Second virial coefficient of a generalized Lennard-Jones potential.
González-Calderón, Alfredo; Rocha-Ichante, Adrián
2015-01-21
We present an exact analytical solution for the second virial coefficient of a generalized Lennard-Jones type of pair potential model. The potential can be reduced to the Lennard-Jones, hard-sphere, and sticky hard-sphere models by tuning the potential parameters corresponding to the width and depth of the well. Thus, the second virial solution can also regain the aforementioned cases. Moreover, the obtained expression strongly resembles the one corresponding to the Kihara potential. In fact, the Fk functions are the same. Furthermore, for these functions, the complete expansions at low and high temperature are given. Additionally, we propose an alternative stickiness parameter based on the obtained second virial coefficient. PMID:25612707
Corresponding states law for a generalized Lennard-Jones potential.
Orea, P; Romero-Martínez, A; Basurto, E; Vargas, C A; Odriozola, G
2015-07-14
It was recently shown that vapor-liquid coexistence densities derived from Mie and Yukawa models collapse to define a single master curve when represented against the difference between the reduced second virial coefficient at the corresponding temperature and that at the critical point. In this work, we further test this proposal for another generalization of the Lennard-Jones pair potential. This is carried out for vapor-liquid coexistence densities, surface tension, and vapor pressure, along a temperature window set below the critical point. For this purpose, we perform molecular dynamics simulations by varying the potential softness parameter to produce from very short to intermediate attractive ranges. We observed all properties to collapse and yield master curves. Moreover, the vapor-liquid curve is found to share the exact shape of the Mie and attractive Yukawa. Furthermore, the surface tension and the logarithm of the vapor pressure are linear functions of this difference of reduced second virial coefficients. PMID:26178115
Modified Jeans instability in Lorentzian dusty self-gravitating plasmas with Lennard-Jones potential
Qian, Y. Z. Chen, H. Liu, S. Q.
2014-11-15
The Jeans instability in self-gravitating plasma with Kappa distributed dust grains is investigated basing on assumption that the mutual interaction among dust grains is governed by Lennard-Jones potential. It is shown that the presence of additional suprathermal particles has significant effects on the range of unstable modes and growth rate of Jeans instability. Compared with Maxwellian scenario, suprathermality stabilized the Jeans instability.
The potential energy landscape for crystallisation of a Lennard-Jones fluid
NASA Astrophysics Data System (ADS)
de Souza, Vanessa K.; Wales, David J.
2016-07-01
Crystallisation pathways are explored by direct analysis of the potential energy landscape for a system of Lennard-Jones particles with periodic boundary conditions. A database of minima and transition states linking liquid and crystalline states is constructed using discrete path sampling and the entire potential energy landscape from liquid to crystal is visualised. We demonstrate that there is a strong negative correlation between the number of atoms in the largest crystalline cluster and the potential energy. In common with previous results we find a strong bias towards the growth of FCC rather than HCP clusters, despite a very small potential energy difference. We characterise three types of perfect crystals with very similar energies: pure FCC, pure HCP, and combinations of FCC and HCP layers. There are also many slightly defective crystalline structures. The effect of the simulation box is analysed for a supercell containing 864 atoms. There are low barriers between some of the different crystalline structures via pathways involving sliding layers, and many different defective structures with FCC layers stacked at an angle to the periodic box. Finally, we compare a binary Lennard-Jones system and visualise the potential energy landscape from supercooled liquid to crystal.
A Lennard-Jones plus Coulomb potential for Al3+ ions in aqueous solutions
NASA Astrophysics Data System (ADS)
Faro, Tatiana M. C.; Thim, Gilmar P.; Skaf, Munir S.
2010-03-01
We developed a simple pair-additive Lennard-Jones plus Coulomb potential for molecular simulations of the trivalent cation Al3+ in water which accounts reasonably well for the behavior of aluminum aqueous solutions. The model predicts an octahedral first hydration shell containing 6 water molecules and a trigonal second shell with 12 molecules on average, in good agreement with the available experimentally determined structure. The peak positions of the cation-oxygen radial distribution function are only slightly compressed compared to the x-ray structure, the hydration enthalpy is 10% too low, and the cation self-diffusion coefficient and the single-particle second rank reorientational time are in excellent agreement with inelastic neutron scattering and NMR spectroscopy data, respectively. The model also captures the essential vibrational features of the hydrated [Al(H2O)6]3+ complex. It predicts the main O-Al-O bending mode frequency to within ˜5%, but significantly overestimates the frequency of the totally symmetric Al-O stretching mode. Overall, the accuracy of the proposed model is as good as the best available classical potentials, if not better in some aspects, with a much simpler functional form, which makes it an attractive alternative for computer simulations of Al3+ in more complex aqueous and biomolecular systems.
Connectivity in the potential energy landscape for binary Lennard-Jones systems
NASA Astrophysics Data System (ADS)
de Souza, Vanessa K.; Wales, David J.
2009-05-01
Connectivity in the potential energy landscape of a binary Lennard-Jones system can be characterized at the level of cage-breaking. We calculate the number of cage-breaking routes from a given local minimum and determine the branching probabilities at different temperatures, along with correlation factors that represent the repeated reversals of cage-breaking events. The number of reversals increases at lower temperatures and for more fragile systems, while the number of accessible connections decreases. We therefore associate changes in connectivity with super-Arrhenius behavior. Reversals in minimum-to-minimum transitions are common, but often correspond to "non-cage-breaking" processes. We demonstrate that the average waiting time within a minimum shows simple exponential behavior with decreasing temperature. To describe the long-term behavior of the system, we consider reversals and connectivity in terms of the "cage-breaking" processes that are pertinent to diffusion [V. K. de Souza and D. J. Wales, J. Chem. Phys. 129, 164507 (2008)]. These cage-breaking events can be modeled by a correlated random walk. Thus, a full correlation factor can be calculated using short simulations that extend up to two cage-breaking events.
NASA Astrophysics Data System (ADS)
Mamedov, Bahtiyar Akber; Somuncu, Elif
2016-04-01
An efficient analytical method to evaluate the third virial coefficient with Lennard-Jones (12-6) type potential is presented. Proposed approach is particularly suitable for analysis of various properties of three body systems. To conform the correctness of the calculation result, a comparison is given with the literature for NO2, SF6 and C2H2 molecules. Calculation results show that obtained formulae provide higher accuracy and efficiency than the proposed approaches in literature.
Taylor, Mark P; Ye, Yuting; Adhikari, Shishir R
2015-11-28
The conformation of a polymer chain in solution is coupled to the local structure of the surrounding solvent and can undergo large changes in response to variations in solvent density and temperature. The many-body effects of solvent on the structure of an n-mer polymer chain can be formally mapped to an exact n-body solvation potential. Here, we use a pair decomposition of this n-body potential to construct a set of two-body potentials for a Lennard-Jones (LJ) polymer chain in explicit LJ solvent. The solvation potentials are built from numerically exact results for 5-mer chains in solvent combined with an approximate asymptotic expression for the solvation potential between sites that are distant along the chain backbone. These potentials map the many-body chain-in-solvent problem to a few-body single-chain problem and can be used to study a chain of arbitrary length, thereby dramatically reducing the computational complexity of the polymer chain-in-solvent problem. We have constructed solvation potentials at a large number of state points across the LJ solvent phase diagram including the vapor, liquid, and super-critical regions. We use these solvation potentials in single-chain Monte Carlo (MC) simulations with n ≤ 800 to determine the size, intramolecular structure, and scaling behavior of chains in solvent. To assess our results, we have carried out full chain-in-solvent MC simulations (with n ≤ 100) and find that our solvation potential approach is quantitatively accurate for a wide range of solvent conditions for these chain lengths. PMID:26627969
NASA Astrophysics Data System (ADS)
Temelkov, K. A.; Slaveeva, S. I.; Fedchenko, Yu I.
2016-03-01
Thermal conductivities of helium, neon, bromine, and hydrogen are calculated on the basis of the (12-6) Lennard-Jones interaction approximation. Where necessary for a more precise approximation, a generalized (n-m) Lennard-Jones interaction potential is used. Thermal conductivities of binary gas systems are calculated and compared through two different empirical methods for the case of gas discharges in He, Ne, and Ne-He mixtures with small admixtures of bromine and hydrogen. A new simple method is proposed for the thermal conductivity determination for the 3- and 4-component gas mixtures of our interest.
Transport theory for the Lennard-Jones dense fluid
Karkheck, J.; Stell, G.; Xu, J.
1988-11-01
A kinetic theory for a fluid of particles interacting via a pair potential with hard-core plus truncated tail is described and used to derive a transport theory for the Lennard-Jones fluid as well as the square-well fluid. Numerical results for shear viscosity, thermal conductivity, and the self-diffusion coefficient are given for the Lennard-Jones fluid and compared with simulation and experimental results. Our Lennard-Jones theory proves quantitatively useful over a wide range of states.
Xantheas, Sotiris S.; Werhahn, Jasper C.
2014-08-14
Based on the formulation of the analytical expression of the potential V(r) describing intermolecular interactions in terms of the dimensionless variables r*=r/rm and !*=V/!, where rm is the separation at the minimum and ! the well depth, we propose more generalized scalable forms for the commonly used Lennard-Jones, Mie, Morse and Buckingham exponential-6 potential energy functions (PEFs). These new generalized forms have an additional parameter from and revert to the original ones for some choice of that parameter. In this respect, the original forms can be considered as special cases of the more general forms that are introduced. We also propose a scalable, but nonrevertible to the original one, 4-parameter extended Morse potential.
Freezing of Lennard-Jones-type fluids
Khrapak, Sergey A.; Chaudhuri, Manis; Morfill, Gregor E.
2011-02-07
We put forward an approximate method to locate the fluid-solid (freezing) phase transition in systems of classical particles interacting via a wide range of Lennard-Jones-type potentials. This method is based on the constancy of the properly normalized second derivative of the interaction potential (freezing indicator) along the freezing curve. As demonstrated recently it yields remarkably good agreement with previous numerical simulation studies of the conventional 12-6 Lennard-Jones (LJ) fluid [S.A.Khrapak, M.Chaudhuri, G.E.Morfill, Phys. Rev. B 134, 052101 (2010)]. In this paper, we test this approach using a wide range of the LJ-type potentials, including LJ n-6 and exp-6 models, and find that it remains sufficiently accurate and reliable in reproducing the corresponding freezing curves, down to the triple-point temperatures. One of the possible application of the method--estimation of the freezing conditions in complex (dusty) plasmas with ''tunable'' interactions--is briefly discussed.
Taylor, Mark P; Adhikari, Shishir R
2011-07-28
The average conformation of a flexible chain molecule in solution is coupled to the local solvent structure. In a dense solvent, local chain structure often mirrors the pure solvent structure, whereas, in a dilute solvent, the chain can strongly perturb the solvent structure which, in turn, can lead to either chain expansion or compression. Here we use Monte Carlo (MC) simulation to study such solvent effects for a short Lennard-Lones (LJ) chain in monomeric LJ solvent. For an n-site chain molecule in solution these many-body solvent effects can be formally mapped to an n-body solvation potential. We have previously shown that for hard-sphere and square-well chain-in-solvent systems this n-body potential can be decomposed into a set of two-body potentials. Here, we show that this decomposition is also valid for the LJ system. Starting from high precision MC results for the n = 5 LJ chain-in-solvent system, we use a Boltzmann inversion technique to compute numerically exact sets of two-body solvation potentials which map the many-body chain-in-solvent problem to a few-body single-chain problem. We have carried out this mapping across the full solvent phase diagram including the dilute vapor, dense liquid, and supercritical regions and find that these sets of solvation potentials are able to encode the complete range of solvent effects found in the LJ chain-in-solvent system. We also show that these two-site solvation potentials can be used to obtain accurate multi-site intramolecular distribution functions and we discuss the application of these exact short chain potentials to the study of longer chains in solvent. PMID:21806157
Phase diagram of power law and Lennard-Jones systems: Crystal phases
Travesset, Alex
2014-10-28
An extensive characterization of the low temperature phase diagram of particles interacting with power law or Lennard-Jones potentials is provided from Lattice Dynamical Theory. For power law systems, only two lattice structures are stable for certain values of the exponent (or softness) (A15, body centered cube (bcc)) and two more (face centered cubic (fcc), hexagonal close packed (hcp)) are always stable. Among them, only the fcc and bcc are equilibrium states. For Lennard-Jones systems, the equilibrium states are either hcp or fcc, with a coexistence curve in pressure and temperature that shows reentrant behavior. The hcp solid never coexists with the liquid. In all cases analyzed, for both power law and Lennard-Jones potentials, the fcc crystal has higher entropy than the hcp. The role of anharmonic terms is thoroughly analyzed and a general thermodynamic integration to account for them is proposed.
The Lennard-Jones melting line and isomorphism
NASA Astrophysics Data System (ADS)
Heyes, D. M.; Brańka, A. C.
2015-12-01
The location of the melting line (ML) of the Lennard-Jones (LJ) system and its associated physical properties are investigated using molecular dynamics computer simulation. The radial distribution function and the behavior of the repulsive and attractive parts of the potential energy indicate that the ML is not a single isomorph, but the isomorphic state evolves gradually with temperature, i.e., it is only "locally isomorphic." The state point dependence of the unitless isomorphic number, X ˜ , for a range of static and dynamical properties of the LJ system in the solid and fluid states, and for fluid argon, are also reported. The quantity X ˜ typically varies most with state point in the vicinity of the triple point and approaches a plateau in the high density (temperature) limit along the ML.
NASA Astrophysics Data System (ADS)
Mamedov, Bahtiyar A.; Somuncu, Elif; Askerov, Iskender M.
2016-08-01
In this work, a new theoretical approach is proposed for calculating fourth virial coefficient with Leonard-Jones potential. The established algorithm can be used to evaluate the thermodynamics properties and the intermolecular interaction potentials of liquids and gases with an improved accuracy. Note that the evaluation of the high-order virial coefficients is very valuable for accurate calculation of thermodynamic parameters. By using the suggested method, the fourth virial coefficient of CH4, Ar,C2H6 and SF6 molecules are evaluated. The calculation results are useful for accurate interpretation of the experimental data and of the determination of related physical properties.
Elastic compliances and stiffnesses of the fcc Lennard-Jones solid
NASA Astrophysics Data System (ADS)
Quesnel, D. J.; Rimai, D. S.; Demejo, L. P.
1993-09-01
The isothermal elastic compliances, stiffnesses, and bulk moduli of a Lennard-Jones solid organized into an fcc crystal structure (256 atoms in 43 unit cells) have been calculated as a function of testing temperature (expressed as the mean kinetic energy per atom). Tests conducted in pure shear were used to determine S44 and C44=G100, where 100 refers to crystallographic directions. Tests imposing axial elongation with fixed lateral dimensions established C11 and C12. Axial deformation with zero lateral pressure (a tension test) was used to determine S11, S12, E100 and ν100. This provided an independent set of results for comparison with the dilatational stiffnesses C11 and C12. The bulk modulus K was obtained by independent triaxial tension testing. The stiffnesses, compliances, and moduli were determined by regression analysis and digital filtering applied to combinations of the stress-tensor and strain-tensor data stored at each iteration during the constant-rate deformation experiments. While the cubic fcc Lennard-Jones solid expectedly obeys the Cauchy relations for central-force potentials, it is not isotropic, allowing ν to take on values other than 1/4 as originally proposed by Poisson. The present calculations show ν100=0.347 for the fcc Lennard-Jones solid with a Young's modulus of E100=61.1ɛ/σ3, an initial (as indicated by superscript 0) shear modulus of G0100=57.2ɛ/σ3, and an initial bulk modulus of K0=71.2ɛ/σ3 at zero temperature. The moduli all decreased with increasing temperature. Reuss, Voigt, and Hashin and Shtrikman [J. Mech. Phys. Solids 10, 335 (1962)] bounds on the isotropic elastic properties of polycrystalline aggregates of Lennard-Jones material were also determined. Computed values of the moduli are in reasonable agreement with experimental results for solid argon and crystalline polyethylene.
Scaling of the dynamics of flexible Lennard-Jones chains: Effects of harmonic bonds
NASA Astrophysics Data System (ADS)
Veldhorst, Arno A.; Dyre, Jeppe C.; Schrøder, Thomas B.
2015-11-01
The previous paper [A. A. Veldhorst et al., J. Chem. Phys. 141, 054904 (2014)] demonstrated that the isomorph theory explains the scaling properties of a liquid of flexible chains consisting of ten Lennard-Jones particles connected by rigid bonds. We here investigate the same model with harmonic bonds. The introduction of harmonic bonds almost completely destroys the correlations in the equilibrium fluctuations of the potential energy and the virial. According to the isomorph theory, if these correlations are strong a system has isomorphs, curves in the phase diagram along which structure, dynamics, and the excess entropy are invariant. The Lennard-Jones chain liquid with harmonic bonds does have curves in the phase diagram along which the structure and dynamics are invariant. The excess entropy is not invariant on these curves, which we refer to as "pseudoisomorphs." In particular, this means that Rosenfeld's excess-entropy scaling (the dynamics being a function of excess entropy only) does not apply for the Lennard-Jones chain with harmonic bonds.
Elastic Lennard-Jones polymers meet clusters: Differences and similarities
NASA Astrophysics Data System (ADS)
Schnabel, Stefan; Bachmann, Michael; Janke, Wolfhard
2009-09-01
We investigate solid-solid and solid-liquid transitions of elastic flexible off-lattice polymers with Lennard-Jones monomer-monomer interaction and anharmonic springs by means of sophisticated variants of multicanonical Monte Carlo methods. We find that the low-temperature behavior depends strongly and nonmonotonically on the system size and exhibits broad similarities to unbound atomic clusters. Particular emphasis is dedicated to the classification of icosahedral and nonicosahedral low-energy polymer morphologies.
Energy landscapes of quantum Lennard-Jones solids.
Chakravarty, Charusita
2011-06-30
To generalize inherent structure analysis to understand structural changes in quantum liquids and solids, differences between classical (V(x)) and quantum-corrected (U(qeff)(x)) energy landscapes are estimated as a function of the de Boer parameter (Λ). Path integral simulations of quantum Lennard-Jones solids are performed at zero pressure and a dimensionless reduced temperature of 0.123, corresponding to an absolute temperature of 4.2K. At constant temperature and pressure, Λ is increased from the classical limit of zero to Λ = 0.28, corresponding to para-H(2). Increasing quantum delocalization effects result in a continuous decrease in density and local order but without a transition to a disordered, liquid state. The inherent structure landscape of bulk systems is strongly dependent on density with the energy and stability of crystalline minima decreasing relative to that of amorphous packing minima as the system is stretched. For Λ ≈ 0.23, the volume fluctuations in quantum solids are sufficient to result in sampling of disordered minima while for Λ = 0.28, the underlying classical inherent structures are completely disordered, indicating that the topography of U(qeff)(x) and V(x) are qualitatively different for such values of Λ. To assess the nature of the quantum-corrected energy landscape, effective pair potentials are defined by u(qeff)(r) = -kT ln g(r) using the pair correlation function (g(r)) of the quantum system in the neighborhood of the first peak. Our results show that as Λ increases, the pair potentials become increasingly softer, shallower, and of increasing range with a shifting of the potential minimum to larger distances. For example, the reduction of the entropy of fusion and melting temperatures of quantum solids with increasing Λ are analogous to the changes in thermodynamics of melting seen in classical solids with increasing range and softness of interactions. The energy landscapes associated with such coarse-grained potentials
Kim, Sun Ung; Monroe, Charles W.
2014-09-15
The inverse problem of parameterizing intermolecular potentials given macroscopic transport and thermodynamic data is addressed. Procedures are developed to create arbitrary-precision algorithms for transport collision integrals, using the Lennard-Jones (12–6) potential as an example. Interpolation formulas are produced that compute these collision integrals to four-digit accuracy over the reduced-temperature range 0.3≤T{sup ⁎}≤400, allowing very fast computation. Lennard-Jones parameters for neon, argon, and krypton are determined by simultaneously fitting the observed temperature dependences of their viscosities and second virial coefficients—one of the first times that a thermodynamic and a dynamic property have been used simultaneously for Lennard-Jones parameterization. In addition to matching viscosities and second virial coefficients within the bounds of experimental error, the determined Lennard-Jones parameters are also found to predict the thermal conductivity and self-diffusion coefficient accurately, supporting the value of the Lennard-Jones (12–6) potential for noble-gas transport-property correlation.
Lennard-Jones and lattice models of driven fluids.
Díez-Minguito, M; Garrido, P L; Marro, J
2005-08-01
We introduce a nonequilibrium off-lattice model for anisotropic phenomena in fluids. This is a Lennard-Jones generalization of the driven lattice-gas model in which the particles' spatial coordinates vary continuously. A comparison between the two models allows us to discuss some exceptional, hardly realistic features of the original discrete system--which has been considered a prototype for nonequilibrium anisotropic phase transitions. We thus help to clarify open issues, and discuss on the implications of our observations for future investigation of anisotropic phase transitions. PMID:16196640
Structure diagram of binary Lennard-Jones clusters
NASA Astrophysics Data System (ADS)
Mravlak, Marko; Kister, Thomas; Kraus, Tobias; Schilling, Tanja
2016-07-01
We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and present a publicly accessible database of 180 000 minimal energy structures (http://softmattertheory.lu/clusters.html). We identify a variety of structures such as core-shell clusters, Janus clusters, and clusters in which the minority species is located at the vertices of icosahedra. Such clusters can be synthesized from nanoparticles in agglomeration experiments and used as building blocks in colloidal molecules or crystals. We discuss the factors that determine the formation of clusters with specific structures.
Structure diagram of binary Lennard-Jones clusters.
Mravlak, Marko; Kister, Thomas; Kraus, Tobias; Schilling, Tanja
2016-07-14
We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and present a publicly accessible database of 180 000 minimal energy structures (http://softmattertheory.lu/clusters.html). We identify a variety of structures such as core-shell clusters, Janus clusters, and clusters in which the minority species is located at the vertices of icosahedra. Such clusters can be synthesized from nanoparticles in agglomeration experiments and used as building blocks in colloidal molecules or crystals. We discuss the factors that determine the formation of clusters with specific structures. PMID:27421400
Phase behavior of the 38-atom Lennard-Jones cluster
Sehgal, Ray M.; Maroudas, Dimitrios E-mail: ford@ecs.umass.edu; Ford, David M. E-mail: ford@ecs.umass.edu
2014-03-14
We have developed a coarse-grained description of the phase behavior of the isolated 38-atom Lennard-Jones cluster (LJ{sub 38}). The model captures both the solid-solid polymorphic transitions at low temperatures and the complex cluster breakup and melting transitions at higher temperatures. For this coarse model development, we employ the manifold learning technique of diffusion mapping. The outcome of the diffusion mapping analysis over a broad temperature range indicates that two order parameters are sufficient to describe the cluster's phase behavior; we have chosen two such appropriate order parameters that are metrics of condensation and overall crystallinity. In this well-justified coarse-variable space, we calculate the cluster's free energy landscape (FEL) as a function of temperature, employing Monte Carlo umbrella sampling. These FELs are used to quantify the phase behavior and onsets of phase transitions of the LJ{sub 38} cluster.
Equation of State for the Lennard-Jones Fluid
NASA Astrophysics Data System (ADS)
Thol, Monika; Rutkai, Gabor; Köster, Andreas; Lustig, Rolf; Span, Roland; Vrabec, Jadran
2016-06-01
An empirical equation of state correlation is proposed for the Lennard-Jones model fluid. The equation in terms of the Helmholtz energy is based on a large molecular simulation data set and thermal virial coefficients. The underlying data set consists of directly simulated residual Helmholtz energy derivatives with respect to temperature and density in the canonical ensemble. Using these data introduces a new methodology for developing equations of state from molecular simulation. The correlation is valid for temperatures 0.5 < T/Tc < 7 and pressures up to p/pc = 500. Extensive comparisons to simulation data from the literature are made. The accuracy and extrapolation behavior are better than for existing equations of state.
Lennard-Jones fluid-fluid interfaces under shear
NASA Astrophysics Data System (ADS)
Galliero, Guillaume
2010-05-01
Using nonequilibrium molecular dynamics simulations on simple Lennard-Jones binary mixtures, we have studied the behavior of planar fluid-fluid interfaces undergoing shear flow. When the miscibility is low enough, a slip together with a partial depletion have been noticed at the interface between the two fluid phases. The slip length can reach a value equal to some molecular diameters and the corresponding interfacial viscosity can be two times smaller than the value in the bulk. It is shown how the omission of this slip may lead to flow-rate misevaluation when dealing with a multiphase flow in a nanoporous medium even for non polymer fluids. In addition, using the simulation results, a simple relation between interfacial tension and interfacial viscosity is proposed for the monoatomic systems studied in this work. Finally, it is shown that the interfacial viscosity cannot be fully accounted for by estimating the local viscosity deduced from the local thermodynamic properties of the interface.
Computationally Useful Bridge Diagram Series. III. Lennard-Jones Mixtures
Dyer, Kippi M.; Perkyns, John S.; Pettitt, Bernard M.
2002-06-01
The first two orders of bridge diagrams for the f-bond expansion and the h-bond expansion are calculated for a binary mixture of Lennard-Jones spheres. The method used follows the Legendre polynomial integration methods outlined in the first two papers of this series. As for the pure fluid cases, the thermodynamic results which follow from these methods are found to be in reasonable agreement with the simulation result. Analysis of the thermodynamic and structural results in comparison to the best current bridge function approximations indicate that accurate descriptions of higher order mixtures will require methods beyond the current mean field treatments which are of utility in simple fluids. The methods given are unfortunately not computationally convenient at highest order; however, the lower order diagrams are both accessible and give reasonable numerical results.
Computationally useful bridge diagram series. III. Lennard-Jones mixtures
NASA Astrophysics Data System (ADS)
Dyer, Kippi; Perkyns, John; Pettitt, B. Montgomery
2002-06-01
The first two orders of bridge diagrams for the f-bond expansion and the h-bond expansion are calculated for a binary mixture of Lennard-Jones spheres. The method used follows the Legendre polynomial integration methods outlined in the first two papers of this series. As for the pure fluid cases, the thermodynamic results which follow from these methods are found to be in reasonable agreement with the simulation result. Analysis of the thermodynamic and structural results in comparison to the best current bridge function approximations indicate that accurate descriptions of higher order mixtures will require methods beyond the current mean field treatments which are of utility in simple fluids. The methods given are unfortunately not computationally convenient at highest order; however, the lower order diagrams are both accessible and give reasonable numerical results.
Freezing point depression in model Lennard-Jones solutions
NASA Astrophysics Data System (ADS)
Koschke, Konstantin; Jörg Limbach, Hans; Kremer, Kurt; Donadio, Davide
2015-09-01
Crystallisation of liquid solutions is of uttermost importance in a wide variety of processes in materials, atmospheric and food science. Depending on the type and concentration of solutes the freezing point shifts, thus allowing control on the thermodynamics of complex fluids. Here we investigate the basic principles of solute-induced freezing point depression by computing the melting temperature of a Lennard-Jones fluid with low concentrations of solutes, by means of equilibrium molecular dynamics simulations. The effect of solvophilic and weakly solvophobic solutes at low concentrations is analysed, scanning systematically the size and the concentration. We identify the range of parameters that produce deviations from the linear dependence of the freezing point on the molal concentration of solutes, expected for ideal solutions. Our simulations allow us also to link the shifts in coexistence temperature to the microscopic structure of the solutions.
Water in the presence of inert Lennard-Jones obstacles
NASA Astrophysics Data System (ADS)
Kurtjak, Mario; Urbic, Tomaz
2014-04-01
Water confined by the presence of a 'sea' of inert obstacles was examined. In the article, freely mobile two-dimensional Mercedes-Benz (MB) water put to a disordered, but fixed, matrix of Lennard-Jones disks was studied by the Monte Carlo computer simulations. For the MB water molecules in the matrix of Lennard-Jones disks, we explored the structures, hydrogen-bond-network formation and thermodynamics as a function of temperature and size and density of matrix particles. We found that the structure of model water is perturbed by the presence of the obstacles. Density of confined water, which was in equilibrium with the bulk water, was smaller than the density of the bulk water and the temperature dependence of the density of absorbed water did not show the density anomaly in the studied temperature range. The behaviour observed as a consequence of confinement is similar to that of increasing temperature, which can for a matrix lead to a process similar to capillary evaporation. At the same occupancy of space, smaller matrix molecules cause higher destruction effect on the absorbed water molecules than the bigger ones. We have also tested the hypothesis that at low matrix densities the obstacles induce an increased ordering and 'hydrogen bonding' of the MB model molecules, relative to pure fluid, while at high densities the obstacles reduce MB water structuring, as they prevent the fluid to form good 'hydrogen-bonding' networks. However, for the size of matrix molecules similar to that of water, we did not observe this effect.
