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
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.
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.
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.
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 ...
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
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.
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
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...
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.)
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
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)
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...
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
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....
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.
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....
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.
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.
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...
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...
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.
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.
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.
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
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.
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.
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
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.
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.
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.
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
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.
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.
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....
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.
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.
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.
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.
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
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.
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.
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.
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.
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.
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
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.
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.
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
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
On the record: Interview with Major General Johan Jooste (Retired ...
African Journals Online (AJOL)
Major General Johan Jooste (Ret) heads the unit. Critical voices have questioned the efficacy of the anti-poaching strategy, suggesting that park authorities are waging a 'war on poaching' with unintended long-term consequences for protected areas management and community relations.1 Scholars have argued that ...
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.
Uhiuus orkester Tallinn Sinfonietta / Ivo Lille ja Risto Joost ; intervjueerinud Kristina Kõrver
Lille, Ivo, 1977-
2009-01-01
Kontserdiagentuurist HIMusic Agency ja Tallinn Sinfoniettast räägivad dirigent R. Joost ja I. Lille. Avakontserdist Vene Kultuurikeskuses, kus oli kavas Mozarti sümfooniad 1, 10 ja 40 ning kontsertaariad bulgaaria soprani Sonya Youncheva esituses
Wang, Zhiming M
2014-01-01
Featuring material from celebrated innovators in this rapidly developing field of research, this book provides a comprehensive survey of recent advances in a subject certain to yield a host of powerful applications in technology and optoelectronics.
Coalescence-induced nanodroplet jumping
Cha, Hyeongyun; Xu, Chenyu; Sotelo, Jesus; Chun, Jae Min; Yokoyama, Yukihiro; Enright, Ryan; Miljkovic, Nenad
2016-10-01
Water vapor condensation on superhydrophobic surfaces has received much attention in recent years due to the ability of such surfaces to shed microscale water droplets via coalescence-induced droplet jumping, resulting in heat transfer, anti-icing, and self-cleaning performance enhancement. Here we report the coalescence-induced removal of water nanodroplets (R ≈500 nm ) from superhydrophobic carbon nanotube (CNT) surfaces. The two-droplet coalescence time is measured for varying droplet Ohnesorge numbers, confirming that coalescence prior to jumping is governed by capillary-inertial dynamics. By varying the conformal hydrophobic coating thickness on the CNT surface, the minimum jumping droplet radius is shown to increase with increasing solid fraction and decreasing apparent advancing contact angle, allowing us to explore both hydrodynamic limitations stemming from viscous dissipation and surface adhesion limitations. We find that, even for the smallest nanostructure length scale (≤100 nm) and lowest surface adhesions, nonideal surface interactions and the evolved droplet morphology play defining roles in limiting the minimum size for jumping on real surfaces. The outcomes of this work demonstrate the ability to passively shed nanometric water droplets, which has the potential to further increase the efficiency of systems that can harness jumping droplets for a wide range of energy and water applications.
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...
Line tension and the shape of nanodroplets.
Schimmele, L; Dietrich, S
2009-12-01
Various factors are discussed which might influence the equilibrium contact angle of nanodroplets placed on a solid substrate. Special emphasis is put on the possible role of the dependence of the solid-liquid interface tension [Formula: see text] on the pressure in the liquid, which in nanodrops considerably exceeds the saturation pressure. We show that certain published data regarding that dependence are meaningless because these have been deduced based on an inconsistent data analysis.
Coalescence-Induced Jumping of Nanodroplets on Textured Surfaces.
Gao, Shan; Liao, Quanwen; Liu, Wei; Liu, Zhichun
2018-01-04
Conducting experimental studies on nanoscale droplet coalescence using traditional microscopes is a challenging research topic, and views differ as to whether the spontaneous removal can occur in the coalescing nanodroplets. Here, a molecular dynamics simulation is carried out to investigate the coalescence process of two equally sized nanodroplets. On the basis of atomic coordinates, we compute the liquid bridge radii for various cases, which is described by a power law of spreading time, and these nanodroplets undergo coalescence in the inertially limited-viscous regime. Moreover, coalescence-induced jumping is also possible for the nanodroplets, and the attraction force between surface and water molecules plays a crucial role in this process, where the merged nanodroplets prefer to jump away from those surfaces with lower attraction force. When the solid-liquid interaction intensity and surface structure parameters are varied, the attraction force is shown to decrease with decreasing surface wettability intensity and solid fraction.
Water nanodroplets confined in zeolite pores.
Coudert, François-Xavier; Cailliez, Fabien; Vuilleumier, Rodolphe; Fuchs, Alain H; Boutin, Anne
2009-01-01
We provide a comprehensive depiction of the behaviour of a nanodroplet of approximately equal to 20 water molecules confined in the pores of a series of 3D-connected isostructural zeolites with varying acidity, by means of molecular simulations. Both grand canonical Monte Carlo simulations using classical interatomic forcefields and first-principles Car-Parrinello molecular dynamics were used in order to characterise the behaviour of confined water by computing a range of properties, from thermodynamic quantities to electronic properties such as dipole moment, including structural and dynamical information. From the thermodynamic point of view, we have identified the all-silica zeolite as hydrophobic, and the cationic zeolites as hydrophilic; the condensation transition in the first case was demonstrated to be of first order. Furthermore, in-depth analysis of the dynamical and electronic properties of water showed that water in the hydrophobic zeolite behaves as a nanodroplet trying to close its hydrogen-bond network onto itself, with a few short-lived dangling OH groups, while water in hydrophilic zeolites "opens up" to form weak hydrogen bonds with the zeolite oxygen atoms. Finally, the dipole moment of confined water is studied and the contributions of water self-polarisation and the zeolite electric field are discussed.
A Nanodroplet Processor for Advanced Microencapsulated Drug Formulations Project
National Aeronautics and Space Administration — The objective of this proposal is to provide a demonstration of a nanodroplet synthesis of multifunctional liposomes for drug delivery based on immiscible...
A Nanodroplet Processor for Advanced Microencapsulated Drug Formulations, Phase I
National Aeronautics and Space Administration — The objective of this proposal is to provide a demonstration of a nanodroplet synthesis of multifunctional liposomes for drug delivery based on immiscible...
A Nanodroplet Processor for Advanced Microencapsulated Drug Formulations, Phase II
National Aeronautics and Space Administration — During this Phase II program we propose to build on the key aspects of the nanodroplet encapsulation technology to demonstrate optimized formulation and...
Thermophoretic Motion of Water Nanodroplets confined inside Carbon Nanotubes
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Koumoutsakos, Petros
2009-01-01
We study the thermophoretic motion of water nanodroplets confined inside carbon nanotubes using molecular dynamics simulations. We find that the nanodroplets move in the direction opposite the imposed thermal gradient with a terminal velocity that is linearly proportional to the gradient....... The translational motion is associated with a solid body rotation of the water nanodroplet coinciding with the helical symmetry of the carbon nanotube. The thermal diffusion displays a weak dependence on the wetting of the water-carbon nanotube interface. We introduce the use of the Moment Scaling Spectrum (MSS......) in order to determine the characteristics of the motion of the nanoparticles inside the carbon nanotube. The MSS indicates that affinity of the nanodroplet with the walls of the carbon nanotubes is important for the isothermal diffusion, and hence for the Soret coefficient of the system....
Reinders, S.; Blom, F.R.E.
2011-01-01
This article analyzes Joost van den Vondel's career strategies and shows that the ambition for obtaining patronage as a poet played a crucial role in the dedications of his consecutive Vergil translations. In the period 1646-1660 Vondel published three Dutch translations of Vergil, one in prose, one
Theoretical Studies Of Nucleation Kinetics And Nanodroplet Microstructure
International Nuclear Information System (INIS)
Wilemski, Gerald
2009-01-01
The goals of this project were to (1) explore ways of bridging the gap between fundamental molecular nucleation theories and phenomenological approaches based on thermodynamic reasoning, (2) test and improve binary nucleation theory, and (3) provide the theoretical underpinning for a powerful new experimental technique, small angle neutron scattering (SANS) from nanodroplet aerosols, that can probe the compositional structure of nanodroplets. This report summarizes the accomplishments of this project in realizing these goals. Publications supported by this project fall into three general categories: (1) theoretical work on nucleation theory (2) experiments and modeling of nucleation and condensation in supersonic nozzles, and (3) experimental and theoretical work on nanodroplet structure and neutron scattering. These publications are listed and briefly summarized in this report.
Dynamics of metal nanodroplets; Dynamik metallischer Nanotroepfchen
Energy Technology Data Exchange (ETDEWEB)
Habenicht, Anja
2007-11-12
In this work flat metal nanostructures on inert substrates like glass, silicon or graphite have been illuminated by single intensive laser pulses with fluences above the melting threshold. The liquid structures produced in this way are far from their equilibrium shape and a dewetting process starts. On a timescale of a few nanoseconds, the liquid but still flat nanostructure transforms toward a sphere. During this deformation the center of mass moves upward, which can lead to detachment of droplets from the surface due to inertia. The velocity of the detaching nanodroplets is measured with a light barrier technique. The experiment shows that the velocity of the detached droplet is constant over a large range of laser energy densities. This supports the model of a dewetting driven process: The droplet gains surface energy by transforming toward a sphere which is then converted into kinetic energy. Loss mechanisms like excitation of droplet oscillations and dissipation due to viscous friction are discussed. With this model the escape velocity was predicted for nanostructures of different materials and forms, hence other material parameters like surface tension or density and has been confirmed experimentally. The droplets are landed on another surface. Two scenarios are found: There are spheres with a similar shape as the droplet or heavily deformed structures. These structures of splashing and rebounding are identical to the structures which can be observed in the macroscopic impact of liquids. The two scenarios can be explained by different temperatures of the droplets when reaching the substrate. (orig.)
Electronic spectroscopy of aniline ions embedded in helium nanodroplets
Brauer, N.B.; Smolarek, S.D.; Zhang, X.; Buma, W.J.; Drabbels, M.
2011-01-01
Excitation spectra of the Ã2A2←X̃2B1 and B̃2B1←X̃2B1 transitions of aniline cations embedded in helium nanodroplets are reported. The spectra are characterized by broad asymmetric resonances that consist of an intrinsically broadened zero-phonon line, which partially overlaps with the accompanying
Femtosecond water dynamics in reverse-micellar nanodroplets
Cringus, D; Lindner, J; Milder, MTW; Pshenichnikov, MS; Vohringer, P; Wiersma, DA; Milder, Maaike T.W.; Pshenichnikov, Maxim S.; Vöhringer, Peter
2005-01-01
Vibrational energy relaxation and ultrafast thermalization following impulsive excitation of the OH-stretching band of water nanodroplets confined to reverse micelles is studied by infrared pump-probe spectroscopy with sub-100 fs time resolution. The self-consistent analysis of experimental data for
Impulsive Laser Induced Alignment of Molecules Dissolved in Helium Nanodroplets
DEFF Research Database (Denmark)
Pentlehner, Dominik; H. Nielsen, Jens; Slenczka, Alkwin
2013-01-01
We show that a 450 fs nonresonant, moderately intense, linearly polarized laser pulse can induce field-free molecular axis alignment of methyliodide (CH3I) molecules dissolved in a helium nanodroplet. Time-resolved measurements reveal rotational dynamics much slower than that of isolated molecules...
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.
Positron probe to study the freezing of nanodroplets
International Nuclear Information System (INIS)
Pujari, P.K.
2010-01-01
Positron is an excellent in situ probe to study the phase behavior of fluid confined in nanodomains. The study of phase behavior (freezing/melting) of nano confined fluid or nanodroplet has great relevance in fundamental research as well as applications in nano-tribology, nanofabrication, membrane separation, interfacial adhesion and lubrication. It is seen that the properties of freezing/melting of nanodroplets are different from their bulk behavior due to the combined effects of finite size, surface force, surface anisotropy, pore disorder and reduced dimensionality. We have used positron annihilation spectroscopy (PAS) to study the freezing/melting behavior of different organic liquids like benzene, ethylene glycol and isopropanol confined in nanopores of ZSM5 zeolite and silica gel
Influence of contact-line curvature on the evaporation of nanodroplets from solid substrates.
Zhang, Jianguo; Leroy, Frédéric; Müller-Plathe, Florian
2014-07-25
The effect of the three-phase contact-line curvature on the evaporation mechanism of nanoscopic droplets from smooth and chemically homogenous substrates is studied by molecular dynamics simulations. Spherical droplets, whose three-phase contact line is curved, and cylindrical droplets, whose contact radius is infinite, are compared. It is found that the evaporation of cylindrical droplets takes place at constant contact angle, while spherical droplets evaporate by simultaneous reduction of their contact area and their contact angle. This is independent of the substrate-liquid interaction strength. The dependence of the evaporation mechanism on the contact-line curvature can be rationalized with the help of the concept of a contact-line tension, and the evaporation simulations of the spherical droplets are used to extract the line tension on each surface. The corresponding values for the Lennard-Jones systems studied here are of the order of 10(-11)N, which is in a good agreement with previous theoretical and experimental estimates. With this order of magnitude, the line tension is expected to have an effect on the contact angle of spherical droplets only, when their diameter is less than about 100 nm. The observed difference in evaporation mechanism is interpreted as a manifestation of the line tension whose existence has been controversial.
Atomic Scale Imaging of Nucleation and Growth Trajectories of an Interfacial Bismuth Nanodroplet.
Li, Yingxuan; Bunes, Benjamin R; Zang, Ling; Zhao, Jie; Li, Yan; Zhu, Yunqing; Wang, Chuanyi
2016-02-23
Because of the lack of experimental evidence, much confusion still exists on the nucleation and growth dynamics of a nanostructure, particularly of metal. The situation is even worse for nanodroplets because it is more difficult to induce the formation of a nanodroplet while imaging the dynamic process with atomic resolution. Here, taking advantage of an electron beam to induce the growth of Bi nanodroplets on a SrBi2Ta2O9 platelet under a high resolution transmission electron microscope (HRTEM), we directly observed the detailed growth pathways of Bi nanodroplets from the earliest stage of nucleation that were previously inaccessible. Atomic scale imaging reveals that the dynamics of nucleation involves a much more complex trajectory than previously predicted based on classical nucleation theory (CNT). The monatomic Bi layer was first formed in the nucleation process, which induced the formation of the prenucleated clusters. Following that, critical nuclei for the nanodroplets formed both directly from the addition of atoms to the prenucleated clusters by the classical growth process and indirectly through transformation of an intermediate liquid film based on the Stranski-Krastanov growth mode, in which the liquid film was induced by the self-assembly of the prenucleated clusters. Finally, the growth of the Bi nanodroplets advanced through the classical pathway and sudden droplet coalescence. This study allows us to visualize the critical steps in the nucleation process of an interfacial nanodroplet, which suggests a revision of the perspective of CNT.
Transport of lipid nano-droplets through MDCK epithelial cell monolayer.
Khatri, Pulkit; Shao, Jun
2017-05-01
This study aims to investigate the transport of lipid nano-droplets through MDCK epithelial cell monolayer. Nanoemulsions of self-nano-emulsifying drug delivery systems (SNEDDS) labeled with radioactive C18 triglyceride were developed. The effect of droplet size and lipid composition on the transport was investigated. The results showed that the lipid nano-droplet transport through MDCK cell monolayer was as high as 2.5%. The transport of lipid nano-droplets was higher for nanoemulsions of medium chain glycerides than the long chain glycerides. The transport was reduced by more than half when the average lipid nano-droplet size increased from 38nm to 261nm. The droplet size measurement verified the existence of lipid nano-droplets in the receiver chamber only when the nanoemulsions were added to the donor chamber but not when the surfactant or saline solution was added. Cryo-TEM images confirmed the presence of lipid nano-droplets in both donor and receiver chamber at the end of transport study. In conclusion, lipid nano-droplets can be transported through the cell monolayer. This finding may help to further explore the oral and other non-invasive delivery of macromolecules loaded inside SNEDDS. Copyright © 2017 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Mike Keirsbilck
2012-08-01
Full Text Available In 1625 Joost van den Vondel published Palamedes, a play that is usually readas an allegory on the execution of Johan van Oldenbarnevelt. When reading Spinoza's Theological-Political Treatise (1670 it appears that the history of thisexecution still was relevant. Because the two authors share this topic one would suppose a certain connection. Yet, in the factual Vondel and Spinoza studies, the dominant theory states there is little that binds the two authors. With my analyses of their texts I would like to show that it could be useful to approach their connection from another perspective.
Evaluating the Laplace pressure of water nanodroplets from simulations
Malek, Shahrazad M. A.; Sciortino, Francesco; Poole, Peter H.; Saika-Voivod, Ivan
2018-04-01
We calculate the components of the microscopic pressure tensor as a function of radial distance r from the centre of a spherical water droplet, modelled using the TIP4P/2005 potential. To do so, we modify a coarse-graining method for calculating the microscopic pressure (Ikeshoji et al 2003 Mol. Simul. 29 101) in order to apply it to a rigid molecular model of water. As test cases, we study nanodroplets ranging in size from 776 to 2880 molecules at 220 K. Beneath a surface region comprising approximately two molecular layers, the pressure tensor becomes approximately isotropic and constant with r. We find that the dependence of the pressure on droplet radius is that expected from the Young-Laplace equation, despite the small size of the droplets.
Directory of Open Access Journals (Sweden)
Sophie Reinders
2012-03-01
Full Text Available This article analyzes Joost van den Vondel's career strategies and shows that the ambition for obtaining patronage as a poet played a crucial role in the dedications of his consecutive Vergil translations. In the period 1646-1660 Vondel published three Dutch translations of Vergil, one in prose, one 'preview' of the poetry translation, and a final translation of the complete works rendered in verse. For each of the individual dedicatees, the Prince of Orange, the son of the Amsterdam burgomaster Cornelis de Graeff, and the mighty burgomaster himself, the publications' paratexts work to achieve a single goal by means of this work of art: obtaining structural patronage for composing an epic.
Lithium atoms on helium nanodroplets: Rydberg series and ionization dynamics
Lackner, Florian; Krois, Günter; Ernst, Wolfgang E.
2017-11-01
The electronic excitation spectrum of lithium atoms residing on the surface of helium nanodroplets is presented and analyzed employing a Rydberg-Ritz approach. Utilizing resonant two-photon ionization spectroscopy, two different Rydberg series have been identified: one assigned to the nS(Σ) series and the other with predominantly nP(Π) character. For high Rydberg states, which have been resolved up to n = 13, the surrounding helium effectively screens the valence electron from the Li ion core, as indicated by the apparent red-shift of Li transitions and lowered quantum defects on the droplet with respect to their free atom counterparts. For low n states, the screening effect is weakened and the prevailing repulsive interaction gives rise to strongly broadened and blue-shifted transitions. The red-shifts originate from the polarization of nearby He atoms by the positive Li ion core. As a consequence of this effect, the ionization threshold is lowered by 116 ± 10 cm-1 for Li on helium droplets with a radius of about 40 Å. Upon single-photon ionization, heavy complexes corresponding to Li ions attached to intact helium droplets are detected. We conclude that ionization close to the on-droplet ionization threshold triggers a dynamic process in which the Li ion core undergoes a transition from a surface site into the droplet.
Rotovibrational spectroscopy of hydrogen peroxide embedded in superfluid helium nanodroplets.
Raston, Paul L; Knapp, Chrissy J; Jäger, Wolfgang
2011-11-14
We report the infrared depletion spectrum of para- and ortho-hydrogen peroxide embedded in superfluid helium nanodroplets in the OH stretching region. Six transitions were observed in the antisymmetric stretching band (v(5)) of H(2)O(2), and three in the weaker symmetric stretching band (v(1)). While rotations about the b- and c-axes are slowed by a factor of ∼0.4 relative to the gas phase, rotations about the a-axis are not significantly affected; this relates to the rotational speed about the a-axis being too fast for helium density to adiabatically follow. The trans tunneling splitting does not appear to be considerably affected by the helium droplet environment, and is reduced by only 6% relative to the gas phase, under the assumption that the vibrational shifts of the v(5) and v(1) torsional subbands are the same. The linewidths increase with increasing rotorsional energies, and are significantly narrower for energies which fall within the "phonon gap" of superfluid helium. These narrower lines are asymmetrically broadened, indicative of a dynamical coupling between the H(2)O(2) rotor and surrounding helium density.
Laser induced alignment of molecules dissolved in Helium nanodroplets
Stapelfeldt, Henrik
2013-05-01
Laser induced alignment, the method to confine the principal axes of molecules along axes fixed in the laboratory frame, is now used in a range of applications in physics and chemistry. With a few exceptions all studies have focused on isolated molecules in the gas phase. In this talk we present experimental studies of laser induced alignment of molecules embedded in the solvent of a superfluid helium nanodroplet. Alignment is conducted in both the adiabatic and the nonadiabtic regime where the alignment pulse is much longer or shorter, respectively, than the rotational period of the molecules. In the nonadiabatic limit, induced by a few-hundred femtosecond long laser pulse, we show that methyliodide molecules reach an alignment maximum 20 ps after the alignment pulse and gradually loose the alignment completely in another 60 ps. This dynamics is completely different from that of isolated methyliodide molecules where alignment occurs in regularly spaced (by 33.3 ps), narrow time windows, termed revivals. Adiabatic alignment, induced by 10 ns laser pulses, resembles the gas phase behavior although the observed degree of alignment falls below that of isolated molecules. Work done in collaboration with Dominik Pentkehner, Department of Chemistry, Aarhus University; Jens Hedegaard Nielsen, Department of Physics, Aarhus University; Alkwin Slenczka, Department of Chemistry, Regensburg University; and Klaus Mølmer, Department of Physics, Aarhus University.
Thermophoretic transport of water nanodroplets conﬁned in carbon nanotubes: the role of friction
DEFF Research Database (Denmark)
Oyarzua, Elton; Walther, Jens Honore; Zambrano, Harvey
The development of eﬃcient nanoﬂuidic devices requires driving mechanisms that provide controlled transport of ﬂuids through nanoconduits. Temperature gradients have been proposed as a mechanism to drive particles, fullerenes and nanodroplets inside carbon nanotubes (CNTs). In this work, molecula...
Electronic Relaxation Processes of Transition Metal Atoms in Helium Nanodroplets
Kautsch, Andreas; Lindebner, Friedrich; Koch, Markus; Ernst, Wolfgang E.
