and MM sub-systems are described by empirical Lennard-Jones parameters which must be adapted to the hybrid potential considered. Parameters on oxygen atoms were optimized. For the cations, two sets of Parameters were tested: Aqvist empirical parameters, derived to represent cation/water interactions in classical dynamics (set 2), and a new set of parameters which we calculated from dispersion coefficients available in the literature (set 1). The latter gave better results for the interactions with the crown. In the sodium complex, the cation interacts with only four oxygen atoms of the crown, whereas in the complex with cesium, the interaction involves six oxygen atoms. Distortion of the BC6 is therefore less with sodium and favors the corresponding complex by 4 kcal/mol. The cation/BC6 van der Waals energy is very weak for the two complexes. Hence the interaction between the cation and BC6 is primarily electrostatic. The BC6 polarization energy due

  4. 78 FR 66317 - Special Conditions: Learjet Inc. Model LJ-200-1A10; Airplane Fuselage Post-Crash Fire Survivability

    Science.gov (United States)

    2013-11-05

    ... Existing regulations do not adequately ensure that composite structure offers passengers the same... feature associated with advanced composite materials in the construction of its fuselage and wings. The... Directorate, Aircraft Certification Service, 1601 Lind Avenue SW., Renton, Washington, 98057-3356; telephone...

  5. 78 FR 14155 - Special Conditions: Learjet Inc., Model LJ-200-1A10 Airplane; Use of Automatic Power Reserve (APR...

    Science.gov (United States)

    2013-03-05

    ... critical time interval begins at point A on a 2.5 degree approach glide path. (Point A is the point on that.... ADDRESSES: Send comments identified by docket number FAA-2013-0154 using any of the following methods... during a critical point in the approach, landing, or go-around operations precluded further consideration...

  6. The Design and Implementation of a Pedagogical Relational Database System.

    Science.gov (United States)

    1979-12-15

    environment, the student’s ability to quickly grasp the fundamentals of the language is very important in that the less time spent learning and the more...addition, priviledged operations such as an initialization command may be used only by the DBM acting in a special mode. 43 , i LJ -J Im- LC 0C 0ii cj...alone provide it with enough intel- ligence to out-perform a confused or less than proficient user. The design chosen for this implementation is pictured

  7. Test of a new heat-flow equation for dense-fluid shock waves

    Science.gov (United States)

    Holian, Brad Lee; Mareschal, Michel; Ravelo, Ramon

    2010-09-01

    Using a recently proposed equation for the heat-flux vector that goes beyond Fourier's Law of heat conduction, we model shockwave propagation in the dense Lennard-Jones fluid. Disequilibrium among the three components of temperature, namely, the difference between the kinetic temperature in the direction of a planar shock wave and those in the transverse directions, particularly in the region near the shock front, gives rise to a new transport (equilibration) mechanism not seen in usual one-dimensional heat-flow situations. The modification of the heat-flow equation was tested earlier for the case of strong shock waves in the ideal gas, which had been studied in the past and compared to Navier-Stokes-Fourier solutions. Now, the Lennard-Jones fluid, whose equation of state and transport properties have been determined from independent calculations, allows us to study the case where potential, as well as kinetic contributions are important. The new heat-flow treatment improves the agreement with nonequilibrium molecular-dynamics simulations under strong shock wave conditions, compared to Navier-Stokes.

  8. Interface bonding in silicon oxide nanocontacts: interaction potentials and force measurements

    Science.gov (United States)

    Wierez-Kien, M.; Craciun, A. D.; Pinon, A. V.; Le Roux, S.; Gallani, J. L.; Rastei, M. V.

    2018-04-01

    The interface bonding between two silicon-oxide nanoscale surfaces has been studied as a function of atomic nature and size of contacting asperities. The binding forces obtained using various interaction potentials are compared with experimental force curves measured in vacuum with an atomic force microscope. In the limit of small nanocontacts (typically measured with sensitive probes the bonding is found to be influenced by thermal-induced fluctuations. Using interface interactions described by Morse, embedded atom model, or Lennard-Jones potential within reaction rate theory, we investigate three bonding types of covalent and van der Waals nature. The comparison of numerical and experimental results reveals that a Lennard-Jones-like potential originating from van der Waals interactions captures the binding characteristics of dry silicon oxide nanocontacts, and likely of other nanoscale materials adsorbed on silicon oxide surfaces. The analyses reveal the importance of the dispersive surface energy and of the effective contact area which is altered by stretching speeds. The mean unbinding force is found to decrease as the contact spends time in the attractive regime. This contact weakening is featured by a negative aging coefficient which broadens and shifts the thermal-induced force distribution at low stretching speeds.

  9. Comparison of potentials for polymeric liquids

    International Nuclear Information System (INIS)

    Jung, Hae Young

    2002-01-01

    Many theories for polymeric liquids are based on the concepts of cell, hole, free volume of lattice etc. In this theories, van der Waals potential, Lennard-Jones 6-12 potential and their modified potentials are commonly used. In this work, Mie(p,6)potential was applied to the Continuous Lattice Fluid Theory (which extends the discrete lattices of Lattice Fluid Theory to classically continuous lattices) and Dee-Walsch's Cell Theory (which modifies Flory's Equation of State Theory). Both of them are known to be successful theories for polymeric liquids. Thus, PVT values changing with p (the exponent in the repulsion potential) were calculated and compared with experimental values. And, calculated values of Lattice Fluid theory, Flory's Equation of State Theory and Cho-Sanchez Theory using perturbation method were also compared. Through the calculated results, van der Waals potential, Lennard-Jones 6-12 potential and Mie(p,6) potential for polymeric liquids were compared with each other

  10. Solvation in atomic liquids: connection between Gaussian field theory and density functional theory

    Directory of Open Access Journals (Sweden)

    V. Sergiievskyi

    2017-12-01

    Full Text Available For the problem of molecular solvation, formulated as a liquid submitted to the external potential field created by a molecular solute of arbitrary shape dissolved in that solvent, we draw a connection between the Gaussian field theory derived by David Chandler [Phys. Rev. E, 1993, 48, 2898] and classical density functional theory. We show that Chandler's results concerning the solvation of a hard core of arbitrary shape can be recovered by either minimising a linearised HNC functional using an auxiliary Lagrange multiplier field to impose a vanishing density inside the core, or by minimising this functional directly outside the core — indeed a simpler procedure. Those equivalent approaches are compared to two other variants of DFT, either in the HNC, or partially linearised HNC approximation, for the solvation of a Lennard-Jones solute of increasing size in a Lennard-Jones solvent. Compared to Monte-Carlo simulations, all those theories give acceptable results for the inhomogeneous solvent structure, but are completely out-of-range for the solvation free-energies. This can be fixed in DFT by adding a hard-sphere bridge correction to the HNC functional.

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

    KAUST Repository

    Wu, Congmin

    2010-07-07

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

  12. Lattice model theory of the equation of state covering the gas, liquid, and solid phases

    Science.gov (United States)

    Bonavito, N. L.; Tanaka, T.; Chan, E. M.; Horiguchi, T.; Foreman, J. C.

    1975-01-01

    The three stable states of matter and the corresponding phase transitions were obtained with a single model. Patterned after Lennard-Jones and Devonshires's theory, a simple cubic lattice model containing two fcc sublattices (alpha and beta) is adopted. The interatomic potential is taken to be the Lennard-Jones (6-12) potential. Employing the cluster variation method, the Weiss and the pair approximations on the lattice gas failed to give the correct phase diagrams. Hybrid approximations were devised to describe the lattice term in the free energy. A lattice vibration term corresponding to a free volume correction is included semi-phenomenologically. The combinations of the lattice part and the free volume part yield the three states and the proper phase diagrams. To determine the coexistence regions, the equalities of the pressure and Gibbs free energy per molecule of the coexisting phases were utilized. The ordered branch of the free energy gives rise to the solid phase while the disordered branch yields the gas and liquid phases. It is observed that the triple point and the critical point quantities, the phase diagrams and the coexistence regions plotted are in good agreement with the experimental values and graphs for argon.

  13. An adaptive immune optimization algorithm with dynamic lattice searching operation for fast optimization of atomic clusters

    International Nuclear Information System (INIS)

    Wu, Xia; Wu, Genhua

    2014-01-01

    Highlights: • A high efficient method for optimization of atomic clusters is developed. • Its performance is studied by optimizing Lennard-Jones clusters and Ag clusters. • The method is proved to be quite efficient. • A new Ag 61 cluster with stacking-fault face-centered cubic motif is found. - Abstract: Geometrical optimization of atomic clusters is performed by a development of adaptive immune optimization algorithm (AIOA) with dynamic lattice searching (DLS) operation (AIOA-DLS method). By a cycle of construction and searching of the dynamic lattice (DL), DLS algorithm rapidly makes the clusters more regular and greatly reduces the potential energy. DLS can thus be used as an operation acting on the new individuals after mutation operation in AIOA to improve the performance of the AIOA. The AIOA-DLS method combines the merit of evolutionary algorithm and idea of dynamic lattice. The performance of the proposed method is investigated in the optimization of Lennard-Jones clusters within 250 atoms and silver clusters described by many-body Gupta potential within 150 atoms. Results reported in the literature are reproduced, and the motif of Ag 61 cluster is found to be stacking-fault face-centered cubic, whose energy is lower than that of previously obtained icosahedron

  14. A simple extrapolation of thermodynamic perturbation theory to infinite order.

    Science.gov (United States)

    Ghobadi, Ahmadreza F; Elliott, J Richard

    2015-09-21

    Recent analyses of the third and fourth order perturbation contributions to the equations of state for square well spheres and Lennard-Jones chains show trends that persist across orders and molecular models. In particular, the ratio between orders (e.g., A3/A2, where A(i) is the ith order perturbation contribution) exhibits a peak when plotted with respect to density. The trend resembles a Gaussian curve with the peak near the critical density. This observation can form the basis for a simple recursion and extrapolation from the highest available order to infinite order. The resulting extrapolation is analytic and therefore cannot fully characterize the critical region, but it remarkably improves accuracy, especially for the binodal curve. Whereas a second order theory is typically accurate for the binodal at temperatures within 90% of the critical temperature, the extrapolated result is accurate to within 99% of the critical temperature. In addition to square well spheres and Lennard-Jones chains, we demonstrate how the method can be applied semi-empirically to the Perturbed Chain - Statistical Associating Fluid Theory (PC-SAFT).

  15. Quantum complex rotation and uniform semiclassical calculations of complex energy eigenvalues

    International Nuclear Information System (INIS)

    Connor, J.N.L.; Smith, A.D.

    1983-01-01

    Quantum and semiclassical calculations of complex energy eigenvalues have been carried out for an exponential potential of the form V 0 r 2 exp(-r) and Lennard-Jones (12,6) potential. A straightforward method, based on the complex coordinate rotation technique, is described for the quantum calculation of complex eigenenergies. For singular potentials, the method involves an inward and outward integration of the radial Schroedinger equation, followed by matching of the logarithmic derivatives of the wave functions at an intermediate point. For regular potentials, the method is simpler, as only an inward integration is required. Attention is drawn to the World War II researches of Hartree and co-workers who anticipated later quantum mechanical work on the complex rotation method. Complex eigenenergies are also calculated from a uniform semiclassical three turning point quantization formula, which allows for the proximity of the outer pair of complex turning points. Limiting cases of this formula, which are valid for very narrow or very broad widths, are also used in the calculations. We obtain good agreement between the semiclassical and quantum results. For the Lennard-Jones (12,6) potential, we compare resonance energies and widths from the complex energy definition of a resonance with those obtained from the time delay definition

  16. Heat conduction in diatomic chains with correlated disorder

    Science.gov (United States)

    Savin, Alexander V.; Zolotarevskiy, Vadim; Gendelman, Oleg V.

