Energy Technology Data Exchange (ETDEWEB)
Mamedov, Bahtiyar A. [Department of Physics, Gaziosmanpaşa University, 60250, Tokat (Turkey); Somuncu, Elif; Askerov, Iskender M. [Department of Physics, Giresun University, Giresun (Turkey)
2016-08-10
In this work, a new theoretical approach is proposed for calculating fourth virial coefficient with Lennard-Jones potential. The established algorithm can be used to evaluate the thermodynamics properties and the intermolecular interaction potentials of liquids and gases with an improved accuracy. Note that the evaluation of the high-order virial coefficients is very valuable for accurate calculation of thermodynamic parameters. By using the suggested method, the fourth virial coefficient of CH{sub 4}, Ar, C{sub 2}H{sub 6} and SF{sub 6} molecules are evaluated. The calculation results are useful for accurate interpretation of the experimental data and of the determination of related physical properties.
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)
Third-order WKBJ eigenvalues for Lennard-Jones and Varshni V potentials
International Nuclear Information System (INIS)
Kesarwani, R.N.; Varshni, Y.P.
1978-01-01
The WKBJ method is applied to the third order for obtaining the eigenvalues for the fifth potential of Varshni, and the relevant integrals are analytically evaluated. Numerical results are obtained for the Lennard-Jones Potential, which is a special case of the Varshni V potential, and are compared to the results of Harrison and Bernstein obtained by a numerical integration of the wave equation. Error estimates are made. It is shown that for diatomic potentials, the Langer correction is not needed if the WKBJ approximation is carried to second and higher orders. (author)
The potential energy landscape in the Lennard-Jones binary mixture model
International Nuclear Information System (INIS)
Sampoli, M; Benassi, P; Eramo, R; Angelani, L; Ruocco, G
2003-01-01
The potential energy landscape in the Kob-Andersen Lennard-Jones binary mixture model has been studied carefully from the liquid down to the supercooled regime, from T = 2 down to 0.46. One thousand independent configurations along the time evolution locus have been examined at each temperature investigated. From the starting configuration, we searched for the nearest saddle (or quasi-saddle) and minimum of the potential energy. The vibrational densities of states for the starting and the two derived configurations have been evaluated. Besides the number of negative eigenvalues of the saddles other quantities show some signature of the approach of the dynamical arrest temperature
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....
Hoheisel, C.
1988-09-01
Equilibrium molecular dynamics calculations with constraints have been performed for model liquids SF6 and CF4. The computations were carried out with four- and six-center Lennard-Jones potentials and up to 2×105 integration steps. Shear, bulk viscosity and the thermal conductivity have been calculated with use of Green-Kubo relations in the formulation of ``molecule variables.'' Various thermodynamic states were investigated. For SF6, a detailed comparison with experimental data was possible. For CF4, the MD results could only be compared with experiment for one liquid state. For the latter liquid, a complementary comparison was performed using MD results obtained with a one-center Lennard-Jones potential. A limited test of the particle number dependence of the results is presented. Partial and total correlations functions are shown and discussed with respect to findings obtained for the one-center Lennard-Jones liquid.
Freezing of Lennard-Jones-type fluids
International Nuclear Information System (INIS)
Khrapak, Sergey A.; Chaudhuri, Manis; Morfill, Gregor E.
2011-01-01
We put forward an approximate method to locate the fluid-solid (freezing) phase transition in systems of classical particles interacting via a wide range of Lennard-Jones-type potentials. This method is based on the constancy of the properly normalized second derivative of the interaction potential (freezing indicator) along the freezing curve. As demonstrated recently it yields remarkably good agreement with previous numerical simulation studies of the conventional 12-6 Lennard-Jones (LJ) fluid [S.A.Khrapak, M.Chaudhuri, G.E.Morfill, Phys. Rev. B 134, 052101 (2010)]. In this paper, we test this approach using a wide range of the LJ-type potentials, including LJ n-6 and exp-6 models, and find that it remains sufficiently accurate and reliable in reproducing the corresponding freezing curves, down to the triple-point temperatures. One of the possible application of the method--estimation of the freezing conditions in complex (dusty) plasmas with ''tunable'' interactions--is briefly discussed.
International Nuclear Information System (INIS)
Lin, T.; Bian, X.F.; Jiang, J.
2006-01-01
Two metallic bulk glasses, Cu 60 Zr 30 Ti 10 and Cu 47 Ti 33 Zr 11 Ni 8 Si 1 , with a diameter of 3 mm were prepared by copper mold casting method. Dilatometric measurement was carried out on the two glassy alloys to obtain information about the average nearest-neighbour distance r 0 and the effective depth of pair potential V 0 . By assuming a Lennard-Jones potential, r 0 and V 0 were calculated to be 0.28 nm and 0.16 eV for Cu 60 Zr 30 Ti 10 and 0.27 nm and 0.13 eV for Cu 47 Ti 33 Zr 11 Ni 8 Si 1 , respectively. It was found that the glassy alloy Cu 60 Zr 30 Ti 10 was more stable than Cu 47 Ti 33 Zr 11 Ni 8 Si 1 against heating from both experiment and calculation
Hoheisel, C.
1989-01-01
For several liquid states of CF4 and SF4, the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints was chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3×105 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF4, while for SF6 the transport coefficients fall below the experimental ones by about 30%.
International Nuclear Information System (INIS)
Hoheisel, C.
1989-01-01
For several liquid states of CF 4 and SF 6 , the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints were chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3 x 10 5 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF 4 , while for SF 6 the transport coefficients fall below the experimental ones by about 30%
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.
DEFF Research Database (Denmark)
Friisberg, Ida Marie; Costigliola, Lorenzo; Dyre, Jeppe C.
2017-01-01
This paper investigates the relation between the density-scaling exponent γ and the virial potentialenergy coefficient R at several thermodynamic state points in three dimensions for the generalized (2n, n) Lennard-Jones (LJ) system for n = 4, 9, 12, 18, as well as for the standard n = 6 LJ syste...
Thermal decay of Lennard-Jones clusters
International Nuclear Information System (INIS)
Garzon, I.L.; Avalos-Borja, M.
1989-01-01
The decay mechanisms of argon clusters have been studied using molecular dynamics simulations and Lennard-Jones potentials. Heating up processes were applied to Ar 13 up to temperatures in the melting region. In this range of temperatures large fluctuations in the mean kinetic energy of the system are present and a sequential evaporation is observed. The thermal decay of these aggregates occurs in a time scale of nanoseconds. (orig.)
Phase diagram of a modified Lennard-Jones system
International Nuclear Information System (INIS)
Sakagami, Takahiro; Fuchizaki, Kazuhiro
2010-01-01
The well-known Lennard-Jones potential is modified in such a way that it smoothly vanishes at a certain distance. A system whose interparticle interaction is given by such a potential is referred to as a modified Lennard-Jones system, and is served as a standard system describing simple solids and fluids. A phase diagram is determined based on the free energies obtained through thermodynamic integration.
Effect of surface tension on the behavior of adhesive contact based on Lennard-Jones potential law
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.
Evaporation of Lennard-Jones clusters
International Nuclear Information System (INIS)
Roman, C.E.; Garzon, I.L.
1991-01-01
Extensive molecular dynamics simulations have been done to study the evaporation of a 13-atom Lennard-Jones cluster. The survival probability and the evaporative lifetime are calculated as a function of the cluster total energy from a classical trajectory analysis. The results are interpreted in terms of the RRK theory of unimolecular dissociation. The calculation of the binding energy of the evaporated species from the evaporation rate and the average kinetic energy release is discussed. (orig.)
DEFF Research Database (Denmark)
D'ovidio, Francesco; Bohr, Henrik; Lindgård, Per-Anker
2005-01-01
We study the propagation of solitons along the hydrogen bonds of an alpha helix. Modeling the hydrogen and peptide bonds with Lennard-Jones potentials, we show that the solitons can appear spontaneously and have long lifetimes. Remarkably, even if no explicit solution is known for the Lennard-Jones...... potential, the solitons can be characterized analytically with a good quantitative agreement using formulas for a Toda potential with parameters fitted to the Lennard-Jones potential. We also discuss and show the robustness of the family of periodic solutions called cnoidal waves, corresponding to phonons...
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
Phase diagram of power law and Lennard-Jones systems: Crystal phases
International Nuclear Information System (INIS)
Travesset, Alex
2014-01-01
An extensive characterization of the low temperature phase diagram of particles interacting with power law or Lennard-Jones potentials is provided from Lattice Dynamical Theory. For power law systems, only two lattice structures are stable for certain values of the exponent (or softness) (A15, body centered cube (bcc)) and two more (face centered cubic (fcc), hexagonal close packed (hcp)) are always stable. Among them, only the fcc and bcc are equilibrium states. For Lennard-Jones systems, the equilibrium states are either hcp or fcc, with a coexistence curve in pressure and temperature that shows reentrant behavior. The hcp solid never coexists with the liquid. In all cases analyzed, for both power law and Lennard-Jones potentials, the fcc crystal has higher entropy than the hcp. The role of anharmonic terms is thoroughly analyzed and a general thermodynamic integration to account for them is proposed
Atomic size effect on the formation of ionized cluster beam epitaxy in Lennard-Jones systems
International Nuclear Information System (INIS)
Hsieh Horngming; Averback, R.S.
1991-01-01
Ionized cluster beam deposition is studied by molecular dynamics simulations in which the atomic size of incident cluster atoms is different from the size of substrate atoms. Lennard-Jones interatomic potentials are used for the two-component system. The results provide the morphologies of the overlayers for various atomic sizes and are compared to simulation results of molecular beam epitaxy. (orig.)
Evaporation of Lennard-Jones fluids.
Cheng, Shengfeng; Lechman, Jeremy B; Plimpton, Steven J; Grest, Gary S
2011-06-14
Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature T/T(c), where T(c) is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.
Scaling of the dynamics of flexible Lennard-Jones chains
DEFF Research Database (Denmark)
Veldhorst, Arno; Dyre, Jeppe C.; Schrøder, Thomas
2015-01-01
The previous paper [A. A. Veldhorst et al., J. Chem. Phys. 141, 054904 (2014)] demonstrated that the isomorph theory explains the scaling properties of a liquid of flexible chains consisting of ten Lennard-Jones particles connected by rigid bonds. We here investigate the same model with harmonic......, dynamics, and the excess entropy are invariant. The Lennard-Jones chain liquid with harmonic bondsdoes have curves in the phase diagram along which the structure and dynamics are invariant. The excess entropy is not invariant on these curves, which we refer to as “pseudoisomorphs.” In particular......, this means that Rosenfeld’s excess-entropy scaling (the dynamics being a function of excess entropy only) does not apply for the Lennard-Jones chain with harmonic bonds...
Cluster fusion algorithm: application to Lennard-Jones clusters
DEFF Research Database (Denmark)
Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter
2006-01-01
paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence......We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...
Cluster fusion algorithm: application to Lennard-Jones clusters
DEFF Research Database (Denmark)
Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter
2008-01-01
paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence......We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...
International Nuclear Information System (INIS)
Kim, Soon-Chul; Lee, Song Hi
2004-01-01
A density functional perturbation approximation (DFPT), which is based both on the fundamental-measure theory (FMT) to the hard-sphere repulsion and on the weighted-density approximations (WDAs) to the attractive contribution, has been proposed for studying the structural properties of model fluids with an attractive part of the potential. The advantage of the present theory is the simplicity of the calculation of the weight function due to the attractive contribution. It has been applied to predict the equilibrium particle density distributions and adsorption isotherms of Lennard-Jones fluids at interfaces. The theoretical results show that the present theory describes quite well the adsorption isotherms of a Lennard-Jones ethane in a graphite slit pore as well as the equilibrium particle density distributions of a Lennard-Jones fluid near a planar slit pore
Stability of relaxed Lennard-Jones models made of 500 to 6000 atoms
International Nuclear Information System (INIS)
Raoult, B.; Farges, J.; Feraudy, M.F. de; Torchet, G.
1989-01-01
We present a study of the stability of clusters models made of a number N of atoms in the range 500 to 6000 atoms, freely interacting through the Lennard-Jones potential. The potential energy per atom, calculated for relaxed models, shows that stable models belong to an icosahedral sequence when N<1600 and to a decahedral sequence beyond. A coexistence size range of both structures is discussed in connection with experimental results on argon clusters in free jet expansions. (orig.)
Effect of Energy Polydispersity on the Nature of Lennard-Jones Liquids
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...
Contact angle of sessile drops in Lennard-Jones systems.
Becker, Stefan; Urbassek, Herbert M; Horsch, Martin; Hasse, Hans
2014-11-18
Molecular dynamics simulations are used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and dewetting is investigated by varying the solid-fluid dispersive interaction energy. The temperature is varied between the triple point and the critical temperature. A correlation is obtained for the contact angle in dependence of the temperature and the dispersive interaction energy. Size effects are studied by varying the number of fluid particles at otherwise constant conditions, using up to 150,000 particles. For particle numbers below 10,000, a decrease of the contact angle is found. This is attributed to a dependence of the solid-liquid surface tension on the droplet size. A convergence to a constant contact angle is observed for larger system sizes. The influence of the wall model is studied by varying the density of the wall. The effective solid-fluid dispersive interaction energy at a contact angle of θ = 90° is found to be independent of temperature and to decrease linearly with the solid density. A correlation is developed that describes the contact angle as a function of the dispersive interaction, the temperature, and the solid density. The density profile of the sessile drop and the surrounding vapor phase is described by a correlation combining a sigmoidal function and an oscillation term.
Dynamics of an assembly of finite-size Lennard-Jones spheres
International Nuclear Information System (INIS)
Singh, P.
1996-01-01
The time-averaged Fourier spectra of the number density, velocity, and force fields are obtained numerically for an assembly of spherical particles interacting via the Lennard-Jones potential. The magnitude spectra determine the dominant wave numbers, and the phase difference between the Lennard-Jones force and number density spectra determines the nature of the particle dynamics. The latter is used to show that for every wave number k there is a critical frequency ω c (k), such that when ω c (k) the phase difference is π/2 and when ω approx-gt ω c (k) the phase difference is -π/2. The ratio of the frequency and the wave number at which the phase difference changes sign is used to define an effective sound speed for the particle system. The effective sound speed is shown to be a function of the dimensionless wave number, and is locally minimum at the same dimensionless wave numbers for which the static structure factor is minimum. It is also shown that the dynamical response of the particle system for waves with speeds greater than the effective sound speed is similar to the response of the hyperbolic systems of equations, and for waves with speeds smaller than the effective sound speed the response is similar to the response of the elliptic systems. The convection effects are shown to be of the same order of magnitude as the Lennard-Jones forces, and the change of type of the equations from hyperbolic to elliptic occurs when the magnitude of the convection term is comparable to the magnitude of the Lennard-Jones force term. It is also shown that the change of type cannot occur in a theory where the convection term is neglected. copyright 1996 The American Physical Society
Free energy of the Lennard-Jones solid
Hoef, van der M.A.
2000-01-01
We have determined a simple expression for the absolute Helmholtz free energy of the fcc Lennard-Jones solid from molecular dynamics simulations. The pressure and energy data from these simulations have been fitted to a simple functional form (18 parameters) for densities ranging from around
Scaling of the dynamics of flexible Lennard-Jones chains
DEFF Research Database (Denmark)
Veldhorst, Arno; Dyre, J. C.; Schrøder, Thomas
2014-01-01
functions of excess entropy) which has been observed in simulations of both molecular and polymeric systems. Doing molecular dynamics simulations of flexible Lennard-Jones chains (LJC) with rigid bonds, we here provide the first detailed test of the isomorph theory applied to flexible chain molecules. We...
Thermal conductivity of the Lennard-Jones chain fluid model.
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.
Equilibrium spherically curved two-dimensional Lennard-Jones systems
Voogd, J.M.; Sloot, P.M.A.; van Dantzig, R.
2005-01-01
To learn about basic aspects of nano-scale spherical molecular shells during their formation, spherically curved two-dimensional N-particle Lennard-Jones systems are simulated, studying curvature evolution paths at zero-temperature. For many N-values (N < 800) equilibrium configu- rations are traced
International Nuclear Information System (INIS)
Costigliola, Lorenzo; Schrøder, Thomas B.; Dyre, Jeppe C.
2016-01-01
The recent theoretical prediction by Maimbourg and Kurchan [e-print http://arxiv.org/abs/1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2, 3, 4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized by high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly.
Phase diagram of a Lennard-Jones solid
International Nuclear Information System (INIS)
Choi, Y.; Ree, T.; Ree, F.H.
1993-01-01
A phase diagram of a Lennard-Jones solid at kT/ε≥0.8 is constructed by our recent perturbation theory. It shows the stability of the face-centered-cubic phase except within a small pressure and temperature domain, where the hexagonal-close packed phase may occur. The theory predicts anharmonic contributions to the Helmholtz free energy (important to the crystal stability) in good agreement with Monte Carlo data
Crystallisation of a Lennard-Jones fluid by large scale molecular dynamics simulation
International Nuclear Information System (INIS)
Snook, I.
1998-01-01
Full text: The evolution of the structure of a large system of atoms interacting via a Lennard-Jones pair potential was simulated by the use of the Molecular Dynamics computer simulation technique. The system was initially equilibrated in the one phase region of the phase diagram at a temperature above critical then a temperature quench was performed which placed the system in a region were the single fluid phase was unstable. Quenches to below the triple point temperature gave rise to crystallisation The mechanism and final morphology is shown to depend strongly on the starting conditions e.g. the starting density
Radiation damage in an amorphous Lennard-Jones solid
International Nuclear Information System (INIS)
Chaki, T.K.; Li, J.C.M.
1985-01-01
A molecular-dynamics simulation of radiation damage in an amorphous Lennard-Jones solid has been undertaken. A three-dimensional structure of 685 atoms with periodic boundary conditions was used. An atom was injected inward from the middle of one surface, and as it lost its energy its velocity and position were recorded. The temperature profile around the injection direction was also calculated. The amorphous structure was examined before and after irradiation by calculating the volume distribution of the Voronoi polyhedra and its time evolution. The production of vacancies and interstitials was observed. The interstitials were found to disappear rapidly, and the vacancies slowly. (author)
Binding energy of large icosahedral and cuboctahedral Lennard-Jones clusters
International Nuclear Information System (INIS)
Northby, J.A.; Xie, J.
1989-01-01
It is widely believed that the lowest energy configurations for small rare gas clusters have icosahedral symmetry. This contrasts with the bulk crystal structures which have cuboctahedral fcc symmetry. It is of interest to understand the transition between this finite and bulk behavior. To model this transition in rare gas clusters we have undertaken optimization studies within the Lennard-Jones pair potential model. Using a combination of Monte Carlo and Partan Search optimization methods, the lowest energy relaxed structures of Lennard-Jones clusters having icosahedral and cuboctahedral symmetry were found. Studies were performed for complete shell clusters ranging in size from one shell having 13 atoms to 14 shells having 10,179 atoms. It was found that the icosahedral structures are lower in energy than the cuboctahedral structures for cluster sizes having 13 shells or fewer. Additional studies were performed using the more accurate Aziz-Chen [HFD-C] pair potential parameterized for argon. The conclusions appear to be relatively insensitive to the form of the potential. (orig.)
Icosahedral binary clusters of glass-forming Lennard-Jones binary alloy
International Nuclear Information System (INIS)
Iwamatsu, Masao
2007-01-01
It is widely believed that the local icosahedral structure is related to the formation of bulk metallic glasses (BMGs). Specifically the existence of 13-atom icosahedral cluster in undercooled liquid is imagined to play a key role to initiate the glass formation as the seed of amorphous structure or to block the nucleation of regular crystal as the impurity. The existence of 13-atom icosahedral clusters in one-component liquids was predicted more than half a century ago by Frank from his total energy calculation for isolated clusters. In BMG alloys, however, the situation is less clear. In this report, we present the lowest-energy structures of 13-atom Lennard-Jones binary cluster calculated from the modified space-fixed genetic algorithm. We study, in particular, the artificial Lennard-Jones potential designed by Kob and Andersen [W. Kob, H.C. Andersen, Phys. Rev. E 51 (1995) 4626] that is known to form BMG. Curiously, the lowest-energy structures of 13-atom cluster are non-icosahedral for almost all compositions. Our result suggests that the existence of the icosahedral cluster is not a necessary condition but only a sufficient condition for glass formation
A Lennard-Jones-like perspective on first order transitions in biological helices
DEFF Research Database (Denmark)
Oskolkov, Nikolay N.; Bohr, Jakob
2013-01-01
Helical structures with Lennard-Jones self-interactions are studied for optimal conformations. For this purpose, their self-energy is analyzed for extrema with respect to the geometric parameters of the helices. It is found that Lennard-Jones helices exhibit a first order phase transition from...
International Nuclear Information System (INIS)
Garcia, N.
1978-01-01
The GR method for solving the scattering equations of atoms from a hard corrugated surface is applied on accelerated particles above a hard corrugated surface and a hard corrugated surface with an attractive well. The solutions are given for the Rayleigh hypothesis that under the range of corrugation presented in this paper leads to the exact ones. Threshold resonances are studied observing that the appearance and disappearance of beams must be for a general theory with vertical tangent. The structure of the Lennard-Jones resonances given for the model mentioned above. For the first time it is stressed that Lennard-Jones resonances are not observed in metal surfaces in general, and, accordingly, they are unobserved in compact metallic surfaces. This is correlated with the fact that diffraction has not been observed. Both facts are due to the very weak corrugation of the gas-metal interaction potential. According to our results, the Lennard-Jones resonances in metals present greater difficulties to be observed experimentally. It is also noted that the absence of diffraction in compact metal surfaces is because they are almost plane and not because of the Debye-Waller effect. Finally, the lifetimes of the atoms at the crystal surfaces are calculated. These are larger, the smaller the incident energy and the larger the corrugation. But the lifetimes are particularly large at resonance conditions (10 -11 s). (Auth.)
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
Glass of monatomic Lennard-Jones system at nanoscale
International Nuclear Information System (INIS)
Vo Van Hoang
2010-01-01
Structure and stability of glass of monatomic Lennard-Jones (LJ) system at nanoscale compared with those of the bulk counterparts have been studied using the classical molecular dynamics (MD) method. Models have been obtained by cooling from the melts. Structure of the systems was analyzed via radial distribution function (RDF), interatomic distances, the Honeycutt-Andersen analysis and coordination number distributions. Surface and core structures of LJ nanoparticles have been analyzed in details. Density dependence and cooling rate effects on structure of the systems have been found and discussed. In addition, size dependence of structure and properties of nanoparticles has been analyzed in detail. Indeed, we found glass formation in monatomic LJ systems; however, their stability is not high. Evolution of structure and thermodynamics of the systems upon cooling from the melts was found. We also discussed annealing-induced crystallization of LJ glass.
Phase behavior of the 38-atom Lennard-Jones cluster
International Nuclear Information System (INIS)
Sehgal, Ray M.; Maroudas, Dimitrios; Ford, David M.
2014-01-01
We have developed a coarse-grained description of the phase behavior of the isolated 38-atom Lennard-Jones cluster (LJ 38 ). The model captures both the solid-solid polymorphic transitions at low temperatures and the complex cluster breakup and melting transitions at higher temperatures. For this coarse model development, we employ the manifold learning technique of diffusion mapping. The outcome of the diffusion mapping analysis over a broad temperature range indicates that two order parameters are sufficient to describe the cluster's phase behavior; we have chosen two such appropriate order parameters that are metrics of condensation and overall crystallinity. In this well-justified coarse-variable space, we calculate the cluster's free energy landscape (FEL) as a function of temperature, employing Monte Carlo umbrella sampling. These FELs are used to quantify the phase behavior and onsets of phase transitions of the LJ 38 cluster
Water in the presence of inert Lennard-Jones obstacles
Kurtjak, Mario; Urbic, Tomaz
2014-04-01
Water confined by the presence of a 'sea' of inert obstacles was examined. In the article, freely mobile two-dimensional Mercedes-Benz (MB) water put to a disordered, but fixed, matrix of Lennard-Jones disks was studied by the Monte Carlo computer simulations. For the MB water molecules in the matrix of Lennard-Jones disks, we explored the structures, hydrogen-bond-network formation and thermodynamics as a function of temperature and size and density of matrix particles. We found that the structure of model water is perturbed by the presence of the obstacles. Density of confined water, which was in equilibrium with the bulk water, was smaller than the density of the bulk water and the temperature dependence of the density of absorbed water did not show the density anomaly in the studied temperature range. The behaviour observed as a consequence of confinement is similar to that of increasing temperature, which can for a matrix lead to a process similar to capillary evaporation. At the same occupancy of space, smaller matrix molecules cause higher destruction effect on the absorbed water molecules than the bigger ones. We have also tested the hypothesis that at low matrix densities the obstacles induce an increased ordering and 'hydrogen bonding' of the MB model molecules, relative to pure fluid, while at high densities the obstacles reduce MB water structuring, as they prevent the fluid to form good 'hydrogen-bonding' networks. However, for the size of matrix molecules similar to that of water, we did not observe this effect.
A molecular dynamics study of Lennard-Jones physisorption on W(100)
International Nuclear Information System (INIS)
Broughton, J.Q.
1980-01-01
The physisorption of Xe on W(100) was modeled by Lennard-Jones pair-wise interaction potentials and the dynamics of coverages ranging from one to four adlayers obtained by molecular dynamics simulation. At 115 K, the first two layers were well-ordered and each adsorbed with c(2 x 2) symmetry. Further adsorption produced a surface similar to that of a distorted Xe(100) face. In accord with the work of Broughton and Woodcock, the top layers of the three- and four-adlayer coverages were rough and had liquid-like diffusion coefficients. The potential energies of all layers other than the first were similar, thus corroborating one of the postulates of BET theory. Generally, the effect of adsorbing a layer was to reduce the entropy of all those beneath. (orig.)
Shear viscosity of the Lennard-Jones fluid near the triple point: Green-Kubo results
International Nuclear Information System (INIS)
Erpenbeck, J.J.
1988-01-01
The long-standing disagreement over the shear viscosity coefficient of the Lennard-Jones fluid near the triple point is reexamined through a series of very extensive Monte Carlo molecular-dynamics calculations of this transport coefficient based on the Green-Kubo theory. The stress autocorrelation function is shown to exhibit a slow decay, principally in the kinetic-potential and the potential-potential terms, which is large compared with the kinetic-kinetic long-time tail predicted by simple mode-coupling theory. Nonetheless, the viscosity coefficient, exclusive of any correction for this tail for times greater than are accessible numerically, is found to agree with that of Schoen and Hoheisel (who discounted the existence of such a tail) as well as nonequilibrium molecular-dynamics calculations. The large value of the viscosity coefficient found by Levesque and co-workers for 864 particles is brought into statistical agreement with the present results by a modest, but not unrealistic, increase in its statistical uncertainty. The pressure is found to exhibit an anomalous dependence on the size of the system, but the viscosity as well as the self-diffusion constant appear to be linear in the inverse of the number of particles, within the precision of our calculations. The viscosity coefficient, including a long-time-tail contribution based on the extended mode-coupling theory is (3.796 +- 0.068)σepsilon-c/m)/sup 1/2/ for the Lennard-Jones potential, fitted to a cubic spline, and (3.345 +- 0.068)σepsilon-c/m)/sup 1/2/ for the potential truncated at 2.5σ
Crystal phases of a glass-forming Lennard-Jones mixture
International Nuclear Information System (INIS)
Fernandez, Julian R.; Harrowell, Peter
2003-01-01
We compare the potential energy at zero temperature of a range of crystal structures for a glass-forming binary mixture of Lennard-Jones particles. The lowest-energy ordered state consists of coexisting phases of a single component face centered cubic structure and an equimolar cesium chloride structure. An infinite number of layered crystal structures are identified with energies close to this ground state. We demonstrate that the finite size increase of the energy of the coexisting crystal with incoherent interfaces is sufficient to destabilize this ordered phase in simulations of typical size. Two specific local coordination structures are identified as of possible structural significance in the amorphous state. We observe rapid crystal growth in the equimolar mixture
Longitudinal and bulk viscosities of Lennard-Jones fluids
Tankeshwar, K.; Pathak, K. N.; Ranganathan, S.
1996-12-01
Expressions for the longitudinal and bulk viscosities have been derived using Green Kubo formulae involving the time integral of the longitudinal and bulk stress autocorrelation functions. The time evolution of stress autocorrelation functions are determined using the Mori formalism and a memory function which is obtained from the Mori equation of motion. The memory function is of hyperbolic secant form and involves two parameters which are related to the microscopic sum rules of the respective autocorrelation function. We have derived expressions for the zeroth-, second-and fourth- order sum rules of the longitudinal and bulk stress autocorrelation functions. These involve static correlation functions up to four particles. The final expressions for these have been put in a form suitable for numerical calculations using low- order decoupling approximations. The numerical results have been obtained for the sum rules of longitudinal and bulk stress autocorrelation functions. These have been used to calculate the longitudinal and bulk viscosities and time evolution of the longitudinal stress autocorrelation function of the Lennard-Jones fluids over wide ranges of densities and temperatures. We have compared our results with the available computer simulation data and found reasonable agreement.
Vacancy behavior in a compressed fcc Lennard-Jones crystal
International Nuclear Information System (INIS)
Beeler, J.R. Jr.
1981-12-01
This computer experiment study concerns the determination of the stable vacancy configuration in a compressed fcc Lennard-Jones crystal and the migration of this defect in a compressed crystal. Isotropic and uniaxial compression stress conditions were studied. The isotropic and uniaxial compression magnitudes employed were 0.94 less than or equal to eta less than or equal to 1.5, and 1.0 less than or equal to eta less than or equal to 1.5, respectively. The site-centered vacancy (SCV) was the stable vacancy configuration whenever cubic symmetry was present. This includes all of the isotropic compression cases and the particular uniaxial compression case (eta = √2) that give a bcc structure. In addition, the SCV was the stable configuration for uniaxial compression eta 1.20, the SV-OP is an extended defect and, therefore, a saddle point for SV-OP migration could not be determined. The mechanism for the transformation from the SCV to the SV-OP as the stable form at eta = 1.29 appears to be an alternating sign [101] and/or [011] shear process
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
Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts
International Nuclear Information System (INIS)
Chremos, Alexandros; Nikoubashman, Arash; Panagiotopoulos, Athanassios Z.
2014-01-01
In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric–isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments
Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts
Energy Technology Data Exchange (ETDEWEB)
Chremos, Alexandros, E-mail: achremos@imperial.ac.uk [Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Nikoubashman, Arash, E-mail: arashn@princeton.edu; Panagiotopoulos, Athanassios Z. [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States)
2014-02-07
In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric–isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments.
Simulation of depositions of a Lennard-Jones cluster on a crystalline surface
International Nuclear Information System (INIS)
Saitoh, Kuniyasu; Hayakawa, Hisao
2009-01-01
Depositions of amorphous Lennard-Jones clusters on a crystalline surface are numerically investigated. From the results of the molecular dynamics simulation, we found that the deposited clusters exhibit a transition from multilayered adsorption to monolayered adsorption at a critical incident speed. Employing the energy conservation law, we can explain the behavior of the ratio of the number of atoms adsorbed on the substrate to the cluster size. The boundary shape of the deposited cluster depends strongly on the incident speed, and some unstable modes grow during the spread of the deposited cluster on the substrate. We also discuss the wettability between different Lennard-Jones atoms. (author)
International Nuclear Information System (INIS)
Olivi-Tran, N.; Faivre, A.
2009-01-01
We computed a Lennard-Jones frozen liquid with a free surface using classical molecular dynamics. The structure factor curves on the free surface of this sample were calculated for different depths knowing that we have periodic boundary conditions on the other parts of the sample. The resulting structure factor curves show an horizontal shift of their first peak depending on how deep in the sample the curves are computed. We analyze our resulting curves in the light of spatial correlation functions during melting. The conclusion is that the differences between bulk and surface are quite small during melting and that at the end of melting, only the very surface happens to be less dense than the bulk. This result is intrinsic to the shape of the Lennard-Jones potential and does not depend on any other parameter.
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
International Nuclear Information System (INIS)
Adebayo, G.A.; Anusionwu, B.C.; Njah, A.N.; Adeniran, O.J.; Mathew, B.; Sunmonu, R.S.
2009-01-01
Arising from the inability of theoretical calculations to give accurate descriptions of (shear) viscosity in rare gases at high densities, we investigated the likely cause of discrepancy between theory and experiments. Molecular Dynamics simulations were performed to calculate transport coefficients and collision frequency of rare gases at high densities and different temperatures using a Lennard-Jones modelled pair potential. The results, when compared with experiments show an underestimation of the viscosity calculated through the Green-Kubo formalism, but in agreement with some other calculations performed by other groups. In the present work the origin of the underestimation is considered. Analyses of the transport coefficients show a very high collision frequency which suggests an atom may spend much less time in the neighbourhood of the fields of force of another atom and that the distribution in the systems studied adjusts itself to a nearly Maxwellian type which resulted in a locally and temporarily slowly varying temperature. We show that the time spent in the fields of force is so small compared with relaxation time thereby leading to a possible reduction in local velocity auto-correlation between atoms. (author)
Modeling Aggregation Processes of Lennard-Jones particles Via Stochastic Networks
Forman, Yakir; Cameron, Maria
2017-07-01
We model an isothermal aggregation process of particles/atoms interacting according to the Lennard-Jones pair potential by mapping the energy landscapes of each cluster size N onto stochastic networks, computing transition probabilities from the network for an N-particle cluster to the one for N+1, and connecting these networks into a single joint network. The attachment rate is a control parameter. The resulting network representing the aggregation of up to 14 particles contains 6427 vertices. It is not only time-irreversible but also reducible. To analyze its transient dynamics, we introduce the sequence of the expected initial and pre-attachment distributions and compute them for a wide range of attachment rates and three values of temperature. As a result, we find the configurations most likely to be observed in the process of aggregation for each cluster size. We examine the attachment process and conduct a structural analysis of the sets of local energy minima for every cluster size. We show that both processes taking place in the network, attachment and relaxation, lead to the dominance of icosahedral packing in small (up to 14 atom) clusters.
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.
Liquid-vapour phase behaviour of a polydisperse Lennard-Jones fluid
International Nuclear Information System (INIS)
Wilding, Nigel B; Sollich, Peter
2005-01-01
We describe a simulation study of the liquid-vapour phase behaviour of a model polydisperse fluid. Particle interactions are given by a Lennard-Jones potential in which polydispersity features both in the particle sizes and the amplitude of their interactions. We address the computational problem of accurately locating the cloud curve for such a system using Monte Carlo simulations within the grand canonical ensemble. The strongly nonlinear variation of the fractional volumes of the phases across the coexistence region precludes naive extrapolation to determine the cloud point density. Instead we propose an improved estimator for the cloud point location and use scaling arguments to predicts its finite-size behaviour. Excellent agreement is found with the simulation results. Application of the method reveals that the measured cloud curve is highly sensitive to the presence of large particles, even when they are extremely rare. This finding is expected to have implications for the reproducibility of experimentally measured phase diagrams in colloids and polymers
RISM theory distribution functions for Lennard--Jones interaction site fluids
International Nuclear Information System (INIS)
Johnson, E.; Hazoume, R.P.
1978-01-01
Reference interaction site model (RISM) theory distribution functions for Lennard-Jones interaction site fluids are discussed. The comparison with computer simulation results suggests that these distribution functions are as accurate as RISM distribution functions for fused hard sphere molecular fluids
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...
Application of the RISM theory to Lennard-Jones interaction site molecular fluids
International Nuclear Information System (INIS)
Johnson, E.; Hazoume, R.P.
1979-01-01
It seems that reference interaction site model (RISM) theory atom--atom distribution functions have been obtained directly from the RISM equations only for fused hard sphere molecular fluids. RISM distribution functions for Lennard-Jones interaction site fluids are presented. Results presented suggest that these distribution functions are as accurate as RISM distribution functions for fused hard sphere molecular fluids
Molecular dynamics study of the hydration of Lennard-Jones solutes
International Nuclear Information System (INIS)
Geiger, A.; Rahman, A.; Stillinger, F.H.
1979-01-01
In order to clarify the nature of hydrophobic interactions in water, we have used the molecular dynamics simulation method to study a system comprising two Lennard-Jones solute particles and 214 water molecules. Although the solutes were placed initially in contact, forces in the system drive them slightly apart to permit formation of vertex-sharing solvent ''cages.'' Definite orientational preferences have been observed for water molecules in the first solvation layer around the Lennard-Jones solutes; these preferences are loosely reminiscent of structure in clathrates. Nevertheless, substantial local disorder is obviously present. The dynamical data show that translational and rotational motions of solvation--sheath water molecules are perceptibly slower (by at least 20%) than those in pure bulk water
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
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
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
Analytic Debye-Grüneisen equation of state for a generalized Lennard-Jones solids
Institute of Scientific and Technical Information of China (English)
孙久勋; 吴强; 蔡灵仓; 经福谦
2003-01-01
The approximate method to treat the practical quantum anharmonic solids proposed by Hardy,Lacks and Shukla is reformulated with explicit physical meanings.It is shown that the quantum effect is important at low temperature,it can be treated in the harmonic framework; and the anharmonic effect is important at high temperature and tends to zero at low temperature,it can be treated by using a classical approximation.The alternative formulation is easier for various applications,and is applied to a Debye-Gruneisen solid with the generalized Lennard-Jones intermolecular interaction.The expressions for the Debye temperature and Gruneisen parameter as a function of volume are analytically derived.The analytic equation of state is applied to predict the thermodynamic properties of solid xenon at normal-pressure with the nearest-neighbour Lennard-Jones interaction,and is further applied to research the properties of solid xenon and krypton at high pressure by using an all-neighbour Lennard-Jones interaction.The theoretical results are in agreement with the experiments.
Reinisch, S; Schweiger, K; Pablik, E; Collet-Fenetrier, B; Peyrin-Biroulet, L; Alfaro, I; Panés, J; Moayyedi, P; Reinisch, W
2016-09-01
The Lennard-Jones criteria are considered the gold standard for diagnosing Crohn's disease (CD) and include the items granuloma, macroscopic discontinuity, transmural inflammation, fibrosis, lymphoid aggregates and discontinuous inflammation on histology. The criteria have never been subjected to a formal validation process. To develop a validated and improved diagnostic index based on the items of Lennard-Jones criteria. Included were 328 adult patients with long-standing CD (median disease duration 10 years) from three centres and classified as 'established', 'probable' or 'non-CD' by Lennard-Jones criteria at time of diagnosis. Controls were patients with ulcerative colitis (n = 170). The performance of each of the six diagnostic items of Lennard-Jones criteria was modelled by logistic regression and a new index based on stepwise backward selection and cut-offs was developed. The diagnostic value of the new index was analysed by comparing sensitivity, specificity and accuracy vs. Lennard-Jones criteria. By Lennard-Jones criteria 49% (n = 162) of CD patients would have been diagnosed as 'non-CD' at time of diagnosis (sensitivity/specificity/accuracy, 'established' CD: 0.34/0.99/0.67; 'probable' CD: 0.51/0.95/0.73). A new index was derived from granuloma, fibrosis, transmural inflammation and macroscopic discontinuity, but excluded lymphoid aggregates and discontinuous inflammation on histology. Our index provided improved diagnostic accuracy for 'established' and 'probable' CD (sensitivity/specificity/accuracy, 'established' CD: 0.45/1/0.72; 'probable' CD: 0.8/0.85/0.82), including the subgroup isolated colonic CD ('probable' CD, new index: 0.73/0.85/0.79; Lennard-Jones criteria: 0.43/0.95/0.69). We developed an index based on items of Lennard-Jones criteria providing improved diagnostic accuracy for the differential diagnosis between CD and UC. © 2016 John Wiley & Sons Ltd.
Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions.
Fischer, Nina M; van Maaren, Paul J; Ditz, Jonas C; Yildirim, Ahmet; van der Spoel, David
2015-07-14
In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http
Numerical simulation of pool boiling of a Lennard-Jones liquid
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.
Numerical simulation of pool boiling of a Lennard-Jones liquid
Inaoka, Hajime; Ito, Nobuyasu
2013-01-01
We performed a numerical simulation of pool boiling by a molecular dynamics model. In the simulation, a liquid composed of Lennard-Jones particles in a uniform gravitational field is heated by a heat source at the bottom of the system. The model successfully reproduces the change in regimes of boiling from nucleate boiling to film boiling with the increase of the heat source temperature. We present the pool boiling curve by the model, whose general behavior is consistent with those observed in experiments of pool boiling. © 2013 Elsevier B.V. All rights reserved.
Cell-model prediction of the melting of a Lennard-Jones solid
International Nuclear Information System (INIS)
Holian, B.L.
1980-01-01
The classical free energy of the Lennard-Jones 6-12 solid is computed from a single-particle anharmonic cell model with a correction to the entropy given by the classical correlational entropy of quasiharmonic lattice dynamics. The free energy of the fluid is obtained from the Hansen-Ree analytic fit to Monte Carlo equation-of-state calculations. The resulting predictions of the solid-fluid coexistence curves by this corrected cell model of the solid are in excellent agreement with the computer experiments
Self-diffusion coefficients of the metastable Lennard-Jones vapor
International Nuclear Information System (INIS)
Nie Chu; Zhou Youhua; Marlow, W H; Hassan, Y A
2008-01-01
Self-diffusion coefficients of a metastable Lennard-Jones vapor were obtained using the memory function formalism and the frequency moments of the velocity autocorrelation function at reduced temperatures from 0.75 to 1.0. The radial density distribution functions used to evaluate the second, fourth and sixth frequency moments of the velocity autocorrelation function were obtained from the restricted canonical ensemble Monte Carlo simulation (Corti and Debenedetti 1994 Chem. Eng. Sci. 49 2717). The self-diffusion coefficients at reduced temperature 0.75 do not vary monotonically as the density increases, and for the other three temperatures the self-diffusion coefficients vary normally
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.
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
Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids
International Nuclear Information System (INIS)
De Leeuw, S.W.; Brakkee, M.J.D.