2014-06-01
Spectroscopy of doped superfluid helium nanodroplets (He_N) gives information about the influence of this cold, chemically inert, and least interacting matrix environment on the excitation and relaxation dynamics of dopant atoms and molecules. We present the results from laser induced fluorescence (LIF), photoionization (PI), and mass spectroscopy of Cr and Cu doped He_N. From these results, we can draw a comprehensive picture of the complex behavior of such transition metal atoms in He_N upon photo-excitation. The strong Cr and Cu ground state transitions show an excitation blueshift and broadening with respect to the bare atom transitions which can be taken as indication for the solvation inside the droplet. From the originally excited states the atoms relax to energetically lower states and are ejected from the He_N. The relaxation processes include bare atom spin-forbidden transitions, which clearly bears the signature of the He_N influence. Two-color resonant two-photon ionization (2CR2PI) also shows the formation of bare atoms and small Cr-He_n and Cu-He_n clusters in their ground and metastable states ^c. Currently, Cr dimer excitation studies are in progress and a brief outlook on the available results will be given. C. Callegari and W. E. Ernst, Helium Droplets as Nanocryostats for Molecular Spectroscopy - from the Vacuum Ultraviolet to the Microwave Regime, in Handbook of High-Resolution Spectroscopy, eds. M. Quack and F. Merkt, John Wiley & Sons, Chichester, 2011. A. Kautsch, M. Koch, and W. E. Ernst, J. Phys. Chem. A, 117 (2013) 9621-9625, DOI: 10.1021/jp312336m F. Lindebner, A. Kautsch, M. Koch, and W. E. Ernst, Int. J. Mass Spectrom. (2014) in press, DOI: 10.1016/j.ijms.2013.12.022 M. Koch, A. Kautsch, F. Lackner, and W. E. Ernst, submitted to J. Phys. Chem. A
Baghbani, Fatemeh; Moztarzadeh, Fathollah
2017-05-01
Ultrasound-responsive perfluorocarbon nanoemulsions are a class of new multifunctional smart nanocarriers which combine diagnostic properties with therapeutic properties and release their drug payload in a controlled manner in response to ultrasound. Therefore, combination therapy using chemotherapeutic and chemosensitizing agents co-entrapped in these nanocarriers seems beneficial for cancer treatment. In the present study, multifunctional smart alginate/perfluorohexane nanodroplets were developed for co-delivery of doxorubicin and curcumin (a strong chemosensitizer). The nanodroplets with the average particle size of 55.1nm were synthesized via nanoemulsion process. The entrapment efficiency of doxorubicin was 92.3%. To improve curcumin entrapment into the alginate shell, Span 60 was added to the formulation as a co-surfactant and finally curcumin entrapment of about 40% was achieved. Ultrasound-mediated drug release kinetic was evaluated at two different frequencies of 28kHz (low frequency) and 1MHz (high frequency). Low frequency ultrasound resulted in higher triggered drug release from nanodroplets. The nanodroplets showed strong ultrasound contrast via droplet to bubble transition as confirmed via B-mode ultrasound imaging. Enhanced cytotoxicity in adriamycin-resistant A2780 ovarian cancer cells was observed for Dox-Cur-NDs compared to Dox-NDs because of the synergistic effects of doxorubicin and curcumin. However, ultrasound irradiation significantly increased the cytotoxicity of Dox-Cur-NDs. Finally, in vivo ovarian cancer treatment using Dox/Cur-NDs combined with ultrasound irradiation resulted in efficient tumor regression. According to the present study, nanotherapy of multidrug resistant human ovarian cancer using ultrasound responsive doxorubicin/curcumin co-loaded alginate-shelled nanodroplets combined with ultrasound irradiation could be a promising modality for the future of cancer treatment. Copyright © 2017 Elsevier B.V. All rights reserved.
Wang, Long-Hai; Xu, Xiao-Man; Hong, Chun-Yan; Wu, De-Cheng; Yu, Zhi-Qiang; You, Ye-Zi
2014-09-04
Generally, it is very difficult to control the size of large compound vesicles. Here, we introduce a novel method for the preparation of biodegradable large compound vesicles with controlled size and narrow size distribution by using aqueous nanodroplets as templates.
Molecular rotation and dynamics in superfluid ^4He nanodroplets
Callegari, Carlo
2001-05-01
Cavity-enhanced laser radiation, coupled to molecular-beam bolometric detection has been used to study the spectroscopy of acetylenic molecules embedded in helium nanodroplets. The 2ν1 transition (CH stretch overtone) of HCN, DCCH, NCCCH, CH_3CCH, CF_3CCH, (CH_3)_3CCCH, (CH_3)_3SiCCH, has been investigated in the 1.5 μm spectral region by means of a color center laser coupled to a resonant buildup cavity, which enhances the laser power experienced by the molecules in the beam by up to a factor of 400, thus overcoming the weakness of the (harmonically forbidden) transitions. All molecules are observed to rotate freely in the liquid cluster environment, with strongly enhanced moments of inertia, but with negligible matrix induced shifts (less than 1 cm-1). We show that this enhancement is largely accounted for by hydrodynamic effects, which we have modeled and numerically calculated. While in the gas phase the rotational lines have instrument-limited widths (a few MHz), in the droplets we have observed linewidths ranging from 600 MHz for (CH_3)_3SiCCH to 2.8 GHz for (CH_3)_3CCCH. To investigate the nature of the broadening (which was widely believed to be homogeneous), we have performed a series of infrared (IR) saturation experiments on the 2ν1 transition. We have also thoroughly investigated NCCCH by means of microwave (MW) single-resonance experiments (on rotational transitions) and double-resonance (MW-MW and MW-IR) experiments. The results demonstrate that the spectral features of molecules in He droplets are inhomogeneously broadened, and allow an estimate of the importance of the different broadening contributions. In particular, MW-IR measurements show that the size of the cluster greatly affects the way rotational energy is relaxed. Large clusters seem to follow a ``strong collision model'' where memory of the initial rotational state is completely lost after each ``relaxation'' event, while for smaller clusters relaxation rates are probably affected by
Molecular rotation and dynamics in superfluid helium-4 nanodroplets
Callegari, Carlo
2000-11-01
Cavity-enhanced laser radiation, coupled to molecular- beam bolometric detection has been used to study the spectroscopy of acetylenic molecules embedded in helium nanodroplets. The 2ν1 transition (CH stretch overtone) of HCN, DCCH, NCCCH, CH3CCH, CF3CCH, (CH 3)3CCCH, (CH3)3SiCCH, has been investigated in the 1.5 μm spectral region by means of a color center laser coupled to a resonant build-up cavity, which enhances the laser power experienced by the molecules in the beam by up to a factor of 400, thus overcoming the weakness of the (dipole forbidden) transitions. All molecules are observed to rotate freely in the liquid cluster environment, with strongly enhanced moments of inertia, but with negligible matrix induced shifts (less than 1 cm-1). We show that this enhancement is largely accounted for by hydrodynamic effects, which we have modeled and numerically calculated. While in the gas phase the rotational lines have instrument-limited widths (a few MHZ), in the droplets we have observed linewidths ranging from 600 MHz for (CH3)3SiCCH to 2.8GHz for (CH3) 3CCCH. To investigate the nature of the broadening (which was widely believed to be homogeneous), we have performed a series of infrared (IR) saturation experiments on the 2ν1 transition. We have also thoroughly investigated NCCCH by means of microwave (MW) single-resonance experiments (on rotational transitions) and double-resonance (MW-MW and MW-IR) experiments. The results demonstrate that the spectral features of molecules in He droplets are inhomogeneously broadened, and allow an estimate of the importance of the different broadening contributions. In particular, MW-IR measurements show that the size of the cluster greatly affects the way rotational energy is relaxed. Large clusters seem to follow a ``strong collision model'' where memory of the initial rotational state is completely lost after each ``relaxation'' event, while for smaller clusters relaxation rates are probably affected by the lower
Horne, Joseph E; Lavrik, Nickolay V; Terrones, Humberto; Fuentes-Cabrera, Miguel
2015-06-30
In an effort to enhance our knowledge on how to control the movement of metallic nanodroplets, here we have used classical molecular dynamics simulations to investigate whether Cu nanostructures deposited on nanopillared substrates can be made to jump at desired angles. We find that such control is possible, especially for Cu nanostructures that are symmetric; for asymmetric nanostructures, however, control is more uncertain. The work presented here borrows ideas from two seemingly different fields, metallic droplets and water droplets in the dynamic Leidenfrost regime. Despite the differences in the respective systems, we find common ground in their behavior on nanostructured surfaces. Due to this, we suggest that the ongoing research in Leidenfrost droplets is a fertile area for scientists working on metallic nanodroplets.
Liquid nanodroplet formation through phase explosion mechanism in laser-irradiated metal targets.
Mazzi, Alberto; Gorrini, Federico; Miotello, Antonio
2015-09-01
Some quantitative aspects of laser-irradiated pure metals, while approaching phase explosion, are still not completely understood. Here, we develop a model that describes the main quantities regulating the liquid-vapor explosive phase transition and the expulsion of liquid nanodroplets that, by solidifying, give rise to nanoparticle formation. The model combines both a thermodynamics description of the explosive phase change and a Monte Carlo simulation of the randomly generated critical vapor bubbles. The calculation is performed on a set of seven metals (Al, Fe, Co, Ni, Cu, Ag, and Au) which are frequently used in pulsed laser ablation experiments. Our final predictions about the size distribution of the liquid nanodroplets and the number ratio of liquid/vapor ejected atoms are compared, whenever possible, with available molecular dynamics simulations and experimental data.
Wu, Shih-Ying; Fix, Samantha M.; Arena, Christopher B.; Chen, Cherry C.; Zheng, Wenlan; Olumolade, Oluyemi O.; Papadopoulou, Virginie; Novell, Anthony; Dayton, Paul A.; Konofagou, Elisa E.
2018-02-01
Focused ultrasound with nanodroplets could facilitate localized drug delivery after vaporization with potentially improved in vivo stability, drug payload, and minimal interference outside of the focal zone compared with microbubbles. While the feasibility of blood-brain barrier (BBB) opening using nanodroplets has been previously reported, characterization of the associated delivery has not been achieved. It was hypothesized that the outcome of drug delivery was associated with the droplet’s sensitivity to acoustic energy, and can be modulated with the boiling point of the liquid core. Therefore, in this study, octafluoropropane (OFP) and decafluorobutane (DFB) nanodroplets were used both in vitro for assessing their relative vaporization efficiency with high-speed microscopy, and in vivo for delivering molecules with a size relevant to proteins (40 kDa dextran) to the murine brain. It was found that at low pressures (300-450 kPa), OFP droplets vaporized into a greater number of microbubbles compared to DFB droplets at higher pressures (750-900 kPa) in the in vitro study. In the in vivo study, successful delivery was achieved with OFP droplets at 300 kPa and 450 kPa without evidence of cavitation damage using ¼ dosage, compared to DFB droplets at 900 kPa where histology indicated tissue damage due to inertial cavitation. In conclusion, the vaporization efficiency of nanodroplets positively impacted the amount of molecules delivered to the brain. The OFP droplets due to the higher vaporization efficiency served as better acoustic agents to deliver large molecules efficiently to the brain compared with the DFB droplets.
Helium Nanodroplet Isolation of Ionic Liquid Vapor: Inrared Laser Spectroscopy of [EMIM][Tf_2N
Flynn, Steven D.; Douberly, Gary E.
2012-06-01
The Infrared spectrum of the vapor produced upon thermal vaporization of the [emim][Tf_2N] ionic liquid has been obtained using the helium nanodroplet isolation method. Despite the low vapor pressure of [emim][Tf_2N], sufficient gas phase densities are produced, allowing for efficient helium nanodroplet pick-up. The mass spectrum of the emim[Tf_2N] doped droplet beam shows signatures that have been attributed in gas phase measurements to the presence of isolated, intact [emim][Tf_2N] ion-pairs. Furthermore, the mass spectrometry results indicate that emim[Tf_2N] does not undergo thermal decomposition at 410 K. Comparisons are made between the experimental measurements and ab initio calculations (mp2/6-311++g(d,p)) of the CH stretch vibrational bands and permanent electric dipole moments for several [emim][Tf_2N] low energy isomers. The helium nanodroplet infrared spectrum of this species provides rather definitive support to the previously suggested vaporization mechanism of ionic liquids. [emim][Tf_2N] is defined as 1-ethyl-3-methylimidazolium[bis(trifluoromethylsulfonyl)imide] Armstrong, J.P.; Hurst, C.; Jones, R. G.; Licence, P.; Lovelock, K. R. J.; Satterley, C. J.; Villar-Garcia, I. J. Physical Chemistry Chemical Physics 2007, 9, 982. Strasser, D.; Goulay, F.; Belau, L.; Kostko, O.; Koh, C.; Chambreau, S. D.; Vaghjiani, G. L.; Ahmed, M.; Leone, S. R. Journal of Physical Chemistry A 2010, 114, 879. Strasser, D.; Goulay, F.; Kelkar, M. S.; Maginn, E. J.; Leone, S. R. Journal of Physical Chemistry A 2007, 111, 3191. Chambreau, S. D.; Vaghjiani, G. L.; To, A.; Koh, C.; Strasser, D.; Kostko, O.; Leone, S. R. Journal of Physical Chemistry B 2010, 114, 1361. Maginn, E. J.; Kelkar, M. S. Journal of Physical Chemistry B 2007, 111, 9424.
Interaction of SO2 with the Surface of a Water Nanodroplet.
Zhong, Jie; Zhu, Chongqin; Li, Lei; Richmond, Geraldine L; Francisco, Joseph S; Zeng, Xiao Cheng
2017-11-29
We present a comprehensive computational study of interaction of a SO 2 with water molecules in the gas phase and with the surface of various sized water nanodroplets to investigate the solvation behavior of SO 2 in different atmospheric environments. Born-Oppenheimer molecular dynamics (BOMD) simulation shows that, in the gas phase and at a temperature of 300 K, the dominant interaction between SO 2 and H 2 O is (SO 2 ) S···O (H 2 O) , consistent with previous density-functional theory (DFT) computation at 0 K. However, at the surface of a water nanodroplet, BOMD simulation shows that the hydrogen-bonding interaction of (SO 2 ) O···H (H 2 O) becomes increasingly important with the increase of droplet size, reflecting a marked effect of the water surface on the SO 2 solvation. This conclusion is in good accordance with spectroscopy evidence obtained previously (J. Am. Chem. Soc. 2005, 127, 16806; J. Am. Chem. Soc. 2006, 128, 3256). The prevailing interaction (SO 2 ) O···H (H 2 O) on a large droplet is mainly due to favorable exposure of H atoms of H 2 O at the air-water interface. Indeed, the conversion of the dominant interaction in the gas phase (SO 2 ) S···O (H 2 O) to the dominant interaction on the water nanodroplet (SO 2 ) O···H (H 2 O) may incur effects on the SO 2 chemistry in atmospheric aerosols because the solvation of SO 2 at the water surface can affect the reactive sites and electrophilicity of SO 2 . Hence, the solvation of SO 2 on the aerosol surface may have new implications when studying SO 2 chemistry in the aerosol-containing troposphere.
Paproski, Robert J; Jovel, Juan; Wong, Gane Ka-Shu; Lewis, John D; Zemp, Roger J
2017-01-01
The feasibility of personalized medicine approaches will be greatly improved by the development of noninvasive methods to interrogate tumor biology. Extracellular vesicles shed by solid tumors into the bloodstream have been under recent investigation as a source of tumor-derived biomarkers such as proteins and nucleic acids. We report here an approach using submicrometer perfluorobutane nanodroplets and focused ultrasound to enhance the release of extracellular vesicles from specific locations in tumors into the blood. The released extracellular vesicles were enumerated and characterized using micro flow cytometry. Only in the presence of nanodroplets could ultrasound release appreciable levels of tumor-derived vesicles into the blood. Sonication of HT1080-GFP tumors did not increase the number of circulating tumor cells or the metastatic burden in the tumor-bearing embryos. A variety of biological molecules were successfully detected in tumor-derived extracellular vesicles, including cancer-associated proteins, mRNAs, and miRNAs. Sonication of xenograft HT1080 fibrosarcoma tumors released extracellular vesicles that contained detectable RAC1 mRNA with the highly tumorigenic N92I mutation known to exist in HT1080 cells. Deep sequencing serum samples of embryos with sonicated tumors allowed the identification of an additional 13 known heterozygous mutations in HT1080 cells. Applying ultrasound to HT1080 tumors increased tumor-derived DNA in the serum by two orders of magnitude. This work is the first demonstration of enhanced extracellular vesicle release by ultrasound stimulation and suggests that nanodroplets/ultrasound offers promise for genetic profiling of tumor phenotype and aggressiveness by stimulating the release of extracellular vesicles. Cancer Res; 77(1); 3-13. ©2016 AACR. ©2016 American Association for Cancer Research.
International Nuclear Information System (INIS)
Lu, Gui; Hu, Han; Sun, Ying; Duan, Yuanyuan
2013-01-01
In this Letter, dynamic wetting of water nano-droplets containing non-surfactant gold nanoparticles on a gold substrate is examined via molecular dynamics simulations. The results show that the addition of non-surfactant nanoparticles hinders the nano-second droplet wetting process, attributed to the increases in both surface tension of the nanofluid and friction between nanofluid and substrate. The droplet wetting kinetics decreases with increasing nanoparticle loading and water-particle interaction energy. The observed wetting suppression and the absence of nanoparticle ordering near the contact line of nano-sized droplets differ from the wetting behaviors reported from nanofluid droplets of micron size or larger
Communication: X-ray coherent diffractive imaging by immersion in nanodroplets
Directory of Open Access Journals (Sweden)
Rico Mayro P. Tanyag
2015-09-01
Full Text Available Lensless x-ray microscopy requires the recovery of the phase of the radiation scattered from a specimen. Here, we demonstrate a de novo phase retrieval technique by encapsulating an object in a superfluid helium nanodroplet, which provides both a physical support and an approximate scattering phase for the iterative image reconstruction. The technique is robust, fast-converging, and yields the complex density of the immersed object. Images of xenon clusters embedded in superfluid helium droplets reveal transient configurations of quantum vortices in this fragile system.
Kontrastide maa Brasiilia / Meelis Joost
Joost, Meelis
2011-01-01
Artikli autor kuulus Euroopa Majandus- ja Sotsiaalkomitee delegatsioon, mis külastas lihavõttenädalale järgneval nädalal Brasiilia Majandus– ja Sotsiaalnõukogu kutsel Brasiilia Föderatsiooni pealinna Brasíliat ning riigi esimest pealinna, praegust Bahia osariigi pealinna Salvadori, et osaleda 4. EL– Brasiilia kodanikuühiskonna ümarlaual
Dynamics of liquid nanodroplet formation in nanosecond laser ablation of metals
Mazzi, A.; Gorrini, F.; Miotello, A.
2017-10-01
The laser ablation mechanisms of metallic targets leading to liquid nanodroplet ejection are of wide interest both from a fundamental point of view and for applications in various fields, especially when nanoparticle synthesis is required. The phase explosion process was recognized as the driving mechanism of the expulsion of a mixture of vapor and liquid nanodroplets in the short pulse laser ablation of metals. A model based on thermodynamics that links the theory of homogeneous vapor bubble nucleation to the size distribution of the generated liquid nanoclusters has been recently proposed. The present work aims to take a step ahead to remove some assumptions made in previous work. Here an improved computational approach allows us to describe time-dependent nucleation in a homogeneous system with no temperature spatial gradients under nanosecond laser irradiation. Numerical results regarding the size distribution of formed liquid clusters and the time evolution of the process are shown for aluminum, iron, cobalt, nickel, copper, silver and gold. Connections with experimental data and molecular dynamics simulations, when available from literature, are reported and discussed.
Molecular Dynamics Simulation of Water Nanodroplets on Silica Surfaces at High Air Pressures
DEFF Research Database (Denmark)
Zambrano, Harvey A; Jaffe, Richard Lawrence; Walther, Jens Honore
2010-01-01
e.g., nanobubbles. In the present work we study the role of air on the wetting of hydrophilic systems. We conduct molecular dynamics simulations of a water nanodroplet on an amorphous silica surface at different air pressures. The interaction potentials describing the silica, water, and air...... are obtained from the literature. The silica surface is modeled by a large 32 ⨯ 32 ⨯ 2 nm amorphous SiO2 structure consisting of 180000 atoms. The water consists of 18000 water molecules surrounded by N2 and O2 air molecules corresponding to air pressures of 0 bar (vacuum), 50 bar, 100 bar and 200 bar. We...... the effect of air and find a consistent increase in the water contact angle reaching 53º at 200 bar air pressure. These results are important for the creation and stability of nanobubbles at hydrophilic interfaces....
Fragmentation dynamics of ionized neon trimer inside helium nanodroplets: a theoretical study.
Bonhommeau, David; Viel, Alexandra; Halberstadt, Nadine
2004-06-22
We report a theoretical study of the fragmentation dynamics of Ne(3) (+) inside helium nanodroplets, following vertical ionization of the neutral neon trimer. The motion of the neon atoms is treated classically, while transitions between the electronic states of the ionic cluster are treated quantum mechanically. A diatomics-in-molecules description of the potential energy surfaces is used, in a minimal basis set consisting of three effective p orbitals on each neon atom for the missing electron. The helium environment is modeled by a friction force acting on the neon atoms when their speed exceeds the Landau velocity. A reasonable range of values for the corresponding friction coefficient is obtained by comparison with existing experimental measurements. (c) 2004 American Institute of Physics.
International Nuclear Information System (INIS)
Gamero-Castano, Manuel
2009-01-01
The determination of the mass of a nanoparticle via time-of-flight typically requires a direct measurement of its charge. This can be done with a differential retarding potential analyzer and an induction charge detector operating in tandem. The spectrometer described in this article selects a particle with a specified retarding potential from a beam and directs it to an induction charge detector where both its velocity and charge are measured. The retarding potential, velocity, and charge also yield the particle's mass. The particle is analyzed without the need to collect it, and therefore can be employed in a subsequent experiment. The high charge sensitivity of the induction charge detector and the capability for working at low retarding potentials make the characterization of electrosprayed nanodroplets possible for the first time.
Tramonto, F.; Salvestrini, P.; Nava, M.; Galli, D. E.
2015-07-01
By means of the Path Integral Monte Carlo method, we have performed a detailed microscopic study of 4He nanodroplets doped with an argon ion, Ar, at K. We have computed density profiles, energies, dissociation energies, and characterized the local order around the ion for nanodroplets with a number of 4He atoms ranging from 10 to 64 and also 128. We have found the formation of a stable solid structure around the ion, a "snowball", consisting of three concentric shells in which the 4He atoms are placed at the vertices of platonic solids: the first inner shell is an icosahedron (12 atoms); the second one is a dodecahedron with 20 atoms placed on the faces of the icosahedron of the first shell; the third shell is again an icosahedron composed of 12 atoms placed on the faces of the dodecahedron of the second shell. The "magic numbers" implied by this structure, 12, 32, and 44 helium atoms, have been observed in a recent experimental study (Bartl et al., J Phys Chem A 118:8050, 2014) of these complexes; the dissociation energy curve computed in the present work shows jumps in correspondence with those found in the nanodroplets abundance distribution measured in that experiment, strengthening the agreement between theory and experiment. The same structures were predicted in Galli et al. (J Phys Chem A 115:7300, 2011) in a study regarding Na+@4He when ; a comparison between Ar+@4He and Na+@4He complexes is also presented.