Pressure-energy correlations and thermodynamic scaling in viscous Lennard-Jones liquids
NASA Astrophysics Data System (ADS)
Coslovich, D.; Roland, C. M.
2009-01-01
We use molecular dynamics simulation results on viscous binary Lennard-Jones mixtures to examine the correlation between the potential energy and the virial. In accord with a recent proposal [U. R. Pedersen et al., Phys. Rev. Lett. 100, 015701 (2008)], the fluctuations in the two quantities are found to be strongly correlated, exhibiting a proportionality constant, Γ, numerically equal to one-third the slope of an inverse power law approximation to the intermolecular potential function. The correlation is stronger at higher densities, where interatomic separations are in the range where the inverse power law approximation is more accurate. These same liquids conform to thermodynamic scaling of their dynamics, with the scaling exponent equal to Γ. Thus, the properties of strong correlation between energy and pressure and thermodynamic scaling both reflect the ability of an inverse power law representation of the potential to capture interesting features of the dynamics of dense, highly viscous liquids.
NASA Astrophysics Data System (ADS)
Cameron, M. K.
2013-08-01
The large time behavior of a stochastic system with infinitesimally small noise can be described in terms of Freidlin's cycles. We show that if the system is gradient and the potential satisfies certain non-restrictive conditions, the hierarchy of cycles has a structure of a full binary tree, and each cycle is exited via the lowest saddle adjacent to it. Exploiting this property, we propose an algorithm for computing the asymptotic zero-temperature path and building a hierarchy of Freidlin's cycles associated with the transition process between two given local equilibria. This algorithm is suitable for systems with a complex potential energy landscape with numerous minima. We apply it to find the asymptotic zero-temperature path and Freidlin's cycles involved into the transition process between the two lowest minima of the Lennard-Jones cluster of 38 atoms. D. Wales's stochastic network of minima and transition states of this cluster is used as an input.
Molecular Dynamic Study of a Single Dislocation in a Two-Dimensional Lennard Jones System
NASA Astrophysics Data System (ADS)
Robles, Miguel; Mustonen, Ville; Kaski, Kimmo
In this work the motion of a single dislocation in a two-dimensional triangular lattice is studied by using classical Molecular Dynamics method with the Lennard Jones inter-atomic potential. The dislocation motion is investigated with an interactive simulation program developed to track automatically the movement of lattice defects. Constant strain and constant strain-rate deformations were applied to the system. From constant strain simulations a curve of shear stress versus dislocation velocity is obtained, showing a nonlinear power law relation. An equation of motion for the dislocation is proposed and found to be applicable when the movement of dislocation follows a quasi-static process. Numerical simulations at different strain rates show an elastic-to-plastic transition that modifies the dynamics of the dislocation motion.
Density-functional theory of elastic moduli: Hard-sphere and Lennard-Jones crystals
NASA Astrophysics Data System (ADS)
Jarić, Marko V.; Mohanty, Udayan
1988-03-01
We propose a density-functional method for calculating elastic moduli of crystalline solids. The method is based on the second-order Ramakrishnan-Yussouff (RY) expansion of the variational grand-canonical potential around a uniform liquid state. The densities of the strained and unstrained crystal are represented as sums of narrow Gaussians. We express the crystal moduli in terms of the liquid structure factor its first and second derivatives evaluated at the reciprocal-lattice points of the crystal. We evaluate the elastic moduli for fcc hard-sphere and Lennard-Jones crystals using the Percus-Yevick and computer-simulation liquid structure factors, respectively. An indirect comparison with available experimental and theoretical values shows that although our calculated moduli are accurate to an order of magnitude, higher-order terms in the RY expansion might be significant. We find important contributions from density equilibration within the strained unit cell.
Melting transition of Lennard-Jones fluid in cylindrical pores
Das, Chandan K.; Singh, Jayant K.
2014-05-28
Three-stage pseudo-supercritical transformation path and multiple-histogram reweighting technique are employed for the determination of solid-liquid coexistence of the Lennard-Jones (12-6) fluid, in a structureless cylindrical pore of radius, R, ranging from 4 to 20 molecular diameters. The Gibbs free energy difference is evaluated using thermodynamic integration method by connecting solid and liquid phases under confinement via one or more intermediate states without any first order phase transition among them. The thermodynamic melting temperature, T{sub m}, is found to oscillate for pore size, R < 8, which is in agreement with the behavior observed for the melting temperature in slit pores. However, T{sub m} for almost all pore sizes is less than the bulk case, which is contrary to the behavior seen for the slit pore. The oscillation in T{sub m} decays at around pore radius R = 8, and beyond that shift in the melting temperature with respect to the bulk case is in line with the prediction of the Gibbs-Thomson equation.
Metastable Lennard-Jones fluids. II. Thermal conductivity.
Baidakov, Vladimir G; Protsenko, Sergey P
2014-06-01
The method of equilibrium molecular dynamics with the use of the Green-Kubo formalism has been used to calculate the thermal conductivity λ in stable and metastable regions of a Lennard-Jones fluid. Calculations have been made in the range of reduced temperatures 0.4 ≤ T* = k(b)T/ε ≤ 2.0 and densities 0.01 ≤ ρ* = ρσ³ ≤ 1.2 on 15 isotherms for 234 states, 130 of which refer to metastable regions: superheated and supercooled liquids, supersaturated vapor. Equations have been built up which describe the dependence of the regular part of the thermal conductivity on temperature and density, and also on temperature and pressure. It has been found that in (p, T) variables in the region of a liquid-gas phase transition a family of lines of constant value of excess thermal conductivity Δλ = λ - λ0, where λ0 is the thermal conductivity of a dilute gas, has an envelope which coincides with the spinodal. Thus, at the approach to the spinodal of a superheated liquid and supersaturated vapor (∂Δλ/∂p)T → ∞, (∂Δλ/∂T)p → ∞. PMID:24908025
Solid-liquid phase equilibrium for binary Lennard-Jones mixtures
NASA Astrophysics Data System (ADS)
Hitchcock, Monica R.; Hall, Carol K.
1999-06-01
Solid-liquid phase diagrams are calculated for binary mixtures of Lennard-Jones spheres using Monte Carlo simulation and the Gibbs-Duhem integration technique of Kofke. We calculate solid-liquid phase diagrams for the model Lennard-Jones mixtures: argon-methane, krypton-methane, and argon-krypton, and compare our simulation results with experimental data and with Cottin and Monson's recent cell theory predictions. The Lennard-Jones model simulation results and the cell theory predictions show qualitative agreement with the experimental phase diagrams. One of the mixtures, argon-krypton, has a different phase diagram than its hard-sphere counterpart, suggesting that attractive interactions are an important consideration in determining solid-liquid phase behavior. We then systematically explore Lennard-Jones parameter space to investigate how solid-liquid phase diagrams change as a function of the Lennard-Jones diameter ratio, σ11/σ22, and well-depth ratio, ɛ11/ɛ22. This culminates in an estimate of the boundaries separating the regions of solid solution, azeotrope, and eutectic solid-liquid phase behavior in the space spanned by σ11/σ22 and ɛ11/ɛ22 for the case σ11/σ22<0.85.
Bárcenas, M; Reyes, Y; Romero-Martínez, A; Odriozola, G; Orea, P
2015-02-21
Coexistence and interfacial properties of a triangle-well (TW) fluid are obtained with the aim of mimicking the Lennard-Jones (LJ) potential and approach the properties of noble gases. For this purpose, the scope of the TW is varied to match vapor-liquid densities and surface tension. Surface tension and coexistence curves of TW systems with different ranges were calculated with replica exchange Monte Carlo and compared to those data previously reported in the literature for truncated and shifted (STS), truncated (ST), and full Lennard-Jones (full-LJ) potentials. We observed that the scope of the TW potential must be increased to approach the STS, ST, and full-LJ properties. In spite of the simplicity of TW expression, a remarkable agreement is found. Furthermore, the variable scope of the TW allows for a good match of the experimental data of argon and xenon. PMID:25702023
Systematic investigation of theories of transport in the Lennard-Jones fluid
NASA Astrophysics Data System (ADS)
Dyer, Kippi M.; Pettitt, B. M.; Stell, George
2007-01-01
Three kinetic theories of transport are investigated for the single-species Lennard-Jones model fluid. Transport coefficients, including diffusion, shear, and bulk viscosity, are calculated from these theories for the Lennard-Jones fluid across the fluid regions of the phase diagram. The results are systematically compared against simulation. It is found that for each transport property considered, there is at least one theoretical result based on approximations that have been systematically derived from a first-principles starting point that is quantitatively useful over a wide range of densities and temperatures. To the authors' knowledge, this article constitutes the first such compendium of results for the Lennard-Jones model fluid that has been assembled.
Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts
NASA Astrophysics Data System (ADS)
Chremos, Alexandros; Nikoubashman, Arash; Panagiotopoulos, Athanassios Z.
2014-02-01
In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric-isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments.
NASA Astrophysics Data System (ADS)
Hoang, Hai; Galliero, Guillaume
2013-12-01
This work aims at providing a tractable approach to model the local shear viscosity of strongly inhomogeneous dense fluids composed of spherical molecules, in which the density variations occur on molecular distance. The proposed scheme, which relies on the local density average model, has been applied to the quasi-hard-sphere, the Week-Chandler-Andersen and the Lennard-Jones fluids. A weight function has been developed to deal with the hard-sphere fluid given the specificities of momentum exchange. To extend the approach to the smoothly repulsive potential, we have taken into account that the non-local contributions to the viscosity due to the interactions of particles separated by a given distance are temperature dependent. Then, using a simple perturbation scheme, the approach is extended to the Lennard-Jones fluids. It is shown that the viscosity profiles of inhomogeneous dense fluids deduced from this approach are consistent with those directly computed by non-equilibrium molecular dynamics simulations.
Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts.
Chremos, Alexandros; Nikoubashman, Arash; Panagiotopoulos, Athanassios Z
2014-02-01
In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric-isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments. PMID:24511981
Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts
Chremos, Alexandros; Nikoubashman, Arash Panagiotopoulos, Athanassios Z.
2014-02-07
In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric–isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments.
Thermodynamic stability of soft-core Lennard-Jones fluids and their mixtures
NASA Astrophysics Data System (ADS)
Heyes, D. M.
2010-02-01
Thermodynamic stability of model single component and binary mixture fluids is considered with the Fisher-Ruelle (FR) stability criteria, which apply in the thermodynamic limit, and molecular dynamics (MD) simulation for finite periodic systems. Two soft-core potential forms are considered, ϕ6,1(r)=4[1/(a +r6)2-1/(a +r6)] and ϕ2,3(r)=4[1/(a +r2)6-1/(a+r2)3], where r is the separation between the particle centers. According to FR these are unstable in the thermodynamic limit if a >ac=1/2 and a >ac=(7/32)1/3, respectively. MD simulations with single-component particles show, however, that this transition on typical simulation times is more gradual for finite periodic systems with variation in a on either side of ac. For a
Molecular Dynamics Simulation of the Lennard--Jones Polymers in a Good Solvent
NASA Astrophysics Data System (ADS)
Ciesla, M.; Pawlowicz, J.; Longa, L.
2007-05-01
We carried out united-atom Langevin dynamics simulations of polymer's equilibrium state in a good solvent. Our primary goal was a pedagogical exposition of fundamental equilibrium properties of isolated polymers in dilutions with a model that contains many features of real materials. The polymer was chosen to be a three-dimensional chain of N identical beads (monomers) without internal structure. Each monomer interacted with its two neighbors by a harmonic potential, which modeled a chemical bond. Additionally all monomers within a chain were assumed to interact through the Lennard-Jones (LJ) potential. Interaction with solvent and with other polymers was introduced using Langevin forces. Analyzing internal energy per polymer and radius of gyration as function of temperature we observed a rapid globule to coil phase transition. Also we studied elastic properties of single polymer chain for temperatures below the transition and identified three regions with different elastic behavior. Typical chain lengths in our simulations ranged from 100 to 1000 monomers. The elaborated software package can easily be modified to study {e.g.} the effect of polymer stiffness on thermodynamic behavior.
Effect of Energy Polydispersity on the Nature of Lennard-Jones Liquids.
Ingebrigtsen, Trond S; Tanaka, Hajime
2016-08-11
In the companion paper [ Ingebrigtsen , T. S. ; Tanaka , H. J. Phys. Chem. B 2015 , 119 , 11052 ] 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 simpler than other types of liquids. Moreover, it was shown that size polydisperse LJ liquids have isomorphs to a good approximation. Isomorphs are curves in the phase diagram of RS liquids along which structure, dynamics, and some thermodynamic quantities are invariant in dimensionless (reduced) units. In this paper, we study the effect of energy polydispersity on the nature of LJ liquids. We show that energy polydisperse LJ liquids are RS liquids. However, a tendency of particle segregation, which increases with the degree of polydispersity, leads to a loss of strong virial-potential energy correlation but is mitigated by increasing temperature and/or density. Isomorphs are a good approximation also for energy polydisperse LJ liquids, although particle-resolved quantities display a somewhat poorer scaling compared to the mean quantities along the isomorph. PMID:27434103
Molecular dynamics study of nanobubbles in the equilibrium Lennard-Jones fluid.
Zhukhovitskii, D I
2013-10-28
We employ a model, in which the density fluctuations in a bulk liquid are represented as presence of the clusters of molecules with the lowered number of nearest neighbors (number of bonds). The nanobubble size distribution is calculated on the basis of a close analogy between the surface part of the work of formation for a cluster and for a nanobubble. The pre-exponential factor for this distribution is related to the fluid compressibility. Estimates made for different liquids show that it can be noticeably different from that adopted in the classical nucleation theory (CNT). Molecular dynamics (MD) simulation is performed for a liquid inside a macroscopic droplet of molecules interacting via the Lennard-Jones potential plus a long-range tail. The nanobubbles are identified by clusters of bond-deficient particles with the optimum number of bonds that provide the maximum nanobubble number density and maximum resolvable nanobubble equimolar size. The results of MD simulation are in qualitatively better agreement with proposed theory than with CNT. PMID:24182055
Molecular dynamics study of nanobubbles in the equilibrium Lennard-Jones fluid
NASA Astrophysics Data System (ADS)
Zhukhovitskii, D. I.
2013-10-01
We employ a model, in which the density fluctuations in a bulk liquid are represented as presence of the clusters of molecules with the lowered number of nearest neighbors (number of bonds). The nanobubble size distribution is calculated on the basis of a close analogy between the surface part of the work of formation for a cluster and for a nanobubble. The pre-exponential factor for this distribution is related to the fluid compressibility. Estimates made for different liquids show that it can be noticeably different from that adopted in the classical nucleation theory (CNT). Molecular dynamics (MD) simulation is performed for a liquid inside a macroscopic droplet of molecules interacting via the Lennard-Jones potential plus a long-range tail. The nanobubbles are identified by clusters of bond-deficient particles with the optimum number of bonds that provide the maximum nanobubble number density and maximum resolvable nanobubble equimolar size. The results of MD simulation are in qualitatively better agreement with proposed theory than with CNT.
Understanding the interfacial behavior in isopycnic Lennard-Jones mixtures by computer simulations.
Garrido, José Matías; Piñeiro, Manuel M; Mejía, Andrés; Blas, Felipe J
2016-01-14
The physical characterization of the singular interfacial behavior of heterogeneous fluid systems is a very important step in preliminary stages of the design process, and also in the subsequent procedures for the determination of the optimal operating conditions. Molar isopycnicity or molar density inversion is a special case of phase equilibrium behavior that directly affects the relative position of phases in heterogeneous mixtures, without being affected by gravitational fields. This work is dedicated to characterize the impact of molar density inversion on the interfacial properties of Lennard-Jones binary mixtures. The results and specific trends of the molar density inversion phenomena on the peculiar calculated composition profiles across the interface and interfacial tensions are explored by using canonical molecular dynamics simulations of the Lennard-Jones binary mixtures. Our results show that the density inversion causes drastic changes in the density profiles of the mixtures. In particular, symmetrical and equal-sized Lennard-Jones mixtures always exhibit desorption along the interfacial zone, i.e. the interfacial concentration profiles show a relative minimum at the interface of the total density profiles that increases when the dispersive energy parameter (ε(ij)) between unlike species decreases. However, as the asymmetry of the Lennard-Jones mixtures increases (σ(i) ≠ σ(j)), the concentration profiles display a relative maximum at the interface, which implies the adsorption of the total density profiles along the interfacial zone. PMID:26660062
Freezing and melting equations for the n-6 Lennard-Jones systems
NASA Astrophysics Data System (ADS)
Khrapak, Sergey A.; Ning, Ning
2016-05-01
We generalize previous approach of Khrapak and Morfill [J. Chem. Phys. 134, 094108 (2011)] to construct simple and sufficiently accurate freezing and melting equations for the conventional Lennard-Jones (LJ) system to n-6 LJ systems, using the accurate results for the triple points of these systems published by Sousa et al. [J. Chem. Phys. 136, 174502 (2012)].
Influence of strain on transport in dense Lennard-Jones systems
NASA Astrophysics Data System (ADS)
Petravic, Janka
2004-04-01
We study the shear stress relaxation and temperature dependence of the diffusion coefficient, viscosity, and thermal conductivity along a high-density Lennard-Jones isochore of the reduced density of 1.0, as it crosses the freezing and melting lines, in equilibrium and under constant strain.
Heffelfinger, G.S. ); Swol, F.v. )
1994-05-15
A new approach to calculating diffusivities, both transport as well as equilibrium, is presented. The dual control volume grand canonical molecular dynamics (or DCV-GCMD) method employs two local control volumes for chemical potential control via particle creation/destruction as in grand canonical Monte Carlo (GCMC) simulations. The control volumes are inserted in a standard [ital NVT] molecular dynamics simulation yielding a simulation with stochastic chemical potential control that may be thought of as a hybrid GCMC-MD approach. The geometrical control of the chemical potential enables a steady state chemical potential gradient to be established in the system. By measuring the density profile and flux, Fick's law is used to determine the diffusivity. An example calculation is presented for a simple Lennard-Jones system.
NASA Astrophysics Data System (ADS)
Benjamin, Ronald; Horbach, Jürgen
2015-07-01
Kinetics of crystal-growth is investigated along the solid-liquid coexistence line for the (100), (110), and (111) orientations of the Lennard-Jones (LJ) and Weeks-Chandler-Andersen (WCA) fcc crystal-liquid interface, using non-equilibrium molecular dynamics simulations. A slowing down of the growth kinetics along the coexistence line is observed, which is due to the decrease of the melting enthalpy with increasing coexistence temperature and pressure. Other quantities such as the melting pressure and liquid self-diffusion coefficient have a comparatively lesser impact on the kinetic growth coefficient. Growth kinetics of the LJ and WCA potentials become similar at large values of the melting temperature and pressure, when both resemble a purely repulsive soft-sphere potential. Classical models of crystallization from the melt are in reasonable qualitative agreement with our simulation data. Finally, several one-phase empirical melting/freezing rules are studied with respect to their validity along the coexistence line.
NASA Astrophysics Data System (ADS)
Keshavarzi, Ezat; Namdari, Fatemeh; Jildani, Sediqeh Rabiei
2016-04-01
The modified fundamental measure theory has been employed to investigate some well known regularities of bulk fluid for the Lennard-Jones fluid confined in nanoslit pore. The regularities investigated include common compression point, common bulk modulus point, Tait-Murnaghan equation, and the linear regularity between pressure and temperature for each isochore. All these regularities have been investigated for two different components of pressure for confined fluid. Our results show that the common compression and common bulk modulus point remain valid for fluids confined in nanoslit pores of different sizes and with different wall-fluid potentials. The density of the common compression and common bulk modulus point are different from corresponding ones for the bulk fluid. Our observations also show that the Tait-Murnaghan equation and pressure-temperature linear regularity also hold for confined fluid. The sign of the intercept of pressure-temperature regularity is determined by the difference between attraction and repulsion terms in the compressibility factor.
Crystallization of Lennard-Jones nanodroplets: From near melting to deeply supercooled.
Malek, Shahrazad M A; Morrow, Gregory P; Saika-Voivod, Ivan
2015-03-28
We carry out molecular dynamics (MD) and Monte Carlo (MC) simulations to characterize nucleation in liquid clusters of 600 Lennard-Jones particles over a broad range of temperatures. We use the formalism of mean first-passage times to determine the rate and find that Classical Nucleation Theory (CNT) predicts the rate quite well, even when employing simple modelling of crystallite shape, chemical potential, surface tension, and particle attachment rate, down to the temperature where the droplet loses metastability and crystallization proceeds through growth-limited nucleation in an unequilibrated liquid. Below this crossover temperature, the nucleation rate is still predicted when MC simulations are used to directly calculate quantities required by CNT. Discrepancy in critical embryo sizes obtained from MD and MC arises when twinned structures with five-fold symmetry provide a competing free energy pathway out of the critical region. We find that crystallization begins with hcp-fcc stacked precritical nuclei and differentiation to various end structures occurs when these embryos become critical. We confirm that using the largest embryo in the system as a reaction coordinate is useful in determining the onset of growth-limited nucleation and show that it gives the same free energy barriers as the full cluster size distribution once the proper reference state is identified. We find that the bulk melting temperature controls the rate, even though the solid-liquid coexistence temperature for the droplet is significantly lower. The value of surface tension that renders close agreement between CNT and direct rate determination is significantly lower than what is expected for the bulk system. PMID:25833595
Crystallization of Lennard-Jones nanodroplets: From near melting to deeply supercooled
NASA Astrophysics Data System (ADS)
Malek, Shahrazad M. A.; Morrow, Gregory P.; Saika-Voivod, Ivan
2015-03-01
We carry out molecular dynamics (MD) and Monte Carlo (MC) simulations to characterize nucleation in liquid clusters of 600 Lennard-Jones particles over a broad range of temperatures. We use the formalism of mean first-passage times to determine the rate and find that Classical Nucleation Theory (CNT) predicts the rate quite well, even when employing simple modelling of crystallite shape, chemical potential, surface tension, and particle attachment rate, down to the temperature where the droplet loses metastability and crystallization proceeds through growth-limited nucleation in an unequilibrated liquid. Below this crossover temperature, the nucleation rate is still predicted when MC simulations are used to directly calculate quantities required by CNT. Discrepancy in critical embryo sizes obtained from MD and MC arises when twinned structures with five-fold symmetry provide a competing free energy pathway out of the critical region. We find that crystallization begins with hcp-fcc stacked precritical nuclei and differentiation to various end structures occurs when these embryos become critical. We confirm that using the largest embryo in the system as a reaction coordinate is useful in determining the onset of growth-limited nucleation and show that it gives the same free energy barriers as the full cluster size distribution once the proper reference state is identified. We find that the bulk melting temperature controls the rate, even though the solid-liquid coexistence temperature for the droplet is significantly lower. The value of surface tension that renders close agreement between CNT and direct rate determination is significantly lower than what is expected for the bulk system.
Rydberg-London potential for diatomic molecules and unbonded atom pairs.
Cahill, Kevin; Parsegian, V Adrian
2004-12-01
We propose and test a pair potential that is accurate at all relevant distances and simple enough for use in large-scale computer simulations. A combination of the Rydberg potential from spectroscopy and the London inverse-sixth-power energy, the proposed form fits spectroscopically determined potentials better than the Morse, Varnshi, and Hulburt-Hirschfelder potentials and much better than the Lennard-Jones and harmonic potentials. At long distances, it goes smoothly to the London force appropriate for gases and preserves van der Waals's "continuity of the gas and liquid states," which is routinely violated by coefficients assigned to the Lennard-Jones 6-12 form. PMID:15634034
Phase changes in selected Lennard-Jones X13-nYn clusters.
Sabo, Dubravko; Predescu, Cristian; Doll, J D; Freeman, David L
2004-07-01
Detailed studies of the thermodynamic properties of selected binary Lennard-Jones clusters of the type X13-nYn (where n=1, 2, 3) are presented. The total energy, heat capacity, and first derivative of the heat capacity as a function of temperature are calculated by using the classical and path integral Monte Carlo methods combined with the parallel tempering technique. A modification in the phase change phenomena from the presence of impurity atoms and quantum effects is investigated. PMID:15260616
How to quantify solid-liquid phase transition: Lennard-Jones system case study
NASA Astrophysics Data System (ADS)
Klumov, Boris A.; Klumov
2013-12-01
In this paper we analyzed different measures, characterizing the melting of Lennard-Jones solid, and associated with the properties of both the translational and the orientational local order. It has been shown that the most sensitive indicator of melting is the cumulant of the probability distribution function over w 6 bond-order parameter. The criterion of melting based on the indicator is proposed; the criterion can be used for any solids, having fcc/hcp types of symmetry.
Metastability, spectrum, and eigencurrents of the Lennard-Jones-38 network
Cameron, Maria K.
2014-11-14
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.
Metastability, spectrum, and eigencurrents of the Lennard-Jones-38 network.
Cameron, Maria K
2014-11-14
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. PMID:25399138
Hess, Peter
2014-08-07
An improved microscopic cleavage model, based on a Morse-type and Lennard-Jones-type interaction instead of the previously employed half-sine function, is used to determine the maximum cleavage strength for the brittle materials diamond, tungsten, molybdenum, silicon, GaAs, silica, and graphite. The results of both interaction potentials are in much better agreement with the theoretical strength values obtained by ab initio calculations for diamond, tungsten, molybdenum, and silicon than the previous model. Reasonable estimates of the intrinsic strength are presented for GaAs, silica, and graphite, where first principles values are not available.
Costigliola, Lorenzo; Schrøder, Thomas B; Dyre, Jeppe C
2016-06-21
The recent theoretical prediction by Maimbourg and Kurchan [e-print arXiv:1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2, 3, 4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized by high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly. PMID:27334147
NASA Astrophysics Data System (ADS)
Costigliola, Lorenzo; Schrøder, Thomas B.; Dyre, Jeppe C.
2016-06-01
The recent theoretical prediction by Maimbourg and Kurchan [e-print arXiv:1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2, 3, 4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized by high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly.
Barbante, Paolo; Frezzotti, Aldo; Gibelli, Livio
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.
Solubility Limits in Lennard-Jones Mixtures: Effects of Disparate Molecule Geometries.
Dyer, Kippi M; Perkyns, John S; Pettitt, B Montgomery
2015-07-23
In order to better understand general effects of the size and energy disparities between macromolecules and solvent molecules in solution, especially for macromolecular constructs self-assembled from smaller molecules, we use the first- and second-order exact bridge diagram extensions of the HNC integral equation theory to investigate single-component, binary, ternary, and quaternary mixtures of Lennard-Jones fluids. For pure fluids, we find that the HNCH3 bridge function integral equation (i.e., exact to third order in density) is necessary to quantitatively predict the pure gas and pure liquid sides of the coexistence region of the phase diagram of the Lennard-Jones fluid. For the mixtures, we find that the HNCH2 bridge function integral equation is sufficient to qualitatively predict solubility in the binary, ternary, and quaternary mixtures, up to the nominal solubility limit. The results, as limiting cases, should be useful to several problems, including accurate phase diagram predictions for complex mixtures, design of self-assembling nanostructures via solvent controls, and the solvent contributions to the conformational behavior of macromolecules in complex fluids. PMID:25621892
Solubility Limits in Lennard-Jones Mixtures: Effects of Disparate Molecule Geometries
Dyer, Kippi M.; Perkyns, John S.; Pettitt, B. Montgomery
2016-01-01
In order to better understand general effects of the size and energy disparities between macromolecules and solvent molecules in solution, especially for macromolecular constructs self-assembled from smaller molecules, we use the first- and second-order exact bridge diagram extensions of the HNC integral equation theory to investigate single-component, binary, ternary, and quaternary mixtures of Lennard-Jones fluids. For pure fluids, we find that the HNCH3 bridge function integral equation (i.e., exact to third order in density) is necessary to quantitatively predict the pure gas and pure liquid sides of the coexistence region of the phase diagram of the Lennard-Jones fluid. For the mixtures, we find that the HNCH2 bridge function integral equation is sufficient to qualitatively predict solubility in the binary, ternary, and quaternary mixtures, up to the nominal solubility limit. The results, as limiting cases, should be useful to several problems, including accurate phase diagram predictions for complex mixtures, design of self-assembling nanostructures via solvent controls, and the solvent contributions to the conformational behavior of macromolecules in complex fluids. PMID:25621892
Urrutia, Ignacio; Paganini, Iván E
2016-05-01
We formulate a straightforward scheme of statistical mechanics for inhomogeneous systems that includes the virial series in powers of the activity for the grand free energy and density distributions. There, cluster integrals formulated for inhomogeneous systems play a main role. We center on second order terms that were analyzed in the case of hard-wall confinement, focusing in planar, spherical, and cylindrical walls. Further analysis was devoted to the Lennard-Jones system and its generalization, the 2k-k potential. For these interaction potentials, the second cluster integral was evaluated analytically. We obtained the fluid-substrate surface tension at second order for the planar, spherical, and cylindrical confinement. Spherical and cylindrical cases were analyzed using a series expansion in the radius including higher order terms. We detected a lnR/R(2) dependence of the surface tension for the standard Lennard-Jones system confined by spherical and cylindrical walls, no matter if particles are inside or outside of the hard walls. The analysis was extended to bending and Gaussian curvatures, where exact expressions were also obtained. PMID:27155620
NASA Astrophysics Data System (ADS)
Urrutia, Ignacio; Paganini, Iván E.