    2017-01-01

    The paper considers heat transport in diatomic one-dimensional lattices, containing equal amounts of particles with different masses. Ordering of the particles in the chain is governed by single correlation parameter - the probability for two neighboring particles to have the same mass. As this parameter grows from zero to unity, the structure of the chain varies from regular staggering chain to completely random configuration, and then - to very long clusters of particles with equal masses. Therefore, this correlation parameter allows a control of typical cluster size in the chain. In order to explore different regimes of the heat transport, two interatomic potentials are considered. The first one is an infinite potential wall, corresponding to instantaneous elastic collisions between the neighboring particles. In homogeneous chains such interaction leads to an anomalous heat transport. The other one is classical Lennard-Jones interatomic potential, which leads to a normal heat transport. The simulations demonstrate that the correlated disorder of the particle arrangement does not change the convergence properties of the heat conduction coefficient, but essentially modifies its value. For the collision potential, one observes essential growth of the coefficient for fixed chain length as the limit of large homogeneous clusters is approached. The thermal transport in these models remains superdiffusive. In the Lennard-Jones chain the effect of correlation appears to be not monotonous in the limit of low temperatures. This behavior stems from the competition between formation of long clusters mentioned above, and Anderson localization close to the staggering ordered state.

  17. Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.

    Science.gov (United States)

    Okumura, Hisashi

    2011-01-07

    The partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations samples a wide range of an important part of the potential energy. Although it is a strong technique for structure prediction of biomolecules, the choice of the partial potential energy has not been optimized. In order to find the best choice, partial multicanonical molecular dynamics simulations of an alanine dipeptide in explicit water solvent were performed with 15 trial choices for the partial potential energy. The best choice was found to be the sum of the electrostatic, Lennard-Jones, and torsion-angle potential energies between solute atoms. In this case, the partial multicanonical simulation sampled all of the local-minimum free-energy states of the P(II), C(5), α(R), α(P), α(L), and C states and visited these states most frequently. Furthermore, backbone dihedral angles ϕ and ψ rotated very well. It is also found that the most important term among these three terms is the electrostatic potential energy and that the Lennard-Jones term also helps the simulation to overcome the steric restrictions. On the other hand, multicanonical simulation sampled all of the six states, but visited these states fewer times. Conventional canonical simulation sampled only four of the six states: The P(II), C(5), α(R), and α(P) states.

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

    International Nuclear Information System (INIS)

    Wu Congmin; Qian Tiezheng; Sheng Ping

    2010-01-01

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

  19. Test of a new heat-flow equation for dense-fluid shock waves.

    Science.gov (United States)

    Holian, Brad Lee; Mareschal, Michel; Ravelo, Ramon

    2010-09-21

    Using a recently proposed equation for the heat-flux vector that goes beyond Fourier's Law of heat conduction, we model shockwave propagation in the dense Lennard-Jones fluid. Disequilibrium among the three components of temperature, namely, the difference between the kinetic temperature in the direction of a planar shock wave and those in the transverse directions, particularly in the region near the shock front, gives rise to a new transport (equilibration) mechanism not seen in usual one-dimensional heat-flow situations. The modification of the heat-flow equation was tested earlier for the case of strong shock waves in the ideal gas, which had been studied in the past and compared to Navier-Stokes-Fourier solutions. Now, the Lennard-Jones fluid, whose equation of state and transport properties have been determined from independent calculations, allows us to study the case where potential, as well as kinetic contributions are important. The new heat-flow treatment improves the agreement with nonequilibrium molecular-dynamics simulations under strong shock wave conditions, compared to Navier-Stokes.

  20. An adaptive immune optimization algorithm with dynamic lattice searching operation for fast optimization of atomic clusters

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Xia, E-mail: xiawu@mail.nankai.edu.cn; Wu, Genhua

    2014-08-31

    Highlights: • A high efficient method for optimization of atomic clusters is developed. • Its performance is studied by optimizing Lennard-Jones clusters and Ag clusters. • The method is proved to be quite efficient. • A new Ag{sub 61} cluster with stacking-fault face-centered cubic motif is found. - Abstract: Geometrical optimization of atomic clusters is performed by a development of adaptive immune optimization algorithm (AIOA) with dynamic lattice searching (DLS) operation (AIOA-DLS method). By a cycle of construction and searching of the dynamic lattice (DL), DLS algorithm rapidly makes the clusters more regular and greatly reduces the potential energy. DLS can thus be used as an operation acting on the new individuals after mutation operation in AIOA to improve the performance of the AIOA. The AIOA-DLS method combines the merit of evolutionary algorithm and idea of dynamic lattice. The performance of the proposed method is investigated in the optimization of Lennard-Jones clusters within 250 atoms and silver clusters described by many-body Gupta potential within 150 atoms. Results reported in the literature are reproduced, and the motif of Ag{sub 61} cluster is found to be stacking-fault face-centered cubic, whose energy is lower than that of previously obtained icosahedron.

  1. Biomembrane modeling: molecular dynamics simulation of phospholipid monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, T.R.

    1979-01-01

    As a first step toward a computer model of a biomembrane-like bilayer, a dynamic, deterministric model of a phospholipid monolayer has been constructed. The model moves phospholipid-like centers of force according to an integrated law of motion in finite difference form. Forces on each phospholipid analogue are derived from the gradient of the local potential, itself the sum of Coulombic and short-range terms. The Coulombic term is approximated by use of a finite-difference form of Poisson's equation, while the short-range term results from finite-radius, pairwise summation of a Lennard-Jones potential. Boundary potentials are treated in such a way that the model is effectively infinite in extent in the plane of the monolayer. The two-dimensional virial theorem is used to find the surface pressure of the monolayer as a function of molecular area. Pressure-versus-area curves for simulated monolayers are compared to those of real monolayers. Dependence of the simulator's behavior on Lennard-Jones parameters and the specific geometry of the molecular analogue is discussed. Implications for the physical theory of phospholipid monolayers and bilayers are developed.

  2. How Competitive Interactions Affect the Self-Assembly of Confined Janus Dumbbells.

    Science.gov (United States)

    Bordin, José Rafael; Krott, Leandro B

    2017-04-27

    We explore the self-assembled morphologies of Janus nanoparticles under cylindrical confinement. Langevin dynamics simulations are employed to study the behavior of two types of dimers inside cylinders with distinct radius. The first type of nanoparticle was modeled using one monomer that interacts by a standard Lennard-Jones potential and another monomer that is modeled using a purely repulsive two length scale shoulder potential. The second type is composed by a Lennard-Jones monomer and a repulsive monomer which interacts by the purely repulsive Weeks-Chandler-Andersen potential, which have only one length scale. The two length scale potential used in the first type of nanoparticle models a monomer with competitive interaction. Our results show that the aggregated structures are completely distinct for each type of nanoparticle. Also, our simulations indicate that the cylinder radius can be used to control the type of self-assembled cluster. Small clusters, tubular and donut-like micelles with central holes, with potential application to molecule encapsulation were observed regarding the nanoparticle specificities and the cylinder radii. Also, bilayer lamellae structures were obtained depending on the type of nanoparticle and the cylinder size.

  3. Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields.

    Science.gov (United States)

    Van Vleet, Mary J; Misquitta, Alston J; Stone, Anthony J; Schmidt, J R

    2016-08-09

    Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.

  4. Collision Frequency for Energy Transfer in Unimolecular Reactions.

    Science.gov (United States)

    Matsugi, Akira

    2018-03-01

    Pressure dependence of unimolecular reaction rates is governed by the energy transfer in collisions of reactants with bath gas molecules. Pressure-dependent rate constants can be theoretically determined by solving master equations for unimolecular reactions. In general, master equation formulations describe energy transfer processes using a collision frequency and a probability distribution model of the energy transferred per collision. The present study proposes a novel method for determining the collision frequency from the results of classical trajectory calculations. Classical trajectories for collisions of several polyatomic molecules (ethane, methane, tetrafluoromethane, and cyclohexane) with monatomic colliders (Ar, Kr, and Xe) were calculated on potential energy surfaces described by the third-order density-functional tight-binding method in combination with simple pairwise interaction potentials. Low-order (including non-integer-order) moments of the energy transferred in deactivating collisions were extracted from the trajectories and compared with those derived using some probability distribution models. The comparison demonstrates the inadequacy of the conventional Lennard-Jones collision model for representing the collision frequency and suggests a robust method for evaluating the collision frequency that is consistent with a given probability distribution model, such as the exponential-down model. The resulting collision frequencies for the exponential-down model are substantially higher than the Lennard-Jones collision frequencies and are close to the (hypothetical) capture rate constants for dispersion interactions. The practical adequacy of the exponential-down model is also briefly discussed.

  5. Comparative Physiological and Molecular Analyses of Two Contrasting Flue-Cured Tobacco Genotypes under Progressive Drought Stress

    Directory of Open Access Journals (Sweden)

    Xinhong Su

    2017-05-01

    Full Text Available Drought is a major environmental factor that limits crop growth and productivity. Flue-cured tobacco (Nicotiana tabacum is one of the most important commercial crops worldwide and its productivity is vulnerable to drought. However, comparative analyses of physiological, biochemical and gene expression changes in flue-cured tobacco varieties differing in drought tolerance under long-term drought stress are scarce. In this study, drought stress responses of two flue-cured tobacco varieties, LJ851 and JX6007, were comparatively studied at the physiological and transcriptional levels. After exposing to progressive drought stress, the drought-tolerant LJ851 showed less growth inhibition and chlorophyll reduction than the drought-sensitive JX6007. Moreover, higher antioxidant enzyme activities and lower levels of H2O2, Malondialdehyde (MDA, and electrolyte leakage after drought stress were found in LJ851 when compared with JX6007. Further analysis showed that LJ851 plants had much less reductions than the JX6007 in the net photosynthesis rate and stomatal conductance during drought stress; indicating that LJ851 had better photosynthetic performance than JX6007 during drought. In addition, transcriptional expression analysis revealed that LJ851 exhibited significantly increased transcripts of several categories of drought-responsive genes in leaves and roots under drought conditions. Together, these results indicated that LJ851 was more drought-tolerant than JX6007 as evidenced by better photosynthetic performance, more powerful antioxidant system, and higher expression of stress defense genes during drought stress. This study will be valuable for the development of novel flue-cured tobacco varieties with improved drought tolerance by exploitation of natural genetic variations in the future.

  6. System Budgets

    DEFF Research Database (Denmark)

    Jeppesen, Palle

    1996-01-01

    The lecture note is aimed at introducing system budgets for optical communication systems. It treats optical fiber communication systems (six generations), system design, bandwidth effects, other system impairments and optical amplifiers.......The lecture note is aimed at introducing system budgets for optical communication systems. It treats optical fiber communication systems (six generations), system design, bandwidth effects, other system impairments and optical amplifiers....

  7. Ventilation systems

    International Nuclear Information System (INIS)

    Gossler

    1980-01-01

    The present paper deals with - controlled area ventilation systems - ventilation systems for switchgear-building and control-room - other ventilation systems for safety equipments - service systems for ventilation systems. (orig./RW)

  8. Fulltext PDF

    Indian Academy of Sciences (India)

    0006741

    Translational and rotational entropy of individual water molecules have been calculated at .... LJ(8,4). LJ(18,9). LJ(24,12). LJ(36,18). 2d LJ. 3d LJ. 4d LJ γ d = 3nR. -1000. 0. 1000. 2000. 3000. 4000. 5000. 6000. 0. 0.4. 0.8. 1.2. Relative Intensity. E/cm-1. B3LYP. PBE0 ... polymers and Entangle-like for the large polymers.

  9. Effect of disorder on the melting phase transition

    International Nuclear Information System (INIS)

    Storey, M.