Baghbani, Fatemeh; Chegeni, Mahdieh; Moztarzadeh, Fathollah; Mohandesi, Jamshid Aghazadeh; Mokhtari-Dizaji, Manijhe
2017-08-01
Development of a new class of multifunctional ultrasound-responsive smart nanocarriers that combine therapeutic properties with diagnostic imaging has gained great attention in recent years. Here, we describe the results of ultrasonic nanotherapy of breast cancer using novel alginate-stabilized perfluorohexane nanodroplets. Doxorubicin (Dox)-loaded multifunctional nanodroplets (Dox-NDs) were synthesized via nanoemulsion process and evaluated in vitro and in vivo with focus on cytotoxicity, hemolytic activity, biodistribution, biosafety, and antitumor activity. Echogenic property of nanodroplets was confirmed by B-mode ultrasound imaging. Tumor therapy using Dox-NDs combined with sonication (Dox-ND-US) resulted in strong in vivo antitumor activity characterized by tumor regression which could be because of on demand efficient ultrasound-aided drug release from nanodroplets in tumor tissue under the action of ultrasound. Dox concentration in tumor area for Dox-ND-US treated group reached 10.9μg/g after sonication for 4min (28kHz, 0.034W/cm 2 ), which was 5.2-fold higher compared to non-sonicated Dox-NDs group. The cardiotoxicity of Dox-NDs was much lower than that of free Dox and no hemolytic activity was observed for Dox-NDs. Strong therapeutic effect of these multifunctional nanodroplets combined with their ultrasound-contrast property indicated that this drug delivery system has a great potential in smart cancer-therapy. Copyright © 2017 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Guo H
2017-06-01
Full Text Available Hao Guo,1 Ziming Wang,1 Quanyin Du,1 Pan Li,2 Zhigang Wang,2 Aimin Wang1 1Department of Orthopedics, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China; 2Chongqing Key Laboratory of Ultrasound Molecular Imaging, Institute of Ultrasound Imaging, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China Purpose: Bacterial biofilms on the surface of prostheses are becoming a rising concern in managing prosthetic joint infections. The inherent resistant features of biofilms render traditional antimicrobial therapy unproductive and revision surgery outcomes uncertain. This situation has prompted the exploration of novel antimicrobial strategies. The synergy of ultrasound microbubbles and vancomycin has been proposed as an efficient alternative for biofilm eradication. The purpose of this study was to evaluate the anti-biofilm effect of stimulated phase-shift acoustic nanodroplets (NDs combined with vancomycin.Materials and methods: We fabricated lipid phase-shift NDs with a core of liquid perfluoropentane. A new phase change mode for NDs incorporating an initial unfocused low-intensity pulsed ultrasound for 5 minutes and a subsequent incubation at 37°C into a 24-hour duration was developed. Methicillin-resistant Staphylococcus aureus (MRSA biofilms were incubated with vancomycin and NDs under the hybrid stimulation. Biofilm morphology following treatment was determined using confocal laser scanning microscopy and scanning electron microscopy. Resazurin assay was used to quantify bactericidal efficacy against MRSA biofilm bacteria.Results: NDs treated sequentially with ultrasound and heating at 37°C achieved gradual and substantial ND vaporization and cavitation in a successive process. NDs after stimulation were capable of generating stronger destruction on biofilm structure which was best characterized by residual circular arc margins and more dead bacteria. Furthermore, NDs
Application of Ultrasound to Selectively Localize Nanodroplets for Targeted Imaging and Therapy
Directory of Open Access Journals (Sweden)
Paul A. Dayton
2006-07-01
Full Text Available Lipid-coated perfluorocarbon nanodroplets are submicrometer-diameter liquid-filled droplets with proposed applications in molecularly targeted therapeutics and ultrasound (US imaging. Ultrasonic molecular imaging is unique in that the optimal application of these agents depends not only on the surface chemistry, but also on the applied US field, which can increase receptor-ligand binding and membrane fusion. Theory and experiments are combined to demonstrate the displacement of perfluorocarbon nanoparticles in the direction of US propagation, where a traveling US wave with a peak pressure on the order of megapascals and frequency in the megahertz range produces a particle translational velocity that is proportional to acoustic intensity and increases with increasing center frequency. Within a vessel with a diameter on the order of hundreds of micrometers or larger, particle velocity on the order of hundreds of micrometers per second is produced and the dominant mechanism for droplet displacement is shown to be bulk fluid streaming. A model for radiation force displacement of particles is developed and demonstrates that effective particle displacement should be feasible in the microvasculature. In a flowing system, acoustic manipulation of targeted droplets increases droplet retention. Additionally, we demonstrate the feasibility of US-enhanced particle internalization and therapeutic delivery.
Energy Technology Data Exchange (ETDEWEB)
Douberly, Gary Elliott [Univ. of Georgia, Athens, GA (United States)
2017-11-16
The objective of our experimental research program is to isolate and stabilize transient intermediates and products of prototype combustion reactions. This will be accomplished by Helium Nanodroplet Isolation, a novel technique where liquid helium droplets freeze out high energy metastable configurations of a reacting system, permitting infrared spectroscopic characterizations of products and intermediates that result from hydrocarbon radical reactions with molecular oxygen and other small molecules relevant to combustion environments. The low temperature (0.4 K) and rapid cooling associated with He droplets provides a perfectly suited medium to isolate and probe a broad range of molecular radical and carbene systems important to combustion chemistry. The sequential addition of molecular species to He droplets often leads to the stabilization of high-energy, metastable cluster configurations that represent regions of the potential energy surface far from the global minimum. Single and double resonance IR laser spectroscopy techniques, along with Stark and Zeeman capabilities, are being used to probe the structural and dynamical properties of these systems.
Directory of Open Access Journals (Sweden)
Yuliang Wang
2017-12-01
Full Text Available Interfacial nanobubbles (NBs and nanodroplets (NDs have been attracting increasing attention due to their potential for numerous applications. As a result, the automated segmentation and morphological characterization of NBs and NDs in atomic force microscope (AFM images is highly awaited. The current segmentation methods suffer from the uneven background in AFM images due to thermal drift and hysteresis of AFM scanners. In this study, a two-step approach was proposed to segment NBs and NDs in AFM images in an automated manner. The spherical Hough transform (SHT and a boundary optimization operation were combined to achieve robust segmentation. The SHT was first used to preliminarily detect NBs and NDs. After that, the so-called contour expansion operation was applied to achieve optimized boundaries. The principle and the detailed procedure of the proposed method were presented, followed by the demonstration of the automated segmentation and morphological characterization. The result shows that the proposed method gives an improved segmentation result compared with the thresholding and circle Hough transform method. Moreover, the proposed method shows strong robustness of segmentation in AFM images with an uneven background.
Wang, Yuliang; Lu, Tongda; Li, Xiaolai; Ren, Shuai; Bi, Shusheng
2017-01-01
Interfacial nanobubbles (NBs) and nanodroplets (NDs) have been attracting increasing attention due to their potential for numerous applications. As a result, the automated segmentation and morphological characterization of NBs and NDs in atomic force microscope (AFM) images is highly awaited. The current segmentation methods suffer from the uneven background in AFM images due to thermal drift and hysteresis of AFM scanners. In this study, a two-step approach was proposed to segment NBs and NDs in AFM images in an automated manner. The spherical Hough transform (SHT) and a boundary optimization operation were combined to achieve robust segmentation. The SHT was first used to preliminarily detect NBs and NDs. After that, the so-called contour expansion operation was applied to achieve optimized boundaries. The principle and the detailed procedure of the proposed method were presented, followed by the demonstration of the automated segmentation and morphological characterization. The result shows that the proposed method gives an improved segmentation result compared with the thresholding and circle Hough transform method. Moreover, the proposed method shows strong robustness of segmentation in AFM images with an uneven background.
Energy Technology Data Exchange (ETDEWEB)
Zhu, Ying; Piehowski, Paul D.; Zhao, Rui; Chen, Jing; Shen, Yufeng; Moore, Ronald J.; Shukla, Anil K.; Petyuk, Vladislav A.; Campbell-Thompson, Martha; Mathews, Clayton E.; Smith, Richard D.; Qian, Wei-Jun; Kelly, Ryan T.
2018-02-28
Nanoscale or single cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (Nanodroplet Processing in One pot for Trace Samples) platform as a major advance in overall sensitivity. NanoPOTS dramatically enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive LC-MS, nanoPOTS allows identification of ~1500 to ~3,000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins were consistently identified from as few as 10 cells. Furthermore, we demonstrate robust quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.
Cracks and nanodroplets produced on tungsten surface samples by dense plasma jets
Ticoş, C. M.; Galaţanu, M.; Galaţanu, A.; Luculescu, C.; Scurtu, A.; Udrea, N.; Ticoş, D.; Dumitru, M.
2018-03-01
Small samples of 12.5 mm in diameter made from pure tungsten were exposed to a dense plasma jet produced by a coaxial plasma gun operated at 2 kJ. The surface of the samples was analyzed using a scanning electron microscope (SEM) before and after applying consecutive plasma shots. Cracks and craters were produced in the surface due to surface tensions during plasma heating. Nanodroplets and micron size droplets could be observed on the samples surface. An energy-dispersive spectroscopy (EDS) analysis revealed that the composition of these droplets coincided with that of the gun electrode material. Four types of samples were prepared by spark plasma sintering from powders with the average particle size ranging from 70 nanometers up to 80 μm. The plasma power load to the sample surface was estimated to be ≈4.7 MJ m-2 s-1/2 per shot. The electron temperature and density in the plasma jet had peak values 17 eV and 1.6 × 1022 m-3, respectively.
Chemical solutions in a quantum solvent: anionic electrolytes in 4He nanodroplets.
Coccia, Emanuele; Marinetti, Fabio; Bodo, Enrico; Gianturco, Francesco A
2008-06-23
Variational and diffusion Monte Carlo (VMC and DMC) calculations are presented for anionic electrolytes solvated in (4)He. The electrolytes have the general structure X(-)(He)(N), with X=F, Cl, Br and I, and N varying up to 40 (41 for I(-)). The overall interaction potential is obtained from accurate ab initio data for the two-body components and then using the sum-of-potentials approximation. Our computational scheme is a robust procedure, giving us accurate trial wavefunctions that can be used to perform high-quality DMC calculations. The results indicate very marked delocalization and permanence of the liquid-like quantum features of the solvent adatoms surrounding the anionic impurities. This finding stands in contrast to the more structured, solid-like behavior of the quantum solutions with alkali metal cations embedded in He nanodroplets. While other negatively charged species such as H(-) have shown an overall repulsive interaction with He, the present calculations clearly indicate that the halogen anions remain solvated within liquid-like solvent "bubbles" of species-dependent size.
International Nuclear Information System (INIS)
Pentlehner, D.; Slenczka, A.
2015-01-01
Electronic spectra of organic molecules doped into superfluid helium nanodroplets show characteristic features induced by the helium environment. Besides a solvent induced shift of the electronic transition frequency, in many cases, a spectral fine structure can be resolved for electronic and vibronic transitions which goes beyond the expected feature of a zero phonon line accompanied by a phonon wing as known from matrix isolation spectroscopy. The spectral shape of the zero phonon line and the helium induced phonon wing depends strongly on the dopant species. Phonon wings, for example, are reported ranging from single or multiple sharp transitions to broad (Δν > 100 cm −1 ) diffuse signals. Despite the large number of example spectra in the literature, a quantitative understanding of the helium induced fine structure of the zero phonon line and the phonon wing is missing. Our approach is a systematic investigation of related molecular compounds, which may help to shed light on this key feature of microsolvation in superfluid helium droplets. This paper is part of a comparative study of the helium induced fine structure observed in electronic spectra of anthracene derivatives with particular emphasis on a spectrally sharp multiplet splitting at the electronic origin. In addition to previously discussed species, 9-cyanoanthracene and 9-chloroanthracene will be presented in this study for the first time
Ahadi, Elias; Konermann, Lars
2011-06-22
The ejection of solvated small ions from nanometer-sized droplets plays a central role during electrospray ionization (ESI). Molecular dynamics (MD) simulations can provide insights into the nanodroplet behavior. Earlier MD studies have largely focused on aqueous systems, whereas most practical ESI applications involve the use of organic cosolvents. We conduct simulations on mixed water/methanol droplets that carry excess NH(4)(+) ions. Methanol is found to compromise the H-bonding network, resulting in greatly increased rates of ion ejection and solvent evaporation. Considerable differences in the water and methanol escape rates cause time-dependent changes in droplet composition. Segregation occurs at low methanol concentration, such that layered droplets with a methanol-enriched periphery are formed. This phenomenon will enhance the partitioning of analyte molecules, with possible implications for their ESI efficiencies. Solvated ions are ejected from the tip of surface protrusions. Solvent bridging prior to ion secession is more extensive for methanol/water droplets than for purely aqueous systems. The ejection of solvated NH(4)(+) is visualized as diffusion-mediated escape from a metastable basin. The process involves thermally activated crossing of a ~30 kJ mol(-1) free energy barrier, in close agreement with the predictions of the classical ion evaporation model.
Dynamics of photoexcited Ba{sup +} cations in {sup 4}He nanodroplets
Energy Technology Data Exchange (ETDEWEB)
Leal, Antonio; Pi, Martí [Departament ECM, Facultat de Física, and IN" 2UB, Universitat de Barcelona, Diagonal 645, 08028 Barcelona (Spain); Zhang, Xiaohang; Drabbels, Marcel [Laboratoire de Chimie Physique Moléculaire, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Barranco, Manuel [Departament ECM, Facultat de Física, and IN" 2UB, Universitat de Barcelona, Diagonal 645, 08028 Barcelona (Spain); Laboratoire des Collisions, Agrégats, Réactivité, IRSAMC, UMR 5589, CNRS et Université Paul Sabatier-Toulouse 3, 118 route de Narbonne, F-31062 Toulouse Cedex 09 (France); Cargnoni, Fausto [Istituto di Scienze e Tecnologie Molecolari (ISTM), Consiglio Nazionale delle Ricerche, via Golgi 19, 20133 Milano (Italy); Hernando, Alberto [Social Thermodynamics Applied Research (SThAR), EPFL Innovation Park, Bâtiment C, CH-1015 Lausanne (Switzerland); Mateo, David [Department of Chemistry and Biochemistry, California State University at Northridge, Northridge, California 91330 (United States); Mella, Massimo [Dipartimento di Scienza ed Alta Tecnologia, Università degli Studi dell’Insubria, via Valleggio 11, 22100 Como (Italy)
2016-03-07
We present a joint experimental and theoretical study on the desolvation of Ba{sup +} cations in {sup 4}He nanodroplets excited via the 6p ← 6s transition. The experiments reveal an efficient desolvation process yielding mainly bare Ba{sup +} cations and Ba{sup +}He{sub n} exciplexes with n = 1 and 2. The speed distributions of the ions are well described by Maxwell-Boltzmann distributions with temperatures ranging from 60 to 178 K depending on the excitation frequency and Ba{sup +} He{sub n} exciplex size. These results have been analyzed by calculations based on a time-dependent density functional description for the helium droplet combined with classical dynamics for the Ba{sup +}. In agreement with experiment, the calculations reveal the dynamical formation of exciplexes following excitation of the Ba{sup +} cation. In contrast to experimental observation, the calculations do not reveal desolvation of excited Ba{sup +} cations or exciplexes, even when relaxation pathways to lower lying states are included.
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
Kuma, Susumu; Nakahara, Hiroko; Tsubouchi, Masaaki; Takahashi, Akira; Mustafa, Majd; Sim, Goeun; Momose, Takamasa; Vilesov, Andrey F
2011-06-30
Clusters of tetracene molecules with different numbers of attached (Ar)(N), (Ne)(N) and (H(2))(N) particles (N = 1-2000) are assembled inside superfluid He nanodroplets and studied via laser-induced fluorescence. The frequency shift of the fluorescence spectrum of the tetracene molecules is studied as a function of cluster size and pickup order of tetracene and cluster species. For (Ar)(N) and (Ne)(N) clusters, our results indicate that the tetracene molecules reside inside the clusters when tetracene is captured by the He nanodroplet before the cluster species; conversely, the tetracene molecules stay on the surface of the clusters when tetracene is captured after the cluster species. In the case of (H(2))(N) clusters, however, tetracene molecules reside inside the (H(2))(N) clusters irrespective of the pickup order. We conclude that (Ar)(N) and (Ne)(N) clusters are rigid at T = 0.38 K, while (H(2))(N) clusters of up to N = 2000 remain fluxional at the same temperature. The results may also indicate the occurrence of heterogeneous nucleation of the (H(2))(N) clusters, which is induced by the interaction with tetracene chromophore molecules.
Electrospinning of poly(vinyl alcohol) nanofibers loaded with hexadecane nanodroplets.
Arecchi, A; Mannino, S; Weiss, J
2010-08-01
The feasibility of producing poly(vinyl alcohol) (PVA) nanofibers containing fine-disperse hexadecane droplets by electrospinning a blend of hexadecane-in-water emulsions and PVA was investigated. Hexadecane oil-in-water nanoemulsions (d(10)= 181.2 +/- 0.1 nm) were mixed with PVA at pH 4.5 to yield polymer-emulsion blends containing 0.5 to 1.5 wt% oil droplets and 8-wt% PVA. The solution properties of emulsions and emulsion-PVA blends (viscosity, conductivity, surface tension) were determined. Solutions were electrospun and the morphology and thermal properties of deposited fiber mats characterized by scanning electron microscopy and differential scanning calorimetry. Fiber mats were dissolved in buffer to liberate incorporated hexadecane droplets and the buffer solutions analyzed by optical microscopy, UV-spectroscopy, and light scattering. Analysis of dry fiber mats and their solutions showed that emulsion droplets were indeed part of the electrospun fiber structures. Depending on the concentration of hexadecane in the initial emulsion-polymer blends, droplets were dispersed in the fibers as individual droplets or in form of aggregated flocs of hexadecane droplets. Nanofibers with spindle-like perturbations or nanofibers containing bead-like structures with approximately 5 times larger than the size of droplets in the original nanoemulsion were obtained. Remarkably, incorporation of hexadecane droplets in fibers did not alter size of individual droplets, that is, no coalescence occurred. The manufacture of solid matrix containing nanodroplets could be of substantial interest for manufacturers wishing to develop encapsulation system for lipophilic functional compounds such as lipid-soluble flavors, antimicrobials, antioxidants, and bioactives with tailored release kinetics. Practical Applications: The paper describes the formation of electrospun nanofibers from hydrophilic polymers that contain fine-disperse emulsion droplets. By incorporating emulsion droplets, a
Nandi, Prithwish K.; Burnham, Christian J.; English, Niall J.
2018-01-01
Understanding water solidification, especially in "No Man's Land" (NML) (150 K < T < 235 K) is crucially important (e.g., upper-troposphere cloud processes) and challenging. A rather neglected aspect of tropospheric ice-crystallite formation is inevitably present electromagnetic fields' role. Here, we employ non-equilibrium molecular dynamics of aggressively quenched supercooled water nano-droplets in the gas phase under NML conditions, in externally applied electromagnetic (e/m) fields, elucidating significant differences between effects of static and oscillating fields: although static fields induce "electro-freezing," e/m fields exhibit the contrary - solidification inhibition. This anti-freeze action extends not only to crystal-ice formation but also restricts amorphisation, i.e., suppression of low-density amorphous ice which forms otherwise in zero-field NML environments. E/m-field applications maintain water in the deeply supercooled state in an "entropic trap," which is ripe for industrial impacts in cryo-freezing, etc.
Faridi Esfanjani, Afshin; Jafari, Seid Mahdi; Assadpour, Elham
2017-04-15
The present study illustrates a simple and practical way to produce an adequate delivery system of bioactive compounds of saffron by protein-polysaccharide complex. Frist, crocin, safranal, and picrocrocin were loaded in nanodroplets (WPC)-maltodextrin or WPC-pectin-maltodextrin through water in oil in water (W/O/W) multiple emulsions. The stability and release of loaded crocin, safranal, and picrocrocin in multiple emulsions were investigated during 22days storage. The produced multiple emulsion by WPC-pectin-maltodextrin along with 5% inner aqueous phase showed a high stability and low release of encapsulated compounds over time. This emulsion also provided a high protection of crocin, safranal, and picrocrocin in the gastric condition. Copyright © 2016 Elsevier Ltd. All rights reserved.
Fragmentation dynamics of ionized neon clusters (Ne(n), n=3-14) embedded in helium nanodroplets.
Bonhommeau, David; Halberstadt, Nadine; Viel, Alexandra
2006-01-14
We report a theoretical study of the nonadiabatic fragmentation dynamics of ionized neon clusters embedded in helium nanodroplets for cluster sizes up to n=14 atoms. The dynamics of the neon atoms is modeled using the molecular dynamics with quantum transitions method of Tully [J. Chem. Phys. 93, 1061 (1990)] with the nuclei treated classically and transitions between electronic states quantum mechanically. The potential-energy surfaces are derived from a diatomics-in-molecules model to which induced dipole-induced dipole interactions are added. The effect of the spin-orbit interaction is also discussed. The helium environment is modeled by a friction force acting on charged atoms whose speed exceeds the critical Landau velocity. The dependence of the fragment size distribution on the friction strength and on the initial nanodroplet size is investigated. By comparing with the available experimental data obtained for Ne3+ and Ne4+, a reasonable value for the friction coefficient, the only parameter of the model, is deduced. This value is then used to predict the effect of the helium environment on the dissociation dynamics of larger neon clusters, n=5-14. The results show stabilization of larger fragments than in the gas phase, but fragmentation is not completely caged. In addition, two types of dynamics are characterized for Ne4+: fast and explosive, therefore leaving no time for friction to cool down the process when dynamics starts on one of the highest electronic states, and slower, therefore leading to some stabilization by helium when it starts on one of the lowest electronic states.
Jian, Jia; Liu, Chengbo; Gong, Yuping; Su, Lei; Zhang, Bin; Wang, Zhigang; wang, Dong; Zhou, Yu; Xu, Fenfen; Li, Pan; Zheng, Yuanyi; Song, Liang; Zhou, Xiyuan
2014-01-01
The in vivo applications of gas-core microbubbles have been limited by gas diffusion, rapid body clearance, and poor vascular permeability. To overcome these limitations, using a modified three-step emulsion process, we have developed a first-of-its-kind India ink incorporated optically-triggerable phase-transition perfluorocarbon nanodroplets (INDs) that can provide not only three types of contrast mechanisms—conventional/thermoelastic photoacoustic, phase-transition/nonlinear photoacoustic,...
Jian, Jia; Liu, Chengbo; Gong, Yuping; Su, Lei; Zhang, Bin; Wang, Zhigang; wang, Dong; Zhou, Yu; Xu, Fenfen; Li, Pan; Zheng, Yuanyi; Song, Liang; Zhou, Xiyuan
2014-01-01
The in vivo applications of gas-core microbubbles have been limited by gas diffusion, rapid body clearance, and poor vascular permeability. To overcome these limitations, using a modified three-step emulsion process, we have developed a first-of-its-kind India ink incorporated optically-triggerable phase-transition perfluorocarbon nanodroplets (INDs) that can provide not only three types of contrast mechanisms—conventional/thermoelastic photoacoustic, phase-transition/nonlinear photoacoustic, and ultrasound imaging contrasts, but also a new avenue for photoacoustic effect mediated tumor therapy. Upon pulsed laser illumination above a relatively low energy threshold, liquid-gas phase transition of the INDs has been demonstrated both in vitro and in vivo, offering excellent contrasts for photoacoustic and ultrasound dual-modality imaging. With further increased laser energy, the nanodroplets have been shown to be capable of destructing cancer cells in vivo, presumably due to the photoacoustic effect induced shock-wave generation from the carbon particles of the incorporated India ink. The demonstrated results suggest that the developed multifunctional phase-transition nanodroplets have a great potential for many theranostic biomedical applications, including photoacoustic/ultrasound dual-modality molecular imaging and targeted, localized cancer therapy. PMID:25161702
Jian, Jia; Liu, Chengbo; Gong, Yuping; Su, Lei; Zhang, Bin; Wang, Zhigang; Wang, Dong; Zhou, Yu; Xu, Fenfen; Li, Pan; Zheng, Yuanyi; Song, Liang; Zhou, Xiyuan
2014-01-01
The in vivo applications of gas-core microbubbles have been limited by gas diffusion, rapid body clearance, and poor vascular permeability. To overcome these limitations, using a modified three-step emulsion process, we have developed a first-of-its-kind India ink incorporated optically-triggerable phase-transition perfluorocarbon nanodroplets (INDs) that can provide not only three types of contrast mechanisms-conventional/thermoelastic photoacoustic, phase-transition/nonlinear photoacoustic, and ultrasound imaging contrasts, but also a new avenue for photoacoustic effect mediated tumor therapy. Upon pulsed laser illumination above a relatively low energy threshold, liquid-gas phase transition of the INDs has been demonstrated both in vitro and in vivo, offering excellent contrasts for photoacoustic and ultrasound dual-modality imaging. With further increased laser energy, the nanodroplets have been shown to be capable of destructing cancer cells in vivo, presumably due to the photoacoustic effect induced shock-wave generation from the carbon particles of the incorporated India ink. The demonstrated results suggest that the developed multifunctional phase-transition nanodroplets have a great potential for many theranostic biomedical applications, including photoacoustic/ultrasound dual-modality molecular imaging and targeted, localized cancer therapy.
