Chemical Potential of a Lennard Jones Fluid
Directory of Open Access Journals (Sweden)
Celebonovic, V.
2010-12-01
Full Text Available The aim of this paper is to present results of analytical calculation of chemical potential of a Lennard Jones (LJ fluid performed in two ways: by using the thermodynamical formalism and the formalism of statistical mechanics. The integration range is divided into two regions. In the small distance region, which is $rleqsigma$ in the usual notation, the integration range had to be cut off in order to avoid the occurence of divergences. In the large distance region, the calculation is technically simpler. The calculation reported here will be useful in all kinds of studies concerning phase equilibrium in a LJ fluid. Interesting kinds of such systems are the giant planets and the icy satellites in various planetary systems, but also the (so far hypothetical quark stars.
Chemical potential of a Lennard Jones fluid
Directory of Open Access Journals (Sweden)
Čelebonović V.
2010-01-01
Full Text Available The aim of this paper is to present results of analytical calculation of chemical potential of a Lennard Jones (LJ fluid performed in two ways: by using the thermodynamical formalism and the formalism of statistical mechanics. The integration range is divided into two regions. In the small distance region, which is r ≤ σ in the usual notation, the integration range had to be cut off in order to avoid the occurrence of divergences. In the large distance region, the calculation is technically simpler. The calculation reported here will be useful in all kinds of studies concerning phase equilibrium in a LJ fluid. Interesting kinds of such systems are the giant planets and the icy satellites in various planetary systems, but also the (so far hypothetical quark stars.
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)
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....
Geada, Isidro Lorenzo; Ramezani-Dakhel, Hadi; Jamil, Tariq; Sulpizi, Marialore; Heinz, Hendrik
2018-02-19
Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals.
DEFF Research Database (Denmark)
Friisberg, Ida Marie; Costigliola, Lorenzo; Dyre, Jeppe C.
2017-01-01
This paper investigates the relation between the density-scaling exponent γ and the virial potentialenergy coefficient R at several thermodynamic state points in three dimensions for the generalized (2n, n) Lennard-Jones (LJ) system for n = 4, 9, 12, 18, as well as for the standard n = 6 LJ system...... in two, three, and four dimensions. The state points studied include many low-density states at which the virial potentialenergy correlations are not strong. For these state points we find the roughly linear relation γ ∼= 3n R/d in d dimensions. This result is discussed in light of the approximate...... → 1, a limit that is approached at high densities and/or high temperatures at which the repulsive r−2n term dominates the physics....
Chemical potential and solid-solid equilibrium of near-spherical Lennard-Jones dumbbell crystal
International Nuclear Information System (INIS)
Lee, Sangwon; Kim, Minkyu; Chang, Jaeeon
2016-01-01
We studied the orientational order-disorder transition of crystals made up of near-spherical Lennard-Jones dumbbells, of which reduced bond lengths are 0.225, 0.250 and 0.275. Various techniques of Monte Carlo (MC) simulations are used to calculate the chemical potentials of ordered and disordered crystals, and thereby to predict order disorder phase transition. First, we performed NPT MC simulations to determine crystal structure, equilibrium positions and orientations of the molecules. We then calculated the free energies of the crystals using the expanded ensemble MC simulations combined with the Einstein-molecule method and the thermodynamic integration method. The solid-solid phase equilibrium is determined from the free energy profiles of the individual phases by equating the chemical potential. The predictions of phase transition obtained from the conventional NPT MC simulation and the free energy simulation were in excellent agreement with each other, which confirms the validity of the present method of calculating the chemical potential of crystal. In addition, the Gibbs-Duhem integration was performed to obtain a complete coexistence curve between the two crystal phases. Orientational probability distributions of molecular axes were analyzed to find the characteristic behavior of rotational motion of molecule in the crystal. At sufficiently low temperature, flipping rotation of molecule in the ordered crystal is suppressed. In contrast, the flipping rotation occurs at higher temperature close to the transition while orientationally ordered structure is still maintained. In the free energy calculation, such a unique rotational behavior requires to use a suitable form of external rotational potential with proper symmetry number. The present study demonstrates how one can judiciously choose a correct simulation scheme for the calculation of chemical potentials of molecular crystals.
Köster, Andreas; Mausbach, Peter; Vrabec, Jadran
2017-10-01
The Lennard-Jones potential is used to study the high density fluid and face centered cubic solid state region, including solid-fluid equilibria. Numerous thermodynamic properties are considered, elucidating the behavior of matter in this poorly studied region. The present molecular simulation results are extensively compared to the latest and most accurate equation of state models for fluid and solid phases. It is shown that current models do not cover the thermodynamics of the system adequately near the solid-fluid phase transition. Furthermore, thermodynamic stability is analyzed, indicating that published solid-fluid coexistence data may not be correct at high temperatures. Particular attention is paid to the premelting zone, a range of states close to the melting line, which is characterized by strong variations of several thermodynamic properties. Because the underlying microscopic mechanisms are not yet fully understood, it is hoped that these data may contribute to the development of a theoretical framework for describing premelting effects.
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...
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.
Kaukonen, M; Gulans, A; Havu, P; Kauppinen, E
2012-03-05
Lennard-Jones (LJ) parameters are derived for classical nonpolarizable force fields for carbon nanotubes (CNTs) and for CNT-water interaction from van der Waals (vdW) enhanced density functional calculations. The new LJ parameters for carbon-carbon interactions are of the same order as those previously used in the literature but differ significantly for CNT-water interactions. This may partially originate from the fact that in addition to pure vdW interactions the polarization and other quantum mechanics effects are embedded into the LJ-potential. Copyright © 2012 Wiley Periodicals, Inc.
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
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.
Solitons in a One-Dimensional Lennard-Jones Lattice
Yuji, ISHIMORI; Department of Applied Mathematics and Physics Kyoto University
1982-01-01
Nonlinear waves in a one-dimensional lattice with (2n, n) Lennard-Jones potential are studied in small-amplitude and long-wavelength approximations. Equations derived are classified into three types according to the value of the force-range parameter n. For n=2 and ≧4, we get the Benjamin-Ono equation and the Korteweg-de Vries equation, respectively.
Non-equilibrium surface tension of the vapour-liquid interface of active Lennard-Jones particles
Paliwal, Siddharth; Prymidis, Vasileios; Filion, Laura; Dijkstra, Marjolein
2017-01-01
We study a three-dimensional system of self-propelled Brownian particles interacting via the Lennard-Jones potential. Using Brownian dynamics simulations in an elongated simulation box, we investigate the steady states of vapour-liquid phase coexistence of active Lennard-Jones particles with planar
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
Modified Benedict-Webb-Rubin Equation of State for the Modified Lennard-Jones Fluid
Asano, Yuta; Fuchizaki, Kazuhiro
2014-03-01
We have proposed a modified Lennard-Jones (mLJ) potential to deal with problems, such as the accurate determination of the melting condition, in which an attractive interaction plays an essential role, but its range need not necessarily extend to infinity. An accurate phase diagram, including the triple and the critical points of the system characterized by the mLJ potential, has been investigated using mainly thermodynamic integration. To predict the thermodynamic behavior of the system, it is further desired to construct the equation of state (EOS) as accurately as possible. The modified Benedict-Webb-Rubin EOS was employed to this end. The 33 parameters involved in the equation were carefully determined in order for the EOS to be compatible with the temperature dependences of the virial coefficients as well as with an extremely large set of thermodynamic data obtained from our own molecular dynamics simulation performed over a wide fluid region. The resultant EOS was found to be not only sufficiently accurate at temperatures up to twenty times as high as the critical-point temperature but also effective in practical use.
More on the melting of Lennard-Jones clusters
International Nuclear Information System (INIS)
Garzon, I.L.; Avalos-Borja, M.; Blaisten-Barojas, E.
1989-01-01
The melting of 13-atom clusters interacting via Lennard-Jones potentials has been revisited using molecular dynamics coupled to steepest descent quenches. A procedure was devised to account for the fraction of times the global and local minima of the potential energy surface are accessed during a long trajectory. This quantity presents a sigmoid shape. A phenomenological model of melting is given in terms of a correlated walk that maps the short time excursions among the global and local minima in configuration space. Comparison between the simulation results and the theoretical model shows that the melting transition is well described in terms of the temperature changes of the fraction of high energy minima accessed during the cluster trajectory. Cooperativity is clear from the S shape of this quantity, i.e., the access to a local minimum favours the access to other local minima. (orig.)
Mapping the magic numbers in binary Lennard-Jones clusters.
Doye, Jonathan P K; Meyer, Lars
2005-08-05
Using a global optimization approach that directly searches for the composition of greatest stability, we have been able to find the particularly stable structures for binary Lennard-Jones clusters with up to 100 atoms for a range of Lennard-Jones parameters. In particular, we have shown that just having atoms of different sizes leads to a remarkable stabilization of polytetrahedral structures, including both polyicosahedral clusters and at larger sizes structures with disclination lines.
Formation of global energy minimim structures in the growth process of Lennard-Jones clusters
DEFF Research Database (Denmark)
Solov'yov, Ilia; Koshelev, Andrey; Shutovich, Andrey
2003-01-01
that in this way all known global minimum structures of the Lennard-Jones (LJ) clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic numbers sequence for the clusters of noble gases atoms and compare...... for the clusters of noble gases atoms. Our method serves an efficient alternative to the global optimization techniques based on the Monte-Carlo simulations and it can be applied for the solution of a broad variety of problems in which atomic cluster structure is important....
Cluster fusion algorithm: application to Lennard-Jones clusters
DEFF Research Database (Denmark)
Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter
2008-01-01
We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing...... paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...
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.
Cluster fusion algorithm: application to Lennard-Jones clusters
DEFF Research Database (Denmark)
Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter
2006-01-01
We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing ...
Origin of line tension for a Lennard-Jones nanodroplet
Weijs, Joost; Weijs, Joost H.; Marchand, Antonin; Andreotti, Bruno; Lohse, Detlef; Snoeijer, Jacobus Hendrikus
2011-01-01
The existence and origin of line tension has remained controversial in literature. To address this issue, we compute the shape of Lennard-Jones nanodrops using molecular dynamics and compare them to density functional theory in the approximation of the sharp kink interface. We show that the
Free energy of the Lennard-Jones solid
van der Hoef, Martin Anton
2000-01-01
We have determined a simple expression for the absolute Helmholtz free energy of the fcc Lennard-Jones solid from molecular dynamics simulations. The pressure and energy data from these simulations have been fitted to a simple functional form (18 parameters) for densities ranging from around
Gas-solid coexistence of the Lennard-Jones system
van der Hoef, Martin Anton
2002-01-01
Recently, the absolute free energies of the Lennard-Jones system at solid–liquid and solid–gas coexistence were computed from Monte Carlo simulations [J. Chem. Phys. 116, 7145 (2002)]. In this note, we show that the values along the sublimation line are in good agreement with the results from an
DEFF Research Database (Denmark)
D'ovidio, Francesco; Bohr, Henrik; Lindgård, Per-Anker
2005-01-01
We study the propagation of solitons along the hydrogen bonds of an alpha helix. Modeling the hydrogen and peptide bonds with Lennard-Jones potentials, we show that the solitons can appear spontaneously and have long lifetimes. Remarkably, even if no explicit solution is known for the Lennard-Jon...
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.
Goujon, Florent; Ghoufi, Aziz; Malfreyt, Patrice
2018-02-01
We report Monte Carlo (MC) simulations of the Lennard-Jones (LJ) fluid at the liquid-vapor interface in the critical region. A slab-based tail method is associated with the MC simulations to approach as close as possible the critical point (T∗ = 0.98 TC∗) . We investigate then the impact of system-sizes on the surface tension and coexisting densities by considering very large box dimensions for which the surface tension is independent of system-sizes at low temperatures.
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 ...
Origin of line tension for a Lennard-Jones nanodroplet
Weijs, Joost H.; Marchand, Antonin; Andreotti, Bruno; Lohse, Detlef; Snoeijer, Jacco H.
2011-02-01
The existence and origin of line tension has remained controversial in literature. To address this issue, we compute the shape of Lennard-Jones nanodrops using molecular dynamics and compare them to density functional theory in the approximation of the sharp kink interface. We show that the deviation from Young's law is very small and would correspond to a typical line tension length scale (defined as line tension divided by surface tension) similar to the molecular size and decreasing with Young's angle. We propose an alternative interpretation based on the geometry of the interface at the molecular scale.
Non-equilibrium surface tension of the vapour-liquid interface of active Lennard-Jones particles
Paliwal, Siddharth; Prymidis, Vasileios; Filion, Laura; Dijkstra, Marjolein
2017-08-01
We study a three-dimensional system of self-propelled Brownian particles interacting via the Lennard-Jones potential. Using Brownian dynamics simulations in an elongated simulation box, we investigate the steady states of vapour-liquid phase coexistence of active Lennard-Jones particles with planar interfaces. We measure the normal and tangential components of the pressure tensor along the direction perpendicular to the interface and verify mechanical equilibrium of the two coexisting phases. In addition, we determine the non-equilibrium interfacial tension by integrating the difference of the normal and tangential components of the pressure tensor and show that the surface tension as a function of strength of particle attractions is well fitted by simple power laws. Finally, we measure the interfacial stiffness using capillary wave theory and the equipartition theorem and find a simple linear relation between surface tension and interfacial stiffness with a proportionality constant characterized by an effective temperature.
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
Scaling of the dynamics of flexible Lennard-Jones chains
DEFF Research Database (Denmark)
Veldhorst, Arno; Dyre, J. C.; Schrøder, Thomas
2014-01-01
S/T , where ρ is density, T is temperature, and γ S is a material specific scaling exponent) is an approximation to a more general scaling predicted by the isomorph theory. Furthermore, the isomorph theory provides an explanation for Rosenfeld scaling (relaxation times and transport coefficients being...... functions of excess entropy) which has been observed in simulations of both molecular and polymeric systems. Doing molecular dynamics simulations of flexible Lennard-Jones chains (LJC) with rigid bonds, we here provide the first detailed test of the isomorph theory applied to flexible chain molecules. We...... confirm the existence of isomorphs, which are curves in the phase diagram along which the dynamics is invariant in the appropriate reduced units. This holds not only for the relaxation times but also for the full time dependence of the dynamics, including chain specific dynamics such as the end...
Sumi, Tomonari; Maruyama, Yutaka; Mitsutake, Ayori; Koga, Kenichiro
2016-06-14
In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.
International Nuclear Information System (INIS)
Ohtori, Norikazu; Ishii, Yoshiki
2015-01-01
Explicit expressions of the self-diffusion coefficient, D i , and shear viscosity, η sv , are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m −3 . The scaling equations obtained by multiplying all the single-variable dependences can well express D i and η sv evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for D i can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on D i . The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions
Energy Technology Data Exchange (ETDEWEB)
Ohtori, Norikazu, E-mail: ohtori@chem.sc.niigata-u.ac.jp [Department of Chemistry, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181 (Japan); Ishii, Yoshiki [Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181 (Japan)
2015-10-28
Explicit expressions of the self-diffusion coefficient, D{sub i}, and shear viscosity, η{sub sv}, are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m{sup −3}. The scaling equations obtained by multiplying all the single-variable dependences can well express D{sub i} and η{sub sv} evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for D{sub i} can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on D{sub i}. The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions.
Sweatman, Martin B; Atamas, Alexander; Leyssale, Jean-Marc
2009-01-14
The self-referential (SR) method incorporating thermodynamic integration (TI) [Sweatman et al., J. Chem. Phys. 128, 064102 (2008)] is extended to treat systems of rigid linear bodies. The method is then applied to obtain the canonical ensemble Helmholtz free energy of the alpha-N(2) and plastic face centered cubic phases of systems of hard and Lennard-Jones dumbbells using Monte Carlo simulations. Generally good agreement with reference literature data is obtained, which indicates that the SR-TI method is potentially very general and robust.
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
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.
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.
Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory
Evans, Robert; Stewart, Maria C.; Wilding, Nigel B.
2017-07-01
We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory, we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, i.e., in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent ν∥, which controls the parallel correlation length, i.e., the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. Possible reasons for this discrepancy are discussed in the light of fresh insights into the nature of near critical finite-size effects.
Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory.
Evans, Robert; Stewart, Maria C; Wilding, Nigel B
2017-07-28
We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory, we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, i.e., in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent ν ∥ , which controls the parallel correlation length, i.e., the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. Possible reasons for this discrepancy are discussed in the light of fresh insights into the nature of near critical finite-size effects.
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
African Journals Online (AJOL)
has provided many new insights into cellular biology and opened up new and novel therapeutic possibilities. ... to endocrinology and bone mineral metabolism is briefly reviewed. Numerous reviews and articles have been ... prenylation in endocrinology and bone and mineral metabolism are briefly discussed. The potential ...
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
Doi, Hideo; Yasuoka, Kenji
2017-05-01
Confined systems exhibit interesting properties that are applied to the fields of lubrication, adhesion and nanotechnology. The replica exchange molecular simulation method was applied to calculate the phase equilibrium points of Lennard-Jones particles in a two-dimensional confined system. The liquid-solid phase equilibrium points and the solid structure with a dependency of the slit width were determined and the order parameter of the solid structure was analyzed. Such confined systems are shown to be favorable for manipulation of the phase equilibrium points.
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.
Nonlinear transport processes and fluid dynamics: Cylindrical Couette flow of Lennard-Jones fluids
International Nuclear Information System (INIS)
Khayat, R.E.; Eu, B.C.
1988-01-01
In this paper we report on calculations of flow profiles for cylindrical Couette flow of a Lennard-Jones fluid. The flow is subjected to a temperature gradient and thermoviscous effects are taken into consideration. We apply the generalized fluid dynamic equations which are provided by the modified moment method for the Boltzmann equation reported previously. The results of calculations are in good agreement with the Monte Carlo direct simulation method by K. Nanbu [Phys. Fluids 27, 2632 (1984)] for most of Knudsen numbers for which the simulation data are available
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.
Stability limits for the supercooled liquid and superheated crystal of Lennard-Jones particles.
Loscar, Ernesto S; Martin, Daniel A; Grigera, Tomás S
2017-07-21
We have studied the limits of stability in the first order liquid-solid phase transition in a Lennard-Jones system by means of the short-time relaxation method and using the bond-orientational order parameter Q 6 . These limits are compared with the melting line. We have paid special attention to the supercooled liquid, comparing our results with the point where the free energy cost of forming a nucleating droplet goes to zero. We also indirectly estimate the dimension associated to the critical nucleus at the spinodal, expected to be fractal according to mean field theories of nucleation.
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.
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.
Ikeshoji, T; Torchet, G; de Feraudy, M F; Koga, K
2001-03-01
We studied finite-temperature ensembles of solid clusters produced by cooling liquid droplets either by evaporation or by a thermostat through a molecular dynamics calculation using the Lennard-Jones potential. The ensembles consist of either single or binary component clusters with 25% of the atoms 8% smaller in diameter than the other 75%. These clusters (380 clusters in total) exhibit various structures in the size range of n=160-2200, where n is the number of atoms in a cluster. For increasing size, the clusters show a gradual transition from icosahedral to a variety of structures: decahedral, face centered cubic, a small amount of hexagonal, and some icosahedral structures. They are asymmetrical or faulted. Electron diffraction patterns calculated with average structure factors of clusters after grouping them into several size regions are very similar to those experimentally observed. The size transition is around n=450 for single component clusters whatever the cooling process, evaporation or thermostat. This size is smaller than the experimental transition size estimated for argon clusters formed in a supersonic expansion. The transition size for binary component clusters is around n=600 for evaporative cooling, and larger for thermostatic cooling. The larger transition size found for the binary component clusters is consistent with the large icosahedral Au-Fe and Au-Cu alloy clusters observed experimentally.
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.
An equation of state for two-center Lennard-Jones fluids
Mecke, M.; Müller, A.; Winkelmann, J.; Fischer, J.
1997-05-01
A new equation of state (EOS) is proposed for the Helmholzt energy F of two-center Lennard-Jones fluids. The EOS is written in the form of a generalized van der Waals equation, F=F H + F A , where F H accounts for the hard-body interaction and F A for the attractive dispersion forces. The equation is constructed on the basis of previously published data sets and results from new extensive computer simulation studies. It correlates pressures and internal energies over a wide fluid range for two-center model fluids with elongations up to 0.67 in reduced units with a high accuracy and shows an excellent description of the vapor-liquid coexistence properties. Comparisons of results from the new EOS with other data sets and recently published VLE from the NpT plus test particle method show very good agreement.
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.
Viscoelastic crack propagation and closing with Lennard-Jones surface forces
International Nuclear Information System (INIS)
Greenwood, J A
2007-01-01
An analysis of the opening and closing of a crack in a viscoelastic solid has been made assuming a Lennard-Jones law of force acting between the crack faces. The results are compared with those of an earlier analysis in which a simple Dugdale model of the surface forces was assumed. The approximate 'reciprocal rule' between the apparent surface energies for opening and closing cracks is confirmed. At low speeds a linear relation between the apparent surface energy and the crack speed is found. The lengths of the process zone for opening and closing cracks are found to be very similar and so presumably are not responsible for the very different values of the apparent surface energy
Viscoelastic crack propagation and closing with Lennard-Jones surface forces
Energy Technology Data Exchange (ETDEWEB)
Greenwood, J A [Department of Engineering, Trumpington Street, Cambridge, CB2 1PZ (United Kingdom)
2007-03-21
An analysis of the opening and closing of a crack in a viscoelastic solid has been made assuming a Lennard-Jones law of force acting between the crack faces. The results are compared with those of an earlier analysis in which a simple Dugdale model of the surface forces was assumed. The approximate 'reciprocal rule' between the apparent surface energies for opening and closing cracks is confirmed. At low speeds a linear relation between the apparent surface energy and the crack speed is found. The lengths of the process zone for opening and closing cracks are found to be very similar and so presumably are not responsible for the very different values of the apparent surface energy.
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.
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...
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.
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.
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.
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
Fusion process of Lennard-Jones clusters: global minima and magic numbers formation
DEFF Research Database (Denmark)
Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter
2004-01-01
measured for the clusters of noble gas atoms. Our method serves as an efficient alternative to the global optimization techniques based on the Monte-Carlo simulations and it can be applied for the solutions of a broad variety of problems in which atomic cluster structure is important.......We present a new theoretical framework for modeling the fusion process of Lennard–Jones (LJ) clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing paths up to the cluster size of 150 atoms....... We demonstrate that in this way all known global minima structures of the (LJ)-clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence for the clusters of noble gas atoms and compare...
Zimmerman, Paul M; Head-Gordon, Martin; Bell, Alexis T
2011-06-14
Quantum mechanics/molecular mechanics (QM/MM) models are an appealing method for performing zeolite simulations. In QM/MM, a small cluster chosen to encompass the active center is described by QM, while the rest of the zeolite is described by MM. In the present study, we demonstrate that the charges and Lennard-Jones parameters on Si and O must be chosen properly for QM/MM calculations of adsorption energies and activation energies to agree closely with full QM calculations. The selection of parameters for Si and O is based on using the ωB97X-D functional for DFT calculations of the QM region, which is effective in capturing the effects of van der Waals interactions. A comparison of the heats of adsorption for a variety of adsorbates and activation energies for the cracking of propane and butane reveals that energies derived from QM/MM calculation carried out with appropriately selected MM parameters agree to within an rms error of ∼1.5 kcal/mol with QM calculations. To avoid reparametrization for new substrates, Lennard-Jones zeolite parameters are chosen to be compatible with existing CHARMM parameters. Transferability of these parameters is demonstrated by tests utilizing the B3LYP density functional and simulations of MFI and FAU zeolites. Moreover, the computational time for QM/MM calculations is considerably lower than that for QM calculations, and the ratio of computational times decreases rapidly with increasing size of the cluster used to represent the zeolite.
Separdar, L.; Davatolhagh, S.
2016-12-01
Molecular dynamics simulations at constant (N , V , T) are used to study the mutual effects of gold nanoparticles on the structure and dynamics of Kob-Andersen binary Lennard-Jones (BLJ) liquid within the framework of mode coupling theory of dynamic glass transition in the reciprocal space. The results show the 'softening' effect of the gold nanoparticles on the liquid dynamics in terms of (i) reducing the mode coupling crossover temperature Tc with respect to that of the bulk BLJ (i.e. BLJ without nanoparticles), (ii) decreasing the time interval of β-relaxation, and (iii) decreasing the exponent γ characterizing the power-law behavior of the α-relaxation time. This softening effect is explained in terms of the van der Waals attraction between the gold atoms comprising the nanoparticle and the BLJ host atoms, such that adsorption of host atoms onto the nanoparticle surface creates more space or free-volume for the other atoms to diffuse. By the same token interactions of purely excluded-volume-type are expected to result in the opposite effect. It is also noted that, much unlike BLJ host particles, the dynamics of gold nanoparticles is much less dependent on the wave-vector and that it exhibits a nearly exponential behavior in the α-relaxation regime.
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.
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
Vapour-liquid equilibria of two-centre Lennard-Jones fluids from the NpT plus test particle method
Kriebel, Christian; Müller, Andreas; Winkelmann, Jochen; Fischer, Johann
Vapour-liquid phase equilibria (VLE) are determined from the NpT plus test particle method for two-centre Lennard-Jones fluids of elongations L* = 0·22, 0·3292, 0·505, and 0·67. The resulting vapour pressures as well as the saturated vapour and liquid densities are correlated by simple equations. The thermodynamic consistency of the VLE data is confirmed on the basis of the Clausius-Clapeyron equation. Comparison is made with results from previous simulations, and from perturbation theory.
Kronome, Gergely; Liszi, Janos; Szalai, Istvan
The vapour pressures, saturated liquid and vapour densities, enthalpies of vaporization, isobaric, and saturation heat capacities are calculated for ethane and ethylene along their vapour-liquid equilibrium (VLE) curves from Monte Carlo simulations using the extended NpT plus test particle (XNpT + TP) method (Boda, D., Liszi, J., and Szalai, I., 1995, Chem. Phys. Lett. , 235, 140). The substances are modelled by two-centre Lennard-Jones molecules of elongations L * = 0.67 for ethane and L * = 0.74 for ethylene. Simulation results are compared with correlated experimental data. In the case of ethylene new values are required for the model parameters to obtain a good agreement with experimental data along the VLE curve. Our results show that the XNpT + TP method is appropriate for the simulation of caloric properties of molecular fluids along the VLE curve.
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.
Optimization of long range potential interaction parameters in ion mobility spectrometry
Wu, Tianyang; Derrick, Joseph; Nahin, Minal; Chen, Xi; Larriba-Andaluz, Carlos
2018-02-01
The problem of optimizing Lennard-Jones (L-J) potential parameters to perform collision cross section (CCS) calculations in ion mobility spectrometry has been undertaken. The experimental CCS of 16 small organic molecules containing carbon, hydrogen, oxygen, nitrogen, and fluoride in N2 was compared to numerical calculations using Density Functional Theory (DFT). CCS calculations were performed using the momentum transfer algorithm IMoS and a 4-6-12 potential without incorporating the ion-quadrupole potential. A ceteris paribus optimization method was used to optimize the intercept σ and potential well-depth ɛ for the given atoms. This method yields important information that otherwise would remain concealed. Results show that the optimized L-J parameters are not necessarily unique with intercept and well-depth following an exponential relation at an existing line of minimums. Similarly, the method shows that some molecules containing atoms of interest may be ill-conditioned candidates to perform optimizations of the L-J parameters. The final calculated CCSs for the chosen parameters differ 1% on average from their experimental counterparts. This result conveys the notion that DFT calculations can indeed be used as potential candidates for CCS calculations and that effects, such as the ion-quadrupole potential or diffuse scattering, can be embedded into the L-J parameters without loss of accuracy but with a large increase in computational efficiency.
Lennard-Jones fluids in a nanochannel
Hartkamp, Remco; Luding, Stefan; Nuernberg Messe GmbH,
2010-01-01
During the past few decades molecular dynamics has been a widely applied tool to simulate fluid confined in micro/nano geometries. What makes interfacial fluids fundamentally different from the bulk fluid is the fact that their density varies considerably over microscopic distances. A class of such
Reif, Maria M.; Hünenberger, Philippe H.
2011-04-01
The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [M. A. Kastenholz and P. H. Hünenberger, J. Chem. Phys. 124, 224501 (2006), 10.1529/biophysj.106.083667; M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144103 (2010)], the application of appropriate correction terms permits to obtain methodology-independent results. The corrected values are then exclusively characteristic of the underlying molecular model including in particular the ion-solvent van der Waals interaction parameters, determining the effective ion size and the magnitude of its dispersion interactions. In the present study, the comparison of calculated (corrected) hydration free energies with experimental data (along with the consideration of ionic polarizabilities) is used to calibrate new sets of ion-solvent van der Waals (Lennard-Jones) interaction parameters for the alkali (Li+, Na+, K+, Rb+, Cs+) and halide (F-, Cl-, Br-, I-) ions along with either the SPC or the SPC/E water models. The experimental dataset is defined by conventional single-ion hydration free energies [Tissandier et al., J. Phys. Chem. A 102, 7787 (1998), 10.1021/jp982638r; Fawcett, J. Phys. Chem. B 103, 11181] along with three plausible choices for the (experimentally elusive) value of the absolute (intrinsic) hydration free energy of the proton, namely, Δ G_hyd^{ominus }[H+] = -1100, -1075 or -1050 kJ mol-1, resulting in three sets L, M, and H for the SPC water model and three sets LE, ME, and HE for the SPC/E water model (alternative sets can easily be interpolated to intermediate Δ G_hyd^{ominus }[H+] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective ionic radius entering into the calculation of the correction terms is
Kuzyk, Raya
2011-01-01
This article presents a list of the best audiobooks of 2010. Among the past year's most memorable audiobooks, all recipients of starred "Library Journal" reviews, are four "LJ" Best Books, two postapocalyptic trilogy starters, two nonfiction tracts on marriage, a baseball novella, an adult/YA crossover novel, and an Obama biography.
Sun, Rui; Dubessy, Jean
2010-04-01
Molecular based equations of state (EOS) are attractive because they can take into account the energetic contribution of the main types of molecular interactions. This study models vapor-liquid equilibrium (VLE) and PVTx properties of the H 2O-CO 2 binary system using a Lennard-Jones (LJ) referenced SAFT (Statistical Associating Fluid Theory) EOS. The improved SAFT-LJ EOS is defined in terms of the residual molar Helmholtz energy, which is a sum of four terms representing the contributions from LJ segment-segment interactions, chain-forming among the LJ segments, short-range associations and long-range multi-polar interactions. CO 2 is modeled as a linear chain molecule with a constant quadrupole moment, and H 2O is modeled as a spherical molecule with four association sites and a dipole moment. The multi-polar contribution to Helmholtz energy, including the dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole contribution for H 2O-CO 2 system, is calculated using the theory of Gubbins and Twu (1978). Six parameters for pure H 2O and four parameters for pure CO 2 are needed in our model. The Van der Waals one-fluid mixing rule is used to calculate the Lennard-Jones energy parameter and volume parameter for the mixture. Two or three binary parameters are needed for CO 2-H 2O mixtures, which are evaluated from phase equilibrium data of the binary system. Comparison with the experimental data shows that our model represents the PVT properties of CO 2 better than other SAFT EOS without a quadrupole contribution. For the CO 2-H 2O system, our model agrees well with the vapor-liquid equilibrium data from 323-623 K. The average relative deviation for CO 2 solubility (expressed in mole fraction) in water is within 6%. Our model can also predict the PVTx properties of CO 2-H 2O mixtures up to 1073 K and 3000 bar. The good performance of this model indicates that: (1) taking account of the multi-polar contribution explicitly improves the agreement of calculated
From Dimer to Crystal: Calculating the Cohesive Energy of Rare Gas Solids
Halpern, Arthur M.
2012-01-01
An upper-level undergraduate project is described in which students perform high-level ab initio computational scans of the potential energy curves for Ne[subscript 2] and Ar[subscript 2] and obtain the respective Lennard-Jones (LJ) potential parameters [sigma] and [epsilon] for the dimers. Using this information, along with the summation of…
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
African Journals Online (AJOL)
containing bisphosphonates including alendronate inhibit prenylation.'" They act directly on the osteoclast by causing apoptosis via Mstl kinase cleavage and the activation of caspases, and these effects can be mimicked by lovastatin and reversed by ...
Hopping in a supercooled binary Lennard-Jones liquid
DEFF Research Database (Denmark)
Schrøder, Thomas; Dyre, Jeppe
1998-01-01
A binary LennardJones liquid has been investigated by molecular dynamics at equilibrium supercooled conditions. At the lowest temperature investigated, hopping is present in the system as indicated by a secondary peak in 4r2Gs(r,t), where Gs(r,t) is the van Hove self correlation function...
Hopping in a supercooled binary Lennard-Jones liquid
DEFF Research Database (Denmark)
Schrøder, Thomas; Dyre, Jeppe
1998-01-01
A binary LennardJones liquid has been investigated by molecular dynamics at equilibrium supercooled conditions. At the lowest temperature investigated, hopping is present in the system as indicated by a secondary peak in 4r2Gs(r,t), where Gs(r,t) is the van Hove self correlation function......", as often argued, and that the system has a single-peaked distribution of hopping-distances centered around the characteristic intermolecular distance....
Equilibrium fluctuations of the Lennard-Jones cluster surface
Zhukhovitskii, D. I.
2008-11-01
Spectra of the cluster surface equilibrium fluctuations are treated by decomposition into the bulk and net capillary ones. The bulk fluctuations without capillary ones are simulated by the surface of a cluster truncated by a sphere. The bulk fluctuation spectrum is shown to be generated primarily by the discontinuity in the spatial distribution of cluster internal particles. The net capillary fluctuation slice spectrum is obtained in molecular dynamics simulation by subtraction of the bulk fluctuation spectrum from the total one. This net spectrum is in the best agreement with a theoretical estimation if we assume the intrinsic surface tension to be independent of the wave number. The wave number cutoff is brought in balance with the intrinsic surface tension and excess surface area induced by the capillary fluctuations. It is shown that the ratio of the ordinary surface tension to the intrinsic one can be considered as a universal constant independent of the temperature and cluster size.
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
On the potential energy landscape of supercooled liquids and glasses
DEFF Research Database (Denmark)
Rodney, D.; Schrøder, Thomas
2011-01-01
The activation-relaxation technique (ART), a saddle-point search method, is applied to determine the potential energy landscape around supercooled and glassy configurations of a three-dimensional binary Lennard-Jones system. We show a strong relation between the distribution of activation energies...... of transitions undergone by the same supercooled liquid during a time trajectory simulated by molecular dynamics. We find that ART is biased towards more heterogeneous transitions with higher activation energies and more broken bonds than the MD simulation....
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...