1990-01-01
Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs
Nonlinear transport processes and fluid dynamics: Cylindrical Couette flow of Lennard-Jones fluids
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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
Phase Diagram of Kob-Andersen-Type Binary Lennard-Jones Mixtures
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.
International Nuclear Information System (INIS)
Vorob'ev, V.S.
2003-01-01
We suggest a concept of multiple disordering scaling of the crystalline state. Such a scaling procedure applied to a crystal leads to the liquid and (in low density limit) gas states. This approach provides an explanation to a high value of configuration (common) entropy of liquefied noble gases, which can be deduced from experimental data. We use the generalized nearest-neighbor approach to calculate free energy and pressure of the Lennard-Jones systems after performing this scaling procedure. These thermodynamic functions depend on one parameter characterizing the disordering only. Condensed states of the system (liquid and solid) correspond to small values of this parameter. When this parameter tends to unity, we get an asymptotically exact equation of state for a gas involving the second virial coefficient. A reasonable choice of the values for the disordering parameter (ranging between zero and unity) allows us to find the lines of coexistence between different phase states in the Lennard-Jones systems, which are in a good agreement with the available experimental data
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.
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.
An accurate expression for radial distribution function of the Lennard-Jones fluid
International Nuclear Information System (INIS)
Morsali, Ali; Goharshadi, Elaheh K.; Ali Mansoori, G.; Abbaspour, Mohsen
2005-01-01
A simple and accurate expression for radial distribution function (RDF) of the Lennard-Jones fluid is presented. The expression explicitly states the RDF as a continuous function of reduced interparticle distance, temperature, and density. It satisfies the limiting conditions of zero density and infinite distance imposed by statistical thermodynamics. The distance dependence of this expression is expressed by an equation which contains 11 adjustable parameters. These parameters are fitted to 353 RDF data, obtained by molecular dynamics calculations, and then expressed as functions of reduced distance, temperature and density. This expression, having a total of 65 constants, reproduces the RDF data with an average root-mean-squared deviation of 0.0152 for the range of state variables of 0.5= * = * = * =ρσ 3 are reduced temperature and density, respectively). The expression predicts the pressure and the internal energy of the Lennard-Jones fluid with an uncertainty that is comparable to that obtained directly from the molecular dynamics simulations
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.
International Nuclear Information System (INIS)
Dowell, F.
1983-01-01
Two average-environment simple cubic lattice models: a refined model and a simple model, both having site-site (segmental) pair Lennard-Jones (LJ) interactions: for molecules composed of rigid cores having semiflexible tails are presented. The calculated values of the following properties at the nematic-isotropic transition for rigid rods of varying length are compared with relevant experimental data for PAA (p-azoxyanisole, or 4,4'-dimethoxyazoxybenzene): temperature, core orientational order parameter, nematic density and volume, relative density change, and relative entropy change. The temperature change as a function of volume change at constant order parameter is also discussed. In general, both LJ models give considerably better quantitative agreement with experiment, especially for the temperature and the relative density change, than do the earlier lattice models with hard repulsions, with or without constant segmental pair interaction energies. In most aspects, these LJ models give good quantitative agreement with experiment. These LJ models elucidate the importance of realistic intermolecular potentials, especially the role of soft repulsions, in describing an order-disorder transition between two condensed phases
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...
The Monte Carlo dynamics of a binary Lennard-Jones glass-forming mixture
International Nuclear Information System (INIS)
Berthier, L; Kob, W
2007-01-01
We use a standard Monte Carlo algorithm to study the slow dynamics of a binary Lennard-Jones glass-forming mixture at low temperature. We find that the Monte Carlo approach is by far the most efficient way to simulate a stochastic dynamics since the relaxation is about 10 times faster than in Brownian dynamics and about 30 times faster than in stochastic dynamics. Moreover, the average dynamical behaviour of the system is in quantitative agreement with that obtained using Newtonian dynamics, apart from at very short times where thermal vibrations are suppressed. We show, however, that dynamic fluctuations quantified by four-point dynamic susceptibilities do retain a dependence on the microscopic dynamics, as recently predicted theoretically
The effect of atom mismatch on the fragility of supercooled Lennard-Jones binary mixtures
International Nuclear Information System (INIS)
Sun Minhua; Sun Yongli; Wang Aiping; Ma Congxiao; Li Jiayun; Cheng Weidong; Liu Fang
2006-01-01
The shear viscosity of the well-known binary Lennard-Jones mixture is simulated under constant temperature and constant volume conditions (NVT) by a molecular-dynamics (MD) method. The effect of atomic size mismatch on the fragility parameter and glass-forming ability is studied. The fragility parameters calculated from shear viscosity data decrease with the increment of the atomic size mismatch. The value of the fragility changes from 168.963 to 22.976 when the mismatch changes from 0.023 to 0.25. It is shown that the fragility parameter is sensitive to the atomic size mismatch. The calculated pair distribution functions and mean square displacements indicate that the glass-forming ability increases with the atomic size mismatch
Dynamics of vacancies in two-dimensional Lennard-Jones crystals
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.
Theoretical prediction of crystallization kinetics of a supercooled Lennard-Jones fluid
Gunawardana, K. G. S. H.; Song, Xueyu
2018-05-01
The first order curvature correction to the crystal-liquid interfacial free energy is calculated using a theoretical model based on the interfacial excess thermodynamic properties. The correction parameter (δ), which is analogous to the Tolman length at a liquid-vapor interface, is found to be 0.48 ± 0.05 for a Lennard-Jones (LJ) fluid. We show that this curvature correction is crucial in predicting the nucleation barrier when the size of the crystal nucleus is small. The thermodynamic driving force (Δμ) corresponding to available simulated nucleation conditions is also calculated by combining the simulated data with a classical density functional theory. In this paper, we show that the classical nucleation theory is capable of predicting the nucleation barrier with excellent agreement to the simulated results when the curvature correction to the interfacial free energy is accounted for.
Thermal conductivity of the Lennard-Jones fluid: An empirical correlation
International Nuclear Information System (INIS)
Bugel, Mathilde; Galliero, Guillaume
2008-01-01
In this work, is presented an empirical correlation on the thermal conductivity of the Lennard-Jones fluid based on extensive non-equilibrium molecular dynamics simulations results (103 points). Finite size and cutoff radius effects are investigated and taken into account to develop the correlation. This last, composed of low-density, residual and critical enhancement contributions, is built for a wide range of thermodynamics states, even at the vicinity of the critical point, and yields an average absolute deviation of 1.29% compared to our simulations. In addition, a careful analysis of the different contributions to the microscopic flux is carried out which sheds light on the underlying mechanism of the results. Finally, are discussed the limitations of the proposed model when applied to real simple fluids and mixtures using a standard corresponding states scheme and the van der Waals one-fluid approximation
Simulasi Sifat Fisis Model Molekuler Dinamik Gas Argon dengan Potensial Lennard-Jones
Directory of Open Access Journals (Sweden)
Wira Bahari Nurdin
2014-01-01
Full Text Available DOWNLOAD PDFTelah dilakukan pembuatan dan pengujian suatu simulasi tentang sifat fisis gasargon dengan menggunakan dinamika molekuler menggunakan potensial Lennard-Jonesdalam sistem terisolasi (ensemble mikrokanonik. Jumlah molekul, energi total sistem danluas kotak simulasi telah divariasikan. Untuk menghitung perubahan posisi digunakanalgoritma Verlet. Sifat fisis yang ditentukan dalam simulasi adalah temperatur dan energitotal sistem untuk menentukan adanya fase transisi. Dari hasil simulasi, terdapatkesesuaian antara simulasi dengan gas argon dan tidak diperoleh adanya fase transisi.Kata kunci: Simulasi dinamika molekul, argon, potensial Lennard-Jones, ensemblemikrokanonik, algoritma Verlet
Phase diagram and universality of the Lennard-Jones gas-liquid system
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.
Freezing and melting line invariants of the Lennard-Jones system
DEFF Research Database (Denmark)
Costigliola, Lorenzo; Schrøder, Thomas; Dyre, Jeppe C.
2016-01-01
The invariance of several structural and dynamical properties of the Lennard-Jones (LJ) system along the freezing and melting lines is interpreted in terms of isomorph theory. First the freezing/melting lines of the LJ system are shown to be approximated by isomorphs. Then we show...... that the invariants observed along the freezing and melting isomorphs are also observed on other isomorphs in the liquid and crystalline phases. The structure is probed by the radial distribution function and the structure factor and dynamics are probed by the mean-square displacement, the intermediate scattering...... function, and the shear viscosity. Studying these properties with reference to isomorph theory explains why the known single-phase melting criteria hold, e.g., the Hansen–Verlet and the Lindemann criteria, and why the Andrade equation for the viscosity at freezing applies, e.g., for most liquid metals. Our...
International Nuclear Information System (INIS)
Erpenbeck, J.J.
1987-01-01
We apply the so-called ''synthetic'' nonequilibrium molecular-dynamics method to the calculation of the self-diffusion constant of a Lennard-Jones fluid at a number density of 0.85/σ 3 and a temperature of 1.08 epsilon-c/k/sub B/ (where epsilon-c and σ are the energy and length parameters of the potential and k/sub B/ is the Boltzmann constant). By comparing with the Green-Kubo calculation for the same state of the system and for the same number of particles, N, we find the latter calculation to yield more precise values of the self-diffusion constant for a given number of molecular-dynamics time steps. Even at small values of the diffusion current, a nontrivial time is needed for the nonequilibrium calculation to reach the steady state. For larger values of the driving force, the steady-state flow appears to become unstable and evidence of a secondary flow pattern is presented. The presence of these instabilities acts as a limit to the range of the driving force for which the steady-state method can be applied. With increasing N the range of stable values of the diffusion current density decreases. For the Green-Kubo calculations, the N dependence of the self-diffusion constant is found to be anomalous for N = 108, with the 1/N dependence only exhibited for at least 500 particles. The nonequilibrium results, while approximately independent of N for 108 and 500 particles, are found to have a similar anomalous N dependence when we extend the calculations to 1372 particles, thereby bringing the Green-Kubo and nonequilibrium results into agreement in the large-system limit
International Nuclear Information System (INIS)
Mulero, A.; Cuadros, F; Faundez, C.A.
1999-01-01
Vapour-liquid equilibrium properties for both three- and two-dimensional Lennard-Jones fluids were obtained using simple cubic-in-density equations of state proposed by the authors. Results were compared with those obtained by other workers from computer simulations and also with results given by other more complex semi-theoretical or semi-empirical equations of state. In the three-dimensional case good agreement is found for all properties and all temperatures. In the two-dimensional case only the coexistence densities were compared, producing good agreement for low temperatures only. The present work is the first to give numerical data for the vapour-liquid equilibrium properties of Lennard-Jones fluids calculated from equations of state. Copyright (1999) CSIRO Australia
Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation
Energy Technology Data Exchange (ETDEWEB)
Kadoura, Ahmad, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa; Sun, Shuyu, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa [Computational Transport Phenomena Laboratory, The Earth Sciences and Engineering Department, The Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia); Siripatana, Adil, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa; Hoteit, Ibrahim, E-mail: ibrahim.hoteit@kaust.edu.sa [Earth Fluid Modeling and Predicting Group, The Earth Sciences and Engineering Department, The Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia); Knio, Omar, E-mail: ahmad.kadoura@kaust.edu.sa, E-mail: adil.siripatana@kaust.edu.sa, E-mail: shuyu.sun@kaust.edu.sa, E-mail: omar.knio@kaust.edu.sa [Uncertainty Quantification Center, The Applied Mathematics and Computational Science Department, The Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900 (Saudi Arabia)
2016-06-07
In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard-Jones (LJ) particles. The main advantage of such surrogates, once generated, is the capability of accurately computing the needed thermodynamic quantities in a few seconds, thus efficiently replacing the computationally expensive MC molecular simulations. Benefiting from the tremendous computational time reduction, the PC surrogates were used to conduct large-scale optimization in order to propose single-site LJ models for several simple molecules. Experimental data, a set of supercritical isotherms, and part of the two-phase envelope, of several pure components were used for tuning the LJ parameters (ε, σ). Based on the conducted optimization, excellent fit was obtained for different noble gases (Ar, Kr, and Xe) and other small molecules (CH{sub 4}, N{sub 2}, and CO). On the other hand, due to the simplicity of the LJ model used, dramatic deviations between simulation and experimental data were observed, especially in the two-phase region, for more complex molecules such as CO{sub 2} and C{sub 2} H{sub 6}.
A test of the mean density approximation for Lennard-Jones mixtures with large size ratios
International Nuclear Information System (INIS)
Ely, J.F.
1986-01-01
The mean density approximation for mixture radial distribution functions plays a central role in modern corresponding-states theories. This approximation is reasonably accurate for systems that do not differ widely in size and energy ratios and which are nearly equimolar. As the size ratio increases, however, or if one approaches an infinite dilution of one of the components, the approximation becomes progressively worse, especially for the small molecule pair. In an attempt to better understand and improve this approximation, isothermal molecular dynamics simulations have been performed on a series of Lennard-Jones mixtures. Thermodynamic properties, including the mixture radial distribution functions, have been obtained at seven compositions ranging from 5 to 95 mol%. In all cases the size ratio was fixed at two and three energy ratios were investigated, 22 / 11 =0.5, 1.0, and 1.5. The results of the simulations are compared with the mean density approximation and a modification to integrals evaluated with the mean density approximation is proposed
A perturbed Lennard-Jones chain equation of state for liquid metals
Energy Technology Data Exchange (ETDEWEB)
Mousazadeh, M H; Marageh, M Ghanadi [AEOI, JIH Research Laboratory, 11365/8486, Tehran (Iran, Islamic Republic of)
2006-05-24
The perturbed Lennard-Jones chain (PLJC) equation of state is formulated based on first-order variational perturbation theory. The model uses two parameters for a monatomic system, segment size, {sigma}, and segment energy, {epsilon}/k. In this work, we employed the PLJC equation to calculate the liquid density of 26 metals, including alkali and alkali earth metals, iron, cobalt, nickel, copper, silver, gold, zinc, cadmium, mercury, aluminium, gallium, indium, thallium, tin, lead, antimony, and bismuth, for which accurate experimental data exist in the literature. The calculations cover a broad range of temperatures ranging from the melting point to close to the critical point and pressures ranging from the vapour-pressure curve up to pressures as high as 2000 bar. The average absolute deviation in the liquid density predicted by the PLJC equation of state in the saturation line compared with experimental data is 1.26%. Also, using the normal melting temperature and liquid density at melting point (T{sub m}, {rho}{sub m}) as input data for the estimation of the equation of state parameters provides a good correlation of liquid density at saturated and compressed pressures.
Spray flow-network flow transition of binary Lennard-Jones particle system
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.
Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems
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.
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.
A model-adaptivity method for the solution of Lennard-Jones based adhesive contact problems
Ben Dhia, Hachmi; Du, Shuimiao
2018-05-01
The surface micro-interaction model of Lennard-Jones (LJ) is used for adhesive contact problems (ACP). To address theoretical and numerical pitfalls of this model, a sequence of partitions of contact models is adaptively constructed to both extend and approximate the LJ model. It is formed by a combination of the LJ model with a sequence of shifted-Signorini (or, alternatively, -Linearized-LJ) models, indexed by a shift parameter field. For each model of this sequence, a weak formulation of the associated local ACP is developed. To track critical localized adhesive areas, a two-step strategy is developed: firstly, a macroscopic frictionless (as first approach) linear-elastic contact problem is solved once to detect contact separation zones. Secondly, at each shift-adaptive iteration, a micro-macro ACP is re-formulated and solved within the multiscale Arlequin framework, with significant reduction of computational costs. Comparison of our results with available analytical and numerical solutions shows the effectiveness of our global strategy.
Dodecagonal order in a two-dimensional Lennard-Jones system
International Nuclear Information System (INIS)
Leung, P.W.; Henley, C.L.; Chester, G.V.
1989-01-01
We investigate a two-dimensional Lennard-Jones mixture with the interaction parameters chosen so as to favor configurations where the large atoms form squares and equilateral triangles. Many such configurations are possible which by our choice of interactions are nearly degenerate in energy. It is hypothesized that a thermal equilibrium state with 12-fold orientational order exists. Several Monte Carlo simulations were performed to cool the system to a temperature approaching zero. The ordering process was studied by following the evolution of the configurations with temperature. The onset of ordering seemed to be very diffuse in space rather than nucleated at a point. The resulting configurations consist of squares and triangles, except for a few dislocations, and thus have perfect orientational order. We also characterized the deviation from ideal quasiperiodicity in terms of the ''phason strain''; this was analyzed both by fitting a linear relation between the physical space coordinates of the atoms and the corresponding ''perpendicular space'' coordinates, and also by calculating the diffraction peaks. The latter are shifted and broadened, relative to an ideal 12-fold diffraction pattern, as in real quasicrystals
Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation
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.
Spray flow-network flow transition of binary Lennard-Jones particle system
Inaoka, Hajime; Yukawa, Satoshi; Ito, Nobuyasu
2010-01-01
We simulate gas-liquid flows caused by rapid depressurization using a molecular dynamics model. The model consists of two types of Lennard-Jones particles, which we call liquid particles and gas particles. These two types of particles are distinguished by their mass and strength of interaction: a liquid particle has heavier mass and stronger interaction than a gas particle. By simulations with various initial number densities of these particles, we found that there is a transition from a spray flow to a network flow with an increase of the number density of the liquid particles. At the transition point, the size of the liquid droplets follows a power-law distribution, while it follows an exponential distribution when the number density of the liquid particles is lower than the critical value. The comparison between the transition of the model and that of models of percolation is discussed. The change of the average droplet size with the initial number density of the gas particles is also presented. © 2010 Elsevier B.V. All rights reserved.
Fowler's approximation for the surface tension and surface energy of Lennard-Jones fluids revisited
International Nuclear Information System (INIS)
Mulero, A; Galan, C; Cuadros, F
2003-01-01
We present a detailed study of the validity of Fowler's approximation for calculating the surface tension and the surface energy of Lennard-Jones fluids. To do so, we consider three different explicit analytical expressions for the radial distribution function (RDF), including one proposed by our research group, together with very accurate expressions for the liquid and vapour densities, also proposed by our group. The calculation of the surface tension from the direct correlation function using both the Percus-Yevick and the hypernetted-chain approximations is also considered. Finally, our results are compared with those obtained by other authors by computer simulations or through relevant theoretical approximations. In particular, we consider the analytical expression proposed by Kalikmanov and Hofmans (1994 J. Phys.: Condens. Matter 6 2207-14) for the surface tension. Our results indicate that the values for the surface energy in Fowler's approximation obtained by other authors are adequate, and can be calculated from the RDF models. For the surface tension, however, the values considered as valid in previous works seem to be incorrect. The correct values can be obtained from our model for the RDF or from the Kalikmanov and Hofmans expression with suitable inputs
International Nuclear Information System (INIS)
Lee, Song Hi
2010-01-01
We presented a molecular dynamics (MD) simulation study of friction behavior between two very massive Brownian particles (BPs) oriented along the z axis with BP centers at -R 12 /2 and R 12 /2 in a Lennard-Jones solvent as a function of the inter-particle separation, R 12 . In order to fix the BPs in space an MD simulation method with the mass of the BP as 10 90 g/mol was employed in which the total momentum of the system was conserved. The cross friction coefficients of x- and y-components are nearly insensitive to R 12 but that of z-component varies with R 12 in good accord with the simple hydrodynamic approximation. On the other hand, the self-friction coefficients are estimated as a very small difference from the single particle friction coefficients, ξ 0 , at all inter-particle separations which agrees with the simple hydrodynamic approximation. Consequently ξ (-) xx is nearly independent of R 12 and equal to its asymptotic value of twice the single particle friction coefficient, and the other relative friction, ξ (-) zz , is in good agreement with the simple hydrodynamic approximation. Molecular theory of Brownian motion of a single heavy particle in a fluid had received a considerable attention in earlier years. After molecular dynamics (MD) simulation technique was utilized, this subject has been widely studied by a variety of MD simulation methods. The common issues here were about the long time behavior of the force and velocity autocorrelation functions, the system size dependent friction coefficient of a massive Brownian particle, and test of the Stokes-Einstein law
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
Liquid-liquid interfacial properties of a symmetrical Lennard-Jones binary mixture
International Nuclear Information System (INIS)
Martínez-Ruiz, F. J.; Blas, F. J.; Moreno-Ventas Bravo, A. I.
2015-01-01
We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ 11 = σ 22 , with the same dispersive energy between like species, ϵ 11 = ϵ 22 , but different dispersive energies between unlike species low enough to induce phase separation. We use the extensions of the improved version of the inhomogeneous long-range corrections of Janecek [J. Phys. Chem. B 110, 6264 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] and Martínez-Ruiz et al. [J. Chem. Phys. 141, 184701 (2014)], to deal with the interaction energy and microscopic components of the pressure tensor. We perform Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of the symmetrical mixture with different cut-off distances r c and in combination with the inhomogeneous long-range corrections. The pressure tensor is obtained using the mechanical (virial) and thermodynamic route. The liquid-liquid interfacial tension is also evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the test-area methodology. This allows to check the validity of the recent extensions presented to deal with the contributions due to long-range corrections for intermolecular energy and pressure tensor in the case of binary mixtures that exhibit liquid-liquid immiscibility. In addition to the pressure tensor and the surface tension, we also obtain density profiles and coexistence densities and compositions as functions of pressure, at a given temperature. According to our results, the main effect of increasing the cut-off distance r c is to sharpen the liquid-liquid interface and to increase the width of the biphasic coexistence region. Particularly interesting is the presence of a relative minimum in the total density profiles of the symmetrical mixture. This minimum is related with a desorption of the
Directory of Open Access Journals (Sweden)
W. Kurniawan
2016-11-01
Full Text Available Penyelesaian persamaan Schrödinger dengan berbagai model potensial sangat penting dilakukan untuk memberikan gambaran perilaku zarah di bawah pengaruh potensial tersebut. Solusinya berupa fungsi gelombang yang memuat informasi penting tentang perilaku gelombang yang ditunjukkan dengan energi terikatnya. Pada penelitian ini kasus yang ingin diteliti adalah model potensial Lennard-Jones dengan menggunakan metode analisa goal seek yang tersedia pada Microsoft excel. Persamaannya dijabarkan dengan metode Euler terlebih dahulu selanjutnya syarat batas ditentukan agar ketelitian hasil diperoleh. Agar perhitungan goal seek dapat dilakukan maka harus diubah dari besaran fisis menjadi besaran yang tidak berdimensi dimana parameter v menunjukkan keklasikan suatu sistem dan nilai ε menunjukkan kuantisasi energi. Hasil yang diperoleh adalah bahwa dengan memasukkan parameter kontrol nilai v tertentu, telah diperoleh beberapa keadaan energi dengan batas zkiri dan zkanan tertentu. Ketika masukan parameter v yang diberikan semakin besar keadaan energinya pun lebih rapat (ditunjukkan energy state yang diperoleh semakin banyak dibandingkan bila masukan v-nya lebih kecil. Penelitian ini bermanfaat untuk menyederhanakan kasus potensial yang lebih rumit, dimana solusinya dapat diperoleh dengan mudah dan konsep kuantisasi energi akibat model potensial L-J dapat dipahami secara utuh. Solution of the Schrödinger equation in various potential model is very important in order to provide an overview of behaviour’s particle under influence of potential model. The solution is a wave function that contains important information are shown by energy state. In this research, the investigated is Lennard Jones potential by using Goal Seek analysis which are available in Microsoft Excel. The equation is described by the Euler method and then boundary condition is determined to perecision result which are obtained. It must be changed in terms dimensionless where
Georgescu, Ionuţ; Mandelshtam, Vladimir A
2012-10-14
The theory of self-consistent phonons (SCP) was originally developed to address the anharmonic effects in condensed matter systems. The method seeks a harmonic, temperature-dependent Hamiltonian that provides the "best fit" for the physical Hamiltonian, the "best fit" being defined as the one that optimizes the Helmholtz free energy at a fixed temperature. The present developments provide a scalable O(N) unified framework that accounts for anharmonic effects in a many-body system, when it is probed by either thermal (ℏ → 0) or quantum fluctuations (T → 0). In these important limits, the solution of the nonlinear SCP equations can be reached in a manner that requires only the multiplication of 3N × 3N matrices, with no need of diagonalization. For short range potentials, such as Lennard-Jones, the Hessian, and other related matrices are highly sparse, so that the scaling of the matrix multiplications can be reduced from O(N(3)) to ~O(N). We investigate the role of quantum effects by continuously varying the de-Boer quantum delocalization parameter Λ and report the N-Λ (T = 0), and also the classical N-T (Λ = 0) phase diagrams for sizes up to N ~ 10(4). Our results demonstrate that the harmonic approximation becomes inadequate already for such weakly quantum systems as neon clusters, or for classical systems much below the melting temperatures.
International Nuclear Information System (INIS)
Johnson, W.R.; Dzuba, V.A.; Safronova, U.I.; Safronova, M.S.
2004-01-01
A finite-field scaling method is applied to evaluate the Lennard-Jones interaction constant C 3 for alkali-metal atoms. The calculations are based on the relativistic single-double approximation in which single and double excitations of Dirac-Hartree-Fock wave functions are included to all orders in perturbation theory
Bazhenov, Alexiev M.; Heyes, David M.
1990-01-01
The thermodynamics, structure, and transport coefficients, as defined by the Green-Kubo integrals, of the one-dimensional Lennard-Jones fluid are evaluated for a wide range of state points by molecular dynamics computer simulation. These calculations are performed for the first time for thermal conductivity and the viscosity. We observe a transition from hard-rod behavior at low number density to harmonic-spring fluid behavior in the close-packed limit. The self-diffusion coefficient decays with increasing density to a finite limiting value. The thermal conductivity increases with density, tending to ∞ in the close-packed limit. The viscosity in contrast maximizes at intermediate density, tending to zero in the zero density and close-packed limits.
International Nuclear Information System (INIS)
Merabia, Samy; Termentzidis, Konstantinos
2012-01-01
We characterize the thermal Kapitza conductance between Lennard-Jones solids using non-equilibrium molecular dynamics simulations. We consider a series of perfect interfaces between mass-mismatched solids. We show that both the acoustic mismatch model (AMM) and the diffuse mismatch model (DMM) fail to predict the interfacial conductance even for large acoustic mismatched solids. This poor agreement may be explained by the use of equilibrium distributions of phonons in the expression of the conductance. On the other hand, we show that an extension of AMM taking into account the out-of-equilibrium phonon distribution on both sides of the interface leads to a good agreement with the simulation results, even for interfaces between almost similar materials. This opens the way to understand interfacial heat transport across real semi-conductors and dielectrics.
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
International Nuclear Information System (INIS)
Staśkiewicz, B.; Okrasiński, W.
2012-01-01
We propose a simple analytical form of the vapor–liquid equilibrium curve near the critical point for Lennard-Jones fluids. Coexistence densities curves and vapor pressure have been determined using the Van der Waals and Dieterici equation of state. In described method the Bernoulli differential equations, critical exponent theory and some type of Maxwell's criterion have been used. Presented approach has not yet been used to determine analytical form of phase curves as done in this Letter. Lennard-Jones fluids have been considered for analysis. Comparison with experimental data is done. The accuracy of the method is described. -- Highlights: ► We propose a new analytical way to determine the VLE curve. ► Simple, mathematically straightforward form of phase curves is presented. ► Comparison with experimental data is discussed. ► The accuracy of the method has been confirmed.
International Nuclear Information System (INIS)
Van Zon, Ramses; Ashwin, S S; Cohen, E G D
2008-01-01
To describe short time (picosecond) and small scale (nanometre) transport in fluids, a Green's function approach was recently developed. This approach relies on an expansion of the distribution of single particle displacements around a Gaussian function, yielding an infinite series of correction terms. Applying a recent theorem (van Zon and Cohen 2006 J. Stat. Phys. 123 1–37) shows that for sufficiently small times the terms in this series become successively smaller, so that truncating the series near or at the Gaussian level might provide a good approximation. In this paper, we derive a theoretical estimate for the time scale at which truncating the series at or near the Gaussian level could be supposed to be accurate for equilibrium nanoscale systems. In order to numerically estimate this time scale, the coefficients for the first few terms in the series are determined in computer simulations for a Lennard-Jones (LJ) fluid, an isotopic LJ mixture and a suspension of a LJ-based model of nanoparticles in a LJ fluid. The results suggest that for LJ fluids an expansion around a Gaussian is accurate at time scales up to a picosecond, while for nanoparticles in suspension (a nanofluid), the characteristic time scale up to which the Gaussian is accurate becomes of the order of 5–10 ps. (invited article)
Fowler's approximation for the surface tension and surface energy of Lennard-Jones fluids revisited
Energy Technology Data Exchange (ETDEWEB)
Mulero, A [Departamento de Fisica, Universidad de Extremadura, 06071-Badajoz (Spain); Galan, C [Departamento de Fisica, Universidad de Extremadura, 06071-Badajoz (Spain); Cuadros, F [Departamento de Fisica, Universidad de Extremadura, 06071-Badajoz (Spain)
2003-04-16
We present a detailed study of the validity of Fowler's approximation for calculating the surface tension and the surface energy of Lennard-Jones fluids. To do so, we consider three different explicit analytical expressions for the radial distribution function (RDF), including one proposed by our research group, together with very accurate expressions for the liquid and vapour densities, also proposed by our group. The calculation of the surface tension from the direct correlation function using both the Percus-Yevick and the hypernetted-chain approximations is also considered. Finally, our results are compared with those obtained by other authors by computer simulations or through relevant theoretical approximations. In particular, we consider the analytical expression proposed by Kalikmanov and Hofmans (1994 J. Phys.: Condens. Matter 6 2207-14) for the surface tension. Our results indicate that the values for the surface energy in Fowler's approximation obtained by other authors are adequate, and can be calculated from the RDF models. For the surface tension, however, the values considered as valid in previous works seem to be incorrect. The correct values can be obtained from our model for the RDF or from the Kalikmanov and Hofmans expression with suitable inputs.
Scaling relation and regime map of explosive gas–liquid flow of binary Lennard-Jones particle system
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.
An EQT-based cDFT approach for a confined Lennard-Jones fluid mixture
Energy Technology Data Exchange (ETDEWEB)
Motevaselian, M. H.; Mashayak, S. Y.; Aluru, N. R., E-mail: aluru@illinois.edu [Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)
2015-09-28
Empirical potential-based quasi-continuum theory (EQT) provides a route to incorporate atomistic detail into continuum framework such as the Nernst-Planck equation. EQT can also be used to construct a grand potential functional for classical density functional theory (cDFT). The combination of EQT and cDFT provides a simple and fast approach to predict the inhomogeneous density, potential profiles, and thermodynamic properties of confined fluids. We extend the EQT-cDFT approach to confined fluid mixtures and demonstrate it by simulating a mixture of methane and hydrogen inside slit-like channels of graphene. We show that the EQT-cDFT predictions for the structure of the confined fluid mixture compare well with the molecular dynamics simulation results. In addition, our results show that graphene slit nanopores exhibit a selective adsorption of methane over hydrogen.
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
International Nuclear Information System (INIS)
Martínez-Ruiz, F. J.; Blas, F. J.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.
2014-01-01
We propose an extension of the improved version of the inhomogeneous long-range corrections of Janeček [J. Phys. Chem. B 110, 6264–6269 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] to account for the intermolecular potential energy of spherical, rigid, and flexible molecular systems, to deal with the contributions to the microscopic components of the pressure tensor due to the dispersive long-range corrections. We have performed Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of spherical Lennard-Jones molecules with different cutoff distances, r c = 2.5, 3, 4, and 5σ. In addition, we have also considered cutoff distances r c = 2.5 and 3σ in combination with the inhomogeneous long-range corrections proposed in this work. The normal and tangential microscopic components of the pressure tensor are obtained using the mechanical or virial route in combination with the recipe of Irving and Kirkwood, while the macroscopic components are calculated using the Volume Perturbation thermodynamic route proposed by de Miguel and Jackson [J. Chem. Phys. 125, 164109 (2006)]. The vapour-liquid interfacial tension is evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the Test-Area methodology. In addition to the pressure tensor and the surface tension, we also obtain density profiles, coexistence densities, vapour pressure, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the cutoff distance and the long-range corrections on these properties. According to our results, the main effect of increasing the cutoff distance (at fixed temperature) is to sharpen the vapour-liquid interface, to decrease the vapour pressure, and to increase the width of the biphasic coexistence region. As a result, the interfacial thickness
Molecular dynamics calculation of half-lives for thermal decay of Lennard-Jones clusters
International Nuclear Information System (INIS)
Smith, R.W.
1991-01-01
Molecular dynamics has been used with a Lenard-Jones (6-12) potential in order to study the decay behavior of neutral Argon clusters containing between 12 and 14 atoms. The clusters were heated to temperatures well above their melting points and then tracked in time via molecular dynamics until evaporation of one or more atoms was observed. In each simulation, the mode of evaporation, energy released during evaporation, and cluster lifetime were recorded. Results from roughly 2000 simulation histories were combined in order to compute statistically significant values of cluster half-lives and decay energies. It was found that cluster half-life decreases with increasing energy and that for a given value of excess energy (defined as E=(E tot -E gnd )/n), the 13 atom cluster is more stable against decay than clusters containing either 12 or 14 atoms. The dominant decay mechanism for all clusters was determined to be single atom emission. (orig.)
Karbowniczek, Paweł; Chrzanowska, Agnieszka
2017-11-01
A two-dimensional Lennard-Jones system in a circular and rotating container has been studied by means of molecular dynamics technique. A nonequilibrium transition to the rotating stage has been detected in a delayed time since an instant switching of the frame rotation. This transition is attributed to the increase of the density at the wall because of the centrifugal force. At the same time the phase transition occurs, the inner system changes its configuration of the solid-state type into the liquid type. Impact of angular frequency and molecular roughness on the transport properties of the nonrotating and rotating systems is analyzed.
Vogelsang, R.; Hoheisel, C.
1987-02-01
Molecular-dynamics (MD) calculations are reported for three thermodynamic states of a Lennard-Jones fluid. Systems of 2048 particles and 105 integration steps were used. The transverse current autocorrelation function, Ct(k,t), has been determined for wave vectors of the range 0.5viscosities which showed a systematic behavior as a function of k. Extrapolation to the hydrodynamic region at k=0 gave shear viscosity coefficients in good agreement with direct Green-Kubo results obtained in previous work. The two-exponential model fit for the memory function proposed by other authors does not provide a reasonable description of the MD results, as the fit parameters show no systematic wave-vector dependence, although the Ct(k,t) functions are somewhat better fitted. Similarly, the semiempirical interpolation formula for the decay time based on the viscoelastic concept proposed by Akcasu and Daniels fails to reproduce the correct k dependence for the wavelength range investigated herein.
International Nuclear Information System (INIS)
Vogelsang, R.; Hoheisel, C.
1987-01-01
For a large region of dense fluid states of a Lennard-Jones system, they have calculated the friction coefficient by the force autocorrelation function of a Brownian-type particle by molecular dynamics (MD). The time integral over the force autocorrelation function showed an interesting behavior and the expected plateau value when the mass of the Brownian particle was chosen to be about a factor of 100 larger than the mass of the fluid particle. Sufficient agreement was found for the friction coefficient calculated by this way and that obtained by calculations of the self-diffusion coefficient using the common relation between these coefficients. Furthermore, a modified friction coefficient was determined by integration of the force autocorrelation function up to the first maximum. This coefficient can successfully be used to derive a reasonable soft part of the friction coefficient necessary for the Rice-Allnatt approximation for the shear velocity and simple liquids
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.
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 ...
International Nuclear Information System (INIS)
Fay, P.J.; Ray, J.R.; Wolf, R.J.
1994-01-01
We present a new, nondestructive, method for determining chemical potentials in Monte Carlo and molecular dynamics simulations. The method estimates a value for the chemical potential such that one has a balance between fictitious successful creation and destruction trials in which the Monte Carlo method is used to determine success or failure of the creation/destruction attempts; we thus call the method a detailed balance method. The method allows one to obtain estimates of the chemical potential for a given species in any closed ensemble simulation; the closed ensemble is paired with a ''natural'' open ensemble for the purpose of obtaining creation and destruction probabilities. We present results for the Lennard-Jones system and also for an embedded atom model of liquid palladium, and compare to previous results in the literature for these two systems. We are able to obtain an accurate estimate of the chemical potential for the Lennard-Jones system at higher densities than reported in the literature
Adsorption of metal atoms at a buckled graphene grain boundary using model potentials
International Nuclear Information System (INIS)
Helgee, Edit E.; Isacsson, Andreas
2016-01-01
Two model potentials have been evaluated with regard to their ability to model adsorption of single metal atoms on a buckled graphene grain boundary. One of the potentials is a Lennard-Jones potential parametrized for gold and carbon, while the other is a bond-order potential parametrized for the interaction between carbon and platinum. Metals are expected to adsorb more strongly to grain boundaries than to pristine graphene due to their enhanced adsorption at point defects resembling those that constitute the grain boundary. Of the two potentials considered here, only the bond-order potential reproduces this behavior and predicts the energy of the adsorbate to be about 0.8 eV lower at the grain boundary than on pristine graphene. The Lennard-Jones potential predicts no significant difference in energy between adsorbates at the boundary and on pristine graphene. These results indicate that the Lennard-Jones potential is not suitable for studies of metal adsorption on defects in graphene, and that bond-order potentials are preferable
International Nuclear Information System (INIS)
Stiegler, Thomas; Sadus, Richard J.
2015-01-01
General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic properties predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form
International Nuclear Information System (INIS)
Brooks, R.; Porter, R.A.R.; Kalos, F.; Grosser, A.E.
1975-01-01
A velocity selected molecular beam of D 2 O was crossed with a nozzle beam of Ar and the angular distribution of the scattered D 2 O was measured mass spectrometrically. By varying the velocity of the D 2 O beam, the differential cross section was measured at two collision energies. The experimental results were compared with synthetic differential cross sections calculated from Lennard-Jones and Kihara-Stockmayer trial potentials to determine potential parameters. Implications for the H 2 O pair potential are discussed
Chemical potential calculations in dense liquids using metadynamics
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.
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
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...
Note: Modification of the Gay-Berne potential for improved accuracy and speed
Persson, Rasmus A. X.
2012-06-01
A modification of the Gay-Berne (GB) potential is proposed which is about 10% to 20% more speed efficient and statistically more accurate in reproducing the energy of interaction of two linear Lennard-Jones tetratomics when averaged over all orientations. For the special cases of end-to-end and side-by-side configurations, the new potential is equivalent to the GB one. A simple generalization to dissimilar particles of D∞h symmetry is presented but does not retain the superior agreement with respect to its GB counterpart, except at close range.
Analysis of bound-state spectra near the threshold of neutral particle interaction potentials
International Nuclear Information System (INIS)
Ou Fang; Cao Zhuangqi; Chen Jianping; Xu Junjie
2006-01-01
It is understood that conventional semiclassical approximations deteriorate towards threshold in a typical neutral particle interaction potential which is important for the study of ultra-cold atoms and molecules. In this Letter we give an example of the Lennard-Jones potential with tuning of the strength parameter on the basis of the analytical transfer matrix (ATM) method. Highly accurate quantum mechanical results, such as number of the bound states, energy level density and the eigenvalues with extremely low energies have been derived
Experimental studies of the NaRb ground-state potential up to the v''=76 level
International Nuclear Information System (INIS)
Docenko, O.; Nikolayeva, O.; Tamanis, M.; Ferber, R.; Pazyuk, E.A.; Stolyarov, A.V.
2002-01-01
Laser induced fluorescence spectra of the C 1 Σ + -X 1 Σ + system of 23 Na 85 Rb and 23 Na 87 Rb have allowed vibrational levels of the electronic ground state up to v '' =76, spanning 99.85% of the potential well to be observed. The ground-state term values have been fitted to a Dunham polynomial expansion, and also to a direct modified Lennard-Jones (MLJ) potential. The analytical MLJ construction allowed us to match previous measured term values for v '' ≤30 with long-range behavior of the potential through the intermediate internuclear distance region covered by the present investigation
Similarity Laws for the Lines of Ideal Free Energy and Chemical Potential in Supercritical Fluids.
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.
Energy Technology Data Exchange (ETDEWEB)
Mokhtari, B.; Enayati, M. [Iranian Offshore Oil Co., Tehran (Iran, Islamic Republic of); Heidaryan, E. [Islamic Azad Univ., Tehran (Iran, Islamic Republic of). Masjidosolayman Branch
2008-07-01
Theoretical methods show that crystalline hydrates can form from single-phase systems consisting of both vapor water with gaseous hydrate former and liquid water with dissolved hydrate former. Two phase systems consist of both liquid water with gaseous hydrate former and with liquid hydrate former on the surface. This paper presented a Langmuir constant related model for the prediction of equilibrium pressures and cage occupancies of pure component hydrates. Intermolecular potentials were fit to quantum mechanical energies to obtain the Langmuir constants, which differed from the procedure utilized with the vdWP model. The paper described the experimental method and model calculations. This included the Fugacity model and Van der Waals and Platteeuw model. The paper also discussed pair potential of non-spherical molecules, including the multicentre (site-site) potential; Gaussian overlap potential; Lennard-Jones potential; and Kihara generalized pair potential. It was concluded that fraction of occupied cavities is a function of pair potentials between hard core and empty hydrate lattice. These pair potentials could be calculated from some model as Kihara cell potential, Gaussian potential, Lennard-Jones potential and multicentre pair potential. 49 refs., 3 figs.
The importance of accurate interaction potentials in the melting of argon nanoclusters
Pahl, E.; Calvo, F.; Schwerdtfeger, P.