Chen, Xiao-Wei; Wang, Jin-Mei; Guo, Jian; Wan, Zhi-Li; Yin, Shou-Wei; Yang, Xiao-Quan
2017-02-22
Herein, we report novel high internal phase emulsions and transparent oleogels that exhibit a hierarchical configuration by manipulating the spatial assembly of a natural small molecular-weight quillaja saponin for color performance. Quillaja saponin (QS) is a natural triterpenoid bidesmosidic from the soapbark tree (Quillaja saponaria Molina). Fairly monodispersed QS-coated nanodroplets (∼154 nm) were prepared using the ultrasonic emulsification strategy, and then used as block stabilizers for the fabrication of stable oil-in-water high internal phase emulsions (HIPEs, ϕ = 0.75). The resulting HIPEs can be easily converted into transparent oleogels with a very high oil loading (99.7%) through oven drying (70 °C). The jelly-like oleogels exhibit weak elastic, shear thinning behavior, good thixotropic recovery, and thermostabilization properties, which might be provided by the percolating 3D network of QS fibrils in the oil phase. We spatially tuned the color performance of the HIPEs and subsequent oleogels by locating the compositions of food colorants in different sections of their hierarchal architecture. The design and construction of hierarchical HIPEs and oleogels provide a promising new route for multitask functional delivery applications in various fields including food, cosmetics, and medical applications.
Directory of Open Access Journals (Sweden)
Giulia Rossana Gulino
2015-01-01
Full Text Available Monocytes play a key role in the inflammatory stage of the healing process. To allow monocyte migration to injured tissues, the balances between secreted matrix metalloproteinases (MMPs and their inhibitors (TIMPs must be finely modulated. However, a reduction of blood supply and local oxygen tension can modify the phenotype of immune cells. Intriguingly, hypoxia might be targeted by new effective oxygenating devices such as 2H,3H-decafluoropentane- (DFP- based oxygen-loaded nanodroplets (OLNs. Here, hypoxia effects on gelatinase/TIMP release from human peripheral monocytes were investigated, and the therapeutic potential of dextran-shelled OLNs was evaluated. Normoxic monocytes constitutively released ~500 ng/mL MMP-9, ~1.3 ng/mL TIMP-1, and ~0.6 ng/mL TIMP-2 proteins. MMP-2 was not detected. After 24 hours, hypoxia significantly altered MMP-9/TIMP-1 balance by reducing MMP-9 and increasing TIMP-1, without affecting TIMP-2 secretion. Interestingly OLNs, not displaying toxicity to human monocytes after cell internalization, effectively counteracted hypoxia, restoring a normoxia-like MMP-9/TIMP-1 ratio. The action of OLNs was specifically dependent on time-sustained oxygen diffusion up to 24 h from their DFP-based core. Therefore, OLNs appear as innovative, nonconventional, cost-effective, and nontoxic therapeutic tools, to be potentially employed to restore the physiological invasive phenotype of immune cells in hypoxia-associated inflammation.
International Nuclear Information System (INIS)
Khadjavi, Amina; Magnetto, Chiara; Panariti, Alice; Argenziano, Monica; Gulino, Giulia Rossana; Rivolta, Ilaria; Cavalli, Roberta; Giribaldi, Giuliana; Guiot, Caterina; Prato, Mauro
2015-01-01
Background: : In chronic wounds, efficient epithelial tissue repair is hampered by hypoxia, and balances between the molecules involved in matrix turn-over such as matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) are seriously impaired. Intriguingly, new oxygenating nanocarriers such as 2H,3H-decafluoropentane-based oxygen-loaded nanodroplets (OLNs) might effectively target chronic wounds. Objective: : To investigate hypoxia and chitosan-shelled OLN effects on MMP/TIMP production by human keratinocytes. Methods: : HaCaT cells were treated for 24 h with 10% v/v OLNs both in normoxia or hypoxia. Cytotoxicity and cell viability were measured through biochemical assays; cellular uptake by confocal microscopy; and MMP and TIMP production by enzyme-linked immunosorbent assay or gelatin zymography. Results: : Normoxic HaCaT cells constitutively released MMP-2, MMP-9, TIMP-1 and TIMP-2. Hypoxia strongly impaired MMP/TIMP balances by reducing MMP-2, MMP-9, and TIMP-2, without affecting TIMP-1 release. After cellular uptake by keratinocytes, nontoxic OLNs abrogated all hypoxia effects on MMP/TIMP secretion, restoring physiological balances. OLN abilities were specifically dependent on time-sustained oxygen diffusion from OLN core. Conclusion: : Chitosan-shelled OLNs effectively counteract hypoxia-dependent dysregulation of MMP/TIMP balances in human keratinocytes. Therefore, topical administration of exogenous oxygen, properly encapsulated in nanodroplet formulations, might be a promising adjuvant approach to promote healing processes in hypoxic wounds. - Highlights: • Hypoxia impairs MMP9/TIMP1 and MMP2/TIMP2 balances in HaCaT human keratinocytes. • Chitosan-shelled oxygen-loaded nanodroplets (OLNs) are internalised by HaCaT cells. • OLNs are not toxic to HaCaT cells. • OLNs effectively counteract hypoxia effects on MMP/TIMP balances in HaCaT cells. • OLNs appear as promising and cost-effective therapeutic tools for hypoxic
Energy Technology Data Exchange (ETDEWEB)
Khadjavi, Amina [Dipartimento di Neuroscienze, Università di Torino, Torino (Italy); Magnetto, Chiara [Istituto Nazionale di Ricerca Metrologica (INRIM), Torino (Italy); Panariti, Alice [Dipartimento di Scienze della Salute, Università di Milano Bicocca, Monza (Italy); Argenziano, Monica [Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Torino (Italy); Gulino, Giulia Rossana [Dipartimento di Oncologia, Università di Torino, Torino (Italy); Rivolta, Ilaria [Dipartimento di Scienze della Salute, Università di Milano Bicocca, Monza (Italy); Cavalli, Roberta [Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Torino (Italy); Giribaldi, Giuliana [Dipartimento di Oncologia, Università di Torino, Torino (Italy); Guiot, Caterina [Dipartimento di Neuroscienze, Università di Torino, Torino (Italy); Prato, Mauro, E-mail: mauro.prato@unito.it [Dipartimento di Neuroscienze, Università di Torino, Torino (Italy); Dipartimento di Scienze della Sanità Pubblica e Pediatriche, Università di Torino, Torino (Italy)
2015-08-01
Background: : In chronic wounds, efficient epithelial tissue repair is hampered by hypoxia, and balances between the molecules involved in matrix turn-over such as matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) are seriously impaired. Intriguingly, new oxygenating nanocarriers such as 2H,3H-decafluoropentane-based oxygen-loaded nanodroplets (OLNs) might effectively target chronic wounds. Objective: : To investigate hypoxia and chitosan-shelled OLN effects on MMP/TIMP production by human keratinocytes. Methods: : HaCaT cells were treated for 24 h with 10% v/v OLNs both in normoxia or hypoxia. Cytotoxicity and cell viability were measured through biochemical assays; cellular uptake by confocal microscopy; and MMP and TIMP production by enzyme-linked immunosorbent assay or gelatin zymography. Results: : Normoxic HaCaT cells constitutively released MMP-2, MMP-9, TIMP-1 and TIMP-2. Hypoxia strongly impaired MMP/TIMP balances by reducing MMP-2, MMP-9, and TIMP-2, without affecting TIMP-1 release. After cellular uptake by keratinocytes, nontoxic OLNs abrogated all hypoxia effects on MMP/TIMP secretion, restoring physiological balances. OLN abilities were specifically dependent on time-sustained oxygen diffusion from OLN core. Conclusion: : Chitosan-shelled OLNs effectively counteract hypoxia-dependent dysregulation of MMP/TIMP balances in human keratinocytes. Therefore, topical administration of exogenous oxygen, properly encapsulated in nanodroplet formulations, might be a promising adjuvant approach to promote healing processes in hypoxic wounds. - Highlights: • Hypoxia impairs MMP9/TIMP1 and MMP2/TIMP2 balances in HaCaT human keratinocytes. • Chitosan-shelled oxygen-loaded nanodroplets (OLNs) are internalised by HaCaT cells. • OLNs are not toxic to HaCaT cells. • OLNs effectively counteract hypoxia effects on MMP/TIMP balances in HaCaT cells. • OLNs appear as promising and cost-effective therapeutic tools for hypoxic
Faulkner, Ty; Miller, Isaac; Raston, Paul L.
2018-01-01
We report high-resolution infrared spectra of OCS isotopologues embedded in helium nanodroplets that were recorded with a newly built spectrometer. For the normal isotopologue, we observed the relatively weak third bending overtone band, in addition to new high J transitions in the C-O stretching fundamental, which has previously been investigated by diode laser spectroscopy [S. Grebenev et al., J. Chem. Phys. 112, 4485 (2000)]. Similar to the gas phase, the overtone band is (only) 45 cm-1 higher in energy than the fundamental, and this leads to additional broadening due to rapid vibrational relaxation that is accompanied by the creation of real/virtual phonon excitations. We also observed spectra in the C-O stretching fundamental for several minor isotopologues of OCS, including 18OCS, O13CS, and OC33S, in addition to some new peaks for OC34S. A rovibrational analysis allowed for determination of the moment of inertia of helium (ΔIHe) that couples to the rotation of OCS for each isotopologue. In the context of the adiabatic following approximation, the helium density structure that follows the rotation of OCS should essentially remain unchanged between the isotopologues, i.e., there should be no dependence of ΔIHe on the gas phase moment of inertia of OCS (IG). While this behavior was expected for the "heavy" OCS rotor investigated here, we instead found an approximately linear 1:1 relation between ΔIHe and IG, which suggests partial breakdown of the adiabatic following approximation, making OCS the heaviest molecule for which evidence for this effect has been obtained.
Chen, Wei-Tsung; Kang, Shih-Tsung; Lin, Jian-Liang; Wang, Chung-Hsin; Chen, Ran-Chou; Yeh, Chih-Kuang
2015-01-01
In this study, we aimed to validate the feasibility of receptor-targeted tumor theranostics with folate-conjugated (FA) and camptothecin-loaded (CPT) acoustic nanodroplets (NDs) (collectively termed FA-CPT-NDs). The ND formulation was based on lipid-stabilized low-boiling perfluorocarbon that can undergo acoustic droplet vaporization (ADV) under ultrasound (US) exposure. Conjugation of folate enhanced the selective delivery to tumors expressing high levels of folate receptor (FR) under mediation by the enhanced permeability and retention effect. In vitro and in vivo studies were performed using FR-positive KB and FR-negative HT-1080 cell lines and mouse xenograft tumor models. Simultaneous therapy and imaging were conducted with a clinical US imaging system at mechanical indices of up to 1.4 at a center frequency of 10 MHz. The results demonstrated that FA-CPT-NDs selectively attached to KB cells, but not HT-1080 cells. The targeted ADV caused instant and delayed damage via mechanical disruption and chemical toxicity to decrease the viability of KB cells by up to 45%, a much higher decrease than that achieved by the NDs without folate conjugation. The in vivo experiments showed that FR-mediated targeting successfully enhanced the EPR of FA-CPT-NDs in KB tumors mainly on the tumor periphery as indicated by immunofluorescence microscopy and US B-mode imaging. Treatments with FA-CPT-NDs at a CPT dose of 50 μg/kg inhibited the growth of KB tumors for up to six weeks, whereas treatment with NDs lacking folate produced a 4.6-fold increase in tumor volume. For HT-1080 tumors, neither the treatments with FA-CPT-NDs nor those with the NDs lacking folate presented tumor growth inhibition. In summary, FR-targeted tumor theranostics has been successfully implemented with FA-CPT-NDs and a clinical US unit. The ligand-directed and EPR-mediated accumulation provides active and passive targeting capabilities, permitting the antitumor effects of FA-CPT-NDs to be exerted
International Nuclear Information System (INIS)
Basilico, Nicoletta; Magnetto, Chiara; D'Alessandro, Sarah; Panariti, Alice; Rivolta, Ilaria; Genova, Tullio; Khadjavi, Amina; Gulino, Giulia Rossana; Argenziano, Monica; Soster, Marco
2015-01-01
In chronic wounds, hypoxia seriously undermines tissue repair processes by altering the balances between pro-angiogenic proteolytic enzymes (matrix metalloproteinases, MMPs) and their inhibitors (tissue inhibitors of metalloproteinases, TIMPs) released from surrounding cells. Recently, we have shown that in human monocytes hypoxia reduces MMP-9 and increases TIMP-1 without affecting TIMP-2 secretion, whereas in human keratinocytes it reduces MMP-2, MMP-9, and TIMP-2, without affecting TIMP-1 release. Provided that the phenotype of the cellular environment is better understood, chronic wounds might be targeted by new oxygenating compounds such as chitosan- or dextran-shelled and 2H,3H-decafluoropentane-cored oxygen-loaded nanodroplets (OLNs). Here, we investigated the effects of hypoxia and dextran-shelled OLNs on the pro-angiogenic phenotype and behavior of human dermal microvascular endothelium (HMEC-1 cell line), another cell population playing key roles during wound healing. Normoxic HMEC-1 constitutively released MMP-2, TIMP-1 and TIMP-2 proteins, but not MMP-9. Hypoxia enhanced MMP-2 and reduced TIMP-1 secretion, without affecting TIMP-2 levels, and compromised cell ability to migrate and invade the extracellular matrix. When taken up by HMEC-1, nontoxic OLNs abrogated the effects of hypoxia, restoring normoxic MMP/TIMP levels and promoting cell migration, matrix invasion, and formation of microvessels. These effects were specifically dependent on time-sustained oxygen diffusion from OLN core, since they were not achieved by oxygen-free nanodroplets or oxygen-saturated solution. Collectively, these data provide new information on the effects of hypoxia on dermal endothelium and support the hypothesis that OLNs might be used as effective adjuvant tools to promote chronic wound healing processes. - Highlights: • Hypoxia enhances MMP-2 and reduces TIMP-1 secretion by dermal HMEC-1 cell line. • Hypoxia compromises migration and matrix invasion abilities of
Observation of the Q(3/2) Λ-doublet transitions for X2Π3/2 OD in helium nanodroplets
Raston, Paul L.; Liang, Tao; Douberly, Gary E.
2014-01-01
The deuteroxyl radical (OD) has been isolated in superfluid helium nanodroplets and characterised by infrared depletion spectroscopy. Two resolved Q(3/2) lines are observed, with a separation that is 4.88 (10) times larger than in the gas phase. This is similar to that previously reported for He-solvated OH (5.30 (2)), for which it was shown that the splitting could be reproduced by a model that assumes a small parity dependence of the rotor's effective moment of inertia [P.L. Raston, T. Liang, and G.E. Douberly, J. Phys. Chem. A (2013). DOI:10.1021/jp312335q]. With this model, the OD Λ-doublet splitting in liquid He is reproduced with Be and Bf rotational constants that differ by ≈0.24%.
Euroopa 2014 aasta valimiste teemaline manifest / Meelis Joost
Joost, Meelis
2014-01-01
Euroopa Puuetega Inimeste Foorumi manifest, mis kutsub üles Euroopa Parlamenti kandideerijaid lisama oma programmi tegevusi, mis aitavad parandada puuetega inimeste sotsiaalset kaasatust kogu Euroopas
Morbidity profile of admissions to GF Jooste Hospital, Manenberg ...
African Journals Online (AJOL)
The International Statistical Classification of Diseases (ICD) directed diagnosis sorting. Disease prevalence was expressed as the percentage of patients allocated to each ICD category among those admitted to the hospital and respective wards and, additionally, the percentage of diagnoses for each ICD subcategory ...
Zhu, Chongqin; Gao, Yurui; Li, Hui; Meng, Sheng; Li, Lei; Francisco, Joseph S; Zeng, Xiao Cheng
2016-11-15
Hydrophobicity of macroscopic planar surface is conventionally characterized by the contact angle of water droplets. However, this engineering measurement cannot be directly extended to surfaces of proteins, due to the nanometer scale of amino acids and inherent nonplanar structures. To measure the hydrophobicity of side chains of proteins quantitatively, numerous parameters were developed to characterize behavior of hydrophobic solvation. However, consistency among these parameters is not always apparent. Herein, we demonstrate an alternative way of characterizing hydrophobicity of amino acid side chains in a protein environment by constructing a monolayer of amino acids (i.e., artificial planar peptide network) according to the primary and the β-sheet secondary structures of protein so that the conventional engineering measurement of the contact angle of a water droplet can be brought to bear. Using molecular dynamics simulations, contact angles θ of a water nanodroplet on the planar peptide network, together with excess chemical potentials of purely repulsive methane-sized Weeks-Chandler-Andersen solute, are computed. All of the 20 types of amino acids and the corresponding planar peptide networks are studied. Expectedly, all of the planar peptide networks with nonpolar amino acids are hydrophobic due to θ [Formula: see text] 90°, whereas all of the planar peptide networks of the polar and charged amino acids are hydrophilic due to θ [Formula: see text] 90°. Planar peptide networks of the charged amino acids exhibit complete-wetting behavior due to θ [Formula: see text] 0°. This computational approach for characterization of hydrophobicity can be extended to artificial planar networks of other soft matter.
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 ...
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.
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 ...
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...
Energy Technology Data Exchange (ETDEWEB)
Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es [Instituto de Física Fundamental (C.S.I.C.), Serrano 123, E-28006 Madrid (Spain); Stoll, Hermann [Institut für Theoretische Chemie, Universität Stuttgart, D-70550 Stuttgart (Germany); Civalleri, Bartolomeo [Dipartimento di Chimica e Centro Interdipartimentale NIS, Universitá di Torino, Via P. Giuria 7, 10125 Torino (Italy); Causà, Mauro [Dipartimento di Ingegneria Chimica, dei Materiali e delle Produzioni Industriali, Universiá di Napoli Federico II, Piazzale Tecchio, 80126 Napoli (Italy); Voloshina, Elena [Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin (Germany); Mitrushchenkov, Alexander O. [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France); Pi, Martí [Department ECM, Facultat de Física, and IN" 2UB, Universitat de Barcelona, Diagonal 645, E-08028 Barcelona (Spain)
2014-10-21
In this work we propose a general strategy to calculate accurate He–surface interaction potentials. It extends the dispersionless density functional approach recently developed by Pernal et al. [Phys. Rev. Lett. 103, 263201 (2009)] to adsorbate-surface interactions by including periodic boundary conditions. We also introduce a scheme to parametrize the dispersion interaction by calculating two- and three-body dispersion terms at coupled cluster singles and doubles and perturbative triples (CCSD(T)) level via the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)]. The performance of the composite approach is tested on {sup 4}He/graphene by determining the energies of the low-lying selective adsorption states, finding an excellent agreement with the best available theoretical data. Second, the capability of the approach to describe dispersionless correlation effects realistically is used to extract dispersion effects in time-dependent density functional simulations on the collision of {sup 4}He droplets with a single graphene sheet. It is found that dispersion effects play a key role in the fast spreading of the {sup 4}He nanodroplet, the evaporation-like process of helium atoms, and the formation of solid-like helium structures. These characteristics are expected to be quite general and highly relevant to explain experimental measurements with the newly developed helium droplet mediated deposition technique.
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
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 ...
leserskring sal geniet. Die boek verdien dit. A. D. Pont. J. P. Jooste ...
African Journals Online (AJOL)
Test
1959, Uitgewer en jaar van publikasie ... Die werk van Van der Vyver wat in Neder land gedruk is toon dat goeie vakmanne dié ... 'n Tweede punt is dat die note nie aan die voet van die bladsy staan waar dit tuishoort nie. Dit word agter in die ...
Method and Apparatus for Forming Nanodroplets
Ackley, Donald; Forster, Anita
2011-01-01
This innovation uses partially miscible fluids to form nano- and microdroplets in a microfluidic droplet generator system. Droplet generators fabricated in PDMS (polydimethylsiloxane) are currently being used to fabricate engineered nanoparticles and microparticles. These droplet generators were first demonstrated in a T-junction configuration, followed by a cross-flow configuration. All of these generating devices have used immiscible fluids, such as oil and water. This immiscible fluid system can produce mono-dispersed distributions of droplets and articles with sizes ranging from a few hundred nanometers to a few hundred microns. For applications such as drug delivery, the ability to encapsulate aqueous solutions of drugs within particles formed from the droplets is desirable. Of particular interest are non-polar solvents that can dissolve lipids for the formation of liposomes in the droplet generators. Such fluids include ether, cyclohexane, butanol, and ethyl acetate. Ethyl acetate is of particular interest for two reasons. It is relatively nontoxic and it is formed from ether and acetic acid, and maybe broken down into its constituents at relatively low concentrations.
Acoustic Studies on Nanodroplets, Microbubbles and Liposomes
Kumar, Krishna Nandan
Microbubbles and droplets are nanometer to micron size biocompatible particles which are primarily used for drug delivery and contrast imaging. Our aim is to broaden the use of microbubbles from contrast imaging to other applications such as measuring blood pressure. The other goal is to develop in situ contrast agents (phase shift droplets) which can be used for applications such as cancer tumor imaging. Therefore, the focus is on developing and validating the concept using experimental and theoretical methods. Below is an overview of each of the projects performed on droplets and microbubbles. Phase shift droplets vaporizable by acoustic stimulation offer many advantages over microbubbles as contrast agents due to their higher stability and possibility of smaller sizes. In this study, the acoustic droplet vaporization (ADV) threshold of a suspension of PFP droplets (400-3000nm) was acoustically measured as a function of the excitation frequency by examining the scattered signals, fundamental, sub- and second-harmonic. This work presents the experimental methodology to determine ADV threshold. The threshold increases with frequency: 1.25 MPa at 2.25 MHz, 2.0 MPa at 5 MHz and 2.5 MPa at 10 MHz. The scattered response from droplets was also found to match well with that of independently prepared lipid-coated microbubble suspension in magnitude as well as trends above the threshold value. Additionally, we have employed classical nucleation theory (CNT) to investigate the ADV, specifically the threshold value of the peak negative pressure required for vaporization. The theoretical analysis predicts that the ADV threshold increases with increasing surface tension of the droplet core and frequency of excitation, while it decreases with increasing temperature and droplet size. The predictions are in qualitative agreement with experimental observations. A technique to measure the ambient pressure using microbubbles was developed. Here we are presenting the results of an in vitro study aimed at developing an ultrasound-aided noninvasive pressure estimation technique using contrast agents-DefinityRTM, a lipid coated microbubble, and an experimental PLA (Poly lactic acid) microbubbles. Scattered responses from these bubbles have been measured in vitro as a function of ambient pressure using a 3.5 MHz acoustic excitation of varying amplitude. At an acoustic pressure of 670 kPa, Definity RTM microbubbles showed a linear decrease in subharmonic signal with increasing ambient pressure, registering a 12dB reduction at an overpressure of 120 mm Hg. Ultrasound contrast microbubbles experience widely varying ambient blood pressure in different organs, which can also change due to diseases. Pressure change can alter the material properties of the encapsulation of these microbubbles. Here the characteristic rheological parameters of contrast agent Definity and Targestar are determined by varying the ambient pressure (in a physiologically relevant range 0-200 mmHg). Four different interfacial rheological models are used to characterize the microbubbles. Both the contrast agents show an increase in their interfacial dilatational viscosity and interfacial dilatational elasticity with ambient pressure. It has been well established that liposomes prepared following a careful multi-step procedure can be made echogenic. Our group as well as others experimentally demonstrated that freeze-drying in the presence of mannitol is a crucial component to ensure echogenicity. Here, we showed that freeze-dried aqueous solutions of excipients such as mannitol, meso-erythritol, glycine, and glucose that assume a crystalline state, when dispersed in water creates bubbles and are echogenic even without any lipids. We also present an explanation for the bubble generation process because of dissolution of mannitol.