Comparison of Hard-Core and Soft-Core Potentials for Modelling Flocking in Free Space
Smith, J. A; Martin, A. M
2009-01-01
An investigation into the properties of a two dimensional (2D+1) system of self propelled particles (known as boids) in free space is conducted using a Lagrangian Individual-Based Model. A potential, associated with each boid is specified and a Lagrangian is subsequently derived in order to obtain the equations of motion for each particle in the flock. The Morse potential and the Lennard-Jones potential, both well understood in atomic and molecular physics, are specified. In contrast to the o...
NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface
DEFF Research Database (Denmark)
Ingebrigtsen, Trond; Toxværd, Søren; Heilmann, Ole
2011-01-01
-potential-energy constraint via standard Lagrangian multipliers. The basic NVU algorithm is tested by single-precision computer simulations of the Lennard-Jones liquid. Excellent numerical stability is obtained if the force cutoff is smoothed and the two initial configurations have identical potential energy within machine...... precision. Nevertheless, just as for NVE algorithms, stabilizers are needed for very long runs in order to compensate for the accumulation of numerical errors that eventually lead to “entropic drift” of the potential energy towards higher values. A modification of the basic NVU algorithm is introduced...
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.
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.
Interface bonding in silicon oxide nanocontacts: interaction potentials and force measurements
Wierez-Kien, M.; Craciun, A. D.; Pinon, A. V.; Le Roux, S.; Gallani, J. L.; Rastei, M. V.
2018-04-01
The interface bonding between two silicon-oxide nanoscale surfaces has been studied as a function of atomic nature and size of contacting asperities. The binding forces obtained using various interaction potentials are compared with experimental force curves measured in vacuum with an atomic force microscope. In the limit of small nanocontacts (typically measured with sensitive probes the bonding is found to be influenced by thermal-induced fluctuations. Using interface interactions described by Morse, embedded atom model, or Lennard-Jones potential within reaction rate theory, we investigate three bonding types of covalent and van der Waals nature. The comparison of numerical and experimental results reveals that a Lennard-Jones-like potential originating from van der Waals interactions captures the binding characteristics of dry silicon oxide nanocontacts, and likely of other nanoscale materials adsorbed on silicon oxide surfaces. The analyses reveal the importance of the dispersive surface energy and of the effective contact area which is altered by stretching speeds. The mean unbinding force is found to decrease as the contact spends time in the attractive regime. This contact weakening is featured by a negative aging coefficient which broadens and shifts the thermal-induced force distribution at low stretching speeds.
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.
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.
Perturbation theory calculations of model pair potential systems
Energy Technology Data Exchange (ETDEWEB)
Gong, Jianwu [Iowa State Univ., Ames, IA (United States)
2016-01-01
Helmholtz free energy is one of the most important thermodynamic properties for condensed matter systems. It is closely related to other thermodynamic properties such as chemical potential and compressibility. It is also the starting point for studies of interfacial properties and phase coexistence if free energies of different phases can be obtained. In this thesis, we will use an approach based on the Weeks-Chandler-Anderson (WCA) perturbation theory to calculate the free energy of both solid and liquid phases of Lennard-Jones pair potential systems and the free energy of liquid states of Yukawa pair potentials. Our results indicate that the perturbation theory provides an accurate approach to the free energy calculations of liquid and solid phases based upon comparisons with results from molecular dynamics (MD) and Monte Carlo (MC) simulations.
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
Effect of the ordering potential on the structure of liquid alloys
Directory of Open Access Journals (Sweden)
Grosdidier B.
2011-05-01
Full Text Available The concept of “ordering or alloying potential” (J. Hafneri: from Hamiltonians to phase diagrams: Springer Berlin 1987 and R. N. Singh and F. Sommerii Rep. Prog. Phys. 60 (1997 57–150 enables the understanding of the different kind of alloys: hetero-coordinated one’s leading to compounds, homocoordinated ones leading to miscibility gap systems and substitutional alloys. The ordering potential is based on the comparison of identical atom interionic potentials (V11 and V22 and different atom interionic potential (V12 It allows the description of the demixing properties of some alloys. In order to understand the concepts, we developed our calculations by using a Lennard-Jones potential, the atomic structure being calculated by molecular dynamics simulation. We obtained surprising and unexpected results putting in evidence the time of simulation and the strength of the ordering potential.
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.
L-J phase in a Cu2.2Mn0.8Al alloy
Jeng, S. C.; Liu, T. F.
1995-06-01
A new type of precipitate (designated L-J phase) with two variants was observed within the (DO3 + L21) matrix in a Cu2.2Mn0.8Al alloy. Transmission electron microscopy examinations indicated that the L-J phase has an orthorhombic structure with lattice parameters a = 0.413 nm, b = 0.254 nm and c = 0.728 nm. The orientation relationship between the L-J phase and the matrix is (100)L-J//(011) m , (010)L-J//(111) m and (001)L-J//(211) m . The rotation axis and rotation angle between two variants of the L-J phase are [021] and 90 deg. The L-J phase has never been observed in various Cu-Al, Cu-Mn, and Cu-Al-Mn alloy systems before.
Pramana – Journal of Physics | Indian Academy of Sciences
Indian Academy of Sciences (India)
We have carried out Monte Carlo simulations in Gibbs ensemble for two-and three-dimensional double Yukawa fluid. We have compared liquid–vapour equilibrium curve with that of Lennard-Jones, when parameters occurring in double Yukawa potential are chosen to fit Lennard-Jones potential. The results are in good ...
Vapour–liquid equilibria of the two-and three-dimensional ...
Indian Academy of Sciences (India)
We have carried out Monte Carlo simulations in Gibbs ensemble for two-and three-dimensional double Yukawa fluid. We have compared liquid–vapour equilibrium curve with that of Lennard-Jones, when parameters occurring in double Yukawa potential are chosen to fit Lennard-Jones potential. The results are in good ...
Equation of state of matter irradiated by short laser pulse and geometry of spalled cupola
Petrov, Yu. V.; Zhakhovskii, V. V.; Inogamov, N. A.; Ashitkov, S. I.; Khokhlov, V. A.; Upadhyay, A. K.; Agranat, M. B.; Anisimov, S. I.; Nishihara, K.; Rethfeld, B.; Urbassek, H. M.
2008-05-01
The motion of both Lennard-Jones solids and metals induced by ultrashort laser irradiation near the ablation threshold is investigated by molecular dynamics simulation. The universality of the ablation threshold fluence with respect to the cohesion energy of solids irradiated by femtosecond laser pulses is demonstrated for Lennard-Jones solid and metals simulated by many-body EAM potentials.
Anion inhibition studies of two α-carbonic anhydrases from Lotus japonicus, LjCAA1 and LjCAA2.
Vullo, Daniela; Flemetakis, Emmanouil; Scozzafava, Andrea; Capasso, Clemente; Supuran, Claudiu T
2014-07-01
The model organism for the investigation of symbiotic nitrogen fixation in legumes Lotus japonicus encodes two carbonic anhydrases (CAs, EC 4.2.1.1) belonging to the α-class, LjCAA1 and LjCAA2. Here we report the kinetic characterization and inhibition of these two CAs with inorganic and complex anions and other molecules interacting with zinc proteins, such as sulfamide, sulfamic acid, and phenylboronic/arsonic acids. LjCAA1 showed a high catalytic activity for the CO2 hydration reaction, with a k(cat) of 7.4∗10(5) s(-1) and a k(cat)/K(m) of 9.6∗10(7) M(-1) s(-1) and was inhibited in the low micromolar range by N,N-diethyldithiocarbamate, sulfamide, sulfamic acid, phenylboronic/arsonic acid (K(I)s of 4-62 μM). LjCAA2 showed a moderate catalytic activity for the physiologic reaction, with a k(cat) of 4.0∗10(5) s(-1) and a k(cat)/K(m) of 4.9∗10(7) M(-1) s(-1). The same anions mentioned above for the inhibition of LjCAA1 showed the best activity against LjCAA2 (K(I)s of 7-29 μM). Nitrate and nitrite, anions involved in nitrogen fixation, showed lower affinity for the two enzymes, with inhibition constants in the range of 3.7-7.0 mM. Halides and sulfate also behaved in a distinct manner towards the two enzymes investigated here. As LjCAA1/2 participate in the pH regulation processes and CO2 metabolism within the nitrogen-fixing nodules of the plant, our studies may shed some light regarding these complex biochemical processes. Copyright © 2014 Elsevier Inc. All rights reserved.
The nonadditive intermolecular potential for water revised
International Nuclear Information System (INIS)
Dang, L.X.
1992-01-01
The results of an improved version of a nonadditive intermolecular model for water that explicitly includes the nonadditive polarization energy are reported. The original polarizable water potential model (POL1), upon which the improved version is based, was developed by Caldwell, Dang, and Kollman [J. Am. Soc. Chem. 112, 9144 (1990)]. To improve the POL1 model, we developed a new set of atomic polarizabilities that reproduce the experimental molecular polarizability for water using the atom--dipole interaction model (Applequist, Carl, and Fung [J. Am. Soc. Chem. 94, 2952 (1972)]). Using the new atomic polarizabilities, we optimized the Lennard-Jones parameters for O--O interactions to improve the model. As expected, the new model has improved the radial distribution functions and the average potential energy for liquid water as well as the density and the average total dipole moment. The model is then used to compute the binding energies of Cs + --water clusters. Without the need for three-body forces (ion--water--water interaction), the agreement between the results of molecular-dynamics simulations and experimental energies of cluster formation is very good
Validity of the Rosenfeld relationship: A comparative study of the ...
Indian Academy of Sciences (India)
In this paper we explore the validity of the Rosenfeld and the Dzugutov relation for the Lennard- Jones (LJ) system, its repulsive counterpart, the WCA system and a network forming liquid, the NTW model. We find that for all the systems both the relations are valid at high temperature regime with an universalexponent close ...
Van Westen, T.; Vlugt, T.J.H.; Gross, J.
2015-01-01
We study the isotropic (vapor and liquid) phase behavior of attractive chain fluids. Special emphasis is placed on the role of molecular flexibility, which is studied by means of a rod-coil model. Two new equations of state (EoSs) are developed for square-well- (SW) and Lennard-Jones (LJ) chain
Nonpolar solvation dynamics for a nonpolar solute in room ...
Indian Academy of Sciences (India)
Home; Journals; Journal of Chemical Sciences; Volume 130; Issue 1. Nonpolar solvation ... Frank-Condon type excitation of the solute, previously in equilibrium inRTIL solvent, has been modelled by abruptly changing the Lennard-Jones(LJ) diameter of the solute atoms and thereby disrupting the equilibrium situation.
Cluster growing process and a sequence of magic numbers
DEFF Research Database (Denmark)
Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter
2003-01-01
demonstrate that in this way all known global minimum structures of the Lennard-Jones (LJ) clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence for the clusters of noble gas atoms...
Pramana – Journal of Physics | Indian Academy of Sciences
Indian Academy of Sciences (India)
dimensional spatial inhomogeneity is parallel to the direction of propagation. pp 269-279 Research Articles. Structures and autocorrelation functions of liquid Al and Mg modelled via Lennard-Jones potential from molecular dynamics simulation.
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 ...
Prakash, Muthuramalingam; Lemaire, Thibault; Di Tommaso, Devis; de Leeuw, Nora; Lewerenz, Marius; Caruel, Matthieu; Naili, Salah
2017-10-01
Water diffusion in the vicinity of hydroxyapatite (HAP) crystals is a key issue to describe biomineralization process. In this study, a configuration of parallel HAP platelets mimicking bone nanopores is proposed to characterize the nanoscopic transport properties of water molecules at HAP-water surface and interfaces using various potential models such as combination of the Core-Shell (CS) model, Lennard-Jones (LJ) potentials with SPC or SPC/E water models. When comparing all these potentials models, it appears that the core-shell potential for HAP together with the SPC/E water model more accurately predicts the diffusion properties of water near HAP surface. Moreover, we have been able to put into relief the possibility of observing hydroxyl (OH-) ion dissociation that modifies the water structure near the HAP surface.
New Aspects of Collective Phenomena at Nanoscales in Quantum Plasmas
Shukla, P. K.; Eliasson, B.
We present two novel collective effects is quantum plasmas. First, we discuss novel attractive force between ions that are shielded by the degenerate electrons in quantum plasmas. Here we show that the electric potential around an isolated ion has a hard core negative part that resembles the Lennard-Jones (LJ)-type potential. Second, we present theory for stimulated scattering instabilities of electromagnetic waves off quantum plasma modes. Our studies are based on the quantum hydrodynamical description of degenerate electrons that are greatly influenced by electromagnetic and quantum forces. The relevance of our investigation to bringing ions closer for fusion in high-energy solid density plasmas at atomic dimensions, and for producing coherent short wavelength radiation in the x-ray regime at nanoscales are discussed.
Kader, Mohamed Sayed Abdel
2002-07-01
Depolarized interaction-induced light scattering spectra of tetrafluoromethane in the frequency range 2-150 cm-1 at 294.5 K and 0.91 mol/l with the interaction pressure virial coefficient and viscosity have been used for deriving the empirical multiparameter Morse-Morse-Morse-Spline-van der Waals (M3SV), Lennard-Jones, Kihara, and exp-6 intermolecular potentials. The line shape at relatively low frequencies is determined largely by the effect of bound and free transitions. At intermediate frequencies it is sensitive to both the attractive part of the potential and the short-range part of the polarizability anisotropy. The high frequency wings are discussed in terms of the collision-induced rotational Raman effect and estimates for the dipole-quadrupole and dipole-octopole polarizabilities A and E, respectively, are obtained. Absolute zeroth and second moments have been measured and compared with theoretical calculations using these models of the intermolecular potentials. The results show that M3SV is the most accurate potential yet reported for this system.
Nurisso, Alessandra; Bravo, Juan; Carrupt, Pierre-Alain; Daina, Antoine
2012-05-25
GOLD is a molecular docking software widely used in drug design. In the initial steps of docking, it creates a list of hydrophobic fitting points inside protein cavities that steer the positioning of ligand hydrophobic moieties. These points are generated based on the Lennard-Jones potential between a carbon probe and each atom of the residues delimitating the binding site. To thoroughly describe hydrophobic regions in protein pockets and properly guide ligand hydrophobic moieties toward favorable areas, an in-house tool, the MLP filter, was developed and herein applied. This strategy only retains GOLD hydrophobic fitting points that match the rigorous definition of hydrophobicity given by the molecular lipophilicity potential (MLP), a molecular interaction field that relies on an atomic fragmental system based on 1-octanol/water experimental partition coefficients (log P(oct)). MLP computations in the binding sites of crystallographic protein structures revealed that a significant number of points considered hydrophobic by GOLD were actually polar according to the MLP definition of hydrophobicity. To examine the impact of this new tool, ligand-protein complexes from the Astex Diverse Set and the PDB bind core database were redocked with and without the use of the MLP filter. Reliable docking results were obtained by using the MLP filter that increased the quality of docking in nonpolar cavities and outperformed the standard GOLD docking approach.
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.
Liu, Yang; Huang, Yin; Ma, Jianyi; Li, Jun
2018-02-15
Collision energy transfer plays an important role in gas phase reaction kinetics and relaxation of excited molecules. However, empirical treatments are generally adopted for the collisional energy transfer in the master equation based approach. In this work, classical trajectory approach is employed to investigate the collision energy transfer dynamics in the C 2 H 2 -Ne system. The entire potential energy surface is described as the sum of the C 2 H 2 potential and interaction potential between C 2 H 2 and Ne. It is highlighted that both parts of the entire potential are highly accurate. In particular, the interaction potential is fit to ∼41 300 configurations determined at the level of CCSD(T)-F12a/cc-pCVTZ-F12 with the counterpoise correction. Collision energy transfer dynamics are then carried out on this benchmark potential and the widely used Lennard-Jones and Buckingham interaction potentials. Energy transfers and related probability densities at different collisional energies are reported and discussed.
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.
Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures.
Chatzieleftheriou, Stavros; Adendorff, Matthew R; Lagaros, Nikos D
2016-10-24
The potential energy of molecules and nanostructures is commonly calculated in the molecular mechanics formalism by superimposing bonded and nonbonded atomic energy terms, i.e. bonds between two atoms, bond angles involving three atoms, dihedral angles involving four atoms, nonbonded terms expressing the Coulomb and Lennard-Jones interactions, etc. In this work a new, generalized numerical simulation is presented for studying the mechanical behavior of three-dimensional nanostructures at the atomic scale. The energy gradient and Hessian matrix of such assemblies are usually computed numerically; a potential energy finite element model is proposed herein where these two components are expressed analytically. In particular, generalized finite elements are developed that express the interactions among atoms in a manner equivalent to that invoked in simulations performed based on the molecular dynamics method. Thus, the global tangent stiffness matrix for any nanostructure is formed as an assembly of the generalized finite elements and is directly equivalent to the Hessian matrix of the potential energy. The advantages of the proposed model are identified in terms of both accuracy and computational efficiency. In the case of popular force fields (e.g., CHARMM), the computation of the Hessian matrix by implementing the proposed method is of the same order as that of the gradient. This analysis can be used to minimize the potential energy of molecular systems under nodal loads in order to derive constitutive laws for molecular systems where the entropy and solvent effects are neglected and can be approximated as solids, such as double stranded DNA nanostructures. In this context, the sequence dependent stretch modulus for some typical base pairs step is calculated.
Okumura, Hisashi; Heyes, David M
2006-12-01
We compare the results of three-dimensional molecular-dynamics (MD) simulations of a Lennard-Jones (LJ) liquid with a hydrostatic (HS) solution of a high temperature liquid channel which is surrounded by a fluid at lower temperature. The maximum temperature gradient, dT/dx , between the two temperature regions ranged from infinity (step function) to dT/dx=0.1 (in the usual LJ units). Because the systems were in stationary-nonequilibrium states with no fluid flow, both MD simulation and the HS solution gave flat profiles for the normal pressure in all temperature-gradient cases. However, the other quantities showed differences between the two methods. The MD-derived density was found to oscillate over the length of ca. 8 LJ particle diameters from the boundary plane in the system with the infinite temperature gradient, while the HS-derived density showed simply a stepwise profile. The MD simulation also showed another anomaly near the boundary in potential energy. We have found systems in which the HS treatment works well and those where the HS approach breaks down, and therefore established the minimum length scale for the HS treatment to be valid. We also compare the kinetic temperature and the configurational temperature in these systems, and show that these can differ in the transition zone between the two temperatures.
Functional domain analysis of the Remorin protein LjSYMREM1 in Lotus japonicus
DEFF Research Database (Denmark)
Tóth, Katalin; Stratil, Thomas F; Madsen, Esben B
2012-01-01
In legumes rhizobial infection during root nodule symbiosis (RNS) is controlled by a conserved set of receptor proteins and downstream components. MtSYMREM1, a protein of the Remorin family in Medicago truncatula, was shown to interact with at least three receptor-like kinases (RLKs) that are ess......In legumes rhizobial infection during root nodule symbiosis (RNS) is controlled by a conserved set of receptor proteins and downstream components. MtSYMREM1, a protein of the Remorin family in Medicago truncatula, was shown to interact with at least three receptor-like kinases (RLKs...... by the Remorin C-terminal region with its coiled-coil domain while the RLK kinase domains transiently interact in vivo and phosphorylate a residue in the N-terminal region of the LjSYMREM1 protein in vitro. These data provide novel insights into the mechanism of this putative molecular scaffold protein...
2012-02-07
..., and the FAA must issue a finding of regulatory adequacy pursuant to Sec. 611 of Public Law 92-574, the ``Noise Control Act of 1972.'' The FAA issues special conditions, as defined in 14 CFR 11.19, in... novel or unusual design features: The Model LJ-200-1A10 airplane flight deck design incorporates a...
PSO Method for Fitting Analytic Potential Energy Functions. Application to I-(H2O).
Bhandari, H N; Ma, X; Paul, A K; Smith, P; Hase, W L
2018-03-13
In this work a particle swarm optimization (PSO) algorithm was used to fit an analytic potential energy function to I - (H 2 O) intermolecular potential energy curves calculated with DFT/B97-1 theory. The analytic function is a sum of two-body terms, each written as a generalized sum of Buckingham and Lennard-Jones terms with only six parameters. Two models were used to describe the two-body terms between I - and H 2 O: a three-site model H 2 O and a four-site model including a ghost atom. The fits are compared with those obtained with a genetic/nonlinear least-squares algorithm. The ghost atom model significantly improves the fitting accuracy for both algorithms. The PSO fits are significantly more accurate and much less time-consuming than those obtained with the genetic/nonlinear least-squares algorithm. Eight I - ---H 2 O potential energy curves, fit with the PSO algorithm for the three- and four-site models, have RMSE of 1.37 and 0.22 kcal/mol and compute times of ∼20 and ∼68 min, respectively. The PSO fit for the four-site model is quite adequate for determining densities of states and partition functions for I - (H 2 O) n clusters at high energies and temperatures, respectively. The PSO algorithm was also applied to the eight potential energy curves, with the four-site model, for a short time ∼8 min fitting. The RMSE was small, only 0.37 kcal/mol, showing the high efficiency of the PSO algorithm with retention of a good fitting accuracy. The PSO algorithm is a good choice for fitting analytic potential energy functions, and for the work presented here was able to find an adequate fit to an I - (H 2 O) analytic intermolecular potential with a small number of parameters.
Computer simulation of liquid-vapor coexistence of confined quantum fluids.
Trejos, Víctor M; Gil-Villegas, Alejandro; Martinez, Alejandro
2013-11-14
The liquid-vapor coexistence (LV) of bulk and confined quantum fluids has been studied by Monte Carlo computer simulation for particles interacting via a semiclassical effective pair potential Veff(r) = VLJ + VQ, where VLJ is the Lennard-Jones 12-6 potential (LJ) and VQ is the first-order Wigner-Kirkwood (WK-1) quantum potential, that depends on β = 1∕kT and de Boer's quantumness parameter Λ=h/σ√mε, where k and h are the Boltzmann's and Planck's constants, respectively, m is the particle's mass, T is the temperature of the system, and σ and ε are the LJ potential parameters. The non-conformal properties of the system of particles interacting via the effective pair potential Veff(r) are due to Λ, since the LV phase diagram is modified by varying Λ. We found that the WK-1 system gives an accurate description of the LV coexistence for bulk phases of several quantum fluids, obtained by the Gibbs Ensemble Monte Carlo method (GEMC). Confinement effects were introduced using the Canonical Ensemble (NVT) to simulate quantum fluids contained within parallel hard walls separated by a distance Lp, within the range 2σ ≤ Lp ≤ 6σ. The critical temperature of the system is reduced by decreasing Lp and increasing Λ, and the liquid-vapor transition is not longer observed for Lp∕σ < 2, in contrast to what has been observed for the classical system.
Computer simulation of liquid-vapor coexistence of confined quantum fluids
Trejos, Víctor M.; Gil-Villegas, Alejandro; Martinez, Alejandro
2013-11-01
The liquid-vapor coexistence (LV) of bulk and confined quantum fluids has been studied by Monte Carlo computer simulation for particles interacting via a semiclassical effective pair potential Veff(r) = VLJ + VQ, where VLJ is the Lennard-Jones 12-6 potential (LJ) and VQ is the first-order Wigner-Kirkwood (WK-1) quantum potential, that depends on β = 1/kT and de Boer's quantumness parameter Λ = h/σ √{mɛ }, where k and h are the Boltzmann's and Planck's constants, respectively, m is the particle's mass, T is the temperature of the system, and σ and ɛ are the LJ potential parameters. The non-conformal properties of the system of particles interacting via the effective pair potential Veff(r) are due to Λ, since the LV phase diagram is modified by varying Λ. We found that the WK-1 system gives an accurate description of the LV coexistence for bulk phases of several quantum fluids, obtained by the Gibbs Ensemble Monte Carlo method (GEMC). Confinement effects were introduced using the Canonical Ensemble (NVT) to simulate quantum fluids contained within parallel hard walls separated by a distance Lp, within the range 2σ ⩽ Lp ⩽ 6σ. The critical temperature of the system is reduced by decreasing Lp and increasing Λ, and the liquid-vapor transition is not longer observed for Lp/σ < 2, in contrast to what has been observed for the classical system.
Results of the radiological survey at 10 Long Valley Road, Lodi, New Jersey (LJ055)
International Nuclear Information System (INIS)
Foley, R.D.; Floyd, L.M.; Carrier, R.F.
1989-11-01
Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 10 Long Valley Road, Lodi, New Jersey (LJ055), was conducted during 1985 and 1986. Results of the survey demonstrated no radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions were not significantly different from normal background levels in the northern New Jersey area. 4 refs., 5 figs., 3 tabs
Results of the radiological survey at 104 Avenue E, Lodi, New Jersey (LJ086)
International Nuclear Information System (INIS)
Foley, R.D.; Floyd, L.M.
1989-12-01
Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 104 Avenue E, Lodi, New Jersey (LJ086), was conducted during 1988. 5 refs., 2 figs., 3 tabs
Results of the radiological survey at 15 John Street, Lodi, New Jersey (LJ087)
International Nuclear Information System (INIS)
Foley, R.D.; Floyd, L.M.
1989-12-01
Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 15 John Street, Lodi, New Jersey (LJ087), was conducted during 1988. 5 refs., 3 figs., 3 tabs
Results of the radiological survey at 105 Garibaldi Avenue, Lodi, New Jersey (LJ065)
International Nuclear Information System (INIS)
Foley, R.D.; Floyd, L.M.; Carrier, R.F.
1989-11-01
Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 105 Garibaldi Avenue, Lodi, New Jersey (LJ065), was conducted during 1987. 4 refs., 4 figs., 3 tabs
Results of the radiological survey at 90 C Avenue, Lodi, New Jersey (LJ079)
International Nuclear Information System (INIS)
Foley, R.D.; Floyd, L.M.
1989-06-01
Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducted an investigative radiological survey during 1988 at 90 C Avenue, Lodi, New Jersey (LJ079), one of the properties in the vicinity of the MCW site. The survey included a gamma radiation scan of the surface and at one meter above the surface, as well as radionuclide sampling of surface and subsurface soil. The survey objective was to determine whether this site was contaminated with radioactive residues derived from MCW, principally 232 Th. Results of the survey demonstrated radionuclide concentrations in excess of DOE remedial action criteria, primarily from the 232 Th decay chain, with some contamination from 226 Ra. The radionuclide distributions are typical of the type of material originating from the MCW site. 5 refs., 3 figs., 3 tabs
Thermodynamic properties of confined square-well fluids with multiple associating sites
Trejos, Víctor M.; Quintana-H, Jacqueline
2018-02-01
In this work, a molecular simulation study of confined hard-spheres particles with square-well (SW) attractive interactions with two and four associating SW sites based on the first-order perturbation form of Wertheim's theory is presented. An extended version of the Gibbs ensemble technique for inhomogeneous fluids [A. Z. Panagiotopoulos, Mol. Phys. 62, 701 (1987)] is used to predict the adsorption density profiles for associating fluids confined between opposite parallel walls. The fluid is confined in four kinds of walls: hard-wall, SW wall, Lennard-Jones (LJ) 12-6 wall potential, and LJ 10-4 wall potential. We analyze the behavior of the confined system for several supercritical temperatures as a function of variation of molecular parameters: potential range λ, bulk densities ρb*, pore width H, cutoff range interaction rc*, and range of the potential and depth of the particle-wall (λw, ɛw*). Additionally, we include predictions for liquid-vapor coexistence of bulk associative particles and how their critical properties are modified by the presence of associative sites in the molecule. The molecular simulation data presented in this work are of prime importance to the development of theoretical approaches for inhomogeneous fluids as classical density functional theory. The simulation results presented here are resourceful for predicting adsorption isotherms of real associating fluids such as water.
Zheng, Zheng; Merz, Kenneth M
2013-05-24
We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the Protein Databank (PDB). Forty-nine (49) types of atomic pairwise interactions were derived using this method, which we call the knowledge-based and empirical combined scoring algorithm (KECSA). Two validation benchmarks were introduced to test the performance of KECSA. The first validation benchmark included two test sets that address the training set and enthalpy/entropy of KECSA. The second validation benchmark suite included two large-scale and five small-scale test sets, to compare the reproducibility of KECSA, with respect to two empirical score functions previously developed in our laboratory (LISA and LISA+), as well as to other well-known scoring methods. Validation results illustrate that KECSA shows improved performance in all test sets when compared with other scoring methods, especially in its ability to minimize the root mean square error (RMSE). LISA and LISA+ displayed similar performance using the correlation coefficient and Kendall τ as the metric of quality for some of the small test sets. Further pathways for improvement are discussed for which would allow KECSA to be more sensitive to subtle changes in ligand structure.
Do, D D; Do, H D
2004-08-17
In this paper, we studied vapor-liquid equilibria (VLE) and adsorption of ethylene on graphitized thermal carbon black and in slit pores whose walls are composed of graphene layers. Simple models of a one-center Lennard-Jones (LJ) potential and a two-center united atom (UA)-LJ potential are investigated to study the impact of the choice of potential models in the description of VLE and adsorption behavior. Here, we used a Monte Carlo simulation method with grand canonical Monte Carlo (GCMC) and Gibbs ensemble Monte Carlo ensembles. The one-center potential model cannot describe adequately the VLE over the practical range of temperature from the triple point to the critical point. On the other hand, the two-center potential model (Wick et al. J. Phys. Chem. B 2000, 104, 8008-8016) performs well in the description of VLE (saturated vapor and liquid densities and vapor pressure) over the wide range of temperature. This UA-LJ model is then used in the study of adsorption of ethylene on graphitized thermal carbon black and in slit pores. Agreement between the GCMC simulation results and the experimental data on graphitized thermal carbon black for moderate temperatures is excellent, demonstrating that the potential of the GCMC method and the proper choice of potential model are essential to investigate adsorption. For slit pores of various sizes, we have found that the behavior of ethylene exhibits a number of features that are not manifested in the study of spherical LJ particles. In particular, the singlet density distribution versus distance across the pore and the angle between the molecular axis and the z direction provide rich information about the way molecules arrange themselves when the pore width is varied. Such an arrangement has been found to be very sensitive to the pore width.
Ghorbanzadeh Ahangari, Morteza; Fereidoon, A.; Hamed Mashhadzadeh, Amin
2017-12-01
In present study, we investigated mechanical, electronic and interlayer properties of mono, bi and 3layer of Boron-Nitride (B-N), Aluminum-Nitride (Al-N) and Gallium-Nitride (Ga-N) graphene sheets and compared these results with results obtained from carbonic graphenes (C-graphenes). For reaching this purpose, first we optimized the geometrical parameters of these graphenes by using density functional theory (DFT) method. Then we calculated Young's modulus of graphene sheet by compressing and then elongating these sheets in small increment. Our results indicates that Young's modulus of graphenes didn't changed obviously by increasing the number of layer sheet. We also found that carbonic graphene has greatest Young's modulus among another mentioned sheets because of smallest equilibrium distance between its elements. Next we modeled the van der Waals interfacial interaction exist between two sheets with classical spring model by using general form of Lennard-Jones (L-J) potential for all of mentioned graphenes. For calculating L-J parameters (ε and σ), the potential energy between layers of mentioned graphene as a function of the separation distance was plotted. Moreover, the density of states (DOS) are calculated to understand the electronic properties of these systems better.
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 periodic solution found by Simó through S (2). For the LJ system, we calculated the index for the solution tending to the figure-eight solution of the a = 6 homogeneous system for the period T \\to ∞ . We obtain N, N c and N e as monotonically increasing functions of T from T \\to ∞ , which start with N=N_c=N_e=0 , jump at the smallest T by 1, and reach N = 12, N_c=4 , and N_e=1 for T \\to ∞ in the other branch.
Effective particle size from molecular dynamics simulations in fluids
Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.
2018-04-01
We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.
Effective particle size from molecular dynamics simulations in fluids
Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.
2017-12-01
We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.
Results of the radiological survey at 9 Redstone Lane, Lodi, New Jersey (LJ069)
International Nuclear Information System (INIS)
Foley, R.D.; Carrier, R.F.
1989-07-01
Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process waste and residues associated with the production and refining of thorium and thorium compounds from monozite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Areas residents used the sandlike waste from this thorium extraction process mixed with teas and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigate radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, 9 Redstone Lane, Lodi, New Jersey (LJ069), was conducted during 1987. Measurements at the private property located at 9 Redstone Lane indicate slightly elevated gamma exposure rates in association with cinder-like material observed in logging holes. These elevated levels result from naturally occurring radioactivity present in such substances as ashes and cinders. They are not related to the deposit of residues from processing operations at the MCW site. All other radiological findings conform to the guidelines established by the DOE for the Maywood, New Jersey, area remedial action plan. 4 refs., 3 figs., 3 tabs
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
Microscopic structure of the hydrogen-xenon mixture
Senesi, R.; Nardone, M.; Ricci, F. P.; Ricci, M. A.; Soper, A. K.
1997-09-01
We report a neutron-diffraction study of the microscopic structure of the H2-Xe binary mixture in the Xe-rich phase, xXe=0.78, at T=283 K and P=170 bars, i.e., in the vicinity of the second-type gas-gas demixing surface. The site-site distribution functions are extracted employing the H-D isotopic substitution technique. We report also molecular-dynamics simulations for a mixture of equivalent Lennard-Jones (LJ) atoms. The experimental results are compared with previous ones obtained for the He-Xe and Ne-Xe mixtures, which show a first- and a second-type gas-gas transition, respectively. The general picture already suggested by the other two mixtures agrees also with the present results, although in this case the center-center distribution functions H2-H2 and H2-Xe are clearly modulated by the Xe-Xe correlations. In particular the features found in the distribution functions of the mixture suggest that the LJ potential model is not able to reproduce at a satisfactory level the H2-H2 and the H2-Xe correlation functions and that a (XeH4) chemical complex is present.