2016-05-01
We formulate a straightforward scheme of statistical mechanics for inhomogeneous systems that includes the virial series in powers of the activity for the grand free energy and density distributions. There, cluster integrals formulated for inhomogeneous systems play a main role. We center on second order terms that were analyzed in the case of hard-wall confinement, focusing in planar, spherical, and cylindrical walls. Further analysis was devoted to the Lennard-Jones system and its generalization, the 2k-k potential. For these interaction potentials, the second cluster integral was evaluated analytically. We obtained the fluid-substrate surface tension at second order for the planar, spherical, and cylindrical confinement. Spherical and cylindrical cases were analyzed using a series expansion in the radius including higher order terms. We detected a lnR/R2 dependence of the surface tension for the standard Lennard-Jones system confined by spherical and cylindrical walls, no matter if particles are inside or outside of the hard walls. The analysis was extended to bending and Gaussian curvatures, where exact expressions were also obtained.
Georgescu, Ionuţ; Brown, Sandra E; Mandelshtam, Vladimir A
2013-04-01
In order to address the issue of whether neon liquid in coexistence with its gas phase can be mapped to a quantum Lennard-Jones (LJ) fluid, we perform a series of simulations using Gibbs ensemble Monte Carlo for a range of de Boer quantum parameters Λ=ℏ/(σ√(mε)). The quantum effects are incorporated by implementing the variational gaussian wavepacket method, which provides an efficient numerical framework for estimating the quantum density at thermal equilibrium. The computed data for the LJ liquid is used to produce its phase diagram as a function of the quantum parameter, 0.065 ≤ Λ ≤ 0.11. These data are then used to fit the experimental phase diagram for neon liquid. The resulting parameters, ε = 35.68 ± 0.03 K and σ = 2.7616 ± 0.0005 Å (Λ = 0.0940), of the LJ pair potential are optimized to best represent liquid neon in coexistence with its gas phase for a range of physically relevant temperatures. This multi-temperature approach towards fitting and assessing a pair-potential is much more consistent than merely fitting a single data point, such as a melting temperature or a second virial coefficient. PMID:23574239
Sharapov, Vladimir A; Mandelshtam, Vladimir A
2007-10-18
We consider systems undergoing very-low-temperature solid-solid transitions associated with minima of similar energy but different symmetry, and separated by a high potential barrier. In such cases the well-known "broken-ergodicity" problem is often difficult to overcome, even using the most advanced Monte Carlo (MC) techniques, including the replica exchange method (REM). The methodology that we develop in this paper is suitable for the above specified cases and is numerically accurate and efficient. It is based on a new MC move implemented within the REM framework, in which trial points are generated analytically using an auxiliary harmonic superposition system that mimics well the true system at low temperatures. Due to the new move, the low-temperature random walks are able to frequently switch the relevant potential energy funnels leading to an efficient sampling. Numerically accurate results are obtained for a number of Lennard-Jones clusters, including those that have so far been treated only by the harmonic superposition approximation (HSA). The latter is believed to provide good estimates for low-temperature equilibrium properties but is manifestly uncontrollable and is difficult to validate. The present results provide a good test for the HSA and demonstrate its reliability, particularly for estimation of the solid-solid transition temperatures in most cases considered. PMID:17685597
Gordiz, Kiarash; Henry, Asegun
2015-01-01
To date, the established methods that describe thermal interface conductance (TIC) and include mode-level dependence have not included anharmonicity. The current intuition is therefore based on the behavior in the harmonic limit, whereby the extent of overlap in the bulk phonon density of states (DoS) (e.g., frequency overlap) dictates the TIC and more frequency overlap leads to higher TIC. Here, we study over 2,000 interfaces described by the Lennard-Jones potential using equilibrium molecular dynamics simulations, whereby we systematically change the mass and stiffness of each side. We show that the trends in TIC do not generally follow that of the bulk phonon DoS overlap, but instead more closely follow the vibrational power spectrum overlap for the interfacial atoms. We then identify the frequency overlap in the interfacial power spectra as an improved descriptor for understanding the qualitative trends in TIC. Although improved, the results show that the basic intuition of frequency overlap is still insufficient to explain all of the features, as the remaining variations are shown to arise from anharmonicity, which is a critical effect to include in interface calculations above cryogenic temperatures. PMID:26678793
NASA Astrophysics Data System (ADS)
Gordiz, Kiarash; Henry, Asegun
2015-12-01
To date, the established methods that describe thermal interface conductance (TIC) and include mode-level dependence have not included anharmonicity. The current intuition is therefore based on the behavior in the harmonic limit, whereby the extent of overlap in the bulk phonon density of states (DoS) (e.g., frequency overlap) dictates the TIC and more frequency overlap leads to higher TIC. Here, we study over 2,000 interfaces described by the Lennard-Jones potential using equilibrium molecular dynamics simulations, whereby we systematically change the mass and stiffness of each side. We show that the trends in TIC do not generally follow that of the bulk phonon DoS overlap, but instead more closely follow the vibrational power spectrum overlap for the interfacial atoms. We then identify the frequency overlap in the interfacial power spectra as an improved descriptor for understanding the qualitative trends in TIC. Although improved, the results show that the basic intuition of frequency overlap is still insufficient to explain all of the features, as the remaining variations are shown to arise from anharmonicity, which is a critical effect to include in interface calculations above cryogenic temperatures.
Explicit expression for the Stokes-Einstein relation for pure Lennard-Jones liquids.
Ohtori, Norikazu; Ishii, Yoshiki
2015-01-01
An explicit expression of the Stokes-Einstein (SE) relation in molecular scale has been determined for pure Lennard-Jones (LJ) liquids on the saturated vapor line using a molecular dynamics calculation with the Green-Kubo formula, as Dη(sv)=kTξ(-1)(N/V)(1/3), where D is the self-diffusion coefficient, η(sv) the shear viscosity, k the Boltzmann constant, T the temperature, ξ the constant, and N the particle number included in the system volume V. To this end, the dependence of D and η(sv) on packing fraction, η, and T has been determined so as to complete their scaling equations. The equations for D and η(sv) in these states are m(-1/2)(N/V)(-1/3)(1-η)(4)ε(-1/2)T and m(1/2)(N/V)(2/3)(1-η)(-4)ε(1/2)T(0), respectively, where m and ε are the atomic mass and characteristic parameter of energy used in the LJ potentials, respectively. The equations can well describe the behaviors of D and η(sv) for both the LJ and the real rare-gas liquids. The obtained SE relation justifies the theoretical equation proposed by Eyring and Ree, although the value of ξ is slightly different from that given by them. The difference of the obtained expression from the original SE relation, Dη(sv)=(kT/2π)σ(-1), where σ means the particle size, is the presence of the η(1/3) term, since (N/V)(1/3)=(6/π)(1/3)σ(-1)η(1/3). Since the original SE relation is based on the fluid mechanics for continuum media, allowing the presence of voids in liquids is the origin of the η(1/3) term. Therefore, also from this viewpoint, the present expression is more justifiable in molecular scale than the original SE relation. As a result, the η(1/3) term cancels out the σ dependence from the original SE relation. The present result clearly shows that it is not necessary to attribute the deviation from the original SE relation to any temperature dependence of particle size or to introduce the fractional SE relation for pure LJ liquids. It turned out that the η dependence of both D and
Explicit expression for the Stokes-Einstein relation for pure Lennard-Jones liquids
NASA Astrophysics Data System (ADS)
Ohtori, Norikazu; Ishii, Yoshiki
2015-01-01
An explicit expression of the Stokes-Einstein (SE) relation in molecular scale has been determined for pure Lennard-Jones (LJ) liquids on the saturated vapor line using a molecular dynamics calculation with the Green-Kubo formula, as D ηsv=k T ξ-1(N/V ) 1 /3 , where D is the self-diffusion coefficient, ηsv the shear viscosity, k the Boltzmann constant, T the temperature, ξ the constant, and N the particle number included in the system volume V . To this end, the dependence of D and ηsv on packing fraction, η , and T has been determined so as to complete their scaling equations. The equations for D and ηsv in these states are m-1 /2(N/V ) -1 /3(1-η ) 4ɛ-1 /2T and m1 /2(N/V ) 2 /3(1-η ) -4ɛ1 /2T0 , respectively, where m and ɛ are the atomic mass and characteristic parameter of energy used in the LJ potentials, respectively. The equations can well describe the behaviors of D and ηsv for both the LJ and the real rare-gas liquids. The obtained SE relation justifies the theoretical equation proposed by Eyring and Ree, although the value of ξ is slightly different from that given by them. The difference of the obtained expression from the original SE relation, D ηsv=(k T /2 π ) σ-1 , where σ means the particle size, is the presence of the η1 /3 term, since (N/V )1 /3=(6/π )1 /3σ-1η1 /3 . Since the original SE relation is based on the fluid mechanics for continuum media, allowing the presence of voids in liquids is the origin of the η1 /3 term. Therefore, also from this viewpoint, the present expression is more justifiable in molecular scale than the original SE relation. As a result, the η1 /3 term cancels out the σ dependence from the original SE relation. The present result clearly shows that it is not necessary to attribute the deviation from the original SE relation to any temperature dependence of particle size or to introduce the fractional SE relation for pure LJ liquids. It turned out that the η dependence of both D and ηsv is similar to
Modelling of disjoining pressure for Lennard-Jones free thin films
NASA Astrophysics Data System (ADS)
Peng, Tiefeng; Gao, Xuechao; Li, Qibin; Yang, Siyuan; Tang, Qizhong
2016-03-01
Development of disjoining pressure was performed to study the symmetric, Lennard-Jones (LJ) free thin films using molecular modelling. A methodology rooted from film thermodynamics was established to derive the disjoining pressure isotherm (Π ‑ h), which is based on the surface tension at varied film thicknesses and can be viewed as a post-processing technique. The results showed that the disjoining pressure of LJ fluid is purely attractive. Compared with the complicated method reported previously, this methodology is demonstrated to be more convenient and readily applicable for other liquid films (e.g. water, aqueous thin films containing electrolyte or surfactants), meanwhile it can be applied at both low and high temperatures.
Properties of the Lennard-Jones dimeric fluid in two dimensions: An integral equation study
Urbic, Tomaz; Dias, Cristiano L.
2014-03-07
The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared with Monte Carlo simulations. The critical parameters for selected types of dimers were also estimated. We analyze the influence of the bond length on critical point as well as tested correctness of site-site integral equation theory with different closures. The integral equations can be used to predict the phase diagram of dimers whose molecular parameters are known.
On the establishment of thermal diffusion in binary Lennard-Jones liquids
NASA Astrophysics Data System (ADS)
Ferrario, M.; Bonella, S.; Ciccotti, G.
2016-07-01
The establishment of thermal diffusion in an Ar-Kr Lennard-Jones mixture is investigated via dynamical non equilibrium molecular dynamics [G. Ciccotti, G. Jacucci, Phys. Rev. Lett. 35, 789 (1975)]. We observe, in particular, the evolution of the density and temperature fields of the system following the onset of the thermal gradient. In stationary conditions, we also compute the Soret coefficient of the mixture. This study confirms that dynamical non equilibrium molecular dynamics is an effective tool to gather information on transient phenomena, even though the full evolution of the mass and energy fluxes associated to the temperature and density fields requires, in this case, a more substantial numerical effort than the one employed here.
Phase diagram and universality of the Lennard-Jones gas-liquid system.
Watanabe, Hiroshi; Ito, Nobuyasu; Hu, Chin-Kun
2012-05-28
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. PMID:22667535
Dynamics of vacancies in two-dimensional Lennard-Jones crystals
NASA Astrophysics Data System (ADS)
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.
Baidakov, Vladimir G; Bobrov, Konstantin S; Teterin, Aleksey S
2011-08-01
Molecular dynamics simulations have been used to investigate the kinetics of spontaneous cavitation and crystallization in a Lennard-Jones liquid at negative pressures in the temperature range where these processes compete with each other. The nucleation rate has been calculated in NVE and NpT ensembles by the method of mean lifetime and the transition interface sampling method with parallel path swapping. The data obtained have been used to determine in the framework of classical nucleation theory the value of the ratio of the solid-liquid and the liquid-void interfacial free energy for critical crystals and cavities and the values of their volumes at points where the cavitation rate of the liquid is equal to the rate of its crystallization. PMID:21823717
Mesoscopic Hamiltonian for the fluctuations of adsorbed Lennard-Jones liquid films.
Fernández, Eva M; Chacón, Enrique; MacDowell, Luis G; Tarazona, Pedro
2015-06-01
We use Monte Carlo simulations of a Lennard-Jones fluid adsorbed on a short-range planar wall substrate to study the fluctuations in the thickness of the wetting layer, and we get a quantitative and consistent characterization of their mesoscopic Hamiltonian, H[ξ]. We have observed important finite-size effects, which were hampering the analysis of previous results obtained with smaller systems. The results presented here support an appealing simple functional form for H[ξ], close but not exactly equal to the theoretical nonlocal proposal made on the basis a generic density-functional analysis by Parry and coworkers. We have analyzed systems under different wetting conditions, as a proof of principle for a method that provides a quantitative bridge between the molecular interactions and the phenomenology of wetting films at mesoscopic scales. PMID:26172722
Dynamics of vacancies in two-dimensional Lennard-Jones crystals
NASA Astrophysics Data System (ADS)
Yao, Zhenwei; de la Cruz, Monica Olvera
2014-12-01
Vacancies represent an important class of crystallographic defects, and their behaviors can be strongly coupled with relevant material properties. In this work, we study the dynamics of generic n -point vacancies in two-dimensional Lennard-Jones crystals in several thermodynamic states. Simulations reveal the spectrum of distinct, size-dependent vacancy dynamics, including the nonmonotonously varying diffusive mobilities of one-, two- and three-point vacancies, and several healing routines of linear vacancies. Specifically, we numerically observe significantly faster diffusion of the two-point vacancy that can be attributed to its rotational degree of freedom. The high mobility of the two-point vacancies opens the possibility of doping two-point vacancies into atomic materials to enhance atomic migration. The rich physics of vacancies revealed in this study may have implications in the engineering of defects in extensive crystalline materials for desired properties.
Clustering of Lennard-Jones particles in water: temperature and pressure effects.
Ferrara, Gastón; McCarthy, Andrés N; Grigera, J Raúl
2007-09-14
While the hydrophobic effect is, for many systems, one of the most relevant interactions, it may be said that in the case of biological systems this effect becomes of determinant importance. Although the matter has been analyzed extensively, certain aspects are yet to be elucidated. Hence, the study on the behavior of the hydrophobic effect with temperature, and particularly with pressure deserves further investigation; model systems may help us in the task. We have analyzed the behavior of Lennard-Jones particles in water by means of molecular dynamics simulation under different conditions of size, concentration, temperature, and pressure. Following the formation of particle aggregates we can observe an increase of the hydrophobic effect with temperature and a strong weakening of the effect at high pressures. The results agree with the experimental evidence and show the ability of molecular dynamics simulation to account for the behavior of nonpolar substances under different conditions, provided that the intermolecular interactions used are adequate. PMID:17867756
Properties of the Lennard-Jones dimeric fluid in two dimensions: An integral equation study
Urbic, Tomaz; Dias, Cristiano L.
2014-01-01
The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared with Monte Carlo simulations. The critical parameters for selected types of dimers were also estimated. We analyze the influence of the bond length on critical point as well as tested correctness of site-site integral equation theory with different closures. The integral equations can be used to predict the phase diagram of dimers whose molecular parameters are known. PMID:24606372
Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids.
Dhabal, Debdas; Nguyen, Andrew Huy; Singh, Murari; Khatua, Prabir; Molinero, Valeria; Bandyopadhyay, Sanjoy; Chakravarty, Charusita
2015-10-28
Molecular dynamics simulations are used to contrast the supercooling and crystallization behaviour of monatomic liquids that exemplify the transition from simple to anomalous, tetrahedral liquids. As examples of simple fluids, we use the Lennard-Jones (LJ) liquid and a pair-dominated Stillinger-Weber liquid (SW16). As examples of tetrahedral, water-like fluids, we use the Stillinger-Weber model with variable tetrahedrality parameterized for germanium (SW20), silicon (SW21), and water (SW(23.15) or mW model). The thermodynamic response functions show clear qualitative differences between simple and water-like liquids. For simple liquids, the compressibility and the heat capacity remain small on isobaric cooling. The tetrahedral liquids in contrast show a very sharp rise in these two response functions as the lower limit of liquid-phase stability is reached. While the thermal expansivity decreases with temperature but never crosses zero in simple liquids, in all three tetrahedral liquids at the studied pressure, there is a temperature of maximum density below which thermal expansivity is negative. In contrast to the thermodynamic response functions, the excess entropy on isobaric cooling does not show qualitatively different features for simple and water-like liquids; however, the slope and curvature of the entropy-temperature plots reflect the heat capacity trends. Two trajectory-based computational estimation methods for the entropy and the heat capacity are compared for possible structural insights into supercooling, with the entropy obtained from thermodynamic integration. The two-phase thermodynamic estimator for the excess entropy proves to be fairly accurate in comparison to the excess entropy values obtained by thermodynamic integration, for all five Lennard-Jones and Stillinger-Weber liquids. The entropy estimator based on the multiparticle correlation expansion that accounts for both pair and triplet correlations, denoted by S(trip), is also studied. S
Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids
NASA Astrophysics Data System (ADS)
Dhabal, Debdas; Nguyen, Andrew Huy; Singh, Murari; Khatua, Prabir; Molinero, Valeria; Bandyopadhyay, Sanjoy; Chakravarty, Charusita
2015-10-01
Molecular dynamics simulations are used to contrast the supercooling and crystallization behaviour of monatomic liquids that exemplify the transition from simple to anomalous, tetrahedral liquids. As examples of simple fluids, we use the Lennard-Jones (LJ) liquid and a pair-dominated Stillinger-Weber liquid (SW16). As examples of tetrahedral, water-like fluids, we use the Stillinger-Weber model with variable tetrahedrality parameterized for germanium (SW20), silicon (SW21), and water (SW23.15 or mW model). The thermodynamic response functions show clear qualitative differences between simple and water-like liquids. For simple liquids, the compressibility and the heat capacity remain small on isobaric cooling. The tetrahedral liquids in contrast show a very sharp rise in these two response functions as the lower limit of liquid-phase stability is reached. While the thermal expansivity decreases with temperature but never crosses zero in simple liquids, in all three tetrahedral liquids at the studied pressure, there is a temperature of maximum density below which thermal expansivity is negative. In contrast to the thermodynamic response functions, the excess entropy on isobaric cooling does not show qualitatively different features for simple and water-like liquids; however, the slope and curvature of the entropy-temperature plots reflect the heat capacity trends. Two trajectory-based computational estimation methods for the entropy and the heat capacity are compared for possible structural insights into supercooling, with the entropy obtained from thermodynamic integration. The two-phase thermodynamic estimator for the excess entropy proves to be fairly accurate in comparison to the excess entropy values obtained by thermodynamic integration, for all five Lennard-Jones and Stillinger-Weber liquids. The entropy estimator based on the multiparticle correlation expansion that accounts for both pair and triplet correlations, denoted by Strip, is also studied. Strip is a
Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids
Dhabal, Debdas; Chakravarty, Charusita; Nguyen, Andrew Huy; Molinero, Valeria; Singh, Murari; Khatua, Prabir; Bandyopadhyay, Sanjoy
2015-10-28
Molecular dynamics simulations are used to contrast the supercooling and crystallization behaviour of monatomic liquids that exemplify the transition from simple to anomalous, tetrahedral liquids. As examples of simple fluids, we use the Lennard-Jones (LJ) liquid and a pair-dominated Stillinger-Weber liquid (SW{sub 16}). As examples of tetrahedral, water-like fluids, we use the Stillinger-Weber model with variable tetrahedrality parameterized for germanium (SW{sub 20}), silicon (SW{sub 21}), and water (SW{sub 23.15} or mW model). The thermodynamic response functions show clear qualitative differences between simple and water-like liquids. For simple liquids, the compressibility and the heat capacity remain small on isobaric cooling. The tetrahedral liquids in contrast show a very sharp rise in these two response functions as the lower limit of liquid-phase stability is reached. While the thermal expansivity decreases with temperature but never crosses zero in simple liquids, in all three tetrahedral liquids at the studied pressure, there is a temperature of maximum density below which thermal expansivity is negative. In contrast to the thermodynamic response functions, the excess entropy on isobaric cooling does not show qualitatively different features for simple and water-like liquids; however, the slope and curvature of the entropy-temperature plots reflect the heat capacity trends. Two trajectory-based computational estimation methods for the entropy and the heat capacity are compared for possible structural insights into supercooling, with the entropy obtained from thermodynamic integration. The two-phase thermodynamic estimator for the excess entropy proves to be fairly accurate in comparison to the excess entropy values obtained by thermodynamic integration, for all five Lennard-Jones and Stillinger-Weber liquids. The entropy estimator based on the multiparticle correlation expansion that accounts for both pair and triplet correlations, denoted by S{sub trip
Enhancement of the droplet nucleation in a dense supersaturated Lennard-Jones vapor.
Zhukhovitskii, D I
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. PMID:27179494
Kadoura, Ahmad; Siripatana, Adil; Sun, Shuyu; Knio, Omar; Hoteit, Ibrahim
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. PMID:27276951
Calero, C; Knorowski, C; Travesset, A
2016-03-28
We investigate a general method to calculate the free energy of crystalline solids by considering the harmonic approximation and quasistatically switching the anharmonic contribution. The advantage of this method is that the harmonic approximation provides an already very accurate estimate of the free energy, and therefore the anharmonic term is numerically very small and can be determined to high accuracy. We further show that the anharmonic contribution to the free energy satisfies a number of exact inequalities that place constraints on its magnitude and allows approximate but fast and accurate estimates. The method is implemented into a readily available general software by combining the code HOODLT (Highly Optimized Object Oriented Dynamic Lattice Theory) for the harmonic part and the molecular dynamics (MD) simulation package HOOMD-blue for the anharmonic part. We use the method to calculate the low temperature phase diagram for Lennard-Jones particles. We demonstrate that hcp is the equilibrium phase at low temperature and pressure and obtain the coexistence curve with the fcc phase, which exhibits reentrant behavior. Several implications of the method are discussed. PMID:27036422
Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation
NASA Astrophysics Data System (ADS)
Kadoura, Ahmad; Siripatana, Adil; Sun, Shuyu; Knio, Omar; Hoteit, Ibrahim
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 (ɛ, 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
NASA Astrophysics Data System (ADS)
Zhukhovitskii, D. I.
2016-05-01
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.
Effect of confinement on the solid-liquid coexistence of Lennard-Jones Fluid
Das, Chandan K.; Singh, Jayant K.
2013-11-07
The solid-liquid coexistence of a Lennard-Jones fluid confined in slit pores of variable pore size, H, is studied using molecular dynamics simulations. Three-stage pseudo-supercritical transformation path of Grochola [J. Chem. Phys. 120(5), 2122 (2004)] and multiple histogram reweighting are employed for the confined system, for various pore sizes ranging from 20 to 5 molecular diameters, to compute the solid-liquid coexistence. The Gibbs free energy difference is evaluated using thermodynamic integration method by connecting solid-liquid phases under confinement via one or more intermediate states without any first order phase transition among them. Thermodynamic melting temperature is found to oscillate with wall separation, which is in agreement with the behavior seen for kinetic melting temperature evaluated in an earlier study. However, thermodynamic melting temperature for almost all wall separations is higher than the bulk case, which is contrary to the behavior seen for the kinetic melting temperature. The oscillation founds to decay at around H = 12, and beyond that pore size dependency of the shift in melting point is well represented by the Gibbs-Thompson equation.
Nucleation of liquid droplets and voids in a stretched Lennard-Jones fcc crystal
Baidakov, Vladimir G. Tipeev, Azat O.
2015-09-28
The method of molecular dynamics simulation has been used to investigate the phase decay of a metastable Lennard-Jones face-centered cubic crystal at positive and negative pressures. It is shown that at high degrees of metastability, crystal decay proceeds through the spontaneous formation and growth of new-phase nuclei. It has been found that there exists a certain boundary temperature. Below this temperature, the crystal phase disintegrates as the result of formation of voids, and above, as a result of formation of liquid droplets. The boundary temperature corresponds to the temperature of cessation of a crystal–liquid phase equilibrium when the melting line comes in contact with the spinodal of the stretched liquid. The results of the simulations are interpreted in the framework of classical nucleation theory. The thermodynamics of phase transitions in solids has been examined with allowance for the elastic energy of stresses arising owing to the difference in the densities of the initial and the forming phases. As a result of the action of elastic forces, at negative pressures, the boundary of the limiting superheating (stretching) of a crystal approaches the spinodal, on which the isothermal bulk modulus of dilatation becomes equal to zero. At the boundary of the limiting superheating (stretching), the shape of liquid droplets and voids is close to the spherical one.
Theory of slope-dependent disjoining pressure with application to Lennard-Jones liquid films.
Yi, Taeil; Wong, Harris
2007-09-15
A liquid film of thickness h<100 nm is subject to additional intermolecular forces, which are collectively called disjoining pressure Pi. Since Pi dominates at small film thicknesses, it determines the stability and wettability of thin films. Current theory derived for uniform films gives Pi=Pi(h). This solution has been applied recently to non-uniform films and becomes unbounded near a contact line as h-->0. Consequently, many different effects have been considered to eliminate or circumvent this singularity. We present a mean-field theory of Pi that depends on the slope h(x) as well as the height h of the film. When this theory is implemented for Lennard-Jones liquid films, the new Pi=Pi(h,h(x)) is bounded near a contact line as h-->0. Thus, the singularity in Pi(h) is artificial because it results from extending a theory beyond its range of validity. We also show that the new Pi can capture all three regimes of drop behavior (complete wetting, partial wetting, and pseudo-partial wetting) without altering the signs of the long and short-range interactions. We find that a drop with a precursor film is linearly stable. PMID:17570389
Calero, C.; Knorowski, C.; Travesset, A.
2016-03-22
We investigate a general method to calculate the free energy of crystalline solids by considering the harmonic approximation and quasistatically switching the anharmonic contribution. The advantage of this method is that the harmonic approximation provides an already very accurate estimate of the free energy, and therefore the anharmonic term is numerically very small and can be determined to high accuracy. We further show that the anharmonic contribution to the free energy satisfies a number of exact inequalities that place constraints on its magnitude and allows approximate but fast and accurate estimates. The method is implemented into a readily available generalmore » software by combining the code HOODLT (Highly Optimized Object Oriented Dynamic Lattice Theory) for the harmonic part and the molecular dynamics (MD) simulation package HOOMD-blue for the anharmonic part. We use the method to calculate the low temperature phase diagram for Lennard-Jones particles. We demonstrate that hcp is the equilibrium phase at low temperature and pressure and obtain the coexistence curve with the fcc phase, which exhibits reentrant behavior. Furthermore, several implications of the method are discussed.« less
Freezing and melting line invariants of the Lennard-Jones system.
Costigliola, Lorenzo; Schrøder, Thomas B; Dyre, Jeppe C
2016-06-01
The invariance of several structural and dynamical properties of the Lennard-Jones (LJ) system along the freezing and melting lines is interpreted in terms of isomorph theory. First the freezing/melting lines of the LJ system are shown to be approximated by isomorphs. Then we show that the invariants observed along the freezing and melting isomorphs are also observed on other isomorphs in the liquid and crystalline phases. The structure is probed by the radial distribution function and the structure factor and dynamics are probed by the mean-square displacement, the intermediate scattering function, and the shear viscosity. Studying these properties with reference to isomorph theory explains why the known single-phase melting criteria hold, e.g., the Hansen-Verlet and the Lindemann criteria, and why the Andrade equation for the viscosity at freezing applies, e.g., for most liquid metals. Our conclusion is that these empirical rules and invariants can all be understood from isomorph theory and that the invariants are not peculiar to the freezing and melting lines, but hold along all isomorphs. PMID:27186598
NASA Astrophysics Data System (ADS)
Calero, C.; Knorowski, C.; Travesset, A.