    1999-01-01

    simplicity in comparison to the full Lennard-Jones potential. The nature of the transition is investigated and the fact that the nature of the transition does riot, change in the temperature-density phase diagram is used. In the disordered case, the particle-pin interaction is given by all attractive Gaussian. Using the same techniques as in the pure case, the effect of disorder on the melting transition is studied. The aim is to make some comparisons with the clean systems transition and find the critical pinning potential at which the transition vanishes completely. Conclusions are drawn front the results of the two-dimensional analytical and the simulation studies of the melting transition ill the presence of disorder. It turns out that it may also be very useful to study the effect of disorder in order to help draw conclusions oil the nature of the transition of the clean system. (author)

  10. Thermal systems; Systemes thermiques

    Energy Technology Data Exchange (ETDEWEB)

    Lalot, S. [Valenciennes Univ. et du Hainaut Cambresis, LME, 59 (France); Lecoeuche, S. [Ecole des Mines de Douai, Dept. GIP, 59 - Douai (France)]|[Lille Univ. des Sciences et Technologies, 59 - Villeneuve d' Ascq (France); Ahmad, M.; Sallee, H.; Quenard, D. [CSTB, 38 - Saint Martin d' Heres (France); Bontemps, A. [Universite Joseph Fourier, LEGI/GRETh, 38 - Grenoble (France); Gascoin, N.; Gillard, P.; Bernard, S. [Laboratoire d' Energetique, Explosion, Structure, 18 - Bourges (France); Gascoin, N.; Toure, Y. [Laboratoire Vision et Robotique, 18 - Bourges (France); Daniau, E.; Bouchez, M. [MBDA, 18 - Bourges (France); Dobrovicescu, A.; Stanciu, D. [Bucarest Univ. Polytechnique, Faculte de Genie Mecanique (Romania); Stoian, M. [Reims Univ. Champagne Ardenne, Faculte des Sciences, UTAP/LTM, 51 (France); Bruch, A.; Fourmigue, J.F.; Colasson, S. [CEA Grenoble, Lab. Greth, 38 (France); Bontemps, A. [Universite Joseph Fourier, LEGI/GRETh, 38 - Grenoble (France); Voicu, I.; Mare, T.; Miriel, J. [Institut National des Sciences Appliquees (INSA), LGCGM, IUT, 35 - Rennes (France); Galanis, N. [Sherbrooke Univ., Genie Mecanique, QC (Canada); Nemer, M.; Clodic, D. [Ecole des Mines de Paris, Centre Energetique et Procedes, 75 (France); Lasbet, Y.; Auvity, B.; Castelain, C.; Peerhossaini, H. [Nantes Univ., Ecole Polytechnique, Lab. de Thermocinetiquede Nantes, UMR-CNRS 6607, 44 (France)

    2005-07-01

    This session about thermal systems gathers 26 articles dealing with: neural model of a compact heat exchanger; experimental study and numerical simulation of the thermal behaviour of test-cells with walls made of a combination of phase change materials and super-insulating materials; hydraulic and thermal modeling of a supercritical fluid with pyrolysis inside a heated channel: pre-dimensioning of an experimental study; energy analysis of the heat recovery devices of a cryogenic system; numerical simulation of the thermo-hydraulic behaviour of a supercritical CO{sub 2} flow inside a vertical tube; mixed convection inside dual-tube exchangers; development of a nodal approach with homogenization for the simulation of the brazing cycle of a heat exchanger; chaotic exchanger for the cooling of low temperature fuel cells; structural optimization of the internal fins of a cylindrical generator; a new experimental approach for the study of the local boiling inside the channels of exchangers with plates and fins; experimental study of the flow regimes of boiling hydrocarbons on a bundle of staggered tubes; energy study of heat recovery exchangers used in Claude-type refrigerating systems; general model of Carnot engine submitted to various operating constraints; the free pistons Stirling cogeneration system; natural gas supplied cogeneration system with polymer membrane fuel cell; influence of the CRN coating on the heat flux inside the tool during the wood unrolling process; transport and mixture of a passive scalar injected inside the wake of a Ahmed body; control of a laser welding-brazing process by infrared thermography; 2D self-adaptative method for contours detection: application to the images of an aniso-thermal jet; exergy and exergy-economical study of an 'Ericsson' engine-based micro-cogeneration system; simplified air-conditioning of telephone switching equipments; parametric study of the 'low-energy' individual dwelling; brief synthesis of

  11. Data Systems vs. Information Systems

    OpenAIRE

    Amatayakul, Margret K.

    1982-01-01

    This paper examines the current status of “hospital information systems” with respect to the distinction between data systems and information systems. It is proposed that the systems currently existing are incomplete data dystems resulting in ineffective information systems.

  12. Nanothermodynamics of iron clusters: Small clusters, icosahedral and fcc-cuboctahedral structures

    Science.gov (United States)

    Angelié, C.; Soudan, J.-M.

    2017-05-01

    towards a more stable structure without regularity. The 38 atom cluster exhibits a nearly glassy relaxation, through a cascade of six metastable states of long life. This behaviour, as that of the 147 atom cluster towards the amorphous state, shows that difficulties to reach ergodicity in the lower half of the solid zone are related to particular features of the potential energy landscape, and not necessarily to a too large size of the system. Comparisons of the cEAM iron system with published results about Lennard-Jones systems and DFT calculations are made. The results of the previous clusters have been combined with that of Paper II to plot the cohesive energy Ec and the melting temperature Tm in terms of the cluster atom number Nat. The Nat -1 /3 linear dependence of the melting temperature (Pawlow law) is observed again for Nat > 150. In contrast, for Nat the curve diverges strongly from the Pawlow law, giving it an overall V-shape, with a linear increase of Tm when Nat goes from 55 to 13 atoms. Surprisingly, the 38 atom cluster is anomalously below the overall curve.

  13. EXPERT SYSTEMS

    OpenAIRE

    Georgiana Marin; Mihai Catalin Andrei

    2011-01-01

    In recent decades IT and computer systems have evolved rapidly in economic informatics field. The goal is to create user friendly information systems that respond promptly and accurately to requests. Informatics systems evolved into decision assisted systems, and such systems are converted, based on gained experience, in expert systems for creative problem solving that an organization is facing. Expert systems are aimed at rebuilding human reasoning on the expertise obtained from experts, sto...

  14. Microbial community diversity associated with moonmilk deposits in a karstic cave system in Ireland

    Science.gov (United States)

    Rooney, D.; Hutchens, E.; Clipson, Nick; McDermott, Frank

    2009-04-01

    has been unaltered by human disturbance or practices. The aim of this study was to examine microbial community diversity associated with moonmilk deposits at Ballynamintra Cave, Ireland using automated ribosomal intergenic spacer analysis (ARISA). The results revealed considerable bacterial and fungal diversity associated with moonmilk in a karstic cave system, suggesting that the microbial community implicated in moonmilk formation may be more diverse than previously thought. These results suggest that microbes may have important functional roles in subterranean environments. Although the moonmilk in this study was largely comprised of calcite, microbial involvement in calcite precipitation could result in the bioavailability of a range of organic compounds for subsequent microbial metabolism. References: Baskar, S., Baskar, R., Mauclaire, L., and McKenzie, J.A. 2006. Microbially induced calcite precipitation in culture experiments: Possible origin for stalactites in Sahastradhara caves, Dehradun, India. Current Science 90: 58-64. Burford, E.P., Fomina, M., Gadd, G. 2003. Fungal involvement in bioweathering and biotrasformations of rocks and minerals. Min Mag 67(6):1172-1155. Engel, A.S., Stern, L.A., Bennett, P.C. 2004. Microbial contributions to cave formation: new insights into sulfuric acid speleogenesis. Geology 32(5): 369-372. Gadd, G.M. (2004). Mycotransformation of organic and inorganic substrates. Mycologist 18: 60-70. Northup, D., Barns, S.M., Yu, Laura, E., Spilde, M.N., Schelble, R.T., Dano, K.E., Crossey, L.J., Connolly, C.A., Boston, P.J., and Dahm, C.N. 2003. Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves. Environmental Microbiology 5(11): 1071-1086.

  15. Emission of water clusters: molecular dynamic simulation

    International Nuclear Information System (INIS)

    Kutliev, U.O.; Kalandarov, K.S.

    2006-01-01

    SPC potential is able to reproduce many of the properties of bulk H 2 O [6]. In the SPC model, the molecular interaction potential U inter consists of an electrostatic component U electrostatic describing the charge-charge interaction between pairs of atoms in the two molecules. In order to describe the dispersion and repulsive interactions between the two oxygen sites, a Lennard- Jones function ULJ is included. The Au-Au interactions are represented by the MD/Monte Carlo corrected effective medium (MD/MC-CEM) potential function for fcc metals [7]. For metal- water systems has been developed a potential by Spohr [8]. The Spohr potential consist a Morse function combined with a corrugation term defining various surface sites for the oxygen-surface interaction and a repulsive term for the hydrogen -surface interaction. For our calculation we used modified Spo hr function. Because we need the metal atoms to move and interact the water molecules, we have modified the Spohr function so that the interactions are pairwise additive between the O and H atoms in the H 2 O molecule and the metal atoms. The process of sputtering water molecules from the metal surface have been investigated by computer simulation. For the 2 layers water molecules on the Au(III) have been obtained mass spectra secondary particles. The mass spectra consists peaks corresponding to the both water molecules and clusters. On the mass spectra also observed peaks of gold atoms. The visual observations shown that at the bombardment observed 'small icebergs' which can not registered by mass detectors. These results are of interest for mass spectrometry of molecules, study of surfaces, biological molecules and medical procedures. (author)

  16. Multibody Systems

    DEFF Research Database (Denmark)

    Wagner, Falko Jens

    1999-01-01

    Multibody Systems is one area, in which methods for solving DAEs are of special interst. This chapter is about multibody systems, why they result in DAE systems and what kind of problems that can arise when dealing with multibody systems and formulating their corresponding DAE system....

  17. Molecular dynamics simulation of supercritical fluids

    Science.gov (United States)

    Branam, Richard D.

    Axisymmetric injectors appear in a multitude of applications ranging from rocket engines to biotechnology. While experimentation is limited to larger injectors, much interest has been shown in the micro- and nano-scales as well. Experimentation at these scales can be cost prohibitive if even possible. Often, the operating regime involves supercritical fluids or complex geometries. Molecular dynamics modeling provides a unique way to explore these flow regimes, calculate hard to measure flow parameters accurately, and determine the value of potential improvements before investing in costly experiments or manufacturing. This research effort modeled sub- and supercritical fluid flow in a cylindrical tube being injected into a quiescent chamber. The ability of four wall models to provide an accurate simulation was compared. The simplest model, the diffuse wall, proved useful in getting results quickly but the results for the higher density cases are questionable, especially with respect to velocity profiles and density distributions. The one zone model, three layers of an fcc solid tethered to the lattice sites with a spring, proved very useful for this research primarily because it did not need as many CPU hours to equilibrate. The two zone wall uses springs as a two body potential and has a second stationary zone to hold the wall in place. The most complicated, the three zone wall, employed a reactionary zone, a stochastic zone and a stationary zone using a Lennard-Jones two body potential. Jet simulations were conducted on argon and nitrogen for liquid tube diameters from 20 to 65 A at both sub and supercritical temperatures (Ar: 130 K and 160 K, N2: 120 K and 130 K). The simulations focused on pressures above the critical pressure (Ar: 6 MPa, N2: 4 MPa). The diffusive wall showed some variation from the analytical velocity profile in the tube while the atomistically modeled walls performed very well. The walls were all able to maintain system temperature to reach

  18. Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code

    Science.gov (United States)

    Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín

    2010-12-01

    Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to

  19. A study of the diffusion mechanism in glasses: a theoretical and experimental study of tracers diffusion in amorphous metallic alloys

    International Nuclear Information System (INIS)

    Loirat, Yanick

    1999-01-01

    The principal aims of this work are a better understanding of the experimental situation in amorphous metallic alloys and a tentative explanation of the role of collective mechanisms in matter transport. Self- and solute-diffusion of Hf, Au and Cu tracers in amorphous Ni Zr alloy have been studied. We study by SIMS analysis the broadening of the concentration profile with temperature and pressure, in thin amorphous layers which were prepared by sputtering and properly relaxed. The diffusion coefficient variation with temperature shows an Arrhenius behaviour for all of our tracers. The activation energy amount to 1.55 eV for Cu, 1.65 eV for Au and 1.78 eV for Hf and corresponds to nearly one half of the corresponding energy in crystalline zirconium. The diffusion coefficients variation with hydrostatic pressure yields an activation volume equal to one half of an average atomic volume of our matrix for medium and large sized tracers Au, Hf and a smaller activation volume for Cu. The second part of our work consists of numerical simulations of atomic displacements in a generic glass by two complementary methods. In a Lennard-Jones alloy with size effect, we observe by molecular dynamics (MD) some correlated displacements which consist of substitution cycles or chains. The associated energy of these collective events represents nearly 15 pc of that found in crystalline Lennard- Jones. The systematic exploration of energy surface in space configuration made with activation-relaxation technique ART yields energy distributions of stable and saddles positions and opens the way to an evaluation of diffusion coefficients. The events found by ART are qualitatively close to MD ones, but the averaged activation energy associated with these events represents only 10 pc of the crystalline one. This clearly points towards the limit of Lennard-Jones potential, which is not enough representative of actual glasses. This is the reason why an interaction model closer to amorphous

  20. Closure system

    International Nuclear Information System (INIS)

    Kube, L.J.