Webbaserad pedagogisk meritportfölj - från idé till verklighet
Directory of Open Access Journals (Sweden)
Jakob Johansson
2011-03-01
åväl sökanden som bedömare. Det finns behov av redovisning av pedagogiska meriter även för andra ändamål än vid tjänstetillsättningar. Många medarbetare (som inte avser att söka akademisk tjänst gör betydande insatser i undervisningen exempelvis i form av administration, föreläsningar, seminarieledning samt klinisk handledning, och dessa prestationer bör användas som underlag för exempelvis planeringssamtal, löneförhandlingar och kompetensutveckling. Många finner det svårt att redovisa dessa undervisningsinsatser. Orsaken till detta är sannolikt delvis bristen på tradition att bokföra pedagogiskt arbetet (i kontrast till vetenskapligt arbete, men också bristen på ett användarvänligt verktyg för bokföring. Detta var startskottet för ett projekt som syftade till att framställa en personlig webbaserad pedagogisk meritportfölj som skulle kunna överbrygga det praktiska bekymret och ge medarbetarna ett smidigt verktyg för dokumentation av och reflektion runt pedagogiska meriter. Detta samtidigt som det skulle vara acceptabelt som instrument för sökande av akademisk tjänst genom att bygga på Uppsala universitets pedagogiska program och riktlinjer för meritvärdering. Denna artikel beskriver processen från idé till färdig webbaserad pedagogisk meritportfölj för vetenskapsområdet för medicin och farmaci vid Uppsala universitet. Även om det sannolikt existerar liknande webb-verktyg för bokföring av pedagogiska meriter så är detta o
Predicting the Function of 4-Coumarate:CoA Ligase (LJ4CL1 in Lonicera japonica
Directory of Open Access Journals (Sweden)
Yuan Yuan
2014-02-01
Full Text Available 4-Coumarate:CoA ligases (4CLs are a group of essential enzymes involved in the pathway of phenylpropanoid-derived compound metabolisms; however it is still difficult to identify orthologs and paralogs of these important enzymes just based on sequence similarity of the conserved domains. Using sequence data of 20 plant species from the public databases and sequences from Lonicera japonica, we define 1252 adenosine monophosphate (AMP-dependent synthetase/ligase sequences and classify them into three phylogenetic clades. 4CLs are in one of the four subgroups, according to their partitioning, with known proteins characterized in A. thaliana and Oryza sativa. We also defined 184 non-redundant sequences that encode proteins containing the GEICIRG motif and the taxonomic distribution of these GEICIRG-containing proteins suggests unique catalytic activities in plants. We further analyzed their transcription levels in L. japonica and L. japonica. var. chinensis flowers and chose the highest expressed genes representing the subgroups for structure and binding site predictions. Coupled with liquid chromatography-mass spectrometry (LC-MS analysis of the L. japonica flowers, the structural study on putative substrate binding amino acid residues, ferulate, and 4-coumaric acid of the conserved binding-site of LJ4CL1 leads to a conclusion that this highly expressed protein group in the flowers may process 4-coumarate that represents 90% of the known phenylpropanoid-derived compounds. The activity of purified crude LJ4CL1 protein was analyzed using 4-coumarate as template and high activity indicating that 4-coumarate is one of the substrates of LJ4CL1.
A practical law to predict the appearance sizes of multiply charged rare-gas and molecular clusters
Bonhommeau, David A.
2017-10-01
A dimensionless law depending on cluster size N is derived from the Rayleigh limit expressed in reduced Lennard-Jones (LJ) units to predict the critical sizes nc (z) of clusters carrying z positive charges. This relationship provides suitable estimates of nc (z) (z = 2 - 4) for rare-gas clusters, including neon clusters whose predicted critical sizes deviate from experimental expectations by less than 12% for different choices of LJ parameters. An extension to 11 nonpolar and 15 polar molecular clusters, from dimers to aromatic hydrocarbons, is achieved that demonstrates the broad applicability of the formula despite inaccuracies for highly polar systems.
Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A
2011-05-19
A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. © 2011 American Chemical Society
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. 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.
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.
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
Indian Academy of Sciences (India)
Structures and autocorrelation functions of liquid Al and Mg modelled via Lennard-Jones potential from molecular dynamics simulation ... Collision frequency of Lennard–Jones fluids at high densities by equilibrium molecular dynamics simulation ... Adhesion energy, surface traction and surface tension in liquid xenon.
Application of the cluster variation method to ordering in an interstitital solid solution
DEFF Research Database (Denmark)
Pekelharing, Marjon I.; Böttger, Amarante; Somers, Marcel A. J.
1999-01-01
The tetrahedron approximation of the cluster variation method (CVM) was applied to describe the ordering on the fcc interstitial sublattice of gamma-Fe[N] and gamma'-Fe4N1-x. A Lennard-Jones potential was used to describe the dominantly strain-induced interactions, caused by misfitting of the N a...
A Computational Study of Rare Gas Clusters: Stepping Stones to the Solid State
Glendening, Eric D.; Halpern, Arthur M.
2012-01-01
An upper-level undergraduate or beginning graduate project is described in which students obtain the Lennard-Jones 6-12 potential parameters for Ne[subscript 2] and Ar[subscript 2] from ab initio calculations and use the results to express pairwise interactions between the atoms in clusters containing up to N = 60 atoms. The students use simulated…
Line Tension and Wettability of Nanodrops on Curved Surfaces
Maheshwari, Shantanu; van der Hoef, Martin Anton; Lohse, Detlef
2016-01-01
In this work we study the formation of nanodrops on curved surfaces (both convex and concave) by means of molecular dynamics simulations, where the particles interact via a Lennard-Jones potential. We find that the contact angle is not affected by the curvature of the substrate, in agreement with
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.)
Thermal conductivity of simple liquids: temperature and packing-fraction dependence.
Ohtori, Norikazu; Ishii, Yoshiki; Togawa, Yoshinori; Oono, Takuya; Takase, Keiichi
2014-02-01
The thermal conductivity of rare gases in liquid and dense fluid states has been evaluated using molecular dynamics simulation with the Lennard-Jones (LJ) potentials and the Green-Kubo (GK) formula. All the calculated thermal conductivities are in very good agreement with experimental results for a wide range of temperature and density. Special attention was paid to temperature and packing-fraction dependence which is nontrivial from dimensional analysis on the LJ potentials and the GK formula. First, the temperature dependence of T(1/4) was determined from the calculations at constant densities. Secondly, in order to obtain the dependence on packing fraction from that on number density separately, a scaling method of particle and/or cell size was introduced. The number density dependence of (N/V)(2/3) which is expected from the dimensional analysis of the GK formulas was confirmed and the packing-fraction dependence of η(3/2) was determined by using the scaling method. It turned out that the summarized functional form of m(-1/2)(N/V)(2/3)η(3/2)T(1/4) can well express both the calculated and experimental thermal conductivities for Ar, Kr, and Xe, where m is the atomic mass. The scaling method has also been applied to molten NaCl and KCl so that it has been found that the thermal conductivity has the packing-fraction dependence of η(2/3) which is much weaker than that of the simple LJ liquids.
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.
Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS
Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan
Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiency has been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume.
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.
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).
Thermodynamics of confined gallium clusters.
Chandrachud, Prachi
2015-11-11
We report the results of ab initio molecular dynamics simulations of Ga13 and Ga17 clusters confined inside carbon nanotubes with different diameters. The cluster-tube interaction is simulated by the Lennard-Jones (LJ) potential. We discuss the geometries, the nature of the bonding and the thermodynamics under confinement. The geometries as well as the isomer spectra of both the clusters are significantly affected. The degree of confinement decides the dimensionality of the clusters. We observe that a number of low-energy isomers appear under moderate confinement while some isomers seen in the free space disappear. Our finite-temperature simulations bring out interesting aspects, namely that the heat capacity curve is flat, even though the ground state is symmetric. Such a flat nature indicates that the phase change is continuous. This effect is due to the restricted phase space available to the system. These observations are supported by the mean square displacement of individual atoms, which are significantly smaller than in free space. The nature of the bonding is found to be approximately jellium-like. Finally we note the relevance of the work to the problem of single file diffusion for the case of the highest confinement.
Marques, Jorge M C; Pereira, Francisco B
2013-03-05
We performed a global minimum search of mixed rare-gas clusters by applying an evolutionary algorithm (EA), which was recently proposed for binary atomic systems (Marques and Pereira, Chem. Phys. Lett. 2010, 485, 211). Before being applied to the potentials used in this work, the EA was further tested against results previously reported for the Ar(N)Xe(38-N) clusters and several new putative global minima were discovered. We employed either simple Lennard-Jones (LJ) potentials or more realistic functions to describe pair interactions in Ar(N)Kr(38-N), Ar(N)Xe(38-N), and Kr(N)Xe(38-N) clusters. The long-range tail of the pair-potentials shows some influence on the energetic features and shape of the structure of clusters. In turn, core-shell type structures are mostly observed for global minima of the binary rare-gas clusters, for both accurate and LJ potentials. However, the long-range tail of the potential may have influence on the type of atoms that segregate on the surface or form the core of the cluster. While relevant differences for the preferential site occupancy occur between the two potentials for Ar(N)Kr(38-N) (for N > 21), the type of atoms that segregate on the surface for Ar(N)Xe(38-N) and Kr(N)Xe(38-N) clusters is unaffected by the accuracy of the long-range part of the interaction in almost all cases. Moreover, the global minimum search for model-potentials in binary systems reveals that the surface-site occupancy is mainly determined by the combination of two parameters: the size ratio of the two types of particles forming the cluster and the minimum-energy ratio corresponding to the pair-interactions between unlike atoms. Copyright © 2012 Wiley Periodicals, Inc.
Phase equilibria of binary mixtures by molecular simulation and cubic equations of state
Directory of Open Access Journals (Sweden)
Cabral V.F.
2001-01-01
Full Text Available Molecular simulation data were used to study the performance of equations of state (EoS and combining rules usually employed in thermodynamic property calculations. The Monte Carlo method and the Gibbs ensemble technique were used for determining composition and densities of vapor and liquid phases in equilibrium for binary mixtures of Lennard-Jones fluids. Simulation results are compared to data in the literature and to those calculated by the t-PR-LJ EoS. The use of adequate combining rules has been shown to be very important for the satisfactory representation of molecular simulation data.
Phase equilibria of binary mixtures by molecular simulation and cubic equations of state
Cabral,V.F.; Pinto,R.R.C.; Tavares,F.W.; Castier,M.
2001-01-01
Molecular simulation data were used to study the performance of equations of state (EoS) and combining rules usually employed in thermodynamic property calculations. The Monte Carlo method and the Gibbs ensemble technique were used for determining composition and densities of vapor and liquid phases in equilibrium for binary mixtures of Lennard-Jones fluids. Simulation results are compared to data in the literature and to those calculated by the t-PR-LJ EoS. The use of adequate combining rule...
African Journals Online (AJOL)
Scand. Supp\\. 25, 9. MILLER, E.L. & 0RSKOV, E.R., 1986. Degradabilityof protein and its prediction. Bulletin of the International. Dairy Federation No. 196/1986. Brussels, Belgium. NRC, 1985. Ruminant nitrogen usage. US National Academy of Science, Washington, DC. ROHR, 1987. Present situation of the modern protein.
African Journals Online (AJOL)
1974-06-15
Jun 15, 1974 ... congenital cataracts, macular degeneration and tapeto- retinal degeneration. ... especially important in the diagnosis of tapetoretinal degeneration. Macular degeneration may be noted, or the cherry-red spot in Tay-Sachs disease. Optokinetic ... Persistence of a particular abnormality necessitates treatment.
Amir, Sahar Z.
2013-05-01
We introduce an efficient thermodynamically consistent technique to extrapolate and interpolate normalized Canonical NVT ensemble averages like pressure and energy for Lennard-Jones (L-J) fluids. Preliminary results show promising applicability in oil and gas modeling, where accurate determination of thermodynamic properties in reservoirs is challenging. The thermodynamic interpolation and thermodynamic extrapolation schemes predict ensemble averages at different thermodynamic conditions from expensively simulated data points. The methods reweight and reconstruct previously generated database values of Markov chains at neighboring temperature and density conditions. To investigate the efficiency of these methods, two databases corresponding to different combinations of normalized density and temperature are generated. One contains 175 Markov chains with 10,000,000 MC cycles each and the other contains 3000 Markov chains with 61,000,000 MC cycles each. For such massive database creation, two algorithms to parallelize the computations have been investigated. The accuracy of the thermodynamic extrapolation scheme is investigated with respect to classical interpolation and extrapolation. Finally, thermodynamic interpolation benefiting from four neighboring Markov chains points is implemented and compared with previous schemes. The thermodynamic interpolation scheme using knowledge from the four neighboring points proves to be more accurate than the thermodynamic extrapolation from the closest point only, while both thermodynamic extrapolation and thermodynamic interpolation are more accurate than the classical interpolation and extrapolation. The investigated extrapolation scheme has great potential in oil and gas reservoir modeling.That is, such a scheme has the potential to speed up the MCMC thermodynamic computation to be comparable with conventional Equation of State approaches in efficiency. In particular, this makes it applicable to large-scale optimization of L-J
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.
A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water.
Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul
2016-03-21
The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.
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.
Czech Academy of Sciences Publication Activity Database
Moučka, F.; Nezbeda, Ivo; Smith, W. R.
2013-01-01
Roč. 9, č. 11 (2013), s. 5076-5085 ISSN 1549-9618 Grant - others:GA MŠMT(CZ) LH12019; NSERCC(CA) OGP1041; UJEP(CZ) GAP208/12/0105 Institutional support: RVO:67985858 Keywords : sodium-chloride * ionic hydration * free-energy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.310, year: 2013
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.
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
Modeling of Hydraulic Fracturing on the Basis of the Particle Method
Berezhnoi, D. V.; Gabsalikova, N. F.; Izotov, V. G.; Miheev, V. V.
2018-01-01
A technique of calculating the deformation of the soil environment when it interacts with a liquid on the basis of the particle method a is realized. To describe the behavior of the solid and liquid phases of the soil, a classical two-parameter Lennard-Jones interaction potential and its modified version proposed by the authors were chosen. The model problem of deformation and partial destruction of a soil massif under strong pressure from the liquid pumped into it is solved. Analysis of the results shows that the use of the modified Lennard-Jones potential for describing the solid phase of the soil environment makes it possible to describe the process of formation of cracks in the soil during hydraulic fracturing of the formation.
Isomorph invariance of Couette shear flows simulated by the SLLOD equations of motion
DEFF Research Database (Denmark)
Separdar, Leila; Bailey, Nicholas; Schrøder, Thomas
2013-01-01
Non-equilibrium molecular dynamics simulations were performed to study the thermodynamic, structural, and dynamical properties of the single-component Lennard-Jones and the Kob-Andersen binary Lennard-Jones liquids. Both systems are known to have strong correlations between equilibrium thermal...... fluctuations of virial and potential energy. Such systems have good isomorphs (curves in the thermodynamic phase diagram along which structural, dynamical, and some thermodynamic quantities are invariant when expressed in reduced units). The SLLOD equations of motion were used to simulate Couette shear flows...... of the two systems. We show analytically that these equations are isomorph invariant provided the reduced strain rate is fixed along the isomorph. Since isomorph invariance is generally only approximate, a range of strain rates were simulated to test for the predicted invariance, covering both the linear...
Scaling of viscous dynamics in simple liquids
DEFF Research Database (Denmark)
Bøhling, Lasse; Ingebrigtsen, Trond; Grzybowski, A.
2012-01-01
Supercooled liquids are characterized by relaxation times that increase dramatically by cooling or compression. From a single assumption follows a scaling law according to which the relaxation time is a function of h(ρ) over temperature, where ρ is the density and the function h(ρ) depends...... on the liquid in question. This scaling is demonstrated to work well for simulations of the Kob–Andersen binary Lennard-Jones mixture and two molecular models, as well as for the experimental results for two van der Waals liquids, dibutyl phthalate and decahydroisoquinoline. The often used power-law density...... scaling, h(ρ)∝ργ, is an approximation to the more general form of scaling discussed here. A thermodynamic derivation was previously given for an explicit expression for h(ρ) for liquids of particles interacting via the generalized Lennard-Jones potential. Here a statistical mechanics derivation is given...
Isomorph invariance of the structure and dynamics of classical crystals
DEFF Research Database (Denmark)
Albrechtsen, Dan; Olsen, Andreas Elmerdahl; Pedersen, Ulf Rørbæk
2014-01-01
This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework......, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics...... of a defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnström binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles...
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.
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
Jackson, Isabel L; Zodda, Andrew; Gurung, Ganga; Pavlovic, Radmila; Kaytor, Michael D; Kuskowski, Michael A; Vujaskovic, Zeljko
2017-12-01
BIO 300 nanosuspension (Humanetics Corporation) is being developed as a medical countermeasure (MCM) for the mitigation of the delayed effects of acute radiation exposure, specifically pneumonitis and fibrosis of the lung. The objective of this study was to determine the best dose and treatment duration of BIO 300 to mitigate lung injury and improve the likelihood for survival in C57L/J mice exposed to whole thorax lung irradiation (WTLI). Age- and sex-matched C57L/J mice received a single dose of 11.0 or 12.5 Gy WTLI. BIO 300 (200 or 400 mg·kg -1 , oral gavage) was administered daily starting 24 h post-exposure for a duration of 2, 4, 6 or, in some cases, 10 weeks. Non-treated controls were included for comparison in both sexes. Animals were observed daily for signs of major morbidity. Respiratory function was assessed biweekly. Lungs were collected, weighed and paraffin embedded for histological evaluation post mortem. BIO 300 administered at an oral dose of 400 mg·kg -1 for 4 to 6 weeks starting 24 h post-WTLI reduced morbidity associated with WTLI. The improvement in survival correlated with reduced respiratory frequency and enhanced pause. The irradiated lungs of mice treated with BIO 300 (400 mg·kg -1 ) for 4 to 6 weeks displayed less morphological damage and airway loss due to oedema, congestion and fibrotic scarring than the untreated, irradiated controls. BIO 300 is a promising MCM candidate to mitigate pneumonitis/fibrosis when administered daily for 4-6 weeks starting 24 h post-exposure. © 2017 The British Pharmacological Society.
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
Intermolecular interactions and the thermodynamic properties of supercritical fluids.
Yigzawe, Tesfaye M; Sadus, Richard J
2013-05-21
The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of β = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids.
Nanoscale colloids in a freely adsorbing polymer solution: a Monte Carlo simulation study.
Marla, Krishna Tej; Meredith, J Carson
2004-02-17
A key issue in nanoscale materials and chemical processing is the need for thermodynamic and kinetic models covering colloid-polymer systems over the mesoscopic length scale (approximately 1-100 nm). We have applied Monte Carlo simulations to attractive nanoscale colloid-polymer mixtures toward developing a molecular basis for models of these complex systems. The expanded ensemble Monte Carlo simulation method is applied to calculate colloid chemical potentials (micro(c)) and polymer adsorption (gamma) in the presence of freely adsorbing Lennard-Jones (LJ) homopolymers (surface modifiers). gamma and micro(c) are studied as a function of nanoparticle diameter (sigma(c)), modifier chain length (n) and concentration, and colloid-polymer attractive strength over 0.3 attractive regime, nanocolloid chemical potential decreases and adsorbed amount increases as sigma(c), or n is increased. The scaling of gamma with n from the simulations agrees with the theory of Aubouy and Raphael (Macromolecules 1998, 31, 4357) in the extreme limits of Rg/sigma(c). When Rg/sigma(c) is large, the "colloid" approaches a molecular size and interacts only locally with a few polymer segments and gamma approximately n. When Rg/sigma(c) is small, the system approaches the conventional colloid-polymer size regime where multiple chains interact with a single particle, and gamma approximately sigma(c)2, independent of n. In contrast, adsorption in the mesoscopic range of Rg/sigma(c) investigated here is represented well by a power law gamma approximately n(p), with 0 attractive strength. Likewise, the chemical potential from our results is fitted well with micro(c) approximately n(q)sigma(c)3, where the cubic term results from the sigma(c) dependence of particle surface area (approximately sigma(c)2) and LJ attractive magnitude (approximately sigma(c)). The q-exponent for micro(c) (micro(c) approximately n(q)) varies with composition and LJ attractive strength but is always very close to the power
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.
International Nuclear Information System (INIS)
Foley, R.D.; Floyd, L.M.; Crutcher, J.W.
1989-08-01
Maywood Chemical Works (MCW) of Maywood, New Jersey, generated process wastes and residues associated with the production and refining of thorium and thorium compounds from monazite ores from 1916 to 1956. MCW supplied rare earth metals and thorium compounds to the Atomic Energy Commission and various other government agencies from the late 1940s to the mid-1950s. Area residents used the sandlike waste from this thorium extraction process mixed with tea and cocoa leaves as mulch in their yards. Some of these contaminated wastes were also eroded from the site into Lodi Brook. At the request of the US Department of Energy (DOE), a group from Oak Ridge National Laboratory conducts investigative radiological surveys of properties in the vicinity of MCW to determine whether a property is contaminated with radioactive residues, principally 232 Th, derived from the MCW site. The survey typically includes direct measurement of the gamma radiation levels and soil sampling for radionuclide analyses. The survey of this site, the Firemen's Memorial Park and Fire Hall number sign 2, Garibaldi Avenue and Kennedy Drive, Lodi, New Jersey (LJ066) was conducted during 1987. Results of the survey demonstrated radionuclide concentrations in excess of the DOE Formerly Utilized Sites Remedial Action Program criteria. The radionuclide distributions are typical of the type of material originating from the MCW site. 4 refs., 10 figs., 3 tabs
Applying inversion techniques to understanding nucleus-nucleus potentials
International Nuclear Information System (INIS)
Mackintosh, R.S.; Cooper, S.G.
1996-01-01
The iterative-perturbative (IP) inversion algorithm makes it possible to determine, essentially uniquely, the complex potential, including spin-orbit component, for spin half particles given the elastic scattering S-matrix S lj . We here report an extension of the method to the determination of energy dependent potentials V(r,E) defined over an energy range for which S lj (E) are provided. This is a natural development of the IP algorithm which has previously been applied to fixed energy, fixed partial wave and the intermediate mixed case inversion. The energy range can include negative energies i.e. V(r,E) can reproduce bound state energies. It can also fit the effective range parameter for low energy scattering. We briefly define the classes of cases which can be studied, outline the IP method itself and briefly review the range of applications. We show the power of the method by presenting nucleon-αV(r,E) for S lj (E) derived from experiments above and below the inelastic threshold and relating them to V(r,E) inverted from S lj (E) for RGM theory. Reference is given to the code IMAGO which embodies the IP algorithm. (author). 38 refs., 5 figs., 4 tabs
Coding coarse grained polymer model for LAMMPS and its application to polymer crystallization
Luo, Chuanfu; Sommer, Jens-Uwe
2009-08-01
We present a patch code for LAMMPS to implement a coarse grained (CG) model of poly(vinyl alcohol) (PVA). LAMMPS is a powerful molecular dynamics (MD) simulator developed at Sandia National Laboratories. Our patch code implements tabulated angular potential and Lennard-Jones-9-6 (LJ96) style interaction for PVA. Benefited from the excellent parallel efficiency of LAMMPS, our patch code is suitable for large-scale simulations. This CG-PVA code is used to study polymer crystallization, which is a long-standing unsolved problem in polymer physics. By using parallel computing, cooling and heating processes for long chains are simulated. The results show that chain-folded structures resembling the lamellae of polymer crystals are formed during the cooling process. The evolution of the static structure factor during the crystallization transition indicates that long-range density order appears before local crystalline packing. This is consistent with some experimental observations by small/wide angle X-ray scattering (SAXS/WAXS). During the heating process, it is found that the crystalline regions are still growing until they are fully melted, which can be confirmed by the evolution both of the static structure factor and average stem length formed by the chains. This two-stage behavior indicates that melting of polymer crystals is far from thermodynamic equilibrium. Our results concur with various experiments. It is the first time that such growth/reorganization behavior is clearly observed by MD simulations. Our code can be easily used to model other type of polymers by providing a file containing the tabulated angle potential data and a set of appropriate parameters. Program summaryProgram title: lammps-cgpva Catalogue identifier: AEDE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU's GPL No. of lines in distributed program
A Four-Site Molecular Model for Simulations of Liquid Methanol and Water-Methanol Mixtures: MeOH-4P.
Martínez-Jiménez, Manuel; Saint-Martin, Humberto
2018-04-17
In this work, we present a new four-site potential for methanol, MeOH-4P, fitted to reproduce the dielectric constant ε, the surface tension γ s , and the liquid density ρ of the pure liquid at T = 298.15 K and p = 1 bar. The partial charges on each site were taken from the OPLS/2016 model with the only difference of putting the negative charge on the fourth site ( M) instead of on the O atom, as done in four-site water models. The original Lennard-Jones (LJ) parameters of OPLS/2016 for the methyl moiety (Me) were modified for the fitting of ρ and γ s , whereas the parameters of the TIP4P-FB water model were used for the O atom without change. Taking into account the energetic cost of the enhanced dipole relative to the isolated molecule, the results from simulations with this model showed good agreement with experiments for ρ, α p , κ T , C p , and Δ H v- l . Also, the temperature dependence of γ s and ε is satisfactory in the interval between 260 and 360 K, and the critical point description is similar to that of OPLS/2016. It is shown that orientational correlations, described by the Kirkwood factor G k , play a prominent role in the appropriate description of dielectric constants in existing models; unfortunately, the enhancement of the dipole moment produced a low diffusion coefficient D MeOH ; thus, a compromise was required between a good reproduction of ε and an acceptable D MeOH . The use of a fourth site resulted in a significant improvement for water-methanol mixtures described with TIP4P-FB and MeOH-4P, respectively, but required the modification of the LJ geometric combination rule to allow a good description of the methanol molar-fraction dependence of ρ, ε, and methanol (water) diffusion coefficients D MeOH ( D H 2 O ) and excess volume of mixing Δ V mix in the entire range of composition. The resulting free energy of hydration Δ G hyd shows excellent agreement with experiments in the interval between 280 and 360 K.
Directory of Open Access Journals (Sweden)
Trond S. Ingebrigtsen
2012-03-01
Full Text Available This paper is an attempt to identify the real essence of simplicity of liquids in John Locke’s understanding of the term. Simple liquids are traditionally defined as many-body systems of classical particles interacting via radially symmetric pair potentials. We suggest that a simple liquid should be defined instead by the property of having strong correlations between virial and potential-energy equilibrium fluctuations in the NVT ensemble. There is considerable overlap between the two definitions, but also some notable differences. For instance, in the new definition simplicity is not a direct property of the intermolecular potential because a liquid is usually only strongly correlating in part of its phase diagram. Moreover, not all simple liquids are atomic (i.e., with radially symmetric pair potentials and not all atomic liquids are simple. The main part of the paper motivates the new definition of liquid simplicity by presenting evidence that a liquid is strongly correlating if and only if its intermolecular interactions may be ignored beyond the first coordination shell (FCS. This is demonstrated by NVT simulations of the structure and dynamics of several atomic and three molecular model liquids with a shifted-forces cutoff placed at the first minimum of the radial distribution function. The liquids studied are inverse power-law systems (r^{-n} pair potentials with n=18,6,4, Lennard-Jones (LJ models (the standard LJ model, two generalized Kob-Andersen binary LJ mixtures, and the Wahnstrom binary LJ mixture, the Buckingham model, the Dzugutov model, the LJ Gaussian model, the Gaussian core model, the Hansen-McDonald molten salt model, the Lewis-Wahnstrom ortho-terphenyl model, the asymmetric dumbbell model, and the single-point charge water model. The final part of the paper summarizes properties of strongly correlating liquids, emphasizing that these are simpler than liquids in general. Simple liquids, as defined here, may be
Ingebrigtsen, Trond S.; Schrøder, Thomas B.; Dyre, Jeppe C.
2012-01-01
This paper is an attempt to identify the real essence of simplicity of liquids in John Locke’s understanding of the term. Simple liquids are traditionally defined as many-body systems of classical particles interacting via radially symmetric pair potentials. We suggest that a simple liquid should be defined instead by the property of having strong correlations between virial and potential-energy equilibrium fluctuations in the NVT ensemble. There is considerable overlap between the two definitions, but also some notable differences. For instance, in the new definition simplicity is not a direct property of the intermolecular potential because a liquid is usually only strongly correlating in part of its phase diagram. Moreover, not all simple liquids are atomic (i.e., with radially symmetric pair potentials) and not all atomic liquids are simple. The main part of the paper motivates the new definition of liquid simplicity by presenting evidence that a liquid is strongly correlating if and only if its intermolecular interactions may be ignored beyond the first coordination shell (FCS). This is demonstrated by NVT simulations of the structure and dynamics of several atomic and three molecular model liquids with a shifted-forces cutoff placed at the first minimum of the radial distribution function. The liquids studied are inverse power-law systems (r-n pair potentials with n=18,6,4), Lennard-Jones (LJ) models (the standard LJ model, two generalized Kob-Andersen binary LJ mixtures, and the Wahnstrom binary LJ mixture), the Buckingham model, the Dzugutov model, the LJ Gaussian model, the Gaussian core model, the Hansen-McDonald molten salt model, the Lewis-Wahnstrom ortho-terphenyl model, the asymmetric dumbbell model, and the single-point charge water model. The final part of the paper summarizes properties of strongly correlating liquids, emphasizing that these are simpler than liquids in general. Simple liquids, as defined here, may be characterized in three quite
van Westen, Thijs; Vlugt, Thijs J. H.; Gross, Joachim
2015-06-01
We study the isotropic (vapor and liquid) phase behavior of attractive chain fluids. Special emphasis is placed on the role of molecular flexibility, which is studied by means of a rod-coil model. Two new equations of state (EoSs) are developed for square-well- (SW) and Lennard-Jones (LJ) chain fluids. The EoSs are developed by applying the perturbation theory of Barker and Henderson (BH) to a reference fluid of hard chain molecules. The novelty of the approach is based on (1) the use of a recently developed hard-chain reference EoS that explicitly incorporates the effects of molecular flexibility, (2) the use of recent molecular simulation data for the radial distribution function of hard-chain fluids, and (3) a newly developed effective segment size, which effectively accounts for the soft repulsion between segments of LJ chains. It is shown that the effective segment size needs to be temperature-, density-, and chain-length dependent. To obtain a simplified analytical EoS, the perturbation terms are fitted by polynomials in density (SW and LJ), chain length (SW and LJ), and temperature (only for LJ). It is shown that the equations of state result in an accurate description of molecular simulation data for vapor-liquid equilibria (VLE) and isotherms of fully flexible SW- and LJ chain fluids and their mixtures. To evaluate the performance of the equations of state in describing the effects of molecular flexibility on VLE, we present new Monte Carlo simulation results for the VLE of rigid linear- and partially flexible SW- and LJ chain fluids. For SW chains, the developed EoS is in a good agreement with simulation results. For increased rigidity of the chains, both theory and simulations predict an increase of the VL density difference and a slight increase of the VL critical temperature. For LJ chains, the EoS proves incapable of reproducing part of these trends.
Nanolayering around and thermal resistivity of the water-hexagonal boron nitride interface
Akıner, Tolga; Mason, Jeremy K.; Ertürk, Hakan
2017-07-01
The water-hexagonal boron nitride interface was investigated by molecular dynamics simulations. Since the properties of the interface change significantly with the interatomic potential, a new method for calibrating the solid-liquid interatomic potential is proposed based on the experimental energy of the interface. The result is markedly different from that given by Lorentz-Berthelot mixing for the Lennard-Jones parameters commonly used in the literature. Specifically, the extent of nanolayering and interfacial thermal resistivity is measured for several interatomic potentials, and the one calibrated by the proposed method gives the least thermal resistivity.
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.
Partial structure factors and orientational correlations in liquid HI
International Nuclear Information System (INIS)
Andreani, C.; Nardone, M.; Ricci, F.P.
1993-01-01
The three atomic partial structure factors of orthobaric liquid HI at 253 K derived from neutron diffraction experiments are presented. The analysis of these structure factors and of the corresponding pair distribution functions indicates that the molecular center of mass distribution function is essentially that of a monoatomic Lennard-Jones fluid and that the anisotropic part of the intermolecular potential is able to build up orientational correlations between molecular axes without however giving rise to well defined correlations between the intermolecular axis and the molecular axis. These findings are consistent with an anisotropic part of the intermolecular potential due essentially to electric multipoles. (authors). 4 figs., 4 refs
Effect of pressure on the structure and lattice dynamics of fullerene crystal C60
International Nuclear Information System (INIS)
Prilutski, Yu.I.; Shapovalov, G.G.
1997-01-01
The low-temperature orientationally ordered crystalline phase of fullerene C 60 was investigated in dependence on the external pressure. An assumption was made that the energy of the lattice includes two contributions: a Lennard-Jones (12-6) potential and electrostatic interaction. The vibrational spectrum of C 60 crystal was calculated using the atom-atom potential method. The frequencies of intermolecular modes as functions of external pressure were studied. The sound velocities, elastic constants and bulk modulus are calculated. The dependence of sound velocities in fullerene crystal C 60 on the external pressure is investigated. The results obtained are in good agreement with the available experimental data. (orig.)
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.)
A new shared-memory programming paradigm for molecular dynamics simulations on the Intel Paragon
Energy Technology Data Exchange (ETDEWEB)
D`Azevedo, E.F.; Romine, C.H.
1994-12-01
This report describes the use of shared memory emulation with DOLIB (Distributed Object Library) to simplify parallel programming on the Intel Paragon. A molecular dynamics application is used as an example to illustrate the use of the DOLIB shared memory library. SOTON-PAR, a parallel molecular dynamics code with explicit message-passing using a Lennard-Jones 6-12 potential, is rewritten using DOLIB primitives. The resulting code has no explicit message primitives and resembles a serial code. The new code can perform dynamic load balancing and achieves better performance than the original parallel code with explicit message-passing.
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....
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.
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.
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....
Pearson, W. E.
1974-01-01
The viscosity and thermal conductivity of nitrogen gas for the temperature range 5 K - 135 K have been computed from the second Chapman-Enskog approximation. Quantum effects, which become appreciable at the lower temperatures, are included by utilizing collision integrals based on quantum theory. A Lennard-Jones (12-6) potential was assumed. The computations yield viscosities about 20 percent lower than those predicted for the high end of this temperature range by the method of corresponding states, but the agreement is excellent when the computed values are compared with existing experimental data.
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.
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
Strong pressure-energy correlations in van der Waals liquids
DEFF Research Database (Denmark)
Pedersen, Ulf Rørbæk; Bailey, Nicholas; Schrøder, Thomas
2008-01-01
in the crystal and glass phases reflect an effective inverse power-law repulsive potential dominating fluctuations, even at zero and slightly negative pressure. In experimental data for supercritical argon, the correlations are found to be approximately 96%. Consequences for viscous liquid dynamics are discussed.......Strong correlations between equilibrium fluctuations of the configurational parts of pressure and energy are found in computer simulations of the Lennard-Jones liquid and other simple liquids, but not for hydrogen-bonding liquids such as methanol and water. The correlations that are present also...
Um modelo para a superfície líquida no estudo da dinâmica do espalhamento de Xe e Ne pelo esqualano
Directory of Open Access Journals (Sweden)
Leal Alexandre S.
2004-01-01
Full Text Available In this work we present a theoretical model to investigate the scattering of Xe and Ne by a liquid squalane surface. The liquid surface is modeled as a grid of harmonic oscillators with frequencies adjusted to experimental vibration as frequencies of the liquid squalane and the atom-surface interaction potential is modeled by a Lennard-Jones function. The three dimensional description of the dynamics of the process which occurs at the gas-liquid interface is obtained by the classical trajectory method. The general characteristics of the dynamics of the scattering process are in good agreement with experimental data.