2016-03-01
We investigate a general method to calculate the free energy of crystalline solids by considering the harmonic approximation and quasistatically switching the anharmonic contribution. The advantage of this method is that the harmonic approximation provides an already very accurate estimate of the free energy, and therefore the anharmonic term is numerically very small and can be determined to high accuracy. We further show that the anharmonic contribution to the free energy satisfies a number of exact inequalities that place constraints on its magnitude and allows approximate but fast and accurate estimates. The method is implemented into a readily available general software by combining the code HOODLT (Highly Optimized Object Oriented Dynamic Lattice Theory) for the harmonic part and the molecular dynamics (MD) simulation package HOOMD-blue for the anharmonic part. We use the method to calculate the low temperature phase diagram for Lennard-Jones particles. We demonstrate that hcp is the equilibrium phase at low temperature and pressure and obtain the coexistence curve with the fcc phase, which exhibits reentrant behavior. Several implications of the method are discussed.
An accurate Van der Waals-type equation of state for the Lennard-Jones fluid
Mecke, M.; Mueller, A.; Winkelmann, J.
1996-03-01
A new equation of state (EOS) is proposed for the Helmholtz energy F of the Lennard-Jones fluid which represents the thermodynamic properties over a wide range of temperatures and densities. The EOS is written in the form of a generalized van der Waals equation, F= F{sub H} + F{sub A}, where F{sub H} is a hard body contribution and FA an attractive dispersion force contribution. The expression for F{sub H} is closely related to the hybrid Barker-Henderson pertubation theory. The construction of FA is accomplished with the Setzmann-Wagner optimization procedure on the basis of virial coefficients and critically assessed computer simulation data. A comparison with the EOS shows improvement in the description of the vapor-liquid coexistence properties, the pvT data, and in peculiar, of the caloric properties. A comparison with the EOS of Kolafa and Nezbeda which appeared after the bulk of this work was finished shows still an improvement in the standard deviations of the pressure and internal energy by about 30%.
NASA Astrophysics Data System (ADS)
McNeil, William J.; Madden, William G.; Haymet, A. D. J.; Rice, Stuart A.
1983-01-01
A recent theory of Haymet, Rice, and Madden (HRM) for the pair and triplet correlation functions is tested at liquid state densities against new molecular dynamics results for the Lennard-Jones (12,6) fluid. The HRM integral equation, based on the Born-Green equation and a topological reduction of the diagrammatic expansion of the triplet correlation function, has been solved for a high temperature state (T*=2.74, ρ*=0.80) and is found to give triplet correlation functions in good agreement with the molecular dynamics results. For a lower-temperature state (T*=0.73, ρ*=0.85), where numerical difficulties have thus far frustrated attempts to obtain a self-consistent solution of the HRM integral equation, direct tests of the HRM closure are made using molecular dynamics pair correlation functions to evaluate the diagrams. Although some striking qualitative features of the triplet correlations are correctly described by the HRM closure for this low-temperature state, the HRM approach is not in quantitative agreement with the molecular dynamics results. Test calculations indicate that the principle source of these errors is the neglect of important higher-order diagrams for the triplet correlation function. A reorganization of the diagrammatic series is suggested which may identify the most important of these neglected diagrams. Additional computer simulation results are also reported for the purely repulsive Weeks-Chandler-Andersen (WCA) ``reference'' fluid and for the underlying hard sphere fluid. The similarity of the pair structures of these fluids, noted by WCA, is also found to hold with high accuracy for the triplet structures. It is suggested that these similarities may be exploited in applying the methods of HRM to the hard sphere fluid.
Klauda, Jeffery B; Wu, Xiongwu; Pastor, Richard W; Brooks, Bernard R
2007-05-01
Molecular dynamics (MD) simulations of heptane/vapor, hexadecane/vapor, water/vapor, hexadecane/water, and dipalmitoylphosphatidylcholine (DPPC) bilayers and monolayers are analyzed to determine the accuracy of treating long-range interactions in interfaces with the isotropic periodic sum (IPS) method. The method and cutoff (rc) dependences of surface tensions, density profiles, water dipole orientation, and electrostatic potential profiles are used as metrics. The water/vapor, heptane/vapor, and hexadecane/vapor interfaces are accurately and efficiently calculated with 2D IPS (rc=10 A). It is demonstrated that 3D IPS is not practical for any of the interfacial systems studied. However, the hybrid method PME/IPS [Particle Mesh Ewald for electrostatics and 3D IPS for Lennard-Jones (LJ) interactions] provides an efficient way to include both types of long-range forces in simulations of large liquid/vacuum and all liquid/liquid interfaces, including lipid monolayers and bilayers. A previously published pressure-based long-range LJ correction yields results similar to those of PME/IPS for liquid/liquid interfaces. The contributions to surface tension of LJ terms arising from interactions beyond 10 A range from 13 dyn/cm for the hexadecane/vapor interface to approximately 3 dyn/cm for hexadecane/water and DPPC bilayers and monolayers. Surface tensions of alkane/vapor, hexadecane/water, and DPPC monolayers based on the CHARMM lipid force fields agree very well with experiment, whereas surface tensions of the TIP3P and TIP4P-Ew water models underestimate experiment by 16 and 11 dyn/cm, respectively. Dipole potential drops (DeltaPsi) are less sensitive to long-range LJ interactions than surface tensions. However, DeltaPsi for the DPPC bilayer (845+/-3 mV proceeding from water to lipid) and water (547+/-2 mV for TIP4P-Ew and 521+/-3 mV for TIP3P) overestimate experiment by factors of 3 and 5, respectively, and represent expected deficiencies in nonpolarizable force fields
Liquid-liquid interfacial properties of a symmetrical Lennard-Jones binary mixture
Martínez-Ruiz, F. J.; Blas, F. J.; Moreno-Ventas Bravo, A. I.
2015-09-14
We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ{sub 11} = σ{sub 22}, with the same dispersive energy between like species, ϵ{sub 11} = ϵ{sub 22}, but different dispersive energies between unlike species low enough to induce phase separation. We use the extensions of the improved version of the inhomogeneous long-range corrections of Janecek [J. Phys. Chem. B 110, 6264 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] and Martínez-Ruiz et al. [J. Chem. Phys. 141, 184701 (2014)], to deal with the interaction energy and microscopic components of the pressure tensor. We perform Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of the symmetrical mixture with different cut-off distances r{sub c} and in combination with the inhomogeneous long-range corrections. The pressure tensor is obtained using the mechanical (virial) and thermodynamic route. The liquid-liquid interfacial tension is also evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the test-area methodology. This allows to check the validity of the recent extensions presented to deal with the contributions due to long-range corrections for intermolecular energy and pressure tensor in the case of binary mixtures that exhibit liquid-liquid immiscibility. In addition to the pressure tensor and the surface tension, we also obtain density profiles and coexistence densities and compositions as functions of pressure, at a given temperature. According to our results, the main effect of increasing the cut-off distance r{sub c} is to sharpen the liquid-liquid interface and to increase the width of the biphasic coexistence region. Particularly interesting is the presence of a relative minimum in the total density profiles of the symmetrical mixture. This minimum is related
Liquid-liquid interfacial properties of a symmetrical Lennard-Jones binary mixture
NASA Astrophysics Data System (ADS)
Martínez-Ruiz, F. J.; Moreno-Ventas Bravo, A. I.; Blas, F. J.
2015-09-01
We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ11 = σ22, with the same dispersive energy between like species, ɛ11 = ɛ22, 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 Janec̆ek [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 rc 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 rc is to sharpen the liquid-liquid interface and to increase the width of the biphasic coexistence region. Particularly interesting is the presence of a relative minimum in the total density profiles of the symmetrical mixture. This minimum is related with a desorption of the molecules
Liquid-liquid interfacial properties of a symmetrical Lennard-Jones binary mixture.
Martínez-Ruiz, F J; Moreno-Ventas Bravo, A I; Blas, F J
2015-09-14
We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ11 = σ22, with the same dispersive energy between like species, ϵ11 = ϵ22, 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 Janec̆ek [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 rc 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 rc is to sharpen the liquid-liquid interface and to increase the width of the biphasic coexistence region. Particularly interesting is the presence of a relative minimum in the total density profiles of the symmetrical mixture. This minimum is related with a desorption of the molecules
Lundrigan, Sarah E. M.; Saika-Voivod, Ivan
2009-09-14
We perform molecular dynamics (MD) and Monte Carlo computer simulations to test the ability of the recently developed formalism of mean first-passage time (MFPT) [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); J. Wedekind and D. Reguera, J. Phys. Chem. B 112, 11060 (2008)] to characterize crystal nucleation in the Lennard-Jones liquid. We find that the nucleation rate, critical embryo size, Zeldovich factor, attachment rate, and the nucleation barrier profile obtained from MFPT all compare very well to the same quantities calculated using other methods. Furthermore, we find that the nucleation rate obtained directly through MD closely matches the prediction of classical nucleation theory.
Separdar, L; Davatolhagh, S
2013-02-01
We investigate the static structure and diffusive dynamics of binary Lennard-Jones mixture upon supercooling in the presence of gold nanoparticle within the framework of the mode-coupling theory of the dynamic glass transition in the direct space by means of constant-NVT molecular dynamics simulations. It is found that the presence of gold nanoparticle causes the energy per particle and the pressure of this system to decrease with respect to the bulk binary Lennard-Jones mixture. Furthermore, the presence of nanoparticle has a direct effect on the liquid structure and causes the peaks of the radial distribution functions to become shorter with respect to the bulk binary Lennard-Jones liquid. The dynamics of the liquid at a given density is found to be consistent with the mode-coupling theory (MCT) predictions in a certain range at low temperatures. In accordance with the idealized MCT, the diffusion constants D(T) show a power-law behavior at low temperatures for both types of binary Lennard-Jones (BLJ) particles as well as the gold atoms comprising the nanoparticle. The mode-coupling crossover temperature T(c) is the same for all particle types; however, T(c)=0.4 is reduced with respect to that of the bulk BLJ liquid, and the γ exponent is found to depend on the particle type. The existence of the nanoparticle causes the short-time β-relaxation regime to shorten and the range of validity of the MCT shrinks with respect to the bulk BLJ. It is also found that at intermediate and low temperatures the curves of the mean-squared displacements (MSDs) versus tD(T) fall onto a master curve. The MSDs follow the master curve in an identical time range with the long-time α-relaxation regime of the mode-coupling theory. By obtaining the viscosity, it is observed that the Stokes-Einstein relation remains valid at high and intermediate temperatures but breaks down as the temperatures approach T(c) as a result of the cooperative motion or activated processes. PMID:23496514
NASA Astrophysics Data System (ADS)
Separdar, L.; Davatolhagh, S.
2013-02-01
We investigate the static structure and diffusive dynamics of binary Lennard-Jones mixture upon supercooling in the presence of gold nanoparticle within the framework of the mode-coupling theory of the dynamic glass transition in the direct space by means of constant-NVT molecular dynamics simulations. It is found that the presence of gold nanoparticle causes the energy per particle and the pressure of this system to decrease with respect to the bulk binary Lennard-Jones mixture. Furthermore, the presence of nanoparticle has a direct effect on the liquid structure and causes the peaks of the radial distribution functions to become shorter with respect to the bulk binary Lennard-Jones liquid. The dynamics of the liquid at a given density is found to be consistent with the mode-coupling theory (MCT) predictions in a certain range at low temperatures. In accordance with the idealized MCT, the diffusion constants D(T) show a power-law behavior at low temperatures for both types of binary Lennard-Jones (BLJ) particles as well as the gold atoms comprising the nanoparticle. The mode-coupling crossover temperature Tc is the same for all particle types; however, Tc=0.4 is reduced with respect to that of the bulk BLJ liquid, and the γ exponent is found to depend on the particle type. The existence of the nanoparticle causes the short-time β-relaxation regime to shorten and the range of validity of the MCT shrinks with respect to the bulk BLJ. It is also found that at intermediate and low temperatures the curves of the mean-squared displacements (MSDs) versus tD(T) fall onto a master curve. The MSDs follow the master curve in an identical time range with the long-time α-relaxation regime of the mode-coupling theory. By obtaining the viscosity, it is observed that the Stokes-Einstein relation remains valid at high and intermediate temperatures but breaks down as the temperatures approach Tc as a result of the cooperative motion or activated processes.
Phase and interface behaviors in type-I and type-V Lennard-Jones mixtures: theory and simulations.
Mejía, Andrés; Pàmies, Josep C; Duque, Daniel; Segura, Hugo; Vega, Lourdes F
2005-07-15
Density gradient theory (DGT) and molecular-dynamics (MD) simulations have been used to predict subcritical phase and interface behaviors in type-I and type-V equal-size Lennard-Jones mixtures. Type-I mixtures exhibit a continuum critical line connecting their pure critical components, which implies that their subcritical phase equilibria are gas liquid. Type-V mixtures are characterized by two critical lines and a heteroazeotropic line. One of the two critical lines begins at the more volatile pure component critical point up to an upper critical end point and the other one comes from the less volatile pure component critical point ending at a lower critical end point. The heteroazeotropic line connects both critical end points and is characterized by gas-liquid-liquid equilibria. Therefore, subcritical states of this type exhibit gas-liquid and gas-liquid-liquid equilibria. In order to obtain a correct characterization of the phase and interface behaviors of these types of mixtures and to directly compare DGT and MD results, the global phase diagram of equal-size Lennard-Jones mixtures has been used to define the molecular parameters of these mixtures. According to our results, DGT and MD are two complementary methodologies able to obtain a complete and simultaneous prediction of phase equilibria and their interfacial properties. For the type of mixtures analyzed here, both approaches have shown excellent agreement in their phase equilibrium and interface properties in the full concentration range. PMID:16080742
NASA Astrophysics Data System (ADS)
Ebato, Yuki; Miyata, Tatsuhiko
2016-05-01
Ornstein-Zernike (OZ) integral equation theory is known to overestimate the excess internal energy, Uex, pressure through the virial route, Pv, and excess chemical potential, μex, for one-component Lennard-Jones (LJ) fluids under hypernetted chain (HNC) and Kovalenko-Hirata (KH) approximatons. As one of the bridge correction methods to improve the precision of these thermodynamic quantities, it was shown in our previous paper that the method to apparently adjust σ parameter in the LJ potential is effective [T. Miyata and Y. Ebato, J. Molec. Liquids. 217, 75 (2016)]. In our previous paper, we evaluated the actual variation in the σ parameter by using a fitting procedure to molecular dynamics (MD) results. In this article, we propose an alternative method to determine the actual variation in the σ parameter. The proposed method utilizes a condition that the virial and compressibility pressures coincide with each other. This method can correct OZ theory without a fitting procedure to MD results, and possesses characteristics of keeping a form of HNC and/or KH closure. We calculate the radial distribution function, pressure, excess internal energy, and excess chemical potential for one-component LJ fluids to check the performance of our proposed bridge function. We discuss the precision of these thermodynamic quantities by comparing with MD results. In addition, we also calculate a corrected gas-liquid coexistence curve based on a corrected KH-type closure and compare it with MD results.
NASA Astrophysics Data System (ADS)
Georgescu, IonuÅ£; Mandelshtam, Vladimir A.
2012-10-01
The theory of self-consistent phonons (SCP) was originally developed to address the anharmonic effects in condensed matter systems. The method seeks a harmonic, temperature-dependent Hamiltonian that provides the "best fit" for the physical Hamiltonian, the "best fit" being defined as the one that optimizes the Helmholtz free energy at a fixed temperature. The present developments provide a scalable O(N) unified framework that accounts for anharmonic effects in a many-body system, when it is probed by either thermal (ℏ → 0) or quantum fluctuations (T → 0). In these important limits, the solution of the nonlinear SCP equations can be reached in a manner that requires only the multiplication of 3N × 3N matrices, with no need of diagonalization. For short range potentials, such as Lennard-Jones, the Hessian, and other related matrices are highly sparse, so that the scaling of the matrix multiplications can be reduced from O(N3) to ˜ O(N). We investigate the role of quantum effects by continuously varying the de-Boer quantum delocalization parameter Λ and report the N-Λ (T = 0), and also the classical N-T (Λ = 0) phase diagrams for sizes up to N ˜ 104. Our results demonstrate that the harmonic approximation becomes inadequate already for such weakly quantum systems as neon clusters, or for classical systems much below the melting temperatures.
Bomont, Jean-Marc; Hansen, Jean-Pierre; Pastore, Giorgio
2015-10-01
The structural and thermodynamic behavior of a deeply supercooled Lennard-Jones liquid, and its random first-order transition (RFOT) to an ideal glass is investigated, using a system of two weakly coupled replicas and the hypernetted chain integral equation for the pair structure of this symmetric binary system. A systematic search in the density-temperature plane points to the existence of two glass branches below a density-dependent threshold temperature. The branch of lower free energy exhibits a rapid growth of the structural overlap order parameter upon cooling and may be identified with the ideal glass phase conjectured by several authors for both spin and structural glasses. The RFOT, signaled by a sharp discontinuity of the order parameter, is predicted to be weakly first order from a thermodynamic viewpoint. The transition temperature T(cr) increases rapidly with density and approximately obeys a scaling relation valid for a reference system of particles interacting via a purely repulsive 1/r(18) potential. PMID:26565249
Munaò, Gianmarco; Costa, Dino; Caccamo, Carlo
2016-10-19
Inspired by significant improvements obtained for the performances of the polymer reference interaction site model (PRISM) theory of the fluid phase when coupled with 'molecular closures' (Schweizer and Yethiraj 1993 J. Chem. Phys. 98 9053), we exploit a matrix generalization of this concept, suitable for the more general RISM framework. We report a preliminary test of the formalism, as applied to prototype square-well homonuclear diatomics. As for the structure, comparison with Monte Carlo shows that molecular closures are slightly more predictive than their 'atomic' counterparts, and thermodynamic properties are equally accurate. We also devise an application of molecular closures to models interacting via continuous, soft-core potentials, by using well established prescriptions in liquid state perturbation theories. In the case of Lennard-Jones dimers, our scheme definitely improves over the atomic one, providing semi-quantitative structural results, and quite good estimates of internal energy, pressure and phase coexistence. Our finding paves the way to a systematic employment of molecular closures within the RISM framework to be applied to more complex systems, such as molecules constituted by several non-equivalent interaction sites. PMID:27548461
A simple water model in the presence of inert Lennard-Jones obstacles II: the hydrophobic effect
NASA Astrophysics Data System (ADS)
Kurtjak, Mario; Urbic, Tomaz
2015-04-01
Using Monte Carlo computer simulations, hydrophobic effect for a non-polar particle with the diameter of a water molecule was studied in water, confined within a disordered matrix. Freely mobile two-dimensional Mercedes-Benz water was put in a disordered, but fixed, matrix of Lennard-Jones disks. Influence of temperature and matrix properties on the thermodynamic quantities of a non-polar solute solvation was studied. The hydrophobic effect is changed by the presence of the obstacles. Smaller matrix particles change the solute-water structure and thermodynamics drastically, as it was also observed for the properties of pure confined water. The study is bringing new scientific important observations in understanding the role of hydrophobic forces under confinement.
NASA Astrophysics Data System (ADS)
Jung, Jiyun; Lee, Jumin; Kim, Jun Soo
2015-03-01
We present a simulation study on the mechanisms of a phase separation in dilute fluids of Lennard-Jones (LJ) particles as a model of self-interacting molecules. Molecular dynamics (MD) and Brownian dynamics (BD) simulations of the LJ fluids are employed to model the condensation of a liquid droplet in the vapor phase and the mesoscopic aggregation in the solution phase, respectively. With emphasis on the cluster growth at late times well beyond the nucleation stage, we find that the growth mechanisms can be qualitatively different: cluster diffusion and coalescence in the MD simulations and Ostwald ripening in the BD simulations. We also show that the rates of the cluster growth have distinct scaling behaviors during cluster growth. This work suggests that in the solution phase the random Brownian nature of the solute dynamics may lead to the Ostwald ripening that is qualitatively different from the cluster coalescence in the vapor phase.
Maddox, M.W.; Gubbins, K.E.
1997-12-01
A combination of grand canonical Monte Carlo and molecular dynamics simulation techniques are used to study the freezing and melting of Lennard-Jones methane in several different cylindrical pores. Two different types of pore wall are considered; a strongly attractive wall, and a weakly attractive wall, each with pore diameters in the range 1.5{endash}3.5 nm. Freezing point depression is observed in the case of the weakly attractive pores, in agreement with several experimental studies. Freezing point elevation is observed at the walls of the strongly attractive pore, but freezing point depression occurs at the center of such pores, due to geometrical constraints. {copyright} {ital 1997 American Institute of Physics.}
NASA Astrophysics Data System (ADS)
Shiba, H.; Onuki, A.
We examine the changeover in the particle configurations and the dynamics in dense Lennard-Jones binary mixtures composed of small and large particles. By varying the composition at a low temperature, we realize crystal with defects, polycrystal with small grains, and glass with various degrees of disorder. In particular, we show configurations where small crystalline regions composed of the majority species are enclosed by percolated amorphous layers composed of the two species. We visualize the dynamics of configuration changes using the method of bond breakage and following the particle displacements. In quiescent jammed states, the dynamics is severely slowed down and is highly heterogeneous at any compositions. We apply shear flow by relative motions of boundary layers. Then plastic deformations multiply occur in relatively fragile regions, growing into large-scale shear bands where the strain is highly localized. Such bands appear on short time scales and evolve on l ong time scales with finite lifetimes.
Nanoscale Poiseuille flow and effects of modified Lennard-Jones potential function
NASA Astrophysics Data System (ADS)
Toghraie Semiromi, D.; Azimian, A. R.
2010-08-01
Numerical simulation of Poiseuille flow of liquid Argon in a nanochannel using the non-equilibrium molecular dynamics simulation (NEMD) is performed. The nanochannel is a three-dimensional rectangular prism geometry where the concerned numbers of Argon atoms are 2,700, 2,550 and 2,400 at 102, 108 and 120 K. Poiseuille flow is simulated by embedding the fluid particles in a uniform force field. An external driving force, ranging from 1 to 11 PN (Pico Newton), is applied along the flow direction to inlet fluid particles during the simulation. To obtain a more uniform temperature distribution across the channel, local thermostating near the wall are used. Also, the effect of other mixing rules (Lorenthz-Berthelot and Waldman-Kugler rules) on the interface structure are examined by comparing the density profiles near the liquid/solid interfaces for wall temperatures 108 and 133 K for an external force of 7 PN. Using Kong and Waldman-Kugler rules, the molecules near the solid walls were more randomly distributed compared to Lorenthz-Berthelot rule. These mean that the attraction between solid-fluid atoms was weakened by using Kong rule and Waldman-Kugler rule rather than the Lorenthz-Berthelot rule. Also, results show that the mean axial velocity has symmetrical distribution near the channel centerline and an increase in external driving force can increase maximum and average velocity values of fluid. Furthermore, the slip length and slip velocity are functions of the driving forces and they show an arising trend with an increase in inlet driving force and no slip boundary condition is satisfied at very low external force (<1 PN).
NASA Astrophysics Data System (ADS)
Sumi, Tomonari; Maruyama, Yutaka; Mitsutake, Ayori; Koga, Kenichiro
2016-06-01
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.
Ohtori, Norikazu; Ishii, Yoshiki
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.
NASA Astrophysics Data System (ADS)
Ohtori, Norikazu; Ishii, Yoshiki
2015-10-01
Explicit expressions of the self-diffusion coefficient, Di, and shear viscosity, ηsv, 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 Di and ηsv evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for Di 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 Di. 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.
Ohtori, Norikazu; Ishii, Yoshiki
2015-10-28
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 Di 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 Di. 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. PMID:26520534
NASA Astrophysics Data System (ADS)
Kikugawa, Gota; Ando, Shotaro; Suzuki, Jo; Naruke, Yoichi; Nakano, Takeo; Ohara, Taku
2015-01-01
In the present study, molecular dynamics (MD) simulations on the monatomic Lennard-Jones liquid in a periodic boundary system were performed in order to elucidate the effect of the computational domain size and shape on the self-diffusion coefficient measured by the system. So far, the system size dependence in cubic computational domains has been intensively investigated and these studies showed that the diffusion coefficient depends linearly on the inverse of the system size, which is theoretically predicted based on the hydrodynamic interaction. We examined the system size effect not only in the cubic cell systems but also in rectangular cell systems which were created by changing one side length of the cubic cell with the system density kept constant. As a result, the diffusion coefficient in the direction perpendicular to the long side of the rectangular cell significantly increases more or less linearly with the side length. On the other hand, the diffusion coefficient in the direction along the long side is almost constant or slightly decreases. Consequently, anisotropy of the diffusion coefficient emerges in a rectangular cell with periodic boundary conditions even in a bulk liquid simulation. This unexpected result is of critical importance because rectangular fluid systems confined in nanospace, which are present in realistic nanoscale technologies, have been widely studied in recent MD simulations. In order to elucidate the underlying mechanism for this serious system shape effect on the diffusion property, the correlation structures of particle velocities were examined.
NASA Astrophysics Data System (ADS)
Li, Ping; Dong, Yunhong; Zhao, Nanrong; Hou, Zhonghuai
2014-04-01
Distance fluctuation of a single molecule, modeled as an idealized bead-spring chain, dissolved in a Lennard-Jones liquid is studied by using a multidimensional generalized Langevin equation, where the friction kernel ζ(t) is calculated from the kinetic mode coupling theory (MCT). Temporal behavior of the distance autocorrelation function shows three typical regimes of time dependence, starting with a constant, followed by a power law of t-α, and finally an exponential decay. Particular attentions are paid to the time span of the power law regime, which corresponds to anomalous subdiffusion behavior, and the MCT framework enables us to investigate thoroughly how this regime depends on microscopic details such as the bead-to-solvent mass ratio MR, chain spring frequency ω, and the chain length N. Interestingly, the exponent α is robust to be 1/2 against the change of these parameters, although the friction kernel ζ(t) shows nontrivial dependence on time. In addition, we find that the starting time of the power-law region t1 scales with Γ-1, with Γ = 4ω2/ζ0 where ζ0 is the zero-frequency friction which decreases rapidly with increasing bead mass. On the other hand, the ending time t2 is not sensitive to varying ω or ζ0, but it increases with N rapidly before it reaches a constant for N larger than some threshold value. Our work may provide a unified strategy starting from the microscopic level to understand the anomalous subdiffusive behavior regarding large scale conformational change of polymers or proteins.
An EQT-based cDFT approach for a confined Lennard-Jones fluid mixture
Motevaselian, M. H.; Mashayak, S. Y.; Aluru, N. R.
2015-09-28
Empirical potential-based quasi-continuum theory (EQT) provides a route to incorporate atomistic detail into continuum framework such as the Nernst-Planck equation. EQT can also be used to construct a grand potential functional for classical density functional theory (cDFT). The combination of EQT and cDFT provides a simple and fast approach to predict the inhomogeneous density, potential profiles, and thermodynamic properties of confined fluids. We extend the EQT-cDFT approach to confined fluid mixtures and demonstrate it by simulating a mixture of methane and hydrogen inside slit-like channels of graphene. We show that the EQT-cDFT predictions for the structure of the confined fluid mixture compare well with the molecular dynamics simulation results. In addition, our results show that graphene slit nanopores exhibit a selective adsorption of methane over hydrogen.
Martínez-Ruiz, F. J.; Blas, F. J.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.
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
NASA Astrophysics Data System (ADS)
Martínez-Ruiz, F. J.; Blas, F. J.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.