    1978-01-01

    This invention relates generally to gas-cooled nuclear reactor systems and, more particularly, to an improved closure system for a pressure vessel in such a system wherein a penetration is provided for accommodating a heat exchanger. (author)

  1. Lymph system

    Science.gov (United States)

    Lymphatic system ... neck, under the arms, and groin. The lymph system includes the: Tonsils Adenoids Spleen Thymus ... JE, Flynn JA, Solomon BS, Stewart RW. Lymphatic system. In: Ball JW, Dains JE, Flynn JA, Solomon ...

  2. Liquid vs Solid Culture Medium to Evaluate Proportion and Time to Change in Management of Suspects of Tuberculosis-A Pragmatic Randomized Trial in Secondary and Tertiary Health Care Units in Brazil.

    Science.gov (United States)

    Moreira, Adriana da Silva Rezende; Huf, Gisele; Vieira, Maria Armanda Monteiro da Silva; Costa, Paulo Albuquerque da; Aguiar, Fábio; Marsico, Anna Grazia; Fonseca, Leila de Souza; Ricks, Mônica; Oliveira, Martha Maria; Detjen, Anne; Fujiwara, Paula Isono; Squire, Stephen Bertel; Kritski, Afranio Lineu

    2015-01-01

    The use of liquid medium (MGIT960) for tuberculosis (TB) diagnosis was recommended by WHO in 2007. However, there has been no evaluation of its effectiveness on clinically important outcomes. A pragmatic trial was carried out in a tertiary hospital and a secondary health care unit in Rio de Janeiro City, Brazil. Participants were 16 years or older, suspected of having TB. They were excluded if only cerebral spinal fluid or blood specimens were available for analysis. MGIT960 technique was compared with the Lowenstein-Jensen (LJ) method for laboratory diagnosis of active TB. Primary outcome was the proportion of patients who had their initial medical management changed within 2 months after randomisation. Secondary outcomes were: mean time for changing the procedure, patient satisfaction with the overall treatment and adverse events. Data were analysed by intention-to-treat. Between April 2008 and September 2011, 693 patients were enrolled (348 to MGIT, 345 to LJ). Smear and culture results were positive for 10% and 15.7% of participants, respectively. Patients in the MGIT arm had their initial medical management changed more frequently than those in the LJ group (10.1% MGIT vs 3.8% LJ, RR 2.67 95% CI 1.44-.96, p = 0.002, NNT 16, 95% CI 10-39). Mean time for changing the initial procedure was greater in LJ group at both sites: 20.0 and 29.6 days in MGIT group and 52.2 and 64.3 in LJ group (MD 33.5, 95% CI 30.6-36.4, p = 0.0001). No other important differences were observed. This study suggests that opting for the MGIT960 system for TB diagnosis provides a promising case management model for improving the quality of care and control of TB. Controlled-Trials.com ISRCTN79888843.

  3. Liquid vs Solid Culture Medium to Evaluate Proportion and Time to Change in Management of Suspects of Tuberculosis-A Pragmatic Randomized Trial in Secondary and Tertiary Health Care Units in Brazil.

    Directory of Open Access Journals (Sweden)

    Adriana da Silva Rezende Moreira

    Full Text Available The use of liquid medium (MGIT960 for tuberculosis (TB diagnosis was recommended by WHO in 2007. However, there has been no evaluation of its effectiveness on clinically important outcomes.A pragmatic trial was carried out in a tertiary hospital and a secondary health care unit in Rio de Janeiro City, Brazil. Participants were 16 years or older, suspected of having TB. They were excluded if only cerebral spinal fluid or blood specimens were available for analysis. MGIT960 technique was compared with the Lowenstein-Jensen (LJ method for laboratory diagnosis of active TB. Primary outcome was the proportion of patients who had their initial medical management changed within 2 months after randomisation. Secondary outcomes were: mean time for changing the procedure, patient satisfaction with the overall treatment and adverse events. Data were analysed by intention-to-treat. Between April 2008 and September 2011, 693 patients were enrolled (348 to MGIT, 345 to LJ. Smear and culture results were positive for 10% and 15.7% of participants, respectively. Patients in the MGIT arm had their initial medical management changed more frequently than those in the LJ group (10.1% MGIT vs 3.8% LJ, RR 2.67 95% CI 1.44-.96, p = 0.002, NNT 16, 95% CI 10-39. Mean time for changing the initial procedure was greater in LJ group at both sites: 20.0 and 29.6 days in MGIT group and 52.2 and 64.3 in LJ group (MD 33.5, 95% CI 30.6-36.4, p = 0.0001. No other important differences were observed.This study suggests that opting for the MGIT960 system for TB diagnosis provides a promising case management model for improving the quality of care and control of TB.Controlled-Trials.com ISRCTN79888843.

  4. Gas–liquid nucleation at large metastability: unusual features and a new formalism

    International Nuclear Information System (INIS)

    Santra, Mantu; Singh, Rakesh S; Bagchi, Biman

    2011-01-01

    to understand the large numerical discrepancy between simulation predictions and experimental results, we carried out a study of the dependence on the range of intermolecular interactions of both the surface tension of an equilibrium planar gas–liquid interface and the free energy barrier of nucleation. Both are found to depend significantly on the range of interaction for the Lennard-Jones potential, both in two and three dimensions. The value of surface tension and also the free energy difference between the gas and the liquid phase increase significantly and converge only when the range of interaction is extended beyond 6–7 molecular diameters. We find, with the full range of interaction potential, that the surface tension shows only a weak dependence on supersaturation, so the reason for the breakdown of CNT (with simulated values of surface tension and free energy gap) cannot be attributed to the supersaturation dependence of surface tension. This remains an unsettled issue at present because of the use of the value of surface tension obtained at coexistence

  5. Interfacial characteristics of propylene carbonate and validation of simulation models for electrochemical applications

    Science.gov (United States)

    You, Xinli

    Supercapacitors have occupy an indispensable role in today's energy storage systems due to their high power density and long life. The introduction of car- bon nanotube (CNT) forests as electrode offers the possibility of nano-scale design and high capacitance. We have performed molecular dynamics simulations on a CNT forest-based electrochemical double-layer capacitor (EDLC) and a widely used electrolyte solution (tetra-ethylammonium tetra-fluoroborate in propylene carbonate, TEABF4 /PC). We compare corresponding primitive model and atomically detailed model of TEABF4 /P, emphasizing the significance of ion clustering in electrolytes. The molecular dynamic simulation results suggests that the arrangement of closest neigh- bors leads to the formation of cation-anion chains or rings. Fuoss's discussion of ion-pairing model provides the approximation for a primitive model of 1-1 electrolyte is not broadly satisfactory for both primitive and atomically detailed cases. A more general Poisson statistical assumption is shown to be satisfactory when coordina- tion numbers are low, as is likely to be the case when ion-pairing initiates. We examined the Poisson-based model over a range of concentrations for both models of TEABF4 /P, and the atomically detailed model results identified solvent-separated nearest-neighbor ion-pairs. Large surface areas plays an essential role in nanomaterial properties, which calls for an accurate description of interfaces through modeling. We studied propylene carbonate, a widely used solvent in EDLC systems. PC wets graphite with a contact angle of 31°. The MD simulation model reproduced this contact angle after reduction 40% of the strength of graphite-C atom Lennard-Jones interactions with the solvent. The critical temperature of PC was accurately evaluated by extrapolating the PC liquid-vapor surface tensions. PC molecules tend to lie flat on the PC liquid-vapor surface, and project the propyl carbon toward the vapor phase. Liquid PC

  6. A sensitivity study of diffusional mass transfer of gases in tropical storm hydrometeors

    Science.gov (United States)

    Ghosh, Satyajit; Gumber, Siddharth; Varotsos, C.

    2017-11-01

    This paper quantifies mass transfer and diffusional uptake rates of gases in liquid and solid hydrometeors within a cyclonic system. The non-availability of transfer rates for trace gases diffusing into storm hydrometeors, particularly over polluted urban conurbations, often constrain modellers the world over; however, this is an essential requirement to quantify the scavenging rates over the region concerned. The present paper seeks to provide modellers with such rates. Further, all of the earlier studies apply only to temperate regimes, and surprisingly identical formulations are assumed even for tropical conditions. The present analysis fills this research gap and couples cloud morphology with the associated thermodynamics through Weather Research and Forecasting (WRF) runs for cyclone Chapala (27 October 2015-04 November 2015) which battered the coasts of Yemen (Skamarock et al. 2008). It was a good example for undertaking this sensitivity study because the vertical extent spanned from around 0.75 to 16 km—enabling uptake rate calculations over both droplet and ice phases. Many of the diffusing gases were polar; the dipole moment of sulphur dioxide (SO2) and water vapour (H2O) was also included using a full Lennard-Jones model to compute the binary diffusivities of these gases as they diffused into the droplets mixed with water vapour. The first-order uptake rate constants ranged from 2.08 × 10-07 to 3.44 × 10-06 (s-1) and 1.97 × 10-07 to 7.81 × 10-07 (s-1) for H2O and SO2 respectively. The rates are of the order of 10-09 (s-1) for diffusion of water vapour into ice crystals further aloft. Closely linked with the gas uptake rates is another crucial parameter—the mass accommodation coefficient, α. The most widely used values are 1 and 0.036 (Pruppacher and Klett 1998)—the chosen values are restrictive and warrants a closer look. In storm systems, the vertical extents are in the kilometre range. Chapala with a large vertical extent warrants a full

  7. INIS system

    International Nuclear Information System (INIS)

    Sokalski, A.

    1982-01-01

    History, organizational structure and operation principles of INIS system are presented. The preparation of input, checking and data processing as well as output production, computer forms of files and information retrieval systems are described in detail. The active participation of Poland in the system is emphasized. The possible ways of system development are presented. (author)

  8. Molecular dynamics simulation for the test of calibrated OPLS-AA force field for binary liquid mixture of tri-iso-amyl phosphate and n-dodecane

    Science.gov (United States)

    Das, Arya; Ali, Sk. Musharaf

    2018-02-01

    performing the non-equilibrium molecular dynamics employing the periodic perturbation method. The calculated shear viscosity of the binary mixture is found to be in excellent agreement with the experimental values. The use of the newly calibrated OPLS force field embedding Mulliken charges is shown to be equally reliable in predicting the structural and dynamical properties for the mixture without incorporating any arbitrary scaling in the force field or Lennard-Jones parameters. Further, the present MD simulation results demonstrate that the Stokes-Einstein relation breaks down at the molecular level. The present methodology might be adopted to evaluate the liquid state properties of an aqueous-organic biphasic system, which is of great significance in the interfacial science and technology.

  9. Systems effectiveness

    CERN Document Server

    Habayeb, A R

    1987-01-01

    Highlights three principal applications of system effectiveness: hardware system evaluation, organizational development and evaluation, and conflict analysis. The text emphasizes the commonality of the system effectiveness discipline. The first part of the work presents a framework for system effectiveness, partitioning and hierarchy of hardware systems. The second part covers the structure, hierarchy, states, functions and activities of organizations. Contains an extended Appendix on mathematical concepts and also several project suggestions.

  10. Reactive Systems

    DEFF Research Database (Denmark)

    Aceto, Luca; Ingolfsdottir, Anna; Larsen, Kim Guldstrand

    A reactive system comprises networks of computing components, achieving their goals through interaction among themselves and their environment. Thus even relatively small systems may exhibit unexpectedly complex behaviours. As moreover reactive systems are often used in safety critical systems......, the need for mathematically based formal methodology is increasingly important. There are many books that look at particular methodologies for such systems. This book offers a more balanced introduction for graduate students and describes the various approaches, their strengths and weaknesses, and when...