Heyes, D. M.; Nuevo, M. J.; Morales, J. J.
Following on from our previous study (Heyes, D. M., Nuevo, M. J, and Morales, J. J., 1996, Molec. Phys., 88, 1503), molecular dynamics simulations have been carried out of translational and rotational diffusion of atomistically rough near-spherical solid Lennard-Jones (LJ) clusters immersed in a Weeks-Chandler-Andersen liquid solvent. A single cluster consisting of up to about 100LJ particles as part of an 8000 atom fluid system was considered in each case. The translational and rotational diffusion coefficients decrease with increasing cluster size and solvent density (roughly in proportion to the molar volume of the solvent). The simulations reveal that for clusters in excess of about 30LJ atoms there is a clear separation of timescales between angular velocity and orientation relaxation which adhere well to the small-step diffusion model encapsulated in Hubbard's relationship. For 100 atom clusters both the StokesEinstein (translation) and Stokes-Einstein-Debye (rotation) equations apply approximately. The small departures from these reference solutions indicate that the translational relaxation experiences a local viscosity in excess of the bulk value (typically by ~ 30%), whereas rotational relaxation experiences a smaller viscosity than the bulk (typically by ~ 30%) reasonably in accord with the Gierer-Wirtz model. Both of these observations are consistent with an observed layering of the liquid molecules next to the cluster observed in our previous study.
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
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.
How Competitive Interactions Affect the Self-Assembly of Confined Janus Dumbbells.
Bordin, José Rafael; Krott, Leandro B
2017-04-27
We explore the self-assembled morphologies of Janus nanoparticles under cylindrical confinement. Langevin dynamics simulations are employed to study the behavior of two types of dimers inside cylinders with distinct radius. The first type of nanoparticle was modeled using one monomer that interacts by a standard Lennard-Jones potential and another monomer that is modeled using a purely repulsive two length scale shoulder potential. The second type is composed by a Lennard-Jones monomer and a repulsive monomer which interacts by the purely repulsive Weeks-Chandler-Andersen potential, which have only one length scale. The two length scale potential used in the first type of nanoparticle models a monomer with competitive interaction. Our results show that the aggregated structures are completely distinct for each type of nanoparticle. Also, our simulations indicate that the cylinder radius can be used to control the type of self-assembled cluster. Small clusters, tubular and donut-like micelles with central holes, with potential application to molecule encapsulation were observed regarding the nanoparticle specificities and the cylinder radii. Also, bilayer lamellae structures were obtained depending on the type of nanoparticle and the cylinder size.
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.
Biomembrane modeling: molecular dynamics simulation of phospholipid monolayers
Energy Technology Data Exchange (ETDEWEB)
Thompson, T.R.
1979-01-01
As a first step toward a computer model of a biomembrane-like bilayer, a dynamic, deterministric model of a phospholipid monolayer has been constructed. The model moves phospholipid-like centers of force according to an integrated law of motion in finite difference form. Forces on each phospholipid analogue are derived from the gradient of the local potential, itself the sum of Coulombic and short-range terms. The Coulombic term is approximated by use of a finite-difference form of Poisson's equation, while the short-range term results from finite-radius, pairwise summation of a Lennard-Jones potential. Boundary potentials are treated in such a way that the model is effectively infinite in extent in the plane of the monolayer. The two-dimensional virial theorem is used to find the surface pressure of the monolayer as a function of molecular area. Pressure-versus-area curves for simulated monolayers are compared to those of real monolayers. Dependence of the simulator's behavior on Lennard-Jones parameters and the specific geometry of the molecular analogue is discussed. Implications for the physical theory of phospholipid monolayers and bilayers are developed.
Lattice model theory of the equation of state covering the gas, liquid, and solid phases
Bonavito, N. L.; Tanaka, T.; Chan, E. M.; Horiguchi, T.; Foreman, J. C.
1975-01-01
The three stable states of matter and the corresponding phase transitions were obtained with a single model. Patterned after Lennard-Jones and Devonshires's theory, a simple cubic lattice model containing two fcc sublattices (alpha and beta) is adopted. The interatomic potential is taken to be the Lennard-Jones (6-12) potential. Employing the cluster variation method, the Weiss and the pair approximations on the lattice gas failed to give the correct phase diagrams. Hybrid approximations were devised to describe the lattice term in the free energy. A lattice vibration term corresponding to a free volume correction is included semi-phenomenologically. The combinations of the lattice part and the free volume part yield the three states and the proper phase diagrams. To determine the coexistence regions, the equalities of the pressure and Gibbs free energy per molecule of the coexisting phases were utilized. The ordered branch of the free energy gives rise to the solid phase while the disordered branch yields the gas and liquid phases. It is observed that the triple point and the critical point quantities, the phase diagrams and the coexistence regions plotted are in good agreement with the experimental values and graphs for argon.
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
Energy Technology Data Exchange (ETDEWEB)
Wu, Xia, E-mail: xiawu@mail.nankai.edu.cn; Wu, Genhua
2014-08-31
Highlights: • A high efficient method for optimization of atomic clusters is developed. • Its performance is studied by optimizing Lennard-Jones clusters and Ag clusters. • The method is proved to be quite efficient. • A new Ag{sub 61} cluster with stacking-fault face-centered cubic motif is found. - Abstract: Geometrical optimization of atomic clusters is performed by a development of adaptive immune optimization algorithm (AIOA) with dynamic lattice searching (DLS) operation (AIOA-DLS method). By a cycle of construction and searching of the dynamic lattice (DL), DLS algorithm rapidly makes the clusters more regular and greatly reduces the potential energy. DLS can thus be used as an operation acting on the new individuals after mutation operation in AIOA to improve the performance of the AIOA. The AIOA-DLS method combines the merit of evolutionary algorithm and idea of dynamic lattice. The performance of the proposed method is investigated in the optimization of Lennard-Jones clusters within 250 atoms and silver clusters described by many-body Gupta potential within 150 atoms. Results reported in the literature are reproduced, and the motif of Ag{sub 61} cluster is found to be stacking-fault face-centered cubic, whose energy is lower than that of previously obtained icosahedron.
Collision Frequency for Energy Transfer in Unimolecular Reactions.
Matsugi, Akira
2018-03-01
Pressure dependence of unimolecular reaction rates is governed by the energy transfer in collisions of reactants with bath gas molecules. Pressure-dependent rate constants can be theoretically determined by solving master equations for unimolecular reactions. In general, master equation formulations describe energy transfer processes using a collision frequency and a probability distribution model of the energy transferred per collision. The present study proposes a novel method for determining the collision frequency from the results of classical trajectory calculations. Classical trajectories for collisions of several polyatomic molecules (ethane, methane, tetrafluoromethane, and cyclohexane) with monatomic colliders (Ar, Kr, and Xe) were calculated on potential energy surfaces described by the third-order density-functional tight-binding method in combination with simple pairwise interaction potentials. Low-order (including non-integer-order) moments of the energy transferred in deactivating collisions were extracted from the trajectories and compared with those derived using some probability distribution models. The comparison demonstrates the inadequacy of the conventional Lennard-Jones collision model for representing the collision frequency and suggests a robust method for evaluating the collision frequency that is consistent with a given probability distribution model, such as the exponential-down model. The resulting collision frequencies for the exponential-down model are substantially higher than the Lennard-Jones collision frequencies and are close to the (hypothetical) capture rate constants for dispersion interactions. The practical adequacy of the exponential-down model is also briefly discussed.
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.
Test of a new heat-flow equation for dense-fluid shock waves
Holian, Brad Lee; Mareschal, Michel; Ravelo, Ramon
2010-09-01
Using a recently proposed equation for the heat-flux vector that goes beyond Fourier's Law of heat conduction, we model shockwave propagation in the dense Lennard-Jones fluid. Disequilibrium among the three components of temperature, namely, the difference between the kinetic temperature in the direction of a planar shock wave and those in the transverse directions, particularly in the region near the shock front, gives rise to a new transport (equilibration) mechanism not seen in usual one-dimensional heat-flow situations. The modification of the heat-flow equation was tested earlier for the case of strong shock waves in the ideal gas, which had been studied in the past and compared to Navier-Stokes-Fourier solutions. Now, the Lennard-Jones fluid, whose equation of state and transport properties have been determined from independent calculations, allows us to study the case where potential, as well as kinetic contributions are important. The new heat-flow treatment improves the agreement with nonequilibrium molecular-dynamics simulations under strong shock wave conditions, compared to Navier-Stokes.
Solvation in atomic liquids: connection between Gaussian field theory and density functional theory
Directory of Open Access Journals (Sweden)
V. Sergiievskyi
2017-12-01
Full Text Available For the problem of molecular solvation, formulated as a liquid submitted to the external potential field created by a molecular solute of arbitrary shape dissolved in that solvent, we draw a connection between the Gaussian field theory derived by David Chandler [Phys. Rev. E, 1993, 48, 2898] and classical density functional theory. We show that Chandler's results concerning the solvation of a hard core of arbitrary shape can be recovered by either minimising a linearised HNC functional using an auxiliary Lagrange multiplier field to impose a vanishing density inside the core, or by minimising this functional directly outside the core — indeed a simpler procedure. Those equivalent approaches are compared to two other variants of DFT, either in the HNC, or partially linearised HNC approximation, for the solvation of a Lennard-Jones solute of increasing size in a Lennard-Jones solvent. Compared to Monte-Carlo simulations, all those theories give acceptable results for the inhomogeneous solvent structure, but are completely out-of-range for the solvation free-energies. This can be fixed in DFT by adding a hard-sphere bridge correction to the HNC functional.
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.
Droplet spreading driven by van der Waals force: a molecular dynamics study
International Nuclear Information System (INIS)
Wu Congmin; Qian Tiezheng; Sheng Ping
2010-01-01
The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t)∼√t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid.
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.
Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields.
Van Vleet, Mary J; Misquitta, Alston J; Stone, Anthony J; Schmidt, J R
2016-08-09
Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.
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.
The impact range for smooth wall–liquid interactions in nanoconfined liquids
DEFF Research Database (Denmark)
Ingebrigtsen, Trond; Dyre, J. C.
2014-01-01
decade. Inspired by these observations, we present results from molecular dynamics computer simulations of four nanoconfined liquids (the single-component Lennard-Jones liquid, the Kob–Andersen binary Lennard-Jones mixture, an asymmetric dumbbell model, and the Dzugutov liquid) demonstrating also...
Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D
2017-08-14
Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.
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)
Loirat, Yanick
1999-01-01
The principal aims of this work are a better understanding of the experimental situation in amorphous metallic alloys and a tentative explanation of the role of collective mechanisms in matter transport. Self- and solute-diffusion of Hf, Au and Cu tracers in amorphous Ni Zr alloy have been studied. We study by SIMS analysis the broadening of the concentration profile with temperature and pressure, in thin amorphous layers which were prepared by sputtering and properly relaxed. The diffusion coefficient variation with temperature shows an Arrhenius behaviour for all of our tracers. The activation energy amount to 1.55 eV for Cu, 1.65 eV for Au and 1.78 eV for Hf and corresponds to nearly one half of the corresponding energy in crystalline zirconium. The diffusion coefficients variation with hydrostatic pressure yields an activation volume equal to one half of an average atomic volume of our matrix for medium and large sized tracers Au, Hf and a smaller activation volume for Cu. The second part of our work consists of numerical simulations of atomic displacements in a generic glass by two complementary methods. In a Lennard-Jones alloy with size effect, we observe by molecular dynamics (MD) some correlated displacements which consist of substitution cycles or chains. The associated energy of these collective events represents nearly 15 pc of that found in crystalline Lennard- Jones. The systematic exploration of energy surface in space configuration made with activation-relaxation technique ART yields energy distributions of stable and saddles positions and opens the way to an evaluation of diffusion coefficients. The events found by ART are qualitatively close to MD ones, but the averaged activation energy associated with these events represents only 10 pc of the crystalline one. This clearly points towards the limit of Lennard-Jones potential, which is not enough representative of actual glasses. This is the reason why an interaction model closer to amorphous
Melting of rare-gas crystals: Monte Carlo simulation versus experiments.
Bocchetti, V; Diep, H T
2013-03-14
We study the melting transition in crystals of rare gas Ar, Xe, and Kr by the use of extensive Monte Carlo simulations with the Lennard-Jones potential. The parameters of this potential have been deduced by Bernardes in 1958 from experiments of rare gas in the gaseous phase. It is amazing that the parameters of such a popular potential were not fully tested so far. Using the Bernardes parameters, we find that the melting temperature of several rare gas is from 13% to 20% higher than that obtained from experiments. We have throughout studied the case of Ar by examining both finite-size and cutoff-distance effects. In order to get a good agreement with the experimental melting temperature, we propose a modification of these parameters to describe better the melting of rare-gas crystals.
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...
Extension of the JCZ product species database
Energy Technology Data Exchange (ETDEWEB)
Hobbs, M.L.; Baer, M.R.; McGee, B.C.
1998-09-01
A database has been created for use with the Jacobs-Cowperthwaite-Zwisler-3 equation-of-state (JCZ3-EOS) to determine thermochemical equilibrium states for energetic materials. The JCZ3-EOS uses the exponential 6 intermolecular potential function to describe interactions between molecules. Product species are characterized by r{sup *}, the radius of the minimum pair potential energy, and {var_epsilon}/{kappa}, the well depth energy normalized by Boltzmann`s constant. These parameters constitute the JCZS (S for Sandia) database describing 750 gases listed in the JANNAF tables and were obtained by using literature values of the Lennard-Jones potential, a corresponding states theory, pure liquid shock Hugoniot data, and fit values to an empirical EOS. Detonation velocities predicted with the JCZS database for a wide variety of explosives are in good agreement with data. Improved predictions of low density explosives is attributed to a better description of molecular interactions at intermediate pressures.
A New Simplified Local Density Model for Adsorption of Pure Gases and Binary Mixtures
Hasanzadeh, M.; Dehghani, M. R.; Feyzi, F.; Behzadi, B.
2010-12-01
Adsorption modeling is an important tool for process simulation and design. Many theoretical models have been developed to describe adsorption data for pure and multicomponent gases. The simplified local density (SLD) approach is a thermodynamic model that can be used with any equation of state and offers some predictive capability with adjustable parameters for modeling of slit-shaped pores. In previous studies, the SLD model has been utilized with the Lennard-Jones potential function for modeling of fluid-solid interactions. In this article, we have focused on application of the Sutherland potential function in an SLD-Peng-Robinson model. The advantages and disadvantages of using the new potential function for adsorption of methane, ethane, carbon dioxide, nitrogen, and three binary mixtures on two types of activated carbon are illustrated. The results have been compared with previous models. It is shown that the new SLD model can correlate adsorption data for different pressures and temperatures with minimum error.
Shape matters: The case for Ellipsoids and Ellipsoidal Water
Tillack, Andreas F.; Robinson, Bruce H.
2017-11-01
We describe the shape potentials used for the van der Waals interactions between soft-ellipsoids used to coarse-grain molecular moieties in Metropolis Monte-Carlo simulation software. The morphologies resulting from different expressions for these van der Waals interaction potentials are discussed for the case of a prolate spheroid system with a strong dipole at the center. We also show that the calculation of ellipsoids is, at worst, only about fivefold more expensive computationally when compared to a simple Lennard-Jones sphere. Finally, as an application of the ellipsoidal shape we parametrize water from the original SPC water model and observe – just through the difference in shape alone – a significant improvement of the O-O radial distribution function when compared to experimental data. ).
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.
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.
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
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)
Anomalous diffusion and diffusion anomaly in confined Janus dumbbells.
B Krott, Leandro; Gavazzoni, Cristina; Bordin, José Rafael
2016-12-28
Self-assembly and dynamical properties of Janus nanoparticles have been studied by molecular dynamic simulations. The nanoparticles are modeled as dimers and they are confined between two flat parallel plates to simulate a thin film. One monomer from the dumbbells interacts by a standard Lennard-Jones potential and the other by a two-length scales shoulder potential, typically used for anomalous fluids. Here, we study the effects of removing the Brownian effects, typical from colloidal systems immersed in aqueous solution, and consider a molecular system, without the drag force and the random collisions from the Brownian motion. Self-assembly and diffusion anomaly are preserved in relation to the Brownian system. Additionally, a superdiffusive regime associated to a collective reorientation in a highly structured phase is observed. Diffusion anomaly and anomalous diffusion are explained in the two length scale framework.
Anomalous diffusion and diffusion anomaly in confined Janus dumbbells
Krott, Leandro B.; Gavazzoni, Cristina; Bordin, José Rafael
2016-12-01
Self-assembly and dynamical properties of Janus nanoparticles have been studied by molecular dynamic simulations. The nanoparticles are modeled as dimers and they are confined between two flat parallel plates to simulate a thin film. One monomer from the dumbbells interacts by a standard Lennard-Jones potential and the other by a two-length scales shoulder potential, typically used for anomalous fluids. Here, we study the effects of removing the Brownian effects, typical from colloidal systems immersed in aqueous solution, and consider a molecular system, without the drag force and the random collisions from the Brownian motion. Self-assembly and diffusion anomaly are preserved in relation to the Brownian system. Additionally, a superdiffusive regime associated to a collective reorientation in a highly structured phase is observed. Diffusion anomaly and anomalous diffusion are explained in the two length scale framework.
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
Stability of surface nanobubbles
Maheshwari, Shantanu; van der Hoef, Martin; Zhang, Xuehua; Lohse, Detlef
2015-11-01
We have studied the stability and dissolution of surface nanobubbles on the chemical heterogenous surface by performing Molecular Dynamics (MD) simulations of binary mixture consists of Lennard-Jones (LJ) particles. Recently our group has derived the exact expression for equilibrium contact angle of surface nanobubbles as a function of oversaturation of the gas concentration in bulk liquid and the lateral length of bubble. It has been showed that the contact line pinning and the oversaturation of gas concentration in bulk liquid is crucial in the stability of surface nanobubbles. Our simulations showed that how pinning of the three-phase contact line on the chemical heterogenous surface lead to the stability of the nanobubble. We have calculated the equilibrium contact angle by varying the gas concentration in bulk liquid and the lateral length of the bubble. Our results showed that the equilibrium contact angle follows the expression derived analytically by our group. We have also studied the bubble dissolution dynamics and showed the ''stick-jump'' mechanism which was also observed experimentally in case of dissolution of nanodrops.
Li, Yongliang; Jiang, Tao; Lin, Shaoliang; Lin, Jiaping; Cai, Chunhua; Zhu, Xingyu
2015-05-01
Self-assembly behavior of a mixture system containing rod-coil block copolymers and rigid homopolymers was investigated by using Brownian dynamics simulations. The morphologies of formed hierarchical self-assemblies were found to be dependent on the Lennard-Jones (LJ) interaction ɛRR between rod blocks, lengths of rod and coil blocks in copolymer, and mixture ratio of block copolymers to homopolymers. As the ɛRR value decreases, the self-assembled structures of mixtures are transformed from an abacus-like structure to a helical structure, to a plain fiber, and finally are broken into unimers. The order parameter of rod blocks was calculated to confirm the structure transition. Through varying the length of rod and coil blocks, the regions of thermodynamic stability of abacus, helix, plain fiber, and unimers were mapped. Moreover, it was discovered that two levels of rod block ordering exist in the helices. The block copolymers are helically wrapped on the homopolymer bundles to form helical string, while the rod blocks are twistingly packed inside the string. In addition, the simulation results are in good agreement with experimental observations. The present work reveals the mechanism behind the formation of helical (experimentally super-helical) structures and may provide useful information for design and preparation of the complex structures.
Monte Carlo Molecular Simulation with Isobaric-Isothermal and Gibbs-NPT Ensembles
Du, Shouhong
2012-05-01
This thesis presents Monte Carlo methods for simulations of phase behaviors of Lennard-Jones fluids. The isobaric-isothermal (NPT) ensemble and Gibbs-NPT ensemble are introduced in detail. NPT ensemble is employed to determine the phase diagram of pure component. The reduced simulation results are verified by comparison with the equation of state by by Johnson et al. and results with L-J parameters of methane agree considerably with the experiment measurements. We adopt the blocking method for variance estimation and error analysis of the simulation results. The relationship between variance and number of Monte Carlo cycles, error propagation and Random Number Generator performance are also investigated. We review the Gibbs-NPT ensemble employed for phase equilibrium of binary mixture. The phase equilibrium is achieved by performing three types of trial move: particle displacement, volume rearrangement and particle transfer. The simulation models and the simulation details are introduced. The simulation results of phase coexistence for methane and ethane are reported with comparison of the experimental data. Good agreement is found for a wide range of pressures. The contribution of this thesis work lies in the study of the error analysis with respect to the Monte Carlo cycles and number of particles in some interesting aspects.
The differential interference in collisional quantum interference on rotational energy transfer
International Nuclear Information System (INIS)
Yang Xin; Wang Weili
2012-01-01
The collisional quantum interference (CQI) on rotational energy transfer was observed in the experiment of the static cell, and the integral interference angles were measured. To obtain more accurate information, the experiment in the molecular beam should be taken, from which the differential interference angle can be obtained. Based on the first-Born approximation of time-dependent perturbation theory, the theoretical model of CQI is developed in an atom-diatom collision system in the condition of the molecular beam. The model has taken into account the Lennard-Jones interaction potentials and 'straight-line' trajectory approximation. The effect factors that the interference angle depend on are investigated. The changing tendencies of the differential interference angle with the impact parameter, velocity, and collision partner are discussed. This theoretical model is important to understand or perform the experiment in the molecular beam. (authors)
Thermodynamic properties of non-conformal soft-sphere fluids with effective hard-sphere diameters.
Rodríguez-López, Tonalli; del Río, Fernando
2012-01-28
In this work we study a set of soft-sphere systems characterised by a well-defined variation of their softness. These systems represent an extension of the repulsive Lennard-Jones potential widely used in statistical mechanics of fluids. This type of soft spheres is of interest because they represent quite accurately the effective intermolecular repulsion in fluid substances and also because they exhibit interesting properties. The thermodynamics of the soft-sphere fluids is obtained via an effective hard-sphere diameter approach that leads to a compact and accurate equation of state. The virial coefficients of soft spheres are shown to follow quite simple relationships that are incorporated into the equation of state. The approach followed exhibits the rescaling of the density that produces a unique equation for all systems and temperatures. The scaling is carried through to the level of the structure of the fluids.
Adhesive contact between a cylinder and a half-space
Energy Technology Data Exchange (ETDEWEB)
Wu, Jiunn-Jong, E-mail: jjw5277@ms19.hinet.ne, E-mail: jjwu@mail.cgu.edu.t [Department of Mechanical Engineering, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan, Taiwan (China)
2009-08-07
Numerical simulation for the adhesive contact between a sphere and a half-space is employed. The numerical simulation is performed for a realistic surface force law based on the Lennard-Jones potential between molecules with the Derjaguin approximation. The result is compared with the two-dimensional Maugis model, which uses the Dugdale law. It is found that the Maugis model gives good results, approximating those obtained by the numerical simulation. It is also found that the usual Maugis parameter governs the transition from the two-dimensional JKR model to the two-dimensional rigid cylinder contact. But the rigid body limit found using the Maugis model is different from that found using the numerical simulation.
Adhesive contact between a cylinder and a half-space
Wu, Jiunn-Jong
2009-08-01
Numerical simulation for the adhesive contact between a sphere and a half-space is employed. The numerical simulation is performed for a realistic surface force law based on the Lennard-Jones potential between molecules with the Derjaguin approximation. The result is compared with the two-dimensional Maugis model, which uses the Dugdale law. It is found that the Maugis model gives good results, approximating those obtained by the numerical simulation. It is also found that the usual Maugis parameter governs the transition from the two-dimensional JKR model to the two-dimensional rigid cylinder contact. But the rigid body limit found using the Maugis model is different from that found using the numerical simulation.
Simulation of wetting and drying at solid-fluid interfaces on the Delft molecular dynamics processor
International Nuclear Information System (INIS)
Sikkenk, J.H.; Indekeu, J.O.; van Leeuwen, J.M.J.; Vossnack, E.O.; Bakker, A.F.
1988-01-01
The adsorption is studied of a fluid at a structured solid substrate by means of computer simulations on the Delft Molecular Dynamics Processor. Two types of particles are present, 2904 of one type for building a three-layer substrate and about 8500 of another type for composing the fluid. Interactions between like and unlike atoms are modeled by pair potentials of Lennard-Jones form cut off at 2.5σ. Simulations are performed at constant temperature and variable ratio of substrate-adsorbate to adsorbate-adsorbate attraction. On the basis of measurements of density profiles, coverages, surface tensions, and contact angles, a wetting as well as a drying phase transition have been identified. Both transitions are of first order
Wu, Shuai; Zhan, Hai-yi; Wang, Hong-ming; Ju, Yan
2012-04-01
The secondary structure of different Iβ cellulose was analyzed by a molecular dynamics simulation with MARTINI coarse-grained force field, where each chain of the cellulose includes 40 D-glucoses units. Calculation gives a satisfied description about the secondary structure of the cellulose. As the chain number increasing, the cellulose becomes the form of a helix, with the diameter of screw growing and spiral rising. Interestingly, the celluloses with chain number N 4 of 6, 24 and 36 do show right-hand twisting. On the contrast, the celluloses with N 8 of 12, 16 chains are left-hand twisting. These simulations indicate that the cellulose with chain number larger than 36 will break down to two parts. Besides, the result indicates that 36-chains cellulose model is the most stable among all models. Furthermore, the Lennard-Jones potential determines the secondary structure. In addition, an equation was set up to analyze the twisting structure.
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.
Huš, Matej; Munaò, Gianmarco; Urbic, Tomaz
2014-01-01
Thermodynamic and structural properties of a coarse-grained model of methanol are examined by Monte Carlo simulations and reference interaction site model (RISM) integral equation theory. Methanol particles are described as dimers formed from an apolar Lennard-Jones sphere, mimicking the methyl group, and a sphere with a core-softened potential as the hydroxyl group. Different closure approximations of the RISM theory are compared and discussed. The liquid structure of methanol is investigated by calculating site-site radial distribution functions and static structure factors for a wide range of temperatures and densities. Results obtained show a good agreement between RISM and Monte Carlo simulations. The phase behavior of methanol is investigated by employing different thermodynamic routes for the calculation of the RISM free energy, drawing gas-liquid coexistence curves that match the simulation data. Preliminary indications for a putative second critical point between two different liquid phases of methanol are also discussed. PMID:25362323
Elastic properties of surfactant monolayers at liquid-liquid interfaces: A molecular dynamics study
DEFF Research Database (Denmark)
Laradji, Mohamed; Mouritsen, Ole G.
2000-01-01
Using a simple molecular model based on the Lennard-Jones potential, we systematically study the elastic properties of liquid-liquid interfaces containing surfactant molecules by means of extensive and large-scale molecular dynamics simulations. The main elastic constants of the interface...... is further increased. Using a Gaussian theory on an interfacial Ginzburg-Landau model of surfactants, we find that the initial decrease of the bending rigidity is attributed to coupling between fluctuations of the surfactant orientation field to those in the interfacial height. (C) 2000 American Institute......, corresponding to the interfacial tension and the mean bending modulus are determined from the analyses of the long-wavelength behavior of the structure factor of the capillary waves. We found that the interfacial tension decreases with increasing surfactant interfacial coverage and/or surfactant chain length...
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.
Molecular Dynamics Simulation Study of Transport Properties of Diatomic Gases
International Nuclear Information System (INIS)
Lee, Song Hi; Kim, Ja Hun
2014-01-01
In this paper, we report thermodynamic and transport properties (diffusion coefficient, viscosity, and thermal conductivity) of diatomic gases (H 2 , N 2 , O 2 , and Cl 2 ) at 273.15 K and 1.00 atm by performing molecular dynamics simulations using Lennard-Jones intermolecular potential and modified Green-Kubo formulas. The results of self-diffusion coefficients of diatomic gases obtained from velocity auto-correlation functions by Green-Kubo relation are in good agreement with those obtained from mean square displacements by Einstein relation. While the results for viscosities of diatomic gases obtained from stress auto-correlation functions underestimate the experimental results, those for thermal conductivities obtained from heat flux autocorrelation functions overestimate the experimental data except H 2
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...
Broadening and shift of the inter-combination spectral line of Cd 326.1 nm perturbed by Kr
Energy Technology Data Exchange (ETDEWEB)
Roston, G D [Physics Department, Faculty of Science, Alexandria University, PO Box 21511, Alexandria (Egypt); Ghatass, Z F, E-mail: dr.gamal_daniel@yahoo.co [Department of Environmental Studies, Institute of Graduate Studies and Research, Alexandria University, 163 Horrya Avenue, PO 832, Shatby, Alexandria (Egypt)
2010-07-15
The line center of the Cd inter-combination spectral line at 326.1 nm (5{sup 1}S{sub 0}-5{sup 3}P{sub 1}) perturbed by Kr has been investigated using a high-resolution scanning Fabry-Perot interferometer. The van der Waals and Lennard-Jones potentials for a Cd-Kr system have been calculated using the Coulomb approximation. The values of the pressure broadening ({beta}) and shift ({delta}) coefficients for the studied line at a temperature of 468 K, density of cadmium N=4.02x10{sup 12} cm{sup -3} and Kr gas pressure ranging from 3 to 95 Torr have been obtained and compared with published theoretical and experimental values.
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
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
Thermophysical properties and some parameters of liquid sodium
International Nuclear Information System (INIS)
Rapeanu, S.; Padureanu, I.; Rotarescu, G.; Craciun, C.; Ion, M.
1982-07-01
In the paper are reported some results on the thermophysical properties of the liquid sodium obtained by means of the neutron scattering and of the theories existing for various physical parameters. The results are based on hard sphere approach and neutron diffraction experiments performed in the region of the small momentum transfer. From this measurement extrapolated at Q → 0, the packing fraction eta as a function of temperature in the range 100-600 deg is obtained. Knowing the parameter eta, the structure factor S(Q) and the radial distribution function g(r) are calculated. To calculate various physical parameters of the liquid sodium like: electrical resistivity, thermoelectric power, viscosity coefficient, electrical conductivity etc., S(Q), g(r) and a Lennard Jones interaction potential phi(r) are used. (authors)
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
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.
Tovbin, Yu. K.; Zaitseva, E. S.; Rabinovich, A. B.
2017-10-01
Size dependences of the surface tension of spherical single-component droplets are calculated using equations of the lattice gas model for 19 compounds. Parameters of the model are found from experimental data on the surface tension of these compounds for a macroscopic planar surface. The chosen low-molecular compounds satisfy the law of corresponding states. To improve agreement with the experimental data, Lennard-Jones potential parameters are varied within 10% deviations. The surface tensions of different sized equilibrium droplets are calculated at elevated and lowered temperatures. It is found that the surface tension of droplets grows monotonically as the droplet size increases from zero to its bulk value. The droplet size R 0 corresponding to zero surface tension corresponds to the critical size of the emergence of a new phase. The critical droplet sizes in the new phase of the considered compounds are estimated for the first time.
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.
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
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.
Buckling instability of circular double-layered graphene sheets.
Natsuki, Toshiaki; Shi, Jin-Xing; Ni, Qing-Qing
2012-04-04
In this paper, we study the buckling properties of circular double-layered graphene sheets (DLGSs), using plate theory. The two graphene layers are modeled as two individual sheets whose interactions are determined by the Lennard-Jones potential of the carbon-carbon bond. An analytical solution of coupled governing equations is proposed for predicting the buckling properties of circular DLGSs. Using the present theoretical approach, the influences of boundary conditions, plate sizes, and buckling-mode shapes on the buckling behaviors are investigated in detail. The buckling stability is significantly affected by the buckling-mode shapes. As a result of van der Waals interactions, the buckling stress of circular DLGSs is much larger for the anti-phase mode than for the in-phase mode. © 2012 IOP Publishing Ltd
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
Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model.
Mohebifar, Mohamad; Johnson, Erin R; Rowley, Christopher N
2017-12-12
London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential using empirically determined parameters. These parameters are generally underdetermined, and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields. The molecular dispersion coefficients for the CGenFF, GAFF, and OPLS models are systematically higher than the XDM-calculated values by a factor of roughly 1.5, likely due to neglect of higher order dispersion terms and premature truncation of the dispersion-energy summation. The XDM dispersion coefficients span a large range for some molecular-mechanical atom types, suggesting an unrecognized source of error in force-field models, which assume that atoms of the same type have the same dispersion interactions. Agreement with the XDM dispersion coefficients is even poorer for the Drude polarizable force field. Popular water models were also examined, and TIP3P was found to have dispersion coefficients similar to the experimental and XDM references, although other models employ anomalously high values. Finally, XDM-derived dispersion coefficients were used to parametrize molecular-mechanical force fields for five liquids-benzene, toluene, cyclohexane, n-pentane, and n-hexane-which resulted in improved accuracy in the
Li, Jun
2013-09-01
We present a single-particle Lennard-Jones (L-J) model for CO2 and N2. Simplified L-J models for other small polyatomic molecules can be obtained following the methodology described herein. The phase-coexistence diagrams of single-component systems computed using the proposed single-particle models for CO2 and N2 agree well with experimental data over a wide range of temperatures. These diagrams are computed using the Markov Chain Monte Carlo method based on the Gibbs-NVT ensemble. This good agreement validates the proposed simplified models. That is, with properly selected parameters, the single-particle models have similar accuracy in predicting gas-phase properties as more complex, state-of-the-art molecular models. To further test these single-particle models, three binary mixtures of CH4, CO2 and N2 are studied using a Gibbs-NPT ensemble. These results are compared against experimental data over a wide range of pressures. The single-particle model has similar accuracy in the gas phase as traditional models although its deviation in the liquid phase is greater. Since the single-particle model reduces the particle number and avoids the time-consuming Ewald summation used to evaluate Coulomb interactions, the proposed model improves the computational efficiency significantly, particularly in the case of high liquid density where the acceptance rate of the particle-swap trial move increases. We compare, at constant temperature and pressure, the Gibbs-NPT and Gibbs-NVT ensembles to analyze their performance differences and results consistency. As theoretically predicted, the agreement between the simulations implies that Gibbs-NVT can be used to validate Gibbs-NPT predictions when experimental data is not available. © 2013 Elsevier Inc.
Jollrnal of EAEA, VoL lJ, 1996
African Journals Online (AJOL)
course in the Electrical Engineering Department of the Faculty of Technology, Addis Ababa University. A list of ... important senior courses in any electrical engineering. cwTiculum. The coverage of the course, however, ... miaoprocessor fundamentals and communication systems. With reference to the outline of the first ...