Critical Landau Velocity in Helium Nanodroplets
Brauer, N.B.; Smolarek, S.; Loginov, E.; Mateo, D.; Hernando, A.; Pi, M.; Barranco, M.; Buma, W.J.; Drabbels, M.
2013-01-01
The best-known property of superfluid helium is the vanishing viscosity that objects experience while moving through the liquid with speeds below the so-called critical Landau velocity. This critical velocity is generally considered a macroscopic property as it is related to the collective
Interatomic Coulombic decay in helium nanodroplets
DEFF Research Database (Denmark)
Shcherbinin, Mykola; Laforge, Aaron; Sharma, Vandana
2017-01-01
, or in the droplet interior. ICD at the surface gives rise to energetic He+ ions as previously observed for free He dimers. ICD deeper inside leads to the ejection of slow He+ ions due to Coulomb explosion delayed by elastic collisions with neighboring He atoms, and to the formation of Hek+ complexes....
ÜRO säästva arengu eesmärgid aastaks 2030 / Meelis Joost
Joost, Meelis
2016-01-01
ÜRO liikmesriikide juhid leppisid 25.‒27. septembril 2015 New Yorgis kokku säästva arengu eesmärkides, mis tuleb saavutada 2030. aastaks. Säästva arengu eesmärgid on kaudselt seotud ka puuetega inimestega. Eesti Puuetega Inimeste Koda huvitab, kuivõrd ligipääsetavus, puuetega inimeste elukvaliteet, kasvav kaasatus ühiskonda ning puuetega inimestele osutatavate sotsiaalteenuste kvaliteet leiab kajastamist säästva arengu tegevuskava elluviimises
Gurjanova, Ilona, 1958-
2016-01-01
Intervjuu Design Management OÜ disaineri ja juhataja, Eesti Disainerite Liidu esimehe, Eesti Disaini Maja endise juhi ja Disainiöö peakorraldaja Ilona Gurjanovaga universaalsest disainist ja selle näidetest
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 ...
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 ...
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 ...
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.
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....
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 ...
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.
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
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…
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…
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, ...
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
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...
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
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.)
Polymer nanodroplet adsorption : continuum theory and computer simulation.
Evangelopoulos, Apostolos Evangelos Alexandros Spyridon
2013-01-01
Compared to the solid and gaseous phases, liquids are more closely related to biological processes and the life sciences. In fact, it is generally believed that abiogenesis occurred in the liquid environment of the primordial sea which, itself, was formed only when appropriate conditions came to prevail on the young Earth, providing a striking illustration of the marginal character of the liquid state, in contrast with the solid and gaseous phases of the same substances, which ...
Homogeneous bulk, surface, and edge nucleation in crystalline nanodroplets
Carvalho, Jessica L.; Dalnoki-Veress, Kari
2011-03-01
We present a study on the homogeneous nucleation of dewetted poly(ethylene oxide) droplets on a substrate that is itself crystallisable. While the chemical properties of the substrate prepared in either the amorphous or crystalline state are identical, the surface landscape varies widely. We observe a large difference in the substrate's nucleating ability depending on how it is prepared. Furthermore, the scaling dependence of the nucleation rate on the size of the droplets depends on the substrate surface properties. The birth of the crystalline state can be directed to originate predominantly within the bulk, at the substrate surface or at the droplet's edge depending on how we tune the substrate. J.L. Carvalho and K. Dalnoki-Veress, Phys. Rev. Lett in press, 2010.
Femtosecond vibrational dynamics in water nano-droplets
Cringus, Gheorghe Dan
2008-01-01
Water is probably the most researched substance on Earth. The interest in water, and redominantly in liquid water, is due to its importance on both macro- and microscopic scales. Although people have been trying to understand water for centuries, this ubiquitous liquid is still surrounded by mystery
Absorption spectrum of Ca atoms attached to He4 nanodroplets
Hernando, Alberto; Barranco, Manuel; Mayol, Ricardo; Pi, Martí; Krośnicki, Marek
2008-01-01
Within density functional theory, we have obtained the structure of He4 droplets doped with neutral calcium atoms. These results have been used, in conjunction with newly determined ab initio Σ1 and Π1 Ca-He pair potentials, to address the 4s4pP11←4s2S01 transition of the attached Ca atom, finding a fairly good agreement with absorption experimental data. We have studied the drop structure as a function of the position of the Ca atom with respect to the center of mass of the helium moiety. The interplay between the density oscillations arising from the helium intrinsic structure and the density oscillations produced by the impurity in its neighborhood plays a role in the determination of the equilibrium state, and hence in the solvation properties of alkaline earth atoms. In a case of study, the thermal motion of the impurity within the drop surface region has been analyzed in a semiquantitative way. We have found that, although the atomic shift shows a sizable dependence on the impurity location, the thermal effect is statistically small, contributing by about 10% to the line broadening. The structure of vortices attached to the calcium atom has been also addressed, and its effect on the calcium absorption spectrum discussed. At variance with previous theoretical predictions, we conclude that spectroscopic experiments on Ca atoms attached to He4 drops will be likely unable to detect the presence of quantized vortices in helium nanodrops.
Nanodroplet real-time PCR system with laser assisted heating
Kim, Hanyoup; Dixit, Sanhita; Green, Christopher J.; Faris, Gregory W.
2011-01-01
We report the successful application of low-power (~30 mW) laser radiation as an optical heating source for high-speed real-time polymerase chain reaction (PCR) amplification of DNA in nanoliter droplets dispersed in an oil phase. Light provides the heating, temperature measurement, and Taqman real-time readout in nanoliter droplets on a disposable plastic substrate. A selective heating scheme using an infrared laser appears ideal for driving PCR because it heats only the droplet, not the oil or plastic substrate, providing fast heating and completing the 40 cycles of PCR in 370 seconds. No microheaters or microfluidic circuitry were deposited on the substrate, and PCR was performed in one droplet without affecting neighboring droplets. The assay performance was quantitative and its amplification efficiency was comparable to that of a commercial instrument. PMID:19129891
Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.
2009-01-01
and DNA microarrays technologies.4,5,6,7,8 Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water,2,9-16 at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle...... computations of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems.3,16,17,18 For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence...... of air. Hence, nanobubles have been observed and proposed as the origin of long range ``hydrophobic'' forces19-30 even for hydrophilic silica-water interfaces unusual phenomena related to nanobubbles have been observed.31-33 In this work we study the role of air on the wetting of amorphous silica...
Kuld, Kirke-Anneli
2015-01-01
Eesti Puuetega Inimeste Koja liikmesorganisatsioonide esindajate ja töövõimereformi võtmes oluliste koostööpartnerite delegatsiooni külaskäigust Norra Kuningriiki 14.-19. jaanuaril, kus saadi ülevaade tööhõivelahendustest, mida pakub Norra töö- ja heaolu direktoraat NAV
Joost, Meelis
2016-01-01
8.–12. jaanuaril osalesid EMP vabaühenduste fondi projekti „Paneme seaduse kehtima!“ partnerite esindajad Islandil poliitikakujundusseminaril ning kohtumistel asutustega, mis mõjutavad elukeskkonna kujundamist
Joost, Meelis
2015-01-01
21.–27. juulil 2015 osales EPIKoja 2-liikmeline meeskond koolitusel Venemaal Nižni Novgorodis, mille korraldas Austria organisatsioon Grenzenlos koostöös Venemaa organisatsiooniga SFERA. Koolituse eesmärgiks oli selgitada, kuidas Euroopa Liidu erinevatesse programmidesse on võimalik paremini kaasata erivajadustega inimesi
de Vries, Rudolf; Dony, Christophe; Habrand, Tanguy; Meesters, Gert
2014-01-01
Taking its cue from selection systems theory, this paper discusses the capabilities of innovative comics artists and publishers to influence their environment in such a way that a certain level of artistic independence can be achieved or sustained. Increased chances of artistic autonomy depend on
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...
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....
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
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
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.
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.
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.
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
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
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.
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.
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
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.
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.
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.
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.
A Polar Isomer of Formic Acid Dimer Formed in Helium Nanodroplets
Czech Academy of Sciences Publication Activity Database
Madeja, F.; Havenith, M.; Nauta, K.; Miller, R. E.; Chocholoušová, Jana; Hobza, Pavel
2004-01-01
Roč. 120, č. 22 (2004), s. 10554-10560 ISSN 0021-9606 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : resolution infrared - spectroscopy * double-resonance spectroscopy * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.105, year: 2004
Hernando, Alberto; Beswick, J Alberto; Halberstadt, Nadine
2013-12-14
The theory of photofragments angular momentum polarization is applied to the photodetachment of an electronically excited alkali atom from a helium nanocluster (N = 200). The alignment of the electronic angular momentum of the bare excited alkali atoms produced is calculated quantum mechanically by solving the excited states coupled equations with potentials determined by density functional theory (DFT). Pronounced oscillations as a function of excitation energy are predicted for the case of Na@(He)200, in marked contrast with the absorption cross-section and angular distribution of the ejected atoms which are smooth functions of the energy. These oscillations are due to quantum interference between different coherently excited photodetachment pathways. Experimentally, these oscillations should be reflected in the fluorescence polarization and polarization-resolved photoelectron yield of the ejected atoms, which are proportional to the electronic angular momentum alignment. In addition, this result is much more general than the test case of NaHe200 studied here. It should be observable for larger droplets, for higher excited electronic states, and for other alkali as well as for alkali-earth atoms. Detection of these oscillations would show that the widely used pseudo-diatomic model can be valid beyond the prediction of absorption spectra and could help in interpreting parts of the dynamics, as already hinted by some experimental results on angular anisotropy of bare alkali fragments.
Atomistic Simulations of Thermophoretic Motion of water Nanodroplets in Carbon Nanotubes
DEFF Research Database (Denmark)
Zambrano, Harvey A; Walther, Jens Honore; Koumoutsakos, Petros
2008-01-01
fabricated nanomotors, and thermodiffusion is expected to allow microscale manipulation and control of flow in nanofluidic devices. In a recent theoretical study, thermophoresis was shown to induce motion of solid gold nanoparticles confined inside carbon nanotubes. In the present investigation, we study......Open-ended nanotubes offer unique possibilities as fluid conduits with applications ranging from molecule separation devices in biocatalysis to encapsulation media for drug storage and delivery. Liquids and solids in nanochannels may be driven by electrophoresis, osmosis, gradients in the surface...... gradients imposed in nanopipes have been used to generate controlled flows for nanoscale applications9, and to enhance electrophoretic motion across carbon nanotube membranes The use of thermal gradients to induce mass transport is known as thermophoresis, the Soret effect or thermodiffusion. The first...
Generation of micro- and nano-droplets containing immiscible solutions in view of optical studies
Nastasa, V.; Karapantsios, T.; Samaras, K.; Dafnopatidou, E.; Pradines, V.; Miller, R.; Pascu, M. L.
2010-08-01
The multiple resistances to treatment, developed by bacteria and malignant tumors require finding alternatives to the existing medicines and treatment procedures. One of them is strengthening the effects of cytostatics by improving the delivery method. Such a method is represented by the use of medicines as micro/nano-droplets. This method can reduce the substance consumption by generating drug micro-droplets incorporated in substances that can favour a faster localization, than the classical mode of medicine administration, to the tumor tissues. This paper contains the results concerning the generation and study of micro/nano-droplets and the generation of micro-droplets with an inner core (medicine) and a thin layer covering it. We have measured the surface tension at water/air interface and water/oil interface for a medicine (Vancomycin) and we have generated and measured droplets of medicine containing a layer of Vitamin A by using a double capillary system. The micro/nano-droplets may be produced by mixing of two immiscible solutions in particular conditions (high rotating speed and/or high pressure difference). For this we have studied the generation of emulsions of vitamin A diluted in sunflower oil and a solution of a surfactant Tween 80 in distilled water. The concentration of surfactant in water was typically 4*10-5M. We have studied in a batch stirred tank system the dependence of the droplet dimensions in emulsion, function of the mixing rotation speed, agitation time and components ratio. The droplet diameters were measured using a Malvern light scattering instrument type Mastersizer Hydro 2000M. We have obtained droplets with diameters smaller than 100 nm; the diameters distribution exhibited a peak at 65 nm.
Energy Technology Data Exchange (ETDEWEB)
Claas, P.
2006-01-15
In the present thesis first studies on the short-time dynamics in alkali dimers and microclusters, which were bound on the surface of superfluid helium droplets, were presented. The experiments comprehended pump-probe measurements on the fs scale on the vibration dynamics on the dimers and on the fragmentation dynamics on the clusters. Generally by the studies it was shown that such extremely short slopes can also be observed on helium droplets by means of the femtosecond spectroscopy.
Magnetic Dichroism of Potassium Atoms on the Surface of Helium Nanodroplets
International Nuclear Information System (INIS)
Nagl, Johann; Auboeck, Gerald; Callegari, Carlo; Ernst, Wolfgang E.
2007-01-01
The population ratio of Zeeman sublevels of atoms on the surface of superfluid helium droplets (T=0.37 K) has been measured. Laser induced fluorescence spectra of K atoms are measured in the presence of a moderately strong magnetic field (2.9 kG). The relative difference between the two states of circular polarization of the exciting laser is used to determine the electron spin polarization of the ensemble. Equal fluorescence levels indicate that the two spin sublevels of the ground-state K atom are equipopulated, within 1%. Thermalization to 0.37 K would give a population ratio of 0.35. We deduce that the rate of spin relaxation induced by the droplet must be 2 triplet dimer we find instead full thermalization of the spin
Rupp, Daniela; Monserud, Nils; Langbehn, Bruno; Sauppe, Mario; Zimmermann, Julian; Ovcharenko, Yevheniy; Möller, Thomas; Frassetto, Fabio; Poletto, Luca; Trabattoni, Andrea; Calegari, Francesca; Nisoli, Mauro; Sander, Katharina; Peltz, Christian; Vrakking, Marc J; Fennel, Thomas; Rouzée, Arnaud
2018-01-16
In the original version of this Article, the affiliation for Luca Poletto was incorrectly given as 'European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Hamburg, Germany', instead of the correct 'CNR, Istituto di Fotonica e Nanotecnologie Padova, Via Trasea 7, 35131 Padova, Italy'. This has now been corrected in both the PDF and HTML versions of the Article.
Ionization and fragmentation of isomeric van der Waals complexes embedded in helium nanodroplets
Lewis, William K.; Lindsay, C. Michael; Miller, Roger E.
2008-11-01
The ionization and charge transfer processes, which occur when a doped helium droplet undergoes electron impact, are studied for droplets doped with van der Waals complexes with various structures and electrostatic moments. The mass spectra of the two isomers of hydrogen cyanide complexed with either cyanoacetylene or acetylene in helium droplets were obtained using optically selected mass spectrometry, and show that the structure of the complex has a large effect on the fragmentation pattern. The resulting fragmentation pattern is consistent with an ionization process in which charge steering strongly influences the site of initial ionization. The observed dissociation products may also be subject to caging by the helium matrix.
Zemp, Roger J.; Paproski, Robert J.
2017-03-01
For emerging tissue-engineering applications, transplants, and cell-based therapies it is important to assess cell viability and function in vivo in deep tissues. Bioluminescence and fluorescence methods are poorly suited to deep monitoring applications with high resolution and require genetically-engineered reporters which are not always feasible. We report on a method for imaging cell viability using deep, high-resolution photoacoustic imaging. We use an exogenous dye, Resazurin, itself weakly fluorescent until it is reduced from blue to a pink color with bright red fluorescence. Upon cell death fluorescence is lost and an absorption shift is observed. The irreversible reaction of resazurin to resorufin is proportional to aerobic respiration. We detect colorimetric absorption shifts using multispectral photoacoustic imaging and quantify the fraction of viable cells. SKOV-3 cells with and without ±80oC heat treatment were imaged after Resazurin treatment. High 575nm:620nm ratiometric absorption and photoacoustic signals in viable cells were observed with a much lower ratio in low-viability populations.
Energy Technology Data Exchange (ETDEWEB)
Kavadiya, Shalinee; Raliya, Ramesh; Schrock, Michael; Biswas, Pratim, E-mail: pbiswas@wustl.edu [Washington University in St. Louis, Aerosol and Air Quality Research Laboratory, Department of Energy, Environmental and Chemical Engineering (United States)
2017-02-15
Restacking of graphene oxide (GO) nanosheets results in loss of surface area and creates limitations in its widespread use for applications. Previously, two-dimensional (2D) GO sheets have been crumpled into 3D structures to prevent restacking using different techniques. However, synthesis of nanometer size crumpled graphene particles and their direct deposition onto a substrate have not been demonstrated under room temperature condition so far. In this work, the evaporative crumpling of GO sheets into very small size (<100 nm) crumpled structures using an electrohydrodynamic atomization technique is described. Systematic study of the effect of different electrohydrodynamic atomization parameters, such as (1) substrate-to-needle distance, (2) GO concentration in the precursor solution, and (3) flow rate (droplet size) on the GO crumpling, is explored. Crumpled GO (CGO) particles are characterized online using a scanning mobility particle sizer (SMPS) and off-line using electron microscopy. The relation between the confinement force and the factors affecting the crumpled structure is established. Furthermore, to expand the application horizons of the structure, crumpled GO–TiO{sub 2} nanocomposites are synthesized. The method described here allows a simple and controlled production of graphene-based particles/composites with direct deposition onto any kind of substrate for a variety of applications.
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.
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....
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.
Ideal and defective vertex configurations in the planar octagonal quasilattice
Baake, M.; Joseph, D.
1990-11-01
The well-known two-dimensional octagonal quasilattice is realized by means of dualization and Klotz construction. We discuss the geometric properties and the extended symmetry of the pattern. The concept of geometric defects is introduced, and an elastic energy measure ΔE is presented that allows a simple sequencing of the forbidden vertices. After a sketchy comparison with Lennard-Jones calculations, some thermodynamic consequences of ΔE are discussed. It turns out that the specific heat should show a significant increase in comparison with the crystallographic case.
Equilibrium properties in the thermodynamic limit from small-sized molecular dynamics simulations
Cortes-Huerto, Robinson; Kremer, Kurt; Potestio, Raffaello
We present an accurate and efficient method to obtain equilibrium thermodynamic properties of bulk systems from small-sized molecular dynamics simulations by introducing finite size effects into integral equations of statistical mechanics. We validate the method by calculating thermodynamic properties of prototypical complex mixtures such as the activity coefficients of aqueous urea mixtures and the Kirkwood-Buff integrals of Lennard-Jones fluids. Moreover, our results demonstrate how to identify simulation conditions under which computer simulations reach the thermodynamic limit. Alexander von Humboldt Foundation.
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.
Variation along liquid isomorphs of the driving force for crystallization
DEFF Research Database (Denmark)
Pedersen, Ulf Rørbæk; Adrjanowicz, Karolina; Niss, Kristine
2017-01-01
at a reference temperature. More general analysis allows interpretation of experimental data for molecular liquids such as dimethyl phthalate and indomethacin, and suggests that the isomorph scaling exponent γ in these cases is an increasing function of density, although this cannot be seen in measurements......We investigate the variation of the driving force for crystallization of a supercooled liquid along isomorphs, curves along which structure and dynamics are invariant. The variation is weak, and can be predicted accurately for the Lennard-Jones fluid using a recently developed formalism and data...
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...
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.
Fluctuations and Linear Response in Supercooled Liquids
DEFF Research Database (Denmark)
Nielsen, Johannes K.
Fluctuation dissipation theorems are derived for thermodynamic properties like frequency dependent specific heat and compressibility. First the case where a systems dynamics are restricted by constant volume and energy is considered. The dynamic linear response to a heat pulse and a volume change...... of the theory in the field of supercooled liquids are showed. First the full frequency dependent thermodynamic response matrix is extracted from simulations of a binary Lennard Jones liquid. Secondly some simple stochastic models of supercooled liquids are analysed in the framework of linear thermodynamic...
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.
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...
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.
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
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.
Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling.
Fačkovec, B; Vanden-Eijnden, E; Wales, D J
2015-07-28
A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.
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.
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
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....
Berim, Gersh O.; Ruckenstein, Eli
2011-02-01
The dependence of the contact angles of nanodrops of Lennard-Jones type fluids in nanocavities on their sizes are calculated using a nonlocal density functional theory in a canonical ensemble. Cavities of various radii and depths, various temperatures, as well as various values of the energy parameter of the fluid-solid interactions were considered. It is argued that this dependence might affect strongly, for instance, the rate of heterogeneous nucleation on rough surfaces, which is usually calculated under the assumption of constant contact angle.
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.
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...
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...
Note: Nonpolar solute partial molar volume response to attractive interactions with water.
Williams, Steven M; Ashbaugh, Henry S
2014-01-07
The impact of attractive interactions on the partial molar volumes of methane-like solutes in water is characterized using molecular simulations. Attractions account for a significant 20% volume drop between a repulsive Weeks-Chandler-Andersen and full Lennard-Jones description of methane interactions. The response of the volume to interaction perturbations is characterized by linear fits to our simulations and a rigorous statistical thermodynamic expression for the derivative of the volume to increasing attractions. While a weak non-linear response is observed, an average effective slope accurately captures the volume decrease. This response, however, is anticipated to become more non-linear with increasing solute size.
DEFF Research Database (Denmark)
Galliero, Guillaume; Medvedev, Oleg; Shapiro, Alexander
2005-01-01
A 322 (2004) 151). In the current study, a fast molecular dynamics scheme has been developed to determine the values of the penetration lengths in Lennard-Jones binary systems. Results deduced from computations provide a new insight into the concept of penetration lengths. It is shown for four different...... binary liquid mixtures of non-polar components that computed penetration lengths, for various temperatures and compositions, are consistent with those deduced from experiments in the framework of the formalism of the fluctuation theory. Moreover, the mutual diffusion coefficients obtained from a coupled...
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.)
Modeling New Adsorbents for Ethylene/Ethane Separations by Adsorption via {Pi}-Complexation
Energy Technology Data Exchange (ETDEWEB)
Blas, F. J.; Vega, L. F.; Gubbins, K. E.
1998-01-01
The adsorption of olefins and paraffins in a novel model porous adsorbent is studied by means of molecular simulations. The adsorbents are synthesized by effective dispersion of CuCI on substrates with hydrocarbon-phobic surfaces, such as {gamma}-A1{sub 2}O{sub 3}. The Cu(I) cations are able to undergo {pi}-complexation with olefin molecules. Ethane and ethylene are studied as adsorbents, and the molecules are modeled as having two Lennard-Jones sites. Ethylene molecules have two additional associating square-well sites placed in the line perpendicular to the symmetry axis of the molecules in order to reproduce the {pi}-complexation.