2014-11-01
We propose an extension of the improved version of the inhomogeneous long-range corrections of Janeček [J. Phys. Chem. B 110, 6264-6269 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] to account for the intermolecular potential energy of spherical, rigid, and flexible molecular systems, to deal with the contributions to the microscopic components of the pressure tensor due to the dispersive long-range corrections. We have performed Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of spherical Lennard-Jones molecules with different cutoff distances, rc = 2.5, 3, 4, and 5σ. In addition, we have also considered cutoff distances rc = 2.5 and 3σ in combination with the inhomogeneous long-range corrections proposed in this work. The normal and tangential microscopic components of the pressure tensor are obtained using the mechanical or virial route in combination with the recipe of Irving and Kirkwood, while the macroscopic components are calculated using the Volume Perturbation thermodynamic route proposed by de Miguel and Jackson [J. Chem. Phys. 125, 164109 (2006)]. The vapour-liquid interfacial tension is evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the Test-Area methodology. In addition to the pressure tensor and the surface tension, we also obtain density profiles, coexistence densities, vapour pressure, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the cutoff distance and the long-range corrections on these properties. According to our results, the main effect of increasing the cutoff distance (at fixed temperature) is to sharpen the vapour-liquid interface, to decrease the vapour pressure, and to increase the width of the biphasic coexistence region. As a result, the interfacial thickness
NASA Astrophysics Data System (ADS)
Ikeshoji, Tamio; Hafskjold, Bjørn; Hashi, Yuichi; Kawazoe, Yoshiyuki
1996-09-01
Cluster formation of Lennard-Jones particles (65 536 atoms in a unit cell with an overall number density equal to 0.0149) was simulated by molecular dynamics. The temperature was set to decrease linearly with time by various thermostats, starting from a gas state temperature and ending at zero temperature. With the Nosé-Hoover thermostat, it was found that the translational temperature of the clusters suddenly decreased almost to zero when the cluster formation drastically increased around a reduced temperature (T*) of 0.5, while the internal temperature decreased linearly. Using the Andersen thermostat, which could simulate the aggregation of particles in an inert gas, both the internal and translational temperatures decreased almost linearly with time. When these thermostats were used, cluster-cluster and cluster-atom collisions did not give any magic number peaks in the size distribution up to 250 atoms/cluster at any temperature. Careful tracing of the cluster growth of 13-atom clusters showed no difference in reactivity between icosahedral and nonicosahedral clusters. To simulate cooling in a supersonic jet, a thermostat which controlled only the translational temperature was introduced. After the clusters were formed by cooling the system with this thermostat, their internal temperature stayed at T*≊0.5, while the translational temperature decreased linearly to zero with time as it was controlled. A long-time evaporation from these high-temperature clusters gave peaks at 13 and 19 (and less significantly at 23 and 26) which are magic number sizes corresponding to single, double, triple, and quadruple icosahedra, respectively. The internal temperatures of 13- and 19-atom clusters were higher than those of other size clusters. Higher evaporation energy was observed for the clusters of 13, 19, 23, and 26 atoms than for other size clusters after the long-time evaporation, but only the 13-atom clusters had the higher evaporation energy after cooling by the
NASA Astrophysics Data System (ADS)
Miyata, Tatsuhiko; Miyazaki, Sanae
2016-08-01
The accuracy of the temperature derivative of radial distribution function obtained under hypernetted chain (HNC), Kovalenko-Hirata (KH), Percus-Yevick (PY) and Verlet-modified (VM) closure approximations is examined for one-component Lennard-Jones fluid. As relevant thermodynamic quantities, constant-volume heat capacity and thermal pressure coefficient are investigated in terms of their accuracy under the above four approximations. It is found that HNC and KH closures overestimate these quantities, whereas PY closure tends to underestimate them. VM closure predicts rather accurately the quantities. A significant cancellation is observed along the integration for the above quantities under HNC and KH closures, especially at high density state.
a Theoretical Investigation on 10-12 Potential of Hydrogen-Hydrogen Covalent Bond
NASA Astrophysics Data System (ADS)
Taneri, Sencer
2013-05-01
This is an analytical investigation of well-known 10-12 potential of hydrogen-hydrogen covalent bond. In this research, we will make an elaboration of the well-known 6-12 Lennard-Jones potential in case of this type of bond. Though the results are illustrated in many text books and literature, an analytical analysis for these potentials is missing almost everywhere. The power laws are valid for small radial distances, which are calculated to some extent. The internuclear separation as well as the binding energy of the hydrogen molecule are evaluated with success.
Oderji, Hassan Yousefi; Ding, Hongbin; Behnejad, Hassan
2011-06-01
The second self-diffusion and viscosity virial coefficients of the Lennard-Jones (LJ) fluid were calculated by a detailed evaluation of the velocity and shear-stress autocorrelation functions using equilibrium molecular dynamics simulations at low and moderate densities. Accurate calculation of these coefficients requires corresponding transport coefficient values with low degrees of uncertainty. These were obtained via very long simulations by increasing the number of particles and by using the knowledge of correlation functions in the Green-Kubo method in conjunction with their corresponding generalized Einstein relations. The values of the self-diffusion and shear viscosity coefficients have been evaluated for systems with reduced densities between 0.0005 and 0.05 and reduced temperatures from 0.7 to 30.0. This provides a new insight into the transport coefficients beyond what can be offered by the Rainwater-Friend theory, which has not been developed for the self-diffusion coefficient. PMID:21797351
NASA Astrophysics Data System (ADS)
Adidharma, Hertanto; Tan, Sugata P.
2016-07-01
Canonical Monte Carlo simulations on face-centered cubic (FCC) and hexagonal closed packed (HCP) Lennard-Jones (LJ) solids are conducted at very low temperatures (0.10 ≤ T∗ ≤ 1.20) and high densities (0.96 ≤ ρ∗ ≤ 1.30). A simple and robust method is introduced to determine whether or not the cutoff distance used in the simulation is large enough to provide accurate thermodynamic properties, which enables us to distinguish the properties of FCC from that of HCP LJ solids with confidence, despite their close similarities. Free-energy expressions derived from the simulation results are also proposed, not only to describe the properties of those individual structures but also the FCC-liquid, FCC-vapor, and FCC-HCP solid phase equilibria.
NASA Astrophysics Data System (ADS)
Somasi, Sweta; Khomami, Bamin; Lovett, Ronald
2000-09-01
On a thermodynamic path proposed by Lutsko, Wolf, and Yip, a solid is transformed at fixed density into an ideal gas. The accuracy of molecular dynamics simulation results for the free energy of solids using this path is compromised by the presence of a singularity on the path and by the nonergodic behavior of the ideal gas. We present calculations of the third law free energies of the face-centered-cubic (fcc) and hexagonal-close-packed (hcp) solids of argon (modeled as a Lennard-Jones system) to illustrate how the singularity and the nonergodic dynamics introduce errors. Strategies for removing the singularity and the nonergodic dynamics are presented. Finally, an analytic expansion around the ideal state is developed to provide an alternate route to the free energy of those states for which simulation estimates give large statistical uncertainties. The quantitative errors in these new approaches to the simulation of the free energy of a solid are given.
NASA Astrophysics Data System (ADS)
Matsumoto, Akira
2014-12-01
The thermodynamic functions for Lennard-Jones (9,6) gases with a hard core that are evaluated till the third virial coefficients, are investigated at an isobaric process. Some thermodynamic functions are analytically expressed as functions of intensive variables, temperature, and pressure. Some thermodynamic quantities for carbon dioxide are calculated numerically and drawn graphically. In critical states, the heat capacity diverges to infinity at the critical point while the Gibbs free energy, volume, enthalpy, and entropy are continuous at the critical point. In the coexistence of two phases, the boiling temperatures and the enthalpy changes of vaporization are obtained by numerical calculations for 20 substances. The Gibbs free energy indicates a polygonal line; entropy, volume, and enthalpy jump from the liquid to gaseous phase at the boiling point. The heat capacity does not diverge to infinity but shows a finite discrepancy at boiling point. This suggests that a first-order phase transition at the boiling point and a second-order phase transition may occur at the critical point.
A new interlayer potential for hexagonal boron nitride.
Akıner, Tolga; Mason, Jeremy K; Ertürk, Hakan
2016-09-28
A new interlayer potential is developed for interlayer interactions of hexagonal boron nitride sheets, and its performance is compared with other potentials in the literature using molecular dynamics simulations. The proposed potential contains Coulombic and Lennard-Jones 6-12 terms, and is calibrated with recent experimental data including the hexagonal boron nitride interlayer distance and elastic constants. The potentials are evaluated by comparing the experimental and simulated values of interlayer distance, density, elastic constants, and thermal conductivity using non-equilibrium molecular dynamics. The proposed potential is found to be in reasonable agreement with experiments, and improves on earlier potentials in several respects. Simulated thermal conductivity values as a function of the number of layers and of temperature suggest that the proposed LJ 6-12 potential has the ability to predict some phonon behaviour during heat transport in the out-of-plane direction. PMID:27452331
NASA Astrophysics Data System (ADS)
van Westen, Thijs; Oyarzún, Bernardo; Vlugt, Thijs J. H.; Gross, Joachim
2015-06-01
We develop an equation of state (EoS) for describing isotropic-nematic (IN) phase equilibria of Lennard-Jones (LJ) chain fluids. The EoS is developed by applying a second order Barker-Henderson perturbation theory to a reference fluid of hard chain molecules. The chain molecules consist of tangentially bonded spherical segments and are allowed to be fully flexible, partially flexible (rod-coil), or rigid linear. The hard-chain reference contribution to the EoS is obtained from a Vega-Lago rescaled Onsager theory. For the description of the (attractive) dispersion interactions between molecules, we adopt a segment-segment approach. We show that the perturbation contribution for describing these interactions can be divided into an "isotropic" part, which depends only implicitly on orientational ordering of molecules (through density), and an "anisotropic" part, for which an explicit dependence on orientational ordering is included (through an expansion in the nematic order parameter). The perturbation theory is used to study the effect of chain length, molecular flexibility, and attractive interactions on IN phase equilibria of pure LJ chain fluids. Theoretical results for the IN phase equilibrium of rigid linear LJ 10-mers are compared to results obtained from Monte Carlo simulations in the isobaric-isothermal (NPT) ensemble, and an expanded formulation of the Gibbs-ensemble. Our results show that the anisotropic contribution to the dispersion attractions is irrelevant for LJ chain fluids. Using the isotropic (density-dependent) contribution only (i.e., using a zeroth order expansion of the attractive Helmholtz energy contribution in the nematic order parameter), excellent agreement between theory and simulations is observed. These results suggest that an EoS contribution for describing the attractive part of the dispersion interactions in real LCs can be obtained from conventional theoretical approaches designed for isotropic fluids, such as a Perturbed
Baker, Christopher M.; Lopes, Pedro E. M.; Zhu, Xiao; Roux, Benoît; MacKerell, Alexander D.
2010-01-01
Lennard-Jones (LJ) parameters for a variety of model compounds have previously been optimized within the CHARMM Drude polarizable force field to reproduce accurately pure liquid phase thermodynamic properties as well as additional target data. While the polarizable force field resulting from this optimization procedure has been shown to satisfactorily reproduce a wide range of experimental reference data across numerous series of small molecules, a slight but systematic overestimate of the hydration free energies has also been noted. Here, the reproduction of experimental hydration free energies is greatly improved by the introduction of pair-specific LJ parameters between solute heavy atoms and water oxygen atoms that override the standard LJ parameters obtained from combining rules. The changes are small and a systematic protocol is developed for the optimization of pair-specific LJ parameters and applied to the development of pair-specific LJ parameters for alkanes, alcohols and ethers. The resulting parameters not only yield hydration free energies in good agreement with experimental values, but also provide a framework upon which other pair-specific LJ parameters can be added as new compounds are parametrized within the CHARMM Drude polarizable force field. Detailed analysis of the contributions to the hydration free energies reveals that the dispersion interaction is the main source of the systematic errors in the hydration free energies. This information suggests that the systematic error may result from problems with the LJ combining rules and is combined with analysis of the pair-specific LJ parameters obtained in this work to identify a preliminary improved combining rule. PMID:20401166
NASA Astrophysics Data System (ADS)
Baidakov, Vladimir G.
2016-02-01
The process of bubble nucleation in a Lennard-Jones (LJ) liquid is studied by molecular dynamics (MD) simulation. The bubble nucleation rate J is determined by the mean life-time method at temperatures above that of the triple point in the region of negative pressures. The results of simulation are compared with classical nucleation theory (CNT) and modified classical nucleation theory (MCNT), in which the work of formation of a critical bubble is determined in the framework of the van der Waals-Cahn-Hilliard gradient theory (GT). It has been found that the values of J obtained in MD simulation systematically exceed the data of CNT, and this excess in the nucleation rate reaches 8-10 orders of magnitude close to the triple point temperature. The results of MCNT are in satisfactory agreement with the data of MD simulation. To describe the properties of vapor-phase nuclei in the framework of GT, an equation of state has been built up which describes stable, metastable and labile regions of LJ fluids. The surface tension of critical bubbles γ has been found from CNT and data of MD simulation as a function of the radius of curvature of the surface of tension R*. The dependence γ(R*) has also been calculated from GT. The Tolman length has been determined, which is negative and in modulus equal to ≈(0.1 - 0.2) σ. The paper discusses the applicability of the Tolman formula to the description of the properties of critical nuclei in nucleation.
Fujiwara, K.; Shibahara, M.
2014-07-21
A classical molecular dynamics simulation was conducted for a system composed of fluid molecules between two planar solid surfaces, and whose interactions are described by the 12-6 Lennard-Jones form. This paper presents a general description of the pressure components and interfacial tension at a fluid-solid interface obtained by the perturbative method on the basis of statistical thermodynamics, proposes a method to consider the pressure components tangential to an interface which are affected by interactions with solid atoms, and applies this method to the calculation system. The description of the perturbative method is extended to subsystems, and the local pressure components and interfacial tension at a liquid-solid interface are obtained and examined in one- and two-dimensions. The results are compared with those obtained by two alternative methods: (a) an evaluation of the intermolecular force acting on a plane, and (b) the conventional method based on the virial expression. The accuracy of the numerical results is examined through the comparison of the results obtained by each method. The calculated local pressure components and interfacial tension of the fluid at a liquid-solid interface agreed well with the results of the two alternative methods at each local position in one dimension. In two dimensions, the results showed a characteristic profile of the tangential pressure component which depended on the direction tangential to the liquid-solid interface, which agreed with that obtained by the evaluation of the intermolecular force acting on a plane in the present study. Such good agreement suggests that the perturbative method on the basis of statistical thermodynamics used in this study is valid to obtain the local pressure components and interfacial tension at a liquid-solid interface.
NASA Astrophysics Data System (ADS)
Nishio, Kengo; Kōga, Junichiro; Yamaguchi, Toshio; Yonezawa, Fumiko
2004-06-01
The purpose of the present paper is to study the freezing procedures of a rare-gas system confined in a nanometer-scale pore as well as the atomic structure of a confined rare-gas solid. To this end, we carry out molecular-dynamics (MD) simulations for Lennard-Jones argon (LJ Ar) confined in an open-ended finite-length pore. Our simulation cell consists of two sections. One section contains a cubic solid with a cylindrical pore, the solid being composed of LJ atoms with interaction parameters appropriate for silica glass. The diameter and length of the cylindrical pore are 10σArAr (3.4 nm) and 20σArAr (6.8 nm), respectively. The other section is a free space into which we insert Ar atoms. The adsorption of Ar atoms into the nanopore proceeds by diffusive mass transfer from the free space. We simulate usual experimental procedures, that is, the pore is first filled with a liquid via capillary condensation, and thereafter the system is cooled. Our results show that, as the temperature is decreased, the freezing of Ar starts from the vicinity of the pore wall. The portion of solidlike Ar atoms increases gradually near the pore wall, while the Ar atoms in the central part of the pore change suddenly from liquidlike to solidlike all at the same time. We find that the structure factor of Ar confined in the pore does not change qualitatively during the freezing process, showing simple-liquid-like behaviors for both the liquid and the solid. This result agrees qualitatively with recently reported x-ray diffraction patterns of confined rare-gas solids. In a bulk LJ Ar system, on the other hand, the atomic structure changes qualitatively during the freezing process. One possible explanation for this difference is that the Ar solid in the pore consists of several different local atomic configurations, each giving distinct contributions to the structure factor of the confined Ar solid. Therefore, analyses beyond the averaged structure are helpful for extending our knowledge
NASA Astrophysics Data System (ADS)
Amon, L. M.; Reinhardt, W. P.
2000-09-01
In this paper four reference states allowing computation of the absolute internal free energies of solid and liquid clusters are introduced and implemented. Three of these are introduced for the first time. Two of these references are useful for highly fluctional liquidlike clusters while the other two are appropriate for more rigid solidlike clusters. These reference states are combined with a finite time variational method to obtain upper and lower bounds to the absolute free energies of clusters of Lennard-Jones (LJ) atoms, LJ4 and LJ55, allowing the efficiency of each of the four reference states to be elucidated. The optimal references are then applied to obtain upper and lower bounds to the internal free energies (the absolute free energy in the cluster center of mass frame) of LJ55 over a series of fixed temperatures including the solid-liquid coexistence regime. The reversible scaling method, recently introduced by de Koning, Antonelli, and Yip, is then used to extend the results over a continuous range of temperatures. Estimation of the rotational free energy allows comparisons to free energies of LJ55 in the nonrotating center of mass frame as estimated by Doye and Wales.
Reif, Maria M.; Huenenberger, Philippe H.
2011-04-14
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. Huenenberger, J. Chem. Phys. 124, 224501 (2006); M. M. Reif and P. H. Huenenberger, 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{sup +}, Na{sup +}, K{sup +}, Rb{sup +}, Cs{sup +}) and halide (F{sup -}, Cl{sup -}, Br{sup -}, I{sup -}) 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); 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, {Delta}G{sub hyd} {sup O-minus} [H{sup +}]=-1100, -1075 or -1050 kJ mol{sup -1}, resulting in three sets L, M, and H for the SPC water model and three sets L{sub E}, M{sub E}, and H{sub E} for the SPC/E water model (alternative sets can easily be interpolated to intermediate {Delta}G{sub hyd} {sup O-minus} [H{sup +}] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective
Energy of Cohesion, Compressibility, and the Potential Energy Functions of the Graphite System
NASA Technical Reports Server (NTRS)
Girifalco, L. A.; Lad, R. A.
1956-01-01
The lattice summations of the potential energy of importance in the graphite system have been computed by direct summation assuming a Lennard-Jones 6-12 potential between carbon atoms. From these summations, potential energy curves were constructed for interactions between a carbon atom and a graphite monolayer, between a carbon atom and a graphite surface, between a graphite monolayer and a semi-infinite graphite crystal and between two graphite semi-infinite crystals. Using these curves, the equilibrium distance between two isolated physically interacting carbon atoms was found to be 2.70 a, where a is the carbon-carbon distance in a graphite sheet. The distance between a surface plane and the rest of the crystal was found to be 1.7% greater than the interlayer spacing. Theoretical values of the energy of cohesion and the compressibility were calculated from the potential curve for the interaction between two semi-infinite crystals. They were (delta)E(sub c) = -330 ergs/sq cm and beta =3.18x10(exp -12)sq cm/dyne, respectively. These compared favorably with the experimental values of (delta)E(sub c) = -260 ergs/sq cm and beta = 2.97 X 10(exp -2) sq cm/dyne.
Effect of intermolecular potential on compressible Couette flow in slip and transitional regimes
NASA Astrophysics Data System (ADS)
Weaver, Andrew B.; Venkattraman, A.; Alexeenko, Alina A.
2014-10-01
The effect of intermolecular potentials on compressible, planar flow in slip and transitional regimes is investigated using the direct simulation Monte Carlo method. Two intermolecular interaction models, the variable hard sphere (VHS) and the Lennard-Jones (LJ) models, are first compared for subsonic and supersonic Couette flows of argon at temperatures of 40, 273, and 1,000 K, and then for Couette flows in the transitional regime ranging from Knudsen numbers (Kn) of 0.0051 to 1. The binary scattering model for elastic scattering using the Lennard-Jones (LJ) intermolecular potential proposed recently [A. Venkattraman and A. Alexeenko, "Binary scattering model for Lennard-Jones potential: Transport coefficients and collision integrals for non-equilibrium gas flow simulations," Phys. Fluids 24, 027101 (2012)] is shown to accurately reproduce both the theoretical collision frequency in an equilibrium gas as well as the theoretical viscosity variation with temperature. The use of a repulsive-attractive instead of a purely repulsive potential is found to be most important in the continuum and slip regimes as well as in flows with large temperature variations. Differences in shear stress of up to 28% between the VHS and LJ models is observed at Kn=0.0051 and is attributed to differences in collision frequencies, ultimately affecting velocity gradients at the wall. For Kn=1 where the Knudsen layer expands the entire domain, the effect of the larger collision frequency in the LJ model relative to VHS diminishes, and a 7% difference in shear stress is observed.
On Stable Pair Potentials with an Attractive Tail, Remarks on Two Papers by A. G. Basuev
NASA Astrophysics Data System (ADS)
de Lima, Bernardo N. B.; Procacci, Aldo; Yuhjtman, Sergio
2016-04-01
We revisit two old and apparently little known papers by Basuev (Teoret Mat Fiz 37(1):130-134, 1978, Teoret Mat Fiz 39(1):94-105, 1979) and show that the results contained there yield strong improvements on current lower bounds of the convergence radius of the Mayer series for continuous particle systems interacting via a very large class of stable and tempered potentials, which includes the Lennard-Jones type potentials. In particular we analyze the case of the classical Lennard-Jones gas under the light of the Basuev scheme and, using also some new results (Yuhjtman in J Stat Phys 160(6): 1684-1695, 2015) on this model recently obtained by one of us, we provide a new lower bound for the Mayer series convergence radius of the classical Lennard-Jones gas, which improves by a factor of the order 105 on the current best lower bound recently obtained in de Lima and Procacci (J Stat Phys 157(3):422-435, 2014).
Zhang, Minhua; Chen, Lihang; Yang, Huaming; Sha, Xijiang; Ma, Jing
2016-07-01
Gibbs ensemble Monte Carlo simulation with configurational bias was employed to study the vapor-liquid equilibrium (VLE) for pure acetic acid and for a mixture of acetic acid and ethylene. An improved united-atom force field for acetic acid based on a Lennard-Jones functional form was proposed. The Lennard-Jones well depth and size parameters for the carboxyl oxygen and hydroxyl oxygen were determined by fitting the interaction energies of acetic acid dimers to the Lennard-Jones potential function. Four different acetic acid dimers and the proportions of them were considered when the force field was optimized. It was found that the new optimized force field provides a reasonable description of the vapor-liquid phase equilibrium for pure acetic acid and for the mixture of acetic acid and ethylene. Accurate values were obtained for the saturated liquid density of the pure compound (average deviation: 0.84 %) and for the critical points. The new optimized force field demonstrated greater accuracy and reliability in calculations of the solubility of the mixture of acetic acid and ethylene as compared with the results obtained with the original TraPPE-UA force field. PMID:27324633
Moučka, Filip; Nezbeda, Ivo; Smith, William R
2013-11-12
It is known that none of the available simple molecular interaction models of aqueous electrolytes based on SPC/E water and their associated force fields are able to reproduce the concentration dependence of important thermodynamic properties of even the simplest electrolyte, NaCl, at ambient conditions over the entire experimentally accessible concentration range [ Mouc̆ka , F. ; Nezbeda , I. ; Smith , W. R. J. Chem. Phys. 2013 , 138 , 154102 ]. This paper explores the possibility of improving their performance by incorporating concentration-dependent experimental data for the total ionic chemical potential and the density into the fitting procedure, in addition to experimental values of solubility and solid chemical potential. We describe a general parameter estimation methodology for a studied class of models that incorporates the aforementioned experimental data. When the entire concentration range is considered, although the resulting force field is a slight improvement over others currently available in the literature, overall quantitative agreement with the experimental data over this range remains unsatisfactory. This indicates an inherent limitation of such simple molecular interaction models and strongly suggests that more complex mathematical forms of such models are required to quantitatively predict the properties of aqueous electrolyte solutions when the entire concentration range is of interest. Our parameter estimation methodology is also applicable to such cases. PMID:26583422
Equilibrium fluctuations of the Lennard-Jones cluster surface
NASA Astrophysics Data System (ADS)
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.
Velaga, Srinath C; Anderson, Brian J
2014-01-16
Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations. PMID:24328234
Classical scattering in strongly attractive potentials
NASA Astrophysics Data System (ADS)
Khrapak, S. A.
2014-03-01
Scattering in central attractive potentials is investigated systematically, in the limit of strong interaction, when large-angle scattering dominates. In particular, three important model interactions (Lennard-Jones, Yukawa, and exponential), which are qualitatively different from each other, are studied in detail. It is shown that for each of these interactions the dependence of the scattering angle on the properly normalized impact parameter exhibits a quasiuniversal behavior. This implies simple scaling of the transport cross sections with energy in the considered limit. Accurate fits for the momentum transfer cross section are suggested. Applications of the obtained results are discussed.
Classical scattering in strongly attractive potentials.
Khrapak, S A
2014-03-01
Scattering in central attractive potentials is investigated systematically, in the limit of strong interaction, when large-angle scattering dominates. In particular, three important model interactions (Lennard-Jones, Yukawa, and exponential), which are qualitatively different from each other, are studied in detail. It is shown that for each of these interactions the dependence of the scattering angle on the properly normalized impact parameter exhibits a quasiuniversal behavior. This implies simple scaling of the transport cross sections with energy in the considered limit. Accurate fits for the momentum transfer cross section are suggested. Applications of the obtained results are discussed. PMID:24730827
NASA Astrophysics Data System (ADS)
Sadeghi, F.; Ansari, R.; Darvizeh, M.
2016-06-01
In this research, a continuum-based model is presented to explore potential energy, force distribution and oscillatory motion of ions, and in particular chloride ion, inside carbon nanotubes (CNTs) decorated by functional groups at two ends. To perform this, van der Waals (vdW) interactions between ion and nanotube are modeled by the 6-12 Lennard-Jones (LJ) potential, whereas the electrostatic interactions between ion and functional groups are modeled by the Coulomb potential and the total interactions are analytically derived by summing the vdW and electrostatic interactions. Making the assumption that carbon atoms and charge of functional groups are all uniformly distributed over the nanotube surface and the two ends of nanotube, respectively, a continuum approach is utilized to evaluate the related interactions. Based on the actual force distribution, the equation of motion is also solved numerically to arrive at the time history of displacement and velocity of inner core. With respect to the proposed formulations, comprehensive studies on the variations of potential energy and force distribution are carried out by varying functional group charge and nanotube length. Moreover, the effects of these parameters together with initial conditions on the oscillatory behavior of system are studied and discussed in detail. It is found out that chloride ion escapes more easily from negatively charged CNTs which is followed by uncharged and positively charged ones. It is further shown that the presence of functional groups leads to enhancing the operating frequency of such oscillatory systems especially when the electric charges of ion and functional groups have different signs.
The second virial coefficient and critical point behavior of the Mie Potential.
Heyes, D M; Rickayzen, G; Pieprzyk, S; Brańka, A C
2016-08-28
Aspects of the second virial coefficient, b2, of the Mie m : n potential are investigated. The Boyle temperature, T0, is shown to decay monotonically with increasing m and n, while the maximum temperature, Tmax, exhibits a minimum at a value of m which increases as n increases. For the 2n : n special case T0 tends to zero and Tmax approaches the value of 7.81 in the n → ∞ limit which is in quantitative agreement with the expressions derived in Rickayzen and Heyes [J. Chem. Phys. 126, 114504 (2007)] in which it was shown that the 2n : n potential in the n → ∞ limit approaches Baxter's sticky-sphere model. The same approach is used to estimate the n - dependent critical temperature of the 2n : n potential in the large n limit. The ratio of T0 to the critical temperature tends to unity in the infinite n limit for the 2n : n potential. The rate of convergence of expansions of b2 about the high temperature limit is investigated, and they are shown to converge rapidly even at quite low temperatures (e.g., 0.05). In contrast, a low temperature expansion of the Lennard-Jones 12 : 6 potential is shown to be an asymptotic series. Two formulas that resolve b2 into its repulsive and attractive terms are derived. The convergence at high temperature of the Lennard-Jones b2 to the m = 12 inverse power value is slow (e.g., requiring T ≃ 10(4) just to attain two significant figure accuracy). The behavior of b2 of the ∞ : n and the Sutherland potential special case, n = 6, is explored. By fitting to the exact b2 values, a semiempirical formula is derived for the temperature dependence of b2 of the Lennard-Jones potential which has the correct high and low temperature limits. PMID:27586933
A Computational Study of Rare Gas Clusters: Stepping Stones to the Solid State
ERIC Educational Resources Information Center
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…
Note: Modification of the Gay-Berne potential for improved accuracy and speed
NASA Astrophysics Data System (ADS)
Persson, Rasmus A. X.
2012-06-01
A modification of the Gay-Berne (GB) potential is proposed which is about 10% to 20% more speed efficient and statistically more accurate in reproducing the energy of interaction of two linear Lennard-Jones tetratomics when averaged over all orientations. For the special cases of end-to-end and side-by-side configurations, the new potential is equivalent to the GB one. A simple generalization to dissimilar particles of D∞h symmetry is presented but does not retain the superior agreement with respect to its GB counterpart, except at close range.
NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface
NASA Astrophysics Data System (ADS)
Ingebrigtsen, Trond S.; Toxvaerd, Søren; Heilmann, Ole J.; Schrøder, Thomas B.; Dyre, Jeppe C.
2011-09-01
An algorithm is derived for computer simulation of geodesics on the constant-potential-energy hypersurface of a system of N classical particles. First, a basic time-reversible geodesic algorithm is derived by discretizing the geodesic stationarity condition and implementing the constant-potential-energy constraint via standard Lagrangian multipliers. The basic NVU algorithm is tested by single-precision computer simulations of the Lennard-Jones liquid. Excellent numerical stability is obtained if the force cutoff is smoothed and the two initial configurations have identical potential energy within machine 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 that ensures potential-energy and step-length conservation; center-of-mass drift is also eliminated. Analytical arguments confirmed by simulations demonstrate that the modified NVU algorithm is absolutely stable. Finally, we present simulations showing that the NVU algorithm and the standard leap-frog NVE algorithm have identical radial distribution functions for the Lennard-Jones liquid.
Solid phase stability of a double-minimum interaction potential system
Suematsu, Ayumi; Yoshimori, Akira Saiki, Masafumi; Matsui, Jun; Odagaki, Takashi
2014-06-28
We study phase stability of a system with double-minimum interaction potential in a wide range of parameters by a thermodynamic perturbation theory. The present double-minimum potential is the Lennard-Jones-Gauss potential, which has a Gaussian pocket as well as a standard Lennard-Jones minimum. As a function of the depth and position of the Gaussian pocket in the potential, we determine the coexistence pressure of crystals (fcc and bcc). We show that the fcc crystallizes even at zero pressure when the position of the Gaussian pocket is coincident with the first or third nearest neighbor site of the fcc crystal. The bcc crystal is more stable than the fcc crystal when the position of the Gaussian pocket is coincident with the second nearest neighbor sites of the bcc crystal. The stable crystal structure is determined by the position of the Gaussian pocket. These results show that we can control the stability of the solid phase by tuning the potential function.
Graph-based analysis of kinetics on multidimensional potential-energy surfaces
NASA Astrophysics Data System (ADS)
Okushima, T.; Niiyama, T.; Ikeda, K. S.; Shimizu, Y.
2009-09-01
The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters.
Graph-based analysis of kinetics on multidimensional potential-energy surfaces.
Okushima, T; Niiyama, T; Ikeda, K S; Shimizu, Y
2009-09-01
The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters. PMID:19905185
A new interlayer potential for hexagonal boron nitride
NASA Astrophysics Data System (ADS)
Akıner, Tolga; Mason, Jeremy K.; Ertürk, Hakan
2016-09-01
A new interlayer potential is developed for interlayer interactions of hexagonal boron nitride sheets, and its performance is compared with other potentials in the literature using molecular dynamics simulations. The proposed potential contains Coulombic and Lennard-Jones 6–12 terms, and is calibrated with recent experimental data including the hexagonal boron nitride interlayer distance and elastic constants. The potentials are evaluated by comparing the experimental and simulated values of interlayer distance, density, elastic constants, and thermal conductivity using non-equilibrium molecular dynamics. The proposed potential is found to be in reasonable agreement with experiments, and improves on earlier potentials in several respects. Simulated thermal conductivity values as a function of the number of layers and of temperature suggest that the proposed LJ 6–12 potential has the ability to predict some phonon behaviour during heat transport in the out-of-plane direction.
Effects of interatomic potentials on mechanical deformation of glasses
NASA Astrophysics Data System (ADS)
Chen, Wei-Ren; Iwashita, Takuya; Egami, Takeshi
2013-03-01
Apparently glasses behave like an elastic solid, which shows a linear relationship between stress and strain in mechanical deformation. However the understanding of the mechanical response of glasses remains elusive because of structural disorder. Mechanical deformation of monatomic model glasses was studied using athermal quasi-static shear (AQS) simulation and with three different potentials. As the interatomic potentials we employed the 12-6 Lennard-Jones (LJ) potential, modified Johnson (mJ) potential, and Dzugutov (Dz) potential, respectively. For mJ and Dz glasses the shear modulus keeps constant below a critical strain, below which it decreases rapidly or discontinuously with strain. Such changes in shear modulus were mostly related to the change in local topology of atomic connectivity or anelasticity. In contrast LJ glass shows a gradual decrease in shear modulus in a continuous manner. The results indicated that the difference arises from the nature of the potentials if the topology of atomic connectivity can be clearly defined.
Visualizing the orientational dependence of an intermolecular potential
NASA Astrophysics Data System (ADS)
Sweetman, Adam; Rashid, Mohammad A.; Jarvis, Samuel P.; Dunn, Janette L.; Rahe, Philipp; Moriarty, Philip
2016-02-01
Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard-Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation.
Kuszewski, J; Gronenborn, A M; Clore, G M
1996-06-01
A new conformational database potential involving dihedral angle relationships in databases of high-resolution highly refined protein crystal structures is presented as a method for improving the quality of structures generated from NMR data. The rationale for this procedure is based on the observation that uncertainties in the description of the nonbonded contacts present a key limiting factor in the attainable accuracy of protein NMR structures and that the nonbonded interaction terms presently used have poor discriminatory power between high- and low-probability local conformations. The idea behind the conformational database potential is to restrict sampling during simulated annealing refinement to conformations that are likely to be energetically possible by effectively limiting the choices of dihedral angles to those that are known to be physically realizable. In this manner, the variability in the structures produced by this method is primarily a function of the experimental restraints, rather than an artifact of a poor nonbonded interaction model. We tested this approach with the experimental NMR data (comprising an average of about 30 restraints per residue and consisting of interproton distances, torsion angles, 3JHN alpha coupling constants, and 13C chemical shifts) used previously to calculate the solution structure of reduced human thioredoxin (Qin J, Clore GM, Gronenborn AM, 1994, Structure 2:503-522). Incorporation of the conformational database potential into the target function used for refinement (which also includes terms for the experimental restraints, covalent geometry, and nonbonded interactions in the form of either a repulsive, repulsive-attractive, or 6-12 Lennard-Jones potential) results in a significant improvement in various quantitative measures of quality (Ramachandran plot, side-chain torsion angles, overall packing). This is achieved without compromising the agreement with the experimental restraints and the deviations from
Correlation of fragility with mechanical moduli in double-well potential for glass-forming liquid
NASA Astrophysics Data System (ADS)
Cao, Wan Qiang
2012-02-01
The shoving model and the Vogel-Fulcher relation are employed to derive correlation of the fragility with the mechanical moduli for glass-forming simple liquids. The result shows that a liquid with smaller fragility will have larger ratio of K∞/G∞ in dilute liquid system. Based on radial distribution function with the Lennard-Jones potential modified by the Gaussian potential with a second minimum, fragility of the supercooled simple liquid is derived from the correlation between viscosity and shear modulus via configurational entropy. The results demonstrate that the fragility is determined by two parts: thermodynamic components and mechanical moduli. For a weak Gaussian potential liquid, the fragility is proportional to the Tg, while for a strong one, the fragility is inversely proportional to the Tg, and the Gaussian potential will increase fragility.
Li, Arvin H.-T.; Chao, S.D.
2006-01-15
To verify the recently calculated intermolecular interaction potentials of the methane dimer within the density functional theory using the (Perdew) local density approximation (LDA) [Chen et al., Phys. Rev. A 69, 034701 (2004)], we have performed a parallel series of calculations using the LDA/6-311++G (3df, 3pd) level of theory with selected exchange functionals (B, G96, MPW, O, PBE, PW91, S, and XA). None of the above calculated intermolecular interaction potentials from the local density approximation reproduce the results reported in the commented paper. In addition, we point out the inappropriateness of using the Lennard-Jones function to model the long-range parts of the calculated intermolecular interaction potentials, as suggested positively by Chen et al.
NASA Astrophysics Data System (ADS)
Wu, Lei; Liu, Haihu; Zhang, Yonghao; Reese, Jason M.
2015-08-01
The Boltzmann equation with an arbitrary intermolecular potential is solved by the fast spectral method. As examples, noble gases described by the Lennard-Jones potential are considered. The accuracy of the method is assessed by comparing both transport coefficients with variational solutions and mass/heat flow rates in Poiseuille/thermal transpiration flows with results from the discrete velocity method. The fast spectral method is then applied to Fourier and Couette flows between two parallel plates, and the influence of the intermolecular potential on various flow properties is investigated. It is found that for gas flows with the same rarefaction parameter, differences in the heat flux in Fourier flow and the shear stress in Couette flow are small. However, differences in other quantities such as density, temperature, and velocity can be very large.
NASA Astrophysics Data System (ADS)
Sierra-Suarez, Jonatan A.; Majumdar, Shubhaditya; McGaughey, Alan J. H.; Malen, Jonathan A.; Higgs, C. Fred
2016-04-01
This work formulates a rough surface contact model that accounts for adhesion through a Morse potential and plasticity through the Kogut-Etsion finite element-based approximation. Compared to the commonly used Lennard-Jones (LJ) potential, the Morse potential provides a more accurate and generalized description for modeling covalent materials and surface interactions. An extension of this contact model to describe composite layered surfaces is presented and implemented to study a self-assembled monolayer (SAM) grown on a gold substrate placed in contact with a second gold substrate. Based on a comparison with prior experimental measurements of the thermal conductance of this SAM junction [Majumdar et al., Nano Lett. 15, 2985-2991 (2015)], the more general Morse potential-based contact model provides a better prediction of the percentage contact area than an equivalent LJ potential-based model.
Influence of the interatomic potential on the structure of dislocations in a monolayer
NASA Astrophysics Data System (ADS)
Joós, B.; Ren, Q.; Duesbery, M. S.
1994-02-01
Using atomic relaxation techniques, dislocation dipoles of various sizes and orientations have been studied for monolayers with the Lennard-Jones potential (LJP) and nearest-neighbour piecewise linear force (PLF) interactions. In the LJP system the lower energy vacancy dipoles have over a wide range of angles an energy which is mainly a function of the vacancy content of the dipole. There is a competition between the elastic forces and the topological constraints which favour a five-fold coordinate vacancy (FCV) at the centre of each core. For the short range PLF system the lattice usually compresses upon the introduction of a dislocation, a consequence of the soft core of the interaction potential, and interstitial dipoles are lower in energy. For the long range LJP system the dislocations are mobile whereas for the PLF system they are pinned. The relevance of these results to existing theories of melting are discussed.
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.
Poiseuille flow of Lennard-Jones fluids in narrow slit pores
NASA Astrophysics Data System (ADS)
Travis, Karl P.; Gubbins, Keith E.
2000-01-01
We present results from nonequilibrium molecular dynamics (NEMD) simulations of simple fluids undergoing planar Poiseuille flow in a slit pore only a few molecular diameters in width. The calculations reported in this publication build on previous results by including the effects of attractive forces and studying the flow at narrower pore widths. Our aims are: (1) to examine the role of attractive forces in determining hydrodynamic properties, (2) to provide clearer evidence for the existence of a non-Markovian generalization of Newtons law, (3) to examine the slip-stick boundary conditions in more detail by using a high spatial resolution of the streaming velocity profiles, (4) to investigate the significance of the recently proposed cross-coupling coefficient on the temperature profiles. The presence of attractive interactions gives rise to interesting packing effects, but otherwise, does not significantly alter the spatial dependence of hydrodynamic quantities. We find the strongest evidence to date that Newton's Law breaks down for very narrow pores; the shear viscosity exhibits singularities. We suggest a method to test the validity of the non-Markovian generalization of Newton's Law. No-slip boundary conditions are found to apply, even at these microscopic length scales, provided one takes into account the finite size of the wall atoms. The effects of any strain rate induced coupling to the heat flow are found to be insignificant.
A multiscale transport model for Lennard-Jones binary mixtures based on interfacial friction.
Bhadauria, Ravi; Aluru, N R
2016-08-21
We propose a one-dimensional isothermal hydrodynamic transport model for non-reacting binary mixtures in slit shaped nanochannels. The coupled species momentum equations contain viscous dissipation and interspecies friction term of Maxwell-Stefan form. Species partial viscosity variations in the confinement are modeled using the van der Waals one fluid approximation and the local average density method. Species specific macroscopic friction coefficient based Robin boundary conditions are provided to capture the species wall slip effects. The value of this friction coefficient is computed using a species specific generalized Langevin formulation. Gravity driven flow of methane-hydrogen and methane-argon mixtures confined between graphene slit shaped nanochannels are considered as examples. The proposed model yields good quantitative agreement with the velocity profiles obtained from the non-equilibrium molecular dynamics simulations. The mixtures considered are observed to behave as single species pseudo fluid, with the interfacial friction displaying linear dependence on molar composition of the mixture. The results also indicate that the different species have different slip lengths, which remain unchanged with the channel width. PMID:27544095
NASA Astrophysics Data System (ADS)
Xu, H.; Wittmer, J. P.; Polińska, P.; Baschnagel, J.
2012-10-01
The truncation of a pair potential at a distance rc is well known to imply, in general, an impulsive correction to the pressure and other moments of the first derivatives of the potential. That, depending on rc, the truncation may also be of relevance to higher derivatives is shown theoretically for the Born contributions to the elastic moduli obtained using the stress-fluctuation formalism in d dimensions. Focusing on isotropic liquids for which the shear modulus G must vanish by construction, the predicted corrections are tested numerically for binary mixtures and polydisperse Lennard-Jones beads in, respectively, d=3 and 2 dimensions. Both models being glass formers, we comment briefly on the temperature (T) dependence of the (corrected) shear modulus G(T) around the glass transition temperature Tg.
Lubna, Nusrat; Kamath, Ganesh; Potoff, Jeffrey J; Rai, Neeraj; Siepmann, J Ilja
2005-12-22
An extension of the transferable potentials for phase equilibria united-atom (TraPPE-UA) force field to thiol, sulfide, and disulfide functionalities and thiophene is presented. In the TraPPE-UA force field, nonbonded interactions are governed by a Lennard-Jones plus fixed point charge functional form. Partial charges are determined through a CHELPG analysis of electrostatic potential energy surfaces derived from ab initio calculations at the HF/6-31g+(d,p) level. The Lennard-Jones well depth and size parameters for four new interaction sites, S (thiols), S(sulfides), S(disulfides), and S(thiophene), were determined by fitting simulation data to pure-component vapor-equilibrium data for methanethiol, dimethyl sulfide, dimethyl disulfide, and thiophene, respectively. Configurational-bias Monte Carlo simulations in the grand canonical ensemble combined with histogram-reweighting methods were used to calculate the vapor-liquid coexistence curves for methanethiol, ethanethiol, 2-methyl-1-propanethiol, 2-methyl-2-propanethiol, 2-butanethiol, pentanethiol, octanethiol, dimethyl sulfide, diethyl sulfide, ethylmethyl sulfide, dimethyl disulfide, diethyl disulfide, and thiophene. Excellent agreement with experiment is achieved, with unsigned errors of less than 1% for saturated liquid densities and less than 3% for critical temperatures. The normal boiling points were predicted to within 1% of experiment in most cases, although for certain molecules (pentanethiol) deviations as large as 5% were found. Additional calculations were performed to determine the pressure-composition behavior of ethanethiol+n-butane at 373.15 K and the temperature-composition behavior of 1-propanethiol+n-hexane at 1.01 bar. In each case, a good reproduction of experimental vapor-liquid equilibrium separation factors is achieved; both of the coexistence curves are somewhat shifted because of overprediction of the pure-component vapor pressures. PMID:16375402
NASA Astrophysics Data System (ADS)
Molinari, Vincenzo; Mostacci, Domiziano
2015-10-01
He-4 is known to become superfluid at very low temperatures. This effect is now generally accepted to be connected with BEC (Bose-Einstein Condensation). The dispersion relation of pressure waves in superfluid He-4 has been determined at 1.1 °K by Yarnell et al., and exhibits a non monotonic behavior-with a maximum and a minimum-usually explained in terms of excitations called rotons, introduced by Landau. In the present work an attempt is made to describe the phenomenon within the Bohmian interpretation of QM. To this end, the effects of the intermolecular potential, taken to be essentially of the Lennard-Jones type modified to account for molecule finiteness, are included as a Vlasov-type self-consistent field. A dispersion relation is found, that is in quite good agreement with Yarnell's curve.
Statistical systems with nonintegrable interaction potentials
NASA Astrophysics Data System (ADS)
Yukalov, V. I.
2016-07-01
Statistical systems composed of atoms interacting with each other trough nonintegrable interaction potentials are considered. Examples of these potentials are hard-core potentials and long-range potentials, for instance, the Lennard-Jones and dipolar potentials. The treatment of such potentials is known to confront several problems, e.g., the impossibility of using the standard mean-field approximations, such as Hartree and Hartree-Fock approximations, the impossibility of directly introducing coherent states, the difficulty in breaking the global gauge symmetry, which is required for describing Bose-Einstein condensed and superfluid systems, the absence of a correctly defined Fourier transform, which hampers the description of uniform matter as well as the use of local-density approximation for nonuniform systems. A novel iterative procedure for describing such systems is developed, starting from a correlated mean-field approximation, allowing for a systematic derivation of higher orders, and meeting no problems listed above. The procedure is applicable to arbitrary systems, whether equilibrium or nonequilibrium. The specification for equilibrium systems is presented. The method of extrapolating the expressions for observable quantities from weak coupling to strong coupling is described.
Statistical systems with nonintegrable interaction potentials.
Yukalov, V I
2016-07-01
Statistical systems composed of atoms interacting with each other trough nonintegrable interaction potentials are considered. Examples of these potentials are hard-core potentials and long-range potentials, for instance, the Lennard-Jones and dipolar potentials. The treatment of such potentials is known to confront several problems, e.g., the impossibility of using the standard mean-field approximations, such as Hartree and Hartree-Fock approximations, the impossibility of directly introducing coherent states, the difficulty in breaking the global gauge symmetry, which is required for describing Bose-Einstein condensed and superfluid systems, the absence of a correctly defined Fourier transform, which hampers the description of uniform matter as well as the use of local-density approximation for nonuniform systems. A novel iterative procedure for describing such systems is developed, starting from a correlated mean-field approximation, allowing for a systematic derivation of higher orders, and meeting no problems listed above. The procedure is applicable to arbitrary systems, whether equilibrium or nonequilibrium. The specification for equilibrium systems is presented. The method of extrapolating the expressions for observable quantities from weak coupling to strong coupling is described. PMID:27575076
46 CFR 12.01-6-12.01-7 - [Reserved
Code of Federal Regulations, 2010 CFR
2010-10-01
... 46 Shipping 1 2010-10-01 2010-10-01 false 12.01-6-12.01-7 Section 12.01-6-12.01-7 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MERCHANT MARINE OFFICERS AND SEAMEN REQUIREMENTS FOR RATING ENDORSEMENTS General §§ 12.01-6-12.01-7...
36 CFR 6.12 - Prohibited acts and penalties.
Code of Federal Regulations, 2010 CFR
2010-07-01
... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Prohibited acts and penalties. 6.12 Section 6.12 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR SOLID WASTE DISPOSAL SITES IN UNITS OF THE NATIONAL PARK SYSTEM § 6.12 Prohibited acts and penalties. (a) The following are prohibited:...
Molecular Multipole Potential Energy Functions for Water.
Tan, Ming-Liang; Tran, Kelly N; Pickard, Frank C; Simmonett, Andrew C; Brooks, Bernard R; Ichiye, Toshiko
2016-03-01
Water is the most common liquid on this planet, with many unique properties that make it essential for life as we know it. These properties must arise from features in the charge distribution of a water molecule, so it is essential to capture these features in potential energy functions for water to reproduce its liquid state properties in computer simulations. Recently, models that utilize a multipole expansion located on a single site in the water molecule, or "molecular multipole models", have been shown to rival and even surpass site models with up to five sites in reproducing both the electrostatic potential around a molecule and a variety of liquid state properties in simulations. However, despite decades of work using multipoles, confusion still remains about how to truncate the multipole expansions efficiently and accurately. This is particularly important when using molecular multipole expansions to describe water molecules in the liquid state, where the short-range interactions must be accurate, because the higher order multipoles of a water molecule are large. Here, truncation schemes designed for a recent efficient algorithm for multipoles in molecular dynamics simulations are assessed for how well they reproduce results for a simple three-site model of water when the multipole moments and Lennard-Jones parameters of that model are used. In addition, the multipole analysis indicates that site models that do not account for out-of-plane electron density overestimate the stability of a non-hydrogen-bonded conformation, leading to serious consequences for the simulated liquid. PMID:26562223
A New Shared-Memory Programming Paradigm for Molecular Dynamics Simulations on the Intel Paragon
D'Azevedo, E.F.
1995-01-01
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.
A new shared-memory programming paradigm for molecular dynamics simulations on the Intel Paragon
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.
NASA Astrophysics Data System (ADS)
Somer, Frank
2005-03-01
Results of recent molecular dynamics simulations of a two-dimensional glass forming system are presented. The system's inherent structures are investigated over a wide range of temperature and cooling rate and compared to previous results for three-dimensional liquids and glasses. A method for analyzing the regions of the energy landscape sampled under various conditions is introduced and used to characterize the glass transition. Connections with inherent-structures theory, mode-coupling theory, and spatially inhomogeneous dynamics are discussed.
Anisotropic united-atoms (AUA) potential for alcohols.
Pérez-Pellitero, Javier; Bourasseau, Emeric; Demachy, Isabelle; Ridard, Jacqueline; Ungerer, Philippe; Mackie, Allan D
2008-08-14
An anisotropic united-atom (AUA4) intermolecular potential has been derived for the family of alkanols by first optimizing a set of charges to reproduce the electrostatic potential of the isolated molecules of methanol and ethanol and then by adjusting the parameters of the OH group to fit selected equilibrium properties. In particular, the proposed potential includes additional extra-atomic charges in order to improve the matching to the electrostatic field. Gibbs ensemble Monte Carlo simulations were performed to determine the phase equilibria, while the critical region was explored by means of grand canonical Monte Carlo simulations combined with histogram reweighting techniques. In order to increase the transferability of the model, only the parameters of the Lennard-Jones OH group have been fitted, the parameters of the other AUA groups are taken from previous works. Nevertheless, a good level of agreement was obtained for all compounds considered in this work. In particular, excellent results were obtained for the Henry constants calculation of different gases in alkanols. PMID:18646801
An efficient fully atomistic potential model for dense fluid methane
NASA Astrophysics Data System (ADS)
Jiang, Chuntao; Ouyang, Jie; Zhuang, Xin; Wang, Lihua; Li, Wuming
2016-08-01
A fully atomistic model aimed to obtain a general purpose model for the dense fluid methane is presented. The new optimized potential for liquid simulation (OPLS) model is a rigid five site model which consists of five fixed point charges and five Lennard-Jones centers. The parameters in the potential model are determined by a fit of the experimental data of dense fluid methane using molecular dynamics simulation. The radial distribution function and the diffusion coefficient are successfully calculated for dense fluid methane at various state points. The simulated results are in good agreement with the available experimental data shown in literature. Moreover, the distribution of mean number hydrogen bonds and the distribution of pair-energy are analyzed, which are obtained from the new model and other five reference potential models. Furthermore, the space-time correlation functions for dense fluid methane are also discussed. All the numerical results demonstrate that the new OPLS model could be well utilized to investigate the dense fluid methane.
Formulation of wide-ranging embedded-atom-type potentials: the role of mechanical stability
NASA Astrophysics Data System (ADS)
Pechenik, Eugene; Kelson, Itzhak; Makov, Guy
2013-01-01
Wide-ranging inter-atomic potentials are necessary for modeling many problems in material physics that involve multiple atomic environments and phases. The domains of thermodynamic and mechanical stability of embedded-atom-type potentials are examined for the cubic phases. It is shown that the choice of the pair potential is critical in determining the domain of stability of embedded-atom-type potentials. In particular, the Lennard-Jones embedded-atom potential is shown not to stabilize the bcc phase. A simple four-parameter universal equation of state-based embedded-atom potential is shown to have a domain of stability for all the cubic phases and to reproduce the high-pressure equation of state. A model phase diagram for the three cubic phases is presented. This potential is fitted to 17 elemental systems and found to be able to reproduce both the elastic constants and the ground state crystalline structure. For elements with a low degree of elastic anisotropy, this potential can also reproduce the high-pressure behavior.
NASA Astrophysics Data System (ADS)
Ziegenhain, Gerolf; Hartmaier, Alexander; Urbassek, Herbert M.
2009-09-01
Molecular-dynamics simulation can give atomistic information on the processes occurring in nanoindentation experiments. In particular, the nucleation of dislocation loops, their growth, interaction and motion can be studied. We investigate how realistic the interatomic potentials underlying the simulations have to be in order to describe these complex processes. Specifically we investigate nanoindentation into a Cu single crystal. We compare simulations based on a realistic many-body interaction potential of the embedded-atom-method type with two simple pair potentials, a Lennard-Jones and a Morse potential. We find that qualitatively many aspects of nanoindentation are fairly well reproduced by the simple pair potentials: elastic regime, critical stress and indentation depth for yielding, dependence on the crystal orientation, and even the level of the hardness. The quantitative deficits of the pair potential predictions can be traced back: (i) to the fact that the pair potentials are unable in principle to model the elastic anisotropy of cubic crystals and (ii) as the major drawback of pair potentials we identify the gross underestimation of the stable stacking fault energy. As a consequence these potentials predict the formation of too large dislocation loops, the too rapid expansion of partials, too little cross slip and in consequence a severe overestimation of work hardening.
The Potential Field of Carbon Bodies as a Basis for Sorption Properties of Barrier Gas Systems
NASA Astrophysics Data System (ADS)
Bubenchikov, A. M.; Bubenchikov, M. A.; Potekaev, A. I.; Libin, É. E.; Khudobina, Yu. P.
2015-11-01
A modification of the Lennard-Jones potential allowed us, via integration over the volume of the bodies of different shapes, to determine the integral action (potential energy barrier) generated by the distributed force centers. The body generating the potential barrier was a carbon plate and the test particles overcoming this barrier were atoms or molecules of a number of gases (hydrogen, helium and methane). When considering the transit of particles (gas atoms or molecules) over this barrier, use was made of the energy barrier wave theory and the potential of a continuous body was used as a barrier. In so doing, the Schrödinger equation was integrated numerically for the molecular density. This integration yielded the expected wave pattern of the process of transit and reflection of the molecules, so a phase averaging procedure had to be applied. By varying the parameters of the layer containing force centers - field sources, the dimensions and density of the carbon plate possessing high selectivity towards separation of gas mixture containing helium, hydrogen and methane were determined. The data obtained provide an interpretation of the sorption properties of barrier carbon systems capable of filtering or separating gases.
Qin, Sanbo; Zhou, Huan-Xiang
2016-08-25
Chemical potential is a fundamental property for determining thermodynamic equilibria involving exchange of molecules, such as between two phases of molecular systems. Previously, we developed the fast Fourier transform (FFT)-based method for Modeling Atomistic Protein-crowder interactions (FMAP) to calculate excess chemical potentials according to the Widom insertion. Intermolecular interaction energies were expressed as correlation functions and evaluated via FFT. Here, we extend this method to calculate liquid-liquid phase equilibria of macromolecular solutions. Chemical potentials are calculated by FMAP over a wide range of molecular densities, and the condition for coexistence of low- and high-density phases is determined by the Maxwell equal-area rule. When benchmarked on Lennard-Jones fluids, our method produces an accurate phase diagram at 18% of the computational cost of the current best method. Importantly, the gain in computational speed increases dramatically as the molecules become more complex, leading to many orders of magnitude in speed up for atomistically represented proteins. We demonstrate the power of FMAP by reporting the first results for the liquid-liquid coexistence curve of γII-crystallin represented at the all-atom level. Our method may thus open the door to accurate determination of phase equilibria for macromolecular mixtures such as protein-protein mixtures and protein-RNA mixtures, that are known to undergo liquid-liquid phase separation, both in vitro and in vivo. PMID:27327881
Systematic and Simulation-Free Coarse-Graining of Polymer Melts using Soft Potentials
NASA Astrophysics Data System (ADS)
Yang, Delian; Wang, Qiang
2014-03-01
Full atomistic simulations of multi-chain systems are not feasible at present due to their formidable computational requirements. Molecular simulations with coarse-grained models have to be used instead, where each segment represents, for example, the center-of-mass of a group of atoms or real monomers. While atoms interact with hard excluded-volume interactions (e.g., the Lennard-Jones potential) and cannot overlap, the coarse-grained segments can certainly overlap and should therefore interact with soft potentials that allow complete particle overlapping. Coarse-grained models, however, reduce the chain conformational entropy, which plays an essential role in the behavior of polymeric systems. In this work, we use integral-equation theories, instead of molecular simulations, to perform both the structure-based and relative-entropy-based coarse-graining of homopolymer melts, and systematically examine how the coarse-grained soft potential varies with N (the number of segments on each chain) and how well the coarse-grained models reproduce both the structural and thermodynamic properties of the original system. This provides us with a quantitative basis for choosing small N-values that can still capture the chain conformational entropy, a characteristics of polymers.