  11. Bitcoin System

    Directory of Open Access Journals (Sweden)

    Jan Lánský

    2017-06-01

    Full Text Available Cryptocurrency systems are purely digital and decentralized systems that use cryptographic principles to confirm transactions. Bitcoin is the first and also the most widespread cryptocurrency. The aim of this article is to introduce Bitcoin system using a language understandable also to readers without computer science education. This article captures the Bitcoin system from three perspectives: internal structure, network and users. Emphasis is placed on brief and clear definitions (system components and their mutual relationships. A new system view of the stated terms constitutes author’s own contribution.

  12. Phosalone-Induced Changes in Regional Cholinesterase Activities ...

    African Journals Online (AJOL)

    Nekky Umera

    Arnal, F., Cote, L.J., Ginsburg, S., Lawrence, G.D., Naini, A. and Sano, M. (1990). Studies on new centrally active reversible acetylcholinesterase inhibitors. Neurochem. Res. 15: 587-599. Balasundaram, K. and Selvarajan, V.R. (1990). Inhibition of acetylcholinesterase in the central nervous system of Rana tigrina.

  13. Basic Aerodynamics of Combustion Chambers,

    Science.gov (United States)

    1981-05-20

    there are viscous shear force-s ,(8/)[/a If, at a place of adhesion to the wall (&1/00) = 0, r =0; theng the flow layer will adhere to the wall...cylindrical coordinate system . I . .’ .I: --m ’ .lj . ***# .., A, (b) , plane Fi. 5.5 I r, , z Cylindrie’. Coordirate Sistem and a Cro- Section

  14. Journal ofEAEA, Vo116,1999

    African Journals Online (AJOL)

    In thispaper, the combined heat and mass transfer of water-vapor into a cylindrical zeolite adsorber has been numerically simulated The two- dimensional heat and mass transfer equations are numerically solved using gPROMS program - a general Process Modeling System {lJ program, inserting the proper initial and ...

  15. Intelligent Systems

    Data.gov (United States)

    National Aeronautics and Space Administration — The autonomous systems (AS) project, led by NASA Ames, is developing software for system operation automation. AS technology will help astronauts make more decisions...

  16. Crystal Systems.

    Science.gov (United States)

    Schomaker, Verner; Lingafelter, E. C.

    1985-01-01

    Discusses characteristics of crystal systems, comparing (in table format) crystal systems with lattice types, number of restrictions, nature of the restrictions, and other lattices that can accidently show the same metrical symmetry. (JN)

  17. Filter systems

    International Nuclear Information System (INIS)

    Vanin, V.R.

    1990-01-01

    The multidetector systems for high resolution gamma spectroscopy are presented. The observable parameters for identifying nuclides produced simultaneously in the reaction are analysed discussing the efficiency of filter systems. (M.C.K.)

  18. Tear System

    Science.gov (United States)

    ... and symptoms may result from the tear drainage system becoming obstructed at any point from the puncta ... specializes in the eyelids, orbit, and tear drain system. It’s also important that he or she is ...

  19. Biliary system

    Science.gov (United States)

    The biliary system creates, moves, stores, and releases bile into the duodenum . This helps the body digest food. It also assists ... from the liver to the duodenum. The biliary system includes: The gallbladder Bile ducts and certain cells ...

  20. Expert systems

    International Nuclear Information System (INIS)

    Haldy, P.A.

    1988-01-01

    The definitions of the terms 'artificial intelligence' and 'expert systems', the methodology, areas of employment and limits of expert systems are discussed. The operation of an expert system is described, especially the presentation and organization of knowledge as well as interference and control. Methods and tools for expert system development are presented and their application in nuclear energy are briefly addressed. 7 figs., 2 tabs., 6 refs

  1. Watchdog System

    DEFF Research Database (Denmark)

    Madsen, Tanja Kidholm Osmann; Bahnsen, Chris Holmberg; Jensen, Morten Bornø

    This deliverable is part of WP4. Overall WP4 is motivated by the need for automatic systems that can ease the task of annotating massive amounts of traffic data. Concretely this deliverable is related to WP4.2 - the watchdog system. The idea with the watchdog is to develop a system that can remov...

  2. Embedded Systems

    Indian Academy of Sciences (India)

    system programmers should take into consideration all possi- bilities and write programs that do not fail. Responsiveness: Embedded systems should respond to events as soon as possible. For example, a patient monitoring system should process the patient'S heart signals quickly and immedi- ately notify if any abnormality ...

  3. Systems Engineering

    Science.gov (United States)

    Pellerano, Fernando

    2015-01-01

    This short course provides information on what systems engineering is and how the systems engineer guides requirements, interfaces with the discipline leads, and resolves technical issues. There are many system-wide issues that either impact or are impacted by the thermal subsystem. This course will introduce these issues and illustrate them with real life examples.

  4. Creative Systems

    DEFF Research Database (Denmark)

    Manelius, Anne-Mette; Beim, Anne

    2007-01-01

    Opsamling af diskussioner på konferencen og udstillingen Creative Systems i september/oktober 2007. Konferencen og Udstillingen Creative Systems sætter fokus på systemer som en positiv drivkraft i den kreative skabelsesproces. CINARK inviterede fire internationale kapaciteter, som indenfor hver...

  5. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    Systems biology seeks to study biological systems as a whole, contrary to the reductionist approach that has dominated biology. Such a view of biological systems emanating from strong foundations of molecular level understanding of the individual components in terms of their form, function and interactions is promising to ...

  6. Digestive System

    Science.gov (United States)

    ... Staying Safe Videos for Educators Search English Español Digestive System KidsHealth / For Parents / Digestive System What's in this ... the body can absorb and use. About the Digestive System Almost all animals have a tube-type digestive ...

  7. Embedded Systems

    Indian Academy of Sciences (India)

    sumer electronic systems, they are cost sensitive. Thus their cost must be low. Robustness: Embedded systems should be robust since they operate in a harsh environment. They should endure vibrations, power supply fluctuations and excessive heat. Due to limited power supply in an embedded system, the power ...

  8. Operating systems

    CERN Document Server

    Tsichritzis, Dionysios C; Rheinboldt, Werner

    1974-01-01

    Operating Systems deals with the fundamental concepts and principles that govern the behavior of operating systems. Many issues regarding the structure of operating systems, including the problems of managing processes, processors, and memory, are examined. Various aspects of operating systems are also discussed, from input-output and files to security, protection, reliability, design methods, performance evaluation, and implementation methods.Comprised of 10 chapters, this volume begins with an overview of what constitutes an operating system, followed by a discussion on the definition and pr

  9. Multifunction system

    International Nuclear Information System (INIS)

    Wauthier, J.; Fiori, R.

    1990-01-01

    The development, the characteristics and the applications of a multifunction system are presented. The system is used on the RBES laboratory pipes, at Marcoule. The system was developed in order to allow, without time loss, the modification of the circuit function by replacing only one component. The following elements form the multifunction system: a fixed base, which is part of the tube, a removable piece, which is inserted into the base, a cover plate and its locking system. The material, chosen among commercial trade marks, required small modifications in order to be used in the circuit [fr

  10. Nonequilibrium thermodynamics of an interface

    Science.gov (United States)

    Schweizer, Marco; Öttinger, Hans Christian; Savin, Thierry

    2016-05-01

    Interfacial thermodynamics has deep ramifications in understanding the boundary conditions of transport theories. We present a formulation of local equilibrium for interfaces that extends the thermodynamics of the "dividing surface," as introduced by Gibbs, to nonequilibrium settings such as evaporation or condensation. By identifying the precise position of the dividing surface in the interfacial region with a gauge degree of freedom, we exploit gauge-invariance requirements to consistently define the intensive variables for the interface. The model is verified under stringent conditions by employing high-precision nonequilibrium molecular-dynamics simulations of a coexisting vapor-liquid Lennard-Jones fluid. We conclude that the interfacial temperature is determined using the surface tension as a "thermometer," and it can be significantly different from the temperatures of the adjacent phases. Our findings lay foundations for nonequilibrium interfacial thermodynamics.

  11. Parameter-free dissipation in simulated sliding friction

    Science.gov (United States)

    Benassi, A.; Vanossi, A.; Santoro, G. E.; Tosatti, E.

    2010-08-01

    Nonequilibrium molecular-dynamics simulations, of crucial importance in sliding friction, are hampered by arbitrariness and uncertainties in the way Joule heat is removed. We implement in a realistic frictional simulation a parameter-free, non-Markovian, stochastic dynamics, which, as expected from theory, absorbs Joule heat precisely as a semi-infinite harmonic substrate would. Simulating stick-slip friction of a slider over a two-dimensional Lennard-Jones solid, we compare our virtually exact frictional results with approximate ones from commonly adopted empirical dissipation schemes. While the latter are generally in serious error, we show that the exact results can be closely reproduced by a viscous Langevin dissipation at the boundary layer, once the backreflected frictional energy is variationally optimized.

  12. 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......The traditional view that the physical properties of a simple liquid are determined primarily by its repulsive forces was recently challenged by Berthier and Tarjus, who showed that in some cases ignoring the attractions leads to large errors in the dynamics [L. Berthier and G. Tarjus, Phys. Rev...... are included in the simulations. What matters is whether or not interactions are included from all particles within the first coordination shell – the attractive forces can thus be ignored, but only at extremely high densities. The recognition of the importance of a local shell in condensed fluids goes back...

  13. Cantilever-based sensing: the origin of surface stress and optimization strategies

    International Nuclear Information System (INIS)

    Godin, Michel; Tabard-Cossa, Vincent; Miyahara, Yoichi; Grutter, Peter; Monga, Tanya; Bruce Lennox, R; Williams, P J; Beaulieu, L Y

    2010-01-01

    Many interactions drive the adsorption of molecules on surfaces, all of which can result in a measurable change in surface stress. This article compares the contributions of various possible interactions to the overall induced surface stress for cantilever-based sensing applications. The surface stress resulting from adsorption-induced changes in the electronic density of the underlying surface is up to 2-4 orders of magnitude larger than that resulting from intermolecular electrostatic or Lennard-Jones interactions. We reveal that the surface stress associated with the formation of high quality alkanethiol self-assembled monolayers on gold surfaces is independent of the molecular chain length, supporting our theoretical findings. This provides a foundation for the development of new strategies for increasing the sensitivity of cantilever-based sensors for various applications.

  14. Adhesive contact between a cylinder and a half-space

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Jiunn-Jong, E-mail: jjw5277@ms19.hinet.ne, E-mail: jjwu@mail.cgu.edu.t [Department of Mechanical Engineering, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan, Taiwan (China)

    2009-08-07

    Numerical simulation for the adhesive contact between a sphere and a half-space is employed. The numerical simulation is performed for a realistic surface force law based on the Lennard-Jones potential between molecules with the Derjaguin approximation. The result is compared with the two-dimensional Maugis model, which uses the Dugdale law. It is found that the Maugis model gives good results, approximating those obtained by the numerical simulation. It is also found that the usual Maugis parameter governs the transition from the two-dimensional JKR model to the two-dimensional rigid cylinder contact. But the rigid body limit found using the Maugis model is different from that found using the numerical simulation.

  15. Adhesive contact between a cylinder and a half-space

    Science.gov (United States)

    Wu, Jiunn-Jong

    2009-08-01

    Numerical simulation for the adhesive contact between a sphere and a half-space is employed. The numerical simulation is performed for a realistic surface force law based on the Lennard-Jones potential between molecules with the Derjaguin approximation. The result is compared with the two-dimensional Maugis model, which uses the Dugdale law. It is found that the Maugis model gives good results, approximating those obtained by the numerical simulation. It is also found that the usual Maugis parameter governs the transition from the two-dimensional JKR model to the two-dimensional rigid cylinder contact. But the rigid body limit found using the Maugis model is different from that found using the numerical simulation.

  16. Simulating prescribed particle densities in the grand canonical ensemble using iterative algorithms.

    Science.gov (United States)

    Malasics, Attila; Gillespie, Dirk; Boda, Dezso

    2008-03-28

    We present two efficient iterative Monte Carlo algorithms in the grand canonical ensemble with which the chemical potentials corresponding to prescribed (targeted) partial densities can be determined. The first algorithm works by always using the targeted densities in the kT log(rho(i)) (ideal gas) terms and updating the excess chemical potentials from the previous iteration. The second algorithm extrapolates the chemical potentials in the next iteration from the results of the previous iteration using a first order series expansion of the densities. The coefficients of the series, the derivatives of the densities with respect to the chemical potentials, are obtained from the simulations by fluctuation formulas. The convergence of this procedure is shown for the examples of a homogeneous Lennard-Jones mixture and a NaCl-CaCl(2) electrolyte mixture in the primitive model. The methods are quite robust under the conditions investigated. The first algorithm is less sensitive to initial conditions.