Jollrnal of EAEA, VoL lJ, 1996
African Journals Online (AJOL)
OICh are also given [4-7). Most of the reference books in the sccood group, however, do not concentrate on electrical-electronic aspects of imtnmeotltioo systems. Besides, the relatively new coocq>ts of intelligent instrumentation and intelligent.
Steven MacCall: Winner of LJ's 2010 Teaching Award
Berry, John N., III
2010-01-01
This article profiles Steven L. MacCall, winner of "Library Journal's" 2010 Teaching Award. An associate professor at the School of Library and Information Studies (SLIS) at the University of Alabama, Tuscaloosa, MacCall was nominated by Kathie Popadin, known as "Kpop" to the members of her cohort in the online MLIS program at SLIS. Sixteen of…
Inman, Matthew Clay
A novel, open-cathode direct methanol fuel cell (DMFC ) has been designed and built by researchers at the University of North Florida and University of Florida. Foremost among the advances of this system over previous DMFC architectures is a passive water recovery system which allows product water to replenish that consumed at the anode. This is enabled by a specially-designed water pathway combined with a liquid barrier layer (LBL ). The LBL membrane is positioned between the cathode catalyst layer and the cathode gas diffusion layer, and must exhibit high permeability and low diffusive resistance to both oxygen and water vapor, bulk hydrophobicity to hold back the product liquid water, and must remain electrically conductive. Maintaining water balance at optimum operating temperatures is problematic with the current LBL design, forcing the system to run at lower temperatures decreasing the overall system efficiency. This research presents a novel approach to nanoporous membrane design whereby flux of a given species is determined based upon the molecular properties of said species and those of the diffusing medium, the pore geometry, and the membrane thickness. A molecular dynamics (MD ) model is developed for tracking Knudsen regime flows of a Lennard-Jones (LJ ) fluid through an atomistic pore structure, hundreds of thousands of wall collision simulations are performed on the University of Florida HiPerGator supercomputer, and the generated trajectory information is used to develop number density and axial velocity profiles for use in a rigorous approach to total flux calculation absent in previously attempted MD models. Results are compared to other published approaches and diffusion data available in the literature. The impact of this study on various applications of membrane design is discussed and additional simulations and model improvements are outlined for future consideration.
Orabi, Esam A; Lamoureux, Guillaume
2014-08-12
A polarizable model for hydrogen sulfide (H2S) is optimized based on the experimental properties of the monomer and of the bulk liquid. The model is characterized by rigid SH bonds but flexible HSH angle and the polarizability is based on the Drude oscillator model. Bonded parameters and atomic charges are based on the experimental properties of the gaseous monomer. Atomic Lennard-Jones (LJ) parameters are adjusted based on the density of H2S around the critical point (in the temperature range 363-393 K and pressure range 8.023-10.013 MPa). The model gives binding energies for H2S dimers, trimers, and tetramers in good agreement with ab initio MP2(full)/6-311++G(d,p) results. It shows a liquid structure in very good agreement with neutron diffraction data. The model also gives density, self-diffusion coefficient, heat of vaporization, and dielectric constant of liquid hydrogen sulfide at the normal boiling point in good agreement with experimental data. In addition, the model is transferable to high temperature and pressure conditions, as evidenced from simulations up to 542.2 K and 40 MPa. The model is used in combination with the SWM4-NDP water model, with LJ parameters between the S and O atoms adjusted to reproduce the experimental hydration free energy of H2S. Simulations suggest that, in its first solvation shell, a single H2O molecule is solvated by 10 H2S molecules while a single H2S molecule is solvated by 20.5 H2O molecules. Pair-specific LJ parameters between alkali ions (Li(+), Na(+), K(+), Rb(+), Cs(+)) and the S atom are adjusted to reproduce ab initio binding energies of the ion-H2S pairs at the CCSD(T) level. Simulations based on these parameters show that alkali ions have higher coordination numbers and lower solvation free energies in liquid H2S than in liquid water or liquid ammonia. The model is also used to investigate the preferential solvation of the ions in aqueous solutions with a 10% H2S mole fraction. Results show that the ions are
Moustafa, Sabry Gad Al-Hak Mohammad
shown to vary slowly with system-size. This allow us to get the FE in the thermodynamic limit by extrapolating the one isomer results to infinity and correct for that by the effect from considering proton-disorder measured at a small system. These techniques are applied to empty hydrates (of types: SI, SII, and SH) to estimate their thermodynamic stability. For conditions where the harmonic model fails, performing MS is needed to estimate rigorously the full (harmonic plus anharmonic) quantity. Although several MS methods are available for that purpose, they do not benefit from the harmonic nature of crystals---which represents the main contribution and is cheap to compute. In other words, those "conventional" methods always "start from scratch" even at states where anharmonic part is negligible. In this work, we develop very efficient MS methods that leverage information, on-the-fly, from the harmonic behavior of configurations such that the anharmonic contributions are directly measured. The approach is named harmonically-mapped averaging (HMA) for the rest of this thesis. Since the major contribution of thermodynamic properties comes from the harmonic nature of crystal, the fluctuations in the anharmonic quantities is to be small; hence, uncertainty associated with the HMA method is small. The HMA method is given in a general formulation such that it can handle properties related to both first- and second-derivatives of free energy. The HMA approach is first applied to Lennard-Jones (LJ) model. First- and second-derivatives of FE with respect to temperature and volume yield the following properties: energy, pressure, isochoric heat capacity, bulk modulus, and thermal pressure coefficient. A considerable improvement in the efficiency of measuring those properties is observed even at melting conditions where anharmonicity is non-negligible. First-derivative properties are computed with 100 to 10,000 times less computational effort, while speedup for the second
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
Füglistaler, A.; Pfenniger, D.
2016-06-01
Context. Molecular clouds typically consist of 3/4 H2, 1/4 He and traces of heavier elements. In an earlier work we showed that at very low temperatures and high densities, H2 can be in a phase transition leading to the formation of ice clumps as large as comets or even planets. However, He has very different chemical properties and no phase transition is expected before H2 in dense interstellar medium conditions. The gravitational stability of fluid mixtures has been studied before, but these studies did not include a phase transition. Aims: We study the gravitational stability of binary fluid mixtures with special emphasis on when one component is in a phase transition. The numerical results are aimed at applications in molecular cloud conditions, but the theoretical results are more general. Methods: First, we study the gravitational stability of van der Waals fluid mixtures using linearized analysis and examine virial equilibrium conditions using the Lennard-Jones intermolecular potential. Then, combining the Lennard-Jones and gravitational potentials, the non-linear dynamics of fluid mixtures are studied via computer simulations using the molecular dynamics code LAMMPS. Results: Along with the classical, ideal-gas Jeans instability criterion, a fluid mixture is always gravitationally unstable if it is in a phase transition because compression does not increase pressure. However, the condensed phase fraction increases. In unstable situations the species can separate: in some conditions He precipitates faster than H2, while in other conditions the converse occurs. Also, for an initial gas phase collapse the geometry is essential. Contrary to spherical or filamentary collapses, sheet-like collapses starting below 15 K easily reach H2 condensation conditions because then they are fastest and both the increase of heating and opacity are limited. Conclusions: Depending on density, temperature and mass, either rocky H2 planetoids, or gaseous He planetoids form. H2
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)
Well-Posedness of the Iterative Boltzmann Inversion
Hanke, Martin
2018-02-01
The iterative Boltzmann inversion is a fixed point iteration to determine an effective pair potential for an ensemble of identical particles in thermal equilibrium from the corresponding radial distribution function. Although the method is reported to work reasonably well in practice, it still lacks a rigorous convergence analysis. In this paper we provide some first steps towards such an analysis, and we show under quite general assumptions that the associated fixed point operator is Lipschitz continuous (in fact, differentiable) in a suitable neighborhood of the true pair potential, assuming that such a potential exists. In other words, the iterative Boltzmann inversion is well-defined in the sense that if the kth iterate of the scheme is sufficiently close to the true pair potential then the k+1st iterate is an admissible pair potential, which again belongs to the domain of the fixed point operator. On our way we establish important properties of the cavity distribution function and provide a proof of a statement formulated by Groeneveld concerning the rate of decay at infinity of the Ursell function associated with a Lennard-Jones type potential.
Oh, B. K.; Kim, S. K.
1974-01-01
A model of helium adsorption on an argon crystal is built up from the premise that local adsorption predominates in the first layer and nonlocal adsorption in the second. Application of the virial expansion theorem to the second layer gives a series in which the first term represents the motion of a single molecule in the external potential field and the second a two-body interaction under this field. The thermodynamic functions of the adsorbed phase are calculated ab initio, the gas-solid interaction potential being derived from lattice summation and the partition function from an appropriate choice of a site-spacing polynomial to describe the periodic potential. The mutual interaction of adsorbed molecules is calculated with a two-dimensional Lennard-Jones potential. The second virial coefficient is calculated and its dependence on temperature and choice of potential is studied. It is found that the second virial coefficient is very well approximated by a two-dimensional gas in free space. The adsorption isotherm, isosteric heat, and specific heat are obtained and compared with the results of Ross and Steele, giving excellent agreement.
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.
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.
Collective behavior of penetrable self-propelled rods in two dimensions
Abkenar, Masoud; Marx, Kristian; Auth, Thorsten; Gompper, Gerhard
2013-12-01
Collective behavior of self-propelled particles is observed on a microscale for swimmers such as sperm and bacteria as well as for protein filaments in motility assays. The properties of such systems depend both on their dimensionality and the interactions between their particles. We introduce a model for self-propelled rods in two dimensions that interact via a separation-shifted Lennard-Jones potential. Due to the finite potential barrier, the rods are able to cross. This model allows us to efficiently simulate systems of self-propelled rods that effectively move in two dimensions but can occasionally escape to the third dimension in order to pass each other. Our quasi-two-dimensional self-propelled particles describe a class of active systems that encompasses microswimmers close to a wall and filaments propelled on a substrate. Using Monte Carlo simulations, we first determine the isotropic-nematic transition for passive rods. Using Brownian dynamics simulations, we characterize cluster formation of self-propelled rods as a function of propulsion strength, noise, and energy barrier. Contrary to rods with an infinite potential barrier, an increase of the propulsion strength does not only favor alignment but also effectively decreases the potential barrier that prevents crossing of rods. We thus find a clustering window with a maximum cluster size at medium propulsion strengths.
Structural behavior of supercritical fluids under confinement
Ghosh, Kanka; Krishnamurthy, C. V.
2018-01-01
The existence of the Frenkel line in the supercritical regime of a Lennard-Jones (LJ) fluid shown through molecular dynamics (MD) simulations initially and later corroborated by experiments on argon opens up possibilities of understanding the structure and dynamics of supercritical fluids in general and of the Frenkel line in particular. The location of the Frenkel line, which demarcates two distinct physical states, liquidlike and gaslike within the supercritical regime, has been established through MD simulations of the velocity autocorrelation (VACF) and radial distribution function (RDF). We, in this article, explore the changes in the structural features of supercritical LJ fluid under partial confinement using atomistic walls. The study is carried out across the Frenkel line through a series of MD simulations considering a set of thermodynamics states in the supercritical regime (P =5000 bar, 240 K ≤T ≤1500 K ) of argon well above the critical point. Confinement is partial, with atomistic walls located normal to z and extending to "infinity" along the x and y directions. In the "liquidlike" regime of the supercritical phase, particles are found to be distributed in distinct layers along the z axis with layer spacing less than one atomic diameter and the lateral RDF showing amorphous-like structure for specific spacings (packing frustration) and non-amorphous-like structure for other spacings. Increasing the rigidity of the atomistic walls is found to lead to stronger layering and increased structural order. For confinement with reflective walls, layers are found to form with one atomic diameter spacing and the lateral RDF showing close-packed structure for the smaller confinements. Translational order parameter and excess entropy assessment confirms the ordering taking place for atomistic wall and reflective wall confinements. In the "gaslike" regime of the supercritical phase, particle distribution along the spacing and the lateral RDF exhibit features
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.
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.
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)
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.
Coarse-grained Monte Carlo simulations of non-equilibrium systems.
Liu, Xiao; Crocker, John C; Sinno, Talid
2013-06-28
We extend the scope of a recent method for generating coarse-grained lattice Metropolis Monte Carlo simulations [X. Liu, W. D. Seider, and T. Sinno, Phys. Rev. E 86, 026708 (2012); and J. Chem. Phys. 138, 114104 (2013)] from continuous interaction potentials to non-equilibrium situations. The original method has been shown to satisfy detailed balance at the coarse scale and to provide a good representation of various equilibrium properties in both atomic and molecular systems. However, we show here that the original method is inconsistent with non-equilibrium trajectories generated by full-resolution Monte Carlo simulations, which, under certain conditions, have been shown to correspond to Langevin dynamics. The modified coarse-grained method is generated by simultaneously biasing the forward and backward transition probability for every possible move, thereby preserving the detailed balance of the original method. The resulting coarse-grained Monte Carlo simulations are shown to provide trajectories that are consistent with overdamped Langevin (Smoluchowski) dynamics using a sequence of simple non-equilibrium examples. We first consider the purely diffusional spreading of a Gaussian pulse of ideal-gas particles and then include an external potential to study the influence of drift. Finally, we validate the method using a more general situation in which the particles interact via a Lennard-Jones interparticle potential.
Thermophoresis of a Brownian particle driven by inhomogeneous thermal fluctuation
Tsuji, Tetsuro; Saita, Sho; Kawano, Satoyuki
2018-03-01
Brownian motion of a spherical particle induced by the interaction with surrounding molecules is considered. If the particle is larger than the molecules and the temperature of surrounding media is spatially non-uniform, the interaction between an individual molecule and the particle is also position-dependent. That is, the particle is subject to inhomogeneous thermal fluctuation. In this paper, we investigate the contribution of the inhomogeneous thermal fluctuation to the thermophoresis, i.e., the Soret coefficient or thermal diffusion factor. The problem is simplified by assuming a hard-sphere potential between the particle and the surrounding molecules and is investigated using the kinetic theory, namely, we consider a linear Boltzmann-type equation for the velocity distribution function of the particle. Using the perturbation analysis with respect to the square root of mass ratio between the molecule and the particle, the drift-diffusion equation of the particle is derived. It is found that the Soret coefficient, or thermal diffusion factor, is dependent on the mass ratio and the excluded volume of the particle. In particular, when the ratio of the mass density of the particle to that of the surrounding media decreases, the Soret coefficient also decreases and may take negative value. The present result well describes the mass-dependency of thermal diffusion factor obtained by the molecular dynamics simulation carried out in an existing study and the one in the present study, where soft potentials of Lennard-Jones-type are used instead of hard-sphere potential.
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.
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
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
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.
Universality and non-universality in the heteronuclear Efimov scenario with large mass imbalance
Energy Technology Data Exchange (ETDEWEB)
Ulmanis, Juris
2015-07-09
This thesis investigates universal and non-universal aspects of few-body physics in a mass-imbalanced mixture of ultracold bosonic {sup 133}Cs and fermionic {sup 6}Li atoms. For this purpose an experimental apparatus for the creation of quantum degenerate gases has been constructed. Using radio-frequency association of weakly-bound LiCs molecules and additional atom-loss spectroscopy we determine the two-body interaction properties between Li and Cs atoms at low collision energies. The analysis with a coupled-channels calculation yields precise singlet and triplet electronic ground state molecular potential curves, from which scattering lengths and positions of Fano-Feshbach resonances are extracted. These results represent almost a tenfold improvement over the previous determination, and are used to study few-body recombination processes and, for the first time, their dependence on the interaction strength between the heavy atoms close to two broad scattering resonances at various temperatures. Measurements of three-body loss rates reveal two series of three and two consecutive LiCs{sub 2} Efimov resonances that demonstrate the universal scaling factor 4.9 between the first and second excited state resonances. The ground state resonance deviates from the discrete scaling law. By the use of hyperspherical formalism with either pairwise zero-range or Lennard-Jones model potentials we identify the van der Waals interaction between Cs atoms as a significant source of these modifications.
Rodríguez-López, Tonalli; Moreno-Razo, J Antonio; del Río, Fernando
2013-03-21
In this work, we explore transport properties of a special type of repulsive spheres that exhibit remarkable scaling of their thermodynamic properties. In order to accomplish that we propose a new way to derive and express effective hard-sphere diameters for transport properties of simple fluids. The procedure relies on mapping the system's transport properties, in the low density limit, to the hard-sphere fluid. We have chosen a set of soft-sphere systems characterised by a well-defined variation of their softness. These systems represent an extension of the repulsive Lennard-Jones potential widely used in statistical mechanics of fluids and are an accurate representation of the effective repulsive potentials of real systems. The self-diffusion coefficient of the soft-sphere fluids is obtained by equilibrium molecular dynamics. The soft-sphere collision integrals of different systems are shown to follow quite simple relationships between each other. These collision integrals are incorporated, through the definition of the effective hard-sphere diameter, in the resulting equation for the self-diffusion coefficient. The approach followed exhibits a density rescaling that leads to a single master curve for all systems and temperatures. The scaling is carried through to the level of the mean-squared displacement.
Energy Technology Data Exchange (ETDEWEB)
Fröhlich, Markus G., E-mail: FroehlichM@missouri.edu, E-mail: ThompsonDon@missouri.edu; Sewell, Thomas D., E-mail: SewellT@missouri.edu; Thompson, Donald L., E-mail: FroehlichM@missouri.edu, E-mail: ThompsonDon@missouri.edu [Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211-7600 (United States)
2014-01-14
The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s{sup −1}, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ∼0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.
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
Klebe, Gerhard; Abraham, Ute
1999-01-01
Comparative molecular field analysis has been applied to a data set of thermolysin inhibitors. Fields expressed in terms of molecular similarity indices (CoMSIA) have been used instead of the usually applied Lennard-Jones- and Coulomb-type potentials (CoMFA). Five different properties, assumed to cover the major contributions responsible for ligand binding, have been considered: steric, electrostatic, hydrophobic, and hydrogen-bond donor or acceptor properties. The statistical evaluation of the field properties by PLS analysis reveals a similar predictive potential to CoMFA. However, significantly improved and easily interpretable contour maps are obtained. The features in these maps intuitively suggest where to modify a molecular structure in terms of physicochemical properties and functional groups in order to improve its binding affinity. They can also be interpreted with respect to the known structural protein environment of thermolysin. Most of the highlighted regions in the maps are mirrored by features in the surrounding environment required for binding. Using the derived correlation model, different members of a combinatorial library designed for thermolysin inhibition have been scored for affinity. The results obtained demonstrate the prediction power of the CoMSIA method.
Cao, Fenglei; Deetz, Joshua D; Sun, Huai
2017-01-23
The free energy based Lennard-Jones 12-6 (FE-12-6) coarse-grained (CG) force field developed for alkanes1 has been extended to model small molecules of light hydrocarbons (methane, ethane, propane, butane, and isobutane), nitrogen, oxygen, and carbon dioxide. The adjustable parameters of the FE-12-6 potential are determined by fitting against experimental vapor-liquid equilibrium (VLE) curves and heat of vaporization (HOV) data for pure substance liquids. Simulations using the optimized FE-12-6 parameters correctly reproduced experimental measures of the VLE, HOV, density, vapor pressure, compressibility, critical point, and surface tension for pure substances over a wide range of thermodynamic states. The force field parameters optimized for pure substances were tested on methane/butane, nitrogen/decane, and carbon dioxide/decane binary mixtures to predict their vapor-liquid equilibrium phase diagrams. It is found that for nonpolar molecules represented by different sized beads, a common scaling factor (0.08) that reduces the strength of the interaction potential between unlike beads, generated using Lorentz-Berthelot (LB) combination rules, is required to predict vapor-liquid phase equilibria accurately.
Molecular Dynamics Simulation of Coarse-Grain Model of Silicon Functionalized Graphene
Directory of Open Access Journals (Sweden)
Hui Zhixin
2015-01-01
Full Text Available The electronic transport, the storage capacity and the service life of the anode material for lithium ion batteries will be reduced seriously in the event of the material layering or cracking, so the anode material must have strong mechanical reliability. Firstly, in view of the traditional molecular dynamics (MD limited by the geometric scales of the model of Silicon functionalized graphenen (SFG as lithium ion batteries anode material, some full atomic models of SFG were established using Tersoff potential and Lennard-Jones potential, and used to calculate the modulus and the adhesion properties. What’s more, the assertion of mechanical equilibrium condition and energy conservation between full atomic and coarse-grain models through elastic strain energy were enforced to arrive at model parameters. The model of SFG coarse-grain bead-spring elements and its system energy function were obtained via full atomic simulations. Finally, the validity of the SFG coarse-grain model was verified by comparing the tensile property of coarse-grain model with full atoms model.
Translocation of a Polymer Chain across a Nanopore: A Brownian Dynamics Simulation Study
Tian, Pu; Smith, Grant D.
2003-01-01
We carried out Brownian dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an applied field (chemical potential gradient). The translocation process can be either dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical gradient across the wall), we focused on the latter case in our studies. Calculation of radius of gyrations at the two opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tubelike pore geometry, more than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied, attraction facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of polymer chain. The width of the translocation time distribution was found to decrease with increasing temperature, increasing field strength, and decreasing pore diameter.
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.
Chaudhury, Pinaki; Bhattacharyya, S. P.
1999-03-01
It is demonstrated that Genetic Algorithm in a floating point realisation can be a viable tool for locating critical points on a multi-dimensional potential energy surface (PES). For small clusters, the standard algorithm works well. For bigger ones, the search for global minimum becomes more efficient when used in conjunction with coordinate stretching, and partitioning of the strings into a core part and an outer part which are alternately optimized The method works with equal facility for locating minima, local as well as global, and saddle points (SP) of arbitrary orders. The search for minima requires computation of the gradient vector, but not the Hessian, while that for SP's requires the information of the gradient vector and the Hessian, the latter only at some specific points on the path. The method proposed is tested on (i) a model 2-d PES (ii) argon clusters (Ar 4-Ar 30) in which argon atoms interact via Lennard-Jones potential, (iii) Ar mX, m=12 clusters where X may be a neutral atom or a cation. We also explore if the method could also be used to construct what may be called a stochastic representation of the reaction path on a given PES with reference to conformational changes in Ar n clusters.
Chemical Dynamics Simulations of Intermolecular Energy Transfer: Azulene + N2 Collisions.
Kim, Hyunsik; Paul, Amit K; Pratihar, Subha; Hase, William L
2016-07-14
Chemical dynamics simulations were performed to investigate collisional energy transfer from highly vibrationally excited azulene (Az*) in a N2 bath. The intermolecular potential between Az and N2, used for the simulations, was determined from MP2/6-31+G* ab initio calculations. Az* is prepared with an 87.5 kcal/mol excitation energy by using quantum microcanonical sampling, including its 95.7 kcal/mol zero-point energy. The average energy of Az* versus time, obtained from the simulations, shows different rates of Az* deactivation depending on the N2 bath density. Using the N2 bath density and Lennard-Jones collision number, the average energy transfer per collision ⟨ΔEc⟩ was obtained for Az* as it is collisionally relaxed. By comparing ⟨ΔEc⟩ versus the bath density, the single collision limiting density was found for energy transfer. The resulting ⟨ΔEc⟩, for an 87.5 kcal/mol excitation energy, is 0.30 ± 0.01 and 0.32 ± 0.01 kcal/mol for harmonic and anharmonic Az potentials, respectively. For comparison, the experimental value is 0.57 ± 0.11 kcal/mol. During Az* relaxation there is no appreciable energy transfer to Az translation and rotation, and the energy transfer is to the N2 bath.
Berim, Gersh O.; Ruckenstein, Eli
2009-01-01
The density distributions and contact angles of nanodrops on smooth solid surfaces are calculated on the basis of a nonlocal density functional theory in wide ranges of temperature and parameters of the Lennard-Jones potentials representing the fluid-fluid and fluid-solid interactions. A simple linear dependence of the contact angle on the fluid-solid energy parameter ɛfs was found for various temperatures, hard core fluid-solid parameters σfs, and average fluid density of the system. A simple expression is suggested which represents all the above results in a unified form that relates the contact angle θ to the parameters of the interaction potentials and temperature. The most intriguing feature was that for each considered σfs there is a value ɛfs0 of ɛfs for which the contact angle θ=θ0 can be considered independent of temperature and of σfs. It is shown that ɛfs=ɛfs0 divides the materials for which θ increases from those for which θ decreases with increasing temperature. The results obtained for the dependence of the contact angle on the parameters of the model are in qualitative agreement with known molecular dynamics results.
A study of τ , the critical exponent of nuclear fragmentation
International Nuclear Information System (INIS)
Cardenas, R.; Lopez, J.A.; Barranon, A.; Dorso, C.O.
2001-01-01
Full text: When nuclei break into pieces, fragments with different sizes mass and charge numbers, are generated. Using the Fisher droplet model this fragmentation process can be characterized as a second order phase transitions of the excited nuclear matter. For breakups occurring near the critical point, the mass distribution should obeys a power law of the form ∼ A - τ , with τ being a critical exponent, apparently universal to processes at different scales with values within 2 ≤ τ ≤3. In this work we study the behavior of this exponent considering four different models. In summary the findings are as follows. Using percolation theory for a cubic system with 216 sites, a value of τ = 2.3 was obtained. A spherical system, also yielded a value of τ = 2.3. The third model, consisting of two 74-particle colliding nuclei interacting via a Lennard-Jones potential, also produced fragments with a power law distribution of τ = 2.3. Finally, studying a series of collisions of 147-particle nuclei using a more realistic potential (Pandharipande), a τ = 1.92 was obtained. This last result, however, can be expected for breakups not occurring near the critical point. Further refinements of this last study are in progress. JAL acknowledges support from the National Science Foundation, through grant PHY-96-00038. (Author)
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.
Offset configurations for single- and double-strand DNA inside single-walled carbon nanotubes.
Alshehri, Mansoor H; Cox, Barry J; Hill, James M
2014-01-01
Nanotechnology is a rapidly expanding research area, and it is believed that the unique properties of molecules at the nano-scale will prove to be of substantial benefit to mankind, especially so in medicine and electronics. Here we use applied mathematical modelling exploiting the basic principles of mechanics and the 6-12 Lennard-Jones potential function together with the continuum approximation, which assumes that intermolecular interactions can be approximated by average atomic surface densities. We consider the equilibrium offset positions for both single-strand and double-strand DNA molecules inside a single-walled carbon nanotube, and we predict offset positions with reference to the cross-section of the carbon nanotube. For the double-strand DNA, the potential energy is determined for the general case for any helical phase angle ϕ, but we also consider a special case when ϕ = π, which leads to a substantial simplification in the analytical expression for the energy. As might be expected, our results confirm that the global minimum energy positions for a single-strand DNA molecule and a double-strand DNA molecule will lie off axis and they become closer to the tube wall as the radius of the tube increases.
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) \
From lime to silica and alumina: systematic modeling of cement clinkers using a general force-field.
Freitas, A A; Santos, R L; Colaço, R; Bayão Horta, R; Canongia Lopes, J N
2015-07-28
Thirteen different cement-clinker crystalline phases present in the lime-silica-alumina system have been systematically modeled using a simple and general force field. This constitutes a new type of approach towards the study of lime-silica-alumina systems, where the simpler and more transferable Lennard-Jones potential was used instead of the more traditional Buckingham potential. The results were validated using experimental density and structural data. The elastic properties were also considered. Six amorphous phases (corresponding to calcium/silicon ratios corresponding to belite, rankinite, wollastonite and alumina-doped amorphous wollastonite with 5%, 10% and 15% alumina content) were also studied using molecular dynamics simulations. The obtained MD trajectories were used to characterize the different crystalline and amorphous phases in terms of the corresponding radial distribution functions, aggregate analyses and connectivity among silica groups. These studies allowed a direct comparison between the crystalline and amorphous phases and revealed how the structure of the silica network was modified in the amorphous materials or by the inclusion of other structural units such as alumina. The knowledge at an atomistic level of such modifications is paramount for the formulation of new cement-clinker phases.
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
DEFF Research Database (Denmark)
Mikkelsen, Henrik Hvenegaard; Søgaard, Thomas Friis
2015-01-01
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...... today abandoned headhunting, the potentials for violence and dominance, which the act of headhunting sought to elicit, remains a critical aspect of masculinity. We propose that a focus on the social significance of performative violent potentiality among Bugkalot men can 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....
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...
Mamatkulov, Shavkat; Schwierz, Nadine
2018-02-01
Metal cations are essential in many vital processes. In order to capture the role of different cations in all-atom molecular dynamics simulations of biological processes, an accurate parametrization is crucial. Here, we develop force field parameters for the metal cations Li+, Na+, K+, Cs+, Mg2+, Ca2+, Sr2+, and Ba2+ in combination with the TIP3P water model that is frequently used in biomolecular simulations. In progressing toward improved force fields, the approach presented here is an extension of previous efforts and allows us to simultaneously reproduce thermodynamic and kinetic properties of aqueous solutions. We systematically derive the parameters of the 12-6 Lennard-Jones potential which accurately reproduces the experimental solvation free energy, the activity derivative, and the characteristics of water exchange from the first hydration shell of the metal cations. In order to reproduce all experimental properties, a modification of the Lorentz-Berthelot combination rule is required for Mg2+. Using a balanced set of solution properties, the optimized force field parameters aim to capture the fine differences between distinct metal cations including specific ion binding affinities and the kinetics of cation binding to biologically important anionic groups.
Interface structure and mechanics between graphene and metal substrates: a first-principles study
International Nuclear Information System (INIS)
Xu Zhiping; Buehler, Markus J
2010-01-01
Graphene is a fascinating material not only for technological applications, but also as a test bed for fundamental insights into condensed matter physics due to its unique two-dimensional structure. One of the most intriguing issues is the understanding of the properties of graphene and various substrate materials. In particular, the interfaces between graphene and metal substrates are of critical importance in applications of graphene in integrated electronics, as thermal materials, and in electromechanical devices. Here we investigate the structure and mechanical interactions at a graphene-metal interface through density functional theory (DFT)-based calculations. We focus on copper (111) and nickel (111) surfaces adhered to a monolayer of graphene, and find that their cohesive energy, strength and electronic structure correlate directly with their atomic geometry. Due to the strong coupling between open d-orbitals, the nickel-graphene interface has a much stronger cohesive energy with graphene than copper. We also find that the interface cohesive energy profile features a well-and-shoulder shape that cannot be captured by simple pair-wise models such as the Lennard-Jones potential. Our results provide a detailed understanding of the interfacial properties of graphene-metal systems, and help to predict the performance of graphene-based nanoelectronics and nanocomposites. The availability of structural and energetic data of graphene-metal interfaces could also be useful for the development of empirical force fields for molecular dynamics simulations.
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.
Classical Fractals and Quantum Chaos in Ultracold Dipolar Collisions.
Yang, B C; Pérez-Ríos, Jesús; Robicheaux, F
2017-04-14
We examine a dipolar-gas model to address fundamental issues regarding the correspondence between classical chaos and quantum observations in ultracold dipolar collisions. The theoretical model consists of a short-range Lennard-Jones potential well with an anisotropic, long-range dipole-dipole interaction between two atoms. Both the classical and quantum dynamics are explored for the same Hamiltonian of the system. The classical chaotic scattering is revealed by the fractals developed in the scattering function (defined as the final atom separation as a function of initial conditions), while the quantum chaotic features lead to the repulsion of the eigenphases from the corresponding quantum S matrix. The nearest-eigenphase-spacing statistics have an intermediate behavior between the Poisson and the Wigner-Dyson distributions. The character of the distribution can be controlled by changing an effective Planck constant or the dipole moment. The degree of quantum chaos shows a good correspondence with the overall average of the classical scattering function. The results presented here also provide helpful insights for understanding the role of the inherent dipole-dipole interaction in the currently ongoing experiments on ultracold collisions of highly magnetic atoms.
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)
Pothapragada, Seetha; Zhang, Peng; Sheriff, Jawaad; Livelli, Mark; Slepian, Marvin J; Deng, Yuefan; Bluestein, Danny
2015-03-01
We developed a phenomenological three-dimensional platelet model to characterize the filopodia formation observed during early stage platelet activation. Departing from continuum mechanics based approaches, this coarse-grained molecular dynamics (CGMD) particle-based model can deform to emulate the complex shape change and filopodia formation that platelets undergo during activation. The platelet peripheral zone is modeled with a two-layer homogeneous elastic structure represented by spring-connected particles. The structural zone is represented by a cytoskeletal assembly comprising of a filamentous core and filament bundles supporting the platelet's discoid shape, also modeled by spring-connected particles. The interior organelle zone is modeled by homogeneous cytoplasm particles that facilitate the platelet deformation. Nonbonded interactions among the discrete particles of the membrane, the cytoskeletal assembly, and the cytoplasm are described using the Lennard-Jones potential with empirical constants. By exploring the parameter space of this CGMD model, we have successfully simulated the dynamics of varied filopodia formations. Comparative analyses of length and thickness of filopodia show that our numerical simulations are in agreement with experimental measurements of flow-induced activated platelets. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.
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
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.
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
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
Transport coefficients of typical biomass equimolar CO-H2 plasma
International Nuclear Information System (INIS)
Aubreton, J; Elchinger, M-F; Hacala, A; Michon, U
2009-01-01
Knowledge of the transport properties of biomass gases is important for modelling plasma flow processes and heat transfer. In this study, calculations were performed for typical biomass equimolar CO-H 2 plasma in a temperature range from 500 to 30 000 K at pressures of 1.0, 2.0, 5.0 and 10.0 bar. Herein, the plasma composition was determined at equilibrium using the Gibbs free energy equation. First, we restricted the species number to 18 for CO-H 2 plasma. Second, the most recent data on potential interactions and elastic differential cross sections were carefully investigated in order to choose those most appropriate to define the collision integrals. Due to a lack of data we used an improvement of the Lennard-Jones function. Third, we tested our collision integrals by comparing (1) the viscosity to experimental data of CO 2 , CH 4 and CO (low temperature) and (2) the thermal conductivity and viscosity to theoretical results for CO 2 plasma (up to 17 000 K). Finally, the viscosity, thermal conductivity and electrical conductivity were calculated for different pressures.
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.
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
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.
Density functional theory formulation for fluid adsorption on correlated random surfaces
Aslyamov, Timur; Khlyupin, Aleksey
2017-10-01
We provide novel random surface density functional theory (RSDFT) formulation in the case of geometric heterogeneous surfaces of solid media which is essential for the description of thermodynamic properties of confined fluids. The major difference of our theoretical approach from the existing ones is a stochastic model of solid surfaces which takes into account the correlation properties of geometry. The main building blocks are effective fluid-solid potentials developed in the work of Khlyupin and Aslyamov [J. Stat. Phys. 167, 1519 (2017)] and geometry-based modification of the Helmholtz free energy for Lennard-Jones fluids. The efficiency of RSDFT is demonstrated in the calculation of argon and nitrogen low temperature adsorption on real heterogeneous surfaces (BP280 carbon black). These results are in good agreement with experimental data published in the literature. Also several models of corrugated materials are developed in the framework of RSDFT. Numerical analysis demonstrates a strong influence of surface roughness characteristics on adsorption isotherms. Thus the developed formalism provides a connection between a rigorous description of the stochastic surface and confined fluid thermodynamics.