Optimization of intermolecular potential parameters for the CO2/H2O mixture.
Orozco, Gustavo A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z
2014-10-01
Monte Carlo simulations in the Gibbs ensemble were used to obtain optimized intermolecular potential parameters to describe the phase behavior of the mixture CO2/H2O, over a range of temperatures and pressures relevant for carbon capture and sequestration processes. Commonly used fixed-point-charge force fields that include Lennard-Jones 12-6 (LJ) or exponential-6 (Exp-6) terms were used to describe CO2 and H2O intermolecular interactions. For force fields based on the LJ functional form, changes of the unlike interactions produced higher variations in the H2O-rich phase than in the CO2-rich phase. A major finding of the present study is that for these potentials, no combination of unlike interaction parameters is able to adequately represent properties of both phases. Changes to the partial charges of H2O were found to produce significant variations in both phases and are able to fit experimental data in both phases, at the cost of inaccuracies for the pure H2O properties. By contrast, for the Exp-6 case, optimization of a single parameter, the oxygen-oxygen unlike-pair interaction, was found sufficient to give accurate predictions of the solubilities in both phases while preserving accuracy in the pure component properties. These models are thus recommended for future molecular simulation studies of CO2/H2O mixtures. PMID:25198539
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. PMID:22462609
Werhahn, Jasper C.; Akase, Dai; Xantheas, Sotiris S.
2014-08-14
The scaled versions of the newly introduced [S. S. Xantheas and J. C. Werhahn, J. Chem. Phys.141, 064117 (2014)] generalized forms of some popular potential energy functions (PEFs) describing intermolecular interactions – Mie, Lennard-Jones, Morse, and Buckingham exponential-6 – have been used to fit the ab initio relaxed approach paths and fixed approach paths for the halide-water, X^{-}(H_{2}O), X = F, Cl, Br, I, and alkali metal-water, M^{+}(H_{2}O), M = Li, Na, K, Rb, Cs, interactions. The generalized forms of those PEFs have an additional parameter with respect to the original forms and produce fits to the ab initio data that are between one and two orders of magnitude better in the χ^{2} than the original PEFs. They were found to describe both the long-range, minimum and repulsive wall of the respective potential energy surfaces quite accurately. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gBe-6) potentials were found to best fit the ab initio data for these two classes of ion-water interactions. Finally, the fitted values of the parameter of the (eM) and (gBe-6) PEFs that control the repulsive wall of the potential correlate remarkably well with the ionic radii of the halide and alkali metal ions.
Folman, M.; Fastow, M.; Kozirovski, Y.
1997-03-05
In our recent investigation of the IR spectrum of CO physically adsorbed on C{sub 60} films, two well-resolved absorption bands at 2135 and 2128 cm{sup -1} were found, suggesting that the molecule is adsorbed on two different sites. To determine the nature of these adsorption sites, calculations of adsorption potentials and spectral shifts for the CO/C{sub 60} system were performed. The calculations were done for the fcc (100), fcc (111) hcp (001), and hcp (111) surface planes. In the calculations the 6-exponential and the Lennard-Jones potentials were used. A number of adsorption sites were chosen. These included the void space between four, three, and two neighboring C{sub 60} molecules and the center of the hexagon and the pentagon on the C{sub 60} surface. The calculated potentials and spectral shifts clearly indicate that adsorption sites in the voids between the C{sub 60} molecules are energetically preferred over sites on top of single C{sub 60} molecules. Comparison is made between results obtained with the two potentials and with results obtained previously with the two other carbon allotropes: graphite and diamond. 11 refs., 4 figs., 3 tabs.
Using a Checking Account. Grades 6-12.
ERIC Educational Resources Information Center
Trey, Frances
Instructions and exercises on the use of checking accounts are provided for students in grades 6-12. The following topics are included: (1) reasons for opening a checking account; (2) how to open a checking account; (3) how to fill out deposit slips; (4) the elements of a check and how to write a check correctly; (5) checking account rules; (6)…
A Stress Control Workbook for Youth Grades 6-12.
ERIC Educational Resources Information Center
Trotter, Jennie C.
Stress is an inevitable part of students' lives, but too much stress can have damaging consequences. Ways in which children can respond positively are covered in this stress booklet. Intended for students in grades 6-12, the booklet is divided into 20 lessons on stress. Each lesson features various activities, role plays, exercises, and checklists…
Parallel Curriculum Units for Science, Grades 6-12
ERIC Educational Resources Information Center
Leppien, Jann H.; Purcell, Jeanne H.
2011-01-01
Based on the best-selling book "The Parallel Curriculum", this professional development resource gives multifaceted examples of rigorous learning opportunities for science students in Grades 6-12. The four sample units revolve around genetics, the convergence of science and society, the integration of language arts and biology, and the periodic…
36 CFR 6.12 - Prohibited acts and penalties.
Code of Federal Regulations, 2013 CFR
2013-07-01
... (4) Operating a solid waste disposal site in violation of 40 CFR Parts 257 or 258, or in violation of... INTERIOR SOLID WASTE DISPOSAL SITES IN UNITS OF THE NATIONAL PARK SYSTEM § 6.12 Prohibited acts and penalties. (a) The following are prohibited: (1) Operating a solid waste disposal site without a...
Van der Waals correlation between two 4He monolayers on the opposite sides of graphene
NASA Astrophysics Data System (ADS)
Kwon, Yongkyung
2015-06-01
Path-integral Monte Carlo calculations have been performed to study the correlation between two 4He monolayers adsorbed on opposite sides of a graphene sheet. Here, the 4He-substrate interaction is described by the pairwise sum of the 4He-C interatomic potentials. We employ two different anisotropic 4He-C pair potentials proposed to fit the helium scattering data on a graphite surface, namely, a 6-12 Lennard-Jones potential and a Yukawa-6 potential. With the Lennard-Jones substrate potential, we do not observe any noticeable correlation between two oppositeside 4He monolayers, which is consistent with the prediction of the previous theoretical studies based on the same substrate potential. When the Yukawa-6 substrate potential is used, however, two incommensurate triangular solids, which are realized at the first-layer completion density of 0.12 Å -2, are found to favor an AA stacking order, two triangular lattices on top of each other, over an AB stacking. Finally, the effects of this interlayer correlation on the formation of stable mobile vacancies are discussed.
Lopes, Juliana Fedoce; Rocha, Willian R; Dos Santos, Hélio F; De Almeida, Wagner B
2008-04-28
In this work, a systematic study of the interaction of neutral cisplatin ([Pt(NH(3))(2)Cl(2)]) and their charged aquated species ([Pt(NH(3))(2)Cl(H(2)O)](+) and [Pt(NH(3))(2)(H(2)O)(2)](2+)) with water was carried out. The potential energy surface (PES) was analyzed by considering 35 spatial orientations for the interacting species. The calculations were performed at various levels of theory including Moller-Plesset fourth order perturbation theory and density functional theory (DFT-B3LYP) using extended basis sets. Lennard-Jones (12-6) plus Coulomb classical potential was also used to assess the repulsion-dispersion and electrostatic contributions. The effect of atomic charges on the interaction energies is discussed using Mulliken, charges from electrostatic potential grid method and natural bond orbital schemes. The outcomes show that the electrostatic term plays a primary role on the calculation of interaction energies, with the absolute values of atomic charges from different approaches significantly affecting the overall interaction. Unusual results were revealed by basis set superposition error calculations for the structures located on the platinum-water PES. PMID:18447507
NASA Astrophysics Data System (ADS)
Rizzi, F.; Jones, R. E.; Debusschere, B. J.; Knio, O. M.
2013-05-01
This article extends the uncertainty quantification analysis introduced in Paper I for molecular dynamics (MD) simulations of concentration driven ionic flow through a silica nanopore. Attention is now focused on characterizing, for a fixed pore diameter of D = 21 Å, the sensitivity of the system to the Lennard-Jones energy parameters, \\varepsilon _{Na^+} and \\varepsilon _{Cl^-}, defining the depth of the potential well for the two ions Na+ and Cl-, respectively. A forward propagation analysis is applied to map the uncertainty in these parameters to the MD predictions of the ionic fluxes. Polynomial chaos expansions and Bayesian inference are exploited to isolate the effect of the intrinsic noise, stemming from thermal fluctuations of the atoms, and properly quantify the impact of parametric uncertainty on the target MD predictions. A Bayes factor analysis is then used to determine the most suitable regression model to represent the MD noisy data. The study shows that the response surface of the Na+ conductance can be effectively inferred despite the substantial noise level, whereas the noise partially hides the underlying trend in the Cl- conductance data over the studied range. Finally, the dependence of the conductances on the uncertain potential parameters is analyzed in terms of correlations with key bulk transport coefficients, namely, viscosity and collective diffusivities, computed using Green-Kubo time correlations.
Hess, S; Kröger, M
2001-07-01
A short-range polynomial interaction potential is introduced which has both a repulsive core and an attractive part. It is cut off smoothly such that its first and second derivatives vanish at the cutoff distance. The potential therefore enables efficient simulation studies of a model material that exhibits similarities to a full (but computationally expensive) classical Lennard-Jones system. Thermophysical properties of the model are calculated by (nonequilibrium) molecular dynamics computer simulations and compared with analytical results. Among the quantities studied is the pressure as a function of the density for various temperatures. Equations of state for the fluid and the solid are tested. The coexistence of gaseous, (metastable) liquid, and fcc solid phases is found for a range of temperatures. Bulk and shear moduli are computed. The response of the system to a shear deformation with a constant shear rate is analyzed. The liquid shows viscoelastic behavior that can be described with a Maxwell model. The solid behaves as an elastic medium up to a finite deformation and then undergoes a transition to plastic flow, which is stick-slip-like at small shear rates and continuous at higher ones. PMID:11461234
Lattice model theory of the equation of state covering the gas, liquid, and solid phases
NASA Technical Reports Server (NTRS)
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.
Keasler, Samuel J; Charan, Sophia M; Wick, Collin D; Economou, Ioannis G; Siepmann, J Ilja
2012-09-13
While the transferable potentials for phase equilibria-united atom (TraPPE-UA) force field has generally been successful at providing parameters that are highly transferable between different molecules, the polarity and polarizability of a given functional group can be significantly perturbed in small cyclic structures, which limits the transferability of parameters obtained for linear molecules. This has motivated us to develop a version of the TraPPE-UA force field specifically for five- and six-membered cyclic alkanes and ethers. The Lennard-Jones parameters for the methylene group obtained from cyclic alkanes are transferred to the ethers for each ring size, and those for the oxygen atom are common to all compounds for a given ring size. However, the partial charges are molecule specific and parametrized using liquid-phase dielectric constants. This model yields accurate saturated liquid densities and vapor pressures, critical temperatures and densities, normal boiling points, heat capacities, and isothermal compressibilities for the following molecules: cyclopentane, tetrahydrofuran, 1,3-dioxolane, cyclohexane, oxane, 1,4-dioxane, 1,3-dioxane, and 1,3,5-trioxane. The azeotropic behavior and separation factor for the binary mixtures of 1,3-dioxolane/cyclohexane and ethanol/1,4-dioxane are qualitively reproduced. PMID:22900670
A Redox Economical Synthesis of Bioactive 6,12-Guaianolides
Wen, Bo; Hexum, Joseph K.; Widen, John C.
2013-01-01
Syntheses of two 6,12-guaianolide analogs are reported within. The scope of the tandem allylboration/lactonization chemistry is expanded to provide a functionalized alleneyne-containing α-methylene butyrolactone that undergoes a Rh(I)-catalyzed cyclocarbonylation reaction to afford a 5-7-5 ring system. The resulting cycloadducts bear a structural resemblance to other NF-κB inhibitors such as cumambrin A and indeed were shown to inhibit NF-κB signaling and cancer cell growth. PMID:23662902
[CrIII8MII6]12+ Coordination Cubes (MII=Cu, Co)**
Sanz, Sergio; O'Connor, Helen M; Pineda, Eufemio Moreno; Pedersen, Kasper S; Nichol, Gary S; Mønsted, Ole; Weihe, Høgni; Piligkos, Stergios; McInnes, Eric J L; Lusby, Paul J; Brechin, Euan K
2015-01-01
[CrIII8MII6]12+ (MII=Cu, Co) coordination cubes were constructed from a simple [CrIIIL3] metalloligand and a “naked” MII salt. The flexibility in the design proffers the potential to tune the physical properties, as all the constituent parts of the cage can be changed without structural alteration. Computational techniques (known in theoretical nuclear physics as statistical spectroscopy) in tandem with EPR spectroscopy are used to interpret the magnetic behavior. PMID:25891167
Rai, Neeraj; Siepmann, J Ilja
2007-09-13
The explicit hydrogen version of the transferable potentials for phase equilibria (TraPPE-EH) force field is extended to benzene, pyridine, pyrimidine, pyrazine, pyridazine, thiophene, furan, pyrrole, thiazole, oxazole, isoxazole, imidazole, and pyrazole. While the Lennard-Jones parameters for carbon, hydrogen (two types), nitrogen (two types), oxygen, and sulfur are transferable for all 13 compounds, the partial charges are specific for each compound. The benzene dimer energies for sandwich, T-shape, and parallel-displaced configurations obtained for the TraPPE-EH force field compare favorably with high-level electronic structure calculations. Gibbs ensemble Monte Carlo simulations were carried out to compute the single-component vapor-liquid equilibria for benzene, pyridine, three diazenes, and eight five-membered heterocycles. The agreement with experimental data is excellent with the liquid densities and vapor pressures reproduced within 1 and 5%, respectively. The critical temperatures and normal boiling points are predicted with mean deviations of 0.8 and 1.6%, respectively. PMID:17713943
Fritsche, Miriam; Pandey, Ras B.; Farmer, Barry L.; Heermann, Dieter W.
2012-01-01
Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential. We find a variety of equilibrium structures including global globular configurations at low normalized temperature (), combination of segmental globules and elongated chains (), predominantly elongated chains (), as well as universal SAW conformations at high normalized temperature (). The radius of gyration of the protein exhibits a non-monotonic temperature dependence with a maximum at a characteristic temperature () where a crossover occurs from a positive (stretching at ) to negative (contraction at ) thermal response on increasing . PMID:22442661
NASA Astrophysics Data System (ADS)
Fritsche, Miriam; Heermann, Dieter; Pandey, Ras; Farmer, Barry
2012-02-01
Using a coarse-grained bond fluctuating model, we investigate structure and dynamics of two histones, H2AX (143 residues) and H3.1 (136 residues) as a function of temperature (T). A knowledged based contact matrix is used as an input for a phenomenological residue-residue interaction in a generalized Lennard-Jones potential. Metropolis algorithm is used to execute stochastic movement of each residue. A number of local and global physical quantities are analyzed. Despite unique energy and mobility profiles of its residues in a specific sequence, the histone H3.1 appears to undergo a structural transformation from a random coil to a globular conformation on reducing the temperature. The radius of gyration of the histone H2AX, in contrast, exhibits a non-monotonic dependence on temperature with a maximum at a characteristic temperature (Tc) where crossover occurs from a positive (stretching below Tc) to negative (contraction above Tc) thermal response on increasing T. Multi-scale structures of the proteins are examined by a detailed analysis of their structure functions.
Pigment Spectra and Intermolecular Interaction Potentials in Glasses and Proteins
Renge, I.; van Grondelle, R.; Dekker, J. P.
2007-01-01
A model is proposed for chromophore optical spectra in solids over a wide range of temperatures and pressures. Inhomogeneous band shapes and their pressure dependence, as well as baric shift coefficients of spectral lines, selected by the frequency, were derived using Lennard-Jones potentials of the ground and excited states. Quadratic electron-phonon coupling constants, describing the thermal shift and broadening of zero-phonon lines, were also calculated. Experimentally, thermal shift and broadening of spectral holes were studied between 5 and 40 K for a synthetic pigment, chlorin, embedded in polymer hosts. The baric effects on holes were determined by applying hydrostatic He gas pressure up to 200 bar, at 6 K. Absorption spectra of pheophytin a, chlorophyll a, and β-carotene in polymers and plant photosystem II CP47 complex were measured between 5 (or 77) and 300 K, and subject to Voigtian deconvolution. A narrowing of inhomogeneous bandwidth with increasing temperature, predicted on the basis of hole behavior, was observed as the shrinking of Gaussian spectral component. The Lorentzian broadening was ascribed to optical dephasing up to 300 K in transitions with weak to moderate linear electron-phonon coupling strength. The thermal broadening is purely Gaussian in multiphonon transitions (S2 band of β-carotene, Soret bands of tetrapyrrolic pigments), and the Lorentz process appears to be suppressed, indicating a lack of exponential dephasing. Density, polarity, polarizability, compressibility, and other local parameters of the pigment binding sites in biologically relevant systems can be deduced from spectroscopic data, provided that sufficient background information is available. PMID:17557783
Intermolecular potential parameters and combining rules determined from viscosity data
Bastien, Lucas A.J.; Price, Phillip N.; Brown, Nancy J.
2010-05-07
The Law of Corresponding States has been demonstrated for a number of pure substances and binary mixtures, and provides evidence that the transport properties viscosity and diffusion can be determined from a molecular shape function, often taken to be a Lennard-Jones 12-6 potential, that requires two scaling parameters: a well depth {var_epsilon}{sub ij} and a collision diameter {sigma}{sub ij}, both of which depend on the interacting species i and j. We obtain estimates for {var_epsilon}{sub ij} and {sigma}{sub ij} of interacting species by finding the values that provide the best fit to viscosity data for binary mixtures, and compare these to calculated parameters using several 'combining rules' that have been suggested for determining parameter values for binary collisions from parameter values that describe collisions of like molecules. Different combining rules give different values for {sigma}{sub ij} and {var_epsilon}{sub ij} and for some mixtures the differences between these values and the best-fit parameter values are rather large. There is a curve in ({var_epsilon}{sub ij}, {sigma}{sub ij}) space such that parameter values on the curve generate a calculated viscosity in good agreement with measurements for a pure gas or a binary mixture. The various combining rules produce couples of parameters {var_epsilon}{sub ij}, {sigma}{sub ij} that lie close to the curve and therefore generate predicted mixture viscosities in satisfactory agreement with experiment. Although the combining rules were found to underpredict the viscosity in most of the cases, Kong's rule was found to work better than the others, but none of the combining rules consistently yields parameter values near the best-fit values, suggesting that improved rules could be developed.
He-broadening and shift coefficients of water vapor lines in infrared spectral region
NASA Astrophysics Data System (ADS)
Petrova, T. M.; Solodov, A. M.; Solodov, A. A.; Deichuli, V. M.; Starikov, V. I.
2015-11-01
The water vapor line broadening and shift coefficients in the ν1+ν2, ν2+ν3, ν1+ν3, 2ν3, 2ν1, 2ν2+ν3, and ν1+2ν2 vibrational bands induced by helium pressure were measured using a Bruker IFS 125HR spectrometer. The vibrational bands 2ν3 and ν1+2ν2 were investigated for the first time. The interaction potential used in the calculations of broadening and shift coefficients was chosen as the sum of pair potentials, which were modeled by the Lennard-Jones (6-12) potentials. The vibrational and rotational contributions to this potential were obtained by use of the intermolecular potential parameters and intramolecular parameters of H2O molecule. The calculated values of the broadening and shift coefficients were compared with the experimental data.
Calculating excess chemical potentials using dynamic simulations in the fourth dimension
Pomes, R.; Eisenmesser, E.; Post, C.B.; Roux, B.
1999-08-01
A general method for computing excess chemical potentials is presented. The excess chemical potential of a solute or ligand molecule is estimated from the potential of mean-force (PMF) calculated along a nonphysical fourth spatial dimension, {ital w}, into which the molecule is gradually inserted or from which it is gradually abstracted. According to this {open_quotes}4D-PMF{close_quotes} (four dimensional) scheme, the free energy difference between two limiting states defines the excess chemical potential: At w={plus_minus}{infinity}, the molecule is not interacting with the rest of the system, whereas at w=0, it is fully interacting. Use of a fourth dimension avoids the numerical instability in the equations of motion encountered upon growing or shrinking solute atoms in conventional free energy perturbation simulations performed in three dimensions, while benefiting from the efficient sampling of configurational space afforded by PMF calculations. The applicability and usefulness of the method are illustrated with calculations of the hydration free energy of simple Lennard-Jones (LJ) solutes, a water molecule, and camphor, using molecular dynamics simulations and umbrella sampling. Physical insight into the nature of the PMF profiles is gained from a continuum treatment of short- and long-range interactions. The short-range barrier for dissolution of a LJ solute in the added dimension provides an apparent surface tension of the solute. An approximation to the long-range behavior of the PMF profiles is made in terms of a continuum treatment of LJ dispersion and electrostatic interactions. Such an analysis saves the need for configurational sampling in the long-range limit of the fourth dimension. The 4D-PMF method of calculating excess chemical potentials should be useful for neutral solute and ligand molecules with a wide range of sizes, shapes, and polarities. {copyright} {ital 1999 American Institute of Physics.}
Wang, Jiyao; Deng, Yuqing; Roux, Benoît
2006-01-01
The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned “on” and “off.” Second, sampling of the ligand conformation is enforced by a restraining potential based on the root mean-square deviation relative to the bound state conformation. The effect of all the restraining potentials is rigorously unbiased, and it is shown explicitly that the final results are independent of all artificial restraints. Third, the repulsive and dispersive free energy contribution arising from the Lennard-Jones interactions of the ligand with its surrounding (protein and solvent) is calculated using the Weeks-Chandler-Andersen separation. This separation also improves convergence of the FEP/MD calculations. Fourth, to decrease the computational cost, only a small number of atoms in the vicinity of the binding site are simulated explicitly, while all the influence of the remaining atoms is incorporated implicitly using the generalized solvent boundary potential (GSBP) method. With GSBP, the size of the simulated FKBP12/ligand systems is significantly reduced, from ∼25,000 to 2500. The computations are very efficient and the statistical error is small (∼1 kcal/mol). The calculated binding free energies are generally in good agreement with available experimental data and previous calculations (within ∼2 kcal/mol). The present results indicate that a strategy based on FEP/MD simulations of a reduced GSBP atomic model sampled with conformational, translational, and orientational restraining
40 CFR 721.524 - Alcohols, C6-12, ethoxylated, reaction product with maleic anhydride.
Code of Federal Regulations, 2014 CFR
2014-07-01
... New Uses for Specific Chemical Substances § 721.524 Alcohols, C6-12, ethoxylated, reaction product... chemical substance identified generically as alcohols, C6-12, ethoxylated, reaction product with maleic... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Alcohols, C6-12, ethoxylated,...
40 CFR 721.524 - Alcohols, C6-12, ethoxylated, reaction product with maleic anhydride.
Code of Federal Regulations, 2012 CFR
2012-07-01
... New Uses for Specific Chemical Substances § 721.524 Alcohols, C6-12, ethoxylated, reaction product... chemical substance identified generically as alcohols, C6-12, ethoxylated, reaction product with maleic... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Alcohols, C6-12, ethoxylated,...
40 CFR 721.524 - Alcohols, C6-12, ethoxylated, reaction product with maleic anhydride.
Code of Federal Regulations, 2011 CFR
2011-07-01
... New Uses for Specific Chemical Substances § 721.524 Alcohols, C6-12, ethoxylated, reaction product... chemical substance identified generically as alcohols, C6-12, ethoxylated, reaction product with maleic... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Alcohols, C6-12, ethoxylated,...
40 CFR 721.524 - Alcohols, C6-12, ethoxylated, reaction product with maleic anhydride.
Code of Federal Regulations, 2013 CFR
2013-07-01
... New Uses for Specific Chemical Substances § 721.524 Alcohols, C6-12, ethoxylated, reaction product... chemical substance identified generically as alcohols, C6-12, ethoxylated, reaction product with maleic... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Alcohols, C6-12, ethoxylated,...
40 CFR 721.524 - Alcohols, C6-12, ethoxylated, reaction product with maleic anhydride.
Code of Federal Regulations, 2010 CFR
2010-07-01
... New Uses for Specific Chemical Substances § 721.524 Alcohols, C6-12, ethoxylated, reaction product... chemical substance identified generically as alcohols, C6-12, ethoxylated, reaction product with maleic... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Alcohols, C6-12, ethoxylated,...
41 CFR 51-6.12 - Specification changes and similar actions.
Code of Federal Regulations, 2010 CFR
2010-07-01
... 41 Public Contracts and Property Management 1 2010-07-01 2010-07-01 true Specification changes and similar actions. 51-6.12 Section 51-6.12 Public Contracts and Property Management Other Provisions Relating to Public Contracts COMMITTEE FOR PURCHASE FROM PEOPLE WHO ARE BLIND OR SEVERELY DISABLED 6-PROCUREMENT PROCEDURES § 51-6.12...
NASA Astrophysics Data System (ADS)
Loeffler, Troy D.; Chen, Bin
2013-12-01
The aggregation-volume-bias Monte Carlo method was employed to study surface-induced nucleation of Lennard-Jonesium on an implicit surface below the melting point. It was found that surfaces catalyze not only the formation of the droplets (where the nucleation free energy barriers were shown to decrease with increasing surface interaction strength), but also the transition of these droplets into crystal structures due to the surface-induced layering effects. However, this only occurs under suitable interaction strength. When surface attraction is too strong, crystallization is actually inhibited due to the spread of the particles across the surface and corresponding formation of two-dimensional clusters. The simulation results were also used to examine the bulk-droplet based classical nucleation theory for surface-induced nucleation, particularly the additional contact angle term used to describe both the nucleation free energy barrier heights and the critical cluster sizes compared to its homogeneous nucleation formalism. Similar to what has been found previously for homogeneous nucleation, the theory does poorly toward the high-supersaturation region when the critical clusters are small and fractal, but the theoretical predictions on both barrier heights and critical cluster sizes improve rapidly with the decrease of the supersaturation.
Nanoparticle interaction potentials constructed by multiscale computation
NASA Astrophysics Data System (ADS)
Lee, Cheng K.; Hua, Chi C.
2010-06-01
The van der Waals (vdW) potentials governing macroscopic objects have long been formulated in the context of classical theories, such as Hamaker's microscopic theory and Lifshitz's continuum theory. This work addresses the possibility of constructing the vdW interaction potentials of nanoparticle species using multiscale simulation schemes. Amorphous silica nanoparticles were considered as a benchmark example for which a series of (SiO2)n (n being an integer) has been systematically surveyed as the potential candidates of the packing units that reproduce known bulk material properties in atomistic molecular dynamics simulations. This strategy led to the identification of spherical Si6O12 molecules, later utilized as the elementary coarse-grained (CG) particles to compute the pair interaction potentials of silica nanoparticles ranging from 0.62 to 100 nm in diameter. The model nanoparticles so built may, in turn, serve as the children CG particles to construct nanoparticles assuming arbitrary sizes and shapes. Major observations are as follows. The pair interaction potentials for all the investigated spherical silica nanoparticles can be cast into a semiempirical, generalized Lennard-Jones 2α-α potential (α being a size-dependent, large integral number). In its reduced form, we discuss the implied universalities for the vdW potentials governing a certain range of amorphous nanoparticle species as well as how thermodynamic transferability can be fulfilled automatically. In view of future applications with colloidal suspensions, we briefly evaluated the vdW potential in the presence of a "screening" medium mimicking the effects of electrical double layers or grafting materials atop the nanoparticle core. The general observations shed new light on strategies to attain a microscopic control over interparticle attractions. In future perspectives, the proposed multiscale computation scheme shall help bridge the current gap between the modeling of polymer chains and
Interatomic potentials and solvation parameters from protein engineering data for buried residues
Lomize, Andrei L.; Reibarkh, Mikhail Y.; Pogozheva, Irina D.