The melting temperatures of argon clusters ArN (N = 13, 55, 147, 309, 561, and 923) and of bulk argon have been obtained from exchange Monte Carlo simulations and are compared using different two-body interaction potentials, namely the standard Lennard-Jones (LJ), Aziz and extended Lennard-Jones (ELJ) potentials. The latter potential has many advantages: while maintaining the computational efficiency of the commonly used LJ potential, it is as accurate as the Aziz potential but the computer time scales more favorably with increasing cluster size. By applying the ELJ form and extrapolating the cluster data to the infinite system, we are able to extract the melting point of argon already in good agreement with experimental measurements. By considering the additional Axilrod-Teller three-body contribution as well, we calculate a melting temperature of T meltELJ = 84.7 K compared to the experimental value of T meltexp = 83.85 K, whereas the LJ potential underestimates the melting point by more than 7 K. Thus melting temperatures within 1 K accuracy are now feasible.
Solid phase stability of a double-minimum interaction potential system
International Nuclear Information System (INIS)
Suematsu, Ayumi; Yoshimori, Akira; Saiki, Masafumi; Matsui, Jun; Odagaki, Takashi
2014-01-01
We study phase stability of a system with double-minimum interaction potential in a wide range of parameters by a thermodynamic perturbation theory. The present double-minimum potential is the Lennard-Jones-Gauss potential, which has a Gaussian pocket as well as a standard Lennard-Jones minimum. As a function of the depth and position of the Gaussian pocket in the potential, we determine the coexistence pressure of crystals (fcc and bcc). We show that the fcc crystallizes even at zero pressure when the position of the Gaussian pocket is coincident with the first or third nearest neighbor site of the fcc crystal. The bcc crystal is more stable than the fcc crystal when the position of the Gaussian pocket is coincident with the second nearest neighbor sites of the bcc crystal. The stable crystal structure is determined by the position of the Gaussian pocket. These results show that we can control the stability of the solid phase by tuning the potential function
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.
International Nuclear Information System (INIS)
Schwarzer, N
2014-01-01
In order to understand the principle differences between rheological or simple stress tests like the uniaxial tensile test to contact mechanical tests and the differences between quasistatic contact experiments and oscillatory ones, this study resorts to effective first principles. This study will show how relatively simple models simulating bond interactions in solids using effective potentials like Lennard-Jones and Morse can be used to investigate the effect of time dependent stress-induced softening or stiffening of these solids. The usefulness of the current study is in the possibility of deriving relatively simple dependences of the bulk-modulus B on time, shear and pressure P with time t. In cases where it is possible to describe, or at least partially describe a material by Lennard-Jones potential approaches, the above- mentioned dependences are even completely free of microscopic material parameters. Instead of bond energies and length, only specific integral parameters like Young’s modulus and Poisson’s ratio are required. However, in the case of time dependent (viscose) material behavior the parameters are not constants anymore. They themselves depend on time and the actual stress field, especially the shear field. A body completely consisting of so called standard linear solid interacting particles will then phenomenologically show a completely different and usually much more complicated mechanical behavior. The influence of the time dependent pressure-shear-induced Young’s modulus change is discussed with respect to mechanical contact experiments and their analysis in the case of viscose materials. (papers)
International Nuclear Information System (INIS)
Koudriavtsev, A.B.; Linert, W.
2005-01-01
Parameters of the formalism [1-6] describing spin crossover in the solid state have been defined via molecular potentials in model systems of neutral and ionic complexes. In the first instance Lennard-Jones and electric dipole-dipole potentials have been used whereas in ionic systems Lennard-Jones and electric point-charge potentials have been used. Electric dipole-dipole interaction of neutral complexes brings about a positive excess energy controlled by the difference of electric dipole moments of HS and LS molecules. Differences of the order of Δμ = 1-2D cause an abrupt spin crossover in systems with T 1/2 = 100-150K. Magnetic coupling contributes both to the excess energy and excess entropy, however the overall effect is equivalent to a modest positive excess energy. Ionic systems in the absence of specific interactions are characterized by very small excess energies corresponding to practically linear van't Hoff plots. Detectable positive and negative excess energies in these systems may arise from interactions of ligands belonging to neighbouring complexes. The HOMO-LUMO overlap in HS-LS pairs can bring about a nontrivial variation of the shape of transition curves. Examples of regression analysis of experimental transition curves in terms of molecular potentials are given. (author)
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.
Empirical potential for molecular simulation of graphene nanoplatelets
Bourque, Alexander J.; Rutledge, Gregory C.
2018-04-01
A new empirical potential for layered graphitic materials is reported. Interatomic interactions within a single graphene sheet are modeled using a Stillinger-Weber potential. Interatomic interactions between atoms in different sheets of graphene in the nanoplatelet are modeled using a Lennard-Jones interaction potential. The potential is validated by comparing molecular dynamics simulations of tensile deformation with the reported elastic constants for graphite. The graphite is found to fracture into graphene nanoplatelets when subjected to ˜15% tensile strain normal to the basal surface of the graphene stack, with an ultimate stress of 2.0 GPa and toughness of 0.33 GPa. This force field is useful to model molecular interactions in an important class of composite systems comprising 2D materials like graphene and multi-layer graphene nanoplatelets.
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
International Nuclear Information System (INIS)
Damyanova, M; Balabanova, E; Hohm, U
2014-01-01
A temperature-dependent effective intermolecular interaction potential is applied to describe the interaction between two nitrogen fluoride (NF 3 ) molecules in gas phase. To this end, a spherically-symmetric (n-6) Lennard-Jones temperature-dependent potential (LJTDP) is used. The (n-6) LJTDP takes into account the influence of vibrational excitation of the molecules on the potential parameters, namely, the equilibrium distance r m and the potential well depth ε. The potential parameters at T = 0 K were obtained from the very small amount of existing thermophysical equilibrium and transport properties of low-density NF 3 gas. Fitting formulae are tabulated for a fast and reliable prediction of the thermophysical properties and potential parameters in the temperature range between 200 K and 1200 K. A comparison is also presented between our estimates for some thermophysical properties of the NF 3 gas with the available experimental and calculated data.
2010-01-01
... 7 Agriculture 1 2010-01-01 2010-01-01 false Administration. 12.6 Section 12.6 Agriculture Office....6 Administration. (a) General. A determination of ineligibility for benefits in accordance with the... making such determinations, as provided in this section. (b) Administration by FSA. (1) The provisions of...
NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface
DEFF Research Database (Denmark)
Ingebrigtsen, Trond; Toxværd, Søren; Heilmann, Ole
2011-01-01
that ensures potential-energy and step-length conservation; center-of-mass drift is also eliminated. Analytical arguments confirmed by simulations demonstrate that the modified NVU algorithm is absolutely stable. Finally, we present simulations showing that the NVU algorithm and the standard leap-frog NVE......An algorithm is derived for computer simulation of geodesics on the constant-potential-energy hypersurface of a system of N classical particles. First, a basic time-reversible geodesic algorithm is derived by discretizing the geodesic stationarity condition and implementing the constant......-potential-energy constraint via standard Lagrangian multipliers. The basic NVU algorithm is tested by single-precision computer simulations of the Lennard-Jones liquid. Excellent numerical stability is obtained if the force cutoff is smoothed and the two initial configurations have identical potential energy within machine...
Comment on 'Path integral solution for a Mie-type potential'
International Nuclear Information System (INIS)
Steiner, F.
1985-01-01
We comment on several incorrect results given in a recent paper by Erkoc and Sever (ES). In particular, it is pointed out that their path integral formula for the one-dimensional Mie-Lennard-Jones potential is wrong, since a quantum correction proportional to (h/2π) 2 - which is a consequence of the stochastic nature of the Feynman paths - has been overlooked. The correct expression can be obtained from a general path integral formula, which we have derived in a previous paper. For the particular potential discussed in detail by ES, we give a complete path integral treatment, which allows us to derive the energies and normalized wave functions of the discrete spectrum. (orig.)
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.
Fusion process of Lennard-Jones clusters: global minima and magic numbers formation
DEFF Research Database (Denmark)
Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter
2004-01-01
We present a new theoretical framework for modeling the fusion process of Lennard–Jones (LJ) clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing paths up to the cluster size of 150 atoms...
Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems
Watanabe, H.; Suzuki, M.; Ito, N.
2011-01-01
simple spatialdecomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute
Interaction forces between nanoparticles in Lennard-Jones (L-J) solvents
International Nuclear Information System (INIS)
Sinha, Indrajit; Mukherjee, Ashim K
2014-01-01
Molecular simulations, such as Monte Carlo (MC) and molecular dynamics (MD) have been recently used for understanding the forces between colloidal nanoparticles that determine the dispersion and stability of nanoparticle suspensions. Herein we review the current status of research in the area of nanoparticles immersed in L-J solvents. The first study by Shinto et al. used large smooth spheres to depict nanoparticles in L-J and soft sphere solvents. The nanoparticles were held fixed at a particular interparticle distance and only the solvents were allowed to equilibrate. Both Van-der-waals and solvation forces were computed at different but fixed interparticle separation. Later Qin and Fitchthorn improved on this model by considering the nanoparticles as collection of molecules, thus taking into the account the effect of surface roughness of nanoparticles. Although the inter particle distance was fixed, the rotation of such nanoparticles with respect to each other was also investigated. Recently, in keeping with the experimental situation, we modified this model by allowing the nanoparticles to move and rotate freely. Solvophilic, neutral and solvophobic interactions between the solvent atoms and those that make up the nanoparticles were modelled. While neutral and solvophobic nanoparticles coalesce even at intermediate distances, solvophilic nanoparticles are more stable in solution due to the formation of a solvent shield
Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation
Kadoura, Ahmad Salim; Siripatana, Adil; Sun, Shuyu; Knio, Omar; Hoteit, Ibrahim
2016-01-01
In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard
Effective pair potentials for spherical nanoparticles
International Nuclear Information System (INIS)
Van Zon, Ramses
2009-01-01
An effective description for rigid spherical nanoparticles in a fluid of point particles is presented. The points inside the nanoparticles and the point particles are assumed to interact via spherically symmetric additive pair potentials, while the distribution of points inside the nanoparticles is taken to be spherically symmetric and smooth. The resulting effective pair interactions between a nanoparticle and a point particle, as well as between two nanoparticles, are then given by spherically symmetric potentials. If overlap between particles is allowed, as can occur for some forms of the pair potentials, the effective potential generally has non-analytic points. It is shown that for each effective potential the expressions for different overlapping cases can be written in terms of one analytic auxiliary potential. Even when only non-overlapping situations are possible, the auxiliary potentials facilitate the formulation of the effective potentials. Effective potentials for hollow nanoparticles (appropriate e.g. for buckyballs) are also considered and shown to be related to those for solid nanoparticles. For hollow nanoparticles overlap is more physical, since this covers the case of a smaller particle embedded in a larger, hollow nanoparticle. Finally, explicit expressions are given for the effective potentials derived from basic pair potentials of power law and exponential form, as well as from the commonly used London–van der Waals, Morse, Buckingham, and Lennard-Jones potentials. The applicability of the latter is demonstrated by comparison with an atomic description of nanoparticles with an internal face centered cubic structure
Thermodynamical Properties of the Solidified Rare Gases
Energy Technology Data Exchange (ETDEWEB)
Ebbsjoe, I
1971-12-15
Lattice parameter, isothermal bulk modulus and specific heat at constant volume are calculated from Helmholtz free energy for solid Ne, Ar, Kr and Xe. The lattice potential energy is expanded to the fourth order in the nuclear displacements. A perturbation treatment in the quasi harmonic approximation of the partition function includes the cubic anharmonic term to second order and the quartic to first order. Detailed numerical calculations are presented for two interatomic pair potentials, the Lennard-Jones (12,6) and the (exp,a,6). The three nearest neighbours have been taken into account. It is shown that earlier nearest neighbour calculations exaggerate the breakdown of the theory at higher temperatures
Theoretical Assessment of Compressibility Factor of Gases by Using Second Virial Coefficient
Mamedov, Bahtiyar A.; Somuncu, Elif; Askerov, Iskender M.
2018-01-01
We present a new analytical approximation for determining the compressibility factor of real gases at various temperature values. This algorithm is suitable for the accurate evaluation of the compressibility factor using the second virial coefficient with a Lennard-Jones (12-6) potential. Numerical examples are presented for the gases H2, N2, He, CO2, CH4 and air, and the results are compared with other studies in the literature. Our results showed good agreement with the data in the literature. The consistency of the results demonstrates the effectiveness of our analytical approximation for real gases.
Molecular Simulation of the Vapor-Liquid Phase Behavior of Lennard-Jones Mixtures in Porous Solids
2006-09-01
sur la Catalyse, Centre National de la Recherche Scientifique, Group de Chimie Theorique, 2 Avenue Albert Einstein, 69626 Villeurbanne Cedex, France...and Group de Chimie Theorique, Ecole Normale Superieure de Lyon, 46 Allee d’Italie, 69364 Lyon, Cedex 07, France 14. ABSTRACT We present vapor...Scientifique, Group de Chimie Theorique, 2 Avenue Albert Einstein, 69626 Villeurbanne Cedex, France and Group de Chimie Theorique, Ecole Normale
Scaling relation and regime map of explosive gas–liquid flow of binary Lennard-Jones particle system
Inaoka, Hajime; Yukawa, Satoshi; Ito, Nobuyasu
2012-01-01
liquid droplets, and gas particles, which remain supercritical gaseous states under the depressurization realized by simulations. The system has a pipe-like structure similar to the model of a shock tube. We observed physical quantities and flow regimes
International Nuclear Information System (INIS)
Hoover, W.G.; Evans, D.J.; Hickman, R.B.; Ladd, A.J.C.; Ashurst, W.T.; Moran, B.
1980-01-01
A new Hamiltonian method for deformation simulations is related to the Green-Kubo fluctuation theory through perturbation theory and linear-response theory. Numerical results for the bulk and shear viscosity coefficients are compared to corresponding Green-Kubo calculations. Both viscosity coefficients depend similarly on frequency, in a way consistent with enhanced ''long-time tails.''
Lennard-Jones fluids in two-dimensional nano-pores. Multi-phase coexistence and fluid structure
Yatsyshin, Petr; Savva, Nikos; Kalliadasis, Serafim
2014-03-01
We present a number of fundamental findings on the wetting behaviour of nano-pores. A popular model for fluid confinement is a one-dimensional (1D) slit pore formed by two parallel planar walls and it exhibits capillary condensation (CC): a first-order phase transition from vapour to capillary-liquid (Kelvin shift). Capping such a pore at one end by a third orthogonal wall forms a prototypical two-dimensional (2D) pore. We show that 2D pores possess a wetting temperature such that below this temperature CC remains of first order, above it becomes a continuous phase transition manifested by a slab of capillary-liquid filling the pore from the capping wall. Continuous CC exhibits hysteresis and can be preceded by a first-order capillary prewetting transition. Additionally, liquid drops can form in the corners of the 2D pore (remnant of 2D wedge prewetting). The three fluid phases, vapour, capillary-liquid slab and corner drops, can coexist at the pore triple point. Our model is based on the statistical mechanics of fluids in the density functional formulation. The fluid-fluid and fluid-substrate interactions are dispersive. We analyze in detail the microscopic fluid structure, isotherms and full phase diagrams. Our findings also suggest novel ways to control wetting of nano-pores. We are grateful to the European Research Council via Advanced Grant No. 247031 for support.
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 ...
Addendum to ''Density fluctuations in liquid rubidium''
International Nuclear Information System (INIS)
Haan, S.W.; Mountain, R.D.; Hsu, C.S.; Rahman, A.
1980-01-01
We performed molecular-dynamics simulations of liquid rubidium and the Lennard-Jones fluid at several densities and temperatures, and of a system whose pair potential is the repulsive core of the rubidium potential. In all cases, propagating density fluctuations occurred in the rubidiumlike systems at much shorter wavelengths than in the Lennard-Jones system. This indicates that the repulsive part of the pair potential is the dominant factor in determining the relaxation of short-wavelength density fluctuations
Adhesive contact: from atomistic model to continuum model
International Nuclear Information System (INIS)
Fan Kang-Qi; Jia Jian-Yuan; Zhu Ying-Min; Zhang Xiu-Yan
2011-01-01
Two types of Lennard-Jones potential are widely used in modeling adhesive contacts. However, the relationships between the parameters of the two types of Lennard-Jones potential are not well defined. This paper employs a self-consistent method to derive the Lennard-Jones surface force law from the interatomic Lennard-Jones potential with emphasis on the relationships between the parameters. The effect of using correct parameters in the adhesion models is demonstrated in single sphere-flat contact via continuum models and an atomistic model. Furthermore, the adhesion hysteresis behaviour is investigated, and the S-shaped force-distance relation is revealed by the atomistic model. It shows that the adhesion hysteresis loop is generated by the jump-to-contact and jump-off-contact, which are illustrated by the S-shaped force-distance curve. (atomic and molecular physics)
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
A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces.
Schneider, Julian; Ciacchi, Lucio Colombi
2011-02-08
The behavior of titanium implants in physiological environments is governed by the thin oxide layer that forms spontaneously on the metal surface and mediates the interactions with adsorbate molecules. In order to study the adsorption of biomolecules on titanium in a realistic fashion, we first build up a model of an oxidized Ti surface in contact with liquid water by means of extensive first-principles molecular dynamics simulations. Taking the obtained structure as reference, we then develop a classical potential to model the Ti/TiOx/water interface. This is based on the mapping with Coulomb and Lennard-Jones potentials of the adsorption energy landscape of single water and ammonia molecules on the rutile TiO2(110) surface. The interactions with arbitrary organic molecules are obtained via standard combination rules to established biomolecular force fields. The transferability of our potential to the case of organic molecules adsorbing on the oxidized Ti surface is checked by comparing the classical potential energy surfaces of representative systems to quantum mechanical results at the level of density functional theory. Moreover, we calculate the heat of immersion of the TiO2 rutile surface and the detachment force of a single tyrosine residue from steered molecular dynamics simulations, finding good agreement with experimental reference data in both cases. As a first application, we study the adsorption behavior of the Arg-Gly-Asp (RGD) peptide on the oxidized titanium surface, focusing particularly on the calculation of the free energy of desorption.
Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential
International Nuclear Information System (INIS)
Zhou Shiqi
2005-01-01
A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.
Jover, J; Haslam, A J; Galindo, A; Jackson, G; Müller, E A
2012-10-14
We present a continuous pseudo-hard-sphere potential based on a cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). Using this potential one can mimic the volumetric, structural, and dynamic properties of the discontinuous hard-sphere potential over the whole fluid range. The continuous pseudo potential has the advantage that it may be incorporated directly into off-the-shelf molecular-dynamics code, allowing the user to capitalise on existing hardware and software advances. Simulation results for the compressibility factor of the fluid and solid phases of our pseudo hard spheres are presented and compared both to the Carnahan-Starling equation of state of the fluid and published data, the differences being indistinguishable within simulation uncertainty. The specific form of the potential is employed to simulate flexible chains formed from these pseudo hard spheres at contact (pearl-necklace model) for m(c) = 4, 5, 7, 8, 16, 20, 100, 201, and 500 monomer segments. The compressibility factor of the chains per unit of monomer, m(c), approaches a limiting value at reasonably small values, m(c) theory. Simulation results are also presented for highly asymmetric mixtures of pseudo hard spheres, with diameter ratios of 3:1, 5:1, 20:1 over the whole composition range.
Kapranov, Sergey V.; Kouzaev, Guennadi A.
2018-01-01
Variations of effective diffusion coefficient of polar molecules exposed to microwave electric fields in a surface potential are studied by solving coupled stochastic differential equations of motion with a deterministic component of the surface force. Being an essential tool for the simulation interpretation, a theoretical approach to effective diffusion in surface potential is first developed. The effective diffusion coefficient is represented as the product of the normal diffusion coefficient and potential-dependent correction function, whose temperature dependence is close to the Arrhenius form. The analytically found zero-diffusion condition defines the state of thermal equilibrium at the surface. The diffusion of a water-like dipole molecule in the potential of graphite surface is simulated in the field-free conditions and in the presence of the alternating electric fields of various magnitude intensities and frequencies. Temperature dependence of the correction function exhibits field-induced variations of the effective Lennard-Jones energy parameter. It demonstrates maximum departure from the zero-field value at certain frequencies and intensities, which is associated with variations in the rotational dynamics. A concept of the amplitude-frequency resonance put forward to interpret the simulation results is explained using a heuristic reasoning and is corroborated by semi-quantitative considerations in terms of the Dissado-Hill cluster theory of dielectric relaxation.
Pair Potential That Reproduces the Shape of Isochrones in Molecular Liquids
DEFF Research Database (Denmark)
Veldhorst, Arno; Schrøder, Thomas; Dyre, Jeppe C.
2016-01-01
-dependent function of density, h(ρ), which for real liquids is well approximated by a power law, ργ. However, in simulations, a power law is not adequate when density changes are large; typical models, such as Lennard-Jones liquids, show that γ(ρ) ≡ d ln h(ρ)/d ln ρ is a decreasing function of density. This article...... presents results from computer simulations using a new pair potential that diverges at a nonzero distance and can be tuned to give a more realistic shape of γ(ρ). Our results indicate that the finite size of molecules is an important factor to take into account when modeling liquids over a large density......Many liquids have curves (isomorphs) in their phase diagrams along which structure, dynamics, and some thermodynamic quantities are invariant in reduced units. A substantial part of their phase diagrams is thus effectively one dimensional. The shapes of these isomorphs are described by a material...
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.
Directory of Open Access Journals (Sweden)
Miriam Fritsche
Full Text Available Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential.We find a variety of equilibrium structures including global globular configurations at low normalized temperature (T* = 0.014, combination of segmental globules and elongated chains (T* = 0.016,0.017, predominantly elongated chains (T* = 0.019,0.020, as well as universal SAW conformations at high normalized temperature (T* ≥ 0.023. The radius of gyration of the protein exhibits a non-monotonic temperature dependence with a maximum at a characteristic temperature (T(c* = 0.019 where a crossover occurs from a positive (stretching at T* ≤ T(c* to negative (contraction at T* ≥ T(c* thermal response on increasing T*.
Dynamical phases of attractive particles sliding on a structured surface
International Nuclear Information System (INIS)
Hasnain, J; Jungblut, S; Dellago, C
2015-01-01
Inspired by experiments on quartz crystal microbalance setups, we study the mobility of a monolayer of Lennard-Jones particles driven over a hexagonal external potential. We pay special attention to the changes in the dynamical phases that arise when the lattice constant of the external substrate potential and the Lennard-Jones interaction are mismatched. We find that if the average particle separation is such that the particles repel each other, or interact harmonically, the qualitative behavior of the system is akin to that of a monolayer of purely repulsive Yukawa particles. On the other hand, if the particles typically attract each other, the ensuing dynamical states are determined entirely by the relative strength of the Lennard-Jones interaction with respect to that of the external potential. (paper)
Equation of state of a hard core fluid with a two-Yukawa tail: toward a simple analytic theory
International Nuclear Information System (INIS)
Jedrzejek, C.
1980-01-01
Thermodynamic properties of simple fluids are calculated using variational theory for a system of hard-core potential with a two-Yukawa tail. Likewise one Yukawa-tail case the working formulas are analytic. Five parameters of the two Yukawa system are chosen so as to get the best fit to a real argon potential or an ''argon-like'' Lennard-Jones potential. The results are fairly good in light of the extreme simplicity of the method. The discrepancies result from using the variational method and a different shape of Yukawa type potential in comparision to the real argon and Lennard-Jones potentials. (author)
Theoretical-experimental study of the solvation enthalpy of acetone in dilute aqueous solution
International Nuclear Information System (INIS)
Arroyo, S. Tolosa; Martin, J.A. Sanson; Garcia, A. Hidalgo
2005-01-01
The present paper describes molecular dynamics simulations of aqueous solutions at infinite dilution with acetone as solute. Lennard-Jones with electrostatic term (12-6-1 potentials) were employed to describe the solute-solvent interactions. The Morokuma decomposition scheme of ab initio interaction energies at the SCF level and the ESIE charges on the solute atoms were used to reproduce the exchange and Coulomb electrostatic contributions of the solute-water interaction potential. Some extensions, such as including the dispersion component evaluated at MP2 level, were added to the traditional calculation procedures in order to improve the results of the solvation enthalpy. The results obtained with the EX-DIS-ES model were compared with the experimental calorimetry values, the observed agreement being acceptable
Characterizing water-metal interfaces and machine learning potential energy surfaces
Ryczko, Kevin
In this thesis, we first discuss the fundamentals of ab initio electronic structure theory and density functional theory (DFT). We also discuss statistics related to computing thermodynamic averages of molecular dynamics (MD). We then use this theory to analyze and compare the structural, dynamical, and electronic properties of liquid water next to prototypical metals including platinum, graphite, and graphene. Our results are built on Born-Oppenheimer molecular dynamics (BOMD) generated using density functional theory (DFT) which explicitly include van der Waals (vdW) interactions within a first principles approach. All calculations reported use large simulation cells, allowing for an accurate treatment of the water-electrode interfaces. We have included vdW interactions through the use of the optB86b-vdW exchange correlation functional. Comparisons with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional are also shown. We find an initial peak, due to chemisorption, in the density profile of the liquid water-Pt interface not seen in the liquid water-graphite interface, liquid watergraphene interface, nor interfaces studied previously. To further investigate this chemisorption peak, we also report differences in the electronic structure of single water molecules on both Pt and graphite surfaces. We find that a covalent bond forms between the single water molecule and the platinum surface, but not between the single water molecule and the graphite surface. We also discuss the effects that defects and dopants in the graphite and graphene surfaces have on the structure and dynamics of liquid water. Lastly, we introduce artificial neural networks (ANNs), and demonstrate how they can be used to machine learn electronic structure calculations. As a proof of principle, we show the success of an ANN potential energy surfaces for a dimer molecule with a Lennard-Jones potential.
Low pressure broadening and shift of the 540.06 nm line of neon
International Nuclear Information System (INIS)
Bielski, A.; Dokurno, W.; Szudy, J.; Wolnikowski, J.
1980-01-01
The collision broadening and shift of the 540.06 nm line of neon emitted from a low pressure glow discharge in pure neon and a neon-helium mixture have been measured. The values of the broadening and shift coefficients were determined and compared with the results of calculations based on the Lindholm-Foley impact theory assuming a Lennard-Jones potential. The results for pure neon demonstrate the inadequacy of the Lennard-Jones potential for the Ne-Ne interaction. (orig.)
Effects of Mn addition on microstructure and hardness of Al-12.6Si alloy
Biswas, Prosanta; Patra, Surajit; Mondal, Manas Kumar
2018-03-01
In this work, eutectic Al-12.6Si alloy with and without manganese (Mn) have been developed through gravity casting route. The effect of Mn concentration (0.0 wt.%, 1 wt%, 2 wt% and 3 wt%) on microstructural morphology and hardness property of the alloy has been investigated. The eutectic Al-12.6 Si alloy exhibits the presence of combine plate, needle and rod-like eutectic silicon phase with very sharp corners and coarser primary silicon particles within the α-Al phase. In addition of 1wt.% of Mn in the eutectic Al-12.6Si alloy, sharp corners of the primary Si and needle-like eutectic Si are became blunt and particles size is reduced. Further, increase in Mn concentration (2.0 wt.%) in the Al-12.6Si alloy, irregular plate shape Al6(Mn,Fe) intermetallics are formed inside the α-Al phase, but the primary and eutectic phase morphology is similar to the eutectic Al-12.6Si alloy. The volume fraction of Al6(Mn,Fe) increases and Al6(Mn,Fe) particles appear as like chain structure in the alloy with 3 wt.% Mn. An increase in Mn concentration in the Al-12.6Si alloys result in the increase in bulk hardness of the alloy as an effects of microstructure modification as well as the presence of harder Al6(Mn,Fe) phase in the developed alloy.
Su, Pin-Chih; Johnson, Michael E
2016-04-05
Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the parahalogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme. © 2015 Wiley Periodicals, Inc.
Calculation of Liquid Water-Hydrate-Methane Vapor Phase Equilibria from Molecular Simulations
DEFF Research Database (Denmark)
Jensen, Lars; Thomsen, Kaj; von Solms, Nicolas
2010-01-01
using the TIP4P/ice potential and a united-atom Lennard-Jones potential. respectively. The equilibrium calculation method for this system has three components, (i) thermodynamic integration from a supercritical ideal gas to obtain the fluid-phase chemical potentials. (ii) calculation of the chemical...
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
Elastic properties of surfactant monolayers at liquid-liquid interfaces: A molecular dynamics study
DEFF Research Database (Denmark)
Laradji, Mohamed; Mouritsen, Ole G.
2000-01-01
Using a simple molecular model based on the Lennard-Jones potential, we systematically study the elastic properties of liquid-liquid interfaces containing surfactant molecules by means of extensive and large-scale molecular dynamics simulations. The main elastic constants of the interface, corres...
Stochasticity thresholds in the Fermi-Pasta-Ulam model
International Nuclear Information System (INIS)
Callegari, B.; Galgani, L.; Milan Univ.
1979-01-01
The authors consider the celebrated model of Fermi, Pasta and Ulam and give a numerical estimate for its thresholds of stochasticity, thus determining a critical energy as a function of the frequency of the corresponding oscillators. The results turn out to be qualitatively similar to those already obtained for a chain of particles with nearest-neighbour Lennard-Jones interaction potential. (author)
Stochasticity thresholds in the Fermi-Pasta-Ulam model
Energy Technology Data Exchange (ETDEWEB)
Callegari, B [Ferrara Univ. (Italy). Ist. di Matematica; Carotta, M C; Ferrario, C [Ferrara Univ. (Italy). Ist. di Fisica; Lo Vecchio, G [Ferrara Univ. (Italy). Ist. di Fisica; Gruppo Nazionale di Struttura della Materia, Ferrara (Italy)); Galgani, L [Milan Univ. (Italy). Ist. di Fisica; Milan Univ. (Italy). Ist. di Matematica)
1979-12-11
The authors consider the celebrated model of Fermi, Pasta and Ulam and give a numerical estimate for its thresholds of stochasticity, thus determining a critical energy as a function of the frequency of the corresponding oscillators. The results turn out to be qualitatively similar to those already obtained for a chain of particles with nearest-neighbour Lennard-Jones interaction potential.
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.
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.
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.
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.)
Crystal structure and conformational flexibility of the unligated FK506-binding protein FKBP12.6
Energy Technology Data Exchange (ETDEWEB)
Chen, Hui; Mustafi, Sourajit M. [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); LeMaster, David M. [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); University at Albany – SUNY, Empire State Plaza, Albany, NY 12201 (United States); Li, Zhong [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); Héroux, Annie [Brookhaven National Laboratory, Upton, NY 11973 (United States); Li, Hongmin; Hernández, Griselda, E-mail: griselda@wadsworth.org [New York State Department of Health, Empire State Plaza, Albany, NY 12201 (United States); University at Albany – SUNY, Empire State Plaza, Albany, NY 12201 (United States)
2014-03-01
Two crystal forms of unligated FKBP12.6 exhibit multiple conformations in the active site and in the 80s loop, the primary site for known protein-recognition interactions. The previously unreported NMR backbone assignment of FKBP12.6 revealed extensive doubling of amide resonances, which reflects a slow conformational transition centered in the 80s loop. The primary known physiological function of FKBP12.6 involves its role in regulating the RyR2 isoform of ryanodine receptor Ca{sup 2+} channels in cardiac muscle, pancreatic β islets and the central nervous system. With only a single previously reported X-ray structure of FKBP12.6, bound to the immunosuppressant rapamycin, structural inferences for this protein have been drawn from the more extensive studies of the homologous FKBP12. X-ray structures at 1.70 and 1.90 Å resolution from P2{sub 1} and P3{sub 1}21 crystal forms are reported for an unligated cysteine-free variant of FKBP12.6 which exhibit a notable diversity of conformations. In one monomer from the P3{sub 1}21 crystal form, the aromatic ring of Phe59 at the base of the active site is rotated perpendicular to its typical orientation, generating a steric conflict for the immunosuppressant-binding mode. The peptide unit linking Gly89 and Val90 at the tip of the protein-recognition ‘80s loop’ is flipped in the P2{sub 1} crystal form. Unlike the >30 reported FKBP12 structures, the backbone conformation of this loop closely follows that of the first FKBP domain of FKBP51. The NMR resonances for 21 backbone amides of FKBP12.6 are doubled, corresponding to a slow conformational transition centered near the tip of the 80s loop, as recently reported for 31 amides of FKBP12. The comparative absence of doubling for residues along the opposite face of the active-site pocket in FKBP12.6 may in part reflect attenuated structural coupling owing to increased conformational plasticity around the Phe59 ring.
Work hardening characteristics in Al base alloys with 12.6 and 45 wt.% Zn
International Nuclear Information System (INIS)
Abd El-Salam, F.; Mostafa, M.M.; Wahab, L.A.; Mostafa, M.T.; Abd El-Aziz, Sh.M.
2008-01-01
The stress-strain curves were obtained for Al-Zn alloys of 12.6 wt.% Zn (alloy I) and 45 wt.% Zn (alloy II) with elements of purity (99.99). The monotonic shift of these curves towards lower flow stress and higher ductility was interrupted at the transformation temperatures 483 K (alloy I) and both 543, 603 K (alloy II). By increasing deformation temperature, Young's modulus, Y, yield and fracture stresses, σ y and σ f , respectively, fracture time, t f , the coefficient of parabolic work hardening, χ, decreased while fracture strain, ε f , and dislocation slip distance, L, increased. From the obtained X-rays diffraction patterns the lattice strain, ε, crystallite size, η, and dislocation density, ρ, were obtained at different deformation temperatures around transformation
NVU dynamics. II. Comparing to four other dynamics
DEFF Research Database (Denmark)
Ingebrigtsen, Trond; Toxværd, Søren; Schrøder, Thomas
2011-01-01
-potential-energy hypersurface. Here, simulations of NVU dynamics are compared to results for four other dynamics, both deterministic and stochastic. First, NVU dynamics is compared to the standard energy-conserving Newtonian NVE dynamics by simulations of the Kob-Andersen binary Lennard-Jones liquid, its WCA version (i.......e., with cut-off's at the pair potential minima), and the Lennard-Jones Gaussian liquid. We find identical results for all quantities probed: radial distribution functions, incoherent intermediate scattering functions, and mean-square displacement as function of time. Arguments are presented...... on the constant-potential-energy hypersurface, and to Nos-Hoover NVT dynamics. If time is scaled for the two stochastic dynamics to make single-particle diffusion constants identical to that of NVE dynamics, the simulations show that all five dynamics are equivalent at low temperatures except at short times....
Kinetic energy of solid and liquid para-hydrogen: a path integral Monte Carlo simulation
International Nuclear Information System (INIS)
Zoppi, M.; Neumann, M.
1992-01-01
The translational (center of mass) kinetic energy of solid and liquid para-hydrogen have been recently measured by means of Deep Inelastic Neutron Scattering. We have evaluated the same quantity, in similar thermodynamic conditions, by means of Path Integral Monte Carlo computer simulation, modelling the system as composed of a set of spherical molecules interacting through a pairwise additive Lennard-Jones potential. In spite of the crude approximations on the interaction potential, the agreement is excellent. The pressure was also computed by means of the same simulations. This quantity, compared with the equation of state for solid para-hydrogen given by Driessen and Silvera, gives an agreement of a lesser quality and a negative value for the liquid state. We attribute this discrepancy to the limitations of the Lennard-Jones potential. (orig.)
Equilibrium properties of dense hydrogen isotope gases based on the theory of simple fluids.
Kowalczyk, Piotr; MacElroy, J M D
2006-08-03
We present a new method for the prediction of the equilibrium properties of dense gases containing hydrogen isotopes. The proposed approach combines the Feynman-Hibbs effective potential method and a deconvolution scheme introduced by Weeks et al. The resulting equations of state and the chemical potentials as functions of pressure for each of the hydrogen isotope gases depend on a single set of Lennard-Jones parameters. In addition to its simplicity, the proposed method with optimized Lennard-Jones potential parameters accurately describes the equilibrium properties of hydrogen isotope fluids in the regime of moderate temperatures and pressures. The present approach should find applications in the nonlocal density functional theory of inhomogeneous quantum fluids and should also be of particular relevance to hydrogen (clean energy) storage and to the separation of quantum isotopes by novel nanomaterials.
Effective diameters and corresponding states of fluids
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.
International Nuclear Information System (INIS)
Bertagnolli, H.
1978-01-01
For the case of special molecular models representing the acetonitrile molecule the expansion coefficients of the molecular par distribution function are calculated by use of pertubation theory. These results are used to get theoretical access to scattering intensities in the frame of several approximations. The first model describes the molecule by three hard spheres and uses a hard sphere liquid as reference. In the second cast the calculations are based on an anisotropic Lennard-Jones potential by application of a model of overlapping ellipsoids and by use of a Lennard-Jones liquid as a reference system. In the third model dipolar attractive forces are taken into account with an anisotropic hard-sphere liquid as a reference. In the third model dipolar attractive forces are taken into account with an anisotropic hard-sphere liquid as a reference. Finally all the calculations with different intermolecular potentials are compared with neutron scattering experiments. (orig.) 891 HK [de
Koperwas, K.; Affouard, F.; Gerges, J.; Valdes, L.-C.; Adrjanowicz, K.; Paluch, M.
2017-12-01
In this paper, we examine, in terms of the classical nucleation theory, how the strengthening of the attractive intermolecular interactions influences the crystallization process for systems like Lennard-Jones at different isobaric conditions. For this purpose, we modify the standard Lennard-Jones potential, and as a result, we obtain three different systems characterized by various strengths of attractive potentials occurring between molecules, which are in direct relationship to the physical quantities describing molecules, e.g., its polarizability or dipole moment. Based on performed analysis, we demonstrate that the molecular attraction primarily impacts the thermodynamics of the interface between liquid and crystal. This is reflected in the behavior of nucleation and overall crystallization rates during compression of the system.
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
Molecular dynamic simulation of Copper and Platinum nanoparticles Poiseuille flow in a nanochannels
Toghraie, Davood; Mokhtari, Majid; Afrand, Masoud
2016-10-01
In this paper, simulation of Poiseuille flow within nanochannel containing Copper and Platinum particles has been performed using molecular dynamic (MD). In this simulation LAMMPS code is used to simulate three-dimensional Poiseuille flow. The atomic interaction is governed by the modified Lennard-Jones potential. To study the wall effects on the surface tension and density profile, we placed two solid walls, one at the bottom boundary and the other at the top boundary. For solid-liquid interactions, the modified Lennard-Jones potential function was used. Velocity profiles and distribution of temperature and density have been obtained, and agglutination of nanoparticles has been discussed. It has also shown that with more particles, less time is required for the particles to fuse or agglutinate. Also, we can conclude that the agglutination time in nanochannel with Copper particles is faster that in Platinum nanoparticles. Finally, it is demonstrated that using nanoparticles raises thermal conduction in the channel.
On the equivalence of continuum and lattice models for fluids
International Nuclear Information System (INIS)
Panagiotopoulos, Athanassios Z.
2000-01-01
It was demonstrated that finely discretized lattice models for fluids with particles interacting via Lennard-Jones or exponential-6 potentials have essentially identical thermodynamic and structural properties to their continuum counterparts. Grand canonical histogram reweighting Monte Carlo calculations were performed for systems with repulsion exponents between 11 and 22. Critical parameters were determined from mixed-field finite-size scaling methods. Numerical equivalence of lattice and continuous space models, within simulation uncertainties, was observed for lattices with ratio of particle diameter σ to grid spacing of 10. The lattice model calculations were more efficient computationally by factors between 10 and 20. It was also shown that Lennard-Jones and exponential-6 based models with identical critical properties can be constructed by appropriate choice of the repulsion exponent. (c) 2000 American Institute of Physics
Graphene on Cu(111) at the nonzero temperatures: Molecular dynamic simulation
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.
Isomorph invariance of Couette shear flows simulated by the SLLOD equations of motion
DEFF Research Database (Denmark)
Separdar, Leila; Bailey, Nicholas; Schrøder, Thomas
2013-01-01
fluctuations of virial and potential energy. Such systems have good isomorphs (curves in the thermodynamic phase diagram along which structural, dynamical, and some thermodynamic quantities are invariant when expressed in reduced units). The SLLOD equations of motion were used to simulate Couette shear flows......Non-equilibrium molecular dynamics simulations were performed to study the thermodynamic, structural, and dynamical properties of the single-component Lennard-Jones and the Kob-Andersen binary Lennard-Jones liquids. Both systems are known to have strong correlations between equilibrium thermal...... of the two systems. We show analytically that these equations are isomorph invariant provided the reduced strain rate is fixed along the isomorph. Since isomorph invariance is generally only approximate, a range of strain rates were simulated to test for the predicted invariance, covering both the linear...
Cluster pair correlation function of simple fluids: energetic connectivity criteria
Pugnaloni, Luis A.; Zarragoicoechea, Guillermo J.; Vericat, Fernando
2006-01-01
We consider the clustering of Lennard-Jones particles by using an energetic connectivity criterion proposed long ago by T.L. Hill [J. Chem. Phys. 32, 617 (1955)] for the bond between pairs of particles. The criterion establishes that two particles are bonded (directly connected) if their relative kinetic energy is less than minus their relative potential energy. Thus, in general, it depends on the direction as well as on the magnitude of the velocities and positions of the particles. An integ...
The second virial coefficients of some halogenated ethanes
Kohler, Friedrich; van Nhu, Nguyen
The second virial coefficients of 1,1-difluoroethane, 1,1,1-trifluoroethane, 1,1,1,2-tetrafluoroethane and 1-chloro-1,1-difluoroethane have been calculated on the basis of two-centre-Lennard-Jones + superimposed dipole model potentials and compared with experimental results. These can be explained taking into account the reduced dipole moments and the angle between dipole moment and molecular axis.
First order phase transition of expanding matter and its fragmentation
International Nuclear Information System (INIS)
Chikazumi, Shinpei; Iwamoto, Akira
2002-01-01
Using an expanding matter model with a Lennard-Jones potential, the instability of the expanding system is investigated. The pressure, the temperature, and the density fluctuations are calculated as functions of density during the time evolution of the expanding matter, which are compared to the coexistence curve calculated by the Gibbs ensemble. The expanding matter undergoes the first order phase transition in the limit of the quasistatic expansion. The resultant fragment mass distributions are also investigated. (author)
Condensation and Evaporation Transitions in Deep Capillary Grooves
Malijevský, A. (Alexandr); Parry, A.O.