Rubner, Oliver; Heuer, Andreas
2008-07-01
We show that the dynamics of supercooled liquids, analyzed from computer simulations of the binary mixture Lennard-Jones system, can be described in terms of a continuous-time random walk (CTRW). The required discretization comes from mapping the dynamics on transitions between metabasins. This yields a quantitative link between the elementary step and the full structural relaxation. The analysis involves a verification of the CTRW conditions as well as a quantitative test of the predictions. The wave-vector dependence of the relaxation time and the degree of nonexponentiality can be expressed in terms of the first moments of the waiting time distribution.
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...
Computer simulation of the thermal pressure in solids and the equation of state
International Nuclear Information System (INIS)
Welch, D.O.; Dienes, G.J.; Paskin, A.
1976-01-01
The equation of state of solids was investigated with molecular dynamics techniques by obtaining the pressure as a function of temperature over a wide range of compressions. Data were obtained for fcc crystals with Lennard--Jones interactions and for bcc crystals with Morse interactions. The results were analyzed in terms of the Mie--Gruneisen equation of state. The Gruneisen constant at zero temperature is found to be essentially that obtained from the volume dependence of the mean-squared lattice vibration frequency, and its temperature dependence can be approximated well with a self-consistent cell model. Calculated results are compared with experimental data for argon along the melting line
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.
Põneva kappkemmerguga mõisahoones hakkab sõitma lift / Vilja Kohler
Kohler, Vilja, 1966-
2005-01-01
Tartumaal asuva Tammistu mõisa rekonstrueerimisest, projekt AS Restor arhitektidelt Mart Keskkülalt ja Reet Saluverelt. Peahoonesse tuleb puuetega laste rehabilitatsioonikeskus. Kommenteerib Meelis Joost
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.
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.
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
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.
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
A simple extrapolation of thermodynamic perturbation theory to infinite order.
Ghobadi, Ahmadreza F; Elliott, J Richard
2015-09-21
Recent analyses of the third and fourth order perturbation contributions to the equations of state for square well spheres and Lennard-Jones chains show trends that persist across orders and molecular models. In particular, the ratio between orders (e.g., A3/A2, where A(i) is the ith order perturbation contribution) exhibits a peak when plotted with respect to density. The trend resembles a Gaussian curve with the peak near the critical density. This observation can form the basis for a simple recursion and extrapolation from the highest available order to infinite order. The resulting extrapolation is analytic and therefore cannot fully characterize the critical region, but it remarkably improves accuracy, especially for the binodal curve. Whereas a second order theory is typically accurate for the binodal at temperatures within 90% of the critical temperature, the extrapolated result is accurate to within 99% of the critical temperature. In addition to square well spheres and Lennard-Jones chains, we demonstrate how the method can be applied semi-empirically to the Perturbed Chain - Statistical Associating Fluid Theory (PC-SAFT).
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Pressure control in interfacial systems: Atomistic simulations of vapor nucleation
Marchio, S.; Meloni, S.; Giacomello, A.; Valeriani, C.; Casciola, C. M.
2018-02-01
A large number of phenomena of scientific and technological interest involve multiple phases and occur at constant pressure of one of the two phases, e.g., the liquid phase in vapor nucleation. It is therefore of great interest to be able to reproduce such conditions in atomistic simulations. Here we study how popular barostats, originally devised for homogeneous systems, behave when applied straightforwardly to heterogeneous systems. We focus on vapor nucleation from a super-heated Lennard-Jones liquid, studied via hybrid restrained Monte Carlo simulations. The results show a departure from the trends predicted for the case of constant liquid pressure, i.e., from the conditions of classical nucleation theory. Artifacts deriving from standard (global) barostats are shown to depend on the size of the simulation box. In particular, for Lennard-Jones liquid systems of 7000 and 13 500 atoms, at conditions typically found in the literature, we have estimated an error of 10-15 kBT on the free-energy barrier, corresponding to an error of 104-106 s-1σ-3 on the nucleation rate. A mechanical (local) barostat is proposed which heals the artifacts for the considered case of vapor nucleation.
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.
Ruffino, F.; Canino, A.; Grimaldi, M. G.; Giannazzo, F.; Roccaforte, F.; Raineri, V.
2009-11-01
Si nanowires grown by the vapour-liquid-solid technique acquired fundamental relevance in the design of innovative nanostructured devices for electronic and optoelectronic applications. Au clusters deposited on Si are widely used as catalysts of the Si nanowires growth. It has been recognized that the starting Au nanoclusters size distribution strongly influences the final distribution of the Si nanowires and therefore the performances of the nanostructured devices based on them. In the present work we illustrate the formation of Au/Si droplets by the deposition of a thick Au film on Si(100) and annealing at 873K for different times. We focus our attention on the study of the evolution of the droplets size distribution and center-to-center distance distribution as a function of the annealing time at 873K using microscopic techniques such as atomic force microscopy, and scanning electron microscopy. The droplets isothermal-induced self-organization is shown to be a ripening process of hemispherical three dimensional structures limited by the Au surface diffusion. The application of the ripening theory allowed us to calculate the surface diffusion coefficient and all the other parameters needed to describe the entire process.
2015-06-01
resolution live cell imaging,” Lab Chip 11(3), 484–489 (2011). 6. C. Fang, L. Shao, Y. Zhao, J. Wang, and H. Wu, “A gold nanocrystal /poly...FOL 1402PLY-617-1457, Furukawa Electric ) of wavelength 1.46 μm for heating the microdroplet. A current source (LDX-3620, ILX Lightwave
2013-09-01
Unclassified c. THIS PAGE Unclassified SAR 31 19b. TELEPHONE NO (include area code ) 661-525-5449 Standard Form 298 (Rev. 8-98) Prescribed by ANSI...D.; Massone, K.; Szarvas, L.; Nemeth , B.; Veszpremi, T.; Nyulaszi, L. Carbenes in Ionic Liquids. New J. Chem. 2010, 34, 3004-3009. 88
Formation of Nanodroplets in N2/H2O/SO2 under Irradiation of Fast Proton Beams
DEFF Research Database (Denmark)
Nakai, Youchi; Shigeoka, Tomita; Funada, Shuhei
The droplet formation induced by cosmic ray in the terrestrial atmosphere attract certainattention in recent decades because this process could be important to understand thepossible relationship between cosmic ray and climate on the earth. The role of energetic ionsfor the droplet formation would...... measured with adifferential mobility analyzer. We found that the mass yield of generated droplets showedlinear dependence on the amount of SO2 oxidation. This behavior is different from binarynucleation theory of water and H2SO4. The difference might indicates importance ofconsidering the droplet formation...
JPRS Report, Science & Technology: Europe, Economic Competitiveness.
1991-06-27
Venture [Joost Melten; Rijswijk BIOTECHNOLOGIE IN NEDERLAND, Apr 91] 43 Thomson-CSF, British Aerospace End Joint Missile Project [Paris LE MONDE, 16...1991 WEST EUROPE 43 Five Biotech Companies Form Joint Venture 91AN0380 Rijswijk BIOTECHNOLOGIE IN NEDERLAND in Dutch Apr 91 p 37 [Article by Joost
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
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)
Nonequilibrium thermodynamics of an interface
Schweizer, Marco; Öttinger, Hans Christian; Savin, Thierry
2016-05-01
Interfacial thermodynamics has deep ramifications in understanding the boundary conditions of transport theories. We present a formulation of local equilibrium for interfaces that extends the thermodynamics of the "dividing surface," as introduced by Gibbs, to nonequilibrium settings such as evaporation or condensation. By identifying the precise position of the dividing surface in the interfacial region with a gauge degree of freedom, we exploit gauge-invariance requirements to consistently define the intensive variables for the interface. The model is verified under stringent conditions by employing high-precision nonequilibrium molecular-dynamics simulations of a coexisting vapor-liquid Lennard-Jones fluid. We conclude that the interfacial temperature is determined using the surface tension as a "thermometer," and it can be significantly different from the temperatures of the adjacent phases. Our findings lay foundations for nonequilibrium interfacial thermodynamics.
Parameter-free dissipation in simulated sliding friction
Benassi, A.; Vanossi, A.; Santoro, G. E.; Tosatti, E.
2010-08-01
Nonequilibrium molecular-dynamics simulations, of crucial importance in sliding friction, are hampered by arbitrariness and uncertainties in the way Joule heat is removed. We implement in a realistic frictional simulation a parameter-free, non-Markovian, stochastic dynamics, which, as expected from theory, absorbs Joule heat precisely as a semi-infinite harmonic substrate would. Simulating stick-slip friction of a slider over a two-dimensional Lennard-Jones solid, we compare our virtually exact frictional results with approximate ones from commonly adopted empirical dissipation schemes. While the latter are generally in serious error, we show that the exact results can be closely reproduced by a viscous Langevin dissipation at the boundary layer, once the backreflected frictional energy is variationally optimized.
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.
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. ).
DEFF Research Database (Denmark)
Toxværd, Søren; Dyre, J. C.
2011-01-01
. Lett. 103, 170601 (2009);10.1103/PhysRevLett.103.170601 J. Chem. Phys. 134, 214503 (2011)10.1063/1.3592709] . We present simulations of the standard Lennard-Jones liquid at several condensed-fluid state points, including a fairly low density state and a very high density state, as well as simulations......The traditional view that the physical properties of a simple liquid are determined primarily by its repulsive forces was recently challenged by Berthier and Tarjus, who showed that in some cases ignoring the attractions leads to large errors in the dynamics [L. Berthier and G. Tarjus, Phys. Rev...... are included in the simulations. What matters is whether or not interactions are included from all particles within the first coordination shell – the attractive forces can thus be ignored, but only at extremely high densities. The recognition of the importance of a local shell in condensed fluids goes back...
Probing heterogeneous dynamics from spatial density correlation in glass-forming liquids.
Li, Yan-Wei; Zhu, You-Liang; Sun, Zhao-Yan
2016-12-01
We numerically investigate the connection between spatial density correlation and dynamical heterogeneity in glass-forming liquids. We demonstrate that the cluster size defined by the spatial aggregation of densely packed particles (DPPs) can better capture the difference between the dynamics of the Lennard-Jones glass model and the Weeks-Chandler-Andersen truncation model than the commonly used pair correlation functions. More interestingly, we compare the mobility of DPPs and loosely packed particles, and we find that high local density correlates well with slow dynamics in systems with relatively hard repulsive interactions but links to mobile ones in the system with soft repulsive interactions at one relaxation time scale. Our results show clear evidence that the above model dependence behavior stems from the hopping motion of DPPs at the end of the caging stage due to the compressive nature of soft repulsive spheres, which activates the dynamics of DPPs in the α relaxation stage.
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.
Energy Technology Data Exchange (ETDEWEB)
Geysermans, P.; Pontikis, V. [Centre National de la Recherche Scientifique (CNRS), 94 - Vitry-sur-Seine (France). Centre d' Etudes de Chimie Metallurgique
2002-09-01
The atomic structure of the solid-liquid heterophase interface was investigated by using molecular dynamics. Two kinds of systems were studied; the first one was crystalline copper with (100) and (111) surface terminations in contact with liquid aluminium, while in the second one the interface was modelled by two systems in contact made of Lennard-Jones particles with different size ({sigma}) and energy ({epsilon}) parameters. We found that at the interface the liquid was layered whatever the crystallographic orientation of the surface. The layering of the liquid is still preserved when the ratio of particles sites ({chi}={sigma}{sub 1}/{sigma}{sub 2}) changes while an epitaxial relationship is always found between the crystal and the first liquid layer. The average density of the latter is closely related to the {chi} value. (authors)
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.
Cantilever-based sensing: the origin of surface stress and optimization strategies
International Nuclear Information System (INIS)
Godin, Michel; Tabard-Cossa, Vincent; Miyahara, Yoichi; Grutter, Peter; Monga, Tanya; Bruce Lennox, R; Williams, P J; Beaulieu, L Y
2010-01-01
Many interactions drive the adsorption of molecules on surfaces, all of which can result in a measurable change in surface stress. This article compares the contributions of various possible interactions to the overall induced surface stress for cantilever-based sensing applications. The surface stress resulting from adsorption-induced changes in the electronic density of the underlying surface is up to 2-4 orders of magnitude larger than that resulting from intermolecular electrostatic or Lennard-Jones interactions. We reveal that the surface stress associated with the formation of high quality alkanethiol self-assembled monolayers on gold surfaces is independent of the molecular chain length, supporting our theoretical findings. This provides a foundation for the development of new strategies for increasing the sensitivity of cantilever-based sensors for various applications.
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.
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.
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.
Isoviscosity lines and the liquid-glass transition in simple liquids.
Fomin, Yu D; Brazhkin, V V; Ryzhov, V N
2012-07-01
This article presents the study of the generic behavior of viscosity of liquids based on some simple theoretical models, the soft-spheres and Lennard-Jones systems. The use of these simple models allows us to investigate in detail the viscosity behavior in a wide range of temperatures and pressures including the high-temperature-high-pressure limits. Based on the simulation results, we discuss the shape of isoviscosity lines and analyze the glass transition at high temperatures and high pressures. Despite the fact that the viscosity drastically increases in the limit of high temperatures and high pressures along the melting line, the relaxation time rapidly decreases in this region, and the system becomes further from the glass transition.
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.
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.
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.
Hatch, Harold W.; Jiao, Sally; Mahynski, Nathan A.; Blanco, Marco A.; Shen, Vincent K.
2017-12-01
Virial coefficients are predicted over a large range of both temperatures and model parameter values (i.e., alchemical transformation) from an individual Mayer-sampling Monte Carlo simulation by statistical mechanical extrapolation with minimal increase in computational cost. With this extrapolation method, a Mayer-sampling Monte Carlo simulation of the SPC/E (extended simple point charge) water model quantitatively predicted the second virial coefficient as a continuous function spanning over four orders of magnitude in value and over three orders of magnitude in temperature with less than a 2% deviation. In addition, the same simulation predicted the second virial coefficient if the site charges were scaled by a constant factor, from an increase of 40% down to zero charge. This method is also shown to perform well for the third virial coefficient and the exponential parameter for a Lennard-Jones fluid.
Cumulative distribution functions associated with bubble-nucleation processes in cavitation
Watanabe, Hiroshi
2010-11-15
Bubble-nucleation processes of a Lennard-Jones liquid are studied by molecular dynamics simulations. Waiting time, which is the lifetime of a superheated liquid, is determined for several system sizes, and the apparent finite-size effect of the nucleation rate is observed. From the cumulative distribution function of the nucleation events, the bubble-nucleation process is found to be not a simple Poisson process but a Poisson process with an additional relaxation time. The parameters of the exponential distribution associated with the process are determined by taking the relaxation time into account, and the apparent finite-size effect is removed. These results imply that the use of the arithmetic mean of the waiting time until a bubble grows to the critical size leads to an incorrect estimation of the nucleation rate. © 2010 The American Physical Society.
International Nuclear Information System (INIS)
Matsuyama, M.; Miyake, H.; Ashida, K.; Watanabe, K.
1982-01-01
Tetrafluoroethylene (TFE) is widely used for conventional tritium handling systems such as vacuum seals, tubing and so on. We measured the permeation of the three hydrogen isotopes, methane and the inert gases through a TFE film at room temperature by means of the time-lag method in order to establish the physicochemical properties which determine the solubility and diffusivity of those gases. It was found that the diffusion constant of the inert gases changed exponentially with the heat of vaporization and the solubility was an exponential function of the Lennard-Jones force constant of the gases. On the other hand, hydrogen isotopes and methane deviated from these relations. It is concluded that chemical interactions between the solute and the solvent play an important role for the dissolution and the diffusion of these gases in TFE. (orig.)
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.
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.
Moore, Elaine A.; Mortimer, Michael; Wigglesworth, Christopher; Williams, Martin A. K.
1999-07-01
Molecular modelling is used to calculate the barrier heights to reorientation for the trifluoromethyl group, CF 3, in both lithium trifluoromethanesulphonate, LiCF 3SO 3, and the crystalline complex of this salt with poly(ethylene oxide), PEO. The calculated barrier heights are compared with those determined from 19F spin-lattice relaxation studies. In the case of LiCF 3SO 3, fluorine-fluorine non-bonded interactions are shown to play a dominant role in determining the barrier height to CF 3 group reorientation and optimised Lennard-Jones parameters for this interaction are determined. In the crystalline complex, PEO 3·LiCF 3SO 3, it is suggested that CF 3 group reorientation is strongly influenced by segmental motions of the PEO chain.
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.
Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus.
Herruzo, Elena T; Garcia, Ricardo
2012-01-01
Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip-surface forces such as the Lennard-Jones and Derjaguin-Muller-Toporov forces.
Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus
Directory of Open Access Journals (Sweden)
Elena T. Herruzo
2012-03-01
Full Text Available Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip–surface forces such as the Lennard-Jones and Derjaguin–Muller–Toporov forces.
Yin, Jian; Fenley, Andrew T.; Henriksen, Niel M.; Gilson, Michael K.
2015-01-01
Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by non-optimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery. PMID:26181208
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.
Multilayer approximation for a confined fluid in a slit pore
Directory of Open Access Journals (Sweden)
V. A. Kuz
2010-02-01
Full Text Available A simple Lennard-Jones fluid confined in a slit nanopore with hard walls is studied on the basis of a multilayer structured model. Each layer is homogeneous and parallel to the walls of the pore. The Helmholtz energy of this system is constructed following van der Waals-like approximations, with the advantage that the model geometry permits to obtain analytical expressions for the integrals involved. Being the multilayer system in thermodynamic equilibrium, a system of non-linear equations is obtained for the densities and widths of the layers. A numerical solution of the equations gives the density profile and the longitudinal pressures. The results are compared with Monte Carlo simulations and with experimental data for Nitrogen, showing very good agreement.Received: 23 December 2009, Accepted: 24 February 2010; Edited by: D. A. Stariolo; DOI: 10.4279/PIP.020002
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...
Gas Permeation Characteristics across Nano-Porous Inorganic Membranes
Directory of Open Access Journals (Sweden)
M.R Othman, H. Mukhtar
2012-10-01
Full Text Available An overview of parameters affecting gas permeation in inorganic membranes is presented. These factors include membrane physical characteristics, operational parameters and gas molecular characteristics. The membrane physical characteristics include membrane materials and surface area, porosity, pore size and pore size distribution and membrane morphology. The operational parameters include feed flow rate and concentration, stage cut, temperature and pressure. The gas molecular characteristics include gas molecular weight, diameter, critical temperature, critical pressure, Lennard-Jones parameters and diffusion volumes. The current techniques of material characterization may require complementary method in describing microscopic heterogeneity of the porous ceramic media. The method to be incorporated in the future will be to apply a stochastic model and/or fractal dimension. Keywords: Inorganic membrane, surface adsorption, Knudsen diffusion, Micro-porous membrane, permeation, gas separation.
Comparing crystal-melt interfacial free energies through homogeneous nucleation rates
International Nuclear Information System (INIS)
Bai Xianming; Li Mo
2008-01-01
In this work, we compared several available crystal-melt interfacial free energies via homogeneous nucleation rates in a pure Lennard-Jones model system using both model fitting and numerical methods. We examined the homogeneous nucleation temperature obtained from the classical nucleation theory using the available interfacial free energies from three different methods as inputs, i.e. the free energy integration method, the interface fluctuation method and the classical nucleation theory based method. We found that the critical temperature obtained by using the interfacial free energy calculated recently (Bai and Li 2006 J. Chem. Phys. 124 124707) is in better agreement with that obtained from spontaneous crystallization in an independent molecular dynamics simulation. The discrepancies among the interface energies are discussed in light of these results
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...
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
Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model
Invernizzi, Michele; Valsson, Omar; Parrinello, Michele
2017-03-01
A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg-Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard-Jones fluid in the region close to the liquid-vapor critical point. The procedure is general and can be adapted to other coarse-grained models.
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.
Statistical ensembles and molecular dynamics studies of anisotropic solids. II
International Nuclear Information System (INIS)
Ray, J.R.; Rahman, A.
1985-01-01
We have recently discussed how the Parrinello--Rahman theory can be brought into accord with the theory of the elastic and thermodynamic behavior of anisotropic media. This involves the isoenthalpic--isotension ensemble of statistical mechanics. Nose has developed a canonical ensemble form of molecular dynamics. We combine Nose's ideas with the Parrinello--Rahman theory to obtain a canonical form of molecular dynamics appropriate to the study of anisotropic media subjected to arbitrary external stress. We employ this isothermal--isotension ensemble in a study of a fcc→ close-packed structural phase transformation in a Lennard-Jones solid subjected to uniaxial compression. Our interpretation of the Nose theory does not involve a scaling of the time variable. This latter fact leads to simplifications when studying the time dependence of quantities
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...
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)
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.
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.
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
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.
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.
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.
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.
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
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)
Hamed Mashhadzadeh, A.; Fereidoon, A.; Ghorbanzadeh Ahangari, M.
2017-11-01
In present work, we performed Density Functional Theory calculation (DFT) to prepare polypropylene (PP) and polyvinyl chloride (PVC) nanocomposite. For mentioned purpose, we chose Boron-Nitride graphene (BN-graphene) sheet as nano reinforcement. Next, we calculated adsorbed energy between these two polymeric matrixes with BN-monolayer sheet. Our DFT results demonstrated that interaction energy between PP/BN-graphene and PVC/BN-graphene are equal, approximately, because in mentioned two nanocomposite systems, polymer matrix approached to nano reinforcement from hydrogen atom in optimized structure. Then, the adsorbed energy and equilibrium distance between mentioned polymeric matrixes and BN-graphene sheet in nanocomposite with increasing the number of polymer monomers onto surface of BN-graphene were calculated. Finally, we modeled van der Waals interfacial interaction between polymer matrixes and nano reinforcement with linear classical spring by using lennard-jones parameters.
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
Monte Carlo simulation of continuous-space crystal growth
International Nuclear Information System (INIS)
Dodson, B.W.; Taylor, P.A.
1986-01-01
We describe a method, based on Monte Carlo techniques, of simulating the atomic growth of crystals without the discrete lattice space assumed by conventional Monte Carlo growth simulations. Since no lattice space is assumed, problems involving epitaxial growth, heteroepitaxy, phonon-driven mechanisms, surface reconstruction, and many other phenomena incompatible with the lattice-space approximation can be studied. Also, use of the Monte Carlo method circumvents to some extent the extreme limitations on simulated timescale inherent in crystal-growth techniques which might be proposed using molecular dynamics. The implementation of the new method is illustrated by studying the growth of strained-layer superlattice (SLS) interfaces in two-dimensional Lennard-Jones atomic systems. Despite the extreme simplicity of such systems, the qualitative features of SLS growth seen here are similar to those observed experimentally in real semiconductor systems
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.
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
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
Energy Technology Data Exchange (ETDEWEB)
Liu, T.K.
1980-03-01
The thermogravimetric method was used to study high temperature corrosion under SO/sub 2//O/sub 2/ atmosphere applied to Armco 18SR alloys with different heat treatment histories, Armco T310 and pure chromium between 750 and 1100/sup 0/C. The weight gain follows the parabolic rate law. The volatilization of the protective Cr/sub 2/O/sub 3/ layer via formation of CrO/sub 3/ was taken into account above 900/sup 0/C for long time runs. The parabolic rate and the volatilization rate, derived from fitting the experimental data to the modified Tedmon's non-linear model, were correlated using the Arrhenius equation. Armco 18SR-C has the best corrosion resistance of the Armco 18SR alloys. Armco T310 is not protective at high temperatures. The available rate data on the oxidation of chromium oxide, chlorination of chromium, oxidation-chlorination of chromium oxide, chlorination of nickel and chlorination of iron were found to be predictable. The calculation of high temperature volatilization rate was performed using the available fluid correlation equations and the Lennard-Jones parameters derived from the molecule with similar structure and from the low temperature viscosity measurement. The lower predicted volatilization rate is due to the use of the Chapman-Enskog equation with the Lennard-Jones parameters mostly derived from the low temperature viscosity measurement. This was substantiated by comparing the reliable high temperature diffusion rate in the literature with the above mentioned calculational method. The experimental volatilization rates of this study are compared with the other related studies and the mass transfer predictions.