  17. Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer

    Directory of Open Access Journals (Sweden)

    Casuyac Miqueas

    2016-01-01

    Full Text Available This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNRusing the classical molecular dynamic (MD simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator. The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H2 on SiNR. By varying the temperatures (60 K Δ 130 K, we observed that the Δxdisplacement of H2 on the surface SiNR shows a Brownian motion on a Lennard-Jones potential and a Gaussian probability distribution can be plotted describing the diffusion of H2. The calculated mean square displacement (MSD was approximately increasing in time and the activation energy barrier for diffusion has been found to be 43.23meV.

  18. Communication: Predicting virial coefficients and alchemical transformations by extrapolating Mayer-sampling Monte Carlo simulations

    Science.gov (United States)

    Hatch, Harold W.; Jiao, Sally; Mahynski, Nathan A.; Blanco, Marco A.; Shen, Vincent K.

    2017-12-01

    Virial coefficients are predicted over a large range of both temperatures and model parameter values (i.e., alchemical transformation) from an individual Mayer-sampling Monte Carlo simulation by statistical mechanical extrapolation with minimal increase in computational cost. With this extrapolation method, a Mayer-sampling Monte Carlo simulation of the SPC/E (extended simple point charge) water model quantitatively predicted the second virial coefficient as a continuous function spanning over four orders of magnitude in value and over three orders of magnitude in temperature with less than a 2% deviation. In addition, the same simulation predicted the second virial coefficient if the site charges were scaled by a constant factor, from an increase of 40% down to zero charge. This method is also shown to perform well for the third virial coefficient and the exponential parameter for a Lennard-Jones fluid.

  19. Melting of rare-gas crystals: Monte Carlo simulation versus experiments.

    Science.gov (United States)

    Bocchetti, V; Diep, H T

    2013-03-14

    We study the melting transition in crystals of rare gas Ar, Xe, and Kr by the use of extensive Monte Carlo simulations with the Lennard-Jones potential. The parameters of this potential have been deduced by Bernardes in 1958 from experiments of rare gas in the gaseous phase. It is amazing that the parameters of such a popular potential were not fully tested so far. Using the Bernardes parameters, we find that the melting temperature of several rare gas is from 13% to 20% higher than that obtained from experiments. We have throughout studied the case of Ar by examining both finite-size and cutoff-distance effects. In order to get a good agreement with the experimental melting temperature, we propose a modification of these parameters to describe better the melting of rare-gas crystals.

  20. The energy barrier to reorientational motion of the trifluoromethyl group in lithium trifluoromethanesulphonate and its complex with poly(ethylene oxide): a comparison between modelling and NMR relaxation measurements

    Science.gov (United States)

    Moore, Elaine A.; Mortimer, Michael; Wigglesworth, Christopher; Williams, Martin A. K.

    1999-07-01

    Molecular modelling is used to calculate the barrier heights to reorientation for the trifluoromethyl group, CF 3, in both lithium trifluoromethanesulphonate, LiCF 3SO 3, and the crystalline complex of this salt with poly(ethylene oxide), PEO. The calculated barrier heights are compared with those determined from 19F spin-lattice relaxation studies. In the case of LiCF 3SO 3, fluorine-fluorine non-bonded interactions are shown to play a dominant role in determining the barrier height to CF 3 group reorientation and optimised Lennard-Jones parameters for this interaction are determined. In the crystalline complex, PEO 3·LiCF 3SO 3, it is suggested that CF 3 group reorientation is strongly influenced by segmental motions of the PEO chain.

  1. Simulation of wetting and drying at solid-fluid interfaces on the Delft molecular dynamics processor

    International Nuclear Information System (INIS)

    Sikkenk, J.H.; Indekeu, J.O.; van Leeuwen, J.M.J.; Vossnack, E.O.; Bakker, A.F.

    1988-01-01

    The adsorption is studied of a fluid at a structured solid substrate by means of computer simulations on the Delft Molecular Dynamics Processor. Two types of particles are present, 2904 of one type for building a three-layer substrate and about 8500 of another type for composing the fluid. Interactions between like and unlike atoms are modeled by pair potentials of Lennard-Jones form cut off at 2.5σ. Simulations are performed at constant temperature and variable ratio of substrate-adsorbate to adsorbate-adsorbate attraction. On the basis of measurements of density profiles, coverages, surface tensions, and contact angles, a wetting as well as a drying phase transition have been identified. Both transitions are of first order

  2. Secondary Structure Analysis of Native Cellulose by Molecular Dynamics Simulations with Coarse Grained Model

    Science.gov (United States)

    Wu, Shuai; Zhan, Hai-yi; Wang, Hong-ming; Ju, Yan

    2012-04-01

    The secondary structure of different Iβ cellulose was analyzed by a molecular dynamics simulation with MARTINI coarse-grained force field, where each chain of the cellulose includes 40 D-glucoses units. Calculation gives a satisfied description about the secondary structure of the cellulose. As the chain number increasing, the cellulose becomes the form of a helix, with the diameter of screw growing and spiral rising. Interestingly, the celluloses with chain number N 4 of 6, 24 and 36 do show right-hand twisting. On the contrast, the celluloses with N 8 of 12, 16 chains are left-hand twisting. These simulations indicate that the cellulose with chain number larger than 36 will break down to two parts. Besides, the result indicates that 36-chains cellulose model is the most stable among all models. Furthermore, the Lennard-Jones potential determines the secondary structure. In addition, an equation was set up to analyze the twisting structure.

  3. Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus.

    Science.gov (United States)

    Herruzo, Elena T; Garcia, Ricardo

    2012-01-01

    Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip-surface forces such as the Lennard-Jones and Derjaguin-Muller-Toporov forces.

  4. Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus

    Directory of Open Access Journals (Sweden)

    Elena T. Herruzo

    2012-03-01

    Full Text Available Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip–surface forces such as the Lennard-Jones and Derjaguin–Muller–Toporov forces.

  5. Gas Permeation Characteristics across Nano-Porous Inorganic Membranes

    Directory of Open Access Journals (Sweden)

    M.R Othman, H. Mukhtar

    2012-10-01

    Full Text Available An overview of parameters affecting gas permeation in inorganic membranes is presented. These factors include membrane physical characteristics, operational parameters and gas molecular characteristics. The membrane physical characteristics include membrane materials and surface area, porosity, pore size and pore size distribution and membrane morphology. The operational parameters include feed flow rate and concentration, stage cut, temperature and pressure. The gas molecular characteristics include gas molecular weight, diameter, critical temperature, critical pressure, Lennard-Jones parameters and diffusion volumes. The current techniques of material characterization may require complementary method in describing microscopic heterogeneity of the porous ceramic media. The method to be incorporated in the future will be to apply a stochastic model and/or fractal dimension. Keywords: Inorganic membrane, surface adsorption, Knudsen diffusion, Micro-porous membrane, permeation, gas separation.

  6. Properties of a soft-core model of methanol: An integral equation theory and computer simulation study

    Science.gov (United States)

    Huš, Matej; Munaò, Gianmarco; Urbic, Tomaz

    2014-01-01

    Thermodynamic and structural properties of a coarse-grained model of methanol are examined by Monte Carlo simulations and reference interaction site model (RISM) integral equation theory. Methanol particles are described as dimers formed from an apolar Lennard-Jones sphere, mimicking the methyl group, and a sphere with a core-softened potential as the hydroxyl group. Different closure approximations of the RISM theory are compared and discussed. The liquid structure of methanol is investigated by calculating site-site radial distribution functions and static structure factors for a wide range of temperatures and densities. Results obtained show a good agreement between RISM and Monte Carlo simulations. The phase behavior of methanol is investigated by employing different thermodynamic routes for the calculation of the RISM free energy, drawing gas-liquid coexistence curves that match the simulation data. Preliminary indications for a putative second critical point between two different liquid phases of methanol are also discussed. PMID:25362323

  7. 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...... is further increased. Using a Gaussian theory on an interfacial Ginzburg-Landau model of surfactants, we find that the initial decrease of the bending rigidity is attributed to coupling between fluctuations of the surfactant orientation field to those in the interfacial height. (C) 2000 American Institute......, corresponding to the interfacial tension and the mean bending modulus are determined from the analyses of the long-wavelength behavior of the structure factor of the capillary waves. We found that the interfacial tension decreases with increasing surfactant interfacial coverage and/or surfactant chain length...

  8. Statistical ensembles and molecular dynamics studies of anisotropic solids. II

    International Nuclear Information System (INIS)

    Ray, J.R.; Rahman, A.

    1985-01-01

    We have recently discussed how the Parrinello--Rahman theory can be brought into accord with the theory of the elastic and thermodynamic behavior of anisotropic media. This involves the isoenthalpic--isotension ensemble of statistical mechanics. Nose has developed a canonical ensemble form of molecular dynamics. We combine Nose's ideas with the Parrinello--Rahman theory to obtain a canonical form of molecular dynamics appropriate to the study of anisotropic media subjected to arbitrary external stress. We employ this isothermal--isotension ensemble in a study of a fcc→ close-packed structural phase transformation in a Lennard-Jones solid subjected to uniaxial compression. Our interpretation of the Nose theory does not involve a scaling of the time variable. This latter fact leads to simplifications when studying the time dependence of quantities

  9. Exploring the free energy surfaces of clusters using reconnaissance metadynamics

    Science.gov (United States)

    Tribello, Gareth A.; Cuny, Jérôme; Eshet, Hagai; Parrinello, Michele

    2011-09-01

    A new approach is proposed for exploring the low-energy structures of small to medium-sized aggregates of atoms and molecules. This approach uses the recently proposed reconnaissance metadynamics method [G. A. Tribello, M. Ceriotti, and M. Parrinello. Proc. Natl. Acad. Sci. U.S.A. 107(41), 17509 (2010), 10.1073/pnas.1011511107] in tandem with collective variables that describe the average structure of the coordination sphere around the atoms/molecules. We demonstrate this method on both Lennard-Jones and water clusters and show how it is able to quickly find the global minimum in the potential energy surface, while exploring the finite temperature free energy surface.

  10. Molecular Dynamics Simulation Study of Transport Properties of Diatomic Gases

    International Nuclear Information System (INIS)

    Lee, Song Hi; Kim, Ja Hun

    2014-01-01

    In this paper, we report thermodynamic and transport properties (diffusion coefficient, viscosity, and thermal conductivity) of diatomic gases (H 2 , N 2 , O 2 , and Cl 2 ) at 273.15 K and 1.00 atm by performing molecular dynamics simulations using Lennard-Jones intermolecular potential and modified Green-Kubo formulas. The results of self-diffusion coefficients of diatomic gases obtained from velocity auto-correlation functions by Green-Kubo relation are in good agreement with those obtained from mean square displacements by Einstein relation. While the results for viscosities of diatomic gases obtained from stress auto-correlation functions underestimate the experimental results, those for thermal conductivities obtained from heat flux autocorrelation functions overestimate the experimental data except H 2

  11. Computer simulations of nanoindentation in Mg-Cu and Cu-Zr metallic glasses

    DEFF Research Database (Denmark)

    Paduraru, Anca; Andersen, Ulrik Grønbjerg; Thyssen, Anders

    2010-01-01

    The formation of shear bands during plastic deformation of Cu0.50Zr0.50 and Mg0.85Cu0.15 metallic glasses is studied using atomic-scale computer simulations. The atomic interactions are described using realistic many-body potentials within the effective medium theory, and are compared with similar...... simulations using a Lennard-Jones description of the material. The metallic glasses are deformed both in simple shear and in a simulated nanoindentation experiment. Plastic shear localizes into shear bands with a width of approximately 5 nm in CuZr and 8 nm in MgCu. In simple shear, the shear band formation...... is very clear, whereas only incipient shear bands are seen in nanoindentation. The shear band formation during nanoindentation is sensitive to the indentation velocity, indenter radius and the cooling rate during the formation of the metallic glass. For comparison, a similar nanoindentation simulation...