2014-01-01
We study the order of capillary condensation and evaporation transitions of a simple fluid adsorbed in a deep capillary groove using a fundamental measure density functional theory (DFT). The walls of the capillary interact with the fluid particles via long-ranged, dispersion, forces while the fluid-fluid interaction is modelled as a truncated Lennard-Jones-like potential. We find that below the wetting temperature $T_w$ condensation is first-order and evaporation is continuous with the metas...
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
Parsing partial molar volumes of small molecules: a molecular dynamics study.
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.
Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids
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
Phase transitions of quadrupolar fluids
International Nuclear Information System (INIS)
OShea, S.F.; Dubey, G.S.; Rasaiah, J.C.
1997-01-01
Gibbs ensemble simulations are reported for Lennard-Jones particles with embedded quadrupoles of strength Q * =Q/(εσ 5 ) 1/2 =2.0 where ε and σ are the Lennard-Jones parameters. Calculations revealing the effect of the dispersive forces on the liquid endash vapor coexistence were carried out by scaling the attractive r -6 term in the Lennard-Jones pair potential by a factor λ ranging from 0 to 1. Liquid endash vapor coexistence is observed for all values of λ including λ=0 for Q * =2.0, unlike the corresponding dipolar fluid studied by van Leeuwen and Smit et al. [Phys. Rev. Lett. 71, 3991 (1993)] which showed no phase transition below λ=0.35 when the reduced dipole moment μ * =2.0. The simulation data are analyzed to estimate the critical properties of the quadrupolar fluid and their dependence on the strength λ of the dispersive force. The critical temperature and pressure show a clear quadratic dependence on λ, while the density is less confidently identified as being linear in λ. The compressibility is roughly linear in λ. copyright 1997 American Institute of Physics
Fluids in micropores. V. Effects of thermal motion in the walls of a slit-micropore
International Nuclear Information System (INIS)
Diestler, D.J.; Schoen, M.
1996-01-01
Previous articles in this series have concerned the prototypal slit-pore with rigid walls, in which a Lennard-Jones (12,6) monatomic film is constrained between two plane-parallel walls comprising like atoms fixed in the face-centered-cubic (fcc) (100) configuration. The behavior of molecularly thin films in the rigid-wall prototype is governed by the template effect, whereby solid films can form epitaxially when the walls are properly aligned in the lateral directions. In this article the influence of thermal motion of the wall atoms on the template effect is investigated. The walls are treated as Einstein solids, the atoms moving independently in harmonic potentials centered on rigidly fixed equilibrium positions in the fcc (100) configuration. The force constant f c is a measure of the stiffness of the walls, the rigid-wall limit being f c =∞. Formal thermodynamic and statistical mechanical analyses of the system are carried out. The results of grand canonical ensemble Monte Carlo simulations indicate that for values of f c characteristic of a soft (e.g., noble-gas) crystal dynamic coupling between wall and film has a substantial influence on such equilibrium properties as normal stress (load) and interfacial tensions. In general, the softer the walls (i.e., the smaller the value of f c ), the weaker the template effect and hence the softer and more disordered the confined film. copyright 1996 American Institute of Physics
Interfacial layering and capillary roughness in immiscible liquids.
Geysermans, P; Pontikis, V
2010-08-21
The capillary roughness and the atomic density profiles of extended interfaces between immiscible liquids are determined as a function of the interface area by using molecular dynamics and Lennard-Jones (12-6) potentials. We found that with increasing area, the interface roughness diverges logarithmically, thus fitting the theoretical mean-field prediction. In systems small enough for the interfacial roughness not to blur the structural details, atomic density profiles across the fluid interface are layered with correlation length in the range of molecular correlations in liquids. On increasing the system size, the amplitude of the thermally excited position fluctuations of the interface increases, thus causing layering to rapidly vanish, if density profiles are computed without special care. In this work, we present and validate a simple method, operating in the direct space, for extracting from molecular dynamics trajectories the "intrinsic" structure of a fluid interface that is the local density profile of the interface cleaned from capillary wave effects. Estimated values of interfacial properties such as the tension, the intrinsic width, and the lower wavelength limit of position fluctuations are in agreement with results collected from the literature.
Picciochi, Ricardo; Canongia Lopes, José N; Diogo, Hermínio P; Minas da Piedade, Manuel E
2008-10-16
The standard molar enthalpy of sublimation of monoclinic cyclopentadienyltricarbonylmanganese, Mn(eta (5)-C 5H 5)(CO) 3, at 298.15 K, was determined as Delta sub H m (o)[Mn(eta (5)-C 5H 5)(CO) 3] = 75.97 +/- 0.37 kJ x mol (-1) from Knudsen effusion and Calvet-drop microcalorimetry measurements, thus considerably improving the very large inaccuracy (>10 kJ x mol (-1)) of the published data. The obtained value was used to assess the extension of the OPLS-based all-atom force field we previously developed for iron metallocenes to manganese organometallic compounds. The modified force field was able to reproduce the volumetric properties (density and unit-cell volume) of crystalline Mn(eta (5)-C 5H 5)(CO) 3 with a deviation of 0.6% and the experimentally determined enthalpy of sublimation with an accuracy of 1 kJ x mol (-1). The interaction (epsilon) and atomic-diameter (sigma) parameters of the Lennard-Jones (12-6) potential function used to calculate dispersion contributions within the framework of the force field were found to be transferable from iron to manganese.
International Nuclear Information System (INIS)
Guseva, D. V.; Komarov, P. V.; Lyulin, Alexey V.
2014-01-01
Constant temperature–constant pressure (NpT) molecular-dynamics computer simulations have been carried out for the united-atom model of a non-crosslinked (1,4) cis-polyisoprene (PI) melt confined between two amorphous, fully coordinated silica surfaces. The Lennard-Jones 12-6 potential was implemented to describe the polymer–silica interactions. The thickness H of the produced PI–silica film has been varied in a wide range, 1 g g is the individual PI chain radius of gyration measured under the imposed confinement. After a thorough equilibration, the PI film stratified structure and polymer segmental dynamics have been studied. The chain structure in the middle of the films resembles that in a corresponding bulk, but the polymer-density profile shows a pronounced ordering of the polymer segments in the vicinity of silica surfaces; this ordering disappears toward the film middles. Tremendous slowing down of the polymer segmental dynamics has been observed in the film surface layers, with the segmental relaxation more than 150 times slower as compared to that in a PI bulk. This effect increases with decreasing the polymer-film thickness. The segmental relaxation in the PI film middles shows additional relaxation process which is absent in a PI bulk. Even though there are fast relaxation processes in the film middle, its overall relaxation is slower as compared to that in a bulk sample. The interpretation of the results in terms of polymer glassy bridges has been discussed
International Nuclear Information System (INIS)
Lamb, W.E. Jr.
1978-07-01
The molecule SF 6 is treated as a classical dynamical system obeying Newton's laws of motion. This report describes how the current SF 6 potential is determined. The initial approach is described in terms of a pair of Lennard--Jones potential functions with arbitrary coefficients. A method for determining the potential constants is developed. The SF 6 spectrum was reproduced by including three-body forces. By specifying certain parameters such as the 1/r 6 F-F constant and the total dissociation energy of the molecule, a satisfactory global potential was obtained. The laser-molecule interaction energy was developed
Thermal motion in proteins: Large effects on the time-averaged interaction energies
International Nuclear Information System (INIS)
Goethe, Martin; Rubi, J. Miguel; Fita, Ignacio
2016-01-01
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.
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.
Estimated Viscosities and Thermal Conductivities of Gases at High Temperatures
Svehla, Roger A.
1962-01-01
Viscosities and thermal conductivities, suitable for heat-transfer calculations, were estimated for about 200 gases in the ground state from 100 to 5000 K and 1-atmosphere pressure. Free radicals were included, but excited states and ions were not. Calculations for the transport coefficients were based upon the Lennard-Jones (12-6) potential for all gases. This potential was selected because: (1) It is one of the most realistic models available and (2) intermolecular force constants can be estimated from physical properties or by other techniques when experimental data are not available; such methods for estimating force constants are not as readily available for other potentials. When experimental viscosity data were available, they were used to obtain the force constants; otherwise the constants were estimated. These constants were then used to calculate both the viscosities and thermal conductivities tabulated in this report. For thermal conductivities of polyatomic gases an Eucken-type correction was made to correct for exchange between internal and translational energies. Though this correction may be rather poor at low temperatures, it becomes more satisfactory with increasing temperature. It was not possible to obtain force constants from experimental thermal conductivity data except for the inert atoms, because most conductivity data are available at low temperatures only (200 to 400 K), the temperature range where the Eucken correction is probably most in error. However, if the same set of force constants is used for both viscosity and thermal conductivity, there is a large degree of cancellation of error when these properties are used in heat-transfer equations such as the Dittus-Boelter equation. It is therefore concluded that the properties tabulated in this report are suitable for heat-transfer calculations of gaseous systems.
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.
Free energy evaluation in polymer translocation via Jarzynski equality
International Nuclear Information System (INIS)
Mondaini, Felipe; Moriconi, L.
2014-01-01
We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.
Effect of pairwise additivity on finite-temperature behavior of classical ideal gas
Shekaari, Ashkan; Jafari, Mahmoud
2018-05-01
Finite-temperature molecular dynamics simulations have been applied to inquire into the effect of pairwise additivity on the behavior of classical ideal gas within the temperature range of T = 250-4000 K via applying a variety of pair potentials and then examining the temperature dependence of a number of thermodynamical properties. Examining the compressibility factor reveals the most deviation from ideal-gas behavior for the Lennard-Jones system mainly due to the presence of both the attractive and repulsive terms. The systems with either attractive or repulsive intermolecular potentials are found to present no resemblance to real gases, but the most similarity to the ideal one as temperature rises.
Oscillations of spherical fullerenes interacting with graphene sheet
Energy Technology Data Exchange (ETDEWEB)
Ghavanloo, Esmaeal, E-mail: ghavanloo@shirazu.ac.ir; Fazelzadeh, S. Ahmad
2017-01-01
In the present study, the oscillations of spherical fullerenes in the vicinity of a fully constrained graphene sheet are investigated. Using the continuous approximation and Lennard-Jones potential, the van der Waals (vdW) potential energy and interaction forces are obtained. The equation of motion is derived and directly solved based on the actual force distribution between the fullerene molecules and the graphene sheet. Numerical results are obtained and shown that the oscillation is sensitive to the size of the fullerene as well as the distance between the center of the fullerene and the graphene sheet.
2011-03-01
have been developed ranging from measuring surface details to modifying surface structures . This chapter focuses on aspects of AFM modeling the- ory and...how far apart they are. An example of a poten- tial function is the Lennard-Jones potential, which is also called the 6-12 potential. It can be...γ1 + γ2 + γ12, (31) where γ1 and γ2 are the surface energies of the two adhering spheres, and γ12 is the interfacial energy between the two spheres
Light hydrogen isotopes in the single - walled carbon nano tube
International Nuclear Information System (INIS)
Khugaev, A.V.; Sultanov, R.A.; Guster, D.
2007-01-01
Full text: Progress of our understanding of the molecular hydrogen behavior in the nano tube interior open an intriguing possibility for the applications of these knowledge's to the solution of the hydrogen storage problem and light isotopes gas selectivity. That can strongly change the situation at the energy production in the world and completely change our civil life. These investigations underline the influence of the quantum effects on the properties of molecular hydrogen in the nano tube interior and it leads to the pure quantum-mechanical reformulation of the problem for the hydrogen behavior inside carbon nano tube as a problem of molecular quantum system behavior in the external field induced by the regular nano tube surface. In the present paper the molecular hydrogen behavior in the carbon nano tube was considered in the simple quantum mechanical manner. The main attention was paid to the investigation of the quantum sieving selectivity in the dependence of nano tube composition, radius and symmetry properties. For the interaction potential between hydrogen and nano tube surface was taken some phenomenological LJ(12,6) - (Lennard - Jones) potential and the external field induced by the nano tube in its interior is considered as a simple sum over the all nano tube carbon atoms. Influence of the structure of rotation (vibration) spectrum of the energy levels of diatomic molecules, such as H 2 , HD and D 2 on the final results and finite size of the nano tube along the axis of symmetry, its boundary effects is discussed in details. Thermal oscillations of nano tube surface were considered separately in the dependence of the temperature gradient along of the axis of symmetry
Time-dependent friction and solvation time correlation function
International Nuclear Information System (INIS)
Samanta, Alok; Ali, Sk Musharaf; Ghosh, Swapan K
2005-01-01
We have derived a new relation between the time-dependent friction and solvation time correlation function (STCF) for non-polar fluids. The friction values calculated using this relation and simulation results on STCF for a Lennard-Jones fluid are shown to have excellent agreement with the same obtained through mode-coupling theory. Also derived is a relation between the time-dependent dielectric friction and STCF for polar fluids. Routes are thus provided to obtain the time-dependent friction (non-polar as well as dielectric) from an experimentally measured quantity like STCF, even if the interparticle interaction potential is not known
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.)
Communication: Simple liquids' high-density viscosity
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.
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....
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....
Theory of warm ionized gases: equation of state and kinetic Schottky anomaly.
Capolupo, A; Giampaolo, S M; Illuminati, F
2013-10-01
Based on accurate Lennard-Jones-type interaction potentials, we derive a closed set of state equations for the description of warm atomic gases in the presence of ionization processes. The specific heat is predicted to exhibit peaks in correspondence to single and multiple ionizations. Such kinetic analog in atomic gases of the Schottky anomaly in solids is enhanced at intermediate and low atomic densities. The case of adiabatic compression of noble gases is analyzed in detail and the implications on sonoluminescence are discussed. In particular, the predicted plasma electron density in a sonoluminescent bubble turns out to be in good agreement with the value measured in recent experiments.
Geysermans, P; Elyeznasni, N; Russier, V
2005-11-22
We present a study of the structure in the interface between two immiscible liquids by density-functional theory and molecular-dynamics calculations. The liquids are modeled by Lennard-Jones potentials, which achieve immiscibility by suppressing the attractive interaction between unlike particles. The density profiles of the liquids display oscillations only in a limited part of the simple liquid-phase diagram (rho,T). When approaching the liquid-vapor coexistence, a significant depletion appears while the layering behavior of the density profile vanishes. By analogy with the liquid-vapor interface and the analysis of the adsorption this behavior is suggested to be strongly related to the drying transition.
On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems
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.
Communication: Simple liquids' high-density viscosity.
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.
International Nuclear Information System (INIS)
Vallee, O.; Ranson, P.; Chapelle, J.
1977-01-01
AI line broadening was studied from collisions between neutral argon atoms (3p 5 4p-3p 5 4s transitions) in a weakly ionised plasma jet (neutral atoms temperature T 0 approximately 4000K, electrons temperature Tsub(e) approximately 6000K, electronic density Nsub(e) 15 cm -3 , ionisation rate α -4 , and pressure range from 1 to 3 kg/cm 2 ). A satisfactory description of Van der Waals broadened lines is obtained by means of a Lennard-Jones potential. Measurement of line widths whose corresponding transitions occur on resonant levels, gives with relatively good accuracy the oscillator strength of the argon resonance lines [fr
Capillary condensation in pores with rough walls: a density functional approach.
Bryk, P; Rzysko, W; Malijevsky, Al; Sokołowski, S
2007-09-01
The effect of surface roughness of slit-like pore walls on the capillary condensation of a spherical particles and short chains is studied. The gas molecules interact with the substrate by a Lennard-Jones (9,3) potential. The rough layer at each pore wall has a variable thickness and density and consists of a disordered quenched matrix of spherical particles. The system is described in the framework of a density functional approach and using computer simulations. The contribution due to attractive van der Waals interactions between adsorbate molecules is described by using first-order mean spherical approximation and mean-field approximation.
Modulation of capillary condensation by trace component
Directory of Open Access Journals (Sweden)
Shiqi Zhou
2011-06-01
Full Text Available Impact of trace component on capillary condensation (CC is investigated systematically using a classical density functional theory. It is discovered that (i presence of the trace component makes the CC to occur at much lower condensation pressure than when its absence; (ii Lennard-Jones potential parameters like size parameter and energy parameter of the trace component, and its concentration in the bulk adsorption system, show their effects the most remarkably within a particular range beyond which the effects eventually become insignificant. The present discoveries have implications in low pressure storage of gases, separation and enrichment of low concentration component, and easy control of CC transition, etc.
Microscopic theory of warm ionized gases: equation of state and kinetic Schottky anomaly
International Nuclear Information System (INIS)
Capolupo, A; Giampaolo, S M; Illuminati, F
2013-01-01
Based on accurate Lennard-Jones type interaction potentials, we derive a closed set of state equations for the description of warm atomic gases in the presence of ionization processes. The specific heat is predicted to exhibit peaks in correspondence to single and multiple ionizations. Such kinetic analogue in atomic gases of the Schottky anomaly in solids is enhanced at intermediate and low atomic densities. The case of adiabatic compression of noble gases is analyzed in detail and the implications on sonoluminescence are discussed.
Chaotic dynamics in dense fluids
International Nuclear Information System (INIS)
Posch, H.A.; Hoover, W.G.
1987-09-01
We present calculations of the full spectra of Lyapunov exponents for 8- and 32-particle systems with periodic boundary conditions and interacting with the repulsive part of a Lennard-Jones potential both in equilibrium and nonequilibrium steady states. Lyapunov characteristic exponents λ/sub n/ describe the mean exponential rates of divergence and convergence of neighbouring trajectories in phase-space. They are useful in characterizing the stochastic properties of a dynamical system. A new algorithm for their calculation is presented which incorporates ideas from control theory and constraint nonequilibrium molecular dynamics. 4 refs., 1 fig
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
Um modelo para a superfície líquida no estudo da dinâmica do espalhamento de Xe e Ne pelo esqualano
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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.
Complexity, rate of energy exchanges and stochasticity
International Nuclear Information System (INIS)
Casartelli, M.; Sello, S.
1987-01-01
The complexity of trajectories in the phase of anharmonic crystal (mostly a Lennard-Jones chain) is analysed by the variance of microcanonical density and by new parameters P and chi defined, respectively, as the mean value of the time averages and the relative variance of the absolute exchange rate of energies among the normal modes. Evidence is given to the trapping action of residual invariant surfaces in low stochastic regime of motion. The parameter chi, moreover, proves efficient in exploring the border of stochasticity. A simple power law for P vs. the specific energy is obtained and proved to be independent of stochasticity and of the type of anharmonic potential
International Nuclear Information System (INIS)
Xiao-Guang, Zhang; Guang-Qing, Fang; Xin-Yuan, Zhao; Wen-Bo, Zhang; Li-Xia, Xi; Qian-Jin, Xiong; Xi-Xiang, Li; Guang-Yong, Zhang
2010-01-01
This paper reports on an experiment about a novel method of polarization stabilization. The polarization stabilizer proposed here has an additional function of polarization transformation from any state of polarization into any others. The particle swarm optimization is introduced as a control algorithm in the process of either searching or endless tracking. The tracking speed of the stabilizer is obtained up to 12.6 krad/s by using hardware we have in the laboratory, which means that we can achieve a higher speed practical polarization stabilizer if we have faster hardware. (classical areas of phenomenology)
Bernardes, Carlos E S; Canongia Lopes, José N; Minas da Piedade, Manuel E
2013-10-31
A previously developed OPLS-based all-atom force field for organometallic compounds was extended to a series of first-, second-, and third-row transition metals based on the study of M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) complexes. For materials that are solid at ambient temperature and pressure (M = Cr, Mo, W) the validation of the force field was based on reported structural data and on the standard molar enthalpies of sublimation at 298.15 K, experimentally determined by Calvet-drop microcalorimetry using samples corresponding to a specific and well-characterized crystalline phase: Δ(sub)H(m)° = 72.6 ± 0.3 kJ·mol(–1) for Cr(CO)(6), 73.4 ± 0.3 kJ·mol(–1) for Mo(CO)(6), and 77.8 ± 0.3 kJ·mol(–1) for W(CO)(6). For liquids, where problems of polymorphism or phase mixtures are absent, critically analyzed literature data were used. The force field was able to reproduce the volumetric properties of the test set (density and unit cell volume) with an average deviations smaller than 2% and the experimentally determined enthalpies of sublimation and vaporization with an accuracy better than 2.3 kJ·mol(–1). The Lennard-Jones (12-6) potential function parameters used to calculate the repulsive and dispersion contributions of the metals within the framework of the force field were found to be transferable between chromium, iron, and nickel (first row) and between molybdenum and ruthenium (second row).
de Mello, Ramon Andrade; Ferreira, Mónica; Soares-Pires, Filipa; Costa, Sandra; Cunha, João; Oliveira, Pedro; Hespanhol, Venceslau; Reis, Rui Manuel
2013-01-01
Introduction Polymorphic variants in the 5p15, 6p12, 6p21, and 15q25 loci were demonstrated to potentially contribute to lung cancer carcinogenesis. Therefore, this study was performed to assess the role of those variants in non-small cell lung cancer (NSCLC) risk and prognosis in a Portuguese population. Materials and Methods Blood from patients with NSCLC was prospectively collected. To perform an association study, DNA from these patients and healthy controls were genotyped for a panel of 19 SNPs using a Sequenom® MassARRAY platform. Kaplan-Meier curves were used to assess the overall survival (OS) and progression-free survival (PFS). Results One hundred and forty-four patients with NSCLC were successfully consecutively genotyped for the 19 SNPs. One SNP was associated with NSCLC risk: rs9295740 G/A. Two SNPs were associated with non-squamous histology: rs3024994 (VEGF intron 2) T/C and rs401681 C/T. Three SNPs were associated with response rate: rs3025035 (VEGF intron 7) C/T, rs833061 (VEGF –460) C/T and rs9295740 G/A. One SNP demonstrated an influence on PFS: rs401681 C/T at 5p15, p = 0.021. Four SNPs demonstrated an influence on OS: rs2010963 (VEGF +405 G/C), p = 0.042; rs3025010 (VEGF intron 5 C/T), p = 0.047; rs401681 C/T at 5p15, p = 0.046; and rs31489 C/A at 5p15, p = 0.029. Conclusions Our study suggests that SNPs in the 6p12, 6p21, and 5p15 loci may serve as risk, predictive and prognostic NSCLC biomarkers. In the future, SNPs identified in the genomes of patients may improve NSCLC screening strategies and therapeutic management as well. PMID:24039754
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.
Heat conduction in diatomic chains with correlated disorder
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.
Combination Rules for Morse-Based van der Waals Force Fields.
Yang, Li; Sun, Lei; Deng, Wei-Qiao
2018-02-15
In traditional force fields (FFs), van der Waals interactions have been usually described by the Lennard-Jones potentials. Conventional combination rules for the parameters of van der Waals (VDW) cross-termed interactions were developed for the Lennard-Jones based FFs. Here, we report that the Morse potentials were a better function to describe VDW interactions calculated by highly precise quantum mechanics methods. A new set of combination rules was developed for Morse-based FFs, in which VDW interactions were described by Morse potentials. The new set of combination rules has been verified by comparing the second virial coefficients of 11 noble gas mixtures. For all of the mixed binaries considered in this work, the combination rules work very well and are superior to all three other existing sets of combination rules reported in the literature. We further used the Morse-based FF by using the combination rules to simulate the adsorption isotherms of CH 4 at 298 K in four covalent-organic frameworks (COFs). The overall agreement is great, which supports the further applications of this new set of combination rules in more realistic simulation systems.
The thermodynamic properties of normal liquid helium 3
Modarres, M.; Moshfegh, H. R.
2009-09-01
The thermodynamic properties of normal liquid helium 3 are calculated by using the lowest order constrained variational (LOCV) method. The Landau Fermi liquid model and Fermi-Dirac distribution function are considered as our statistical model for the uncorrelated quantum fluid picture and the Lennard-Jones and Aziz potentials are used in our truncated cluster expansion (LOCV) to calculate the correlated energy. The single particle energy is treated variationally through an effective mass. The free energy, pressure, entropy, chemical potential and liquid phase diagram as well as the helium 3 specific heat are evaluated, discussed and compared with the corresponding available experimental data. It is found that the critical temperature for the existence of the pure gas phase is about 4.90 K (4.45 K), which is higher than the experimental prediction of 3.3 K, and the helium 3 flashing temperature is around 0.61 K (0.50 K) for the Lennard-Jones (Aziz) potential.
A study on the contact angles of a water droplet on smooth and rough solid surfaces
International Nuclear Information System (INIS)
Park, Ju Young; Ha, Man Yeong; Choi, Ho Jin; Hong, Seung Do; Yoon, Hyun Sik
2011-01-01
We investigated the wetting characteristics such as contact angle, wetting radius and topography of water droplets on smooth and random solid surfaces. Molecular dynamic simulation is employed to analyze the wetting behavior of water droplets on smooth and rough surfaces by considering different potential energy models of bond, angle, Lennard-Jones and Coulomb to calculate the interacting forces between water molecules. The Lennard-Jones potential energy model is adopted as an interaction model between water molecules and solid surface atoms. The randomly rough surface is generated by changing the standard deviation of roughness height from 1 A to 3 A with the fixed autocorrelation length. The size of water droplet considered is in the range from 2,000 to 5,000 molecules. The contact angles increase generally with increasing number of water molecules. For a hydrophobic surface whose characteristic energy is 0.1 kcal/mol, the contact angles depend rarely on the standard deviation of the roughness height. However, when the surface energy is 0.5 and 1.0 kcal/mol, the contact angles depend on both the roughness height of surfaces and droplet size
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
Termodinâmica estatística de líquidos com o método de Monte Carlo. II. O líquido clorofórmio
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Barlette Vania Elisabeth
1999-01-01
Full Text Available Thermodynamic properties and radial distribution functions for liquid chloroform were calculated using the Monte Carlo method implemented with Metropolis algorithm in the NpT ensemble at 298 K and 1 atm. A five site model was developed to represent the chloroform molecules. A force field composed by Lennard-Jones and Coulomb potential functions was used to calculate the intermolecular energy. The partial charges needed to represent the Coulombic interactions were obtained from quantum chemical ab initio calculations. The Lennard-Jones parameters were adjusted to reproduce experimental values for density and enthalpy of vaporization for pure liquid. All thermodynamic results are in excelent agreement with experimental data. The correlation functions calculated are in good accordance with theoretical results avaliable in the literature. The free energy for solvating one chloroform molecule into its own liquid at 298 K and 1 atm was computed as an additional test of the potential model. The result obtained compares well with the experimental value. The medium effects on cis/trans convertion of a hypotetical solute in water TIP4P and chloroform solvents were also accomplished. The results obtained from this investigation are in agreement with estimates of the continuous theory of solvation.
Divergence of activity expansions: Is it actually a problem?
Ushcats, M. V.; Bulavin, L. A.; Sysoev, V. M.; Ushcats, S. Yu.
2017-12-01
For realistic interaction models, which include both molecular attraction and repulsion (e.g., Lennard-Jones, modified Lennard-Jones, Morse, and square-well potentials), the asymptotic behavior of the virial expansions for pressure and density in powers of activity has been studied taking power terms of high orders into account on the basis of the known finite-order irreducible integrals as well as the recent approximations of infinite irreducible series. Even in the divergence region (at subcritical temperatures), this behavior stays thermodynamically adequate (in contrast to the behavior of the virial equation of state with the same set of irreducible integrals) and corresponds to the beginning of the first-order phase transition: the divergence yields the jump (discontinuity) in density at constant pressure and chemical potential. In general, it provides a statistical explanation of the condensation phenomenon, but for liquid or solid states, the physically proper description (which can turn the infinite discontinuity into a finite jump of density) still needs further study of high-order cluster integrals and, especially, their real dependence on the system volume (density).
Carbon nanotori as traps for atoms and ions
International Nuclear Information System (INIS)
Chan Yue; Cox, Barry J.; Hill, James M.
2012-01-01
Carbon nanotori surely represent an ideal location to trap both charged and uncharged atoms, since they are open, accessible and possess strong attractive energy. In this paper, we investigate the plausibility of carbon nanotori as atomic traps and we use the continuum approximation together with the Lennard-Jones potential to model the encapsulation of an atom or ion by a nanotorus. The critical geometric factors such as the minor and major radii, i.e. r and R of the nanotorus, for which the maximum interaction between the atom and the nanotorus occurs, are determined. For various atoms, assumed situated along the axis of the torus, the minimum potential energy between the atom and the nanotorus is calculated and compared, and shown to be approximately kηεσ 2 , where η is the uniform atomic density, ε and σ are the Lennard-Jones well depth and the van der Waals radius, respectively, and k is a universal non-dimensional constant with the approximate value -12.42. The results given in this paper might be used for future drug delivery and biosensing design.
Simplicity of condensed matter at its core: generic definition of a Roskilde-simple system.
Schrøder, Thomas B; Dyre, Jeppe C
2014-11-28
The isomorph theory is reformulated by defining Roskilde-simple systems by the property that the order of the potential energies of configurations at one density is maintained when these are scaled uniformly to a different density. If the potential energy as a function of all particle coordinates is denoted by U(R), this requirement translates into U(Ra) < U(Rb) ⇒ U(λRa) < U(λRb). Isomorphs remain curves in the thermodynamic phase diagram along which structure, dynamics, and excess entropy are invariant, implying that the phase diagram is effectively one-dimensional with respect to many reduced-unit properties. In contrast to the original formulation of the isomorph theory, however, the density-scaling exponent is not exclusively a function of density and the isochoric heat capacity is not an exact isomorph invariant. A prediction is given for the latter quantity's variation along the isomorphs. Molecular dynamics simulations of the Lennard-Jones and Lennard-Jones Gaussian systems validate the new approach.
Yuhara, Daisuke; Brumby, Paul E.; Wu, David T.; Sum, Amadeu K.; Yasuoka, Kenji
2018-05-01
To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.
Solvation in atomic liquids: connection between Gaussian field theory and density functional theory
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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.
Test of a new heat-flow equation for dense-fluid shock waves.
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.
Energy Technology Data Exchange (ETDEWEB)
Kadoura, Ahmad; Sun, Shuyu, E-mail: shuyu.sun@kaust.edu.sa; Salama, Amgad
2014-08-01
Accurate determination of thermodynamic properties of petroleum reservoir fluids is of great interest to many applications, especially in petroleum engineering and chemical engineering. Molecular simulation has many appealing features, especially its requirement of fewer tuned parameters but yet better predicting capability; however it is well known that molecular simulation is very CPU expensive, as compared to equation of state approaches. We have recently introduced an efficient thermodynamically consistent technique to regenerate rapidly Monte Carlo Markov Chains (MCMCs) at different thermodynamic conditions from the existing data points that have been pre-computed with expensive classical simulation. This technique can speed up the simulation more than a million times, making the regenerated molecular simulation almost as fast as equation of state approaches. In this paper, this technique is first briefly reviewed and then numerically investigated in its capability of predicting ensemble averages of primary quantities at different neighboring thermodynamic conditions to the original simulated MCMCs. Moreover, this extrapolation technique is extended to predict second derivative properties (e.g. heat capacity and fluid compressibility). The method works by reweighting and reconstructing generated MCMCs in canonical ensemble for Lennard-Jones particles. In this paper, system's potential energy, pressure, isochoric heat capacity and isothermal compressibility along isochors, isotherms and paths of changing temperature and density from the original simulated points were extrapolated. Finally, an optimized set of Lennard-Jones parameters (ε, σ) for single site models were proposed for methane, nitrogen and carbon monoxide.
Droplet spreading driven by van der Waals force: a molecular dynamics study
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.
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.
Yuhara, Daisuke; Brumby, Paul E; Wu, David T; Sum, Amadeu K; Yasuoka, Kenji
2018-05-14
To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.
Unusual mechanism of capillary condensation in pores modified with chains forming pillars.
Borówko, M; Patrykiejew, A; Sokołowski, S
2011-08-07
Density functional approach is applied to study the phase behavior of Lennard-Jones(12,6) fluid in pillared slit-like pores. Our focus is in the evaluation of phase transitions in fluid adsorbed in the pore of a fixed width. If the length of pillars is sufficiently large, we observe additional phase transitions of the first and second order due to the symmetry breaking of the distribution of chain segments and fluid species with respect to the slit-like pore center. Re-entrant symmetry changes and additional critical, critical end points and tricritical points then are observed. The scenario of phase changes is sensitive to the energy of fluid-solid interaction, the amount, and the length of the pillars. Quantitative trends and qualitative changes of the phase diagrams topology are examined depending on the values of these parameters.
International Nuclear Information System (INIS)
Sharma, Poonam; Dhawan, Anil; Jayraj, J.; Kamachi Mudali, U.
2013-01-01
The potentiodynamic polarization studies were carried out on Zr based bulk amorphous alloy Zr 57 Cu 15.4 Ni 12.6 Al 10 Nb 5 and Zr 59 Cu 20 Ni 8 Al 10 Ti 3 in solutions of 1 M, 6 M and 11.5 M HNO 3 aqueous media at room temperature. As received specimens of Zr 57 Cu 15.4 Ni 12.6 Al 10 Nb 5 (5 mm diameter rod) and Zr 59 Cu 20 Ni 8 Al 10 Ti 3 (3 mm diameter rod) were polished with SiC paper before testing them for potentiodynamic polarization studies. The amorphous nature of the specimens was checked by X-ray diffraction. The bulk amorphous alloy Zr 59 Cu 20 Ni 8 Al 10 Ti 3 shows the better corrosion resistance than Zr 57 Cu 15.4 Ni 12.6 Al 10 Nb 5 alloy in the aqueous HNO 3 media as the value of the corrosion current density (I corr ) for Zr 57 Cu 15.4 Ni 12.6 Al 10 Nb 5 alloy were found to be more than Zr 59 Cu 20 Ni 8 Al 10 Ti 3 alloy in aqueous HNO 3 media. The improved corrosion resistance of Zr 59 Cu 20 Ni 8 Al 10 Ti 3 alloy is possibly due to the presence of Ti and formation of TiO 2 during anodic oxidation. Both Zr based bulk amorphous alloys shows wider passive range at lower concentration of nitric acid and the passive region gets narrowed down with the increase in concentration. A comparison of data obtained from both the Zr-based bulk amorphous alloys is made and results are discussed in the paper. (author)
Molecular interactions and thermal transport in ionic liquids with carbon nanomaterials.
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
Simulating prescribed particle densities in the grand canonical ensemble using iterative algorithms.
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.
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.
International Nuclear Information System (INIS)
Fedin, V.P.; Kalinina, I.V.; Virovets, A.V.; Fenske, D.
2001-01-01
A new cubane cluster complex K 6 [Ta 4 (μ 4 -O)(μ 3 -Te) 4 (CN) 12 ] · KOH · 4H 2 O was prepared by high-temperature synthesis from a mixture of TaTe 4 and KCN with subsequent crystallization from aqueous solutions. The compound was characterized by the methods of cyclic voltammetry, X-ray diffraction analysis, IR, Raman and absorption spectroscopies. Comparative study of clusters [M 4 OTe 4 (CN) 12 ] 6- (M=Nb, Ta) containing μ 4 -O-ligands and being the first examples of molecular chalcogenide cubane complexes for group 5 metals of the Periodic System, was made [ru
MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.
Klett, Javier; Núñez-Salgado, Alfonso; Dos Santos, Helena G; Cortés-Cabrera, Álvaro; Perona, Almudena; Gil-Redondo, Rubén; Abia, David; Gago, Federico; Morreale, Antonio
2012-09-11
An ultrafast and accurate scoring function for protein-protein docking is presented. It includes (1) a molecular mechanics (MM) part based on a 12-6 Lennard-Jones potential; (2) an electrostatic component based on an implicit solvent model (ISM) with individual desolvation penalties for each partner in the protein-protein complex plus a hydrogen bonding term; and (3) a surface area (SA) contribution to account for the loss of water contacts upon protein-protein complex formation. The accuracy and performance of the scoring function, termed MM-ISMSA, have been assessed by (1) comparing the total binding energies, the electrostatic term, and its components (charge-charge and individual desolvation energies), as well as the per residue contributions, to results obtained with well-established methods such as APBSA or MM-PB(GB)SA for a set of 1242 decoy protein-protein complexes and (2) testing its ability to recognize the docking solution closest to the experimental structure as that providing the most favorable total binding energy. For this purpose, a test set consisting of 15 protein-protein complexes with known 3D structure mixed with 10 decoys for each complex was used. The correlation between the values afforded by MM-ISMSA and those from the other methods is quite remarkable (r(2) ∼ 0.9), and only 0.2-5.0 s (depending on the number of residues) are spent on a single calculation including an all vs all pairwise energy decomposition. On the other hand, MM-ISMSA correctly identifies the best docking solution as that closest to the experimental structure in 80% of the cases. Finally, MM-ISMSA can process molecular dynamics trajectories and reports the results as averaged values with their standard deviations. MM-ISMSA has been implemented as a plugin to the widely used molecular graphics program PyMOL, although it can also be executed in command-line mode. MM-ISMSA is distributed free of charge to nonprofit organizations.
Si-coated single-walled carbon nanotubes under axial loads: An atomistic simulation study
International Nuclear Information System (INIS)
Song Haiyang; Zha Xinwei
2007-01-01
The mechanical properties of the Si-coated imperfect (5, 5) single-walled carbon nanotube (SWCNT), the imperfect (5, 5) SWCNT and several perfect armchair SWCNTs under axial loads were investigated using molecular dynamics simulation. The interactions between atoms were modeled using the empirical Tersoff potential and the Tersoff-Brenner potential coupled with the Lennard-Jones potential. We get Young's modulus of the defective (5, 5) nanotube with and without the Si coating under axial tension 1107.92 and 1076.02 GPa, respectively. The results also show that the structure failure of the Si-coated imperfect (5, 5) SWCNT under axial compression occurs at a slightly higher strain than for the perfect (5, 5) SWCNT. Therefore, we can confirm the protective effect of Si as a coating material for defective SWCNTs. We also obtain the critical buckling strains of perfect SWCNTs
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...
Shukla-Eliasson attractive force: Revisited
Akbari-Moghanjoughi, M.; Akbari-Moghanjoughi
2013-04-01
By investigating the dielectric response of the Fermi-Dirac plasma in the linear limit and evaluating the electrostatic potential around the positive stationary test charge, we find that the Shukla-Eliasson attractive force is present for the plasma density range expected in the interiors of large planets for a wide range of plasma atomic number. This research, which is based on the generalized electron Fermi-momentum, further confirms the existence of the newly discovered Lennard-Jones-like attractive potential and its inevitable role in plasma crystallization in the cores of planets. Moreover, it is observed that the characteristics of the attractive potential are strongly sensitive to the variation of plasma density and composition. Current research can also have applications in the study of strong laser-matter interactions and inertially confined plasmas.
Longhurst, M. J.; Quirke, N.
2006-11-01
We have previously shown that the upshift in the radial breathing mode (RBM) of closed (or infinite) carbon nanotubes in solution is almost entirely due to coupling of the RBM with an adsorbed layer of fluid on the nanotube surface. The upshift can be modeled analytically by considering the adsorbed fluid as an infinitesimally thin shell, which interacts with the nanotube via a continuum Lennard-Jones potential. Here we extend the model to include internally as well as externally adsorbed waterlike molecules, and find that filling the nanotubes leads to an additional upshift of two to six wave numbers. We show that using molecular dynamics, the RBM can be accurately reproduced by replacing the fluid molecules with a mean field harmonic shell potential, greatly reducing simulation times.
The effect of normal load on polytetrafluoroethylene tribology.
Barry, Peter R; Chiu, Patrick Y; Perry, Scott S; Sawyer, W Gregory; Phillpot, Simon R; Sinnott, Susan B
2009-04-08
The tribological behavior of oriented poly(tetrafluoroethylene) (PTFE) sliding surfaces is examined as a function of sliding direction and applied normal load in classical molecular dynamics (MD) simulations. The forces are calculated with the second-generation reactive empirical bond-order potential for short-range interactions, and with a Lennard-Jones potential for long-range interactions. The range of applied normal loads considered is 5-30 nN. The displacement of interfacial atoms from their initial positions during sliding is found to vary by a factor of seven, depending on the relative orientation of the sliding chains. However, within each sliding configuration the magnitude of the interfacial atomic displacements exhibits little dependence on load over the range considered. The predicted friction coefficients are also found to vary with chain orientation and are in excellent quantitative agreement with experimental measurements.
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.
Numerical investigation of elastic mechanical properties of graphene structures
International Nuclear Information System (INIS)
Georgantzinos, S.K.; Giannopoulos, G.I.; Anifantis, N.K.
2010-01-01
The computation of the elastic mechanical properties of graphene sheets, nanoribbons and graphite flakes using spring based finite element models is the aim of this paper. Interatomic bonded interactions as well as van der Waals forces between carbon atoms are simulated via the use of appropriate spring elements expressing corresponding potential energies provided by molecular theory. Each layer is idealized as a spring-like structure with carbon atoms represented by nodes while interatomic forces are simulated by translational and torsional springs with linear behavior. The non-bonded van der Waals interactions among atoms which are responsible for keeping the graphene layers together are simulated with the Lennard-Jones potential using appropriate spring elements. Numerical results concerning the Young's modulus, shear modulus and Poisson's ratio for graphene structures are derived in terms of their chilarity, width, length and number of layers. The numerical results from finite element simulations show good agreement with existing numerical values in the open literature.