Using the k-d Tree Data Structure to Accelerate Monte Carlo Simulations.
Chen, Qile P; Xue, Bai; Siepmann, J Ilja
2017-04-11
The k-d tree data structure is implemented in a Monte Carlo (MC) molecular simulation program to accelerate the range search for particles or interaction sites within the cutoff distance when Lennard-Jones and Coulomb interactions are computed. MC simulations are performed for different molecules in various ensembles to assess the efficiency enhancements due to the k-d tree data structure. It is found that the use of k-d trees accelerates significantly simulations for Lennard-Jones particles in the NVT and NVT-Gibbs ensembles and for n-butane and 2,4,6,8,10,12,14,16,18,20,22-undecamethylpentacosane represented by the TraPPE-UA force field in the NpT ensemble. Simulations for TraPPE-UA ethanol in the NpT ensemble and for the rigid TIP4P water model in the Gibbs ensemble gain slightly in efficiency with the k-d tree, whereas simulations for TIP4P water in the NpT ensemble do not benefit from the use of the k-d tree. The speed-up can be attributed to the reduction in the number of distance calculations in the range search from scaling as [Formula: see text] to [Formula: see text]. In addition, these tests suggest that the efficiency gain from the use of the k-d tree data structure depends on the flexibility of the molecular model (requiring configurational-bias MC moves to sample changes in conformation), on the ensemble (with open ensembles requiring special MC moves to aid particle transfers), and on the number of interaction sites per molecule (with compact multisite models not seeing an efficiency gain). Overall, the use of the k-d tree data structure can substantially enhance MC simulation efficiency for a variety of systems, and it will enable simulations for larger system sizes in the future.
Wilhelmsen, Øivind; Trinh, Thuat T.; Lervik, Anders
2018-01-01
Density gradient theory for fluids has played a key role in the study of interfacial phenomena for a century. In this work, we revisit its fundamentals by examining the vapor-liquid interface of argon, represented by the cut and shifted Lennard-Jones fluid. The starting point has traditionally been a Helmholtz energy functional using mass densities as arguments. By using rather the internal energy as starting point and including the entropy density as an additional argument, following thereby the phenomenological approach from classical thermodynamics, the extended theory suggests that the configurational part of the temperature has different contributions from the parallel and perpendicular directions at the interface, even at equilibrium. We find a similar anisotropy by examining the configurational temperature in molecular dynamics simulations and obtain a qualitative agreement between theory and simulations. The extended theory shows that the temperature anisotropy originates in nonlocal entropic contributions, which are currently missing from the classical theory. The nonlocal entropic contributions discussed in this work are likely to play a role in the description of both equilibrium and nonequilibrium properties of interfaces. At equilibrium, they influence the temperature- and curvature-dependence of the surface tension. Across the vapor-liquid interface of the Lennard Jones fluid, we find that the maximum in the temperature anisotropy coincides precisely with the maximum in the thermal resistivity relative to the equimolar surface, where the integral of the thermal resistivity gives the Kapitza resistance. This links the temperature anisotropy at equilibrium to the Kapitza resistance of the vapor-liquid interface at nonequilibrium.
Scaled-particle theory analysis of cylindrical cavities in solution.
Ashbaugh, Henry S
2015-04-01
The solvation of hard spherocylindrical solutes is analyzed within the context of scaled-particle theory, which takes the view that the free energy of solvating an empty cavitylike solute is equal to the pressure-volume work required to inflate a solute from nothing to the desired size and shape within the solvent. Based on our analysis, an end cap approximation is proposed to predict the solvation free energy as a function of the spherocylinder length from knowledge regarding only the solvent density in contact with a spherical solute. The framework developed is applied to extend Reiss's classic implementation of scaled-particle theory and a previously developed revised scaled-particle theory to spherocylindrical solutes. To test the theoretical descriptions developed, molecular simulations of the solvation of infinitely long cylindrical solutes are performed. In hard-sphere solvents classic scaled-particle theory is shown to provide a reasonably accurate description of the solvent contact correlation and resulting solvation free energy per unit length of cylinders, while the revised scaled-particle theory fitted to measured values of the contact correlation provides a quantitative free energy. Applied to the Lennard-Jones solvent at a state-point along the liquid-vapor coexistence curve, however, classic scaled-particle theory fails to correctly capture the dependence of the contact correlation. Revised scaled-particle theory, on the other hand, provides a quantitative description of cylinder solvation in the Lennard-Jones solvent with a fitted interfacial free energy in good agreement with that determined for purely spherical solutes. The breakdown of classical scaled-particle theory does not result from the failure of the end cap approximation, however, but is indicative of neglected higher-order curvature dependences on the solvation free energy.
MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease.
Gunner, M R; Zhu, Xuyu; Klein, Max C
2011-12-01
The pK(a)s of 96 acids and bases introduced into buried sites in the staphylococcal nuclease protein (SNase) were calculated using the multiconformation continuum electrostatics (MCCE) program and the results compared with experimental values. The pK(a)s are obtained by Monte Carlo sampling of coupled side chain protonation and position as a function of pH. The dependence of the results on the protein dielectric constant (ε(prot)) in the continuum electrostatics analysis and on the Lennard-Jones non-electrostatics parameters was evaluated. The pK(a)s of the introduced residues have a clear dependence on ε(prot,) whereas native ionizable residues do not. The native residues have electrostatic interactions with other residues in the protein favoring ionization, which are larger than the desolvation penalty favoring the neutral state. Increasing ε(prot) scales both terms, which for these residues leads to small changes in pK(a). The introduced residues have a larger desolvation penalty and negligible interactions with residues in the protein. For these residues, changing ε(prot) has a large influence on the calculated pK(a). An ε(prot) of 8-10 and a Lennard-Jones scaling of 0.25 is best here. The X-ray crystal structures of the mutated proteins are found to provide somewhat better results than calculations carried out on mutations made in silico. Initial relaxation of the in silico mutations by Gromacs and extensive side chain rotamer sampling within MCCE can significantly improve the match with experiment. Copyright © 2011 Wiley-Liss, Inc.
African Journal of Health Professions Education - Vol 9, No 4 (2017)
African Journals Online (AJOL)
Research: Self-leadership traits of academics to conform to a changing highereducation environment · EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT. K. Jooste, J. Frantz, 199-202 ...
Tudengid noorukese Mozarti armastuse aias / Tiiu Levald
Levald, Tiiu, 1940-
2009-01-01
Mozarti "La finta giardiniera" ("Armastuse pärast aednikuneiu") EMTA ooperistuudio ja Sümfooniaorkestri koostöös, dirigent Risto Joost, lavastaja Thomas Wiedenhofer, kunstnik Inga Vares, 4. ja 5. mail Estonia teatris
Journal of Consumer Sciences - Vol 40 (2012)
African Journals Online (AJOL)
Sensory analysis of cooked fresh meat sausages containing beef offal · EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT. MM Magoro, BI Zondagh, PJ Jooste, L Morey ...
Czech Academy of Sciences Publication Activity Database
Uras-Aytemiz, N.; Cwiklik, Lukasz; Devlin, J. P.
2012-01-01
Roč. 137, č. 20 (2012), s. 204501 ISSN 0021-9606 Institutional support: RVO:61388955 Keywords : Fourier transform infrared emission spectra * clathrate hydrate * simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.164, year: 2012
Qu, Fei; Li, Chilin; Wang, Zumin; Wen, Yuren; Richter, Gunther; Strunk, Horst P.
2015-05-01
Building porosity in monolithic materials is highly desired to design 3D electrodes, however ex-situ introduction or in-situ generation of nano-scale sacrificial template is still a great challenge. Here Al-Si eutectic droplet templates are uniformly injected into bulk Si through Al-induced solid-solid convection to construct a highly porous Si framework. This process is concomitant with process-inherent conformal coating of ion-conductive oxide. Such an all-in-one method has generated a (continuously processed) high-capacity Si anode integrating longevity and stable electrolyte-anode diaphragm for Li-ion batteries (e.g. a reversible capacity as large as ~1800 mAh/g or ~350 μAh/cm2-μm with a CE of ~99% at 0.1 C after long-term 400 cycles).
Leong, Kai-Yang; Wang, Feng
2018-04-01
The surface tension of nanoscale droplets of water was studied with molecular dynamics simulations using the BLYPSP-4F water potential. The internal pressure of the droplet was measured using an empirical correlation between the pressure and density, established through a series of bulk simulations performed at pressures from 1 to 1000 bars. Such a procedure allows for reliable determination of internal pressure without the need to calculate the local virial. The surface tension, estimated with the Young-Laplace relation, shows good agreement with the Tolman equation with a Tolman length of -0.48 Å. The interface of a liquid water droplet is shown to be around 1.1-1.3 nm thick depending on radii. The fairly thick interface region puts a lower limit on the size of droplets that still have a bulk-like interior.
Guillaume-Gentil, Orane; Zahn, Raphael; Lindhoud, Saskia; Graf, Norma; Voros, Janos; Zambelli, Tomaso
2011-01-01
Using atomic force microscopy, we investigated how the morphology of layer-by-layer deposited polyelectrolyte multilayers is influenced by the physical properties of the supporting substrate. The surface coverage of the assembly and its topography were found to be dependent on the dielectric
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
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
Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten
2017-11-01
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.
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)
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.
Non-equilibrium phase stabilization versus bubble nucleation at a nanoscale-curved Interface
Schiffbauer, Jarrod; Luo, Tengfei
Using continuum dynamic van der Waals theory in a radial 1D geometry with a Lennard-Jones fluid model, we investigate the nature of vapor bubble nucleation near a heated, nanoscale-curved convex interface. Vapor bubble nucleation and growth are observed for interfaces with sufficiently large radius of curvature while phase stabilization of a superheated fluid layer occurs at interfaces with smaller radius. The hypothesis that the high Laplace pressure required for stable equilibrium of very small bubbles is responsible for phase stability is tested by effectively varying the parameter which controls liquid-vapor surface tension. In doing so, the liquid-vapor surface tension- hence Laplace pressure-is shown to have limited effect on phase stabilization vs. bubble nucleation. However, the strong dependence of nucleation on leading-order momentum transport, i.e. viscous dissipation, near the heated inner surface is demonstrated. We gratefully acknowledge ND Energy for support through the ND Energy Postdoctoral Fellowship program and the Army Research Office, Grant No. W911NF-16-1-0267, managed by Dr. Chakrapani Venanasi.
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.
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.
International Nuclear Information System (INIS)
Kamberaj, Hiqmet
2015-01-01
In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4, 5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias
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
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.
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.
Sun, Shuyu
2013-06-01
This paper introduces an efficient technique to generate new molecular simulation Markov chains for different temperature and density conditions, which allow for rapid extrapolation of canonical ensemble averages at a range of temperatures and densities different from the original conditions where a single simulation is conducted. Obtained information from the original simulation are reweighted and even reconstructed in order to extrapolate our knowledge to the new conditions. Our technique allows not only the extrapolation to a new temperature or density, but also the double extrapolation to both new temperature and density. The method was implemented for Lennard-Jones fluid with structureless particles in single-gas phase region. Extrapolation behaviors as functions of extrapolation ranges were studied. Limits of extrapolation ranges showed a remarkable capability especially along isochors where only reweighting is required. Various factors that could affect the limits of extrapolation ranges were investigated and compared. In particular, these limits were shown to be sensitive to the number of particles used and starting point where the simulation was originally conducted.
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.
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.
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.
Lin, Fang-Yu; MacKerell, Alexander D
2018-02-13
The quality of the force field is crucial to ensure the accuracy of simulations used in molecular modeling, including computer-aided drug design (CADD). To perform more accurate modeling and simulations of halogenated molecules, in this study the polarizable force field based on the classical Drude oscillator model was extended to both aliphatic and aromatic systems using halogenated ethane and benzene model compounds for the halogens F, Cl, Br, and I. The force field parameters were optimized targeting quantum mechanical dipole moments, water interactions, and molecular polarizabilities as well as experimental observables, including enthalpies of vaporization, molecular volumes, hydration free energies, and dielectric constants. The developed halogenated polarizable force field is capable of reproducing QM relative energies and geometries of both halogen bonds and halogen-hydrogen bond donor interactions at an unprecedented level due to the inclusion of a virtual particle and anisotropic atomic polarizability on the halogen and, notably, the inclusion of Lennard-Jones parameters on the halogen Drude particle. The model was validated on the basis of its ability to accurately reproduce pure solvent properties for halogenated naphthalenes and alkanes, including species analogous to those used as refrigerants. Accordingly, it is anticipated that the model will be applicable for the study of halogenated derivatives in CADD as well as in other chemical and biophysical studies.
Systematic coarse-graining in nucleation theory
Energy Technology Data Exchange (ETDEWEB)
Schweizer, M., E-mail: marco.schweizer@math.ethz.ch [Department of Materials, Polymer Physics, ETH Zurich, Vladimir-Prelog-Weg 5, 8093 Zurich (Switzerland); Sagis, L. M. C., E-mail: leonard.sagis@wur.nl [Department of Materials, Polymer Physics, ETH Zurich, Vladimir-Prelog-Weg 5, 8093 Zurich (Switzerland); Food Physics Group, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen (Netherlands)
2015-08-21
In this work, we show that the standard method to obtain nucleation rate-predictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3 − 5 orders of magnitude from the recent brute-force molecular dynamics simulations [Diemand et al., J. Chem. Phys. 139, 074309 (2013)] conducted in the experimental accessible supersaturation regime for Lennard-Jones argon. We argue that this is due to the truncated state space the literature mostly relies on, where the number of atoms in a nucleus is considered the only relevant order parameter. We here formulate the nonequilibrium statistical mechanics of nucleation in an extended state space, where the internal energy and momentum of the nuclei are additionally incorporated. We show that the extended model explains the lack in agreement between the molecular dynamics simulations by Diemand et al. and the truncated state space. We demonstrate additional benefits of using the extended state space; in particular, the definition of a nucleus temperature arises very naturally and can be shown without further approximation to obey the fluctuation law of McGraw and LaViolette. In addition, we illustrate that our theory conveniently allows to extend existing theories to richer sets of order parameters.
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.
Energy Technology Data Exchange (ETDEWEB)
Aguilar, Charles M.; De Almeida, Wagner B. [Laboratorio de Quimica Computacional e Modelagem Molecular (LQC-MM), Departamento de Quimica - ICEX, Universidade Federal de Minas Gerais 31270-901, Belo Horizonte, MG (Brazil); Rocha, Willian R. [Laboratorio de Quimica Computacional e Modelagem Molecular (LQC-MM), Departamento de Quimica - ICEX, Universidade Federal de Minas Gerais 31270-901, Belo Horizonte, MG (Brazil)], E-mail: wrocha@ufmg.br
2008-11-03
A sequential Monte Carlo/Quantum Mechanics approach was used to investigate the solvent effects on d {yields} d transition of the Ni{sup 2+} ion in aqueous and ammonia solutions. A set of Lennard-Jones parameters were generated by modification of the UFF Force Field. The structural results obtained for the liquid structure around the Ni{sup 2+} ion are in very good agreement with the experimental findings. The water molecules in the second coordination shell interact strongly with the first shell, with hydrogen bonds of -14.6 {+-} 3.3 kcal mol{sup -1} which is 30% stronger than in the ammonia complex. The electronic spectrum was evaluated within the TD-DFT approach on the gas phase geometry and also on the Monte Carlo generated clusters, including the long range solvent effects by means of the PCM continuum model. We show that the computed electronic transitions are all red-shifted compared with the experimental results and, the agreement with the experimental values are only qualitative.
International Nuclear Information System (INIS)
Aguilar, Charles M.; De Almeida, Wagner B.; Rocha, Willian R.
2008-01-01
A sequential Monte Carlo/Quantum Mechanics approach was used to investigate the solvent effects on d → d transition of the Ni 2+ ion in aqueous and ammonia solutions. A set of Lennard-Jones parameters were generated by modification of the UFF Force Field. The structural results obtained for the liquid structure around the Ni 2+ ion are in very good agreement with the experimental findings. The water molecules in the second coordination shell interact strongly with the first shell, with hydrogen bonds of -14.6 ± 3.3 kcal mol -1 which is 30% stronger than in the ammonia complex. The electronic spectrum was evaluated within the TD-DFT approach on the gas phase geometry and also on the Monte Carlo generated clusters, including the long range solvent effects by means of the PCM continuum model. We show that the computed electronic transitions are all red-shifted compared with the experimental results and, the agreement with the experimental values are only qualitative
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)
Directory of Open Access Journals (Sweden)
Alberto G. Albesa
2010-01-01
Full Text Available Se describe un modelo de carbón nanoporoso que consiste en moléculas poliaromáticas que poseen diferentes números de anillos, de forma tal de obtener diferentes unidades básicas estructurales. La adsorción de nitrógeno y la obtención del calor isostérico de adsorción son modeladas mediante simulaciones Monte Carlo. El nitrógeno es descrito mediante el modelo de 1 centro de Lennard Jones y se utiliza una interacción tomada de a pares. Las áreas específicas de los sustratos muestran una buena correlación con los datos obtenidos experimentalmente, como así también las isotermas simuladas. Los resultados muestran que no existe un efecto significativo del tamaño de los agregados (clusters en la capacidad de adsorción ni en los calores isostéricos, excepto para el caso de los cluster mas pequeños, donde un aumento del calor isostérico es observado con mayores cargas.
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.
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.
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.
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
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...
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
Local order and crystallization of dense polydisperse hard spheres
Coslovich, Daniele; Ozawa, Misaki; Berthier, Ludovic
2018-04-01
Computer simulations give precious insight into the microscopic behavior of supercooled liquids and glasses, but their typical time scales are orders of magnitude shorter than the experimentally relevant ones. We recently closed this gap for a class of models of size polydisperse fluids, which we successfully equilibrate beyond laboratory time scales by means of the swap Monte Carlo algorithm. In this contribution, we study the interplay between compositional and geometric local orders in a model of polydisperse hard spheres equilibrated with this algorithm. Local compositional order has a weak state dependence, while local geometric order associated to icosahedral arrangements grows more markedly but only at very high density. We quantify the correlation lengths and the degree of sphericity associated to icosahedral structures and compare these results to those for the Wahnström Lennard-Jones mixture. Finally, we analyze the structure of very dense samples that partially crystallized following a pattern incompatible with conventional fractionation scenarios. The crystal structure has the symmetry of aluminum diboride and involves a subset of small and large particles with size ratio approximately equal to 0.5.
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.
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.
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.
The barrier to ice nucleation in monatomic water
Prestipino, Santi
2018-03-01
Crystallization from a supercooled liquid initially proceeds via the formation of a small solid embryo (nucleus), which requires surmounting an activation barrier. This phenomenon is most easily studied by numerical simulation, using specialized biased-sampling techniques to overcome the limitations imposed by the rarity of nucleation events. Here, I focus on the barrier to homogeneous ice nucleation in supercooled water, as represented by the monatomic-water model, which in the bulk exhibits a complex interplay between different ice structures. I consider various protocols to identify solidlike particles on a computer, which perform well enough for the Lennard-Jones model, and compare their respective impact on the shape and height of the nucleation barrier. It turns out that the effect is stronger on the nucleus size than on the barrier height. As a by-product of the analysis, I determine the structure of the nucleation cluster, finding that the relative amount of ice phases in the cluster heavily depends on the method used for classifying solidlike particles. Moreover, the phase which is most favored during the earlier stages of crystallization may happen, depending on the nucleation coordinate adopted, to be different from the stable polymorph. Therefore, the quality of a reaction coordinate cannot be assessed simply on the basis of the barrier height obtained. I explain how this outcome is possible and why it just points out the shortcoming of collective variables appropriate to simple fluids in providing a robust method of particle classification for monatomic water.
Set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data.
Eckl, Bernhard; Vrabec, Jadran; Hasse, Hans
2008-10-09
A parametrization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e., vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl ether, sulfur dioxide, dimethyl sulfide, thiophene, hydrogen cyanide, acetonitrile, and nitromethane. Most of the models are able to describe the experimental VLE data with deviations of a few percent.
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.
Assessment of numerical optimization algorithms for the development of molecular models
Hülsmann, Marco; Vrabec, Jadran; Maaß, Astrid; Reith, Dirk
2010-05-01
In the pursuit to study the parameterization problem of molecular models with a broad perspective, this paper is focused on an isolated aspect: It is investigated, by which algorithms parameters can be best optimized simultaneously to different types of target data (experimental or theoretical) over a range of temperatures with the lowest number of iteration steps. As an example, nitrogen is regarded, where the intermolecular interactions are well described by the quadrupolar two-center Lennard-Jones model that has four state-independent parameters. The target data comprise experimental values for saturated liquid density, enthalpy of vaporization, and vapor pressure. For the purpose of testing algorithms, molecular simulations are entirely replaced by fit functions of vapor-liquid equilibrium (VLE) properties from the literature to assess efficiently the diverse numerical optimization algorithms investigated, being state-of-the-art gradient-based methods with very good convergency qualities. Additionally, artificial noise was superimposed onto the VLE fit results to evaluate the numerical optimization algorithms so that the calculation of molecular simulation data was mimicked. Large differences in the behavior of the individual optimization algorithms are found and some are identified to be capable to handle noisy function values.
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.
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.
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.
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.
Kazachenko, Sergey; Giovinazzo, Mark; Hall, Kyle Wm; Cann, Natalie M
2015-09-15
A custom code for molecular dynamics simulations has been designed to run on CUDA-enabled NVIDIA graphics processing units (GPUs). The double-precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse-grained and atomistic models, holonomic constraints, Nosé-Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard-Jones and Gay-Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n-hexane/2-propanol mixture; and a liquid crystal mesogen, 2-(4-butyloxyphenyl)-5-octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33-119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69-287 fold improvement and three GPUs yield a 101-377 fold speedup. © 2015 Wiley Periodicals, Inc.
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.
The interpretation of polycrystalline coherent inelastic neutron scattering from aluminium
Roach, Daniel L.; Ross, D. Keith; Gale, Julian D.; Taylor, Jon W.