  12. New theories for smectic and nematic liquid crystalline polymers

    International Nuclear Information System (INIS)

    Dowell, F.

    1987-01-01

    A summary of results from new statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with LCPs is presented. Thermodynamic and molecular ordering properties (including odd-even effects) have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories have been used to design new LCPs and new solvents and to predict and explain properties

  13. Thermophysical properties and some parameters of liquid sodium

    International Nuclear Information System (INIS)

    Rapeanu, S.; Padureanu, I.; Rotarescu, G.; Craciun, C.; Ion, M.

    1982-07-01

    In the paper are reported some results on the thermophysical properties of the liquid sodium obtained by means of the neutron scattering and of the theories existing for various physical parameters. The results are based on hard sphere approach and neutron diffraction experiments performed in the region of the small momentum transfer. From this measurement extrapolated at Q → 0, the packing fraction eta as a function of temperature in the range 100-600 deg is obtained. Knowing the parameter eta, the structure factor S(Q) and the radial distribution function g(r) are calculated. To calculate various physical parameters of the liquid sodium like: electrical resistivity, thermoelectric power, viscosity coefficient, electrical conductivity etc., S(Q), g(r) and a Lennard Jones interaction potential phi(r) are used. (authors)

  14. New theories for smectic and nematic liquid-crystal polymers: Backbone LCPs [liquid crystalline polymers] and their mixtures and side-chain LCPs

    International Nuclear Information System (INIS)

    Dowell, F.

    1987-01-01

    A summary of predictions and explanations from statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with backbone LCPs are presented. Trends in the thermodynamic and molecular ordering properties have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. The theoretical results are found to be in good agreement with existing experimental data. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories can be used to design new LCPs and new solvents as well as to predict and explain properties. 27 refs., 4 tabs

  15. Extension of the JCZ product species database

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-09-01

    A database has been created for use with the Jacobs-Cowperthwaite-Zwisler-3 equation-of-state (JCZ3-EOS) to determine thermochemical equilibrium states for energetic materials. The JCZ3-EOS uses the exponential 6 intermolecular potential function to describe interactions between molecules. Product species are characterized by r{sup *}, the radius of the minimum pair potential energy, and {var_epsilon}/{kappa}, the well depth energy normalized by Boltzmann`s constant. These parameters constitute the JCZS (S for Sandia) database describing 750 gases listed in the JANNAF tables and were obtained by using literature values of the Lennard-Jones potential, a corresponding states theory, pure liquid shock Hugoniot data, and fit values to an empirical EOS. Detonation velocities predicted with the JCZS database for a wide variety of explosives are in good agreement with data. Improved predictions of low density explosives is attributed to a better description of molecular interactions at intermediate pressures.

  16. Weak temperature dependence of ageing of structural properties in atomistic model glassformers

    Science.gov (United States)

    Jenkinson, Thomas; Crowther, Peter; Turci, Francesco; Royall, C. Patrick

    2017-08-01

    Ageing phenomena are investigated from a structural perspective in two binary Lennard-Jones glassformers, the Kob-Andersen and Wahnström mixtures. In both, the geometric motif assumed by the glassformer upon supercooling, the locally favoured structure (LFS), has been established. The Kob-Andersen mixture forms bicapped square antiprisms; the Wahnström model forms icosahedra. Upon ageing, we find that the structural relaxation time has a time-dependence consistent with a power law. However, the LFS population and potential energy increase and decrease, respectively, in a logarithmic fashion. Remarkably, over the time scales investigated, which correspond to a factor of 104 change in relaxation times, the rate at which these quantities age appears almost independent of temperature. Only at temperatures far below the Vogel-Fulcher-Tamman temperature do the ageing dynamics slow.

  17. Surface tension of different sized single-component droplets, according to macroscopic data obtained using the lattice gas model and the critical droplet size during phase formation

    Science.gov (United States)

    Tovbin, Yu. K.; Zaitseva, E. S.; Rabinovich, A. B.

    2017-10-01

    Size dependences of the surface tension of spherical single-component droplets are calculated using equations of the lattice gas model for 19 compounds. Parameters of the model are found from experimental data on the surface tension of these compounds for a macroscopic planar surface. The chosen low-molecular compounds satisfy the law of corresponding states. To improve agreement with the experimental data, Lennard-Jones potential parameters are varied within 10% deviations. The surface tensions of different sized equilibrium droplets are calculated at elevated and lowered temperatures. It is found that the surface tension of droplets grows monotonically as the droplet size increases from zero to its bulk value. The droplet size R 0 corresponding to zero surface tension corresponds to the critical size of the emergence of a new phase. The critical droplet sizes in the new phase of the considered compounds are estimated for the first time.

  18. Sub- and super-Maxwellian evaporation of simple gases from liquid water

    International Nuclear Information System (INIS)

    Kann, Z. R.; Skinner, J. L.

    2016-01-01

    Non-Maxwellian evaporation of light atoms and molecules (particles) such as He and H 2 from liquids has been observed experimentally. In this work, we use simulations to study systematically the evaporation of Lennard-Jones particles from liquid water. We find instances of sub- and super-Maxwellian evaporation, depending on the mass of the particle and the particle-water interaction strength. The observed trends are in qualitative agreement with experiment. We interpret these trends in terms of the potential of mean force and the effectiveness and frequency of collisions during the evaporation process. The angular distribution of evaporating particles is also analyzed, and it is shown that trends in the energy from velocity components tangential and normal to the liquid surface must be understood separately in order to interpret properly the angular distributions.

  19. Computational study of heat transport in compositionally disordered binary crystals

    International Nuclear Information System (INIS)

    Lyver, John W.; Blaisten-Barojas, Estela

    2006-01-01

    The thermal conductivity of compositionally disordered binary crystals with atoms interacting through Lennard-Jones potentials has been studied as a function of temperature. The two species in the crystal differ in mass, hard-core atomic diameter, well depth and relative concentration. The isobaric Monte Carlo was used to equilibrate the samples at near-zero pressure. The isoenergy molecular dynamics combined with the Green-Kubo approach was taken to calculate the heat current time-dependent autocorrelation function and determine the lattice thermal conductivity of the sample. The inverse temperature dependence of the lattice thermal conductivity was shown to fail at low temperatures when the atomic diameters of the two species differ. Instead, the thermal conductivity was nearly a constant across temperatures for species with different atomic diameters. Overall, it is shown that there is a dramatic decrease of the lattice thermal conductivity with increasing atomic radii ratio between species and a moderate decrease due to mass disorder

  20. Application of Statistical Thermodynamics in Refrigeration

    International Nuclear Information System (INIS)

    Avsec, J.; Marcic, M.

    1999-01-01

    The paper presents the mathematical model for computing the thermodynamical properties in the liquid, gas and two-phase domain by means of statistical thermodynamics. The paper features all important components (translation, rotation, internal rotation, vibration, intermolecular potential energy and influence of electron and nuclei excitation). To calculate the thermodynamic properties of real gases, we have developed the cluster theory, which yields better results than the virial equation. In case of real liquids, the Johnson-Zollweg-Gubbins model based on the modified Benedict-Webb-Rubin (BWR) equation was applied. The Lennard-Jones intermolecular potential was used. The analytical results are compared with the thermodynamical data and models obtained from classical thermodynamics, and they show relatively good agreement. (author)

  1. Buckling instability of circular double-layered graphene sheets.

    Science.gov (United States)

    Natsuki, Toshiaki; Shi, Jin-Xing; Ni, Qing-Qing

    2012-04-04

    In this paper, we study the buckling properties of circular double-layered graphene sheets (DLGSs), using plate theory. The two graphene layers are modeled as two individual sheets whose interactions are determined by the Lennard-Jones potential of the carbon-carbon bond. An analytical solution of coupled governing equations is proposed for predicting the buckling properties of circular DLGSs. Using the present theoretical approach, the influences of boundary conditions, plate sizes, and buckling-mode shapes on the buckling behaviors are investigated in detail. The buckling stability is significantly affected by the buckling-mode shapes. As a result of van der Waals interactions, the buckling stress of circular DLGSs is much larger for the anti-phase mode than for the in-phase mode. © 2012 IOP Publishing Ltd

  2. Cluster dynamics: A classical trajectory study of A + A/sub n/arrow-right-leftA*/sub n/+1

    International Nuclear Information System (INIS)

    Brady, J.W.; Doll, J.D.; Thompson, D.L.

    1979-01-01

    The dynamics of the collision of an atom A with a small cluster of atoms, A/sub n/, leading to the formation of a quasibound A*/sub n/+1 complex, which subsequently decays, has been studied using classical trajectories. Pairwise Lennard-Jones potentials (with parameters appropriate for argon) were used to describe the identical point masses (Ar). The results illustrate the feasibility of direct calculations of microscopic rates for nucleation processes. The dissociation of collisionally formed A*/sub n/+1 (n=3,4, and 5) occurs by first-order exponential decay. Furthermore the energy dependence of the dissociation rate constants appears to be well described by the RRK functional form

  3. A New Simplified Local Density Model for Adsorption of Pure Gases and Binary Mixtures

    Science.gov (United States)

    Hasanzadeh, M.; Dehghani, M. R.; Feyzi, F.; Behzadi, B.

    2010-12-01

    Adsorption modeling is an important tool for process simulation and design. Many theoretical models have been developed to describe adsorption data for pure and multicomponent gases. The simplified local density (SLD) approach is a thermodynamic model that can be used with any equation of state and offers some predictive capability with adjustable parameters for modeling of slit-shaped pores. In previous studies, the SLD model has been utilized with the Lennard-Jones potential function for modeling of fluid-solid interactions. In this article, we have focused on application of the Sutherland potential function in an SLD-Peng-Robinson model. The advantages and disadvantages of using the new potential function for adsorption of methane, ethane, carbon dioxide, nitrogen, and three binary mixtures on two types of activated carbon are illustrated. The results have been compared with previous models. It is shown that the new SLD model can correlate adsorption data for different pressures and temperatures with minimum error.

  4. Cognitive Systems

    DEFF Research Database (Denmark)

    The tutorial will discuss the definition of cognitive systems as the possibilities to extend the current systems engineering paradigm in order to perceive, learn, reason and interact robustly in open-ended changing environments. I will also address cognitive systems in a historical perspective an...... in cognitive systems include e.g. personalized information systems, sensor network systems, social dynamics system and Web2.0, and cognitive components analysis. I will use example from our own research and link to other research activities.......The tutorial will discuss the definition of cognitive systems as the possibilities to extend the current systems engineering paradigm in order to perceive, learn, reason and interact robustly in open-ended changing environments. I will also address cognitive systems in a historical perspective...... to be modeled within a limited set of predefined specifications. There will inevitably be a need for robust decisions and behaviors in novel situations that include handling of conflicts and ambiguities based on the capability and knowledge of the artificial cognitive system. Further, there is a need...

  5. Expert System

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas Troels; Cattani, Gian Luca

    2016-01-01

    An expert system is a computer system for inferring knowledge from a knowledge base, typically by using a set of inference rules. When the concept of expert systems was introduced at Stanford University in the early 1970s, the knowledge base was an unstructured set of facts. Today the knowledge...... base of expert systems is often given in terms of an ontology, extracted and built from various data sources by employing natural language-processing and statistics. To emphasize such capabilities, the term “expert” is now often replaced by “cognitive,” “knowledge,” “knowledge-based,” or “intelligent......” system. With very few exceptions, general-purpose expert systems have failed to emerge so far. However, expert systems are applied in specialized domains, particularly in healthcare. The increasing availability of large quantities of data to organizations today provides a valuable opportunity...

  6. Ternary systems

    International Nuclear Information System (INIS)

    Kagan, D.N.; Hubberstey, P.; Barker, M.G.

    1985-01-01

    The paper reviews the experimental and theoretical studies carried out on multicomponent alkali metal systems. Solid-liquid phase equilibria studies are mainly concerned with the systems Na-K-Rb and Na-K-Cs, and data on the liquidus temperatures in these systems are presented. The thermodynamic properties of the ternary Na-K-Cs eutectic system have been determined experimentally, and the enthalpy, heat capacity and excess functions of the alloy are given. An analysis of calculational methods used in determining thermodynamic functions of ternary liquid metals systems is described. Finally, data are tabulated for the density, compressibility, saturated vapour pressure, viscosity and thermal conductivity of the ternary Na-K-Cs eutectic system. (UK)

  7. Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model.