Coronene molecules in helium clusters: Quantum and classical studies of energies and configurations
Energy Technology Data Exchange (ETDEWEB)
Rodríguez-Cantano, Rocío; Pérez de Tudela, Ricardo; Bartolomei, Massimiliano; Hernández, Marta I.; Campos-Martínez, José; González-Lezana, Tomás, E-mail: t.gonzalez.lezana@csic.es; Villarreal, Pablo [Instituto de Física Fundamental, IFF-CSIC, Serrano 123, 28006 Madrid (Spain); Hernández-Rojas, Javier; Bretón, José [Departamento de Física and IUdEA, Universidad de La Laguna, 38205 Tenerife (Spain)
2015-12-14
Coronene-doped helium clusters have been studied by means of classical and quantum mechanical (QM) methods using a recently developed He–C{sub 24}H{sub 12} global potential based on the use of optimized atom-bond improved Lennard-Jones functions. Equilibrium energies and geometries at global and local minima for systems with up to 69 He atoms were calculated by means of an evolutive algorithm and a basin-hopping approach and compared with results from path integral Monte Carlo (PIMC) calculations at 2 K. A detailed analysis performed for the smallest sizes shows that the precise localization of the He atoms forming the first solvation layer over the molecular substrate is affected by differences between relative potential minima. The comparison of the PIMC results with the predictions from the classical approaches and with diffusion Monte Carlo results allows to examine the importance of both the QM and thermal effects.
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
Molecular Dynamics Simulations of a Linear Nanomotor Driven by Thermophoretic Forces
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.
Molecular Dynamics of a Linear Nanomotor Driven by Thermophoresis Harvey A. Zambrano1, Jens H. Walther1,2 and Richard L. Jaffe3 1Department of Mechanical Engineering, Fluid Mechanics, Technical University of Denmark, DK-2800 Lyngby, Denmark; 2Computational Science and Engineering Laboratory, ETH...... future molecular machines a complete understanding of the friction forces involved on the transport process at the molecular level have to be addressed.18 In this work we perform Molecular Dynamics (MD) simulations using the MD package FASTTUBE19 to study a molecular linear motor consisting of coaxial...... the valence forces within the CNT using Morse, harmonic angle and torsion potentials.19We include a nonbonded carbon-carbon Lennard-Jones potential to describe the vdW interaction between the carbon atoms within the double wall portion of the system. We equilibrate the system at 300K for 0.1 ns, by coupling...
Molecular simulation of water removal from simple gases with zeolite NaA.
Csányi, Eva; Ható, Zoltán; Kristóf, Tamás
2012-06-01
Water vapor removal from some simple gases using zeolite NaA was studied by molecular simulation. The equilibrium adsorption properties of H(2)O, CO, H(2), CH(4) and their mixtures in dehydrated zeolite NaA were computed by grand canonical Monte Carlo simulations. The simulations employed Lennard-Jones + Coulomb type effective pair potential models, which are suitable for the reproduction of thermodynamic properties of pure substances. Based on the comparison of the simulation results with experimental data for single-component adsorption at different temperatures and pressures, a modified interaction potential model for the zeolite is proposed. In the adsorption simulations with mixtures presented here, zeolite exhibits extremely high selectivity of water to the investigated weakly polar/non-polar gases demonstrating the excellent dehydration ability of zeolite NaA in engineering applications.
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)
Long-range interaction of anisotropic systems
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.
International Nuclear Information System (INIS)
Li Yongqing; Song Peng; Chen Yuehui; Wang Weili; Ma Fengcai
2005-01-01
In our previous theoretical studies [Meng-Tao Sun, Yong-Qing Lee, and Feng-Cai Ma, Chem. Phys. Lett. 371 (2003) 342], we have reported the quantum interference on collision-induced rotational energy transfer on CO (A 1 Π, v = 3) with inert gases, which originates from the difference between the two Λ-related collision potential energy surfaces. The interference angle, which measures the degree of coherence, is presented in this paper. Based on the time-dependent first order Born approximation, taking into account the anisotropic Lennard-Jones interaction potentials, the relation of the interference angle with the factors, including experimental temperature, partner, and rotational quantum number, are obtained. The changing tendencies with them are discussed. This theoretical model is important to understanding and performing this kind of experiment.
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.
Long-range interaction of anisotropic systems
Zhang, Junyi; Schwingenschlö gl, Udo
2015-01-01
The first-order electrostatic interaction energy between two far-apart anisotropic atoms depends not only on the distance between them but also on their relative orientation, according to Rayleigh-Schrödinger perturbation theory. Using the first-order interaction energy and the continuum model, we study the long-range interaction between a pair of parallel pristine graphene sheets at zero temperature. The asymptotic form of the obtained potential density, &epsi:(D) &prop: ?D ?3 ?O(D?4), is consistent with the random phase approximation and Lifshitz theory. Accordingly, neglectance of the anisotropy, especially the nonzero first-order interaction energy, is the reason why the widely used Lennard-Jones potential approach and dispersion corrections in density functional theory give a wrong asymptotic form ε(D) &prop: ?D?4. © EPLA, 2015.
Berim, Gersh O; Ruckenstein, Eli
2012-08-07
Adsorption isoterms and capillary condensation in an open slit with walls decorated with arrays of pillars are examined using the density functional theory. Compared with the main substrate, the pillars can have the same or different parameters in the Lennard-Jones interaction potential between them and the fluid in the slit. The roughness of the solid surface, defined as the ratio between the area of the actual surface and the area of the surface free of pillars, is controlled by the height of the pillars. It is shown that the capillary condensation pressure first increases with increasing roughness, passes through a maximum, and then decreases. The amount of adsorbed fluid at constant volume of the slit has, in general, a nonmonotonic dependence on roughness. These features of adsorption and capillary condensation are results of increased surface area and changes in the fluid-solid potential energy due to changes in roughness.
Mechanical properties of pillared-graphene nanostructures using molecular dynamics simulations
International Nuclear Information System (INIS)
Wang, Chih-Hao; Fang, Te-Hua; Sun, Wei-Li
2014-01-01
The deformation behaviour and mechanical properties of three-dimensional (3D) pillared graphene are investigated using molecular dynamics simulations. The Tersoff–Brenner many-body potential model is employed to evaluate the interactions between 3D pillared-graphene carbon atoms and nanotube carbons. The Lennard-Jones potential model is used to compute the interactions between a conical indenter and 3D pillared-graphene carbon atoms. The effects of the size and geometric structure of 3D pillared-graphene are evaluated in terms of the indentation force and contact stiffness. The simulation results for an armchair nanotube of 3D pillared graphene show that the contact stiffness increases with increasing chiral vector of the 3D-pillared graphene. However, the adhesive force sharply decreases with increasing chiral vector of the 3D-pillared graphene. A zigzag nanotube of 3D-pillared graphene exhibits better mechanical properties compared with those of the armchair nanotube. (paper)
Classical square-plus-triangle well fluid
International Nuclear Information System (INIS)
Boghdadi, M.
1984-01-01
A simplified model for the intermolecular-potential function which consists of a hard core and a square-plus-triangle well is proposed. The square width is taken to be lambda 1 -1 and the triangle width is lambda 2 -lambda 1 , where the diameter of the molecules is assumed to be epsilon. Under the restriction that the area under the potential well should be equal to 0.5epsilon, which has its own reason, it is shown that the appropriate choice of lambda 1 and lambda 2 that best mimics the Lennard-Jones (LJ) cut-off results is 1.15 and 1.85 respectively. With this choice for lambda 1 and lambda 2 , the proposed model is effective and satisfactory
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)
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
Molecular dynamics investigation of tracer diffusion in a simple liquid
International Nuclear Information System (INIS)
Ould-Kaddour, F.; Barrat, J.L.
1991-05-01
Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs
International Nuclear Information System (INIS)
Fang, T.-H.; Chang, W.-J.; Lin, S.-L.
2006-01-01
This paper uses molecular dynamics simulation based on the Lennard-Jones potential to study the effects that temperature and velocity have on, the nanojet droplet ejection process, when the droplet is ejected at an angle onto a moving plate's surface. According to the analysis, it was found that the width of the spreading droplet increased as the temperature and the time were increased. Also found was an energy wave phenomenon. The contact angle of the droplet deposited on the plate decreased as the temperature was increased. Furthermore, the layer phenomena became apparent when the atoms were deposited on a moving plate. Thinner film layers were obtained as the velocity of the moving plate was increased. The contact angle on the left side of the droplet was larger than that on the right side when the plate was moving from right to left
Molecular dynamics of contact behavior of self-assembled monolayers on gold using nanoindentation
Energy Technology Data Exchange (ETDEWEB)
Fang, Te-Hua [Institute of Mechanical and Electromechanical Engineering National Formosa University, Yunlin 632, Taiwan (China); Chang, Win-Jin, E-mail: changwj@mail.ksu.edu.tw [Department of Mechanical Engineering Kun Shan University, Tainan 710, Taiwan (China); Fan, Yu-Cheng [Institute of Mechanical and Electromechanical Engineering National Formosa University, Yunlin 632, Taiwan (China); Weng, Cheng-I [Department of Mechanical Engineering National Cheng Kung University, Tainan, 710, Taiwan (China)
2009-08-15
Molecular dynamics simulation is used to study nanoindentation of the self-assembled monolayers (SAMs) on an Au surface. The interaction of SAM atoms is described by a general universal force field (UFF), the tight-binding second-moment approximation (TB-SMA) is used for Au substrate, and the Lennard-Jones potential function is employed to describe interaction among the indenter, the SAMs, and the Au substrate atoms. The model consists of a planar Au substrate with n-hexadecanethiol SAM chemisorbed to the substrate. The simulation results show that the contact pressure increases as the SAMs temperature increases. In addition, the contact pressure also increases as the depth and velocity of indentation increase.
Molecular dynamics of contact behavior of self-assembled monolayers on gold using nanoindentation
International Nuclear Information System (INIS)
Fang, Te-Hua; Chang, Win-Jin; Fan, Yu-Cheng; Weng, Cheng-I
2009-01-01
Molecular dynamics simulation is used to study nanoindentation of the self-assembled monolayers (SAMs) on an Au surface. The interaction of SAM atoms is described by a general universal force field (UFF), the tight-binding second-moment approximation (TB-SMA) is used for Au substrate, and the Lennard-Jones potential function is employed to describe interaction among the indenter, the SAMs, and the Au substrate atoms. The model consists of a planar Au substrate with n-hexadecanethiol SAM chemisorbed to the substrate. The simulation results show that the contact pressure increases as the SAMs temperature increases. In addition, the contact pressure also increases as the depth and velocity of indentation increase.
Local elastic properties of nano-confined fluids: A density functional study
Energy Technology Data Exchange (ETDEWEB)
Sun, Zongli, E-mail: zongli_sun@163.com [Science and Technology College, North China Electric Power University, Baoding 071051 (China); Kang, Yanshuang [College of Science, Agriculture University of Hebei, Baoding 071001 (China)
2014-05-01
The understanding of mechanical properties of confined fluids is essential for modeling and manipulating of nano-scaled systems. Unlike the uniform phase, the confined fluids usually display different features in structure and related properties. Due to the presence of the confining geometry, the density profile and many physical and chemical properties may be position-dependent. The aim of our research is to derive an expression for the local elastic property by using the classical elastic theory. Both the bulk and shear moduli are expressed as functional of density of particle. The theoretical result derived is applied to the Lennard-Jones fluids confined in nano-cavity. Comparison of our numerical result and the simulation result is made and qualitative agreement is observed. Further, influence of bulk density, temperature and external potential on moduli is calculated and the physical mechanism is analyzed. Relationship between contact modulus and the interfacial tension is also calculated. Their opposite trend with temperature is observed.
A variational approach to nucleation simulation.
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.
Exploring the free energy surfaces of clusters using reconnaissance metadynamics
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.
Continuum modelling for carbon and boron nitride nanostructures
International Nuclear Information System (INIS)
Thamwattana, Ngamta; Hill, James M
2007-01-01
Continuum based models are presented here for certain boron nitride and carbon nanostructures. In particular, certain fullerene interactions, C 60 -C 60 , B 36 N 36 -B 36 N 36 and C 60 -B 36 N 36 , and fullerene-nanotube oscillator interactions, C 60 -boron nitride nanotube, C 60 -carbon nanotube, B 36 N 36 -boron nitride nanotube and B 36 N 36 -carbon nanotube, are studied using the Lennard-Jones potential and the continuum approach, which assumes a uniform distribution of atoms on the surface of each molecule. Issues regarding the encapsulation of a fullerene into a nanotube are also addressed, including acceptance and suction energies of the fullerenes, preferred position of the fullerenes inside the nanotube and the gigahertz frequency oscillation of the inner molecule inside the outer nanotube. Our primary purpose here is to extend a number of established results for carbon to the boron nitride nanostructures
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.
Sub- and super-Maxwellian evaporation of simple gases from liquid water
Energy Technology Data Exchange (ETDEWEB)
Kann, Z. R.; Skinner, J. L., E-mail: skinner@chem.wisc.edu [Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706 (United States)
2016-04-21
Non-Maxwellian evaporation of light atoms and molecules (particles) such as He and H{sub 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.
Membrane methods for separation of radioactive noble gases
International Nuclear Information System (INIS)
Bekman, I.N.; Bozhenko, E.I.; Ievlev, A.L.; Kazankin, Yu.N.; Nikonov, V.N.; Teplyakov, V.V.; Shvyryaev, A.A.
1984-01-01
Using the different ial permeability method at different temperatures (20-120 deg C) transport characteristics of inert gases, N 2 , O 2 , CH 4 , CQ 2 and H 2 as the main components of waste gases in homogeneous films of arylate-siloxane block-copolymer (silar) of different composition, as well as of its components - polydimethylsiloxane (PDMS) and polyarylate, have been measured. Dependences of diffusion and permeability coefficients on inert gas atom dimensions, and solubility coefficient - on strength constant of the Lennard-Jones potential, are analyzed. It is shown that selectivity of silar gas permbility is determined by the properties of siloxane component, and the values of permeability coefficients decrease with the increase of polyarylate block part due to dominating decrease in diffusion coefficients as compared with solubility coefficients
International Nuclear Information System (INIS)
Corti, Giancarlo; Zhan, Yingqian; Wang, Lidong; Hare, Brian; Cantrell, Timothy; II, Miles Beaux; Prakash, Tej; Ytreberg, F Marty; McIlroy, David N; Miller, Michael A
2013-01-01
Silica nanosprings (NSs) consisting of multiple nanowires intertwined were demonstrated to reversibly store 0.85 wt% hydrogen at 20 bar and room temperature. X-ray photoelectron spectroscopy indicates a mixed 3 + –4 + ionization state of the silicon atoms and partially explains the enhanced surface adsorption of H 2 relative to other forms of silica. Theoretical modeling and simulation using a Lennard-Jones potential demonstrated that interstitial sites between the silica nanowires forming the NS are energetically more favorable adsorption sites relative to single nanowires. The addition of Pd nanoparticles to the surface of the silica NSs was demonstrated to increase the hydrogen storage capacity to ≈3.5 wt% at 66 bar and room temperature. Palladium-nanoparticle-induced hydrogen spillover is attributed to the enhanced storage capacity relative to bare silica NSs. (paper)
Stability of molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren
2012-01-01
The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...
Communication: Thermodynamic analysis of critical conditions of polymer adsorption
International Nuclear Information System (INIS)
Cimino, R.; Neimark, A. V.; Rasmussen, C. J.
2013-01-01
Polymer adsorption to solid surfaces is a ubiquitous phenomenon, which has attracted long-lasting attention. Dependent on the competition between the polymer-solid adsorption and polymer-solvent solvation interactions, a chain may assume either 3d solvated conformation when adsorption is weak or 2d adsorbed conformation when adsorption is strong. The transition between these conformations occurring upon variation of adsorption strength is quite sharp, and in the limit of “infinite” chain length, can be treated as a critical phenomenon. We suggest a novel thermodynamic definition of the critical conditions of polymer adsorption from the equality of incremental chemical potentials of adsorbed and free chains. We show with the example of freely jointed Lennard-Jones chains tethered to an adsorbing surface that this new definition provides a link between thermodynamic and geometrical features of adsorbed chains and is in line with classical scaling relationships for the fraction of adsorbed monomers, chain radii of gyration, and free energy
Interaction energy for a fullerene encapsulated in a carbon nanotorus
Sarapat, Pakhapoom; Baowan, Duangkamon; Hill, James M.
2018-06-01
The interaction energy of a fullerene symmetrically situated inside a carbon nanotorus is studied. For these non-bonded molecules, the main interaction originates from the van der Waals energy which is modelled by the 6-12 Lennard-Jones potential. Upon utilising the continuum approximation which assumes that there are infinitely many atoms that are uniformly distributed over the surfaces of the molecules, the total interaction energy between the two structures is obtained as a surface integral over the spherical and the toroidal surfaces. This analytical energy is employed to determine the most stable configuration of the torus encapsulating the fullerene. The results show that a torus with major radius around 20-22 Å and minor radius greater than 6.31 Å gives rise to the most stable arrangement. This study will pave the way for future developments in biomolecules design and drug delivery system.
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
International Nuclear Information System (INIS)
Bishop, M.; Kalos, M.H.; Frisch, H.L.
1983-01-01
The influence of the attractive portion of the Lennard-Jones potential on the statics and dynamics of both single chain and multichain systems is investigated by reptation and molecular dynamics simulations. There is no significant effect at a reduced temperature of 10.0. At a temperature of 1.7 the single chain and multichain system at low densities (0.1) indicate that the attractions cause both the chains to be significantly more compact and a slowing of the time autocorrelation functions of the square of the end-to-end distance and radius of gyration. At a moderate density of 0.5, the attractions have almost no effect on the static structure, but they still influence the dynamic properties
Density functional study of the pressure tensor for inhomogeneous Lennard—Jones fluids
International Nuclear Information System (INIS)
Sun Zong-Li; Liu Zhi-Cheng; Kang Yan-Shuang; Ma Heng-Xin; Kang Yan-Mei
2012-01-01
Based on classical density functional theory, an expression of the pressure tensor for inhomogeneous fluids is presented. This takes into account greater correlation between particles, especially for systems that are geometrically confined or involve an interface. The density and pressure components of Lennard-Jones fluids confined in hard and softened nano-cavities are calculated. A comparison between the results of this work and IK expression suggests that the agreement depends on temperature. The interfacial tension for hard sphere fluids agrees well with the Monte Carlo result when the bulk density is not too large. The results of the solid-fluid interfacial tension for Lennard—Jones fluids demonstrate that different types of external potentials modulate the interfacial tension in different manners. (condensed matter: structural, mechanical, and thermal properties)
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
Continuous approximation for interaction energy of adamantane encapsulated inside carbon nanotubes
Baowan, Duangkamon; Hill, James M.; Bacsa, Wolfgang
2018-02-01
The interaction energy for two adjacent adamantane molecules and that of adamantane molecules encapsulated inside carbon nanotubes are investigated considering only dipole-dipole induced interaction. The Lennard-Jones potential and the continuous approximation are utilised to derive analytical expressions for these interaction energies. The equilibrium distance 3.281 Å between two adamantane molecules is determined. The smallest carbon nanotube radius b0 that can encapsulate the adamantane molecule and the radius of the tube bmax that gives the maximum suction energy, linearly depend on the adamantane radius, are calculated. For larger diameter tubes, the off axis position has been calculated, and equilibrium distance between molecule and tube wall is found to be close to the interlayer spacing in graphene.
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...
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.
Communication: Thermodynamic analysis of critical conditions of polymer adsorption
Energy Technology Data Exchange (ETDEWEB)
Cimino, R.; Neimark, A. V., E-mail: aneimark@rutgers.edu [Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854 (United States); Rasmussen, C. J. [DuPont Central Research and Development, Corporate Center for Analytical Sciences, Macromolecular Characterization, Route 141 and Henry Clay, Wilmington, Delaware 19803 (United States)
2013-11-28
Polymer adsorption to solid surfaces is a ubiquitous phenomenon, which has attracted long-lasting attention. Dependent on the competition between the polymer-solid adsorption and polymer-solvent solvation interactions, a chain may assume either 3d solvated conformation when adsorption is weak or 2d adsorbed conformation when adsorption is strong. The transition between these conformations occurring upon variation of adsorption strength is quite sharp, and in the limit of “infinite” chain length, can be treated as a critical phenomenon. We suggest a novel thermodynamic definition of the critical conditions of polymer adsorption from the equality of incremental chemical potentials of adsorbed and free chains. We show with the example of freely jointed Lennard-Jones chains tethered to an adsorbing surface that this new definition provides a link between thermodynamic and geometrical features of adsorbed chains and is in line with classical scaling relationships for the fraction of adsorbed monomers, chain radii of gyration, and free energy.
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
Equilibrium location for spherical DNA and toroidal cyclodextrin
Sarapat, Pakhapoom; Baowan, Duangkamon; Hill, James M.
2018-05-01
Cyclodextrin comprises a ring structure composed of glucose molecules with an ability to form complexes of certain substances within its central cavity. The compound can be utilised for various applications including food, textiles, cosmetics, pharmaceutics, and gene delivery. In gene transfer, the possibility of forming complexes depends upon the interaction energy between cyclodextrin and DNA molecules which here are modelled as a torus and a sphere, respectively. Our proposed model is derived using the continuum approximation together with the Lennard-Jones potential, and the total interaction energy is obtained by integrating over both the spherical and toroidal surfaces. The results suggest that the DNA prefers to be symmetrically situated about 1.2 Å above the centre of the cyclodextrin to minimise its energy. Furthermore, an optimal configuration can be determined for any given size of torus and sphere.
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...... atoms in the interstitial octahedral sites. The gamma-Fe[N]/gamma'-Fe4N1-x miscibility gap, short range ordering (SRO), and long-range ordering (LRO) of nitrogen in gamma-Fe[N] and gamma'-Fe4N1-x, respectively, and lattice parameters of gamma and gamm' were calculated. For the first time, N distribution...... parameters,as calculated by CVM, were compared directly to Mössbauer data for specific surroundings of Fe atoms....
Weak temperature dependence of ageing of structural properties in atomistic model glassformers
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.
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.
Response functions for crystals and surfaces, with applications to surface scattering
International Nuclear Information System (INIS)
Barker, J.A.; Steele, W.A.
1978-01-01
A general solution of the equations of forced motion of a harmonic crystal or other vibrating system with arbitrary time-dependent forces acting on the atoms is given. The solution is given in terms of dynamical 'response functions', for which expressions in terms of the normal mode frequencies and eigenvectors (polarization vectors) are given. Numerical calculations of the response functions are described for (111) and (100) surfaces of face-centered cubic crystals interacting with Lennard-Jones 6-12 potentials, and the qualitative features of the surface and bulk response functions are discussed. The use of these functions in problems of atomic scattering from surface is outlined, and convenient parametrized forms for this application are given. (Auth.)
Structural models for amorphous transition metal binary alloys
International Nuclear Information System (INIS)
Ching, W.Y.; Lin, C.C.
1976-01-01
A dense random packing of 445 hard spheres with two different diameters in a concentration ratio of 3 : 1 was hand-built to simulate the structure of amorphous transition metal-metalloid alloys. By introducing appropriate pair potentials of the Lennard-Jones type, the structure is dynamically relaxed by minimizing the total energy. The radial distribution functions (RDF) for amorphous Fe 0 . 75 P 0 . 25 , Ni 0 . 75 P 0 . 25 , Co 0 . 75 P 0 . 25 are obtained and compared with the experimental data. The calculated RDF's are resolved into their partial components. The results indicate that such dynamically constructed models are capable of accounting for some subtle features in the RDF of amorphous transition metal-metalloid alloys
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
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
Batista-Romero, Fidel A; Pajón-Suárez, Pedro; Bernal-Uruchurtu, Margarita I; Hernández-Lamoneda, Ramón
2015-09-07
The performance of local correlation methods is examined for the interactions present in clusters of bromine with water where the combined effect of hydrogen bonding (HB), halogen bonding (XB), and hydrogen-halogen (HX) interactions lead to many interesting properties. Local methods reproduce all the subtleties involved such as many-body effects and dispersion contributions provided that specific methodological steps are followed. Additionally, they predict optimized geometries that are nearly free of basis set superposition error that lead to improved estimates of spectroscopic properties. Taking advantage of the local correlation energy partitioning scheme, we compare the different interaction environments present in small clusters and those inside the 5(12)6(2) clathrate cage. This analysis allows a clear identification of the reasons supporting the use of local methods for large systems where non-covalent interactions play a key role.
Diffusion processes and memory effects
International Nuclear Information System (INIS)
Mokshin, Anatolii V; Yulmetyev, Renat M; Haenggi, Peter
2005-01-01
We report the results of the numerical estimation of statistical memory effects in diffusion for two various systems: Lennard-Jones fluids and the model of the Brownian particle in a one-dimensional harmonic lattice. We have found the relation between the diffusion coefficient and the non-Markovity parameter, which is linear for the Lennard-Jones systems in liquid state. The relation between the memory measure and the excess entropy is also discussed here
38 CFR 12.6 - Cases of living veterans.
2010-07-01
... administrator or executor or as directed in writing by such owner, or his or her executor or administrator. (2... or executor, or as directed in writing by such guardian, executor or administrator. (3) To the...
44 CFR 12.6 - Establishment of advisory committees.
2010-10-01
... the advisory committee to be fairly balanced in terms of the points of view represented in the... employed by it), will be provided adequate quarters, and will have funds available to meet its other... should describe the Agency's plan to attain balanced membership on the proposed committee, as prescribed...
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
The role of pressure in rubber elasticity.
Bower, A F; Weiner, J H
2004-06-22
We describe a series of molecular dynamics computations that reveal an intimate connection at the atomic scale between difference stress (which resists stretches) and pressure (which resists volume changes) in an idealized elastomer, in contrast to the classical theory of rubber elasticity. Our simulations idealize the elastomer as a "pearl necklace," in which the covalent bonds are stiff linear springs, while nonbonded atoms interact through a Lennard-Jones potential with energy epsilon(LJ) and radius sigma(LJ). We calculate the difference stress t(11)-(t(22)+t(33))/2 and mean stress (t(11)+t(22)+t(33))/3 induced by a constant volume extension in the x(1) direction, as a function of temperature T and reduced density rho(*)=Nsigma(IJ) (3)/nu. Here, N is the number of atoms in the simulation cell and nu is the cell volume. Results show that for rho(*)rubber elasticity, which neglects nonbonded interactions. However, data presented by van Krevelen [Properties of Polymers, 3rd ed. (Elsevier, Amsterdam, 1990), p. 79] indicate that rubber at standard conditions corresponds to rho(*)=1.2. For rho(*)>1, the system is entropic for kT/epsilon(LJ)>2, but at lower temperatures the difference stress contains an additional energy component, which increases as rho(*) increases and temperature decreases. Finally, the model exhibits a glass transition for rho(*)=1.2 and kT/epsilon(LJ) approximately 2. The atomic-scale processes responsible for generating stress are explored in detail. Simulations demonstrate that the repulsive portion of the Lennard-Jones potential provides a contribution sigma(nbr)>0 to the difference stress, the attractive portion provides sigma(nba) approximately 0, while the covalent bonds provide sigma(b)nbr)0, and Pi(b)nbr)=-APi(nbr)P(2)(theta(b)), sigma(b)=BPi(b)P(2)(theta(b)), where P(2)(theta(b)) is a measure of the anisotropy of the orientation of the covalent bonds, and A and B are coefficients that depend weakly on rho(*) and temperature. For high
Molar excess volumes of liquid hydrogen and neon mixtures from path integral simulation
International Nuclear Information System (INIS)
Challa, S.R.; Johnson, J.K.
1999-01-01
Volumetric properties of liquid mixtures of neon and hydrogen have been calculated using path integral hybrid Monte Carlo simulations. Realistic potentials have been used for the three interactions involved. Molar volumes and excess volumes of these mixtures have been evaluated for various compositions at 29 and 31.14 K, and 30 atm. Significant quantum effects are observed in molar volumes. Quantum simulations agree well with experimental molar volumes. Calculated excess volumes agree qualitatively with experimental values. However, contrary to the existing understanding that large positive deviations from ideal mixtures are caused due to quantum effects in Ne - H 2 mixtures, both classical as well as quantum simulations predict the large positive deviations from ideal mixtures. Further investigations using two other Ne - H 2 potentials of Lennard - Jones (LJ) type show that excess volumes are very sensitive to the cross-interaction potential. We conclude that the cross-interaction potential employed in our simulations is accurate for volumetric properties. This potential is more repulsive compared to the two LJ potentials tested, which have been obtained by two different combining rules. This repulsion and a comparatively lower potential well depth can explain the positive deviations from ideal mixing. copyright 1999 American Institute of Physics
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)
Non-chiral, molecular model of negative Poisson ratio in two dimensions
International Nuclear Information System (INIS)
Wojciechowski, K W
2003-01-01
A two-dimensional model of tri-atomic molecules (in which 'atoms' are distributed on vertices of equilateral triangles, and which are further referred to as cyclic trimers) is solved exactly in the static (zero-temperature) limit for the nearest-neighbour site-site interactions. It is shown that the cyclic trimers form a mechanically stable and elastically isotropic non-chiral phase of negative Poisson ratio. The properties of the system are illustrated by three examples of atom-atom interaction potentials: (i) the purely repulsive (n-inverse-power) potential, (ii) the purely attractive (n-power) potential and (iii) the Lennard-Jones potential which shows both the repulsive and the attractive part. The analytic form of the dependence of the Poisson ratio on the interatomic potential is obtained. It is shown that the Poisson ratio depends, in a universal way, only on the trimer anisotropy parameter both (1) in the limit of n → ∞ for cases (i) and (ii), as well as (2) at the zero external pressure for any potential with a doubly differentiable minimum, case (iii) is an example
Fuentes-Herrera, M; Moreno-Razo, J A; Guzmán, O; López-Lemus, J; Ibarra-Tandi, B
2016-06-07
Molecular simulations in the canonical and isothermal-isobaric ensembles were performed to study the effect of varying the shape of the intermolecular potential on the phase diagram, critical, and interfacial properties of model fluids. The molecular interactions were modeled by the Approximate Non-Conformal (ANC) theory potentials. Unlike the Lennard-Jones or Morse potentials, the ANC interactions incorporate parameters (called softnesses) that modulate the steepness of the potential in their repulsive and attractive parts independently. This feature allowed us to separate unambiguously the role of each region of the potential on setting the thermophysical properties. In particular, we found positive linear correlation between all critical coordinates and the attractive and repulsive softness, except for the critical density and the attractive softness which are negatively correlated. Moreover, we found that the physical properties related to phase coexistence (such as span of the liquid phase between the critical and triple points, variations in the P-T vaporization curve, interface width, and surface tension) are more sensitive to changes in the attractive softness than to the repulsive one. Understanding the different roles of attractive and repulsive forces on phase coexistence may contribute to developing more accurate models of liquids and their mixtures.
Lukeš, Jaroslav; Netuka, Ivan; Veselý, Jiří
1988-01-01
Within the tradition of meetings devoted to potential theory, a conference on potential theory took place in Prague on 19-24, July 1987. The Conference was organized by the Faculty of Mathematics and Physics, Charles University, with the collaboration of the Institute of Mathematics, Czechoslovak Academy of Sciences, the Department of Mathematics, Czech University of Technology, the Union of Czechoslovak Mathematicians and Physicists, the Czechoslovak Scientific and Technical Society, and supported by IMU. During the Conference, 69 scientific communications from different branches of potential theory were presented; the majority of them are in cluded in the present volume. (Papers based on survey lectures delivered at the Conference, its program as well as a collection of problems from potential theory will appear in a special volume of the Lecture Notes Series published by Springer-Verlag). Topics of these communications truly reflect the vast scope of contemporary potential theory. Some contributions deal...
Energy Technology Data Exchange (ETDEWEB)
Batista-Romero, Fidel A.; Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón, E-mail: ramon@uaem.mx [Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Cuernavaca, Morelos 62209 (Mexico); Pajón-Suárez, Pedro [Instituto Superior de Tecnologías y Ciencias Aplicadas (InSTEC), Habana 6163 (Cuba)
2015-09-07
The performance of local correlation methods is examined for the interactions present in clusters of bromine with water where the combined effect of hydrogen bonding (HB), halogen bonding (XB), and hydrogen-halogen (HX) interactions lead to many interesting properties. Local methods reproduce all the subtleties involved such as many-body effects and dispersion contributions provided that specific methodological steps are followed. Additionally, they predict optimized geometries that are nearly free of basis set superposition error that lead to improved estimates of spectroscopic properties. Taking advantage of the local correlation energy partitioning scheme, we compare the different interaction environments present in small clusters and those inside the 5{sup 12}6{sup 2} clathrate cage. This analysis allows a clear identification of the reasons supporting the use of local methods for large systems where non-covalent interactions play a key role.
International Nuclear Information System (INIS)
Ferreira, P.L.; Tomio, L.
1992-01-01
In this paper, relativistic confining potential models, endowed with bag constants associated to volume energy terms, are investigated. In contrast to the usual bag model, these potential bags are distinguished by having smeared bag surfaces. Based on the dynamical assumptions underlying the fuzzy bag model, these bag constants are derived from the corresponding energy-momentum tensor. Explicit expressions for the single-quark energies and for the nucleon bag constant are obtained by means of an improved analytical version of the saddle-point variational method for the Dirac equation with confining power-law potentials of the scalar plus vector (S + V) or pure scalar (S) type
Dimensional scaling for quasistationary states
International Nuclear Information System (INIS)
Kais, S.; Herschbach, D.R.
1993-01-01
Complex energy eigenvalues which specify the location and width of quasibound or resonant states are computed to good approximation by a simple dimensional scaling method. As applied to bound states, the method involves minimizing an effective potential function in appropriately scaled coordinates to obtain exact energies in the D→∞ limit, then computing approximate results for D=3 by a perturbation expansion in 1/D about this limit. For resonant states, the same procedure is used, with the radial coordinate now allowed to be complex. Five examples are treated: the repulsive exponential potential (e - r); a squelched harmonic oscillator (r 2 e - r); the inverted Kratzer potential (r -1 repulsion plus r -2 attraction); the Lennard-Jones potential (r -12 repulsion, r -6 attraction); and quasibound states for the rotational spectrum of the hydrogen molecule (X 1 summation g + , v=0, J=0 to 50). Comparisons with numerical integrations and other methods show that the much simpler dimensional scaling method, carried to second-order (terms in 1/D 2 ), yields good results over an extremely wide range of the ratio of level widths to spacings. Other methods have not yet evaluated the very broad H 2 rotational resonances reported here (J>39), which lie far above the centrifugal barrier
Transport in simple liquids and dense gases: kinetic mean-field theory and the KAC limit
International Nuclear Information System (INIS)
Karkheck, J.; Stell, G.; Martina, E.
1982-01-01
Maximization of entropy is used in conjunction with the BBGKY hierarchy to obtain a closed one-particle kinetic equation. For an interparticle potential of hard-sphere core plus smooth attractive tail, this equation contains a hard-core collision integral, identical to that of the revised Enskog theory, plus a mean-field term which is linear in the tail strength. The thermodynamics contained therein leads directly to the now-standard statistical-mechanical methods to construct a state-dependent effective hard-core potential in relation to a more realistic potential. These methods induce an extension of the transport coefficients to the Lennard-Jones potential. Predictions of the resulting transport theory compare very favorably with thermal conductivity and shear viscosity experimental results for real simple liquids and dense gases, and also with molecular dynamics simulation results. Poor agreement between theory and experiment is found for moderately dense and dilute gases. The kinetic theory also contains an entropy functional and an H-theorem is proven. Extension to mixtures is straightforward and the Kac-limit is discussed in detail
ABCluster: the artificial bee colony algorithm for cluster global optimization.
Zhang, Jun; Dolg, Michael
2015-10-07
Global optimization of cluster geometries is of fundamental importance in chemistry and an interesting problem in applied mathematics. In this work, we introduce a relatively new swarm intelligence algorithm, i.e. the artificial bee colony (ABC) algorithm proposed in 2005, to this field. It is inspired by the foraging behavior of a bee colony, and only three parameters are needed to control it. We applied it to several potential functions of quite different nature, i.e., the Coulomb-Born-Mayer, Lennard-Jones, Morse, Z and Gupta potentials. The benchmarks reveal that for long-ranged potentials the ABC algorithm is very efficient in locating the global minimum, while for short-ranged ones it is sometimes trapped into a local minimum funnel on a potential energy surface of large clusters. We have released an efficient, user-friendly, and free program "ABCluster" to realize the ABC algorithm. It is a black-box program for non-experts as well as experts and might become a useful tool for chemists to study clusters.
Exponential 6 parameterization for the JCZ3-EOS
Energy Technology Data Exchange (ETDEWEB)
McGee, B.C.; Hobbs, M.L.; Baer, M.R.
1998-07-01
A database has been created for use with the Jacobs-Cowperthwaite-Zwisler-3 equation-of-state (JCZ3-EOS) to determine thermochemical equilibrium for detonation and expansion states of energetic materials. The JCZ3-EOS uses the exponential 6 intermolecular potential function to describe interactions between molecules. All product species are characterized by r*, the radius of the minimum pair potential energy, and {var_epsilon}/k, the well depth energy normalized by Boltzmann`s constant. These parameters constitute the JCZS (S for Sandia) EOS database describing 750 gases (including all the gases in the JANNAF tables), and have been obtained by using Lennard-Jones potential parameters, a corresponding states theory, pure liquid shock Hugoniot data, and fit values using an empirical EOS. This database can be used with the CHEETAH 1.40 or CHEETAH 2.0 interface to the TIGER computer program that predicts the equilibrium state of gas- and condensed-phase product species. The large JCZS-EOS database permits intermolecular potential based equilibrium calculations of energetic materials with complex elemental composition.
African Journals Online (AJOL)
big timmy
4Department of Geology, Ekiti State University, Ado-Ekiti, Nigeria. Corresponding ... integrated for the classification of the study area into different groundwater potential zones. .... table is mainly controlled by subsurface movement of water into ...
International Nuclear Information System (INIS)
Palmer, B.J.
1994-01-01
A method to calculate the thermal diffusivity D T from spontaneous fluctuations in the local heat energy density is presented. Calculations of the thermal diffusivity are performed for the Lennard-Jones fluid, carbon dioxide, and water. The results for the Lennard-Jones fluid are in agreement with calculations of the thermal conductivity using Green-Kubo relations and nonequilibrium molecular-dynamics techniques. The results for carbon dioxide and water give thermal diffusivities within a factor of 2 of the experimental values
1981-07-01
inverted by the first, i.e., at the moment of time t = T, such that i = (2n+)lT, where 0 is the Rabi frequency (Oraevski et al., 1976). . classical... anisotropic molecule present. CW HeNe, Ar+ and Kr+ lasers are used, and the filter method is necessary because of time-scales lo8 - 10ll Hz. Some general...e.g., truncated harmonic oscillator, square well, spherically symmetric Morse or Lennard-Jones, anisotropic (angle-dependent) Morse or Lennard-Jones
Taniya, Abraham; Deepthi, Murali; Padmanabhan, Alapat
2018-06-01
Recent calculations on the change in radial dimensions of reacting (growing) polyethylene in the gas phase experiencing Lennard Jones and Kihara type potentials revealed that a single reacting polyethylene molecule does not experience polymer collapse. This implies that a transition that is the converse of what happens when molten polyethylene crystallizes, i.e. it transforms from random coil like structure to folded rigid rod type structure, occurs. The predicted behaviour of growing polyethylene was explained by treating the head of the growing polymer chain as myopic whereas as the whole chain (i.e. when under equilibrium conditions) being treated as having normal vision, i.e. the growing chain does not see the attractive part of the LJ or Kihara Potentials. In this paper we provide further proof for this argument in two ways. Firstly we carry forward the exact enumeration calculations on growing self avoiding walks reported in that paper to larger values of number of steps by using Monte Carlo type calculations. We thereby assign physical significance to the connective constant of self avoiding walks, which until now was treated as a purely abstract mathematical entity. Secondly since a reacting polymer molecule that grows by addition polymerisation sees only one step ahead at a time, we extend this calculation by estimating the average atmosphere for molecules, with repulsive potential only (growing self avoiding walks in two dimensions), that look at two, three, four, five ...steps ahead. Our calculation shows that the arguments used in the previous work are correct.
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.
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.
International Nuclear Information System (INIS)
Neumann, Martin; Zoppi, Marco
2002-01-01
We have performed extensive path integral Monte Carlo simulations of liquid and solid neon, in order to derive the kinetic energy as well as the single-particle and pair distribution functions of neon atoms in the condensed phases. From the single-particle distribution function n(r) one can derive the momentum distribution and thus obtain an independent estimate of the kinetic energy. The simulations have been carried out using mostly the semiempirical HFD-C2 pair potential by Aziz et al. [R. A. Aziz, W. J. Meath, and A. R. Allnatt, Chem. Phys. 79, 295 (1983)], but, in a few cases, we have also used the Lennard-Jones potential. The differences between the potentials, as measured by the properties investigated, are not very large, especially when compared with the actual precision of the experimental data. The simulation results have been compared with all the experimental information that is available from neutron scattering. The overall agreement with the experiments is very good
International Nuclear Information System (INIS)
Rotarescu, G.
1981-01-01
Measurements of inelastic scattering of soft neutrons on Bi and liquid Pb, applying all the necessary corrections in view of obtaining the dYnamic structure factor S(Q,ω) were performed. The F(Q,t) function of intermediate scattering was obtained by means of the Fourier transformation of S(Q,ω). Special attention was devoted to one multiple scattering correction, especially at small scattering angles, taking into account its influence on the results. A comparison of the experimental results with three recent theoretical models has shown a good agreement in the range of intermediate and high Q values. Measurements of neutron inelastic scattering on liquid sodium at a temperature of 233 Cdeg within a momentum transfer range of 1 A -1 -1 were performed. The scattering law S(α,β) that was compared to a series of theoretical models has been determined from the experimental data. The validity of the theoretical models for different ranges of energy and momenta was thoroughly checked. S(α,β) was calculated for each type of scattering since sodium proves a mixed, coherent and incoherent scattering agent. A study on the influence of the even interaction potential upon the S(Q,ω) dynamic structure factor, the fourth order momentum ω 4 (Q) and uoon the spectral function C(Q,ω) of longitudinal current correlations was performed. For this purpose, four potentials with oscillations at great distances and a Lennard-Jones type potential were used. (author)
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.
Crystallization in Two Dimensions and a Discrete Gauss-Bonnet Theorem
De Luca, L.; Friesecke, G.