2013-01-01
A new approach to the interpretation and analysis of coherent inelastic neutron scattering from polycrystals (poly-CINS) is presented. This article describes a simulation of the one-phonon coherent inelastic scattering from a lattice model of an arbitrary crystal system. The one-phonon component is characterized by sharp features, determined, for example, by boundaries of the (Q, ω) regions where one-phonon scattering is allowed. These features may be identified with the same features apparent in the measured total coherent inelastic cross section, the other components of which (multiphonon or multiple scattering) show no sharp features. The parameters of the model can then be relaxed to improve the fit between model and experiment. This method is of particular interest where no single crystals are available. To test the approach, the poly-CINS has been measured for polycrystalline aluminium using the MARI spectrometer (ISIS), because both lattice dynamical models and measured dispersion curves are available for this material. The models used include a simple Lennard-Jones model fitted to the elastic constants of this material plus a number of embedded atom method force fields. The agreement obtained suggests that the method demonstrated should be effective in developing models for other materials where single-crystal dispersion curves are not available. PMID:24282332
Russel, M G; Nieman, F H; Bergers, J M; Stockbrügger, R W
1996-11-01
Smoking has been reported as influencing disease activity in inflammatory bowel disease. The aim of our study was to elucidate the relationship between smoking and aspects of disease-specific quality of life in inflammatory bowel disease. Cross-sectional study. In 1105 prevalent patients with inflammatory bowel disease, diagnosed according to the criteria of Lennard-Jones and Truelove and Witts, disease-specific quality of life was investigated using the Inflammatory Bowel Disease Questionnaire (IBDQ). In Crohn's disease, smoking females reported a lower quality of life than non-smoking females (all four dimensions of the IBDQ). Using an explanatory model of relationships between the four dimensions for the analysis, it became evident that smoking is associated with more bowel symptoms in young Crohn's disease females, with more emotional dysfunction in all Crohn's disease females, and with more systemic symptoms in all three diagnostic groups with marked bowel symptoms. Moderately smoking male ulcerative colitis patients reported fewer bowel complaints compared with non-smoking male ulcerative colitis patients. There is a relationship between smoking and disease-specific quality of life in both ulcerative colitis and Crohn's disease. The hypothesis is presented that a part of the observed differences in the studied quality of life dimensions with respect to age, sex and disease group are related to concomitant oral contraceptive use.
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.
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.
Molecular dynamics simulation of ion mobility in gases
Lai, Rui; Dodds, Eric D.; Li, Hui
2018-02-01
A force field molecular dynamics method is developed to directly simulate ion drift in buffer gases driven by an electric field. The ion mobility and collision cross sections (CCSs) with relevance to ion mobility spectrometry can be obtained from the simulated drift velocity in high-density buffer gases (pressure ˜50 bars) and high electric fields (˜107 V/m). Compared to trajectory methods, the advantage of the molecular dynamics method is that it can simultaneously sample the internal dynamic motions of the ion and the ion-gas collisions. For ions with less than 100 atoms, the simulated collision cross section values can be converged to within ±1%-2% by running a 100 ns simulation for 5-19 h using one computer core. By using a set of element-based Lennard-Jones parameters that are not tuned for different atomic types in different molecules, the simulated collision cross sections for 15 small molecular ions (number of atoms ranging from 17 to 85, mass ranging from 74.1 to 609.4 g/mol) are consistent with experimental values: the mean unsigned error is 2.6 Å2 for He buffer gas and 4.4 Å2 for N2 buffer gas. The sensitivity of the simulated CCS values to random diffusion, drift velocity, electric field strength, temperature, and buffer gas density is examined.
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.
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
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.
Yan, Bailu; Zhao, Zheng; Zhou, Yingcheng; Yuan, Wenyan; Li, Jian; Wu, Jun; Cheng, Daojian
2017-10-01
Swarm intelligence optimization algorithms are mainstream algorithms for solving complex optimization problems. Among these algorithms, the particle swarm optimization (PSO) algorithm has the advantages of fast computation speed and few parameters. However, PSO is prone to premature convergence. To solve this problem, we develop a new PSO algorithm (RPSOLF) by combining the characteristics of random learning mechanism and Levy flight. The RPSOLF algorithm increases the diversity of the population by learning from random particles and random walks in Levy flight. On the one hand, we carry out a large number of numerical experiments on benchmark test functions, and compare these results with the PSO algorithm with Levy flight (PSOLF) algorithm and other PSO variants in previous reports. The results show that the optimal solution can be found faster and more efficiently by the RPSOLF algorithm. On the other hand, the RPSOLF algorithm can also be applied to optimize the Lennard-Jones clusters, and the results indicate that the algorithm obtains the optimal structure (2-60 atoms) with an extraordinary high efficiency. In summary, RPSOLF algorithm proposed in our paper is proved to be an extremely effective tool for global optimization.
Energy Technology Data Exchange (ETDEWEB)
Kamberaj, Hiqmet, E-mail: hkamberaj@ibu.edu.mk [Department of Computer Engineering, International Balkan University, Tashko Karadza 11A, Skopje (Macedonia, The Former Yugoslav Republic of)
2015-09-28
In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4, 5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.
Kamberaj, Hiqmet
2015-09-28
In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4, 5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.
LAMMPS strong scaling performance optimization on Blue Gene/Q
Energy Technology Data Exchange (ETDEWEB)
Coffman, Paul; Jiang, Wei; Romero, Nichols A.
2014-11-12
LAMMPS "Large-scale Atomic/Molecular Massively Parallel Simulator" is an open-source molecular dynamics package from Sandia National Laboratories. Significant performance improvements in strong-scaling and time-to-solution for this application on IBM's Blue Gene/Q have been achieved through computational optimizations of the OpenMP versions of the short-range Lennard-Jones term of the CHARMM force field and the long-range Coulombic interaction implemented with the PPPM (particle-particle-particle mesh) algorithm, enhanced by runtime parameter settings controlling thread utilization. Additionally, MPI communication performance improvements were made to the PPPM calculation by re-engineering the parallel 3D FFT to use MPICH collectives instead of point-to-point. Performance testing was done using an 8.4-million atom simulation scaling up to 16 racks on the Mira system at Argonne Leadership Computing Facility (ALCF). Speedups resulting from this effort were in some cases over 2x.
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
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
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
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.
International Nuclear Information System (INIS)
Durand, S.
1999-01-01
Molecular dynamics (MD) simulations on lanthanide(III) and alkaline-earth(II) complexes with poly-amino-carboxylates (ethylene-diamino-tetra-acetate EDTA 4- , ethylene-diamino-tri-acetate-acetic acid EDTA(H) 3- , tetra-aza-cyclo-dodecane-tetra-acetate DOTA 4- , methylene-imidine-acetate MIDA 2- ) are reported. First, a consistent set of Lennard-Jones parameters for La 3+ , Eu 3+ and Lu 3+ cations has been derived from free energy calculations in aqueous solution. Observed differences in hydration free energies, coordination distances and hydration numbers are reproduced. Then, the solution structures of 1:1 complexes of alkaline-earth and/or lanthanide cations with EDTA 4- , EDTA(H) 3- , DOTA 4- and 1:2 complexes of lanthanide cations with MIDA 2- were studied by MD in water. In addition, free energy calculations were performed to study, for each ligand, the relative thermodynamic stabilities of complexes with Ca 2+ vs Sr 2+ and vs Ba 2+ on the one hand, and with La 3+ vs Eu 3+ and vs Lu 3+ on the other hand. Model does not take into account explicitly polarization and charge transfer. However, the results qualitatively agree with experimental complexation data (structure and selectivities). (author)
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.
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.
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.
Stick-Slip Motion of Moving Contact Line on Chemically Patterned Surfaces
Wu, Congmin
2009-01-01
Based on our continuum hydrodynamic model for immiscible two-phase flows at solid surfaces, the stick-slip motion has been predicted for moving contact line at chemically patterned surfaces [Wang et al., J. Fluid Mech., 605 (2008), pp. 59-78]. In this paper we show that the continuum predictions can be quantitatively verified by molecular dynamics (MD) simulations. Our MD simulations are carried out for two immiscible Lennard-Jones fluids confined by two planar solid walls in Poiseuille flow geometry. In particular, one solid surface is chemically patterned with alternating stripes. For comparison, the continuum model is numerically solved using material parameters directly measured in MD simulations. From oscillatory fluid-fluid interface to intermittent stick-slip motion of moving contact line, we have quantitative agreement between the continuum and MD results. This agreement is attributed to the accurate description down to molecular scale by the generalized Navier boundary condition in our continuum model. Numerical results are also presented for the relaxational dynamics of fluid-fluid interface, in agreement with a theoretical analysis based on the Onsager principle of minimum energy dissipation. © 2010 Global-Science Press.
Reducing thermal conductivity of binary alloys below the alloy limit via chemical ordering
International Nuclear Information System (INIS)
Duda, John C; English, Timothy S; Jordan, Donald A; Norris, Pamela M; Soffa, William A
2011-01-01
Substitutional solid solutions that exist in both ordered and disordered states will exhibit markedly different physical properties depending on their exact crystallographic configuration. Many random substitutional solid solutions (alloys) will display a tendency to order given the appropriate kinetic and thermodynamic conditions. Such order-disorder transitions will result in major crystallographic reconfigurations, where the atomic basis, symmetry, and periodicity of the alloy change dramatically. Consequently, the dominant scattering mechanism in ordered alloys will be different than that in disordered alloys. In this study, we present a hypothesis that ordered alloys can exhibit lower thermal conductivities than their disordered counterparts at elevated temperatures. To validate this hypothesis, we investigate the phononic transport properties of disordered and ordered AB Lennard-Jones alloys via non-equilibrium molecular dynamics and harmonic lattice dynamics calculations. It is shown that the thermal conductivity of an ordered alloy is the same as the thermal conductivity of the disordered alloy at ∼0.6T melt and lower than that of the disordered alloy above 0.8T melt .
Lushnikov, A. A.; Kulmala, M.
1998-09-01
The dimer stage of nucleation may affect considerably the rate of the nucleation process at high supersaturation of the nucleating vapor. Assuming that the dimer formation limits the nucleation rate, the kinetics of the particle formation-growth process is studied starting with the definition of dimers as bound states of two associating molecules. The partition function of dimer states is calculated by summing the Boltzmann factor over all classical bound states, and the equilibrium population of dimers is found for two types of intermolecular forces: the Lennard-Jones (LJ) and rectangular well+hard core (RW) potentials. The principle of detailed balance is used for calculating the evaporation rate of dimers. The kinetics of the particle formation-growth process is then investigated under the assumption that the trimers are stable with respect to evaporation and that the condensation rate is a power function of the particle mass. If the power exponent λ=n/(n+1) (n is a non-negative integer), the kinetics of the process is described by a finite set of moments of particle mass distribution. When the characteristic time of the particle formation by nucleation is much shorter than that of the condensational growth, n+2 universal functions of a nondimensional time define the kinetic process. These functions are calculated for λ=2/3 (gas-to-particle conversion in the free molecular regime) and λ=1/2 (formation of islands on surfaces).
Stokes-Einstein relation for pure simple fluids
Cappelezzo, M.; Capellari, C. A.; Pezzin, S. H.; Coelho, L. A. F.
2007-06-01
The authors employed the equilibrium molecular dynamics technique to calculate the self-diffusion coefficient and the shear viscosity for simple fluids that obey the Lennard-Jones 6-12 potential in order to investigate the validity of the Stokes-Einstein (SE) relation for pure simple fluids. They performed calculations in a broad range of density and temperature in order to test the SE relation. The main goal of this work is to exactly calculate the constant, here denominated by α, present in the SE relation. Also, a modified SE relation where a fluid density is raised to a power in the usual expression is compared to the classical expression. According to the authors' simulations slip boundary conditions (α=4) can be satisfied in some state points. An intermediate value of α =5 was found in some regions of the phase diagram confirming the mode coupling theory. In addition depending on the phase diagram point and the definition of hydrodynamics radius, stick boundary condition (α=6) can be reproduced. The authors investigated the role of the hydrodynamic radius in the SE relation using three different definitions. The authors also present calculations for α in a hard-sphere system showing that the slip boundary conditions hold at very high density. They discuss possible explanations for their results and the role of the hydrodynamic radius for different definitions in the SE relation.
International Nuclear Information System (INIS)
Cousty, J.P.
1981-12-01
In this work, we have studied the influence of atomic structure of crystal surface on surface self-diffusion in the medium temperature range. Two ways are followed. First, we have measured, using a radiotracer method, the self-diffusion coefficient at 820 K (0.6 T melting) on copper surfaces both the structure and the cleanliness of which were stable during the experiment. We have shown that the interaction between mobile surface defects and steps can be studied through measurements of the anisotropy of surface self diffusion. Second, the behavior of an adatom and a surface vacancy is simulated via a molecular dynamics method, on several surfaces of a Lennard Jones crystal. An inventory of possible migration mechanisms of these surface defects has been drawn between 0.35 and 0.45 Tsub(m). The results obtained with both the methods point out the influence of the surface atomic structure in surface self-diffusion in the medium temperature range [fr
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.
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.
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)
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.
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.
Equilibrium properties of a grafted polyelectrolyte with explicit counterions
Jayasree, Kandiledath; Ranjith, P.; Rao, Madan; Kumar, P. B. Sunil
2009-03-01
We study the equilibrium conformations of a grafted polyelectrolyte (PE) in the presence of explicit counterions (CIs) using Monte Carlo simulations. The interplay between attractive Lennard-Jones interactions (parametrized by ɛ) and electrostatics (parametrized by A =q2lB/a, where q is the CI valency, lB is the Bjerrum length, and a is the monomer diameter) results in a variety of conformations, characterized as extended (E), pearls with m beads (Pm), sausage (S), and globular (G). For large ɛ, we observe a transition from G →P2→P3→…→S→G with increasing A, i.e., a change from poor to good, to re-entrant poor solvent, whereas, at lower ɛ, the sequence of transitions is E →S→G. The conformation changes are directly related to the nature of binding of CI onto the PE. The transition between S →G is continuous and associated with critical fluctuations in the shape driven by fluctuations in the fraction of condensed CI.
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.
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.
Contribution to diffusion mechanism study in amorphous metallic alloys
International Nuclear Information System (INIS)
Delaye, Jean-Marc
1993-01-01
This work is dedicated to the study of the vacancy diffusion mechanism in mono-elementary and binary amorphous Lennard-Jones systems, by a molecular dynamics method. The first chapter is a review of the preceding works performed before the beginning of this thesis, the method of simulation is described in the second chapter. We showed in the following chapters that the vacancies, introduced by the removal of one atom, remain stable on a large percentage of sites, especially in the binary system. By calculating some thermodynamical values, formation and migration enthalpies and entropies, we showed that the vacancy mechanism is magnified in a disordered system, as compared to a crystal of the same composition, and therefore can explain the magnitudes of the experimental diffusion coefficients. In parallel, to measure diffusion coefficients, we have settled an experimental method based on the evolution of the resistivity of a multilayer sample during interdiffusion, a gold-silver multilayer in our case (chapter six). By measurements under pressure, the activation volume is determined and our results agree well with the preceding ones. (author) [fr
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)
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.
Parametric sensitivity analysis for stochastic molecular systems using information theoretic metrics
Energy Technology Data Exchange (ETDEWEB)
Tsourtis, Anastasios, E-mail: tsourtis@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, Crete (Greece); Pantazis, Yannis, E-mail: pantazis@math.umass.edu; Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-70013 Heraklion, Crete (Greece)
2015-07-07
In this paper, we present a parametric sensitivity analysis (SA) methodology for continuous time and continuous space Markov processes represented by stochastic differential equations. Particularly, we focus on stochastic molecular dynamics as described by the Langevin equation. The utilized SA method is based on the computation of the information-theoretic (and thermodynamic) quantity of relative entropy rate (RER) and the associated Fisher information matrix (FIM) between path distributions, and it is an extension of the work proposed by Y. Pantazis and M. A. Katsoulakis [J. Chem. Phys. 138, 054115 (2013)]. A major advantage of the pathwise SA method is that both RER and pathwise FIM depend only on averages of the force field; therefore, they are tractable and computable as ergodic averages from a single run of the molecular dynamics simulation both in equilibrium and in non-equilibrium steady state regimes. We validate the performance of the extended SA method to two different molecular stochastic systems, a standard Lennard-Jones fluid and an all-atom methane liquid, and compare the obtained parameter sensitivities with parameter sensitivities on three popular and well-studied observable functions, namely, the radial distribution function, the mean squared displacement, and the pressure. Results show that the RER-based sensitivities are highly correlated with the observable-based sensitivities.
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)
Density functional theory for adsorption of gas mixtures in metal-organic frameworks.
Liu, Yu; Liu, Honglai; Hu, Ying; Jiang, Jianwen
2010-03-04
In this work, a recently developed density functional theory in three-dimensional space was extended to the adsorption of gas mixtures. Weighted density approximations to the excess free energy with different weighting functions were adopted for both repulsive and attractive contributions. An equation of state for hard-sphere mixtures and a modified Benedict-Webb-Rubin equation for Lennard-Jones mixtures were used to estimate the excess free energy of a uniform fluid. The theory was applied to the adsorption of CO(2)/CH(4) and CO(2)/N(2) mixtures in two metal-organic frameworks: ZIF-8 and Zn(2)(BDC)(2)(ted). To validate the theoretical predictions, grand canonical Monte Carlo simulations were also conducted. The predicted adsorption and selectivity from DFT were found to agree well with the simulation results. CO(2) has stronger adsorption than CH(4) and N(2), particularly in Zn(2)(BDC)(2)(ted). The selectivity of CO(2) over CH(4) or N(2) increases with increasing pressure as attributed to the cooperative interactions of adsorbed CO(2) molecules. The composition of the gas mixture exhibits a significant effect on adsorption but not on selectivity.
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.
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.
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.
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.
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.
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)
Capozza, R.; Vanossi, A.; Benassi, A.; Tosatti, E.
2015-02-01
Electrical charging of parallel plates confining a model ionic liquid down to nanoscale distances yields a variety of charge-induced changes in the structural features of the confined film. That includes even-odd switching of the structural layering and charging-induced solidification and melting, with important changes of local ordering between and within layers, and of squeezout behavior. By means of molecular dynamics simulations, we explore this variety of phenomena in the simplest charged Lennard-Jones coarse-grained model including or excluding the effect a neutral tail giving an anisotropic shape to one of the model ions. Using these models and open conditions permitting the flow of ions in and out of the interplate gap, we simulate the liquid squeezout to obtain the distance dependent structure and forces between the plates during their adiabatic approach under load. Simulations at fixed applied force illustrate an effective electrical pumping of the ionic liquid, from a thick nearly solid film that withstands the interplate pressure for high plate charge to complete squeezout following melting near zero charge. Effective enthalpy curves obtained by integration of interplate forces versus distance show the local minima that correspond to layering and predict the switching between one minimum and another under squeezing and charging.
Free energy of cluster formation and a new scaling relation for the nucleation rate
International Nuclear Information System (INIS)
Tanaka, Kyoko K.; Tanaka, Hidekazu; Diemand, Jürg; Angélil, Raymond
2014-01-01
Recent very large molecular dynamics simulations of homogeneous nucleation with (1 − 8) × 10 9 Lennard-Jones atoms [J. Diemand, R. Angélil, K. K. Tanaka, and H. Tanaka, J. Chem. Phys. 139, 074309 (2013)] allow us to accurately determine the formation free energy of clusters over a wide range of cluster sizes. This is now possible because such large simulations allow for very precise measurements of the cluster size distribution in the steady state nucleation regime. The peaks of the free energy curves give critical cluster sizes, which agree well with independent estimates based on the nucleation theorem. Using these results, we derive an analytical formula and a new scaling relation for nucleation rates: ln J ′ /η is scaled by ln S/η, where the supersaturation ratio is S, η is the dimensionless surface energy, and J ′ is a dimensionless nucleation rate. This relation can be derived using the free energy of cluster formation at equilibrium which corresponds to the surface energy required to form the vapor-liquid interface. At low temperatures (below the triple point), we find that the surface energy divided by that of the classical nucleation theory does not depend on temperature, which leads to the scaling relation and implies a constant, positive Tolman length equal to half of the mean inter-particle separation in the liquid phase
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.
Directory of Open Access Journals (Sweden)
J. A. Pyle
Full Text Available The stratosphere holds a variety of particulates like polar stratospheric clouds (PSCs and sulphate aerosols which catalyse chemical reactions. These reactions cause changes in the composition of the stratosphere, including the redistribution of active chlorine which might lead to ozone destruction. As a result during recent years a lot of effort has been directed towards the quantification of the uptake of trace gases like ClONO2, HCl, etc. into these particulates. However, it has been observed that many of the two and three dimensional models used in such studies are constrained by the lack of adequate rate constant data. This paper describes a theoretical approach to estimate the reaction rate constants for 23 gases on both types of polar stratospheric clouds (type I and II. It is found that for gases like N2O5, ClONO2 and HCl, diffusional uptake is important and contributes significantly to the heterogeneous reaction rate. A complete Lennard-Jones calculation is used to accurately compute the trace gas diffusion coefficients.
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.
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.
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.
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.
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.
Nayak, Bishnupriya; Menon, S. V. G.
2018-01-01
Enthalpy-based equation of state based on a modified soft sphere model for the fluid phase, which includes vaporization and ionization effects, is formulated for highly porous materials. Earlier developments and applications of enthalpy-based approach had not accounted for the fact that shocked states of materials with high porosity (e.g., porosity more than two for Cu) are in the expanded fluid region. We supplement the well known soft sphere model with a generalized Lennard-Jones formula for the zero temperature isotherm, with parameters determined from cohesive energy, specific volume and bulk modulus of the solid at normal condition. Specific heats at constant pressure, ionic and electronic enthalpy parameters and thermal excitation effects are calculated using the modified approach and used in the enthalpy-based equation of state. We also incorporate energy loss from the shock due to expansion of shocked material in calculating porous Hugoniot. Results obtained for Cu, even up to initial porosities ten, show good agreement with experimental data.
Kadoura, Ahmad Salim
2014-03-17
Molecular simulation could provide detailed description of fluid systems when compared to experimental techniques. They can also replace equations of state; however, molecular simulation usually costs considerable computational efforts. Several techniques have been developed to overcome such high computational costs. In this paper, two early rejection schemes, a conservative and a hybrid one, are introduced. In these two methods, undesired configurations generated by the Monte Carlo trials are rejected earlier than it would when using conventional algorithms. The methods are tested for structureless single-component Lennard-Jones particles in both canonical and NVT-Gibbs ensembles. The computational time reduction for both ensembles is observed at a wide range of thermodynamic conditions. Results show that computational time savings are directly proportional to the rejection rate of Monte Carlo trials. The proposed conservative scheme has shown to be successful in saving up to 40% of the computational time in the canonical ensemble and up to 30% in the NVT-Gibbs ensemble when compared to standard algorithms. In addition, it preserves the exact Markov chains produced by the Metropolis scheme. Further enhancement for NVT-Gibbs ensemble is achieved by combining this technique with the bond formation early rejection one. The hybrid method achieves more than 50% saving of the central processing unit (CPU) time.
Speeding up Monte Carlo molecular simulation by a non-conservative early rejection scheme
Kadoura, Ahmad Salim
2015-04-23
Monte Carlo (MC) molecular simulation describes fluid systems with rich information, and it is capable of predicting many fluid properties of engineering interest. In general, it is more accurate and representative than equations of state. On the other hand, it requires much more computational effort and simulation time. For that purpose, several techniques have been developed in order to speed up MC molecular simulations while preserving their precision. In particular, early rejection schemes are capable of reducing computational cost by reaching the rejection decision for the undesired MC trials at an earlier stage in comparison to the conventional scheme. In a recent work, we have introduced a ‘conservative’ early rejection scheme as a method to accelerate MC simulations while producing exactly the same results as the conventional algorithm. In this paper, we introduce a ‘non-conservative’ early rejection scheme, which is much faster than the conservative scheme, yet it preserves the precision of the method. The proposed scheme is tested for systems of structureless Lennard-Jones particles in both canonical and NVT-Gibbs ensembles. Numerical experiments were conducted at several thermodynamic conditions for different number of particles. Results show that at certain thermodynamic conditions, the non-conservative method is capable of doubling the speed of the MC molecular simulations in both canonical and NVT-Gibbs ensembles. © 2015 Taylor & Francis
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.
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.