    Science.gov (United States)

    Mohebifar, Mohamad; Johnson, Erin R; Rowley, Christopher N

    2017-12-12

    London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential using empirically determined parameters. These parameters are generally underdetermined, and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields. The molecular dispersion coefficients for the CGenFF, GAFF, and OPLS models are systematically higher than the XDM-calculated values by a factor of roughly 1.5, likely due to neglect of higher order dispersion terms and premature truncation of the dispersion-energy summation. The XDM dispersion coefficients span a large range for some molecular-mechanical atom types, suggesting an unrecognized source of error in force-field models, which assume that atoms of the same type have the same dispersion interactions. Agreement with the XDM dispersion coefficients is even poorer for the Drude polarizable force field. Popular water models were also examined, and TIP3P was found to have dispersion coefficients similar to the experimental and XDM references, although other models employ anomalously high values. Finally, XDM-derived dispersion coefficients were used to parametrize molecular-mechanical force fields for five liquids-benzene, toluene, cyclohexane, n-pentane, and n-hexane-which resulted in improved accuracy in the

  8. High temperature corrosion studies. A. Iron: based superalloy in SO/sub 2//O/sub 2/ atmospheres. B. Gas: solid reaction with formation of volatile species

    Energy Technology Data Exchange (ETDEWEB)

    Liu, T.K.

    1980-03-01

    The thermogravimetric method was used to study high temperature corrosion under SO/sub 2//O/sub 2/ atmosphere applied to Armco 18SR alloys with different heat treatment histories, Armco T310 and pure chromium between 750 and 1100/sup 0/C. The weight gain follows the parabolic rate law. The volatilization of the protective Cr/sub 2/O/sub 3/ layer via formation of CrO/sub 3/ was taken into account above 900/sup 0/C for long time runs. The parabolic rate and the volatilization rate, derived from fitting the experimental data to the modified Tedmon's non-linear model, were correlated using the Arrhenius equation. Armco 18SR-C has the best corrosion resistance of the Armco 18SR alloys. Armco T310 is not protective at high temperatures. The available rate data on the oxidation of chromium oxide, chlorination of chromium, oxidation-chlorination of chromium oxide, chlorination of nickel and chlorination of iron were found to be predictable. The calculation of high temperature volatilization rate was performed using the available fluid correlation equations and the Lennard-Jones parameters derived from the molecule with similar structure and from the low temperature viscosity measurement. The lower predicted volatilization rate is due to the use of the Chapman-Enskog equation with the Lennard-Jones parameters mostly derived from the low temperature viscosity measurement. This was substantiated by comparing the reliable high temperature diffusion rate in the literature with the above mentioned calculational method. The experimental volatilization rates of this study are compared with the other related studies and the mass transfer predictions.

  9. Temperature anisotropy at equilibrium reveals nonlocal entropic contributions to interfacial properties

    Science.gov (United States)

    Wilhelmsen, Øivind; Trinh, Thuat T.; Lervik, Anders

    2018-01-01

    Density gradient theory for fluids has played a key role in the study of interfacial phenomena for a century. In this work, we revisit its fundamentals by examining the vapor-liquid interface of argon, represented by the cut and shifted Lennard-Jones fluid. The starting point has traditionally been a Helmholtz energy functional using mass densities as arguments. By using rather the internal energy as starting point and including the entropy density as an additional argument, following thereby the phenomenological approach from classical thermodynamics, the extended theory suggests that the configurational part of the temperature has different contributions from the parallel and perpendicular directions at the interface, even at equilibrium. We find a similar anisotropy by examining the configurational temperature in molecular dynamics simulations and obtain a qualitative agreement between theory and simulations. The extended theory shows that the temperature anisotropy originates in nonlocal entropic contributions, which are currently missing from the classical theory. The nonlocal entropic contributions discussed in this work are likely to play a role in the description of both equilibrium and nonequilibrium properties of interfaces. At equilibrium, they influence the temperature- and curvature-dependence of the surface tension. Across the vapor-liquid interface of the Lennard Jones fluid, we find that the maximum in the temperature anisotropy coincides precisely with the maximum in the thermal resistivity relative to the equimolar surface, where the integral of the thermal resistivity gives the Kapitza resistance. This links the temperature anisotropy at equilibrium to the Kapitza resistance of the vapor-liquid interface at nonequilibrium.

  10. Scaled-particle theory analysis of cylindrical cavities in solution.

    Science.gov (United States)

    Ashbaugh, Henry S

    2015-04-01

    The solvation of hard spherocylindrical solutes is analyzed within the context of scaled-particle theory, which takes the view that the free energy of solvating an empty cavitylike solute is equal to the pressure-volume work required to inflate a solute from nothing to the desired size and shape within the solvent. Based on our analysis, an end cap approximation is proposed to predict the solvation free energy as a function of the spherocylinder length from knowledge regarding only the solvent density in contact with a spherical solute. The framework developed is applied to extend Reiss's classic implementation of scaled-particle theory and a previously developed revised scaled-particle theory to spherocylindrical solutes. To test the theoretical descriptions developed, molecular simulations of the solvation of infinitely long cylindrical solutes are performed. In hard-sphere solvents classic scaled-particle theory is shown to provide a reasonably accurate description of the solvent contact correlation and resulting solvation free energy per unit length of cylinders, while the revised scaled-particle theory fitted to measured values of the contact correlation provides a quantitative free energy. Applied to the Lennard-Jones solvent at a state-point along the liquid-vapor coexistence curve, however, classic scaled-particle theory fails to correctly capture the dependence of the contact correlation. Revised scaled-particle theory, on the other hand, provides a quantitative description of cylinder solvation in the Lennard-Jones solvent with a fitted interfacial free energy in good agreement with that determined for purely spherical solutes. The breakdown of classical scaled-particle theory does not result from the failure of the end cap approximation, however, but is indicative of neglected higher-order curvature dependences on the solvation free energy.

  11. MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease.

    Science.gov (United States)

    Gunner, M R; Zhu, Xuyu; Klein, Max C

    2011-12-01

    The pK(a)s of 96 acids and bases introduced into buried sites in the staphylococcal nuclease protein (SNase) were calculated using the multiconformation continuum electrostatics (MCCE) program and the results compared with experimental values. The pK(a)s are obtained by Monte Carlo sampling of coupled side chain protonation and position as a function of pH. The dependence of the results on the protein dielectric constant (ε(prot)) in the continuum electrostatics analysis and on the Lennard-Jones non-electrostatics parameters was evaluated. The pK(a)s of the introduced residues have a clear dependence on ε(prot,) whereas native ionizable residues do not. The native residues have electrostatic interactions with other residues in the protein favoring ionization, which are larger than the desolvation penalty favoring the neutral state. Increasing ε(prot) scales both terms, which for these residues leads to small changes in pK(a). The introduced residues have a larger desolvation penalty and negligible interactions with residues in the protein. For these residues, changing ε(prot) has a large influence on the calculated pK(a). An ε(prot) of 8-10 and a Lennard-Jones scaling of 0.25 is best here. The X-ray crystal structures of the mutated proteins are found to provide somewhat better results than calculations carried out on mutations made in silico. Initial relaxation of the in silico mutations by Gromacs and extensive side chain rotamer sampling within MCCE can significantly improve the match with experiment. Copyright © 2011 Wiley-Liss, Inc.

  12. Material Systems

    DEFF Research Database (Denmark)

    Jensen, Mads Brath; Mortensen, Henrik Rubæk; Mullins, Michael

    2009-01-01

    This paper describes and reflects upon the results of an investigative project which explores the setting up of a material system - a parametric and generative assembly consisting of and taking into consideration material properties, manufacturing constraints and geometric behavior. The project...... approaches the subject through the construction of a logic-driven system aiming to explore the possibilities of a material system that fulfills spatial, structural and performative requirements concurrently and how these are negotiated in situations where they might be conflicting....

  13. Recommender systems

    CERN Document Server

    Kembellec, Gérald; Saleh, Imad

    2014-01-01

    Acclaimed by various content platforms (books, music, movies) and auction sites online, recommendation systems are key elements of digital strategies. If development was originally intended for the performance of information systems, the issues are now massively moved on logical optimization of the customer relationship, with the main objective to maximize potential sales. On the transdisciplinary approach, engines and recommender systems brings together contributions linking information science and communications, marketing, sociology, mathematics and computing. It deals with the understan

  14. Energetic Systems

    Data.gov (United States)

    Federal Laboratory Consortium — The Energetic Systems Division provides full-spectrum energetic engineering services (project management, design, analysis, production support, in-service support,...

  15. Intelligent systems

    CERN Document Server

    Irwin, J David

    2011-01-01

    Technology has now progressed to the point that intelligent systems are replacing humans in the decision making processes as well as aiding in the solution of very complex problems. In many cases intelligent systems are already outperforming human activities. Artificial neural networks are not only capable of learning how to classify patterns, such images or sequence of events, but they can also effectively model complex nonlinear systems. Their ability to classify sequences of events is probably more popular in industrial applications where there is an inherent need to model nonlinear system

  16. Reactive Systems

    DEFF Research Database (Denmark)

    Aceto, Luca; Ingolfsdottir, Anna; Larsen, Kim Guldstrand

    A reactive system comprises networks of computing components, achieving their goals through interaction among themselves and their environment. Thus even relatively small systems may exhibit unexpectedly complex behaviours. As moreover reactive systems are often used in safety critical systems...... they are best used. Milner's CCS and its operational semantics are introduced, together with the notions of behavioural equivalences based on bisimulation techniques and with recursive extensions of Hennessy-Milner logic. In the second part of the book, the presented theories are extended to take timing issues...

  17. Anticipatory systems as linguistic systems

    Science.gov (United States)

    Ekdahl, Bertil

    2000-05-01

    The idea of system is well established although not well defined. What makes up a system depends on the observer. Thinking in terms of systems is only a convenient way to conceptualize organizations, natural or artificial, that show coherent properties. Among all properties, which can be ascribed to systems, one property seems to be more outstanding than others, namely that of being anticipatory. In nature, anticipatory properties are found only in living organizations. In this way it can be said to separate non-living systems from living because there is no indication that any natural phenomenon occurring in systems where there is no indication of life is anticipatory. The characteristic of living systems is that they are exposed to the evolution contrary to causal systems that do not undergo changes due to the influence of the environment. Causal systems are related to the past in such a way that subsequent situations can be calculated from knowledge of past situations. In causal systems the past is the cause of the present and there is no reference to the future as a determining agent, contrary to anticipatory systems where expectations are the cause of the present action. Since anticipatory properties are characteristic of living systems, this property, as all other properties in living systems, is a result of the evolution and can be found in plants as well as in animals. Thus, it is not only tied to consciousness but is found at a more basic level, i.e., in the interplay between genotype and phenotype. Anticipation is part of the genetic language in such a way that appropriate actions, for events in the anticipatory systems environment, are inscribed in the genes. Anticipatory behavior, as a result of the interpretation of the genetic language, has been selected by the evolution. In this paper anticipatory systems are regarded as linguistic systems and I argue that as such anticipation cannot be fragmented but must be holistically studied. This has the

  18. Vacuum system

    OpenAIRE

    Gröbner, Oswald

    2006-01-01

    The vacuum system of a particle accelerator must provide the necessary conditions for the high energy beam to avoid loss of particles and deterioration of the beam quality. In this talk we will review basic design concepts, vacuum components and procedures required for an accelerator vacuum system.

  19. Immune System

    Science.gov (United States)

    ... jobs to do: B lymphocytes are like the body's military intelligence system, seeking out their targets and sending defenses ... like the soldiers, destroying the invaders that the intelligence system has ... that invades the body is called an antigen (pronounced: AN-tih-jun). ...

  20. Retrofitting Systems

    DEFF Research Database (Denmark)

    Rose, Jørgen

    1997-01-01

    This report gives an overview of the different retrofitting possibilities that are available today. The report looks at both external and internal systems for external wall constructions, roof constructions, floor constructions and foundations. All systems are described in detail in respect to use...