International Nuclear Information System (INIS)
Cybulski, Hubert; Bielski, Andrzej; Ciuryło, Roman; Szudy, Józef; Trawiński, Ryszard S.
2013-01-01
The classical phase-shift theory of spectral line shapes is used to examine various aspects of the applicability of the power-law relations to the description of temperature variations of pressure broadening and shifting coefficients of the isolated atomic and rovibronic molecular lines in a wide temperature range. Model calculations performed for potentials of the Lennard-Jones type indicate that the temperature dependence exponents of the broadening and shifting can be related to the details of the intermolecular interactions. It is shown that they are sensitive to the range of temperatures assumed in the fit and therefore extreme care must be taken when the power-law temperature dependence is used as a scaling law. The problems of the failure of the power-law and of variations in the sign of pressure shift coefficients with increasing temperature are discussed. Very good fits of Frost's empirical formula for temperature dependence of pressure shift to the theoretical ones are obtained. -- Highlights: ► Classical theory of line shapes is used to examine the power-law relations. ► The broadening and shifting exponents depend on the range of temperatures in the fit. ► Extreme care must be taken when using the power-law dependence as a scaling law
Generalized linear isotherm regularity equation of state applied to metals
Directory of Open Access Journals (Sweden)
H. Sun
2012-03-01
Full Text Available A three-parameter equation of state (EOS without physically incorrect oscillations is proposed based on the generalized Lennard-Jones (GLJ potential and the approach in developing linear isotherm regularity (LIR EOS of Parsafar and Mason [J. Phys. Chem., 1994, 49, 3049]. The proposed (GLIR EOS can include the LIR EOS therein as a special case. The three-parameter GLIR, Parsafar and Mason (PM [Phys. Rev. B, 1994, 49, 3049], Shanker, Singh and Kushwah (SSK [Physica B, 1997, 229, 419], Parsafar, Spohr and Patey (PSP [J. Phys. Chem. B, 2009, 113, 11980], and reformulated PM and SSK EOSs are applied to 30 metallic solids within wide pressure ranges. It is shown that the PM, PMR and PSP EOSs for most solids, and the SSK and SSKR EOSs for several solids, have physically incorrect turning points, and pressure becomes negative at high enough pressure. The GLIR EOS is capable not only of overcoming the problem existing in other five EOSs where the pressure becomes negative at high pressure, but also gives results superior to other EOSs
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].
Energy Technology Data Exchange (ETDEWEB)
Calado, J.C.G.; Saramago, B.J.V. [Instituto Superior Tecnico, Lisbon (Portugal). Centro de Quimica Estrutural; Santos Mendonca, A.F.S. dos; Soares, V.A.M. [Univ. de Lisboa, Lisbon (Portugal). Centro de Ciencia e Tecnologia de Materiais
1997-01-01
The authors report a study of the surface tension of three binary liquid mixtures of molecular fluids. A microscopic mean field theory (MFT) has been used to calculate the theoretical results enabling the comparison with the experimental data. The mean field theory has been successfully used in the prediction of the surface properties of simple systems composed by quasi-spherical molecules. In the present study the MFT was able to reproduce the essential features of the interfacial properties of the systems CH{sub 4} + Kr, Kr + NO and CH{sub 4} + NO. The pure components were modeled by Lennard-Jones potentials with a set of intermolecular parameters taken from the literature for Kr and calculated from the fitting of the energy parameters to the surface tension, for CH{sub 4} and NO. In the case of the mixtures, it was found that reasonable agreement with experiment can only be obtained by allowing deviations from the Lorentz-Berthelot combining rules. For the CH{sub 4} + Kr system the authors used the binary energy parameter {xi} obtained through a fitting to the bulk properties; for the Kr + NO and CH{sub 4} + NO systems the binary parameter was adjusted to the interfacial properties.
Calado; Mendonca; Saramago; Soares
1997-01-01
We report a study of the surface tension of three binary liquid mixtures of molecular fluids. A microscopic mean field theory (MFT) has been used to calculate the theoretical results enabling the comparison with the experimental data. The mean field theory has been successfully used in the prediction of the surface properties of simple systems composed by quasi-spherical molecules. In the present study the MFT was able to reproduce the essential features of the interfacial properties of the systems CH4 + Kr, Kr + NO and CH4 + NO. The pure components were modeled by Lennard-Jones potentials with a set of intermolecular parameters taken from the literature for Kr and calculated from the fitting of the energy parameters (epsilon) to the surface tension, for CH4 and NO. In the case of the mixtures, it was found that reasonable agreement with experiment can only be obtained by allowing deviations from the Lorentz-Berthelot combining rules. For the CH4 + Kr system we used the binary energy parameter xi obtained through a fitting to the bulk properties; for the Kr + NO and CH4 + NO systems the binary parameter was adjusted to the interfacial properties.
Vibrations and thermal conductivity in inorganic and polymeric glasses.
Shenogin, Sergei; Bodapati, Arun; Keblinski, Pawel
2006-03-01
The mechanism of thermal transport in amorphous materials was studied by means of vibrational mode analysis and classical nonequilibrium molecular dynamics (MD) simulations. We studied four different model systems of (a) Lennard-Jones glass, (b) bead-spring model of an amorphous polymer, (c) amorphous silicon with Stillinger-Weber potential; and (d) all-atom model of glassy polystyrene with PCFF-type force field. For all structures we evaluated thermal conductivity from the harmonic theory of disordered solids [P.B.Allen, and J.L.Feldman, Phys.Rev.B 48, 12581 (1993)] and from direct MD simulations. We found that for all models but polystyrene, the harmonic theory accurately predicts thermal conductivity. By contrast, in the case of polystyrene, only ˜1/2 of thermal conductivity can be explained within the harmonic approximation. Consequently, a major part of the transport has to be attributed to anharmonic coupling between vibrational modes. The reasons for the failure of harmonic theory of disordered solids to model amorphous glassy polymers will be discussed.
Thermodynamics of Aβ16-21 dissociation from a fibril: Enthalpy, entropy, and volumetric properties.
Rao Jampani, Srinivasa; Mahmoudinobar, Farbod; Su, Zhaoqian; Dias, Cristiano L
2015-11-01
Here, we provide insights into the thermodynamic properties of A β16-21 dissociation from an amyloid fibril using all-atom molecular dynamics simulations in explicit water. An umbrella sampling protocol is used to compute potentials of mean force (PMF) as a function of the distance ξ between centers-of-mass of the A β16-21 peptide and the preformed fibril at nine temperatures. Changes in the enthalpy and the entropic energy are determined from the temperature dependence of these PMF(s) and the average volume of the simulation box is computed as a function of ξ. We find that the PMF at 310 K is dominated by enthalpy while the entropic energy does not change significantly during dissociation. The volume of the system decreases during dissociation. Moreover, the magnitude of this volume change also decreases with increasing temperature. By defining dock and lock states using the solvent accessible surface area (SASA), we find that the behavior of the electrostatic energy is different in these two states. It increases (unfavorable) and decreases (favorable) during dissociation in lock and dock states, respectively, while the energy due to Lennard-Jones interactions increases continuously in these states. Our simulations also highlight the importance of hydrophobic interactions in accounting for the stability of A β16-21. © 2015 Wiley Periodicals, Inc.
Bishop, Kevin P.; Roy, Pierre-Nicholas
2018-03-01
Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.
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.
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
Rana, Malay Kumar; Chandra, Amalendu
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.
Arkundato, Artoto; Monado, Fiber; Su'ud, Zaki
2017-05-01
For corrosion mitigation of steels used in a fast nuclear reactor power plant, oxygen gas is one of promising candidates of inhibitors. Many experiments have been conducted to reveal the mechanism of corrosion and mechanism of how to overcome the corrosion. In the previous work, we had shown computationally that the oxygen atom can be used to reduce the corrosion and we had predicted the oxygen contents. In the current work, not only to explore deeeper the ability of oxygen gas to reduce the corrosion, but also to include the variation of used temperature. We still used iron material to represent a real steels. Using MD (molecular dynamics) simulation based on the Lennard-Jones interaction potential, we sought to understand the concentration of oxygen gas as variation of temperature used in the reactor for the best corrosion mitigation. From this work, we conclude that the temperature does not give effect in related with how concentration of injected oxygen. The temparature merely affects to rise the diffusion coefficient of iron in liquid lead, yet it does not influence how much oxygen needed for corrosion mitigation. In this work, all simulations on different series of temperatures (1023°K, 1073°K, 1123°K, 1173°K) reveals that oxygen content of 0.1151wt% will cause the lowest corrosion level of iron in liquid lead.
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)
Towards the modeling of nanoindentation of virus shells: Do substrate adhesion and geometry matter?
Bousquet, Arthur; Dragnea, Bogdan; Tayachi, Manel; Temam, Roger
2016-12-01
Soft nanoparticles adsorbing at surfaces undergo deformation and buildup of elastic strain as a consequence of interfacial adhesion of similar magnitude with constitutive interactions. An example is the adsorption of virus particles at surfaces, a phenomenon of central importance for experiments in virus nanoindentation and for understanding of virus entry. The influence of adhesion forces and substrate corrugation on the mechanical response to indentation has not been studied. This is somewhat surprising considering that many single-stranded RNA icosahedral viruses are organized by soft intermolecular interactions while relatively strong adhesion forces are required for virus immobilization for nanoindentation. This article presents numerical simulations via finite elements discretization investigating the deformation of a thick shell in the context of slow evolution linear elasticity and in presence of adhesion interactions with the substrate. We study the influence of the adhesion forces in the deformation of the virus model under axial compression on a flat substrate by comparing the force-displacement curves for a shell having elastic constants relevant to virus capsids with and without adhesion forces derived from the Lennard-Jones potential. Finally, we study the influence of the geometry of the substrate in two-dimensions by comparing deformation of the virus model adsorbed at the cusp between two cylinders with that on a flat surface.
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.
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)
Line Tension and Wettability of Nanodrops on Curved Surfaces.
Maheshwari, Shantanu; van der Hoef, Martin; Lohse, Detlef
2016-01-12
In this work we study the formation of nanodrops on curved surfaces (both convex and concave) by means of molecular dynamics simulations, where the particles interact via a Lennard-Jones potential. We find that the contact angle is not affected by the curvature of the substrate, in agreement with previous experimental findings. This means that the change in curvature of the drop in response to the change in curvature of the substrate can be predicted from simple geometrical considerations, under the assumption that the drop's shape is a spherical cap, and that the volume remains unchanged through the curvature. The resulting prediction is in perfect agreement with the simulation results, for both convex and concave substrates. In addition, we calculate the line tension, namely, by fitting the contact angle for different size drops to the modified Young equation. We find that the line tension for concave surfaces is larger than for convex surfaces, while for zero curvature it has a clear maximum. This feature is found to be correlated with the number of particles in the first layer of the liquid on the surface.
Surface impacts and collisions of particle-laden nanodrops
Koplik, Joel
2015-08-01
The surface impact and collisions of particle-laden nanodrops are studied using molecular dynamics computer simulations. The drops are composed of Lennard-Jones dimers and the particles are rigid spherical sections of a cubic lattice, with radii about 11 nm and 0.6 nm, respectively. Uniform suspensions of 21% and 42% particle concentrations and particle-coated drops are studied, and their behavior is compared to that of pure fluid drops of the same size. The relative velocities studied span the transition to splashing, and both wetting/miscible and non-wetting/immiscible cases are considered. Impacts normal to the surface and head-on collisions are studied and compared. In surface impact, the behavior of low-density suspensions and liquid marble drops is qualitatively similar to that of pure liquid, while the concentrated drops are solid-like on impact. Collisions produce a splash only at velocities significantly higher than in impact, but the resulting drop morphology shows a similar dependence on solid concentration as in impact. In all cases, the collision or impact produces a strong local enhancement in the kinetic energy density and temperature but not in the particle or potential energy densities. Mixing of the two colliding species is not enhanced by collisions, unless the velocity is so high as to cause drop disintegration.
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.
The structure of a fluid confined by permeable walls
Margaritis, Nikolaos; Rickayzen, Gerald
Osmosis has been studied using the methods of molecular dynamics and for several different models of a semi-permeable barrier. One of these models has also been used in theoretical and Monte Carlo investigations of the effect of such a barrier on the structure of a hard sphere fluid (Marsh, P., Rickayzen, G., and Calleja, M., 1995, Molec. Phys., 84, 799 ; Kim, S.-C., Calleja, M., and Rickayzen, G., 1995, J. Phys.: condens. Matter, 7, 8053). Results presented in these papers showed that this problem also provides a sensitive test for the validity of various density functional theories. In order to bring the theory to bear on the problem of osmosis, this earlier study is extended to the hard core Lennard-Jones fluid. At the same time a new sum rule for the density of a fluid in a periodic potential, which provides a useful check on the computations, is derived. It is again found that the agreement between the computed and the simulated density profiles is good except at the centre of the barrier and when the bulk density and pressure are close to the critical.
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
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.
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)
Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy.
Klocke, Michael; Wolf, Dietrich E
2016-01-01
A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively.
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.
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.
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)
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
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.
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
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.
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.
Structure of the Ne-Xe mixture near the 26-MPa demixing curve at T=275 K
Nardone, M.; Ricci, F. P.; Filabozzi, A.; Postorino, P.
1996-12-01
We report neutron diffraction measurements for two Ne-Xe mixtures at T=275 K and P=26 MPa, having a Xe molar fraction of 0.81 and 0.45, respectively. These thermodynamic points are chosen to be in the single phase region, close to the gas-gas demixing surface. Total structure factors and neutron weighted pair distribution functions have been extracted. Partial pair distribution functions gij(r) have been calculated by means of molecular dynamics simulation using Lennard-Jones interaction potentials and the Lorentz-Berthelot mixing rules, obtaining a good agreement with the experimental data. These partial pair distribution functions have been analyzed in terms of density expansion and also compared with those derived in a previous experiment on a He-Xe mixture. The main difference found between the structural properties of the two mixtures is that, in the Ne containing mixture, a definitely larger fraction of atoms of the lighter species occupies the Xe-Xe first neighbor shell. The model already used in interpreting the thermodynamic behavior of the He-Xe mixture in terms of microscopic properties suggests that this structural difference is related to the different behavior of the pressure-temperature projection of the critical line in the two mixtures.
Memory versus irreversibility in the thermal densification of amorphous glasses
Ovadyahu, Z.
2017-06-01
We report on dynamic effects associated with thermally annealing amorphous indium-oxide films. In this process, the resistance of a given sample may decrease by several orders of magnitude at room temperatures, while its amorphous structure is preserved. The main effect of the process is densification, i.e., increased system density. The study includes the evolution of the system resistivity during and after the thermal treatment, the changes in the conductance noise, and the accompanying changes in the optical properties. The sample resistance is used to monitor the system dynamics during the annealing period as well as the relaxation that ensues after its termination. These reveal slow processes that fit well with a stretched-exponential law, a behavior that is commonly observed in structural glasses. There is an intriguing similarity between these effects and those obtained in high-pressure densification experiments. Both protocols exhibit the "slow spring-back" effect, a familiar response of memory foams. A heuristic picture based on a modified Lennard-Jones potential for the effective interparticle interaction is argued to qualitatively account for these densification-rarefaction phenomena in amorphous materials, whether affected by thermal treatment or by application of high pressure.
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.
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
DEFF Research Database (Denmark)
Mikkelsen, Henrik Hvenegaard; Friis Søgaard, Thomas
2016-01-01
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....... While most Bugkalot men have today abandoned headhunting, the potentials for violence and dominance, which the act of headhunting sought to elicit, remains a critical aspect of masculinity. We propose that a focus on the social significance of performative violent potentiality among Bugkalot men can...... 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....
African Journals Online (AJOL)
big timmy
INTEGRATION OF HYDROGEOPHYSICAL AND REMOTE SENSING DATA IN THE. ASSESSMENT OF GROUNDWATER POTENTIAL OF THE BASEMENT COMPLEX. TERRAIN OF EKITI STATE, SOUTHWESTERN NIGERIA. 1. 2. 3. 4. Bayowa O.G., Olorunfemi M.O., Akinluyi F.O., and Ademilua O.L. 1Department of Earth ...
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 ...
Molecular Dynamics Simulation of Spinodal Decomposition in Three-Dimensional Binary Fluids
DEFF Research Database (Denmark)
Laradji, Mohamed; Toxvaerd, Søren; Mouritsen, Ole G.
1996-01-01
Using large-scale molecular dynamics simulations of a two-component Lennard-Jones model in three dimensions, we show that the late-time dynamics of spinodal decomposition in concentrated binary fluids reaches a viscous scaling regime with a growth exponent n = 1, in agreement with experiments...
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 ...
Weijs, Joost; Snoeijer, Jacobus Hendrikus; Lohse, Detlef
2012-01-01
We study surface nanobubbles using molecular dynamics simulation of ternary (gas, liquid, solid) systems of Lennard-Jones fluids. They form for a sufficiently low gas solubility in the liquid, i.e., for a large relative gas concentration. For a strong enough gas-solid attraction, the surface
Optmizied random phase approximation for the phase diagram of C ...
African Journals Online (AJOL)
Our perturbation/variational approach for the Helmholtz free energy of the C60 molecules is based on the Lennard-Jones intermolecular interaction. We observe that higher accuracy is obtainable by treating all the grid points within the exclusion hole of the pair distribution function as independent variables. Our numerical ...
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
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....
DEFF Research Database (Denmark)
Toxværd, Søren
2016-01-01
nucleation without the use of a thermostat. The simulations of homogeneous nucleation in a Lennard-Jones system from supersaturated vapor at temperatures below Ttr.p. reveals that the nucleation to a liquid-like critical nucleus is initiated by a small cold cluster [S. Toxvaerd, J. Chem. Phys. \\textbf{143...
Use of polydispersity index as control parameter to study melting ...
Indian Academy of Sciences (India)
Use of polydispersity index as control parameter to study melting/freezing of Lennard-Jones system: Comparison among predictions of bifurcation theory with Lindemann criterion, inherent structure analysis and Hansen-Verlet rule. SARMISTHA SARKARa,b, RAJIB BISWASa, PARTHA PRATIM RAYb and BIMAN BAGCHIa, ...
Feasibility of a single-parameter description of equilibrium viscous liquid dynamics
DEFF Research Database (Denmark)
Pedersen, Ulf Rørbæk; Christensen, Tage Emil; Schrøder, Thomas
2008-01-01
-Andersen binary Lennard-Jones mixture as well as for an asymmetric dumbbell model liquid, a single-parameter description works quite well. This is confirmed by time-domain results where it is found that energy and pressure fluctuations are strongly correlated on the alpha time scale in the constant...
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
"LJ" Report "Anaheim, ALA 2008": Amid the Fantasy, Doses of Reality
Blumenstein, Lynn; Berry, John; Fialkoff, Francine; Fox, Bette-Lee; Hadro, Josh; Horrocks, Norman; Oder, Norman; Roncevic, Mirela
2008-01-01
If the resort city of Anaheim, California, home of Disneyland and its "imagineers," marked a departure from the urban reality of the typical American Library Association (ALA) annual conference, it was impossible, at this 2008 meeting, to avoid urgent library issues. How do libraries maintain their value and cultural presence as users…
Shifting with the Paradigm: LJ's Picks & Pans for ALA in Disneyland
Berry, John N., III
2008-01-01
The feelings of librarians planning for the American Library Association (ALA) conference at Disneyland (aka Anaheim, California, June 26-July 2) range from moderate pleasure to dread. Some remember the joys and difficulties of Orlando, especially the exorbitant cab fares and mediocre restaurants. Others quail at screaming kids and tourists in…
LJ van der Veen et S. Bodinga-bwa-Bodinga. Gedandedi sa Geviya
African Journals Online (AJOL)
rbr
intitulé Gedandedi sa Geviya/Dictionnaire Geviya–Français (en abrégé DGF dans les reste de l'article) a été ... de l'accession du Gabon à la souveraineté internationale (Nyangone Assam et. Mavoungou 2000 ... du dictionnaire, la macro- et microstructure du DGF, et le traitement lexicographique des termes de spécialité. 1.
Radiological survey results at 1 Shady Lane, Lodi, New Jersey (LJ095)
International Nuclear Information System (INIS)
Foley, R.D.; Johnson, C.A.
1995-07-01
The US Department of Energy (DOE) conducted remedial action at the Stepan property in Maywood, New Jersey and several vicinity properties in Lodi, New Jersey as part of the Formerly Utilized Sites Remedial Action Program (FUSRAP). These properties are in the vicinity of the DOE-owned Maywood Interim Storage Site (MISS), adjacent to the former Maywood Chemical Works facility. The property at One Shady Lane, Lodi, New Jersey was not one of these vicinity properties but was surveyed by DOE at the request of the owner. At the request of DOE, a team from Oak Ridge National Laboratory conducted a radiological survey at this property. The purpose of the survey, conducted in November 1994, was to confirm whether remedial actions were to be performed on the property in order to be in compliance with the identified Guidelines. The radiological survey included surface gamma scans and gamma readings at 1 meter, and the collection of soil samples for radionuclide analysis. Results of the survey demonstrated that all radiological measurements on the property at One Shady Lane, Lodi, New Jersey, were comparable to background levels in the area, and well within the limits prescribed by DOE radiological guidelines. Based on the results of the radiological survey data, this property does not meet guidelines for inclusion under FUSRAP
Directory of Open Access Journals (Sweden)
Lu Tian
Full Text Available Polyols can serve as a means for the translocation of carbon skeletons and energy between source and sink organs as well as being osmoprotective solutes and antioxidants which may be involved in the resistance of some plants to biotic and abiotic stresses. Polyol/Monosaccharide transporter (PLT proteins previously identified in plants are involved in the loading of polyols into the phloem and are reported to be located in the plasma membrane. The functions of PLT proteins in leguminous plants are not yet clear. In this study, a total of 14 putative PLT genes (LjPLT1-14 were identified in the genome of Lotus japonicus and divided into 4 clades based on phylogenetic analysis. Different patterns of expression of LjPLT genes in various tissues were validated by qRT-PCR analysis. Four genes (LjPLT3, 4, 11, and 14 from clade II were expressed at much higher levels in nodule than in other tissues. Moreover, three of these genes (LjPLT3, 4, and 14 showed significantly increased expression in roots after inoculation with Mesorhizobium loti. Three genes (LjPLT1, 3, and 9 responded when salinity and/or osmotic stresses were applied to L. japonicus. Transient expression of GFP-LjPLT fusion constructs in Arabidopsis and Nicotiana benthamiana protoplasts indicated that the LjPLT1, LjPLT6 and LjPLT7 proteins are localized to the plasma membrane, but LjPLT2 (clade IV, LjPLT3, 4, 5 (clade II and LjPLT8 (clade III proteins possibly reside in the Golgi apparatus. The results suggest that members of the LjPLT gene family may be involved in different biological processes, several of which may potentially play roles in nodulation in this nitrogen-fixing legume.
Carbon nanotube oscillators for applications as nanothermometers
International Nuclear Information System (INIS)
Rahmat, Fainida; Thamwattana, Ngamta; Hill, James M
2010-01-01
Nanostructures such as carbon nanotubes have a broad range of potential applications such as nanomotors, nano-oscillators and electromechanical nanothermometers, and a proper understanding of the molecular interaction between nanostructures is fundamentally important for these applications. In this paper, we determine the molecular interaction potential of interacting carbon nanotubes for two configurations. The first is a shuttle configuration involving a short outer tube sliding on a fixed inner tube, and the second involves a telescopic configuration for which an inner tube moves both in the region between two outer tubes and through the tubes themselves. For the first configuration we examine two cases of semi-infinite and finite inner carbon nanotubes. We employ the continuum approximation and the 6-12 Lennard-Jones potential for non-bonded molecules to determine the molecular interaction potential and the resulting van der Waals force, and we evaluate the resulting surface integrals numerically. We also investigate the acceptance condition and suction energy for the first configuration. Our results show that for the shuttle configuration with a semi-infinite inner tube, the suction energy is maximum when the difference between the outer and inner tubes radii is approximately 3.4 A, which is the ideal inter-wall spacing between graphene sheets. For the finite inner tube, the potential energy is dependent on both the inner and outer tube lengths as well as on the inter-wall spacing. In terms of the oscillating frequency, the critical issue is the length of the moving outer tube, and the shorter the length, the higher the frequency. Further, for the telescopic configuration with two semi-infinite outer nanotubes of different radii, we find that the interaction energy also depends on the difference of the tube radii. For two outer nanotubes of equal radii we observe that the shorter the distance between the two outer nanotubes, the higher the magnitude of the
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
Flexible equation of state for a hard sphere and Lennard–Jones fluid ...
Indian Academy of Sciences (India)
Equation of state; Lennard–Jones potential; hard-sphere potential; liquid mixture; computer simulation. ... deviation than Barker–Henderson BH2 for LJ fluids, and results are much closer to molecular dynamics (MD) simulations than expectations and reproduce the existing simulation data and present EoS for LJ 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
Satellite potentials for hypergeometric Natanzon potentials
Energy Technology Data Exchange (ETDEWEB)
Codriansky, S. [Departamento de Matematicas y Fisica, Instituto Pedagogico de Caracas, Universidad Pedagogica Experimental Libertador (Venezuela)]. E-mail: codrians@reacciun.ve; Salamo, S. [Universidad Simon Bolivar, Departamento de Fisica, Caracas (Venezuela)]. E-mail: ssalamo@fis.usb.ve
2002-05-17
As a result of the so(2,1) treatment of the hypergeometric Natanzon potentials {l_brace}V{sub N}{r_brace} a set of potentials related to a given one is determined; these are the satellite potentials and all belong to the Natanzon class. The set arises as the result of the action of the so(2,1) generators on the carrier space of an irreducible representation. The results are compared to those obtained from supersymmetric quantum mechanics (SUSYQM) for some Natanzon potentials. The chains of Natanzon potentials constructed using the idea of a satellite potential are, in most cases, different from the SUSYQM chains. (author)
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
Lee, Nicholas Jabari Ouma
Parallel molecular dynamics (MD) simulations are performed to investigate pressure-induced solid-to-solid structural phase transformations in cadmium selenide (CdSe) nanorods. The effects of the size and shape of nanorods on different aspects of structural phase transformations are studied. Simulations are based on interatomic potentials validated extensively by experiments. Simulations range from 105 to 106 atoms. These simulations are enabled by highly scalable algorithms executed on massively parallel Beowulf computing architectures. Pressure-induced structural transformations are studied using a hydrostatic pressure medium simulated by atoms interacting via Lennard-Jones potential. Four single-crystal CdSe nanorods, each 44A in diameter but varying in length, in the range between 44A and 600A, are studied independently in two sets of simulations. The first simulation is the downstroke simulation, where each rod is embedded in the pressure medium and subjected to increasing pressure during which it undergoes a forward transformation from a 4-fold coordinated wurtzite (WZ) crystal structure to a 6-fold coordinated rocksalt (RS) crystal structure. In the second so-called upstroke simulation, the pressure on the rods is decreased and a reverse transformation from 6-fold RS to a 4-fold coordinated phase is observed. The transformation pressure in the forward transformation depends on the nanorod size, with longer rods transforming at lower pressures close to the bulk transformation pressure. Spatially-resolved structural analyses, including pair-distributions, atomic-coordinations and bond-angle distributions, indicate nucleation begins at the surface of nanorods and spreads inward. The transformation results in a single RS domain, in agreement with experiments. The microscopic mechanism for transformation is observed to be the same as for bulk CdSe. A nanorod size dependency is also found in reverse structural transformations, with longer nanorods transforming more
Fan, H. H.; Krotscheck, E.; Lichtenegger, T.; Mateo, D.; Zillich, R. E.
2015-08-01
We present ground-state calculations for low-density Fermi gases described by two model interactions, an attractive square-well potential and a Lennard-Jones potential, of varying strength. We use the optimized Fermi-hypernetted chain integral equation method, which has been proved to provide, in the density regimes of interest here, an accuracy of better than 1%. We first examine the low-density expansion of the energy and compare it with the exact answer of H. Huang and C. N. Yang [Phys. Rev. 105, 767 (1957), 10.1103/PhysRev.105.767]. It is shown that a locally correlated wave function of the Jastrow-Feenberg type does not recover the quadratic term in the expansion of the energy in powers of a0kF , where a0 is the vacuum s -wave scattering length and kF the Fermi wave number. The problem is cured by adding second-order perturbation corrections in a correlated basis. Going to higher densities and/or more strongly coupled systems, we encounter an instability of the normal state of the system which is characterized by a divergence of the in-medium scattering length. We interpret this divergence as a phonon-exchange-driven dimerization of the system, similar to what occurs at zero density when the vacuum scattering length a0 diverges. We then study, in the stable regime, the superfluid gap and its dependence on the density and the interaction strength. We identify two corrections to low-density expansions: One is medium corrections to the pairing interaction, and the other is finite-range corrections. We show that the most important finite-range corrections are a direct manifestation of the many-body nature of the system.
[Using Molecular Simulations to Understand Complex Nanoscale Dynamic Phenomena in Polymer Solutions
Smith, Grant
2004-01-01
The first half of the project concentrated on molecular simulation studies of the translocation of model molecules for single-stranded DNA through a nanosized pore. This has resulted in the publication, Translocation of a polymer chain across a nanopore: A Brownian dynamics simulation study, by Pu Tian and Grant D. Smith, JOURNAL OF CHEMICAL PHYSICS VOLUME 119, NUMBER 21 1 DECEMBER 2003, which is attached to this report. In this work we carried out Brownian dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an applied field (chemical potential gradient) designed to mimic an electrostatic field. The translocation process can be either dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical gradient). We focused on the latter case in our studies. Calculation of radius of gyration of the translocating chain at the two opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tube-like pore geometry, more than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied. Attraction facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of polymer chain. The width of the translocation
Tretyakov, Nikita; Papadopoulos, Periklis; Vollmer, Doris; Butt, Hans-Jürgen; Dünweg, Burkhard; Daoulas, Kostas Ch
2016-10-07
Classical density functional theory is applied to investigate the validity of a phenomenological force-balance description of the stability of the Cassie state of liquids on substrates with nanoscale corrugation. A bulk free-energy functional of third order in local density is combined with a square-gradient term, describing the liquid-vapor interface. The bulk free energy is parameterized to reproduce the liquid density and the compressibility of water. The square-gradient term is adjusted to model the width of the water-vapor interface. The substrate is modeled by an external potential, based upon the Lennard-Jones interactions. The three-dimensional calculation focuses on substrates patterned with nanostripes and square-shaped nanopillars. Using both the force-balance relation and density-functional theory, we locate the Cassie-to-Wenzel transition as a function of the corrugation parameters. We demonstrate that the force-balance relation gives a qualitatively reasonable description of the transition even on the nanoscale. The force balance utilizes an effective contact angle between the fluid and the vertical wall of the corrugation to parameterize the impalement pressure. This effective angle is found to have values smaller than the Young contact angle. This observation corresponds to an impalement pressure that is smaller than the value predicted by macroscopic theory. Therefore, this effective angle embodies effects specific to nanoscopically corrugated surfaces, including the finite range of the liquid-solid potential (which has both repulsive and attractive parts), line tension, and the finite interface thickness. Consistently with this picture, both patterns (stripes and pillars) yield the same effective contact angles for large periods of corrugation.
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.
The phase shifts leading to the broadening and shift of spectral lines
Energy Technology Data Exchange (ETDEWEB)
Roston, G.D. [Department of Physics, Faculty of Science, Alexandria University (Egypt)], E-mail: gamal_daniel@yahoo.com; Ghatass, Z.F. [Department of Environmental Studies, Institute of Graduate Studies and Research, Alexandria University (Egypt); Obaid, F.S. [Department of Mathematics, Faculty of Science, Qubba University (Libyan Arab Jamahiriya)
2009-02-15
The classical theory of collisional broadening and shift parameters ({beta}, {delta}) of an isolated spectral line was used to obtain simple analytical formulas for calculating both {beta} and {delta}. These formulas were obtained on the assumption that the short range interaction is effective only in the broadening while the long range is effective in the shift of the spectral line. These parameters {beta} and {delta} depend on the limiting phase shifts responsible for broadening {eta}{sub b} and shift {eta}{delta}. It was found that the values of {eta}{sub b} and {eta}{sub {delta}} are not equal to each other as was proposed by Weisskopf {eta}{sub b}={eta}{sub {delta}}=1. The maximum and average values of {eta}{sub b} ({eta}{sub bmax}, {eta}{sub bav}) and {eta}{sub {delta}} ({eta}{sub {delta}}{sub max}, {eta}{sub {delta}}{sub av}) were obtained by numerical evaluation, using different inverse power potentials. By introducing these parameters into the approximated formulas for {beta} and {delta} using Van der Waals and Lennard-Jones potential, it was found that the results of calculations for ({beta} and {delta}) with different atomic transitions perturbed by different inert gases are in close agreement with earlier results. Those results, obtained earlier, were based on the Lindholm-Foley theory especially with the average values of {eta}{sub b} [{eta}{sub bav}=0.6057] and the maximum values of {eta}{sub {delta}} [{eta}{sub {delta}}{sub max}=1.57625]. The impact parameters {rho}{sub b} and {rho}{sub {delta}} leading to the broadening and shift of the spectral line were also obtained for different interactions. It was found that the end parameter for the broadening {rho}{sub b} is not equal to the starting parameter for the shift {rho}{sub {delta}}.
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.
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
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
A Force Field for Water over Pt(111): Development, Assessment and Comparison.
Steinmann, Stephan N; Ferreira de Morais, Rodrigo; Götz, Andreas W; Fleurat-Lessard, Paul; Iannuzzi, Marcella; Sautet, Philippe; Michel, Carine
2018-04-16
Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water; (ii) a Gaussian term to improve the surface corrugation and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted against a set of 210 adsorption geometries of water on Pt(111). The performance of GAL17 is compared to several other approaches, that have not been validated against extensive first principles computations yet. Their respective accuracy is evaluated on an extended set of 802 adsorption geometries of H2O on Pt(111), 52 geometries derived from ice-like layers and an MD simulation of an interface between a c(4x6) Pt(111) surface and a water layer of 14 Å thickness. The newly developed GAL17 force field provides a significant improvement over previously existing force fields for Pt(111)/H2O interactions. Its well-balanced performance suggests that it is an ideal candidate to generate relevant geometries for the metal/water interface, paving the way to a representative sampling of the equilibrium distribution at the interface and to predict solvation free energies at the solid/liquid interface.