2018-02-01
We show that the emerging field of discrete differential geometry can be usefully brought to bear on crystallization problems. In particular, we give a simplified proof of the Heitmann-Radin crystallization theorem (Heitmann and Radin in J Stat Phys 22(3):281-287, 1980), which concerns a system of N identical atoms in two dimensions interacting via the idealized pair potential V(r)=+∞ if r1. This is done by endowing the bond graph of a general particle configuration with a suitable notion of discrete curvature, and appealing to a discrete Gauss-Bonnet theorem (Knill in Elem Math 67:1-7, 2012) which, as its continuous cousins, relates the sum/integral of the curvature to topological invariants. This leads to an exact geometric decomposition of the Heitmann-Radin energy into (i) a combinatorial bulk term, (ii) a combinatorial perimeter, (iii) a multiple of the Euler characteristic, and (iv) a natural topological energy contribution due to defects. An analogous exact geometric decomposition is also established for soft potentials such as the Lennard-Jones potential V(r)=r^{-6}-2r^{-12}, where two additional contributions arise, (v) elastic energy and (vi) energy due to non-bonded interactions.
Anomalous vibrational properties in the continuum limit of glasses
Shimada, Masanari; Mizuno, Hideyuki; Ikeda, Atsushi
2018-02-01
The low-temperature thermal properties of glasses are anomalous with respect to those of crystals. These thermal anomalies indicate that the low-frequency vibrational properties of glasses differ from those of crystals. Recent studies revealed that, in the simplest model of glasses, i.e., the harmonic potential system, phonon modes coexist with soft localized modes in the low-frequency (continuum) limit. However, the nature of low-frequency vibrational modes of more realistic models is still controversial. In the present work, we study the Lennard-Jones (LJ) system using large-scale molecular-dynamics (MD) simulation and establish that the vibrational property of the LJ glass converges to coexistence of the phonon modes and the soft localized modes in the continuum limit as in the case of the harmonic potential system. Importantly, we find that the low-frequency vibrations are rather sensitive to the numerical scheme of potential truncation, which is usually implemented in the MD simulation, and this is the reason why contradictory arguments have been reported by previous works. We also discuss the physical origin of this sensitiveness by means of a linear stability analysis.
Ustinov, E A
2015-02-21
This paper presents a refined technique to describe two-dimensional phase transitions in dense fluids adsorbed on a crystalline surface. Prediction of parameters of 2D liquid-solid equilibrium is known to be an extremely challenging problem, which is mainly due to a small difference in thermodynamic functions of coexisting phases and lack of accuracy of numerical experiments in case of their high density. This is a serious limitation of various attempts to circumvent this problem. To improve this situation, a new methodology based on the kinetic Monte Carlo method was applied. The methodology involves analysis of equilibrium gas-liquid and gas-solid systems undergoing an external potential, which allows gradual shifting parameters of the phase coexistence. The interrelation of the chemical potential and tangential pressure for each system is then treated with the Gibbs-Duhem equation to obtain the point of intersection corresponding to the liquid/solid-solid equilibrium coexistence. The methodology is demonstrated on the krypton-graphite system below and above the 2D critical temperature. Using experimental data on the liquid-solid and the commensurate-incommensurate transitions in the krypton monolayer derived from adsorption isotherms, the Kr-graphite Lennard-Jones parameters have been corrected resulting in a higher periodic potential modulation.
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.
Bondarenko, Natalya V; Nedolya, Anatoliy V
2017-12-01
The energy of the isolated iron-nickel nanocluster was calculated by molecular mechanics method using Lennard-Jones potential. The cluster included a carbon atom that drifted from an inside octahedral interstice to a tetrahedral interstice in [Formula: see text] direction and after that in direction to the surface. In addition, one of 14 iron atoms was replaced by a nickel atom, the position of which was changing during simulation.The energy of the nanocluster was estimated at the different interatomic distances. As a result of simulation, the optimal interatomic distances of Fe-Ni-C nanocluster was chosen for the simulation, in which height of the potential barrier was maximal and face-centered cubic (FCC) nanocluster was the most stable.It is shown that there were three main positions of a nickel atom that significantly affected nanocluster's energy.The calculation results indicated that position of the carbon atom in the octahedral interstice was more energetically favorable than tetrahedral interstice in the case of FCC nanocluster. On the other side, the potential barrier was smaller in the direction [Formula: see text] than in the direction .This indicates that there are two ways for carbon atom to drift to the surface of the nanocluster.
Mechanics of single-walled carbon nanotubes inside open single-walled carbon nanocones
International Nuclear Information System (INIS)
Ansari, R.; Hosseinzadeh, M.
2013-01-01
This study investigates the mechanical characteristics of single-walled carbon nanotubes (CNTs) inside open single-walled carbon nanocones (CNCs). New semi-analytical expressions are presented to evaluate van der Waals (vdW) interactions between CNTs and open CNCs. Continuum approximation, along with the the Lennard-Jones (LJ) potential function, is used in this study. The effects of geometrical parameters on alterations in vdW potential energy and the interaction force are extensively examined for the concentric CNT-open CNC configuration. The CNT is assumed to enter the nanocone either through the small end or the wide end of the cone. The preferred position of the CNT with respect to the nanocone axis is fully investigated for various geometrical parameters. The optimum nanotube radius minimizing the total potential energy of the concentric configuration is determined for different radii of the small end of the cone. The examined configuration generates asymmetric oscillation; thus, the system constitutes a nano-oscillator.
Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters
Directory of Open Access Journals (Sweden)
Kenichi Dedachi
2013-01-01
Full Text Available Based on the observation that Ramachandran-type potential energy surfaces of single amino acid units in water are in good agreement with statistical structures of the corresponding amino acid residues in proteins, we recently developed a new all-atom force field called SAAP, in which the total energy function for a polypeptide is expressed basically as a sum of single amino acid potentials and electrostatic and Lennard-Jones potentials between the amino acid units. In this study, the SAAP force field (SAAPFF parameters were improved, and classical canonical Monte Carlo (MC simulation was carried out for short peptide models, that is, Met-enkephalin and chignolin, at 300 K in an implicit water model. Diverse structures were reasonably obtained for Met-enkephalin, while three folded structures, one of which corresponds to a native-like structure with three native hydrogen bonds, were obtained for chignolin. The results suggested that the SAAP-MC method is useful for conformational sampling for the short peptides. A protocol of SAAP-MC simulation followed by structural clustering and examination of the obtained structures by ab initio calculation or simply by the number of the hydrogen bonds (or the hardness was demonstrated to be an effective strategy toward structure prediction for short peptide molecules.
Turbulent resuspension of small nondeformable particles
International Nuclear Information System (INIS)
Lazaridis, M.; Drossinos, Y.
1998-01-01
An energy-balance resuspension model is modified and applied to the resuspension of a monolayer of nondeformable spherical particles. The particle-surface adhesive force is calculated from a microscopic model based on the Lennard-Jones intermolecular potential. Pairwise additivity of intermolecular interactions is assumed and elastic flattening of the particles is neglected. From the resulting particle-surface interaction potential the natural frequency of vibration of a particle on a surface and the depth of the potential well are calculated. The particle resuspension rate is calculated using the results of a previously developed energy-balance model, where the influence of fluid flow on the bound particle motion is recognized. The effect of surface roughness is included by introducing an effective particle radius that results in log-normally distributed adhesive forces. The predictions of the model are compared with experimental results for the resuspension of Al 2 O 3 particles from stainless steel surfaces. Particle resuspension due to turbulent fluid flow is important in the interaction of the atmosphere with various surfaces and in numerous industrial processes. For example, in the nuclear industry, fission-product aerosols released during a postulated severe accident in a Light Water Reactor may deposit and resuspend repeatedly in the vessel circuit and containment
Trajectory study of supercollision relaxation in highly vibrationally excited pyrazine and CO2.
Li, Ziman; Sansom, Rebecca; Bonella, Sara; Coker, David F; Mullin, Amy S
2005-09-01
Classical trajectory calculations were performed to simulate state-resolved energy transfer experiments of highly vibrationally excited pyrazine (E(vib) = 37,900 cm(-1)) and CO(2), which were conducted using a high-resolution transient infrared absorption spectrometer. The goal here is to use classical trajectories to simulate the supercollision energy transfer pathway wherein large amounts of energy are transferred in single collisions in order to compare with experimental results. In the trajectory calculations, Newton's laws of motion are used for the molecular motion, isolated molecules are treated as collections of harmonic oscillators, and intermolecular potentials are formed by pairwise Lennard-Jones potentials. The calculations qualitatively reproduce the observed energy partitioning in the scattered CO(2) molecules and show that the relative partitioning between bath rotation and translation is dependent on the moment of inertia of the bath molecule. The simulations show that the low-frequency modes of the vibrationally excited pyrazine contribute most to the strong collisions. The majority of collisions lead to small DeltaE values and primarily involve single encounters between the energy donor and acceptor. The large DeltaE exchanges result from both single impulsive encounters and chattering collisions that involve multiple encounters.
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
Simplified TiO2 force fields for studies of its interaction with biomolecules
Luan, Binquan; Huynh, Tien; Zhou, Ruhong
2015-06-01
Engineered TiO2 nanoparticles have been routinely applied in nanotechnology, as well as in cosmetics and food industries. Despite active experimental studies intended to clarify TiO2's biological effects, including potential toxicity, the relation between experimentally inferred nanotoxicity and industry standards for safely applying nanoparticles remains somewhat ambiguous with justified concerns. Supplemental to experiments, molecular dynamics simulations have proven to be efficacious in investigating the molecular mechanism of a biological process occurring at nanoscale. In this article, to facilitate the nanotoxicity and nanomedicine research related to this important metal oxide, we provide a simplified force field, based on the original Matsui-Akaogi force field but compatible to the Lennard-Jones potentials normally used in modeling biomolecules, for simulating TiO2 nanoparticles interacting with biomolecules. The force field parameters were tested in simulating the bulk structure of TiO2, TiO2 nanoparticle-water interaction, as well as the adsorption of proteins on the TiO2 nanoparticle. We demonstrate that these simulation results are consistent with experimental data/observations. We expect that simulations will help to better understand the interaction between TiO2 and molecules.
Friction of N-bead macromolecules in solution: Effects of the bead-solvent interaction
International Nuclear Information System (INIS)
Uvarov, Alexander; Fritzsche, Stephan
2006-01-01
The role of the bead-solvent interaction has been studied for its influence on the dynamics of an N-bead macromolecule which is immersed into a solution. Using a Fokker-Planck equation for the phase-space distribution function of the macromolecule, we show that all the effects of the solution can be treated entirely in terms of the friction tensors which are assigned to each pair of interacting beads in the chain. For the high-density as well as for the critical solvent, the properties of these tensors are discussed in detail and are calculated by using several (realistic) choices of the bead-solvent potential. From the friction tensors, moreover, an expression for the center-of-mass friction coefficient of a (N-bead) chain macromolecule is derived. Numerical data for this coefficient for 'truncated' Lennard-Jones bead-solvent potential are compared with results from molecular dynamic simulations and from the phenomenological theoretical data as found in the literature
Compaction simulation of nano-crystalline metals with molecular dynamics analysis
Directory of Open Access Journals (Sweden)
Khoei A.R.
2016-01-01
Full Text Available The molecular-dynamics analysis is presented for 3D compaction simulation of nano-crystalline metals under uniaxial compaction process. The nano-crystalline metals consist of nickel and aluminum nano-particles, which are mixed with specified proportions. The EAM pair-potential is employed to model the formation of nano-particles at different temperatures, number of nano-particles, and mixing ratio of Ni and Al nano-particles to form the component into the shape of a die. The die-walls are modeled using the Lennard-Jones inter-atomic potential between the atoms of nano-particles and die-walls. The forming process is model in uniaxial compression, which is simulated until the full-dense condition is attained at constant temperature. Numerical simulations are performed by presenting the densification of nano-particles at different deformations and distribution of dislocations. Finally, the evolutions of relative density with the pressure as well as the stress-strain curves are depicted during the compaction process.
International Nuclear Information System (INIS)
Ng, T Y; Yeak, S H; Liew, K M
2008-01-01
A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods
Structural organisation and dynamics in king penguin colonies
Gerum, Richard; Richter, Sebastian; Fabry, Ben; Le Bohec, Céline; Bonadonna, Francesco; Nesterova, Anna; Zitterbart, Daniel P.
2018-04-01
During breeding, king penguins do not build nests, however they show strong territorial behaviour and keep a pecking distance to neighbouring penguins. Penguin positions in breeding colonies are highly stable over weeks and appear regularly spaced, but thus far no quantitative analysis of the structural order inside a colony has been performed. In this study, we use the radial distribution function to analyse the spatial coordinates of penguin positions. Coordinates are obtained from aerial images of two colonies that were observed for several years. Our data demonstrate that the structural order in king penguin colonies resembles a 2D liquid of particles with a Lennard-Jones-type interaction potential. We verify this using a molecular dynamics simulation with thermally driven particles, whereby temperature corresponds to penguin movements, the energy well depth ɛ of the attractive potential corresponds to the strength of the colony-forming behaviour, and the repulsive zone corresponds to the pecking radius. We can recapitulate the liquid disorder of the colony, as measured by the radial distribution function, when the particles have a temperature of several (1.4–10) \
Effects of solute--solvent attractive forces on hydrophobic correlations
International Nuclear Information System (INIS)
Pratt, L.R.; Chandler, D.
1980-01-01
A theory is presented for the effect of slowly varying attractive forces on correlations between nonpolar solutes in dilute aqueous solution. We find that hydrophobic correlations are sensitive to relatively long range slowly varying interactions. Thus, it is possible to make qualitative changes in these correlations by introducing small changes in the attractive forces. Several model calculations are presented to illustrate these facts. The contributions of the Lennard-Jones attractive forces to the computer simulation results of Pangali, Rao, and Berne are calculated. For this case it is found that the potential of mean force between spherical nonpolar solutes is hardly affected by inclusion of attractive forces. However, the osmotic second virial coefficient is dominated by the contributions of the attractive forces. For spherical solutes which provide a reasonable model for the methane molecule, inclusion of attractive forces produces a qualitative change in the methane--methane potential of mean force. The connection between these effects of slowly varying attractive forces and the enthalpic part of Ben-Naim's deltaA/sup H/I is discussed
A strategy to find minimal energy nanocluster structures.
Rogan, José; Varas, Alejandro; Valdivia, Juan Alejandro; Kiwi, Miguel
2013-11-05
An unbiased strategy to search for the global and local minimal energy structures of free standing nanoclusters is presented. Our objectives are twofold: to find a diverse set of low lying local minima, as well as the global minimum. To do so, we use massively the fast inertial relaxation engine algorithm as an efficient local minimizer. This procedure turns out to be quite efficient to reach the global minimum, and also most of the local minima. We test the method with the Lennard-Jones (LJ) potential, for which an abundant literature does exist, and obtain novel results, which include a new local minimum for LJ13 , 10 new local minima for LJ14 , and thousands of new local minima for 15≤N≤65. Insights on how to choose the initial configurations, analyzing the effectiveness of the method in reaching low-energy structures, including the global minimum, are developed as a function of the number of atoms of the cluster. Also, a novel characterization of the potential energy surface, analyzing properties of the local minima basins, is provided. The procedure constitutes a promising tool to generate a diverse set of cluster conformations, both two- and three-dimensional, that can be used as an input for refinement by means of ab initio methods. Copyright © 2013 Wiley Periodicals, Inc.
Calculation of the mean force constants of the rare gases and the rectilinear law of mean force
International Nuclear Information System (INIS)
Lee, M.W.; Bigeleisen, J.
1977-01-01
The mean energies, (U), and the mean force constants, (nabla 2 U), have been calculated for liquid argon and liquid krypton using the WCA perturbation theory, and for gaseous argon and krypton along the coexistence line by solution of the PY equation for the radial distribution function. Calculations have been made for the Lennard-Jones, Barker-Henderson, and Maitland-Smith potentials. There is little difference in the values of (U) and (nabla 2 U) calculated for the three potentials. The calculated values are in good agreement with experimental data. Correlation of the calculated values of (nabla 2 U) for the liquid and gas leads to an empirical relationship between (nabla 2 U) and the density of the phase along the coexistence line. When the latter is combined with the law of rectilinear diameters of the density, the rectilinear law of mean force is obtained, which is in good agreement with experimental data on argon. It is shown that the scaling exponent for the mean force constant, (nabla 2 U)/sub l/-(nabla 2 U)/sub g/, is larger than the scaling exponent of the density below the critical temperature and becomes equal to it at the critical temperature. The rationale for the rectilinear law of mean force is provided by an expansion of the radial distribution function of the liquid in powers of the density and the use of the WCA approximation to the radial distribution function
Oscillation of nested fullerenes (carbon onions) in carbon nanotubes
International Nuclear Information System (INIS)
Thamwattana, Ngamta; Hill, James M.
2008-01-01
Nested spherical fullerenes, which are sometimes referred to as carbon onions, of I h symmetries which have N(n) carbon atoms in the nth shell given by N(n) = 60n 2 are studied in this paper. The continuum approximation together with the Lennard-Jones potential is utilized to determine the resultant potential energy. High frequency nanoscale oscillators or gigahertz oscillators created from fullerenes and both single- and multi-walled carbon nanotubes have attracted much attention for a number of proposed applications, such as ultra-fast optical filters and ultra-sensitive nano-antennae that might impact on the development of computing and signalling nano-devices. Further, it is only at the nanoscale where such gigahertz frequencies can be achieved. This paper focuses on the interaction of nested fullerenes and the mechanics of such molecules oscillating in carbon nanotubes. Here we investigate such issues as the acceptance condition for nested fullerenes into carbon nanotubes, the total force and energy of the nested fullerenes, and the velocity and gigahertz frequency of the oscillating molecule. In particular, optimum nanotube radii are determined for which nested fullerenes oscillate at maximum velocity and frequency, which will be of considerable benefit for the design of future nano-oscillating devices
Needlelike motion of prolate ellipsoids in the sea of spheres
Vasanthi, R.; Ravichandran, S.; Bagchi, Biman
2001-05-01
Molecular dynamics simulations of translational motion of isolated prolate ellipsoids in the sea of spheres have been carried out for several different values of the aspect ratio (κ), obtained by changing either the length or the diameter of the ellipsoids, at several different solvent densities. The interaction among the spheres is given by the Lennard-Jones pair potential while that between spheres and ellipsoids is given by a modified Gay-Berne potential. Both the mean-square displacements of the center of mass of the ellipsoids and their orientational time correlation function have been calculated. It is found that at short to intermediate times, the motion of ellipsoids is anisotropic and primarily needlelike—the molecules prefer to move parallel to their long axis. The ratio of these two diffusion constants (D∥ and D⊥) approaches κ, suggesting a decoupling of D∥ from the length of the ellipsoid. The diffusion becomes isotropic in the long time with the total diffusion coefficient given by D∥+2D⊥. The crossover from the anisotropic to the isotropic diffusion is surprisingly sharp and clear in most cases.
Clustering and phase behaviour of attractive active particles with hydrodynamics.
Navarro, Ricard Matas; Fielding, Suzanne M
2015-10-14
We simulate clustering, phase separation and hexatic ordering in a monolayered suspension of active squirming disks subject to an attractive Lennard-Jones-like pairwise interaction potential, taking hydrodynamic interactions between the particles fully into account. By comparing the hydrodynamic case with counterpart simulations for passive and active Brownian particles, we elucidate the relative roles of self-propulsion, interparticle attraction, and hydrodynamic interactions in determining clustering and phase behaviour. Even in the presence of an attractive potential, we find that hydrodynamic interactions strongly suppress the motility induced phase separation that might a priori have been expected in a highly active suspension. Instead, we find only a weak tendency for the particles to form stringlike clusters in this regime. At lower activities we demonstrate phase behaviour that is broadly equivalent to that of the counterpart passive system at low temperatures, characterized by regimes of gas-liquid, gas-solid and liquid-solid phase coexistence. In this way, we suggest that a dimensionless quantity representing the level of activity relative to the strength of attraction plays the role of something like an effective non-equilibrium temperature, counterpart to the (dimensionless) true thermodynamic temperature in the passive system. However there are also some important differences from the equilibrium case, most notably with regards the degree of hexatic ordering, which we discuss carefully.
Ghimire, Sunil; Adhikari, Narayan Prasad
2017-03-01
Molecular dynamics simulation of argon, krypton, and their binary mixtures were performed at different temperatures and constant pressure (P = 1.013 bar) using GROMACS - Groningen Machine for Chemical Simulations. The gases are modeled by Lennard-Jones pair potential, with parameters taken from the literature. The study of radial distribution functions (RDFs) shows a single peak which indicates that there is no packing effect in gaseous state for argon, krypton, and their binary mixtures. The self-diffusion coefficients of argon and krypton is determined by using mean-square displacement(MSD) method and the mutual diffusion coefficients of binary mixtures are determined using Darken's relation. The values of simulated diffusion coefficients are compared with their corresponding theoretical values, numerical estimation, and experimental data. A good agreement between these sets of data is found. The diffusion coefficients obey Arrhenius behavior to a good extent for both pure components and binary mixtures. The values of simulated diffusion coefficient are used to estimate viscosities and thermal conductivities which agree with theoretical values, numerical estimation, and experimental data within 10 %. These results support that the LJ potential is sufficient for description of molecular interactions in argon and krypton.
Morse index for figure-eight choreographies of the planar equal mass three-body problem
Fukuda, Hiroshi; Fujiwara, Toshiaki; Ozaki, Hiroshi
2018-04-01
We report on numerical calculations of the Morse index for figure-eight choreographic solutions to a system of three identical bodies in a plane interacting through the homogeneous potential, -1/r a , or through the Lennard-Jones-type (LJ) potential, 1/r12 - 1/r6 , where r is a distance between the bodies. The Morse index is a number of independent variational functions giving negative second variation S (2) of action functional S. We calculated three kinds of Morse indices, N, N c and N e, in the domain of the periodic, the choreographic and the figure-eight choreographic function, respectively. For the homogeneous system, we obtain N = 4 for 0 ≤slant a index for the solution tending to the figure-eight solution of the a = 6 homogeneous system for the period T \\to ∞ . We obtain N, N c and N e as monotonically increasing functions of T from T \\to ∞ , which start with N=N_c=N_e=0 , jump at the smallest T by 1, and reach N = 12, N_c=4 , and N_e=1 for T \\to ∞ in the other branch.
Lithium ion storage between graphenes
Directory of Open Access Journals (Sweden)
Chan Yue
2011-01-01
Full Text Available Abstract In this article, we investigate the storage of lithium ions between two parallel graphene sheets using the continuous approximation and the 6-12 Lennard-Jones potential. The continuous approximation assumes that the carbon atoms can be replaced by a uniform distribution across the surface of the graphene sheets so that the total interaction potential can be approximated by performing surface integrations. The number of ion layers determines the major storage characteristics of the battery, and our results show three distinct ionic configurations, namely single, double, and triple ion forming layers between graphenes. The number densities of lithium ions between the two graphenes are estimated from existing semi-empirical molecular orbital calculations, and the graphene sheets giving rise to the triple ion layers admit the largest storage capacity at all temperatures, followed by a marginal decrease of storage capacity for the case of double ion layers. These two configurations exceed the maximum theoretical storage capacity of graphite. Further, on taking into account the charge-discharge property, the double ion layers are the most preferable choice for enhanced lithium storage. Although the single ion layer provides the least charge storage, it turns out to be the most stable configuration at all temperatures. One application of the present study is for the design of future high energy density alkali batteries using graphene sheets as anodes for which an analytical formulation might greatly facilitate rapid computational results.
Formation of graphene on BN substrate by vapor deposition method and size effects on its structure
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.
DEFF Research Database (Denmark)
Mikkelsen, Henrik Hvenegaard; Søgaard, Thomas Friis
2015-01-01
” plays a critical role in relation to Bugkalot men’s construction of hegemonic masculinity and the sustaining of complex egalitarian relations. The Bugkalot have a notoriously violent history; until the late 1970s more than half of the adult men engaged in ritual killings. While most Bugkalot men has...... that can also be used in other contexts to understand how men construct hegemonic masculinity by strategically adopting the interspace of civility and violence.......This article explores the social significance of violence as potentiality and performance among former headhunters. Taking its outset in an ethnographic study of violence and masculinity among the Philippine people known as the Bugkalot, we explore how violence as “performed violent potentiality...
Helms, Lester L
2014-01-01
Potential Theory presents a clear path from calculus to classical potential theory and beyond, with the aim of moving the reader into the area of mathematical research as quickly as possible. The subject matter is developed from first principles using only calculus. Commencing with the inverse square law for gravitational and electromagnetic forces and the divergence theorem, the author develops methods for constructing solutions of Laplace's equation on a region with prescribed values on the boundary of the region. The latter half of the book addresses more advanced material aimed at those with the background of a senior undergraduate or beginning graduate course in real analysis. Starting with solutions of the Dirichlet problem subject to mixed boundary conditions on the simplest of regions, methods of morphing such solutions onto solutions of Poisson's equation on more general regions are developed using diffeomorphisms and the Perron-Wiener-Brelot method, culminating in application to Brownian motion. In ...
Wettability of graphitic-carbon and silicon surfaces: MD modeling and theoretical analysis
International Nuclear Information System (INIS)
Ramos-Alvarado, Bladimir; Kumar, Satish; Peterson, G. P.
2015-01-01
The wettability of graphitic carbon and silicon surfaces was numerically and theoretically investigated. A multi-response method has been developed for the analysis of conventional molecular dynamics (MD) simulations of droplets wettability. The contact angle and indicators of the quality of the computations are tracked as a function of the data sets analyzed over time. This method of analysis allows accurate calculations of the contact angle obtained from the MD simulations. Analytical models were also developed for the calculation of the work of adhesion using the mean-field theory, accounting for the interfacial entropy changes. A calibration method is proposed to provide better predictions of the respective contact angles under different solid-liquid interaction potentials. Estimations of the binding energy between a water monomer and graphite match those previously reported. In addition, a breakdown in the relationship between the binding energy and the contact angle was observed. The macroscopic contact angles obtained from the MD simulations were found to match those predicted by the mean-field model for graphite under different wettability conditions, as well as the contact angles of Si(100) and Si(111) surfaces. Finally, an assessment of the effect of the Lennard-Jones cutoff radius was conducted to provide guidelines for future comparisons between numerical simulations and analytical models of wettability
Interactions of hydrogen with graphite at low pressure and elevated temperature
International Nuclear Information System (INIS)
Hoinkis, E.
1991-03-01
The plasma facing components of the vacuum chamber for thermonuclear fusion experiments are clad with graphite. Recycling of gases affects the plasma properties, and the tritium quantity accumulated in the graphite during the operation of Tokamaks with DT must be known. An adsorption isotherm for deuterium on the nuclear grade graphitic Matrix A3-3 was measured by using a volumetric method at 1173 K at pressures c = 2.5 eV/D 2 using Fowler's equation and isotherms were calculated for this E c value. These isotherms predict saturation of the adsorption sites in graphite at T D2 > 0.1 Pa. At T > 1173 K and P D2 -2 Pa the adsorbed quantity is less than 1% of the saturation level. The release kinetics of deuterium was measured at temperatures uo to 2000 K. D 2 desorption commenced at 1170 K. The maximum of the release rate is observed at T p = 1770 K. A Lennard-Jones potential energy diagram was calculated, which suggests a C-H bond energy E b ≅ 3.4 eV/D and an activation energy of desorption E d ≅ 4 eV/D 2 . The partial pressures of hydrocarbons C n ≤3 H m in equilibrium with graphite were calculated. At total pressures -2 Pa the partial pressures of these hydrocarbons are less than 10 -7 Pa in the temperature range 600-1500 K. (orig./MM)
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).
Stokes-Einstein relation for pure simple fluids
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.
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)
Deformation and fracture of Coarse-grained Model of Filled Rubber Composites
Hagita, Katsumi; Morita, Hiroshi; Doi, Masao; Takano, Hiroshi
2011-03-01
We presented a result of coarse-grained Molecular Dynamics simulation of filled polymer melts with Sulfur-crosslink under deformation based on the Kremer-Grest Model. Under uni-axial deformation (extension) by setting Poisson's ratio to less than 0.5, facture of this polymer nanocomoposites occurs due to volume increase for increasing the strain. In order to study facture behavior, we use the original Lennard Jones potential formula (with attractive part) as interaction between polymers. The size of simulation box under periodic boundary conditions (PBC) is set to about 133nm. We put 2048 fillers, 5120 polymer chains of 1024 particles, and many crosslink into the PBC box. Due to the crosslink, all polymer chains are connected to one network gel. One filler consists of 320 particles of the C320 fullerene structure. A repulsive force from the center of the filler is applied to the particles of C320 in order to make a sphere whose diameter is about 7nm. We can observe the fracture occurs due to void created near surface of fillers for the case that interaction between polymer and filler is relatively non- attractive. Various cases of Poisson's ratio and interaction between polymer and filler are examined.
Singh, Jalim; Jose, Prasanth
Results of molecular dynamics simulations of a system of Kremer and Grest linear polymer melts are presented at moderate and high number density. A detailed study of molecular pair distribution function shows that potential of mean force between the molecules has form of Gaussian with an attractive tail at number density ρ = 0.85 (in Lennard-Jones units), which is due to the dominating attractive interactions from temperature T = 0.7. This system shows gelation assisted glass transition, which is interpreted from peaks of molecular structure factor at small wave-numbers. At low temperature, this system phase separate to form dense domains whose local density is high; these domains show many dynamical features of glass transition in monomer and molecular level of relaxation indicating glass transition is assisted by gelation in this system. In the same system, at ρ = 1.0, repulsive interactions dominate, structure does not change even at low temperatures; the system exhibits dynamic heterogeneity and known to undergo glass transition. In this work, we compare and contrast the structure and dynamics of the system near its glass transition. Also, we computed correlation length of systems from the peak value of four-point structural dynamic susceptibility. HPC facility at IIT Mandi.
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
Pavlova, Anna; Parks, Jerry M; Gumbart, James C
2018-02-13
Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co 3+ , Co 2+ , and Co 1+ , and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.
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.
Collision broadening and shift of the potassium 4P-7S and 4P-5D lines by argon
International Nuclear Information System (INIS)
Hohimer, J.P.
1981-01-01
A two-step laser excitation technique has been used to investigate the collisional broadening and shift of excited-state potassium transitions. Values for the argon collisional broadening and shift constants for the potassium 4p-7s and 4p-5d transitions were determined from line shapes for argon pressures up to 100 Torr. The values of these constants (in units of 10 -9 rad s -1 atom -1 cm 3 ) are (4P/sub 1/2/-7S/sub 1/2/): γ=11.60 +- 0.07, β=-6.68 +- 0.11; (4P/sub 3/2/-7S/sub 1/2/): γ=11.49 +- 0.15, β=-6.82 +- 0.14; (4P/sub 1/2/-5D/sub 3/2/): γ=8.64 +- 0.07, β=-4.62 +- 0.04; (4P/sub 3/2/-5D/sub 3/2/): γ=8.58 +- 0.10, β=-3.49 +- 0.32; (4P/sub 3/2/-5D/sub 5/2/): γ=9.13 +- 0.10, β=-4.73 +- 0.09. These broadening and shift constants are interpreted in terms of a Lennard-Jones interaction potential
Simple improvements to classical bubble nucleation models.
Tanaka, Kyoko K; Tanaka, Hidekazu; Angélil, Raymond; Diemand, Jürg
2015-08-01
We revisit classical nucleation theory (CNT) for the homogeneous bubble nucleation rate and improve the classical formula using a correct prefactor in the nucleation rate. Most of the previous theoretical studies have used the constant prefactor determined by the bubble growth due to the evaporation process from the bubble surface. However, the growth of bubbles is also regulated by the thermal conduction, the viscosity, and the inertia of liquid motion. These effects can decrease the prefactor significantly, especially when the liquid pressure is much smaller than the equilibrium one. The deviation in the nucleation rate between the improved formula and the CNT can be as large as several orders of magnitude. Our improved, accurate prefactor and recent advances in molecular dynamics simulations and laboratory experiments for argon bubble nucleation enable us to precisely constrain the free energy barrier for bubble nucleation. Assuming the correction to the CNT free energy is of the functional form suggested by Tolman, the precise evaluations of the free energy barriers suggest the Tolman length is ≃0.3σ independently of the temperature for argon bubble nucleation, where σ is the unit length of the Lennard-Jones potential. With this Tolman correction and our prefactor one gets accurate bubble nucleation rate predictions in the parameter range probed by current experiments and molecular dynamics simulations.
Properties of liquid clusters in large-scale molecular dynamics nucleation simulations
International Nuclear Information System (INIS)
Angélil, Raymond; Diemand, Jürg; Tanaka, Kyoko K.; Tanaka, Hidekazu
2014-01-01
We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with 10 9 atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent statistics for cluster properties over a wide range of cluster sizes. The nucleation rates, cluster growth rates, and size distributions are presented in Diemand et al. [J. Chem. Phys. 139, 74309 (2013)], while this paper analyses the properties of the clusters. We explore the cluster temperatures, density profiles, potential energies, and shapes. A thorough understanding of the properties of the clusters is crucial to the formulation of nucleation models. Significant latent heat is retained by stable clusters, by as much as ΔkT = 0.1ε for clusters with size i = 100. We find that the clusters deviate remarkably from spherical—with ellipsoidal axis ratios for critical cluster sizes typically within b/c = 0.7 ± 0.05 and a/c = 0.5 ± 0.05. We examine cluster spin angular momentum, and find that it plays a negligible role in the cluster dynamics. The interfaces of large, stable clusters are thinner than planar equilibrium interfaces by 10%−30%. At the critical cluster size, the cluster central densities are between 5% and 30% lower than the bulk liquid expectations. These lower densities imply larger-than-expected surface areas, which increase the energy cost to form a surface, which lowers nucleation rates
The energetics and structure of nickel clusters: Size dependence
International Nuclear Information System (INIS)
Cleveland, C.L.; Landman, U.
1991-01-01
The energetics of nickel clusters over a broad size range are explored within the context of the many-body potentials obtained via the embedded atom method. Unconstrained local minimum energy configurations are found for single crystal clusters consisting of various truncations of the cube or octahedron, with and without (110) faces, as well as some monotwinnings of these. We also examine multitwinned structures such as icosahedra and various truncations of the decahedron, such as those of Ino and Marks. These clusters range in size from 142 to over 5000 atoms. As in most such previous studies, such as those on Lennard-Jones systems, we find that icosahedral clusters are favored for the smallest cluster sizes and that Marks' decahedra are favored for intermediate sizes (all our atomic systems larger than about 2300 atoms). Of course very large clusters will be single crystal face-centered-cubic (fcc) polyhedra: the onset of optimally stable single-crystal nickel clusters is estimated to occur at 17 000 atoms. We find, via comparisons to results obtained via atomistic calculations, that simple macroscopic expressions using accurate surface, strain, and twinning energies can usefully predict energy differences between different structures even for clusters of much smaller size than expected. These expressions can be used to assess the relative energetic merits of various structural motifs and their dependence on cluster size
Fast optimization of binary clusters using a novel dynamic lattice searching method
International Nuclear Information System (INIS)
Wu, Xia; Cheng, Wen
2014-01-01
Global optimization of binary clusters has been a difficult task despite of much effort and many efficient methods. Directing toward two types of elements (i.e., homotop problem) in binary clusters, two classes of virtual dynamic lattices are constructed and a modified dynamic lattice searching (DLS) method, i.e., binary DLS (BDLS) method, is developed. However, it was found that the BDLS can only be utilized for the optimization of binary clusters with small sizes because homotop problem is hard to be solved without atomic exchange operation. Therefore, the iterated local search (ILS) method is adopted to solve homotop problem and an efficient method based on the BDLS method and ILS, named as BDLS-ILS, is presented for global optimization of binary clusters. In order to assess the efficiency of the proposed method, binary Lennard-Jones clusters with up to 100 atoms are investigated. Results show that the method is proved to be efficient. Furthermore, the BDLS-ILS method is also adopted to study the geometrical structures of (AuPd) 79 clusters with DFT-fit parameters of Gupta potential
Van Hoang, Vo; Teboul, Victor; Odagaki, Takashi
2015-12-24
Via analysis of spatiotemporal arrangements of atoms based on their dynamics in supercooled liquid and glassy states of a 2D monatomic system with a double-well Lennard-Jones-Gauss (LJG) interaction potential, we find a new scenario of dynamical heterogeneity. Atoms with the same or very close mobility have a tendency to aggregate into clusters. The number of atoms with high mobility (and size of their clusters) increases with decreasing temperature passing over a maximum before decreasing down to zero. Position of the peak moves toward a lower temperature if mobility of atoms in clusters is lower together with an enhancement of height of the peak. In contrast, the number of atoms with very low mobility or solidlike atoms (and size of their clusters) has a tendency to increase with decreasing temperature and then it suddenly increases in the vicinity of the glass transition temperature leading to the formation of a glassy state. A sudden increase in the number of strongly correlated solidlike atoms in the vicinity of a glass transition temperature (Tg) may be an origin of a drastical increase in viscosity of the glass-forming systems approaching the glass transition. In fact, we find that the diffusion coefficient decays exponentially with a fraction of solidlike atoms exhibiting a sudden decrease in the vicinity of the glass transition region.
Ghaffari, Reza; Sauer, Roger A.
2018-06-01
The nonlinear frequencies of pre-stressed graphene-based structures, such as flat graphene sheets and carbon nanotubes, are calculated. These structures are modeled with a nonlinear hyperelastic shell model. The model is calibrated with quantum mechanics data and is valid for high strains. Analytical solutions of the natural frequencies of various plates are obtained for the Canham bending model by assuming infinitesimal strains. These solutions are used for the verification of the numerical results. The performance of the model is illustrated by means of several examples. Modal analysis is performed for square plates under pure dilatation or uniaxial stretch, circular plates under pure dilatation or under the effects of an adhesive substrate, and carbon nanotubes under uniaxial compression or stretch. The adhesive substrate is modeled with van der Waals interaction (based on the Lennard-Jones potential) and a coarse grained contact model. It is shown that the analytical natural frequencies underestimate the real ones, and this should be considered in the design of devices based on graphene structures.
Hu, Han; Sun, Ying
2013-11-01
Disjoining pressure, the excess pressure in an ultra-thin liquid film as a result of van der Waals interactions, is important in lubrication, wetting, flow boiling, and thin film evaporation. The classic theory of disjoining pressure is developed for simple monoatomic liquids. However, real world applications often utilize water, a polar liquid, for which fundamental understanding of disjoining pressure is lacking. In the present study, molecular dynamics (MD) simulations are used to gain insights into the effect of disjoining pressure in a water thin film. Our MD models were firstly validated against Derjaguin's experiments on gold-gold interactions across a water film and then verified against disjoining pressure in an argon thin film using the Lennard-Jones potential. Next, a water thin film adsorbed on a gold surface was simulated to examine the change of vapor pressure with film thickness. The results agree well with the classic theory of disjoining pressure, which implies that the polar nature of water molecules does not play an important role. Finally, the effects of disjoining pressure on thin film evaporation in nanoporous membrane and on bubble nucleation are discussed.
Energy Technology Data Exchange (ETDEWEB)
Rana, Malay Kumar; Chandra, Amalendu, E-mail: amalen@iitk.ac.in [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India)
2015-01-21
Atomistic simulations of model nonpolar nanotubes in a Stockmayer liquid are carried out for varying nanotube diameter and nanotube-solvent interactions to investigate solvophobic interactions in generic dipolar solvents. We have considered model armchair type single-walled nonpolar nanotubes with increasing radii from (5,5) to (12,12). The interactions between solute and solvent molecules are modeled by the well-known Lennard-Jones and repulsive Weeks-Chandler-Andersen potentials. We have investigated the density profiles and microscopic arrangement of Stockmayer molecules, orientational profiles of their dipole vectors, time dependence of their occupation, and also the translational and rotational motion of solvent molecules in confined environments of the cylindrical nanopores and also in their external peripheral regions. The present results of structural and dynamical properties of Stockmayer molecules inside and near atomistically rough nonpolar surfaces including their wetting and dewetting behavior for varying interactions provide a more generic picture of solvophobic effects experienced by simple dipolar liquids without any specific interactions such as hydrogen bonds.
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)
Dong, Dengpan; Vatamanu, Jenel P.; Wei, Xiaoyu; Bedrov, Dmitry
2018-05-01
Atomistic molecular dynamics simulations were conducted to study the wetting states of 1-ethyl-3-methylimidazolium bis(trifluoro-methylsulfonyl)-imide ionic liquid (IL) nanodroplets on surfaces with different strengths of van der Waals (VDW) interactions and in the presence of an electric field. By adjusting the depth of Lennard-Jones potential, the van der Waals interaction between the solid surface and ionic liquid was systematically varied. The shape of the droplets was analyzed to extract the corresponding contact angle utilized to characterize wetting states of the nanodroplets. The explored range of surface-IL interactions allowed contact angles ranging from complete IL spreading on the surface to poor wettability. The effect of the external electrical field was explored by adding point charges to the surface atoms. Systems with two charge densities (±0.002 e/atom and ±0.004 e/atom) that correspond to 1.36 V/nm and 2.72 V/nm electric fields were investigated. Asymmetrical wetting states were observed for both cases. At 1.36 V/nm electric field, contributions of IL-surface VDW interactions and Coulombic interactions to the wetting state were competitive. At 2.72 V/nm field, electrostatic interactions dominate the interaction between the nanodroplet and surface, leading to enhanced wettability on all surfaces.
High-Throughput Characterization of Porous Materials Using Graphics Processing Units
Energy Technology Data Exchange (ETDEWEB)
Kim, Jihan; Martin, Richard L.; Rübel, Oliver; Haranczyk, Maciej; Smit, Berend
2012-05-08
We have developed a high-throughput graphics processing units (GPU) code that can characterize a large database of crystalline porous materials. In our algorithm, the GPU is utilized to accelerate energy grid calculations where the grid values represent interactions (i.e., Lennard-Jones + Coulomb potentials) between gas molecules (i.e., CH$_{4}$ and CO$_{2}$) and material's framework atoms. Using a parallel flood fill CPU algorithm, inaccessible regions inside the framework structures are identified and blocked based on their energy profiles. Finally, we compute the Henry coefficients and heats of adsorption through statistical Widom insertion Monte Carlo moves in the domain restricted to the accessible space. The code offers significant speedup over a single core CPU code and allows us to characterize a set of porous materials at least an order of magnitude larger than ones considered in earlier studies. For structures selected from such a prescreening algorithm, full adsorption isotherms can be calculated by conducting multiple grand canonical Monte Carlo simulations concurrently within the GPU.