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.
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.
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.
Clements, Aspen R; Berk, Brandon; Cooke, Ilsa R; Garrod, Robin T
2018-02-21
Dust grains in cold, dense interstellar clouds build up appreciable ice mantles through the accretion and subsequent surface chemistry of atoms and molecules from the gas. These mantles, of thicknesses on the order of 100 monolayers, are primarily composed of H 2 O, CO, and CO 2 . Laboratory experiments using interstellar ice analogues have shown that porosity could be present and can facilitate diffusion of molecules along the inner pore surfaces. However, the movement of molecules within and upon the ice is poorly described by current chemical kinetics models, making it difficult either to reproduce the formation of experimental porous ice structures or to extrapolate generalized laboratory results to interstellar conditions. Here we use the off-lattice Monte Carlo kinetics model MIMICK to investigate the effects that various deposition parameters have on laboratory ice structures. The model treats molecules as isotropic spheres of a uniform size, using a Lennard-Jones potential. We reproduce experimental trends in the density of amorphous solid water (ASW) for varied deposition angle, rate and surface temperature; ice density decreases when the incident angle or deposition rate is increased, while increasing temperature results in a more-compact water ice. The models indicate that the density behaviour at higher temperatures (≥80 K) is dependent on molecular rearrangement resulting from thermal diffusion. To reproduce trends at lower temperatures, it is necessary to take account of non-thermal diffusion by newly-adsorbed molecules, which bring kinetic energy both from the gas phase and from their acceleration into a surface binding site. Extrapolation of the model to conditions appropriate to protoplanetary disks, in which direct accretion of water from the gas-phase may be the dominant ice formation mechanism, indicate that these ices may be less porous than laboratory ices.
Pandey, R. B.; Farmer, B. L.
2009-01-01
Energy, mobility, and structural profiles of residues in a specific sequence of human immunodeficiency virus (HIV)-1 protease chain and its global conformation and dynamics are studied by a coarse-grained computer simulation model on a cubic lattice. HIV-1 protease is described by a chain of 99 residues (nodes) in a specific sequence (1DIFA) with N- and C-terminals on the lattice, where empty lattice sites represent an effective solvent medium. Internal structures of the residues are ignored but their specificities are captured via an interaction (ɛij) matrix (residue-residue, residue-solvent) of the coefficient (fɛij) of the Lennard-Jones potential. Simulations are performed for a range of interaction strength (f ) with the solvent-residue interaction describing the quality of the solvent. Snapshots of the protein show considerable changes in the conformation of the protein on varying the interaction. From the mobility and energy profiles of the residues, it is possible to identify the active (and not so active) segments of the protein and consequently their role in proteolysis. Contrary to interaction thermodynamics, the hydrophobic residues possess higher configurational energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. Segments of hydrophobic core residues, crucial for the structural evolution of the protein are identified—some of which are consistent with recent molecular dynamics simulation in context to possible clinical observations. Global energy and radius of gyration of the protein exhibit nonmonotonic dependence on the interaction strength (f) with opposite trends, e.g., rapid transition into globular structure with higher energy. Variations of the rms displacement of the protein and that of a tracer residue, Gly49, with the time steps show how they slow down on increasing the interaction strength.
Fujiwara, K; Shibahara, M
2015-03-07
A classical molecular dynamics simulation was conducted for a liquid-solid interfacial system with a nanometer-scale slit pore in order to reveal local thermodynamic states: local pressure components and interfacial tensions of a liquid film in the vicinity of the slit. The simulation also examined the transition mechanism between the two states of the liquid film: (a) liquid film on the slit and (b) liquid film in the slit, based on the local thermodynamic quantities from a molecular point of view. An instantaneous expression of the local pressure components and interfacial tensions, which is based on a volume perturbation, was presented to investigate time-dependent phenomena in molecular dynamics simulations. The interactions between the particles were described by the 12-6 Lennard-Jones potential, and effects of the fluid-solid interaction intensity on the local pressure components and interfacial tensions of the fluid in the vicinity of the slit were examined in detail by the presented perturbative method. The results revealed that the local pressure components tangential to the solid surface in the vicinity of the 1st fluid layer from the solid surface are different in a two dimensional plane, and the difference became pronounced in the vicinity of the corner of the slit, for cases where the fluid-solid interaction intensities are relatively strong. The results for the local interfacial tensions of the fluid inside the slit suggested that the local interfacial tensions in the vicinity of the 2nd and 3rd layers of the solid atoms from the entrance of the slit act as a trigger for the transition between the two states under the influence of a varying fluid-solid interaction.
Drag force, diffusion coefficient, and electric mobility of small particles. II. Application.
Li, Zhigang; Wang, Hai
2003-12-01
We propose a generalized treatment of the drag force of a spherical particle due to its motion in a laminar fluid media. The theory is equally applicable to analysis of particle diffusion and electric mobility. The focus of the current analysis is on the motion of spherical particles in low-density gases with Knudsen number Kn>1. The treatment is based on the gas-kinetic theory analysis of drag force in the specular and diffuse scattering limits obtained in a preceding paper [Z. Li and H. Wang, Phys. Rev. E., 68, 061206 (2003)]. Our analysis considers the influence of van der Waals interactions on the momentum transfer upon collision of a gas molecule with the particle and expresses this influence in terms of an effective, reduced collision integral. This influence is shown to be significant for nanosized particles. In the present paper, the reduced collision integral values are obtained for specular and diffuse scattering, using a Lennard-Jones-type potential energy function suitable for the interactions of a gas molecule with a particle. An empirical formula for the momentum accommodation function, used to determine the effective, reduced collision integral, is obtained from available experimental data. The resulting treatment is shown to be accurate for interpreting the mobility experiments for particles as small as approximately 1 nm in radius. The treatment is subsequently extended to the entire range of the Knudsen number, following a semiempirical, gas-kinetic theory analysis. We demonstrate that the proposed formula predicts very well Millikan's oil-droplet experiments [R. A. Millikan, Philos. Mag. 34, 1 (1917); Phys. Rev. 22, 1 (1923)]. The rigorous theoretical foundation of the proposed formula in the Kn>1 limit makes the current theory far more general than the semiempirical Stokes-Cunningham formula in terms of the particle size and condition of the fluid and, therefore, more attractive than the Stokes-Cunningham formula.
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).
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.
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.
Dislocation-like Structures in a Simulated Liquid
DEFF Research Database (Denmark)
Cotterill, Rodney M J
1979-01-01
The free-volume distribution in a simulated Lennard-Jones liquid is heterogeneous. Chains of holes, appearing as segments rather than a continuous network, have lifetimes that are brief compared with the mean vibration period of the atoms. Larger isolated holes persist for longer times. If the ch......The free-volume distribution in a simulated Lennard-Jones liquid is heterogeneous. Chains of holes, appearing as segments rather than a continuous network, have lifetimes that are brief compared with the mean vibration period of the atoms. Larger isolated holes persist for longer times....... If the chains are interpreted as dislocation cores, the observed dislocation density is 1.0×1014 cm-2, but the actual density is probably higher....
Group leaders optimization algorithm
Daskin, Anmer; Kais, Sabre
2011-03-01
We present a new global optimization algorithm in which the influence of the leaders in social groups is used as an inspiration for the evolutionary technique which is designed into a group architecture. To demonstrate the efficiency of the method, a standard suite of single and multi-dimensional optimization functions along with the energies and the geometric structures of Lennard-Jones clusters are given as well as the application of the algorithm on quantum circuit design problems. We show that as an improvement over previous methods, the algorithm scales as N 2.5 for the Lennard-Jones clusters of N-particles. In addition, an efficient circuit design is shown for a two-qubit Grover search algorithm which is a quantum algorithm providing quadratic speedup over the classical counterpart.
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.)
International Nuclear Information System (INIS)
Kaddour, F.O.; Pastore, G.
1993-07-01
Accurate Molecular Dynamics calculations on highly asymmetric Lennard-Jones mixtures have been performed to check in rather extreme cases the ability of the self-consistent HMSA integral equation to predict the pair correlations in supercooled and glassy mixtures. We find that, in the supercooled region, the HMSA is a reasonable approximation for the structural properties and thermodynamics properties, but systematic deviations from MD data appear when the glass transition is approached. (author). 12 refs, 4 figs, 1 tab
SIMPLE FLUID IN AN ATTRACTIVE, DISORDERED POLYDISPERSE MATRIX
Directory of Open Access Journals (Sweden)
T.Patsahan
2004-01-01
Full Text Available The extension of the replica Ornstein-Zernike (ROZ equations is applied to the study of the structural properties of a Lennard-Jones fluid confined in an attractive polydisperse disordered matrix. The ROZ equations in combination with the orthogonal polynomial expansions for the correlation functions are used. The radial distribution functions are calculated for the adsorbed fluid at different temperatures. The effect of matrix polydispersity on the excess internal energy is considered in our study as well.
Generalized Lyapunov exponents of the random harmonic oscillator: Cumulant expansion approach
Vallejos, Raúl O.; Anteneodo, Celia
2012-02-01
The cumulant expansion is used to estimate generalized Lyapunov exponents of the random-frequency harmonic oscillator. Three stochastic processes are considered: Gaussian white noise, Ornstein-Uhlenbeck, and Poisson shot noise. In some cases, nontrivial numerical difficulties arise. These are mostly solved by implementing an appropriate importance-sampling Monte Carlo scheme. We analyze the relation between random-frequency oscillators and many-particle systems with pairwise interactions like the Lennard-Jones gas.
Kansas Data Access and Support Center — This digital spatial data set provides information on the spatial distribution of potential runoff-contributing areas in Kansas. Potential runoff-contributing areas...
Earth Data Analysis Center, University of New Mexico — Crown fire potential was modeled using FlamMap, an interagency fire behavior mapping and analysis program that computes potential fire behavior characteristics. The...
City and County of Durham, North Carolina — This map shows the average household spending potential for retail goods in the United States in 2012. Spending potential data measures household consumer spending...
Ionization potentials of seaborgium
International Nuclear Information System (INIS)
Johnson, E.; Pershina, V.; Fricke, B.
1999-01-01
Multiconfiguration relativistic Dirac-Fock values were calculated for the first six ionization potentials of seaborgium and of the other group 6 elements. No experimental ionization potentials are available for seaborgium. Accurate experimental values are not available for all of the other ionization potentials. Ionic radii for the 4+ through 6+ ions of seaborgium are also presented. The ionization potentials and ionic radii obtained will be used to predict some physiochemical properties of seaborgium and its compounds
Generalized Rosenbluth potentials
International Nuclear Information System (INIS)
Hassan, M.H.A.
1977-05-01
It is shown that the coefficients of friction and diffusion of the Balescu-Lenard equation can be derived from two ''generalized Rosenbluth potentials'', which reduce to the standard Rosenbluth potentials if wave effects are neglected. The potentials are evaluated explicitly in the case of Maxwellian field particles. The dominant contribution of wave effects to the potentials is due to the interaction of electron field particles with ion sound waves
Molecular simulation of adsorption and transport diffusion of model fluids in carbon nanotubes
Düren, Tina; Keil, Frerich J.; Seaton, Nigel A.
Grand canonical Monte Carlo (GCMC) and dual-control-volume grand canonical molecular dynamics (DCV-GCMD) simulations were carried out with Lennard-Jones model fluids in carbon nanotubes, with the objective of investigating the effect of varying molecular properties on adsorption and diffusion. The influence of the molecular weight, and the Lennard Jones parameters σ (a measure of the molecule size) and ɛ (a measure of the interaction strength) on adsorption isotherms, fluxes, and transport diffusivities was studied. For these simulations, the properties of component 1 in the mixture were held constant and one of the properties of component 2 was changed systematically. Furthermore, the validity of Graham's law, which relates the fluxes of two counter diffusing species to their molecular weight, was investigated on a molecular level. Graham's law is fulfilled for the whole range of molecular weights and Lennard-Jones parameters σ investigated. However, large deviations were observed for large values of ɛ2. Here, the interaction of the two components in the mixture becomes so strong that component 1 is dragged along by component 2.
Hasan, Mohammd; Mandal, Bhabani Prasad
2018-04-01
In this paper we introduce the concept of super periodic potential (SPP) of arbitrary order n, n ∈I+, in one dimension. General theory of wave propagation through SPP of order n is presented and the reflection and transmission coefficients are derived in their closed analytical form by transfer matrix formulation. We present scattering features of super periodic rectangular potential and super periodic delta potential as special cases of SPP. It is found that the symmetric self-similarity is the special case of super periodicity. Thus by identifying a symmetric fractal potential as special cases of SPP, one can obtain the tunnelling amplitude for a particle from such fractal potential. By using the formalism of SPP we obtain the close form expression of tunnelling amplitude of a particle for general Cantor and Smith-Volterra-Cantor potentials.
Directory of Open Access Journals (Sweden)
R. Laval Hunsucker
2007-12-01
the appearance of this article.Among informal methods of scholarly communication and information transfer, conferences (to the investigators’ surprise rated remarkably low.Researchers with large personal collections made more use of the library and its services than those with small collections.Social scientists had little interest in non‐English‐language materials. Line speaks of “a serious foreign language problem” (424.The INFROSS study produced an enormous amount of data. Only 384 of the computer tables produced were made available in 4 separate reports to OSTI. Only 3 tables, 2 of which were abbreviated, appeared in this article. The further raw data were available on request.Conclusion – Line himself was exceedingly cautious in drawing explicit positive conclusions from the INFROSS results. Heeven stated that, “No major patterns were detected which could be of use for information system design purposes” (430. He was freer with his negative and provisional assessments. Two years earlier he had written: “It still remains to be established that there is an information problem in the social sciences, or that, if there is, it is of any magnitude” (“Information Requirements” 3. However, it was now clear to Line that information services and systems for the social scientist were indeed quite inadequate, and that (potential users were not satisfied. He was, furthermore, prepared to go out ona limb with the following assertions and inferences: 1 It was a great strength of INFROSS that it had – in marked contrast to previous science user studies – generated “a mass of comparable [his italics] data within a very broad field, so that every finding can berelated to other findings” (430. 2 There are discernable – and exploitable – differences in the information needs and use patterns among the different social science disciplines (which he often also refers to as the different “subjects”. 3 INFROSS had likewise made more evident the
Ortiz, Luis E.
2015-01-01
Potential games, originally introduced in the early 1990's by Lloyd Shapley, the 2012 Nobel Laureate in Economics, and his colleague Dov Monderer, are a very important class of models in game theory. They have special properties such as the existence of Nash equilibria in pure strategies. This note introduces graphical versions of potential games. Special cases of graphical potential games have already found applicability in many areas of science and engineering beyond economics, including ar...
Schürmann, Michael
2008-01-01
This volume contains the revised and completed notes of lectures given at the school "Quantum Potential Theory: Structure and Applications to Physics," held at the Alfried-Krupp-Wissenschaftskolleg in Greifswald from February 26 to March 10, 2007. Quantum potential theory studies noncommutative (or quantum) analogs of classical potential theory. These lectures provide an introduction to this theory, concentrating on probabilistic potential theory and it quantum analogs, i.e. quantum Markov processes and semigroups, quantum random walks, Dirichlet forms on C* and von Neumann algebras, and boundary theory. Applications to quantum physics, in particular the filtering problem in quantum optics, are also presented.
Handbook of interatomic potentials
International Nuclear Information System (INIS)
Stoneham, A.M.; Taylor, R.
1981-08-01
This Handbook collects together interatomic potentials for a large number of metals. Most of the potentials describe the interactions of host metal atoms with each other, and these, in some cases, may be applied to solid and liquid metals. In addition, there are potentials (a) for a metallic impurity alloyed with the host, (b) for a small number of chemical impurities in the metal (eg H, O), and (c) for rare-gas impurities, notably He. The Handbook is intended to be a convenient source of potentials for bulk, surface and defect calculations, both static and dynamic. (author)
Examining Management Success Potential.
Quatrano, Louis A.
The derivation of a model of management success potential in hospitals or health services administration is described. A questionnaire developed to assess management success potential in health administration students was voluntarily completed by approximately 700 incoming graduate students in 35 university health services administration programs…
Indian Academy of Sciences (India)
2016-01-27
Jan 27, 2016 ... In the following paper, certain black hole dynamic potentials have been developed definitively on the lines of classical thermodynamics. These potentials have been refined in view of the small differences in the equations of the laws of black hole dynamics as given by Bekenstein and those of ...
2012-02-10
... adequacy pursuant to Sec. 611 of Public Law 92-574, the ``Noise Control Act of 1972.'' The FAA issues... flight control systems, autopilots, stability augmentation systems, load alleviation systems, and fuel... flight control systems, autopilots, stability augmentation systems, load alleviation systems, fuel...
Czech Academy of Sciences Publication Activity Database
Moučka, F.; Nezbeda, Ivo; Smith, W. R.
2013-01-01
Roč. 138, č. 15 (2013), s. 154102 ISSN 0021-9606 Grant - others:GA MŠMT(CZ) LH12019; GA ČR(CZ) GAP208/12/0105; NSERCC(CA) OGP1041 Institutional support: RVO:67985858 Keywords : free-energy * computer- simulation * water Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.122, year: 2013
(I lJ.6 - 55 Department of B iochemistr~. Lni,erstl) of.fos. Jos
African Journals Online (AJOL)
BSN
used. The rats were random!) distributed into four groups (A-D• (3 rats per group) and kept in mctabol ic cages. The rats were allowed to stabi I ize on tht normal laborat01") feed for three cla)s thereafter. staned for 2-t hours before feeding \\\\it.i the experimental diets as follows: Group A \\\\Cre fed diet I. Group B \\\\ere fed diet 2.
International Nuclear Information System (INIS)
Foley, R.D.; Johnson, C.A.
1994-02-01
The property at 90 Avenue C, Lodi, New Jersey is one of the vicinity properties of the former Maywood Chemical Works, Maywood, New Jersey designated for remedial action by the US Department of Energy (DOE). In July 1991, Bechtel National, Inc. performed a partial remedial action on this property. At the request of DOE, a team from Oak Ridge National Laboratory conducted an independent radiological verification survey in July, 1991 at this site. The purpose of the verification survey was to ensure the effectiveness of remedial actions performed within FUSRAP and to confirm the site's compliance with DOE guidelines. The radiological survey included surface gamma scans indoors and outdoors, ground-level beta-gamma measurements, and systematic and biased soil and material sampling. Results of the verification survey demonstrated that all radiological measurements on the portions of the property that had been remediated were within DOE guidelines. However, there still remains a portion of the property to be remediated that is not covered by this verification survey
2013-10-31
... the state of technology envisioned in the airworthiness standards for transport category airplanes... (425) 227-1320. SUPPLEMENTARY INFORMATION: Comments Invited We invite interested people to take part in... assessment is largely dependent on the similarities and differences between the new type design and...
L.J. van der Veen et S. Bodinga-bwa-Bodinga. Gedandedi sa Geviya/ Dictionnaire Geviya?Fran?ais
Directory of Open Access Journals (Sweden)
P.A. Mavoungou
2011-10-01
Full Text Available La parution aux ?ditions Peeters de l'ouvrage de r?f?rence lexicographique intitul? Gedandedi sa Geviya/Dictionnaire Geviya?Fran?ais (en abr?g? DGF dans les reste de l'article a ?t? accueilli avec joie et fiert? aussi bien par les locuteurs geviya1 en particulier que par les Gabonais en g?n?ral. Ce dictionnaire, r?sultat d'une longue et fructueuse collaboration scientifique entre Lolke van der Veen et S?bastien Bodinga-bwa-Bodinga, marque le d?but d'une nouvelle ?re dans la r?daction des dictionnaires au Gabon. En effet, la majorit? des ouvrages de r?f?rence lexicographique disponibles dans les langues gabonaises sont des dictionnaires bilingues r?dig?s par les missionnaires catholiques et protestants ou par les administrateurs coloniaux dans la p?riode allant de 1800 ? 1960, date de l'accession du Gabon ? la souverainet? internationale (Nyangone Assam et Mavoungou 2000, Mavoungou 2001.
International Nuclear Information System (INIS)
Nelson, B.A.
1987-01-01
Ion-confining potentials in the Phaedrus tandem mirror are shown to be enhanced over Boltzmann-relations predicted values by radio-frequency (rf) waves in the ion cyclotron range of frequencies (ICRF). The ICRF enhanced potential is larger in the end cell with a lower passing density. Peak potential values decrease with increasing ion endloss current (or central cell density) for a constant rf capacitor bank voltage, and increase with increasing rf-capacitor bank voltage, for a constant ion endloss value (or central cell density). In fully axisymmetric operation, a potential peak is produced in an end cell by the central-cell rf, (with-out end-cell rf) and is found only in the end cell nearer the central-cell antenna. ICRF enhanced potentials are explained as an equilibrium between the electron-collisional filling-in rate and the electron pumping out rate provided by axial time-varying electric fields. Thermal barrier-like potential structures were found in the transition regions between the central cell and end cells, in the fully axisymmetric Phaedrus. Central-cell ICRF trapping effects combined with end-cell μΔ B forces create and pump the barrier potential wells
National Research Council Canada - National Science Library
Wortzel, Larry
1998-01-01
The People's Republic of China (PRC) is seen by many as an economic powerhouse with the world's largest standing military that has the potential to translate economic power into the military sphere...
Elderberry: Botany, Horticulture, Potential
Horticultural Review allows extensive reviews of the state of the knowledge on certain topics or crops. Elderberry: Botany, Horticulture, Potential, is outlined with an Introduction, Botany, Horticulture, Propagation, Uses and Conclusion sections. This review compiles literature from around the w...
DEFF Research Database (Denmark)
Schjerning, Ole; Rosenzweig, Mary; Pottegård, Anton
2016-01-01
BACKGROUND: Several case reports and epidemiological studies have raised concern about the abuse potential of pregabalin, the use of which has increased substantially over the last decade. Pregabalin is, in some cases, used for recreational purposes and it has incurred attention among drug abusers...... for causing euphoric and dissociative effects when taken in doses exceeding normal therapeutic dosages or used by alternative routes of administration, such as nasal insufflation or venous injection. The magnitude of the abuse potential and the mechanism behind it are not fully known. OBJECTIVE: The aim...... of this study was to present a systematic review of the data concerning the abuse potential of pregabalin. METHODS: We performed a systematic literature search and reviewed the preclinical, clinical and epidemiological data on the abuse potential of pregabalin. RESULTS: We included preclinical (n = 17...
Smoothed square well potential
Energy Technology Data Exchange (ETDEWEB)
Salamon, P. [Institute for Nuclear Research Hungarian Academy of Sciences (ATOMKI), Debrecen (Hungary); Vertse, T. [Institute for Nuclear Research Hungarian Academy of Sciences (ATOMKI), Debrecen (Hungary); University of Debrecen, Faculty of Informatics, Debrecen (Hungary)
2017-07-15
The classical square well potential is smoothed with a finite range smoothing function in order to get a new simple strictly finite range form for the phenomenological nuclear potential. The smoothed square well form becomes exactly zero smoothly at a finite distance, in contrast to the Woods-Saxon form. If the smoothing range is four times the diffuseness of the Woods-Saxon shape both the central and the spin-orbit terms of the Woods-Saxon shape are reproduced reasonably well. The bound single-particle energies in a Woods-Saxon potential can be well reproduced with those in the smoothed square well potential. The same is true for the complex energies of the narrow resonances. (orig.)
The Hubble effective potential
Energy Technology Data Exchange (ETDEWEB)
Janssen, T.M.; Miao, S.P.; Prokopec, T. [Institute for Theoretical Physics and Spinoza Institute, Utrecht University, Leuvenlaan 4, Postbus 80.195, 3508 TD Utrecht (Netherlands); Woodard, R.P., E-mail: T.M.Janssen@uu.nl, E-mail: S.Miao@uu.nl, E-mail: T.Prokopec@uu.nl, E-mail: woodard@phys.ufl.edu [Department of Physics, University of Florida, Gainesville, FL 32611 (United States)
2009-05-15
We generalize the effective potential to scalar field configurations which are proportional to the Hubble parameter of a homogeneous and isotropic background geometry. This may be useful in situations for which curvature effects are significant. We evaluate the one loop contribution to the Hubble Effective Potential for a massless scalar with arbitrary conformal and quartic couplings, on a background for which the deceleration parameter is constant. Among other things, we find that inflationary particle production leads to symmetry restoration at late times.
Overview of interatomic potentials
International Nuclear Information System (INIS)
Bonny, G.; Malerba, L.
2005-12-01
In this report an overview on interatomic potentials is given. This overview is by no means complete and it has merely the intention to give the reader an idea of where interatomic potentials come from, as well as to provide the basic ideas behind some commonly used methods for deriving interatomic potentials for molecular dynamics applications. We start by giving a short introduction about the concept of interatomic potential in the framework of quantum mechanics, followed by a short description of commonly used methods for deriving semi-empirical interatomic potentials. After some short theoretical notions on each method, some practical parameterizations of commonly used potentials are given, including very recent ones. An effort has been made to classify existing approaches within a rational and consequent scheme, which is believed to be of use for a thorough comprehension of the topic. Although these approaches can be used in a variety of different materials, we will only discuss the practical cases of metals. Following this, some widespread ad hoc modification of the general methods are discussed. The report is concluded by a generalization of the methods to multi-component materials, in particular metallic alloys. (author)
DEFF Research Database (Denmark)
Kjærgaard, Søren; Canudas-Romo, Vladimir
2017-01-01
, the prospective potential support ratio usually focuses on the current mortality schedule, or period life expectancy. Instead, in this paper we look at the actual mortality experienced by cohorts in a population, using cohort life tables. We analyse differences between the two perspectives using mortality models......, historical data, and forecasted data. Cohort life expectancy takes future mortality improvements into account, unlike period life expectancy, leading to a higher prospective potential support ratio. Our results indicate that using cohort instead of period life expectancy returns around 0.5 extra younger...
Directory of Open Access Journals (Sweden)
Jordi Lucero
2009-01-01
Full Text Available This problem was to calculate the path a robot would take to navigate an obstacle field and get to its goal. Three obstacles were given as negative potential fields which the robot avoided, and a goal was given a positive potential field that attracted the robot. The robot decided each step based on its distance, angle, and influence from every object. After each step, the robot recalculated and determined its next step until it reached its goal. The robot's calculations and steps were simulated with Microsoft Excel.
De Jong, Marvin L.
1993-01-01
Describes the powerful graphing ability of computer algebra systems (CAS) to create three-dimensional graphs or surface graphics of electric potentials. Provides equations along with examples of the printouts. Lists the programs Mathematica, Maple, Derive, Theorist, MathCad, and MATLAB as promising CAS systems. (MVL)
Measurement of Electric Potentials
Tait, A.
1973-01-01
Describes the measurement of electric potentials by means of a flame probe. This method is used extensively in the new Nuffield Advanced Level Physics course, and provides a means of taking reliable quantitative results in an area of most school courses where the majority of the work is qualitative. (JR)
Biomethanation and Its Potential
DEFF Research Database (Denmark)
Angelidaki, Irini; Karakashev, Dimitar Borisov; Batstone, Damien J.
2011-01-01
, plugflow, biofilm, UASB, etc.) and process conditions (retention times, loading rates, temperatures, etc.) in order to maximize the energy output from the waste and also to decrease retention time and enhance process stability. Biomethanation has strong potential for the production of energy from organic...
Energy Technology Data Exchange (ETDEWEB)
Munack, A.; Schroder, O. [Johann Heinrich von Thunen Inst., Braunschweig (Germany); Krahl, J. [Coburg Univ. of Applied Sciences, Coburg (Germany); Bunger, J. [Inst. for Prevention and Occupational Medicine of the German Social Accident Insurance, Ruhr-Univ. Inst., Bochum (Germany)
2010-07-01
This paper discussed the potential of biofuels with particular reference to the situation in Germany and Europe. Emphasis was on technical potential, such as biofuel production, utilization and environmental aspects. The Institute of Agricultural Technology and Biosystems Engineering ran vTI emission tests on diesel engines to evaluate the environmental impacts of biofuels. This testing facility is able to drive heavy-duty diesel engines in both stationary and dynamic test cycles, such as the European ESC and ETC. Additional analyses were conducted to determine the fine and ultra-fine particles, polycyclic aromatic hydrocarbons (PAH), aldehydes, ketones, and the usual regulated exhaust gas compounds. Ames tests were conducted to assess the mutagenic potential of tailpipe emissions. Previous study results showed that neat vegetable oils can render the exhaust high in mutagenic potency. Some of the non-regulated exhaust gas compounds were found to vary nonlinearly with the blend composition. B20 was found to have high mutagenic potential and was subject to sedimentation.
International Nuclear Information System (INIS)
Ruddy, T.
1992-01-01
This article examines the potential market for independent power projects in Germany after the reunification. The topics discussed in the article include legal questions, pricing regulations, pollution regulations, energy efficiency regulations, the carbon tax, the market for modernization of power plants and construction of new capacity, and the future outlook
1973-01-01
The potential of solar energy as a national resource is discussed. Research and development programs for the development of eleven concepts are described to show the proposed funding for each year over a fifteen year period. The estimated energy contributions by period for each of the solar concepts are analyzed. The estimated impact of the solar concepts to the year 2020 are tabulated.
Park, Joseph Sung-Yul
2016-01-01
Language occupies a crucial position in neoliberalism, due to the reimagination of language as commodified skill. This paper studies the role of language ideology in this transformation by identifying a particular ideology that facilitates this process, namely the ideology which views language as pure potential. Neoliberalism treats language as a…
Curtright, Thomas
2011-01-01
Continuous interpolates are described for classical dynamical systems defined by discrete time-steps. Functional conjugation methods play a central role in obtaining the interpolations. The interpolates corrrespond to particle motion in an underlying potential, V. Typically, V has no lower bound and can exhibit switchbacks wherein V changes form when turning points are encountered by the particle. The logistic map is used to illustrate these features.
Potential Vorticity in Magnetohydrodynamics
Webb, G. M.; Mace, R. L.
2014-01-01
A version of Noether's second theorem using Lagrange multipliers is used to investigate fluid relabelling symmetries conservation laws in magnetohydrodynamics (MHD). We obtain a new generalized potential vorticity type conservation equation for MHD which takes into account entropy gradients and the ${\\bf J}\\times{\\bf B}$ force on the plasma due to the current ${\\bf J}$ and magnetic induction ${\\bf B}$. This new conservation law for MHD is derived by using Noether's second theorem in conjuncti...
Sicilian potential biogas production
Directory of Open Access Journals (Sweden)
Antonio Comparetti
2013-09-01
Full Text Available This study is aimed at predicting the Sicilian potential biogas production, using the Organic Fraction of Municipal Solid Waste (OFMSW, animal manure and food industry by-products, in a region where only one biogas plant using MSW and one co-digestion plant are nowadays available. The statistical data about OFMSW, the number of animals bred in medium and large farms and the amounts of by-products of food processing industries were evaluated, in order to compute the Sicilian potential biogas and energy production. The OFMSW produced in Sicily, that is 0.8 million tons ca. per year (37% of MSW, could be used in a bio-reactor, together with other raw materials, for Anaerobic Digestion (AD process, producing biogas and “digestate”. Moreover, 3.03 million tons ca. of manure, collected in medium and large animal husbandry farms (where cows, pigs and poultry are bred, and 350 thousand tons ca. of by-products, collected in food processing industries (pomace from olive oil mills and grape marc from wineries, might be used for AD process. The Sicilian potential biogas production from the AD of the above raw materials is 170.2 millions of m3, that is equal to 1023.4 GWh of energy per year, of which 484 GWh from animal manure, 303 GWh from OFMSW and 236.4 GWh from food industry by-products. The highest biogas production is in the province of Palermo (35.6 millions of m3, Ragusa (30.8 millions of m3 and Catania (22.8 millions of m3, having a potential energy production of 213.8, 185 and 137 GWh, respectively.
Alexandrou, C; Tsapalis, A; Forcrand, Ph. de
2002-01-01
Using state of the art lattice techniques we investigate the static baryon potential. We employ the multi-hit procedure for the time links and a variational approach to determine the ground state with sufficient accuracy that, for distances up to $\\sim 1.2$ fm, we can distinguish the $Y$- and $\\Delta$- Ans\\"atze for the baryonic Wilson area law. Our analysis shows that the $\\Delta$-Ansatz is favoured. This result is also supported by the gauge-invariant nucleon wave function which we measure for the first time.
Electrostatic potential in superconductor
Czech Academy of Sciences Publication Activity Database
Lipavský, Pavel; Koláček, Jan; Morawetz, K.; Brandt, E. H.
2002-01-01
Roč. 65, - (2002), s. 14511-1-14511-18 ISSN 0163-1829 R&D Projects: GA MŠk ME 601; GA ČR GA202/00/0643; GA AV ČR IAA1010806; GA AV ČR IAA1010919 Grant - others:ESF(XX) VORTEX Institutional research plan: CEZ:AV0Z1010914 Keywords : Ginzburg-Landau theory * Bernoulli potential * Abrikosov vortex lattice Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.327, year: 2002
ICT Enhanced Buildings Potentials
DEFF Research Database (Denmark)
Christiansson, Per
2007-01-01
component systems that are accessed and integrated in the real world of building use in different contexts. The ICT systems may be physically or virtually embedded in the building. Already in 1982 AT&T established the 'intelligent buildings', IB, concept due to marketing reasons and the Informart building...... with focus on virtual building models support, new services and user environment definitions and development, virtual spaces and augmented reality, intelligent building components, application ontologies, and ICT systems integration to illustrate ICT enhanced buildings potentials and R&D needs. ...
Compact Polarimetry Potentials
Truong-Loi, My-Linh; Dubois-Fernandez, Pascale; Pottier, Eric
2011-01-01
The goal of this study is to show the potential of a compact-pol SAR system for vegetation applications. Compact-pol concept has been suggested to minimize the system design while maximize the information and is declined as the ?/4, ?/2 and hybrid modes. In this paper, the applications such as biomass and vegetation height estimates are first presented, then, the equivalence between compact-pol data simulated from full-pol data and compact-pol data processed from raw data as such is shown. Finally, a calibration procedure using external targets is proposed.
Zoonotic potential of Giardia.
Ryan, Una; Cacciò, Simone M
2013-11-01
Giardia duodenalis (syn. Giardia lamblia and Giardia intestinalis) is a common intestinal parasite of humans and mammals worldwide. Assessing the zoonotic transmission of the infection requires molecular characterization as there is considerable genetic variation within G. duodenalis. To date eight major genetic groups (assemblages) have been identified, two of which (A and B) are found in both humans and animals, whereas the remaining six (C to H) are host-specific and do not infect humans. Sequence-based surveys of single loci have identified a number of genetic variants (genotypes) within assemblages A and B in animal species, some of which may have zoonotic potential. Multi-locus typing data, however, has shown that in most cases, animals do not share identical multi-locus types with humans. Furthermore, interpretation of genotyping data is complicated by the presence of multiple alleles that generate "double peaks" in sequencing files from PCR products, and by the potential exchange of genetic material among isolates, which may account for the non-concordance in the assignment of isolates to specific assemblages. Therefore, a better understanding of the genetics of this parasite is required to allow the design of more sensitive and variable subtyping tools, that in turn may help unravel the complex epidemiology of this infection. Copyright © 2013. Published by Elsevier Ltd.