International Nuclear Information System (INIS)
Nie, Chu; Geng, Jun; Marlow, William H.
2016-01-01
In order to improve the sampling of restricted microstates in our previous work [C. Nie, J. Geng, and W. H. Marlow, J. Chem. Phys. 127, 154505 (2007); 128, 234310 (2008)] and quantitatively predict thermal properties of supersaturated vapors, an extension is made to the Corti and Debenedetti subcell constraint algorithm [D. S. Corti and P. Debenedetti, Chem. Eng. Sci. 49, 2717 (1994)], which restricts the maximum allowed local density at any point in a simulation box. The maximum allowed local density at a point in a simulation box is defined by the maximum number of particles N m allowed to appear inside a sphere of radius R, with this point as the center of the sphere. Both N m and R serve as extra thermodynamic variables for maintaining a certain degree of spatial homogeneity in a supersaturated system. In a restricted canonical ensemble, at a given temperature and an overall density, series of local minima on the Helmholtz free energy surface F(N m , R) are found subject to different (N m , R) pairs. The true equilibrium metastable state is identified through the analysis of the formation free energies of Stillinger clusters of various sizes obtained from these restricted states. The simulation results of a supersaturated Lennard-Jones vapor at reduced temperature 0.7 including the vapor pressure isotherm, formation free energies of critical nuclei, and chemical potential differences are presented and analyzed. In addition, with slight modifications, the current algorithm can be applied to computing thermal properties of superheated liquids.
Monte Carlo Studies of Phase Separation in Compressible 2-dim Ising Models
Mitchell, S. J.; Landau, D. P.
2006-03-01
Using high resolution Monte Carlo simulations, we study time-dependent domain growth in compressible 2-dim ferromagnetic (s=1/2) Ising models with continuous spin positions and spin-exchange moves [1]. Spins interact with slightly modified Lennard-Jones potentials, and we consider a model with no lattice mismatch and one with 4% mismatch. For comparison, we repeat calculations for the rigid Ising model [2]. For all models, large systems (512^2) and long times (10^ 6 MCS) are examined over multiple runs, and the growth exponent is measured in the asymptotic scaling regime. For the rigid model and the compressible model with no lattice mismatch, the growth exponent is consistent with the theoretically expected value of 1/3 [1] for Model B type growth. However, we find that non-zero lattice mismatch has a significant and unexpected effect on the growth behavior.Supported by the NSF.[1] D.P. Landau and K. Binder, A Guide to Monte Carlo Simulations in Statistical Physics, second ed. (Cambridge University Press, New York, 2005).[2] J. Amar, F. Sullivan, and R.D. Mountain, Phys. Rev. B 37, 196 (1988).
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.
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.
Melting behavior of a model molecular crystalline GeI4
International Nuclear Information System (INIS)
Fuchizaki, Kazuhiro; Asano, Yuta
2015-01-01
A model molecular crystalline GeI 4 was examined using molecular dynamics simulation. The model was constructed in such a way that rigid tetrahedral molecules interact with each other via Lennard-Jones potentials whose centers are located at the vertices of a tetrahedron. Because no other interaction that can “soften” the intermolecular interaction was introduced, the melting curve of the model crystalline material does not exhibit the anomaly that was found for the real substance. However, the current investigation is useful in that it could settle the upper bound of pressure below which the model can predict properties of the molecular liquid. Moreover, singularity-free nature of the melting curve allowed us to analytically treat the melting curve in the light of the Kumari-Dass-Kechin equation. As a result, we could definitely conclude that the well-known Simon equation for the melting curve is merely an approximate expression. The condition for the validity of Simon’s equation was identified. (author)
Theory of static friction: temperature and corrugation effects
International Nuclear Information System (INIS)
Franchini, A; Brigazzi, M; Santoro, G; Bortolani, V
2008-01-01
We present a study of the static friction, as a function of temperature, between two thick solid slabs. The upper one is formed of light particles and the substrate of heavy particles. We focus our attention on the interaction between the phonon fields of the two blocks and on the interface corrugation, among the various mechanisms responsible for the friction. To give evidence of the role played by the dynamical interaction of the substrate with the upper block, we consider both a substrate formed by fixed atoms and a substrate formed by mobile atoms. To study the effect of the corrugation, we model it by changing the range parameter σ in the Lennard-Jones interaction potential. We found that in the case of the mobile substrate there is a large momentum transfer from the substrate to the upper block. This momentum transfer increases on increasing the temperature and produces a large disorder in the upper block favouring a decrease of the static friction with respect to the case for a rigid substrate. Reducing the corrugation, we found that with a rigid substrate the upper block becomes nearly commensurate, producing an enhancement of the static friction with respect to that with a mobile substrate
International Nuclear Information System (INIS)
Piatek, A; Dawid, A; Gburski, Z
2006-01-01
We have simulated (by the molecular dymanics (MD) method) the dynamics of fullerenes (C 60 ) in an extremely small cluster composed of only as many as seven C 60 molecules. The interaction is taken to be the full 60-site pairwise additive Lennard-Jones (LJ) potential which generates both translational and anisotropic rotational motions of each molecule. Our atomically detailed MD simulations discover the plastic phase (no translations but active reorientations of fullerenes) at low energies (temperatures) of the (C 60 ) 7 cluster. We provide the in-depth evidence of the dynamical solid-liquid bistability region in the investigated cluster. Moreover, we confirm the existence of the liquid phase in (C 60 ) 7 , the finding of Gallego et al (1999 Phys. Rev. Lett. 83 5258) obtained earlier on the basis of Girifalco's model, which assumes single-site only and spherically symmetrical interaction between C 60 molecules. We have calculated the translational and angular velocity autocorrelation functions and estimated the diffusion coefficient of fullerene in the liquid phase
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)
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
Monolayer Adsorption of Ar and Kr on Graphite: Theoretical Isotherms and Spreading Pressures
Mulero; Cuadros
1997-02-01
The validity of analytical equations for two-dimensional fluids in the prediction of monolayer adsorption isotherms and spreading pressures of rare gases on graphite is analyzed. The statistical mechanical theory of Steele is used to relate the properties of the adsorbed and two-dimensional fluids. In such theory the model of graphite is a perfectly flat surface, which means that only the first order contribution of the fluid-solid interactions are taken into account. Two analytical equations for two-dimensional Lennard-Jones fluids are used: one proposed by Reddy-O'Shea, based in the fit on pressure and potential energy computer simulated results, and other proposed by Cuadros-Mulero, based in the fit of the Helmholtz free energy calculated from computer simulated results of the radial distribution function. The theoretical results are compared with experimental results of Constabaris et al. (J. Chem. Phys. 37, 915 (1962)) for Ar and of Putnam and Fort (J. Phys. Chem. 79, 459 (1975)) for Kr. Good agreement is found using both equations in both cases.
Analysis of the static properties of cluster formations in symmetric linear multiblock copolymers
International Nuclear Information System (INIS)
Fytas, N G; Theodorakis, P E
2011-01-01
We use molecular dynamics simulations to study the static properties of a single linear multiblock copolymer chain under poor solvent conditions varying the block length N, the number of blocks n, and the solvent quality by variation of the temperature T. We study the most symmetrical case, where the number of blocks of monomers of type A, n A , equals that of monomers B, n B (n A = n B = n/2), the length of all blocks is the same irrespective of their type, and the potential parameters are also chosen symmetrically, as for a standard Lennard-Jones fluid. Under poor solvent conditions the chains collapse and blocks with monomers of the same type form clusters, which are phase separated from the clusters with monomers of the other type. We study the dependence of the size of the clusters formed on n, N and T. Furthermore, we discuss our results with respect to recent simulation data on the phase behaviour of such macromolecules, providing a complete picture for the cluster formations in single multiblock copolymer chains under poor solvent conditions.
Directory of Open Access Journals (Sweden)
Fuxi Shi
2014-01-01
Full Text Available The molecular compressibility, which is a macroscopic quantity to reveal the microcompressibility by additivity of molecular constitutions, is considered as a fixed value for specific organic liquids. In this study, we introduced two calculated expressions of molecular adiabatic compressibility to demonstrate its pressure and temperature dependency. The first one was developed from Wada’s constant expression based on experimental data of density and sound velocity. Secondly, by introducing the 2D fitting expressions and their partial derivative of pressure and temperature, molecular compressibility dependency was analyzed further, and a 3D fitting expression was obtained from the calculated data of the first one. The third was derived with introducing the pressure and temperature correction factors based on analogy to Lennard-Jones potential function and energy equipartition theorem. In wide range of temperatures (293
Fabrication and Molecular Transport Studies of Highly c-Oriented AFI Membranes
Liu, Yang
2017-01-10
The AFI membrane with one-dimensional straight channels is an ideal platform for various applications. In this work, we report the fabrication of a highly c-oriented, compact and stable AFI membrane by epitaxial growth from an almost close-packed and c-oriented monolayer of plate-like seeds that is manually assembled on a porous alumina support. The straight channels in the membrane are not only aligned vertically along the membrane depth, but are also continuous without disruption. The transport resistance is thus minimized and as a result, the membrane shows almost two orders of magnitude greater permeance in pervaporation of hydrocarbons compared to reported values in the literature. The selectivity of p-xylene to 1,3,5-triisopropylbenzene (TIPB) is approximately 850. In addition, through gas permeation studies on a number of gas and liquid molecules, different transport mechanisms including activated Knudsen diffusion, surface diffusion and molecular sieving were discovered for different diffusion species. The ratio of kinetic diameter to channel diameter, dm/dc, and the ratio of the Lennard-Jones length constant to channel diameter, σm/dc, are found very useful in explaining the different transport behaviors. These results should be useful not only for potential industrial applications of the AFI membranes but also for the fundamental understanding of transport in nanoporous structures.
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.
Optimization of linear and branched alkane interactions with water to simulate hydrophobic hydration
Ashbaugh, Henry S.; Liu, Lixin; Surampudi, Lalitanand N.
2011-08-01
Previous studies of simple gas hydration have demonstrated that the accuracy of molecular simulations at capturing the thermodynamic signatures of hydrophobic hydration is linked both to the fidelity of the water model at replicating the experimental liquid density at ambient pressure and an accounting of polarization interactions between the solute and water. We extend those studies to examine alkane hydration using the transferable potentials for phase equilibria united-atom model for linear and branched alkanes, developed to reproduce alkane phase behavior, and the TIP4P/2005 model for water, which provides one of the best descriptions of liquid water for the available fixed-point charge models. Alkane site/water oxygen Lennard-Jones cross interactions were optimized to reproduce the experimental alkane hydration free energies over a range of temperatures. The optimized model reproduces the hydration free energies of the fitted alkanes with a root mean square difference between simulation and experiment of 0.06 kcal/mol over a wide temperature range, compared to 0.44 kcal/mol for the parent model. The optimized model accurately reproduces the temperature dependence of hydrophobic hydration, as characterized by the hydration enthalpies, entropies, and heat capacities, as well as the pressure response, as characterized by partial molar volumes.
Directory of Open Access Journals (Sweden)
Hong Sun
2015-01-01
Full Text Available A molecular dynamic model based on Lennard-Jones Potential, the interaction force between two particles, molecular diffusion, and radial distribution function (RDF is presented. The diffusion of the hydrated ion, triggered by both Grotthuss and vehicle mechanisms, is used to study the proton transfer in Nafion 117. The hydrated ion transfer mechanisms and the effects of the temperature, the water content in the membrane, and the electric field on the diffusion of the hydrated ion are analyzed. The molecular dynamic simulation results are in good agreement with those reported in the literature. The modeling results show that when the water content in Nafion 117 is low, H3O+ is the main transfer ion among the different hydrated ions. However, at higher water content, the hydrated ion in the form of H+(H2O2 is the main transfer ion. It is also found that the negatively charged sulfonic acid group as the fortified point facilitates the proton transfer in Nafion 117 better than the free water molecule. The diffusion of the hydrated ion can be improved by increasing the cell temperature, the water content in Nafion, and the electric field intensity.
Pizzolato, N.; Fiasconaro, A.; Persano Adorno, D.; Spagnolo, B.
2010-09-01
The translocation of molecules across cellular membranes or through synthetic nanopores is strongly affected by thermal fluctuations. In this work we study how the dynamics of a polymer in a noisy environment changes when the translocation process is driven by an oscillating electric field. An improved version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics, by taking into account the harmonic interactions between adjacent monomers and the excluded-volume effect by introducing a Lennard-Jones potential between all beads. A bending recoil torque has also been included in our model. The polymer dynamics is simulated in a two-dimensional domain by numerically solving the Langevin equations of motion. Thermal fluctuations are taken into account by introducing a Gaussian uncorrelated noise. The mean first translocation time of the polymer centre of inertia shows a minimum as a function of the frequency of the oscillating forcing field. This finding represents the first evidence of the resonant activation behaviour in the dynamics of polymer translocation.
Optimized theory for simple and molecular fluids.
Marucho, M; Montgomery Pettitt, B
2007-03-28
An optimized closure approximation for both simple and molecular fluids is presented. A smooth interpolation between Perkus-Yevick and hypernetted chain closures is optimized by minimizing the free energy self-consistently with respect to the interpolation parameter(s). The molecular version is derived from a refinement of the method for simple fluids. In doing so, a method is proposed which appropriately couples an optimized closure with the variant of the diagrammatically proper integral equation recently introduced by this laboratory [K. M. Dyer et al., J. Chem. Phys. 123, 204512 (2005)]. The simplicity of the expressions involved in this proposed theory has allowed the authors to obtain an analytic expression for the approximate excess chemical potential. This is shown to be an efficient tool to estimate, from first principles, the numerical value of the interpolation parameters defining the aforementioned closure. As a preliminary test, representative models for simple fluids and homonuclear diatomic Lennard-Jones fluids were analyzed, obtaining site-site correlation functions in excellent agreement with simulation data.
Santos, Andrés; Manzano, Gema
2010-04-14
As is well known, approximate integral equations for liquids, such as the hypernetted chain (HNC) and Percus-Yevick (PY) theories, are in general thermodynamically inconsistent in the sense that the macroscopic properties obtained from the spatial correlation functions depend on the route followed. In particular, the values of the fourth virial coefficient B(4) predicted by the HNC and PY approximations via the virial route differ from those obtained via the compressibility route. Despite this, it is shown in this paper that the value of B(4) obtained from the virial route in the HNC theory is exactly three halves the value obtained from the compressibility route in the PY theory, irrespective of the interaction potential (whether isotropic or not), the number of components, and the dimensionality of the system. This simple relationship is confirmed in one-component systems by analytical results for the one-dimensional penetrable-square-well model and the three-dimensional penetrable-sphere model, as well as by numerical results for the one-dimensional Lennard-Jones model, the one-dimensional Gaussian core model, and the three-dimensional square-well model.
International Nuclear Information System (INIS)
Murad, S.; Gubbins, K.E.; Gray, C.G.
1983-01-01
We compare several recently proposed theories for the angular pair correlation function g(rω 1 ω 2 ), including first- and second-order perturbation theory (the u-expansion), a Pade approximant to this series, first-order f-expansion, the single superchain, generalized mean field, linearized hypernetted chain, and quadratic hypernetted chain approximations. Numerical results from these theories are compared with available computer simulation data for four model fluids whose intermolecular pair potential is of the form u 0 +usub(a), where u 0 is a hard-sphere of Lennard-Jones model, while usub(a) is a dipole-dipole or quadrupole-quadrupole interaction; we refer to these model fluids as HS+μμ, HS+QQ, LJ+μμ, and LJ+QQ. Properties studied include the angular pair correlation function and its spherical harmonic components, the thermodynamic properties, and the angular correlation parameters G 1 and G 2 that are related to the dielectric and Kerr constants. The second-order perturbation theory is superior to the integral equation theories for the thermodynamic harmonics of g(rω 1 ω 2 ) and for the thermodynamic properties themselves at moderate multipole strengths. For other harmonics and properties, the integral equation theories are better, with the quadratic hypernetted chain approximation being the best overall. (orig.)
Condensation and evaporation transitions in deep capillary grooves.
Malijevský, Alexandr; Parry, Andrew O
2014-09-03
We study the order of capillary condensation and evaporation transitions of a simple fluid adsorbed in a deep capillary groove using a fundamental measure density functional theory (DFT). The walls of the capillary interact with the fluid particles via long-ranged, dispersion, forces while the fluid-fluid interaction is modelled as a truncated Lennard-Jones-like potential. We find that below the wetting temperature Tw condensation is first-order and evaporation is continuous with the metastability of the condensation being well described by the complementary Kelvin equation. In contrast above Tw both phase transitions are continuous and their critical singularities are determined. In addition we show that for the evaporation transition above Tw there is an elegant mapping, or covariance, with the complete wetting transition occurring at a planar wall. Our numerical DFT studies are complemented by analytical slab model calculations which explain how the asymmetry between condensation and evaporation arises out of the combination of long-ranged forces and substrate geometry.
Parallel continuous simulated tempering and its applications in large-scale molecular simulations
Energy Technology Data Exchange (ETDEWEB)
Zang, Tianwu; Yu, Linglin; Zhang, Chong [Applied Physics Program and Department of Bioengineering, Rice University, Houston, Texas 77005 (United States); Ma, Jianpeng, E-mail: jpma@bcm.tmc.edu [Applied Physics Program and Department of Bioengineering, Rice University, Houston, Texas 77005 (United States); Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, Texas 77030 (United States)
2014-07-28
In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); C. Zhang and J. Ma, J. Chem. Phys. 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2–3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard-Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent.
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.
Nanotube bundle oscillators: Carbon and boron nitride nanostructures
International Nuclear Information System (INIS)
Thamwattana, Ngamta; Hill, James M.
2009-01-01
In this paper, we investigate the oscillation of a fullerene that is moving within the centre of a bundle of nanotubes. In particular, certain fullerene-nanotube bundle oscillators, namely C 60 -carbon nanotube bundle, C 60 -boron nitride nanotube bundle, B 36 N 36 -carbon nanotube bundle and B 36 N 36 -boron nitride nanotube bundle are studied using the Lennard-Jones potential and the continuum approach which assumes a uniform distribution of atoms on the surface of each molecule. We address issues regarding the maximal suction energies of the fullerenes which lead to the generation of the maximum oscillation frequency. Since bundles are also found to comprise double-walled nanotubes, this paper also examines the oscillation of a fullerene inside a double-walled nanotube bundle. Our results show that the frequencies obtained for the oscillation within double-walled nanotube bundles are slightly higher compared to those of single-walled nanotube bundle oscillators. Our primary purpose here is to extend a number of established results for carbon to the boron nitride nanostructures.
Theory for the three-dimensional Mercedes-Benz model of water
Bizjak, Alan; Urbic, Tomaz; Vlachy, Vojko; Dill, Ken A.
2009-11-01
The two-dimensional Mercedes-Benz (MB) model of water has been widely studied, both by Monte Carlo simulations and by integral equation methods. Here, we study the three-dimensional (3D) MB model. We treat water as spheres that interact through Lennard-Jones potentials and through a tetrahedral Gaussian hydrogen bonding function. As the "right answer," we perform isothermal-isobaric Monte Carlo simulations on the 3D MB model for different pressures and temperatures. The purpose of this work is to develop and test Wertheim's Ornstein-Zernike integral equation and thermodynamic perturbation theories. The two analytical approaches are orders of magnitude more efficient than the Monte Carlo simulations. The ultimate goal is to find statistical mechanical theories that can efficiently predict the properties of orientationally complex molecules, such as water. Also, here, the 3D MB model simply serves as a useful workbench for testing such analytical approaches. For hot water, the analytical theories give accurate agreement with the computer simulations. For cold water, the agreement is not as good. Nevertheless, these approaches are qualitatively consistent with energies, volumes, heat capacities, compressibilities, and thermal expansion coefficients versus temperature and pressure. Such analytical approaches offer a promising route to a better understanding of water and also the aqueous solvation.
Theory for the three-dimensional Mercedes-Benz model of water.
Bizjak, Alan; Urbic, Tomaz; Vlachy, Vojko; Dill, Ken A
2009-11-21
The two-dimensional Mercedes-Benz (MB) model of water has been widely studied, both by Monte Carlo simulations and by integral equation methods. Here, we study the three-dimensional (3D) MB model. We treat water as spheres that interact through Lennard-Jones potentials and through a tetrahedral Gaussian hydrogen bonding function. As the "right answer," we perform isothermal-isobaric Monte Carlo simulations on the 3D MB model for different pressures and temperatures. The purpose of this work is to develop and test Wertheim's Ornstein-Zernike integral equation and thermodynamic perturbation theories. The two analytical approaches are orders of magnitude more efficient than the Monte Carlo simulations. The ultimate goal is to find statistical mechanical theories that can efficiently predict the properties of orientationally complex molecules, such as water. Also, here, the 3D MB model simply serves as a useful workbench for testing such analytical approaches. For hot water, the analytical theories give accurate agreement with the computer simulations. For cold water, the agreement is not as good. Nevertheless, these approaches are qualitatively consistent with energies, volumes, heat capacities, compressibilities, and thermal expansion coefficients versus temperature and pressure. Such analytical approaches offer a promising route to a better understanding of water and also the aqueous solvation.
Clustering methods for the optimization of atomic cluster structure
Bagattini, Francesco; Schoen, Fabio; Tigli, Luca
2018-04-01
In this paper, we propose a revised global optimization method and apply it to large scale cluster conformation problems. In the 1990s, the so-called clustering methods were considered among the most efficient general purpose global optimization techniques; however, their usage has quickly declined in recent years, mainly due to the inherent difficulties of clustering approaches in large dimensional spaces. Inspired from the machine learning literature, we redesigned clustering methods in order to deal with molecular structures in a reduced feature space. Our aim is to show that by suitably choosing a good set of geometrical features coupled with a very efficient descent method, an effective optimization tool is obtained which is capable of finding, with a very high success rate, all known putative optima for medium size clusters without any prior information, both for Lennard-Jones and Morse potentials. The main result is that, beyond being a reliable approach, the proposed method, based on the idea of starting a computationally expensive deep local search only when it seems worth doing so, is capable of saving a huge amount of searches with respect to an analogous algorithm which does not employ a clustering phase. In this paper, we are not claiming the superiority of the proposed method compared to specific, refined, state-of-the-art procedures, but rather indicating a quite straightforward way to save local searches by means of a clustering scheme working in a reduced variable space, which might prove useful when included in many modern methods.
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
GPU-accelerated Gibbs ensemble Monte Carlo simulations of Lennard-Jonesium
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].
Pazzona, Federico G.; Pireddu, Giovanni; Gabrieli, Andrea; Pintus, Alberto M.; Demontis, Pierfranco
2018-05-01
We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely accepted approach, in which the contributions to the free energy given by the molecules located in two neighboring pores are estimated through Monte Carlo simulations where the two pores are kept separated from the rest of the system, leads to inaccurate results at high sorbate densities. In the coarse-graining strategy that we propose, which is based on the Bethe-Peierls approximation, density-independent interaction terms are instead computed according to local effective potentials that take into account the correlations between the pore pair and its surroundings by means of mean-field correction terms without the need for simulating the pore pair separately. Use of the interaction parameters obtained this way allows the coarse-grained system to reproduce more closely the equilibrium properties of the original one. Results are shown for lattice-gases where the local free energy can be computed exactly and for a system of Lennard-Jones particles under the effect of a static confining field.
Dynamic Simulation of Random Packing of Polydispersive Fine Particles
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.
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)
Analysis of topological relationships and network properties in the interactions of human beings.
Directory of Open Access Journals (Sweden)
Ye Yuan
Full Text Available In the animal world, various kinds of collective motions have been found and proven to be efficient ways of carrying out some activities such as searching for food and avoiding predators. Many scholars research the interactions of collective behaviors of human beings according to the rules of collective behaviors of animals. Based on the Lennard-Jones potential function and a self-organization process, our paper proposes a topological communication model to simulate the collective behaviors of human beings. In the results of simulations, we find various types of collective behavior and fission behavior and discover the threshold for the emergence of collective behavior, which is the range five to seven for the number of topology K. According to the analysis of network properties of the model, the in-degree of individuals is always equal to the number of topology. In the stable state, the out-degrees of individuals distribute around the value of the number of topology K, except that the out-degree of a single individual is approximately double the out-degrees of the other individuals. In addition, under different initial conditions, some features of different kinds of networks emerge from the model. We also find the leader and herd mentality effects in the characteristics of the behaviors of human beings in our model. Thus, this work could be used to discover how to promote the emergence of beneficial group behaviors and prevent the emergence of harmful behaviors.
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
Extension of Kirkwood-Buff theory to the canonical ensemble
Rogers, David M.
2018-02-01
Kirkwood-Buff (KB) integrals are notoriously difficult to converge from a canonical simulation because they require estimating the grand-canonical radial distribution. The same essential difficulty is encountered when attempting to estimate the direct correlation function of Ornstein-Zernike theory by inverting the pair correlation functions. We present a new theory that applies to the entire, finite, simulation volume, so that no cutoff issues arise at all. The theory gives the direct correlation function for closed systems, while smoothness of the direct correlation function in reciprocal space allows calculating canonical KB integrals via a well-posed extrapolation to the origin. The present analysis method represents an improvement over previous work because it makes use of the entire simulation volume and its convergence can be accelerated using known properties of the direct correlation function. Using known interaction energy functions can make this extrapolation near perfect accuracy in the low-density case. Because finite size effects are stronger in the canonical than in the grand-canonical ensemble, we state ensemble correction formulas for the chemical potential and the KB coefficients. The new theory is illustrated with both analytical and simulation results on the 1D Ising model and a supercritical Lennard-Jones fluid. For the latter, the finite-size corrections are shown to be small.
Huge-scale molecular dynamics simulation of multibubble nuclei
Watanabe, Hiroshi
2013-12-01
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.
Interface structure and mechanics between graphene and metal substrates: a first-principles study
Xu, Zhiping; Buehler, Markus J.
2010-12-01
Graphene is a fascinating material not only for technological applications, but also as a test bed for fundamental insights into condensed matter physics due to its unique two-dimensional structure. One of the most intriguing issues is the understanding of the properties of graphene and various substrate materials. In particular, the interfaces between graphene and metal substrates are of critical importance in applications of graphene in integrated electronics, as thermal materials, and in electromechanical devices. Here we investigate the structure and mechanical interactions at a graphene-metal interface through density functional theory (DFT)-based calculations. We focus on copper (111) and nickel (111) surfaces adhered to a monolayer of graphene, and find that their cohesive energy, strength and electronic structure correlate directly with their atomic geometry. Due to the strong coupling between open d-orbitals, the nickel-graphene interface has a much stronger cohesive energy with graphene than copper. We also find that the interface cohesive energy profile features a well-and-shoulder shape that cannot be captured by simple pair-wise models such as the Lennard-Jones potential. Our results provide a detailed understanding of the interfacial properties of graphene-metal systems, and help to predict the performance of graphene-based nanoelectronics and nanocomposites. The availability of structural and energetic data of graphene-metal interfaces could also be useful for the development of empirical force fields for molecular dynamics simulations.
DEFF Research Database (Denmark)
Mikkelsen, Henrik Hvenegaard; Friis Søgaard, Thomas
2016-01-01
as ‘performed violent potentiality’ plays a critical role in relation to Bugkalot men’s construction of hegemonic masculinity and the sustaining of complex egalitarian relations. The Bugkalot have a notoriously violent history; until the late 1970s more than half of the adult men engaged in ritual killings...... provide general insights that can also be used in other contexts to understand how men construct hegemonic masculinity by strategically adopting the interspace of civility and violence.......This article explores the social significance of violence as potentiality and performance among former headhunters engaged in ritual killings. Taking its outset in an ethnographic study of violence and masculinity among the Philippine people known as the Bugkalot, we explore how violence...
Contact angle dependence on the fluid-wall dispersive energy
Horsch, M.; Heitzig, M.; Dan, C.M.; Harting, J.D.R.; Hasse, H.; Vrabec, J.
2010-01-01
Menisci of the truncated and shifted Lennard-Jones fluid between parallel planar walls are investigated by molecular dynamics simulation. Thereby, the characteristic energy of the unlike dispersive interaction between fluid molecules and wall atoms is systematically varied to determine its influence
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
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...
Switching Between the NVT and NpT Ensembles Using the Reweighting and Reconstruction Scheme
Kadoura, Ahmad Salim; Salama, Amgad; Sun, Shuyu
2015-01-01
thermodynamic conditions from a single MC Markov chain. The latter scheme, was first developed to extrapolate quantities in NV T ensemble for struc- tureless Lennard-Jones particles. However, it is evident that for most real life applications the NpT ensemble
Validity of the Rosenfeld relationship: A comparative study of the ...
Indian Academy of Sciences (India)
ATREYEE BANERJEE
we find that the NTW model has mixed characteristics of simple liquids and ionic melts. Our study further ... and the value of the Rosenfeld exponents are differ- ent from that found for ..... Lennard-Jones chains J. Chem. Phys. 129 164904. 4.
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....
Gas Enrichment at Liquid-Wall Interfaces
Dammer, S.M.; Lohse, Detlef
2006-01-01
Molecular dynamics simulations of Lennard-Jones systems are performed to study the effects of dissolved gas on liquid-wall and liquid-gas interfaces. Gas enrichment at walls, which for hydrophobic walls can exceed more than 2 orders of magnitude when compared to the gas density in the bulk liquid,
Density scaling and quasiuniversality of flow-event statistics for athermal plastic flows
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
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 ...
Calculation of partial enthalpies in argon-krypton mixtures by NPT molecular dynamics
Sindzingre, P.; Massobrio, C.; Ciccotti, G.; Frenkel, D.
1989-01-01
In an earlier paper, we have indicated how, by using a particle-insertion technique, partial molar enthalpies and related quantities can be evaluated from simulations on a single state point. In the present paper we apply this method to a Lennard-Jones argon-krypton mixture. For this particular
Boundary layer energies for nonconvex discrete systems
Scardia, L.; Schlömerkemper, A.; Zanini, C.
2011-01-01
In this work we consider a one-dimensional chain of atoms which interact through nearest and next-to-nearest neighbour interactions of Lennard-Jones type. We impose Dirichlet boundary conditions and in addition prescribe the deformation of the second and last but one atoms of the chain. This
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.
Structure and stability of small Li2 +(X2Σ+ g )-Xen (n = 1-6) clusters
Saidi, Sameh; Ghanmi, Chedli; Berriche, Hamid
2014-04-01
We have studied the structure and stability of the Li2 +(X2Σ+ g )Xe n ( n = 1-6) clusters for special symmetry groups. The potential energy surfaces of these clusters, are described using an accurate ab initio approach based on non-empirical pseudopotential, parameterized l-dependent polarization potential and analytic potential forms for the Li+Xe and Xe-Xe interactions. The pseudopotential technique has reduced the number of active electrons of Li2 +(X2Σ+ g )-Xe n ( n = 1-6) clusters to only one electron, the Li valence electron. The core-core interactions for Li+Xe are included using accurate CCSD(T) potential fitted using the analytical form of Tang and Toennies. For the Xe-Xe potential interactions we have used the analytical form of Lennard Jones (LJ6 - 12). The potential energy surfaces of the Li2 +(X2Σ+ g )Xe n ( n = 1-6) clusters are performed for a fixed distance of the Li2 +(X2Σ+ g ) alkali dimer, its equilibrium distance. They are used to extract information on the stability of the Li2 +(X2Σ+ g Xe n ( n = 1-6) clusters. For each n, the stability of the different isomers is examined by comparing their potential energy surfaces. Moreover, we have determined the quantum energies ( D 0), the zero-point-energies (ZPE) and the ZPE%. To our best knowledge, there are neither experimental nor theoretical works realized for the Li2 +(X2Σ+ g Xe n ( n = 1-6) clusters, our results are presented for the first time.
Evaluation of the accuracy of the free-energy-minimization method
International Nuclear Information System (INIS)
Najafabadi, R.; Srolovitz, D.J.
1995-01-01
We have made a detailed comparison between three competing methods for determining the free energies of solids and their defects: the thermodynamic integration of Monte Carlo (TIMC) data, the quasiharmonic (QH) model, and the free-energy-minimization (FEM) method. The accuracy of these methods decreases from the TIMC to QH to FEM method, while the computational efficiency improves in that order. All three methods yield perfect crystal lattice parameters and free energies at finite temperatures which are in good agreement for three different Cu interatomic potentials [embedded atom method (EAM), Morse and Lennard-Jones]. The FEM error (relative to the TIMC) in the (001) surface free energy and in the vacancy formation energy were found to be much larger for the EAM potential than for the other two potentials. Part of the errors in the FEM determination of the free energies are associated with anharmonicities in the interatomic potentials, with the remainder attributed to decoupling of the atomic vibrations. The anharmonicity of the EAM potential was found to be unphysically large compared with experimental vacancy formation entropy determinations. Based upon these results, we show that the FEM method provides a reasonable compromise between accuracy and computational demands. However, the accuracy of this approach is sensitive to the choice of interatomic potential and the nature of the defect to which it is being applied. The accuracy of the FEM is best in high-symmetry environments (perfect crystal, high-symmetry defects, etc.) and when used to describe materials where the anharmonicity is not too large
Thermal transpiration: A molecular dynamics study
Energy Technology Data Exchange (ETDEWEB)
T, Joe Francis [Computational Nanotechnology Laboratory, School of Nano Science and Technology, National Institute of Technology Calicut, Kozhikode (India); Sathian, Sarith P. [Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai (India)
2014-12-09
Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.
Molecular dynamics studies of transport properties and equation of state of supercritical fluids
Nwobi, Obika C.
Many chemical propulsion systems operate with one or more of the reactants above the critical point in order to enhance their performance. Most of the computational fluid dynamics (CFD) methods used to predict these flows require accurate information on the transport properties and equation of state at these supercritical conditions. This work involves the determination of transport coefficients and equation of state of supercritical fluids by equilibrium molecular dynamics (MD) simulations on parallel computers using the Green-Kubo formulae and the virial equation of state, respectively. MD involves the solution of equations of motion of a system of molecules that interact with each other through an intermolecular potential. Provided that an accurate potential can be found for the system of interest, MD can be used regardless of the phase and thermodynamic conditions of the substances involved. The MD program uses the effective Lennard-Jones potential, with system sizes of 1000-1200 molecules and, simulations of 2,000,000 time-steps for computing transport coefficients and 200,000 time-steps for pressures. The computer code also uses linked cell lists for efficient sorting of molecules, periodic boundary conditions, and a modified velocity Verlet algorithm for particle displacement. Particle decomposition is used for distributing the molecules to different processors of a parallel computer. Simulations have been carried out on pure argon, nitrogen, oxygen and ethylene at various supercritical conditions, with self-diffusion coefficients, shear viscosity coefficients, thermal conductivity coefficients and pressures computed for most of the conditions. Results compare well with experimental and the National Institute of Standards and Technology (NIST) values. The results show that the number of molecules and the potential cut-off radius have no significant effect on the computed coefficients, while long-time integration is necessary for accurate determination of the
Polymer deformation in Brownian ratchets: theory and molecular dynamics simulations.
Kenward, Martin; Slater, Gary W
2008-11-01
We examine polymers in the presence of an applied asymmetric sawtooth (ratchet) potential which is periodically switched on and off, using molecular dynamics (MD) simulations with an explicit Lennard-Jones solvent. We show that the distribution of the center of mass for a polymer in a ratchet is relatively wide for potential well depths U0 on the order of several kBT. The application of the ratchet potential also deforms the polymer chains. With increasing U0 the Flory exponent varies from that for a free three-dimensional (3D) chain, nu=35 (U0=0), to that corresponding to a 2D compressed (pancake-shaped) polymer with a value of nu=34 for moderate U0. This has the added effect of decreasing a polymer's diffusion coefficient from its 3D value D3D to that of a pancaked-shaped polymer moving parallel to its minor axis D2D. The result is that a polymer then has a time-dependent diffusion coefficient D(t) during the ratchet off time. We further show that this suggests a different method to operate a ratchet, where the off time of the ratchet, toff, is defined in terms of the relaxation time of the polymer, tauR. We also derive a modified version of the Bader ratchet model [Bader, Proc. Natl. Acad. Sci. U.S.A. 96, 13165 (1999)] which accounts for this deformation and we present a simple expression to describe the time dependent diffusion coefficient D(t). Using this model we then illustrate that polymer deformation can be used to modulate polymer migration in a ratchet potential.
Modeling the liquid-liquid interface and the transfer of a solute by molecular dynamics simulation
International Nuclear Information System (INIS)
Hayoun, Marc
1990-11-01
Molecular Dynamics method and Lennard-Jones potential functions have been employed to model Liquid-Liquid Interfaces. The variation of the miscibilities between the two liquids is obtained by changing the interaction between the two atomic species. The resulting interfaces have a thickness of about three atomic diameters and are stable on the time scale of the simulation. They have been characterized by the density and pressure profiles. The interfacial tension has also been computed and is of the order of magnitude of experimental values. The diffusion process is anisotropic in the interfacial region: the transverse diffusion coefficient (parallelly to the interface) is higher than the normal one. A qualitative explanation of this behaviour is suggested by considering the pressure tensor. The second part of this work, performed by Molecular Dynamics in the canonical ensemble, is devoted to the kinetic study of the transfer of a solute through the interface. A model of a symmetric interface with an atomic solute has been used. The interaction potential between the solute and the solvents has been built in order to obtain an activation barrier to the transfer. We have computed the mean force exerted by the solvent on the solute as a function of its distance to the interface. The resulting mean force potential corresponds to a free energy difference. The height of the energy barrier involved is about 4 kT. The potential energy and entropy profiles have also been calculated and discussed. The diffusion coefficient of the solute has been computed by equilibrium and non-equilibrium methods. We deduced the friction coefficient of the solvent, which is essential to determine the Kramers transmission coefficient. This coefficient is compared to the one obtained by simulation. Finally, the solute transfer rate constant has been calculated. (author) [fr
Towards understanding the structure and capacitance of electrical double layer in ionic liquids
Energy Technology Data Exchange (ETDEWEB)
Fedorov, Maxim V. [Max Planck Institute for Mathematics in the Sciences, D 04103 Leipzig (Germany); Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Kornyshev, Alexei A. [Department of Chemistry, Faculty of Natural Sciences, Imperial College London, SW7 2AZ London (United Kingdom)
2008-10-01
In order to understand basic principles of the double layer formation in room temperature ionic liquids, we have performed Molecular Dynamic simulations for a simplified system: dense assembly of charged Lennard-Jones spheres between charged walls. For simplicity, in this first investigation we have considered the cations and anions of the same size. We have calculated the corresponding values of the double layer capacitance as a function of the electrode potential and compared the results with existing theories. We have found that the capacitance curve does not follow the U-shape of the Gouy-Chapman theory, but has a bell-shape in agreement with the mean-field theory that takes into account the effect of limited maximum packing of ions. The wings of capacitance decrease inversely proportional to the square root of the electrode potential, as prescribed by the mean-field theory and the charge conservation law at large electrode polarizations. We have found, however, that the mean-field theory does not quantitatively reproduce the simulation results at small electrode potentials, having detected their remarkable overscreening effects (ionic correlations). The plots for the distributions of ions near the electrode at different electrode charges show that for the considered system, unlike it is often assumed, the double layer is not one layer thick. The overscreening effects, dominating near the potential of zero charge (p.z.c.), are suppressed by the high electrode polarizations, following the onset of the so-called 'lattice saturation effect'. The maximum of the capacitance coincides with the p.z.c., but it is true only for this 'symmetric' system. If sizes of cations and anions are different the maximum will be shifted away from the p.z.c., and generally the shape of the capacitance curve could be more complicated. (author)
Hiroshi Uno
2007-01-01
This paper proposes a new class of potential games, the nested potential games, which generalize the potential games defined in Monderer and Shapley (1996), as well as the pseudo-potential games defined in Dubey et al. (2006). We show that each maximizer of a nested potential is a Nash equilibrium.
Das, Subir K; Egorov, Sergei A; Virnau, Peter; Winter, David; Binder, Kurt
2018-06-27
Results from Monte Carlo simulations of wall-attached droplets in the three-dimensional Ising lattice gas model and in a symmetric binary Lennard-Jones fluid, confined by antisymmetric walls, are analyzed, with the aim to estimate the dependence of the contact angle [Formula: see text] on the droplet radius [Formula: see text] of curvature. Sphere-cap shape of the wall-attached droplets is assumed throughout. An approach, based purely on 'thermodynamic' observables, e.g. chemical potential, excess density due to the droplet, etc, is used, to avoid ambiguities in the decision which particles belong (or do not belong, respectively) to the droplet. It is found that the results are compatible with a variation [Formula: see text], [Formula: see text] being the contact angle in the thermodynamic limit ([Formula: see text]). The possibility to use such results to estimate the excess free energy related to the contact line of the droplet, namely the line tension, at the wall, is discussed. Various problems that hamper this approach and were not fully recognized in previous attempts to extract the line tension are identified. It is also found that the dependence of wall tensions on the difference of chemical potential of the droplet from that at the bulk coexistence provides effectively a change of the contact angle of similar magnitude. The simulation approach yields precise estimates for the excess density due to wall-attached droplets and the corresponding free energy excess, relative to a system without a droplet at the same chemical potential. It is shown that this information suffices to estimate nucleation barriers, not affected by ambiguities on droplet shape, contact angle and line tension.
Milchev, Andrey; Egorov, Sergei A; Binder, Kurt
2017-03-01
Semiflexible polymers under good solvent conditions interacting with attractive planar surfaces are investigated by Molecular Dynamics (MD) simulations and classical Density Functional Theory (DFT). A bead-spring type potential complemented by a bending potential is used, allowing variation of chain stiffness from completely flexible coils to rod-like polymers whose persistence length by far exceeds their contour length. Solvent is only implicitly included, monomer-monomer interactions being purely repulsive, while two types of attractive wall-monomer interactions are considered: (i) a strongly attractive Mie-type potential, appropriate for a strictly structureless wall, and (ii) a corrugated wall formed by Lennard-Jones particles arranged on a square lattice. It is found that in dilute solutions the former case leads to the formation of a strongly adsorbed surface layer, and the profile of density and orientational order in the z-direction perpendicular to the wall is predicted by DFT in nice agreement with MD. While for very low bulk densities a Kosterlitz-Thouless type transition from the isotropic phase to a phase with power-law decay of nematic correlations is suggested to occur in the strongly adsorbed layer, for larger densities a smectic-C phase in the surface layer is detected. No "capillary nematization" effect at higher bulk densities is found in this system, unlike systems with repulsive walls. This finding is attributed to the reduction of the bulk density (in the center of the slit pore) due to polymer adsorption on the attractive wall, for a system studied in the canonical ensemble. Consequently in a system with two attractive walls nematic order in the slit pore can occur only at a higher density than for a bulk system.
Phonon Scattering and Confinement in Crystalline Films
Parrish, Kevin D.
The operating temperature of energy conversion and electronic devices affects their efficiency and efficacy. In many devices, however, the reference values of the thermal properties of the materials used are no longer applicable due to processing techniques performed. This leads to challenges in thermal management and thermal engineering that demand accurate predictive tools and high fidelity measurements. The thermal conductivity of strained, nanostructured, and ultra-thin dielectrics are predicted computationally using solutions to the Boltzmann transport equation. Experimental measurements of thermal diffusivity are performed using transient grating spectroscopy. The thermal conductivities of argon, modeled using the Lennard-Jones potential, and silicon, modeled using density functional theory, are predicted under compressive and tensile strain from lattice dynamics calculations. The thermal conductivity of silicon is found to be invariant with compression, a result that is in disagreement with previous computational efforts. This difference is attributed to the more accurate force constants calculated from density functional theory. The invariance is found to be a result of competing effects of increased phonon group velocities and decreased phonon lifetimes, demonstrating how the anharmonic contribution of the atomic potential can scale differently than the harmonic contribution. Using three Monte Carlo techniques, the phonon-boundary scattering and the subsequent thermal conductivity reduction are predicted for nanoporous silicon thin films. The Monte Carlo techniques used are free path sampling, isotropic ray-tracing, and a new technique, modal ray-tracing. The thermal conductivity predictions from all three techniques are observed to be comparable to previous experimental measurements on nanoporous silicon films. The phonon mean free paths predicted from isotropic ray-tracing, however, are unphysical as compared to those predicted by free path sampling
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.
Molecular dynamics simulations of bubble nucleation in dark matter detectors.
Denzel, Philipp; Diemand, Jürg; Angélil, Raymond
2016-01-01
Bubble chambers and droplet detectors used in dosimetry and dark matter particle search experiments use a superheated metastable liquid in which nuclear recoils trigger bubble nucleation. This process is described by the classical heat spike model of F. Seitz [Phys. Fluids (1958-1988) 1, 2 (1958)PFLDAS0031-917110.1063/1.1724333], which uses classical nucleation theory to estimate the amount and the localization of the deposited energy required for bubble formation. Here we report on direct molecular dynamics simulations of heat-spike-induced bubble formation. They allow us to test the nanoscale process described in the classical heat spike model. 40 simulations were performed, each containing about 20 million atoms, which interact by a truncated force-shifted Lennard-Jones potential. We find that the energy per length unit needed for bubble nucleation agrees quite well with theoretical predictions, but the allowed spike length and the required total energy are about twice as large as predicted. This could be explained by the rapid energy diffusion measured in the simulation: contrary to the assumption in the classical model, we observe significantly faster heat diffusion than the bubble formation time scale. Finally we examine α-particle tracks, which are much longer than those of neutrons and potential dark matter particles. Empirically, α events were recently found to result in louder acoustic signals than neutron events. This distinction is crucial for the background rejection in dark matter searches. We show that a large number of individual bubbles can form along an α track, which explains the observed larger acoustic amplitudes.
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.
The effect of substrate on thermodynamic and kinetic anisotropies in atomic thin films.
Haji-Akbari, Amir; Debenedetti, Pablo G
2014-07-14
Glasses have a wide range of technological applications. The recent discovery of ultrastable glasses that are obtained by depositing the vapor of a glass-forming liquid onto the surface of a cold substrate has sparked renewed interest in the effects of confinements on physicochemical properties of liquids and glasses. Here, we use molecular dynamics simulations to study the effect of substrate on thin films of a model glass-forming liquid, the Kob-Andersen binary Lennard-Jones system, and compute profiles of several thermodynamic and kinetic properties across the film. We observe that the substrate can induce large oscillations in profiles of thermodynamic properties such as density, composition, and stress, and we establish a correlation between the oscillations in total density and the oscillations in normal stress. We also demonstrate that the kinetic properties of an atomic film can be readily tuned by changing the strength of interactions between the substrate and the liquid. Most notably, we show that a weakly attractive substrate can induce the emergence of a highly mobile region in its vicinity. In this highly mobile region, structural relaxation is several times faster than in the bulk, and the exploration of the potential energy landscape is also more efficient. In the subsurface region near a strongly attractive substrate, however, the dynamics is decelerated and the sampling of the potential energy landscape becomes less efficient than the bulk. We explain these two distinct behaviors by establishing a correlation between the oscillations in kinetic properties and the oscillations in lateral stress. Our findings offer interesting opportunities for designing better substrates for the vapor deposition process or developing alternative procedures for situations where vapor deposition is not feasible.
The effect of substrate on thermodynamic and kinetic anisotropies in atomic thin films
Energy Technology Data Exchange (ETDEWEB)
Haji-Akbari, Amir; Debenedetti, Pablo G., E-mail: pdebene@exchange.princeton.edu [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States)
2014-07-14
Glasses have a wide range of technological applications. The recent discovery of ultrastable glasses that are obtained by depositing the vapor of a glass-forming liquid onto the surface of a cold substrate has sparked renewed interest in the effects of confinements on physicochemical properties of liquids and glasses. Here, we use molecular dynamics simulations to study the effect of substrate on thin films of a model glass-forming liquid, the Kob-Andersen binary Lennard-Jones system, and compute profiles of several thermodynamic and kinetic properties across the film. We observe that the substrate can induce large oscillations in profiles of thermodynamic properties such as density, composition, and stress, and we establish a correlation between the oscillations in total density and the oscillations in normal stress. We also demonstrate that the kinetic properties of an atomic film can be readily tuned by changing the strength of interactions between the substrate and the liquid. Most notably, we show that a weakly attractive substrate can induce the emergence of a highly mobile region in its vicinity. In this highly mobile region, structural relaxation is several times faster than in the bulk, and the exploration of the potential energy landscape is also more efficient. In the subsurface region near a strongly attractive substrate, however, the dynamics is decelerated and the sampling of the potential energy landscape becomes less efficient than the bulk. We explain these two distinct behaviors by establishing a correlation between the oscillations in kinetic properties and the oscillations in lateral stress. Our findings offer interesting opportunities for designing better substrates for the vapor deposition process or developing alternative procedures for situations where vapor deposition is not feasible.
Baker, Thomas A.; Gellene, Gregory I.
2002-10-01
The isotope exchange reaction, and the three-body ozone formation rate proceeding through an ozone complex, have been studied by classical and quasi-classical trajectory techniques. The exchange rate studies indicate that the rate of this reaction is dominantly sensitive to the O+O2 entrance channel characteristics of the potential energy surface. A detailed consideration of the dynamics of the intermediate ozone complex reveals three important classes. In one class, the complex adopts an ozonelike geometry, largely undergoing asymmetric stretchinglike motion until it dissociates. In a second class, the oxygen atom and molecule never visit the ozonelike geometry but rather remain separated by relatively large distances trapped near the angular momentum barrier in the entrance channel of a pseudo-effective potential. These complexes, which cannot undergo exchange, are, nevertheless, found to contribute significantly to ozone formation at high density of the third body suggesting that the association of the high-density effective formation rate constant with twice the exchange rate may not be valid. The third class can be considered a hybrid of the first two, spending some time as an ozonelike complex and some time as a large atom-diatomic complex. This third class provides a mechanism for rearranging atom locations in the complex (e.g., end and middle position swapping) and, consequently, would not be well accounted for by statistical treatments of the ozone complex based on a single ozonelike reference geometry. In general, the survival time distributions of the complexes are found to be nonexponential. However, when the detailed survival time distributions are coupled with a Lennard-Jones collision model for the stabilization step, the experimental ozone formation rate can be adequately modeled over a broad range of temperature and density.
The effect of substrate on thermodynamic and kinetic anisotropies in atomic thin films
International Nuclear Information System (INIS)
Haji-Akbari, Amir; Debenedetti, Pablo G.
2014-01-01
Glasses have a wide range of technological applications. The recent discovery of ultrastable glasses that are obtained by depositing the vapor of a glass-forming liquid onto the surface of a cold substrate has sparked renewed interest in the effects of confinements on physicochemical properties of liquids and glasses. Here, we use molecular dynamics simulations to study the effect of substrate on thin films of a model glass-forming liquid, the Kob-Andersen binary Lennard-Jones system, and compute profiles of several thermodynamic and kinetic properties across the film. We observe that the substrate can induce large oscillations in profiles of thermodynamic properties such as density, composition, and stress, and we establish a correlation between the oscillations in total density and the oscillations in normal stress. We also demonstrate that the kinetic properties of an atomic film can be readily tuned by changing the strength of interactions between the substrate and the liquid. Most notably, we show that a weakly attractive substrate can induce the emergence of a highly mobile region in its vicinity. In this highly mobile region, structural relaxation is several times faster than in the bulk, and the exploration of the potential energy landscape is also more efficient. In the subsurface region near a strongly attractive substrate, however, the dynamics is decelerated and the sampling of the potential energy landscape becomes less efficient than the bulk. We explain these two distinct behaviors by establishing a correlation between the oscillations in kinetic properties and the oscillations in lateral stress. Our findings offer interesting opportunities for designing better substrates for the vapor deposition process or developing alternative procedures for situations where vapor deposition is not feasible
International Nuclear Information System (INIS)
Valkealahti, Seppo.
1987-10-01
Monte Carlo simulation is used to investigate positron and electron slowing down in solid matter. The description of elastic scattering is based on accurate cross sections of effective crystalline atom potentials. Inelastic processes are described separately for each energby level y Gryzinski's excitation function. Various materials are studied and several electron and positron slowing down parameters and distributions are extracted. The results are used to analyze and interprete a number of recent experiments utilizing keV electron and positron beams. Molecular dynamics simulation methods are used to study (i) damage production in aluminum (110) surfaces due to low-energy argon ion bombardment and (ii) the premelting effects of solid noble gas surfaces. Appropriately constructed pair potentials were assigned between the particles and an electronic friction term proportional to the velocity was used for energetic ions. Of particular interest in (i) are the defect and implanted atom distributions, which are compared against recent experiments. In (ii) the simulations show the equilibrium existence of liquid-like layers on the densely packed surfaces well below the bulk melting temperature. In (i) the mean vacancy concentration depth depends only slightly on the incident angle. The total number of vacancies is almost independent of the incident ion dose for very oblique angles of incidence (0>45 deg C). Vancancy profile is found to have a clear peak in the topmost atomic layers and a broader tail deep in the material. The interstitial and Ar + ion profiles are clearly deeper in the material than the vacancy profile. In (ii), a layer-by-layer premelting of Lennard-Jones (111) surfaces is observed. Also the (100) surfaces premelt, but the disordering mechanism for the loosely packed (110) surfaces is roughening. Furthermore, a general rule seems to be that melting proceeds along the directions of high packing densities
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
Low-Dimensional Materials for Optoelectronic and Bioelectronic Applications
Hong, Tu
In this thesis, we first discuss the fundamentals of ab initio electronic structure theory and density functional theory (DFT). We also discuss statistics related to computing thermodynamic averages of molecular dynamics (MD). We then use this theory to analyze and compare the structural, dynamical, and electronic properties of liquid water next to prototypical metals including platinum, graphite, and graphene. Our results are built on Born-Oppenheimer molecular dynamics (BOMD) generated using density functional theory (DFT) which explicitly include van der Waals (vdW) interactions within a first principles approach. All calculations reported use large simulation cells, allowing for an accurate treatment of the water-electrode interfaces. We have included vdW interactions through the use of the optB86b-vdW exchange correlation functional. Comparisons with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional are also shown. We find an initial peak, due to chemisorption, in the density profile of the liquid water-Pt interface not seen in the liquid water-graphite interface, liquid watergraphene interface, nor interfaces studied previously. To further investigate this chemisorption peak, we also report differences in the electronic structure of single water molecules on both Pt and graphite surfaces. We find that a covalent bond forms between the single water molecule and the platinum surface, but not between the single water molecule and the graphite surface. We also discuss the effects that defects and dopants in the graphite and graphene surfaces have on the structure and dynamics of liquid water. Lastly, we introduce artificial neural networks (ANNs), and demonstrate how they can be used to machine learn electronic structure calculations. As a proof of principle, we show the success of an ANN potential energy surfaces for a dimer molecule with a Lennard-Jones potential.
1D momentum-conserving systems: the conundrum of anomalous versus normal heat transport
Li, Yunyun; Liu, Sha; Li, Nianbei; Hänggi, Peter; Li, Baowen
2015-04-01
asymptotic free part (Lennard-Jones model). We compare our findings with recent predictions obtained from nonlinear fluctuating hydrodynamics theory.
Hoda, Nazish; Kumar, Satish
2007-12-01
The adsorption of single polyelectrolyte molecules in shear flow is studied using Brownian dynamics simulations with hydrodynamic interaction (HI). Simulations are performed with bead-rod and bead-spring chains, and electrostatic interactions are incorporated through a screened Coulombic potential with excluded volume accounted for by the repulsive part of a Lennard-Jones potential. A correction to the Rotne-Prager-Yamakawa tensor is derived that accounts for the presence of a planar wall. The simulations show that migration away from an uncharged wall, which is due to bead-wall HI, is enhanced by increases in the strength of flow and intrachain electrostatic repulsion, consistent with kinetic theory predictions. When the wall and polyelectrolyte are oppositely charged, chain behavior depends on the strength of electrostatic screening. For strong screening, chains get depleted from a region close to the wall and the thickness of this depletion layer scales as N1/3Wi2/3 at high Wi, where N is the chain length and Wi is the Weissenberg number. At intermediate screening, bead-wall electrostatic attraction competes with bead-wall HI, and it is found that there is a critical Weissenberg number for desorption which scales as N-1/2κ-3(lB∣σq∣)3/2, where κ is the inverse screening length, lB is the Bjerrum length, σ is the surface charge density, and q is the bead charge. When the screening is weak, adsorbed chains are observed to align in the vorticity direction at low shear rates due to the effects of repulsive intramolecular interactions. At higher shear rates, the chains align in the flow direction. The simulation method and results of this work are expected to be useful for a number of applications in biophysics and materials science in which polyelectrolyte adsorption plays a key role.
International Nuclear Information System (INIS)
Nadler, Boaz; Schuss, Zeev; Singer, Amit; Eisenberg, R S
2004-01-01
Ionic diffusion through and near small domains is of considerable importance in molecular biophysics in applications such as permeation through protein channels and diffusion near the charged active sites of macromolecules. The motion of the ions in these settings depends on the specific nanoscale geometry and charge distribution in and near the domain, so standard continuum type approaches have obvious limitations. The standard machinery of equilibrium statistical mechanics includes microscopic details, but is also not applicable, because these systems are usually not in equilibrium due to concentration gradients and to the presence of an external applied potential, which drive a non-vanishing stationary current through the system. We present a stochastic molecular model for the diffusive motion of interacting particles in an external field of force and a derivation of effective partial differential equations and their boundary conditions that describe the stationary non-equilibrium system. The interactions can include electrostatic, Lennard-Jones and other pairwise forces. The analysis yields a new type of Poisson-Nernst-Planck equations, that involves conditional and unconditional charge densities and potentials. The conditional charge densities are the non-equilibrium analogues of the well studied pair correlation functions of equilibrium statistical physics. Our proposed theory is an extension of equilibrium statistical mechanics of simple fluids to stationary non-equilibrium problems. The proposed system of equations differs from the standard Poisson-Nernst-Planck system in two important aspects. First, the force term depends on conditional densities and thus on the finite size of ions, and second, it contains the dielectric boundary force on a discrete ion near dielectric interfaces. Recently, various authors have shown that both of these terms are important for diffusion through confined geometries in the context of ion channels
Khadem, Masoud H; Wemhoff, Aaron P
2013-02-28
Non-equilibrium molecular dynamics (NEMD) simulations are used to investigate the thermal conductivity of herringbone graphite nanofibers (GNFs) at room temperature by breaking down the axial and transverse conductivity values into intralayer and interlayer components. The optimized Tersoff potential is used to account for intralayer carbon-carbon interactions while the Lennard-Jones potential is used to model the interlayer carbon-carbon interactions. The intralayer thermal conductivity of the graphene layers near room temperature is calculated for different crease angles and number of layers using NEMD with a constant applied heat flux. The edge effect on a layer's thermal conductivity is investigated by computing the thermal conductivity values in both zigzag and armchair directions of the heat flow. The interlayer thermal conductivity is also predicted by imposing hot and cold Nosé-Hoover thermostats on two layers. The limiting case of a 90° crease angle is used to compare the results with those of single-layer graphene and few-layer graphene. The axial and transverse thermal conductivities are then calculated using standard trigonometric conversions of the calculated intralayer and interlayer thermal conductivities, along with calculations of few-layer graphene without a crease. The results show a large influence of the crease angle on the intralayer thermal conductivity, and the saturation of thermal conductivity occurs when number of layers is more than three. The axial thermal conductivity, transverse thermal conductivity in the crease direction, and transverse thermal conductivity normal to the crease for the case of a five-layer herringbone GNF with a 45° crease angle are calculated to be 27 W∕m K, 263 W∕m K, and 1500 W∕m K, respectively, where the axial thermal conductivity is in good agreement with experimental measurements.
Significance of Nanoparticles and the Role of Amino Acids in Structuring Them-A Review.
Kulandaisamy, Arockia Jayalatha; Rayappan, John Bosco Balaguru
2018-08-01
Nanoparticles has occupied an eminent place in our tech-facilitated society. The processes involved in synthesizing nanoparticles are important not only to find their applications, but also to make them eco-friendly. Attempts are being made to replace the use of harmful surfactants/reagents by amino acids, in the due course of nanoparticle synthesis. Especially in synthesizing the multifunctional metal and metal oxide nanoparticles the use of amino acids as surfactant/as catalyst, helps to obtain required size and shape. Amino acids have the inherent property in directing and assembling the superstructures. They have the tendency to act as a capping agent and their presence during the synthesis processes alters the synthesized particles' morphology. Review has been made to study the role of amino acids like histidine, lysine, arginine in structuring ZnO, FeO, Au and Ag nanoparticles. The change in their morphology that resulted due to the addition of amino acids has been compared. It is important to understand the role of amino acids in synthesizing the nanoparticles, and so it is more important to understand the internal energy variation of the same. To achieve this, the interaction between the bio (amino acids) and non-bio (metal and metal oxide) nanoparticles are to be discussed both experimentally and theoretically. At times the theoretical characterization, especially at low dimensions, help us to understand inter-particle interaction and intra-particle interaction by determining their chemical potential and Lennard-Jones potential. This review has been concluded with a model to characterize the precursor solution (amino acids and inorganic materials) by considering the Equation of State for liquids, which could also be extended to determine the structure factor of nanoparticles.
Computational and theoretical studies of globular proteins
Pagan, Daniel L.
Protein crystallization is often achieved in experiment through a trial and error approach. To date, there exists a dearth of theoretical understanding of the initial conditions necessary to promote crystallization. While a better understanding of crystallization will help to create good crystals suitable for structure analysis, it will also allow us to prevent the onset of certain diseases. The core of this thesis is to model and, ultimately, understand the phase behavior of protein particles in solution. Toward this goal, we calculate the fluid-fluid coexistence curve in the vicinity of the metastable critical point of the modified Lennard-Jones potential, where it has been shown that nucleation is increased by many orders of magnitude. We use finite-size scaling techniques and grand canonical Monte Carlo simulation methods. This has allowed us to pinpoint the critical point and subcritical region with high accuracy in spite of the critical fluctuations that hinder sampling using other Monte Carlo techniques. We also attempt to model the phase behavior of the gamma-crystallins, mutations of which have been linked to genetic cataracts. The complete phase behavior of the square well potential at the ranges of attraction lambda = 1.15 and lambda = 1.25 is calculated and compared with that of the gammaII-crystallin. The role of solvent is also important in the crystallization process and affects the phase behavior of proteins in solution. We study a model that accounts for the contribution of the solvent free-energy to the free-energy of globular proteins. This model allows us to model phase behavior that includes solvent.
A fast iterative scheme for the linearized Boltzmann equation
Wu, Lei; Zhang, Jun; Liu, Haihu; Zhang, Yonghao; Reese, Jason M.
2017-06-01
Iterative schemes to find steady-state solutions to the Boltzmann equation are efficient for highly rarefied gas flows, but can be very slow to converge in the near-continuum flow regime. In this paper, a synthetic iterative scheme is developed to speed up the solution of the linearized Boltzmann equation by penalizing the collision operator L into the form L = (L + Nδh) - Nδh, where δ is the gas rarefaction parameter, h is the velocity distribution function, and N is a tuning parameter controlling the convergence rate. The velocity distribution function is first solved by the conventional iterative scheme, then it is corrected such that the macroscopic flow velocity is governed by a diffusion-type equation that is asymptotic-preserving into the Navier-Stokes limit. The efficiency of this new scheme is assessed by calculating the eigenvalue of the iteration, as well as solving for Poiseuille and thermal transpiration flows. We find that the fastest convergence of our synthetic scheme for the linearized Boltzmann equation is achieved when Nδ is close to the average collision frequency. The synthetic iterative scheme is significantly faster than the conventional iterative scheme in both the transition and the near-continuum gas flow regimes. Moreover, due to its asymptotic-preserving properties, the synthetic iterative scheme does not need high spatial resolution in the near-continuum flow regime, which makes it even faster than the conventional iterative scheme. Using this synthetic scheme, with the fast spectral approximation of the linearized Boltzmann collision operator, Poiseuille and thermal transpiration flows between two parallel plates, through channels of circular/rectangular cross sections and various porous media are calculated over the whole range of gas rarefaction. Finally, the flow of a Ne-Ar gas mixture is solved based on the linearized Boltzmann equation with the Lennard-Jones intermolecular potential for the first time, and the difference
Effective potential for non-convex potentials
International Nuclear Information System (INIS)
Fujimoto, Y.; O'Raifeartaigh, L.; Parravicini, G.
1983-01-01
It is shown that the well-known relationship between the effective potential GAMMA and the vacuum graphs μ of scalar QFT follows directly from the translational invariance of the measure, and that it holds for all values of the fields phi if, and only if, the classical potential is convex. In the non-convex case μ appears to become complex for some values of phi, but it is shown that the complexity is only apparent and is due to the failure of the loop expansion. The effective potential actually remains real and well-defined for all phi, and reduces to μ in the neighbourhood of the classical minima. A number of examples are considered, notably potentials which are spontaneously broken. In particular the mechanism by which a spontaneous breakdown may be generated by radiative corrections is re-investigated and some new insights obtained. Finally, it is shown that the renormalization group equations for the parameters may be obtained by inspection from the effective potential, and among the examples considered are SU(n) fields and supermultiplets. In particular, it is shown that for supermultiplets the effective potential is not only real but positive. (orig.)
Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins.
Harris, Robert C; Pettitt, B Montgomery
2016-03-02
The idea that a 'hydrophobic energy' drives protein folding, aggregation, and binding by favoring the sequestration of bulky residues from water into the protein interior is widespread. The solvation free energies (ΔGsolv) of small nonpolar solutes increase with surface area (A), and the free energies of creating macroscopic cavities in water increase linearly with A. These observations seem to imply that there is a hydrophobic component (ΔGhyd) of ΔGsolv that increases linearly with A, and this assumption is widely used in implicit solvent models. However, some explicit-solvent molecular dynamics studies appear to contradict these ideas. For example, one definition (ΔG(LJ)) of ΔGhyd is that it is the free energy of turning on the Lennard-Jones (LJ) interactions between the solute and solvent. However, ΔG(LJ) decreases with A for alanine and glycine peptides. Here we argue that these apparent contradictions can be reconciled by defining ΔGhyd to be a near hard core insertion energy (ΔGrep), as in the partitioning proposed by Weeks, Chandler, and Andersen. However, recent results have shown that ΔGrep is not a simple function of geometric properties of the molecule, such as A and the molecular volume, and that the free energy of turning on the attractive part of the LJ potential cannot be computed from first-order perturbation theory for proteins. The theories that have been developed from these assumptions to predict ΔGhyd are therefore inadequate for proteins.
The Voronoi volume and molecular representation of molar volume: equilibrium simple fluids.
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.
Stochastic characteristics and Second Law violations of atomic fluids in Couette flow
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.
Naden, Levi N; Shirts, Michael R
2016-04-12
We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the computational cost to estimate thermodynamic properties from molecular simulations for over 130,000 tested parameter combinations from over 1000 CPU years to tens of CPU days. This speed increase is achieved primarily by computing the potential energy as a linear combination of basis functions, computed from either modified simulation code or as the difference of energy between two reference states, which can be done without any simulation code modification. The thermodynamic properties are then estimated with the Multistate Bennett Acceptance Ratio (MBAR) as a function of multiple model parameters without the need to define a priori how the states are connected by a pathway. Instead, we adaptively sample a set of points in parameter space to create mutual configuration space overlap. The existence of regions of poor configuration space overlap are detected by analyzing the eigenvalues of the sampled states' overlap matrix. The configuration space overlap to sampled states is monitored alongside the mean and maximum uncertainty to determine convergence, as neither the uncertainty or the configuration space overlap alone is a sufficient metric of convergence. This adaptive sampling scheme is demonstrated by estimating with high precision the solvation free energies of charged particles of Lennard-Jones plus Coulomb functional form with charges between -2 and +2 and generally physical values of σij and ϵij in TIP3P water. We also compute entropy, enthalpy, and radial distribution functions of arbitrary unsampled parameter combinations using only the data from these sampled states and use the estimates of free energies over the entire space to examine the deviation of atomistic simulations from the Born approximation to the solvation free
Simulations of cold nuclear matter at sub-saturation densities
Energy Technology Data Exchange (ETDEWEB)
Giménez Molinelli, P.A., E-mail: pagm@df.uba.ar [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA, CONICET, Ciudad Universitaria, Buenos Aires 1428 (Argentina); Nichols, J.I. [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA, CONICET, Ciudad Universitaria, Buenos Aires 1428 (Argentina); López, J.A. [Department of Physics, University of Texas at El Paso, El Paso, TX 79968 (United States); Dorso, C.O. [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA, CONICET, Ciudad Universitaria, Buenos Aires 1428 (Argentina)
2014-03-01
Ideal nuclear matter is expected to undergo a first order phase transition at the thermodynamic limit. At such phase transitions the size of density fluctuations (bubbles or droplets) scale with the size of the system. This means that simulations of nuclear matter at sub-saturation densities will inexorably suffer from what is vaguely referred to as “finite size effects”. It is usually thought that these finite size effects can be diminished by imposing periodic boundary conditions and making the system large enough, but as we show in this work, that is actually not the case at sub-saturation densities. In this paper we analyze the equilibrium configurations of molecular dynamics simulations of a classical model for symmetric ideal (uncharged) nuclear matter at sub-saturation densities and low temperatures, where phase coexistence is expected at the thermodynamic limit. We show that the most stable configurations in this density range are almost completely determined by artificial aspects of the simulations (i.e. boundary conditions) and can be predicted analytically by surface minimization. This result is very general and is shown to hold true for several well known semi-classical models of nuclear interaction and even for a simple Lennard-Jones potential. Also, in the limit of very large systems, when “small size” effects can be neglected, those equilibrium configurations seem to be restricted to a few structures reminiscent to the “Pasta Phases” expected in Neutron Star matter, but arising from a completely different origin: In Neutron Star matter, the non-homogeneous structures arise from a competition between nuclear and Coulomb interactions while for ideal nuclear matter they emerge from finite (yet not “small”) size effects. The role of periodic boundary conditions and finite size effects in Neutron Star matter simulations are reexamined.
Accuracy of free energies of hydration using CM1 and CM3 atomic charges.
Udier-Blagović, Marina; Morales De Tirado, Patricia; Pearlman, Shoshannah A; Jorgensen, William L
2004-08-01
Absolute free energies of hydration (DeltaGhyd) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CM1 and CM3 procedures of Cramer, Truhlar, and coworkers. Comparisons are made with results using charges fit to the electrostatic potential surface (EPS) from ab initio 6-31G* wave functions and from the OPLS-AA force field. OPLS Lennard-Jones parameters for the organic molecules were used together with the TIP4P water model in Monte Carlo simulations with free energy perturbation theory. Absolute free energies of hydration were computed for OPLS united-atom and all-atom methane by annihilating the solutes in water and in the gas phase, and absolute DeltaGhyd values for all other molecules were computed via transformation to one of these references. Optimal charge scaling factors were determined by minimizing the unsigned average error between experimental and calculated hydration free energies. The PM3-based charge models do not lead to lower average errors than obtained with the EPS charges for the subset of 13 molecules in the original study. However, improvement is obtained by scaling the CM1A partial charges by 1.14 and the CM3A charges by 1.15, which leads to average errors of 1.0 and 1.1 kcal/mol for the full set of 25 molecules. The scaled CM1A charges also yield the best results for the hydration of amides including the E/Z free-energy difference for N-methylacetamide in water. Copyright 2004 Wiley Periodicals, Inc.
Energy Technology Data Exchange (ETDEWEB)
Pang, Yuan-Ping, E-mail: pang@mayo.edu
2015-02-06
Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA){sub 3}-NH{sub 2} to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.
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.
Photodissociation dynamics of CH3C(O)SH in argon matrix: A QM/MM nonadiabatic dynamics simulation
Xia, Shu-Hua; Liu, Xiang-Yang; Fang, Qiu; Cui, Ganglong
2015-11-01
In this work, we have first employed the combined quantum mechanics/molecular mechanics (QM/MM) method to study the photodissociation mechanism of thioacetic acid CH3C(O)SH in the S1, T1, and S0 states in argon matrix. CH3C(O)SH is treated quantum mechanically using the complete active space self-consistent field and complete active space second-order perturbation theory methods; argon matrix is described classically using Lennard-Jones potentials. We find that the C-S bond fission is predominant due to its small barriers of ca. 3.0 and 1.0 kcal/mol in the S1 and T1 states. It completely suppresses the nearby C—C bond fission. After the bond fission, the S1 radical pair of CH3CO and SH can decay to the S0 and T1 states via internal conversion and intersystem crossing, respectively. In the S0 state, the radical pair can either recombine to form CH3C(O)SH or proceed to form molecular products of CH2CO and H2S. We have further employed our recently developed QM/MM generalized trajectory-based surface-hopping method to simulate the photodissociation dynamics of CH3C(O)SH. In 1 ps dynamics simulation, 56% trajectories stay at the Franck-Condon region; the S1 C—S bond fission takes place in the remaining 44% trajectories. Among all nonadiabatic transitions, the S1 → S0 internal conversion is major (55%) but the S1 → T1 intersystem crossing is still comparable and cannot be ignored, which accounts for 28%. Finally, we have found a radical channel generating the molecular products of CH2CO and H2S, which is complementary to the concerted molecular channel. The present work sets the stage for simulating photodissociation dynamics of similar thio-carbonyl systems in matrix.
Bejagam, Karteek K; Singh, Samrendra; Deshmukh, Sanket A
2018-05-05
New Lennard-Jones parameters have been developed to describe the interactions between atomistic model of graphene, represented by REBO potential, and five commonly used all-atom water models, namely SPC, SPC/E, SPC/Fw, SPC/Fd, and TIP3P/Fs by employing particle swarm optimization (PSO) method. These new parameters were optimized to reproduce the macroscopic contact angle of water on a graphene sheet. The calculated line tension was in the order of 10 -11 J/m for the droplets of all water models. Our molecular dynamics simulations indicate the preferential orientation of water molecules near graphene-water interface with one OH bond pointing toward the graphene surface. Detailed analysis of simulation trajectories reveals the presence of water molecules with ≤∼1, ∼2, and ∼4 hydrogen bonds at the surface of air-water interface, graphene-water interface, and bulk region of the water droplet, respectively. Presence of water molecules with ≤∼1 and ∼2 hydrogen bonds suggest the existence of water clusters of different sizes at these interfaces. The trends observed in the libration, bending, and stretching bands of the vibrational spectra are closely associated with these structural features of water. The inhomogeneity in hydrogen bond network of water at the air-water and graphene-water interface is manifested by broadening of the peaks in the libration band for water present at these interfaces. The stretching band for the molecules in water droplet shows a blue shift as compared to the pure bulk water, which conjecture the presence of weaker hydrogen bond network in a droplet. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
A study of highly correlated classical and quantum fluids
International Nuclear Information System (INIS)
Clements, B.E.
1988-01-01
We have determined, by molecular dynamics simulation, the l = 0, 2, 4, and 6 Legendre coefficients of the static pair-pair correlation function Q(r,r'), the dynamic pair-pair correlation function Q(r,r';t) and the dynamic four point correlation function S 4 (k, -k,q, -q;t). The interaction potential was taken to be Lennard-Jones. The simulation was carried out at two different values of density and temperature; one coinciding with that of liquid argon near its triple point and the other coinciding with high density argon at room temperature. We argue that an important contribution to the pair-pair correlation function comes from the thee-body correlations. We find that the Legendre coefficients of Q(r,r') provide strong evidence that, upon freezing, the resulting crystalline structure will be a close-packed structure. A study of dynamical fluctuations characterized by Legendre coefficients of the dynamic pair-pair correlation function support this assertion. Finally, we provide a discussion on a decoupling scheme, used in the literature, to approximate the static and dynamic four point correlation function. A variational calculation with the Penrose-Reatto-Chester-Jastrow density matrix is used to study the finite temperature properties of Bose quantum fluids. This analysis provides a systematic method for adding correction terms to the density matrix approach of Campbell, Ristig, Kurten and Senger. We find that the excitation spectrum for the elementary excitations has the proper temperature dependence in contrast to earlier calculations
Directory of Open Access Journals (Sweden)
Yunxiang Sun
Full Text Available Energetic frustration is becoming an important topic for understanding the mechanisms of protein folding, which is a long-standing big biological problem usually investigated by the free energy landscape theory. Despite the significant advances in probing the effects of folding frustrations on the overall features of protein folding pathways and folding intermediates, detailed characterizations of folding frustrations at an atomic or residue level are still lacking. In addition, how and to what extent folding frustrations interact with protein topology in determining folding mechanisms remains unclear. In this paper, we tried to understand energetic frustrations in the context of protein topology structures or native-contact networks by comparing the energetic frustrations of five homologous Im9 alpha-helix proteins that share very similar topology structures but have a single hydrophilic-to-hydrophobic mutual mutation. The folding simulations were performed using a coarse-grained Gō-like model, while non-native hydrophobic interactions were introduced as energetic frustrations using a Lennard-Jones potential function. Energetic frustrations were then examined at residue level based on φ-value analyses of the transition state ensemble structures and mapped back to native-contact networks. Our calculations show that energetic frustrations have highly heterogeneous influences on the folding of the four helices of the examined structures depending on the local environment of the frustration centers. Also, the closer the introduced frustration is to the center of the native-contact network, the larger the changes in the protein folding. Our findings add a new dimension to the understanding of protein folding the topology determination in that energetic frustrations works closely with native-contact networks to affect the protein folding.
Moon, Gi Jong; Yang, Yu Dong; Oh, Jung Min; Kang, In Seok
2017-11-01
Osmotic pressure plays an important role in the processes of charging and discharging of lithium batteries. In this work, osmotic pressure of the ionic liquids confined inside a nanoslit is calculated by using both MD simulation and continuum approach. In the case of MD simulation, an ionic liquid is modeled as singly charged spheres with a short-ranged repulsive Lennard-Jones potential. The radii of the spheres are 0.5nm, reflecting the symmetry of ion sizes for simplicity. The simulation box size is 11nm×11nm×7.5nm with 1050 ion pairs. The concentration of ionic liquid is about 1.922mol/L, and the total charge on an individual wall varies from +/-60e(7.944 μm/cm2) to +/-600e(79.44 μm/cm2) . In the case of continuum approach, we classify the problems according to the correlation length and steric factor, and considered the four separate cases: 1) zero correlation length and zero steric factor, 2) zero correlation length and non-zero steric factor, 3) non-zero correlation length and zero steric factor, and 4) non-zero correlation and non-zero steric factor. Better understanding of the osmotic pressure of ionic liquids confined inside a nanoslit can be achieved by comparing the results of MD simulation and continuum approach. This research was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MSIP: Ministry of Science, ICT & Future Planning) (No. 2017R1D1A1B05035211).
Oulebsir, Fouad; Vermorel, Romain; Galliero, Guillaume
2018-01-16
With the advent of graphene material, membranes based on single-layer nanoporous solids appear as promising devices for fluid separation, be it liquid or gaseous mixtures. The design of such architectured porous materials would greatly benefit from accurate models that can predict their transport and separation properties. More specifically, there is no universal understanding of how parameters such as temperature, fluid loading conditions, or the ratio of the pore size to the fluid molecular diameter influence the permeation process. In this study, we address the problem of pure supercritical fluids diffusing through simplified models of single-layer porous materials. Basically, we investigate a toy model that consists of a single-layer lattice of Lennard-Jones interaction sites with a slit gap of controllable width. We performed extensive equilibrium and biased molecular dynamics simulations to document the physical mechanisms involved at the molecular scale. We propose a general constitutive equation for the diffusional transport coefficient derived from classical statistical mechanics and kinetic theory, which can be further simplified in the ideal gas limit. This transport coefficient relates the molecular flux to the fluid density jump across the single-layer membrane. It is found to be proportional to the accessible surface porosity of the single-layer porous solid and to a thermodynamic factor accounting for the inhomogeneity of the fluid close to the pore entrance. Both quantities directly depend on the potential of mean force that results from molecular interactions between solid and fluid atoms. Comparisons with the simulations data show that the kinetic model captures how narrowing the pore size below the fluid molecular diameter lowers dramatically the value of the transport coefficient. Furthermore, we demonstrate that our general constitutive equation allows for a consistent interpretation of the intricate effects of temperature and fluid loading
Nasrabad, Afshin Eskandari; Laghaei, Rozita; Eu, Byung Chan
2005-04-28
In previous work on the density fluctuation theory of transport coefficients of liquids, it was necessary to use empirical self-diffusion coefficients to calculate the transport coefficients (e.g., shear viscosity of carbon dioxide). In this work, the necessity of empirical input of the self-diffusion coefficients in the calculation of shear viscosity is removed, and the theory is thus made a self-contained molecular theory of transport coefficients of liquids, albeit it contains an empirical parameter in the subcritical regime. The required self-diffusion coefficients of liquid carbon dioxide are calculated by using the modified free volume theory for which the generic van der Waals equation of state and Monte Carlo simulations are combined to accurately compute the mean free volume by means of statistical mechanics. They have been computed as a function of density along four different isotherms and isobars. A Lennard-Jones site-site interaction potential was used to model the molecular carbon dioxide interaction. The density and temperature dependence of the theoretical self-diffusion coefficients are shown to be in excellent agreement with experimental data when the minimum critical free volume is identified with the molecular volume. The self-diffusion coefficients thus computed are then used to compute the density and temperature dependence of the shear viscosity of liquid carbon dioxide by employing the density fluctuation theory formula for shear viscosity as reported in an earlier paper (J. Chem. Phys. 2000, 112, 7118). The theoretical shear viscosity is shown to be robust and yields excellent density and temperature dependence for carbon dioxide. The pair correlation function appearing in the theory has been computed by Monte Carlo simulations.
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.
Zhakhovsky, Vasily V; Kryukov, Alexei P; Levashov, Vladimir Yu; Shishkova, Irina N; Anisimov, Sergey I
2018-04-16
Boundary conditions required for numerical solution of the Boltzmann kinetic equation (BKE) for mass/heat transfer between evaporation and condensation surfaces are analyzed by comparison of BKE results with molecular dynamics (MD) simulations. Lennard-Jones potential with parameters corresponding to solid argon is used to simulate evaporation from the hot side, nonequilibrium vapor flow with a Knudsen number of about 0.02, and condensation on the cold side of the condensed phase. The equilibrium density of vapor obtained in MD simulation of phase coexistence is used in BKE calculations for consistency of BKE results with MD data. The collision cross-section is also adjusted to provide a thermal flux in vapor identical to that in MD. Our MD simulations of evaporation toward a nonreflective absorbing boundary show that the velocity distribution function (VDF) of evaporated atoms has the nearly semi-Maxwellian shape because the binding energy of atoms evaporated from the interphase layer between bulk phase and vapor is much smaller than the cohesive energy in the condensed phase. Indeed, the calculated temperature and density profiles within the interphase layer indicate that the averaged kinetic energy of atoms remains near-constant with decreasing density almost until the interphase edge. Using consistent BKE and MD methods, the profiles of gas density, mass velocity, and temperatures together with VDFs in a gap of many mean free paths between the evaporation and condensation surfaces are obtained and compared. We demonstrate that the best fit of BKE results with MD simulations can be achieved with the evaporation and condensation coefficients both close to unity.
International Nuclear Information System (INIS)
Pang, Yuan-Ping
2015-01-01
Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA) 3 -NH 2 to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements
Structures of simple liquids in contact with nanosculptured surfaces.
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.
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