International Evoked Potentials Symposium
1980-01-01
The past decade has seen great progress in the measurement of evoked potentials in man; a steady increase in our understanding of their charac teristics, their origins and their usefulness; and a growing application in the field of clinical diagnosis. The topic is a truly multidisciplinary one. Important research contributions have been made by workers of many different backgrounds and clinical applications span the specialities. This book represents a revised and updated version of the work originally presented at the international evoked potential symposium held in Nottingham 4-6 1978. The Nottingham Symposium provided a forum for a state-of-the-art discussion amongst workers from many different disciplines and from many different countries. For each major topic in the field an expert review set the scene for discussion of current research presentations. This format is retained in the book: the chapters in Part A provide the context in which the research presented in Part B is set. The task of selecting m...
The effective nuclear potential
International Nuclear Information System (INIS)
Skyrme, T.H.R.
1994-01-01
An empirical analyses is made of the mean effective internucleon potential required in the shell-model description of nuclei, allowing for the presence of many-body effects as suggested by current theory. A consistent description is found in which the effective two-body interaction acts almost entirely in even states, and the many-body effects are simulated by a repulsive three-body contact interaction. The strength of the two-body interaction is consistent with that expressed by the free scattering matrix of the two-nucleon system, and that of the three-body interaction with the 'rearrangement energy' calculated in the many-body theory. (author). 21 refs, 2 figs, 7 tabs
Potential vorticity in magnetohydrodynamics
Webb, G. M.; Mace, R. L.
2015-01-01
A version of Noether's second theorem using Lagrange multipliers is used to investigate fluid relabelling symmetries conservation laws in magnetohydrodynamics (MHD). We obtain a new generalized potential vorticity type conservation equation for MHD which takes into account entropy gradients and the J × B force on the plasma due to the current J and magnetic induction B. This new conservation law for MHD is derived by using Noether's second theorem in conjunction with a class of fluid relabelling symmetries in which the symmetry generator for the Lagrange label transformations is non-parallel to the magnetic field induction in Lagrange label space. This is associated with an Abelian Lie pseudo algebra and a foliated phase space in Lagrange label space. It contains as a special case Ertel's theorem in ideal fluid mechanics. An independent derivation shows that the new conservation law is also valid for more general physical situations.
Not utilized learning potentials
DEFF Research Database (Denmark)
Kragelund, Linda
-conscious disjuncture, in development of the concept pseudo-everyday life activities and in a categorizing model for and a theory about student nurses' learning processes. The theory includes relations between 4 types of disjuncture, 3 types of content in the learning processes, and factors that provoke...... transformation from one type of disjuncture to another. Students and mentors are not aware that students are in potential learning situations when they interact on their own with patients, and that it is non-routine for students to act with patients in pseudo-everyday life activities. It may be possible...... When the Danish Nursing Education in 2002 became a Bachelor Degree the clinical part of the education was reduced. Therefore, it was necessary to optimize learning in practice. I made a qualitative investigation to describe student nurses' learning processes in non-routine situations where...
Potential for nuclear terrorism
International Nuclear Information System (INIS)
Jenkins, B.M.
1977-05-01
The question of whether or not terrorists will ''go nuclear'' is discussed. It is possible, although there is no historical evidence that any criminal or terrorist group ever made any attempt to acquire nuclear material for use in an explosive or dispersal device. In terms of intentions, psychotics are potential nuclear terrorists, but in terms of capabilities, they are the farthest away from being able to acquire a nuclear weapon. The history of nuclear incidents in the U.S. and abroad is reviewed. As the nuclear industry expands, the number of low-level incidents (bomb threats, pilferage, etc.) will increase also, but not necessarily escalate to more serious incidents. Terrorists may ''go nuclear'' solely for the publicity value; nuclear hoaxes may be attenpted. Nuclear terrorism seems more attractive as a threat than as an action. But the nature of the threat may change in the future, and the danger of imitation of a successful nuclear terrorist act is pointed out
Pseudo potentials and model potentials in atomic collisions
International Nuclear Information System (INIS)
Reyes, O.; Jouin, H.; Fuentealba, P.
1988-01-01
In this work, it is discussed the main differences between the use of pseudo-potentials and model potentials in collision problems . It is shown the potential energy curves for distinct systems obtained with both kinds of potentials. (A.C.A.S.) [pt
Balmer, Bethany F.; Powers, Rachel L.; Zhang, Ting-Hu; Lee, Jihye; Vigant, Frederic; Lee, Benhur; Jung, Michael E.; Purcell, Maureen K.; Snekvik, Kevin; Aguilar, Hector C.
2017-01-01
Many enveloped viruses cause devastating disease in aquaculture, resulting in significant economic impact. LJ001 is a broad-spectrum antiviral compound that inhibits enveloped virus infections by specifically targeting phospholipids in the lipid bilayer via the production of singlet oxygen (1O2). This stabilizes positive curvature and decreases membrane fluidity, which inhibits virus-cell membrane fusion during viral entry. Based on data from previous mammalian studies and the requirement of light for the activation of LJ001, we hypothesized that LJ001 may be useful as a preventative and/or therapeutic agent for infections by enveloped viruses in aquaculture. Here, we report that LJ001 was more stable with a prolonged inhibitory half-life at relevant aquaculture temperatures (15°C), than in mammalian studies at 37°C. When LJ001 was preincubated with our model virus, infectious hematopoietic necrosis virus (IHNV), infectivity was significantly inhibited in vitro (using the epithelioma papulosum cyprini [EPC] fish cell line) and in vivo (using rainbow trout fry) in a dose-dependent and time-dependent manner. While horizontal transmission of IHNV in a static cohabitation challenge model was reduced by LJ001, transmission was not completely blocked at established antiviral doses. Therefore, LJ001 may be best suited as a therapeutic for aquaculture settings that include viral infections with lower virus-shedding rates than IHNV or where higher viral titers are required to initiate infection of naive fish. Importantly, our data also suggest that LJ001-inactivated IHNV elicited an innate immune response in the rainbow trout host, making LJ001 potentially useful for future vaccination approaches.
Substellar fragmentation in self-gravitating fluids with a major phase transition
Füglistaler, A.; Pfenniger, D.
2015-06-01
Context. The observation of various ices in cold molecular clouds, the existence of ubiquitous substellar, cold H2 globules in planetary nebulae and supernova remnants, or the mere existence of comets suggest that the physics of very cold interstellar gas might be much richer than usually envisioned. At the extreme of low temperatures (≲10 K), H2 itself is subject to a phase transition crossing the entire cosmic gas density scale. Aims: This well-known, laboratory-based fact motivates us to study the ideal case of a cold neutral gaseous medium in interstellar conditions for which the bulk of the mass, instead of trace elements, is subject to a gas-liquid or gas-solid phase transition. Methods: On the one hand, the equilibrium of general non-ideal fluids is studied using the virial theorem and linear stability analysis. On the other hand, the non-linear dynamics is studied using computer simulations to characterize the expected formation of solid bodies analogous to comets. The simulations are run with a state-of-the-art molecular dynamics code (LAMMPS) using the Lennard-Jones inter-molecular potential. The long-range gravitational forces can be taken into account together with short-range molecular forces with finite limited computational resources, using super-molecules, provided the right scaling is followed. Results: The concept of super-molecule, where the phase transition conditions are preserved by the proper choice of the particle parameters, is tested with computer simulations, allowing us to correctly satisfy the Jeans instability criterion for one-phase fluids. The simulations show that fluids presenting a phase transition are gravitationally unstable as well, independent of the strength of the gravitational potential, producing two distinct kinds of substellar bodies, those dominated by gravity (planetoids) and those dominated by molecular attractive force (comets). Conclusions: Observations, formal analysis, and computer simulations suggest the
Bioremedication: Potentials and pitfalls
International Nuclear Information System (INIS)
Nichols, A.B.
1992-01-01
The three main types of marine oil spill bioremediation involve fertilizers, seeding, and open-water applications. Fertilizers contain nutrients that trigger the growth of indigenous oil-degrading microorganisms. Seeding involves adding exogenous microbes to an oiled environment to promote increased biodegradation rates. The effectiveness of using either seeding or fertilizers in the open ocean has not been well established and most of the scientific community and many oil professionals remain skeptical about the utility of bioremediation at sea because rigorously controlled and documented experiments have not yet been done. Several companies have advocated using bioremediation for open ocean oil spills, but they have not yet produced convincing evidence that their products work as claimed. A potentially significant problem at sea is keeping the microorganisms in contact with the oil long enough for degradation to occur. The jury is still out regarding regulatory and public acceptance of bioremediation as a technique to clean up oil spills in general. Commercialization of bioremediation products is hindered by lack of protocols for testing and approval, although efforts are underway to devise such mechanisms
Potential dangers of cannabis.
Kaymakçalan, S
1975-01-01
Cannabis is not a harmless drug. The potential dangers of cannabis are briefly reviewed in this report. The above-mentioned observations on cannabis users should be kept in mind and carefully examined by all physicians. One could expect that as more potent cannabis preparations become available, some of the toxic manifestations which now seem rare might become more frequent. Some of the remarks about the dangers of cannabis may not be proved in future studies, and they may represent only our anxiety. However, prior to the elimination of these fears, no steps should be taken toward the legalizing of marijuana. At present there is no scientific evidence that cannabis is less harmful than either tobacco or alcohol. The opposite may be true. The analogy can be drawn between opium and cannabis. The permissive attitude toward the use of opium can easily lead to the use of morphine and other opiates. If we legalize the use of marijuana, we cannot prevent the use of more dangerous derivatives of cannabis; namely, hashish, cannabis oil and THC, itself. In my opinion, in the light of our present knowledge, legalizing of marijuana could be hazardous both for the individual and for society.
Patocka, Jiří; Gupta, Ramesh C; Wu, Qing-hua; Kuca, Kamil
2015-10-01
This review briefly describes the origin, chemistry, molecular mechanism of action, pharmacology, toxicology, and ecotoxicology of palytoxin and its analogues. Palytoxin and its analogues are produced by marine dinoflagellates. Palytoxin is also produced by Zoanthids (i.e. Palythoa), and Cyanobacteria (Trichodesmium). Palytoxin is a very large, non-proteinaceous molecule with a complex chemical structure having both lipophilic and hydrophilic moieties. Palytoxin is one of the most potent marine toxins with an LD50 of 150 ng/kg body weight in mice exposed intravenously. Pharmacological and electrophysiological studies have demonstrated that palytoxin acts as a hemolysin and alters the function of excitable cells through multiple mechanisms of action. Palytoxin selectively binds to Na(+)/K(+)-ATPase with a Kd of 20 pM and transforms the pump into a channel permeable to monovalent cations with a single-channel conductance of 10 pS. This mechanism of action could have multiple effects on cells. Evaluation of palytoxin toxicity using various animal models revealed that palytoxin is an extremely potent neurotoxin following an intravenous, intraperitoneal, intramuscular, subcutaneous or intratracheal route of exposure. Palytoxin also causes non-lethal, yet serious toxic effects following dermal or ocular exposure. Most incidents of palytoxin poisoning have manifested after oral intake of contaminated seafood. Poisonings in humans have also been noted after inhalation, cutaneous/systemic exposures with direct contact of aerosolized seawater during Ostreopsis blooms and/or through maintaining aquaria containing Cnidarian zoanthids. Palytoxin has a strong potential for toxicity in humans and animals, and currently this toxin is of great concern worldwide.
RANGELAND SEQUESTRATION POTENTIAL ASSESSMENT
Energy Technology Data Exchange (ETDEWEB)
Lee Spangler; George F. Vance; Gerald E. Schuman; Justin D. Derner
2012-03-31
Rangelands occupy approximately half of the world's land area and store greater than 10% of the terrestrial biomass carbon and up to 30% of the global soil organic carbon. Although soil carbon sequestration rates are generally low on rangelands in comparison to croplands, increases in terrestrial carbon in rangelands resulting from management can account for significant carbon sequestration given the magnitude of this land resource. Despite the significance rangelands can play in carbon sequestration, our understanding remains limited. Researchers conducted a literature review to identify sustainably management practices that conserve existing rangeland carbon pools, as well as increase or restore carbon sequestration potentials for this type of ecosystem. The research team also reviewed the impact of grazing management on rangeland carbon dynamics, which are not well understood due to heterogeneity in grassland types. The literature review on the impact of grazing showed a wide variation of results, ranging from positive to negative to no response. On further review, the intensity of grazing appears to be a major factor in controlling rangeland soil organic carbon dynamics. In 2003, researchers conducted field sampling to assess the effect of several drought years during the period 1993-2002. Results suggested that drought can significantly impact rangeland soil organic carbon (SOC) levels, and therefore, carbon sequestration. Resampling was conducted in 2006; results again suggested that climatic conditions may have overridden management effects on SOC due to the ecological lag of the severe drought of 2002. Analysis of grazing practices during this research effort suggested that there are beneficial effects of light grazing compared to heavy grazing and non-grazing with respect to increased SOC and nitrogen contents. In general, carbon storage in rangelands also increases with increased precipitation, although researchers identified threshold levels of
Quantum potentiality revisited
Jaeger, Gregg
2017-10-01
Heisenberg offered an interpretation of the quantum state which made use of a quantitative version of an earlier notion, , of Aristotle by both referring to it using its Latin name, potentia, and identifying its qualitative aspect with . The relationship between this use and Aristotle's notion was not made by Heisenberg in full detail, beyond noting their common character: that of signifying the system's objective capacity to be found later to possess a property in actuality. For such actualization, Heisenberg required measurement to have taken place, an interaction with external systems that disrupts the otherwise independent, natural evolution of the quantum system. The notion of state actualization was later taken up by others, including Shimony, in the search for a law-like measurement process. Yet, the relation of quantum potentiality to Aristotle's original notion has been viewed as mainly terminological, even by those who used it thus. Here, I reconsider the relation of Heisenberg's notion to Aristotle's and show that it can be explicated in greater specificity than Heisenberg did. This is accomplished through the careful consideration of the role of potentia in physical causation and explanation, and done in order to provide a fuller understanding of this aspect of Heisenberg's approach to quantum mechanics. Most importantly, it is pointed out that Heisenberg's requirement of an external intervention during measurement that disrupts the otherwise independent, natural evolution of the quantum system is in accord with Aristotle's characterization of spontaneous causation. Thus, the need for a teleological understanding of the actualization of potentia, an often assumed requirement that has left this fundamental notion neglected, is seen to be spurious. This article is part of the themed issue `Second quantum revolution: foundational questions'.
Quantum potentiality revisited.
Jaeger, Gregg
2017-11-13
Heisenberg offered an interpretation of the quantum state which made use of a quantitative version of an earlier notion, [Formula: see text], of Aristotle by both referring to it using its Latin name, potentia , and identifying its qualitative aspect with [Formula: see text] The relationship between this use and Aristotle's notion was not made by Heisenberg in full detail, beyond noting their common character: that of signifying the system's objective capacity to be found later to possess a property in actuality. For such actualization, Heisenberg required measurement to have taken place, an interaction with external systems that disrupts the otherwise independent, natural evolution of the quantum system. The notion of state actualization was later taken up by others, including Shimony, in the search for a law-like measurement process. Yet, the relation of quantum potentiality to Aristotle's original notion has been viewed as mainly terminological, even by those who used it thus. Here, I reconsider the relation of Heisenberg's notion to Aristotle's and show that it can be explicated in greater specificity than Heisenberg did. This is accomplished through the careful consideration of the role of potentia in physical causation and explanation, and done in order to provide a fuller understanding of this aspect of Heisenberg's approach to quantum mechanics. Most importantly, it is pointed out that Heisenberg's requirement of an external intervention during measurement that disrupts the otherwise independent, natural evolution of the quantum system is in accord with Aristotle's characterization of spontaneous causation. Thus, the need for a teleological understanding of the actualization of potentia, an often assumed requirement that has left this fundamental notion neglected, is seen to be spurious.This article is part of the themed issue 'Second quantum revolution: foundational questions'. © 2017 The Author(s).
International Nuclear Information System (INIS)
Soezen, Adnan; Arcaklioglu, Erol
2005-01-01
Most of the locations in Turkey receive abundant solar-energy, because Turkey lies in a sunny belt between 36 deg. and 42 deg. N latitudes. Average annual temperature is 18 to 20 deg. C on the south coast, falls to 14-16 deg. C on the west coat, and fluctuates between 4 and 18 deg. C in the central parts. The yearly average solar-radiation is 3.6 kW h/m 2 day, and the total yearly radiation period is ∼2610 h. In this study, a new formulation based on meteorological and geographical data was developed to determine the solar-energy potential in Turkey using artificial neural-networks (ANNs). Scaled conjugate gradient (SCG), Pola-Ribiere conjugate gradient (CGP), and Levenberg-Marquardt (LM) learning algorithms and logistic sigmoid (logsig) transfer function were used in the networks. Meteorological data for last four years (2000-2003) from 12 cities (Canakkale, Kars, Hakkari, Sakarya, Erzurum, Zonguldak, Balikesir, Artvin, Corum, Konya, Siirt, and Tekirdag) spread over Turkey were used in order to train the neural-network. Meteorological and geographical data (latitude, longitude, altitude, month, mean sunshine-duration, and mean temperature) are used in the input layer of the network. Solar-radiation is in the output layer. The maximum mean absolute percentage error was found to be less than 3.832% and R 2 values to be about 99.9738% for the selected stations. The ANN models show greater accuracy for evaluating solar-resource possibilities in regions where a network of monitoring stations has not been established in Turkey. This study confirms the ability of the ANN to predict solar-radiation values accurately
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
Simulation of self-assembled nanopatterns in binary alloys on the fcc(111) surface
Energy Technology Data Exchange (ETDEWEB)
Weber, Sebastian
2008-07-01
In this PhD thesis, we study the heteroepitaxial crystal growth by means of Monte Carlo simulations. Of particular interest in this work is the influence of the lattice mismatch of the adsorbates relative to the substrate on surface structures. In the framework of an off-lattice model, we consider one monolayer of adsorbate and investigate the emerging nanopatterns in equilibrium and their formation during growth. In chapter 1, a brief introduction is given, which describes the role of computer simulations in the field of the physics of condensed matter. Chapter 2 is devoted to some technical basics of experimental methods of molecular beam epitaxy and the theoretical description. Before a model for the simulation can be designed, it is necessary to make some considerations of the single processes which occur during epitaxial growth. For that purpose we look at an experimental setup and extract the main microscopic processes. Afterwards a brief overview of different theoretical concepts describing that physical procedures is given. In chapter 3, the model used in the simulations is presented. The aim is to investigate the growth of an fcc crystal in the [111] direction. In order to keep the simulation times within a feasible limit a simple pair potential, the Lennard-Jones potential, with continuous particle positions is used, which are necessary to describe effects resulting from the atomic mismatch in the crystal. Furthermore the detailed algorithm is introduced which is based on the idea to calculate the barrier of each diffusion event and to use the barriers in a rejection-free method. Chapter 4 is attended to the simulation of equilibrium. The influence of different parameters on the emerging structures in the first monolayer upon the surface, which is completely covered with two adsorbate materials, is studied. Especially the competition between binding energy and strain leads to very interesting pattern formations like islands or stripes. In chapter 5 the
PV potential and potential PV rent in European regions
DEFF Research Database (Denmark)
Hansen, Anders Chr.; Thorn, Paul
2013-01-01
The paper provides a GIS based model for assessing the potentials of photovoltaic electricity in Europe by NUTS 2 regions. The location specific energy potential per PV-‐panel area is estimated based on observations of solar irradiation, conversion efficiency, levelised costs and the social value...... of PV-‐electricity. Combined with the potential density of PV-‐panel area based on land cover and environental restrictions, the PV energy potential and the potential PV ressource rent is calculated. These calculations enbable the model to estimate the regional patterns at NUTS 2 level...
Vermont Center for Geographic Information — (Link to Metadata) The statewide wind potential layer used in the Act 174 effort represents three combined wind resource layers: Potential Residential and Small and...
Particle rearrangement and softening contributions to the nonlinear mechanical response of glasses
Fan, Meng; Zhang, Kai; Schroers, Jan; Shattuck, Mark D.; O'Hern, Corey S.
2017-09-01
Amorphous materials such as metallic, polymeric, and colloidal glasses exhibit complex preparation-dependent mechanical response to applied shear. In particular, glassy solids yield, with a mechanical response that transitions from elastic to plastic, with increasing shear strain. We perform numerical simulations to investigate the mechanical response of binary Lennard-Jones glasses undergoing athermal, quasistatic pure shear as a function of the cooling rate R used to prepare them. The ensemble-averaged stress versus strain curve 〈σ (γ )〉 resembles the spatial average in the large size limit, which appears smooth and displays a putative elastic regime at small strains, a yielding-related peak in stress at intermediate strain, and a plastic flow regime at large strains. In contrast, for each glass configuration in the ensemble, the stress-strain curve σ (γ ) consists of many short nearly linear segments that are punctuated by particle-rearrangement-induced rapid stress drops. To explain the nonlinearity of 〈σ (γ )〉 , we quantify the shape of the small stress-strain segments and the frequency and size of the stress drops in each glass configuration. We decompose the stress loss [i.e., the deviation in the slope of 〈σ (γ )〉 from that at 〈σ (0 )〉 ] into the loss from particle rearrangements and the loss from softening [i.e., the reduction of the slopes of the linear segments in σ (γ ) ], and then compare the two contributions as a function of R and γ . For the current studies, the rearrangement-induced stress loss is larger than the softening-induced stress loss, however, softening stress losses increase with decreasing cooling rate. We also characterize the structure of the potential energy landscape along the strain direction for glasses prepared with different R , and observe a dramatic change of the properties of the landscape near the yielding transition. We then show that the rearrangement-induced energy loss per strain can serve as
Molecular Dynamics simulations of liquid isoquinoline as a function of temperature
Energy Technology Data Exchange (ETDEWEB)
Ahmad, Norariza [Universiti Sains Malaysia, School of Chemical Sciences, Minden, Penang 11800 (Malaysia); Adnan, Rohana, E-mail: r_adnan@usm.my [Universiti Sains Malaysia, School of Chemical Sciences, Minden, Penang 11800 (Malaysia); Soetens, Jean-Christophe [Universite de Bordeaux 1, ISM, UMR 5255, 351, Cours de la Liberation, Talence F-33405 (France); CNRS, ISM, UMR 5255, 351, Cours de la Liberation, Talence F-33405 (France); Millot, Claude, E-mail: Claude.Millot@univ-lorraine.fr [Universite de Lorraine, SRSMC, UMR 7565, Boulevard des Aiguillettes, BP 70239, Vandoeuvre-les-Nancy F-54506 (France); CNRS, SRSMC, UMR 7565, Boulevard des Aiguillettes, BP 70239, Vandoeuvre-les-Nancy F-54506 (France)
2012-10-15
Highlights: Black-Right-Pointing-Pointer Molecular Dynamics simulations of liquid isoquinoline between 300 and 365 K are done. Black-Right-Pointing-Pointer Dependence on temperature of {sup 13}C T{sub 1} NMR relaxation time is calculated. Black-Right-Pointing-Pointer A small non-Arrhenius behavior is found for translational and rotational diffusion. Black-Right-Pointing-Pointer Comparison with liquid quinoline shows similarities but no clear break temperature. -- Abstract: Molecular Dynamics simulations of isoquinoline in liquid phase have been conducted in the temperature range 300-365 K corresponding to the normal liquid phase in order to investigate the evolution of translational and rotational diffusion with temperature. Molecules are supposed to be rigid and interact through an all-atom potential composed of Coulombic and Lennard-Jones terms. Translational diffusion coefficients are computed from velocity autocorrelation functions and mean square displacement. Anisotropic rotational diffusion coefficients are computed from angular velocity autocorrelation functions. The evolution of the {sup 13}C spin-lattice relaxation time with temperature has been obtained from the simulations and compared with experimental results. A small non-Arrhenius behavior, more pronounced than what was observed experimentally, has been found for this property. The structure has been analyzed in terms of populations of different kinds of first-neighbor dimers. A continuous evolution of the structure with temperature has been observed. The general trend is thus a continuous smooth evolution of the structure at dimer level and a slight non-Arrhenius evolution for diffusion coefficients and reorientational correlation times. These results are compared with those obtained for liquid quinoline where a clear non-Arrhenius break around 290 K was observed for the {sup 13}C spin-lattice relaxation time from experiments [D. Jalabert, J.-B. Robert, H. Roux-Buisson, J.-P. Kintzinger, J.-M. Lehn
Energy Technology Data Exchange (ETDEWEB)
Heusler, Stefan [Duisburg-Essen University, 47057 Duisburg (Germany)
2006-12-08
The main focus of the second, enlarged edition of the book Mathematica for Theoretical Physics is on computational examples using the computer program Mathematica in various areas in physics. It is a notebook rather than a textbook. Indeed, the book is just a printout of the Mathematica notebooks included on the CD. The second edition is divided into two volumes, the first covering classical mechanics and nonlinear dynamics, the second dealing with examples in electrodynamics, quantum mechanics, general relativity and fractal geometry. The second volume is not suited for newcomers because basic and simple physical ideas which lead to complex formulas are not explained in detail. Instead, the computer technology makes it possible to write down and manipulate formulas of practically any length. For researchers with experience in computing, the book contains a lot of interesting and non-trivial examples. Most of the examples discussed are standard textbook problems, but the power of Mathematica opens the path to more sophisticated solutions. For example, the exact solution for the perihelion shift of Mercury within general relativity is worked out in detail using elliptic functions. The virial equation of state for molecules' interaction with Lennard-Jones-like potentials is discussed, including both classical and quantum corrections to the second virial coefficient. Interestingly, closed solutions become available using sophisticated computing methods within Mathematica. In my opinion, the textbook should not show formulas in detail which cover three or more pages-these technical data should just be contained on the CD. Instead, the textbook should focus on more detailed explanation of the physical concepts behind the technicalities. The discussion of the virial equation would benefit much from replacing 15 pages of Mathematica output with 15 pages of further explanation and motivation. In this combination, the power of computing merged with physical intuition
Pyrazine in supercritical xenon: local number density defined by experiment and calculation.
Hrnjez, Bruce J; Kabarriti, Abdo; Dach, Benjamin I; Buldyrev, Sergey V; Asherie, Neer; Natanov, Georgiy R; Balderman, Joshua
2008-12-04
Toward our goal of using supercritical fluids to study solvent effects in physical and chemical phenomena, we develop a method to spatially define the solvent local number density at the solute in the highly compressible regime of a supercritical fluid. Experimentally, the red shift of the pyrazine n-pi* electronic transition was measured at high dilution in supercritical xenon as a function of pressure from 0 to approximately 24 MPa at two temperatures: one (293.2 K) close to the critical temperature and the other (333.2 K) remote. Computationally, several representative stationary points were located on the potential surfaces for pyrazine and 1, 2, 3, and 4 xenons at the MP2/6-311++G(d,p)/aug-cc-pVTZ-PP level. The vertical n-pi* ((1)B(3u)) transition energies were computed for these geometries using a TDDFT/B3LYP/DGDZVP method. The combination of experiment and quantum chemical computation allows prediction of supercritical xenon bulk densities at which the pyrazine primary solvation shell contains an average of 1, 2, 3, and 4 xenon molecules. These density predictions were achieved by graphical superposition of calculated shifts on the experimental shift versus density curves for 293.2 and 333.2 K. Predicted bulk densities are 0.50, 0.91, 1.85, and 2.50 g cm(-3) for average pyrazine primary solvation shell occupancy by 1, 2, 3, and 4 xenons at 293.2 K. Predicted bulk densities are 0.65, 1.20, 1.85, and 2.50 g cm(-3) for average pyrazine primary solvation shell occupancy by 1, 2, 3, and 4 xenons at 333.2 K. These predictions were evaluated with classical Lennard-Jones molecular dynamics simulations designed to replicate experimental conditions at the two temperatures. The average xenon number within 5.0 A of the pyrazine center-of-mass at the predicted densities is 1.3, 2.1, 3.0, and 4.0 at both simulation temperatures. Our three-component method-absorbance measurement, quantum chemical prediction, and evaluation of prediction with classical molecular dynamics
International Nuclear Information System (INIS)
Heusler, Stefan
2006-01-01
The main focus of the second, enlarged edition of the book Mathematica for Theoretical Physics is on computational examples using the computer program Mathematica in various areas in physics. It is a notebook rather than a textbook. Indeed, the book is just a printout of the Mathematica notebooks included on the CD. The second edition is divided into two volumes, the first covering classical mechanics and nonlinear dynamics, the second dealing with examples in electrodynamics, quantum mechanics, general relativity and fractal geometry. The second volume is not suited for newcomers because basic and simple physical ideas which lead to complex formulas are not explained in detail. Instead, the computer technology makes it possible to write down and manipulate formulas of practically any length. For researchers with experience in computing, the book contains a lot of interesting and non-trivial examples. Most of the examples discussed are standard textbook problems, but the power of Mathematica opens the path to more sophisticated solutions. For example, the exact solution for the perihelion shift of Mercury within general relativity is worked out in detail using elliptic functions. The virial equation of state for molecules' interaction with Lennard-Jones-like potentials is discussed, including both classical and quantum corrections to the second virial coefficient. Interestingly, closed solutions become available using sophisticated computing methods within Mathematica. In my opinion, the textbook should not show formulas in detail which cover three or more pages-these technical data should just be contained on the CD. Instead, the textbook should focus on more detailed explanation of the physical concepts behind the technicalities. The discussion of the virial equation would benefit much from replacing 15 pages of Mathematica output with 15 pages of further explanation and motivation. In this combination, the power of computing merged with physical intuition would
Child Abuse Potential: How Persistent?
Haapasalo, Jaana; Aaltonen, Terhi
1999-01-01
Compares mothers whose children had been under supervision of Child Protective Services (CPS) with comparison mothers for child abuse potential using Millner's Child Abuse Potential Inventory. CPS mothers scored significantly higher than the comparison mothers, indicating their persistent elevated child abuse potential; there was no significant…
Pair potentials for fcc metals
International Nuclear Information System (INIS)
Baskes, M.I.; Melius, C.F.
1979-01-01
Long-range pair potentials are presented for the fcc metals Ni, Au, Ag, Pt, Pd, Cu, and Al. Experimental data considered in deriving the potentials include the sublimination energies and stacking-fault energies as well as the lattice parameters, elastic constants, and vacancy-formation and -migration energies. A volume-dependent energy term has been included in the potentials. By scaling the potentials with respect to lattice spacing and a characteristic binding energy, a striking similarity can be seen between the various potentials. These potentials have been used to calculate a variety of point-defect properties including self-interstitial geometries and migration energies. In addition the migration energy of helium and its binding energy to a vacancy have been calculated
The neutron optical model potential
International Nuclear Information System (INIS)
Hodgson, P.E.
1989-01-01
The present status of optical model calculations of neutron scattering and interactions is reviewed, with special emphasis on more recent developments and the more promising lines of research. The use of dispersion relations to provide an extra constraint on the potential is discussed, together with their application to studies of the Fermi surface anomaly. The application of potential inversion techniques to determine the form of the potential is also considered. (author). 39 refs, figs
Oxygen potentials of transuranium oxides
International Nuclear Information System (INIS)
Haruyoshi Otobe; Mituso Akabori; Arai Yasuo; Kazuo Minato
2008-01-01
The oxygen potentials of pyrochlore-type Pu 2 Zr 2 O 7+y , fluorite-type (Pu 0.5 Zr 0.5 )O 2-x and AmO 2-x have been measured by the electromotive force (EMF) method with a zirconia solid-electrolyte. The oxygen potentials of these oxides were reviewed. The phase relations, microstructure, equilibrium state of these oxides were discussed, referring to the isothermal curve of the oxygen potentials. (authors)
Plasmas: Diversity, pervasiveness and potential
Energy Technology Data Exchange (ETDEWEB)
Eastman, Timothy E.
1998-01-01
When considered inclusively, plasma science and technology encompass immense diversity, pervasiveness and potential: diversity through numerous topical areas (see list of nearly 200 in Table II); pervasiveness with examples covering the full range of energy, time and spatial scale; and potential through innumerable current and future applications.
Fertility potential after unilateral orchiopexy
DEFF Research Database (Denmark)
Cortes, D; Thorup, J M; Lindenberg, S
1996-01-01
. CONCLUSIONS: The age matched number of spermatogonia per tubular cross section is significant in regard to fertility potential, and a value of 1% or less (approximately Sertoli cells only) may predict low fertility potential. To our knowledge Sertoli cells only have not been observed before 15 months of life...
Supermodular Games and Potential Games
Brânzei, R.; Mallozzi, L.; Tijs, S.H.
2001-01-01
Potential games and supermodular games are attractive games, especially because under certain conditions they possess pure Nash equilibria. Subclasses of games with a potential are considered which are also strategically equivalent to supermodular games. The focus is on two-person zero-sum games and
Supermodular Games and Potential Games
Brânzei, R.; Mallozzi, L.; Tijs, S.H.
2001-01-01
Potential games and supermodular games are attractive games, especially because under certain conditions they possess pure Nash equilibria. Subclasses of games with a potential are considered which are also strategically equivalent to supermodular games. The focus is on two-person zero-sum games and two-person Cournot games.
Potential photosynthesis of crop surfaces.
Wit, de C.T.
1959-01-01
A formula for calculating the potential photosynthesis of a closed crop surface is proposed, assuming that the leaves of the crop are not arranged in any definite direction. In the Netherlands, values for potential photosynthesis vary from 290 kg. CH2O/ha./day in June to 50 kg./ha./day in December.
Spacetime Metrics from Gauge Potentials
Directory of Open Access Journals (Sweden)
Ettore Minguzzi
2014-03-01
Full Text Available I present an approach to gravity in which the spacetime metric is constructed from a non-Abelian gauge potential with values in the Lie algebra of the group U(2 (or the Lie algebra of quaternions. If the curvature of this potential vanishes, the metric reduces to a canonical curved background form reminiscent of the Friedmann S3 cosmological metric.
A Reappraisal of Children's "Potential"
Beauvais, Clémentine; Higham, Rupert
2016-01-01
What does it mean for a child to fulfil his or her potential? This article explores the contexts and implications of the much-used concept of potential in educational discourses. We claim that many of the popular, political and educational uses of the term in relation to childhood have a problematic blind spot: interpersonality, and the necessary…