2002-01-01
Van der Waals (vdW) interaction energies between different atom types, energies of hydrogen bonds (H-bonds), and atomic solvation parameters (ASPs) have been derived from the published thermodynamic stabilities of 106 mutants with available crystal structures by use of an originally designed model for the calculation of free-energy differences. The set of mutants included substitutions of uncharged, inflexible, water-inaccessible residues in α-helices and β-sheets of T4, human, and hen lysozymes and HI ribonuclease. The determined energies of vdW interactions and H-bonds were smaller than in molecular mechanics and followed the "like dissolves like" rule, as expected in condensed media but not in vacuum. The depths of modified Lennard-Jones potentials were −0.34, −0.12, and −0.06 kcal/mole for similar atom types (polar–polar, aromatic–aromatic, and aliphatic–aliphatic interactions, respectively) and −0.10, −0.08, −0.06, −0.02, and nearly 0 kcal/mole for different types (sulfur–polar, sulfur–aromatic, sulfur–aliphatic, aliphatic–aromatic, and carbon–polar, respectively), whereas the depths of H-bond potentials were −1.5 to −1.8 kcal/mole. The obtained solvation parameters, that is, transfer energies from water to the protein interior, were 19, 7, −1, −21, and −66 cal/moleÅ2 for aliphatic carbon, aromatic carbon, sulfur, nitrogen, and oxygen, respectively, which is close to the cyclohexane scale for aliphatic and aromatic groups but intermediate between octanol and cyclohexane for others. An analysis of additional replacements at the water–protein interface indicates that vdW interactions between protein atoms are reduced when they occur across water. PMID:12142453
Molecular-dynamics simulations of stress relaxation in metals and polymers
NASA Astrophysics Data System (ADS)
Blonski, Slawomir; Brostow, Witold; Kubát, Josef
1994-03-01
Molecular-dynamics simulations of stress relaxation have been performed for models of metals and polymers. A method that employs coupling between the simulation cell and an applied stress as well as an external thermal bath has been used. Two-dimensional models of the materials are defined with interactions described by the Lennard-Jones (Mie 6-12) and harmonic potentials. A special method is employed to generate chains in dense polymeric systems. In agreement with experiments, simulated stress-relaxation curves are similar for metals and polymers. At the same time, there exists an essential difference in the stress-strain behavior of the two kinds of simulated materials. During the relaxation, trajectories of the particles in different materials display a common feature: There exist domains in which movement of the particles is highly correlated. Thus, the simulation results support the cooperative theory of stress relaxation.
A high performance communications and memory caching scheme for molecular dynamics on the CM-5
Beazley, D.M.; Lomdahl, P.S.; Gronbech-Jensen, N.; Tamayo, P.
1993-09-15
In this paper, we provide a brief overview of our general molecular dynamics algorithm and focus on several performance enhancements that have allowed us to achieve high performance on the CM-5. Our use of the CM-5 vector units (VUs) to calculate forces is described along with a memory caching scheme that speeds up the force calculation by as much as 50%. In addition, we discuss a method used to speed up the communication aspects of our algorithm by more than 35%. Lastly, recent timing and scaling results are presented. Our code has been implemented in ANSI C with explicit calls to the CMMD message-passing library. To use the VUs we have written our force calculation in CDPEAC (a C interface to the VU assembler language, DPEAC). We also assume that particles interact according to the Lennard-Jones 6--12 (LJ) potential.
Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions
NASA Astrophysics Data System (ADS)
Ballal, Deepti; Venkataraman, Pradeep; Fouad, Wael A.; Cox, Kenneth R.; Chapman, Walter G.
2014-08-01
Intermolecular potential models for water and alkanes describe pure component properties fairly well, but fail to reproduce properties of water-alkane mixtures. Understanding interactions between water and non-polar molecules like alkanes is important not only for the hydrocarbon industry but has implications to biological processes as well. Although non-polar solutes in water have been widely studied, much less work has focused on water in non-polar solvents. In this study we calculate the solubility of water in different alkanes (methane to dodecane) at ambient conditions where the water content in alkanes is very low so that the non-polar water-alkane interactions determine solubility. Only the alkane-rich phase is simulated since the fugacity of water in the water rich phase is calculated from an accurate equation of state. Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. It is found that an effective water Lennard-Jones energy ɛW/k = 220 K is required to match the experimental water solubility in TraPPE alkanes. This number is much higher than used in most simulation water models (SPC/E—ɛW/k = 78.2 K). It is surprising that the interaction energy obtained here is also higher than the water-alkane interaction energy predicted by studies on solubility of alkanes in water. The reason for this high water-alkane interaction energy is not completely understood. Some factors that might contribute to the large interaction energy, such as polarizability of alkanes, octupole moment of methane, and clustering of water at low concentrations in alkanes, are examined. It is found that, though important, these factors do not completely explain the anomalously strong attraction between alkanes and water observed experimentally.
Benjamin, Ronald; Horbach, Jürgen
2012-07-28
A method is proposed to compute the interfacial free energy of a Lennard-Jones system in contact with a structured wall by molecular dynamics simulation. Both the bulk liquid and bulk face-centered-cubic crystal phase along the (111) orientation are considered. Our approach is based on a thermodynamic integration scheme where first the bulk Lennard-Jones system is reversibly transformed to a state where it interacts with a structureless flat wall. In a second step, the flat structureless wall is reversibly transformed into an atomistic wall with crystalline structure. The dependence of the interfacial free energy on various parameters such as the wall potential, the density and orientation of the wall is investigated. The conditions are indicated under which a Lennard-Jones crystal partially wets a flat wall. PMID:22852644
Bridge function of the repulsive Weeks-Chandler-Andersen (WCA) fluid
NASA Astrophysics Data System (ADS)
Tomazic, Daniel; Hoffgaard, Franziska; Kast, Stefan M.
2014-01-01
The bridge function of a simple liquid is calculated for the repulsive part of the Weeks-Chandler-Andersen (WCA) separation of the Lennard-Jones potential. We employ explicit molecular dynamics simulations of the potential of mean force between constrained dimers in order to extract bridge data near zero separation and illustrate the difference to full Lennard-Jones results. We compare direct, reciprocal space and iterative, real space inversions of the Ornstein-Zernike equation. Bridge functions for various thermodynamic states are analyzed as to their parametric dependence on the renormalized indirect correlation function, which has consequences for the analytic representation of the free energy functional.
41 CFR 51-6.12 - Specification changes and similar actions.
Code of Federal Regulations, 2011 CFR
2011-07-01
... 41 Public Contracts and Property Management 1 2011-07-01 2009-07-01 true Specification changes and similar actions. 51-6.12 Section 51-6.12 Public Contracts and Property Management Other Provisions... Procurement List, including a change that involves the assignment of a new national stock number or...
Su, Pin-Chih; Johnson, Michael E
2016-04-01
Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the parahalogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme. PMID:26666582
From Dimer to Crystal: Calculating the Cohesive Energy of Rare Gas Solids
ERIC Educational Resources Information Center
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…
Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A
2011-05-19
A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. PMID:21500792
Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A.
2011-01-01
A new model of side-chain – side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a Generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parameterized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. PMID:21500792
A Polarizable and Transferable PHAST N2 Potential for Use in Materials Simulation.
Cioce, Christian R; McLaughlin, Keith; Belof, Jonathan L; Space, Brian
2013-12-10
A polarizable and transferable intermolecular potential energy function, potentials with high accuracy, speed, and transferability (PHAST), has been developed from first principles for molecular nitrogen to be used in the modeling of heterogeneous processes such as materials sorption and separations. A five-site (van der Waals and point charge) anisotropic model, that includes many-body polarization, is proposed. It is parametrized to reproduce high-level electronic structure calculations (CCSD(T) using Dunning-type basis sets extrapolated to the CBS limit) for a representative set of dimer potential energy curves. Thus it provides a relatively simple yet robust and broadly applicable representation of nitrogen. Two versions are developed, differing by the type of mixing rules applied to unlike Lennard-Jones potential sites. It is shown that the Waldman-Hagler mixing rules are more accurate than Lorentz-Berthelot. The resulting potentials are demonstrated to be effective in modeling neat nitrogen but are designed to also be useful in modeling N2 interactions in a large array of environments such as metal-organic frameworks and zeolites and at interfaces. In such settings, capturing anisotropic forces and interactions with (open and coordinated) metals and charged/polar environments is essential. In developing the potential, it was found that adding a seemingly redundant dimer orientation, slip-parallel (S), improved the transferability of the potential energy surface (PES). Notably, one of the solid phases of nitrogen was not as accurately represented energetically without including S in the representative set. Liquid simulations, however, were unaffected and worked equally well for both potentials. This suggests that accounting for a wide variety of configurations is critical in designing a potential that is intended for use in heterogeneous environments where many orientations, including those not commonly explored in the bulk, are possible. Testing and
An alternative model for estimating liquid diffusion coefficients requiring no viscosity data
NASA Technical Reports Server (NTRS)
Morales, Wilfredo
1993-01-01
An equation, based on the free volume of a liquid solvent, was derived via dimensional analysis, to predict binary diffusion coefficients. The equation assumed that interaction between the solute and liquid solvent molecules followed a Lennard-Jones potential. The equation was compared to other diffusivity equations and was found to give good results over the temperature range examined.
The calculation of elastic constants from displacement fluctuations
NASA Astrophysics Data System (ADS)
Meyers, M. T.; Rickman, J. M.; Delph, T. J.
2005-09-01
We present a methodology for the accurate and efficient extraction of elastic constants in homogeneous solids via the calculation of the atomic displacement correlation function. This approach is validated for cubic solids parametrized by both Lennard-Jones and embedded-atom method potentials. Finally, we also discuss the extension of this method to obtain the elastic properties of inhomogeneous solids.
Green's function Monte Carlo calculation for the ground state of helium trimers
Cabral, F.; Kalos, M.H.
1981-02-01
The ground state energy of weakly bound boson trimers interacting via Lennard-Jones (12,6) pair potentials is calculated using a Monte Carlo Green's Function Method. Threshold coupling constants for self binding are obtained by extrapolation to zero binding.
Improving the Precollegiate Curriculum on Latin America, Grades 6-12. Final Performance Report.
ERIC Educational Resources Information Center
Wirth, John D.
The Latin America Project, which developed print and nonprint materials for use in grades 6-12, is described. The two-year effort was conducted in five phases: survey of existing materials; the development of curriculum units; review of curriculum by teachers attending summer institutes; field testing and evaluation; and dissemination. Titles of…
Teaching Global Awareness Using the Media. Grades 6-12, Global Awareness Series.
ERIC Educational Resources Information Center
Lamy, Steven L.; And Others
This teaching guide on global awareness contains 15 media-related activities for students in grades 6-12. The objective is to help students see how the media affect their opinions and the roles the media plays in world affairs. The activities are divided into five sections. The first section contains a general survey of the students' knowledge of…
40 CFR 721.10559 - Morpholine, 4-C6-12 acyl derivs.
Code of Federal Regulations, 2013 CFR
2013-07-01
... subject to reporting. (1) The chemical substance identified as morpholine, 4-C6-12 acyl derivs. (PMN P-06...) through (h) are applicable to manufacturers, importers, and processors of this substance. (2) Limitations... SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific...
ERIC Educational Resources Information Center
What Works Clearinghouse, 2011
2011-01-01
The "University of Chicago School Mathematics Project ("UCSMP") 6-12 Curriculum" is a series of yearlong courses--(1) Transition Mathematics; (2) Algebra; (3) Geometry; (4) Advanced Algebra; (5) Functions, Statistics, and Trigonometry; and (6) Precalculus and Discrete Mathematics--emphasizing problem solving, real-world applications, and the use…
Health Problems in the Classroom 6-12: An A-Z Reference Guide for Educators.
ERIC Educational Resources Information Center
Huffman, Dolores M.; Fontaine, Karen Lee; Price, Bernadette K.
This guide provides a resource for middle and high school teachers, teacher aides, administrators, and educators, covering health problems that affect students in grades 6-12. The handbook alphabetically lists the most current health concerns for this age group. Part 1, "Health Issues in the Classroom," includes (1) "Health, Illness, and…
Teens on Target Violence Prevention Curriculum for Grades 6-12.
ERIC Educational Resources Information Center
Becker, Marla G.; Calhoun, Deane
This curriculum is designed to help schools implement programs to prevent violence among students in grades 6-12. It is a six-session, school based curriculum intended for adolescents who are living in communities experiencing high rates of violence. It is facilitated by trained Teens on Target (TNT) members/peer educators, young people who are…
NASA Astrophysics Data System (ADS)
Bresme, Fernando; Abascal, José L. F.; Lomba, Enrique
1996-12-01
Structure and thermodynamics of fluids made of particles that interact via a central force model potential are studied by means of Monte Carlo simulations and integral equation theories. The Hamiltonian has two terms, an intramolecular component represented by a harmonic oscillatorlike potential and an intermolecular interaction of the Lennard-Jones type. The potential does not fulfill the steric saturation condition so it leads to a polydisperse system. First, we investigate the association (clustering) and thermodynamic properties as a function of the potential parameters, such as the intramolecular potential depth, force constant, and bond length. It is shown that the atomic hypernetted chain (HNC) integral equation provides a correct description of the model as compared with simulation results. The calculation of the HNC pseudospinodal curve indicates that the stability boundaries between the vapor and liquid phases are strongly dependent on the bond length and suggests that there might be a direct gas-solid transition for certain elongations. On the other hand, we have assessed the ability of the model to describe the thermodynamics and structure of diatomic liquids such as N2 and halogens. To this end we have devised a procedure to model the intramolecular potential depth to reproduce the complete association limit (i.e., an average number of bonds per particle equal to one). This constraint is imposed on the Ornstein-Zernike integral equation in a straightforward numerical way. The structure of the resulting fluid is compared with results from molecular theories. An excellent agreement between the HNC results for the associating fluid and the reference interaction site model (RISM)-HNC computations for the atom-atom model of the same fluid is obtained. There is also a remarkable coincidence between the simulation results for the molecular and the associating liquids, despite the polydisperse character of the latter. The stability boundaries in the complete
NASA Astrophysics Data System (ADS)
Zarkova, L.; Hohm, U.; Damyanova, M.
2006-09-01
Reference tables of second pVT-virial coefficients B(T ), viscosity η(T ), and self-diffusion ρD(T ) are given for all neat alkanes CnH2n+2, n <6, for temperatures T ⩽1200K starting at 100K for CH4, 150K for C2H6, and 180K for C3H8, n-C4H10, i-C4H10, n-C5H12, i-C5H12, and C(CH3)4. Restricting ourselves to low densities the thermophysical properties are calculated by means of an isotropic (n-6) Lennard-Jones temperature dependent potential (LJTDP). In this model the potential well depth ɛeff(T ) and the separation at minimum energy Rm(eff)(T) are explicitly temperature dependent, whereas the repulsive term n >12 is independent of T. The LJTDP has been used before in order to construct reference tables of thermophysical properties of neat gases [Zarkova and Hohm, J. Phys. Chem. Ref. Data 31, 183 (2002)] and binary mixtures [Zarkova, Hohm, and Damyanova, J. Phys. Chem. Ref. Data 32, 1591 (2003)]. However, those studies were restricted to atoms and globularly shaped nondipolar molecules. Here the approach is extended to elongated, not necessarily spherically symmetric, and in part slightly dipolar molecules. As in previous works the potential parameters ɛ(eff)(T), Rm(eff)(T), and n are determined by minimizing the root-mean-square deviation between calculated and experimentally obtained thermophysical properties B(T ), η(T ), ρD(T ), and the second acoustic virial coefficient β(T ) normalized to their experimental error. In extension of our previous efforts we present a thorough statistical analysis of the experimental input data which gives us the possibility to select primary data which could be used to build up a database.
Anderson, Brian J; Bazant, Martin Z; Tester, Jefferson W; Trout, Bernhardt L
2005-04-28
We present the application of a mathematical method reported earlier by which the van der Waals-Platteeuw statistical mechanical model with the Lennard-Jones and Devonshire approximation can be posed as an integral equation with the unknown function being the intermolecular potential between the guest molecules and the host molecules. This method allows us to solve for the potential directly for hydrates for which the Langmuir constants are computed, either from experimental data or from ab initio data. Given the assumptions made in the van der Waals-Platteeuw model with the spherical-cell approximation, there are an infinite number of solutions; however, the only solution without cusps is a unique central-well solution in which the potential is at a finite minimum at the center to the cage. From this central-well solution, we have found the potential well depths and volumes of negative energy for 16 single-component hydrate systems: ethane (C2H6), cyclopropane (C3H6), methane (CH4), argon (Ar), and chlorodifluoromethane (R-22) in structure I; and ethane (C2H6), cyclopropane (C3H6), propane (C3H8), isobutane (C4H10), methane (CH4), argon (Ar), trichlorofluoromethane (R-11), dichlorodifluoromethane (R-12), bromotrifluoromethane (R-13B1), chloroform (CHCl3), and 1,1,1,2-tetrafluoroethane (R-134a) in structure II. This method and the calculated cell potentials were validated by predicting existing mixed hydrate phase equilibrium data without any fitting parameters and calculating mixture phase diagrams for methane, ethane, isobutane, and cyclopropane mixtures. Several structural transitions that have been determined experimentally as well as some structural transitions that have not been examined experimentally were also predicted. In the methane-cyclopropane hydrate system, a structural transition from structure I to structure II and back to structure I is predicted to occur outside of the known structure II range for the cyclopropane hydrate. Quintuple (L
Electronic properties and carrier mobilities of 6,6,12-graphyne nanoribbons
Ding, Heyu; Huang, Yuanhe; Bai, Hongcun
2015-07-15
Structures, stabilities, electronic properties and carrier mobilities of 6,6,12-graphyne nanoribbons (GyNRs) with armchair and zigzag edges are investigated using the self-consistent field crystal orbital method based on density functional theory. It is found that the 1D GyNRs are more stable than the 2D 6,6,12-graphyne sheet in the view of the Gibbs free energy. The stabilities of these GyNRs decrease as their widths increase. The calculated band structures show that all these GyNRs are semiconductors and that dependence of band gaps on the ribbon width is different from different types of the GyNRs. The carrier mobility was calculated based on the deformation theory and effective mass approach. It is found that the carrier mobilities of these GyNRs can reach the order of 10{sup 5} cm{sup 2} V {sup –1}s{sup –1} at room temperature and are comparable to those of graphene NRs. Moreover, change of the mobilities with change of the ribbon width is quite different from different types of the GyNRs.
Vibrational and thermodynamic properties of α-, β-, γ-, and 6, 6, 12-graphyne structures.
Perkgöz, Nihan Kosku; Sevik, Cem
2014-05-01
Electronic, vibrational, and thermodynamic properties of different graphyne structures, namely α-, β-, γ-, and 6, 6, 12-graphyne, are investigated through first principles-based quasi-harmonic approximation by using phonon dispersions predicted from density-functional perturbation theory. Similar to graphene, graphyne was shown to exhibit a structure with extraordinary electronic features, mechanical hardness, thermal resistance, and very high conductivity from different calculation methods. Hence, characterizing its phonon dispersions and vibrational and thermodynamic properties in a systematic way is of great importance for both understanding its fundamental molecular properties and also figuring out its phase stability issues at different temperatures. Thus, in this research work, thermodynamic stability of different graphyne allotropes is assessed by investigating vibrational properties, lattice thermal expansion coefficients, and Gibbs free energy. According to our results, although the imaginary vibrational frequencies exist for β-graphyne, there is no such a negative behavior for α-, γ-, and 6, 6, 12-graphyne structures. In general, the Grüneisen parameters and linear thermal expansion coefficients of these structures are calculated to be rather more negative when compared to those of the graphene structure. In addition, the predicted difference between the binding energies per atom for the structures of graphene and graphyne points out that graphyne networks have relatively lower phase stability in comparison with the graphene structures. PMID:24737253
Weiss, Vinícius Almir; Faoro, Helisson; Tadra-Sfeir, Michelle Zibbetti; Raittz, Roberto Tadeu; de Souza, Emanuel Maltempi; Monteiro, Rose Adele; Cardoso, Rodrigo Luis Alves; Wassem, Roseli; Chubatsu, Leda Satie; Huergo, Luciano Fernandes; Müller-Santos, Marcelo; Steffens, Maria Berenice Reynaud; Rigo, Liu Un; Pedrosa, Fábio de Oliveira
2012-01-01
Herbaspirillum lusitanum strain P6-12 (DSM 17154) is, so far, the only species of Herbaspirillum isolated from plant root nodules. Here we report a draft genome sequence of this organism. PMID:22815451
Meaningful, Authentic and Place-Based Informal Science Education for 6-12 Students
NASA Astrophysics Data System (ADS)
Ito, E.; Dalbotten, D. M.
2014-12-01
American Indians are underrepresented in STEM and especially in Earth sciences. They have the lowest high school graduation rate and highest unemployment. On the other hand, tribes are in search of qualified young people to work in geo- and hydro-technical fields to manage reservations' natural resources. Dalbotten and her collaborators at the Fond du Lac Band of Lake Superior Chippewa and local 6-12 teachers ran a place-based but non-themed informal monthly science camps (gidakiimanaaniwigamig) for 7 years starting 2003. Camps were held on reservation and some activities focused on observing seasonal changes. The students enjoyed coming to the camps but the camp activities went largely unnoticed by the reservation itself. For the last 5 years, we and the same cast of characters from the gidakiimanaaniwigamig camps ran a very place-based, research-based camp program, manoomin. The research was focused on manoomin (wild rice) which is a culturally important plant and food that grows in local lakes and wetlands. Manmade changes in hydrology, toxic metals from mining, and changing weather patterns due to climate change threaten this precious resource. Our plan was for 6-12 students to investigate the past, the present and the future conditions of manoomin on and around the reservation. It became clear by 3rd year that the research project, as conceived, was overly ambitious and could not be completed at the level we hoped in a camp setting (6 weekend camps = 6 full days per year). However, students felt that they were involved in research that was beneficial to their reservation, reported gaining self-confidence to pursue a career in science, and stated a desired to obtain a college degree. They also became aware of STEM employment opportunities on reservation that they could aim for. The camps also fostered a trusting relationship between researchers at Fond du Lac resource managers and the U. of MN. Based on these experiences, we proposed a new format for these
Iida, T; Tamaru, T; Chang, F C; Goto, J; Nambara, T
1991-04-01
Two new 6-hydroxylated bile acids, 3 beta, 6 alpha, 12 alpha- and 3 beta, 6 beta, 12 alpha-trihydroxy-5 beta-cholanoic acids, were synthesized from deoxycholic acid. In addition, their C-3 epimers, 3 alpha, 6 alpha, 12 alpha- and 3 alpha, 6 beta, 12 alpha-trihydroxy acids, were prepared by a new route. The principal reactions used were 1) 6 beta-hydroxylation of 3-methoxy-3,5-dienes with m-chloroperbenzoic acid in aqueous dioxane; 2) catalytic hydrogenation of the resulting 6 beta-hydroxy-3-oxo-4-enes to the 6 beta-hydroxy-3-oxo-5 beta compounds with palladium on calcium carbonate catalyst in ethanol; and 3) stereoselective reduction of appropriate 3-oxo derivatives with potassium tri-sec-butylborohydride and tert-butylamine-borane complex. The thin-layer chromatographic, gas-liquid chromatographic, and high performance liquid chromatographic mobilities, and 1H- and 13C-nuclear magnetic resonance spectroscopic data of the four stereoisomers are presented. With this work all the 6-hydroxylated derivatives of lithocholic, deoxycholic, chenodeoxycholic, ursodeoxycholic, and cholic acids in the 5 beta series are now known and have been synthesized. PMID:1856610
Whole-grain food consumption in Singaporean children aged 6-12 years.
Neo, Jia En; Binte Mohamed Salleh, Saihah; Toh, Yun Xuan; How, Kesslyn Yan Ling; Tee, Mervin; Mann, Kay; Hopkins, Sinead; Thielecke, Frank; Seal, Chris J; Brownlee, Iain A
2016-01-01
Public health bodies in many countries are attempting to increase population-wide habitual consumption of whole grains. Limited data on dietary habits exist in Singaporean children. The present study therefore aimed to assess whole grain consumption patterns in Singaporean children and compare these with dietary intake, physical activity and health parameters. Dietary intake (assessed by duplicate, multipass, 24-h food recalls), physical activity (by questionnaire) and anthropometric measurements were collected from a cross-section of 561 Singaporean children aged 6-12 years. Intake of whole grains was evaluated using estimates of portion size and international food composition data. Only 38·3 % of participants reported consuming whole grains during the dietary data collection days. Median intake of whole grains in consumers was 15·3 (interquartile range 5·4-34·8) g/d. The most commonly consumed whole-grain food groups were rice (29·5 %), wholemeal bread (28·9 %) and ready-to-eat breakfast cereals (18·8 %). A significantly lower proportion of Malay children (seven out of fifty-eight; P < 0·0001) consumed whole grains than children of other ethnicities. Only 6 % of all children consumed the amount of whole grains most commonly associated with improved health outcomes (48 g/d). There was no relationship between whole grain consumption patterns and BMI, waist circumference or physical activity but higher whole grain intake was associated with increased fruit, vegetable and dairy product consumption (P < 0·001). These findings demonstrate that consumption of whole grain foods is low at a population level and infrequent in Singaporean children. Future drives to increase whole-grain food consumption in this population are likely to require input from multiple stakeholders. PMID:27547396
Yadav, Priya; Das, Soumyajit; Phan, Hoa; Herng, Tun Seng; Ding, Jun; Wu, Jishan
2016-06-17
Although the ground-state and physical properties of zethrene and recently invented 1,2:8,9-dibenzozethrene have been well studied, the other dibenzozethrene isomer, i.e., 5,6:12,13-dibenzozethrene, remained unexplored. A short synthetic route to a kinetically blocked stable 5,6:12,13-dibenzozethrene derivative 5 is presented. The ground state is found to be open-shell singlet experimentally, and the theoretical y0 was enhanced to 0.414, which corroborates nicely with the experimental and theoretical singlet-triplet energy gap. PMID:27227758
Fluid-solid transition in simple systems using density functional theory
NASA Astrophysics Data System (ADS)
Bharadwaj, Atul S.; Singh, Yashwant
2015-09-01
A free energy functional for a crystal which contains both the symmetry-conserved and symmetry-broken parts of the direct pair correlation function has been used to investigate the fluid-solid transition in systems interacting via purely repulsive Weeks-Chandler-Anderson Lennard-Jones potential and the full Lennard-Jones potential. The results found for freezing parameters for the fluid-face centred cubic crystal transition are in very good agreement with simulation results. It is shown that although the contribution made by the symmetry broken part to the grand thermodynamic potential at the freezing point is small compared to that of the symmetry conserving part, its role is crucial in stabilizing the crystalline structure and on values of the freezing parameters.
Statistical distribution of bonding distances in a unidimensional solid
NASA Astrophysics Data System (ADS)
Belousov, Roman; De Gregorio, Paolo; Rondoni, Lamberto; Conti, Livia
2014-10-01
We study a Fermi-Pasta-Ulam-like chain with Lennard-Jones potentials to model a unidimensional solid in contact with heat baths at a given temperature. We formulate an explicit analytical expression for the probability density of bonding distances between neighboring particles, which depends on temperature similarly to the distribution of velocities. For a finite number of particles, its validity is verified with high accuracy through molecular dynamics simulations. We also provide a theoretical framework which is consistent with the numerical findings. We give an analytic expression of the mean bond distance and elastic constant in the case of the square-well and harmonic interparticle potentials: we outline the role played by the hard-core repulsion. We also calculate the same quantities in the case of series expansions of Lennard-Jones potential truncated at different, even series power.
40 CFR 721.6100 - Phosphoric acid, C6-12-alkyl esters, compounds with 2-(dibutylamino) ethanol.
Code of Federal Regulations, 2013 CFR
2013-07-01
..., compounds with 2-(dibutylamino) ethanol. 721.6100 Section 721.6100 Protection of Environment ENVIRONMENTAL..., compounds with 2-(dibutylamino) ethanol. (a) Chemical substances and significant new uses subject to reporting. (1) The chemical substances identified as phosphoric acid, C6-12-alkyl esters, compounds with...
40 CFR 721.6100 - Phosphoric acid, C6-12-alkyl esters, compounds with 2-(dibutylamino) ethanol.
Code of Federal Regulations, 2014 CFR
2014-07-01
..., compounds with 2-(dibutylamino) ethanol. 721.6100 Section 721.6100 Protection of Environment ENVIRONMENTAL..., compounds with 2-(dibutylamino) ethanol. (a) Chemical substances and significant new uses subject to reporting. (1) The chemical substances identified as phosphoric acid, C6-12-alkyl esters, compounds with...
40 CFR 721.6100 - Phosphoric acid, C6-12-alkyl esters, compounds with 2-(dibutylamino) ethanol.
Code of Federal Regulations, 2011 CFR
2011-07-01
..., compounds with 2-(dibutylamino) ethanol. 721.6100 Section 721.6100 Protection of Environment ENVIRONMENTAL..., compounds with 2-(dibutylamino) ethanol. (a) Chemical substances and significant new uses subject to reporting. (1) The chemical substances identified as phosphoric acid, C6-12-alkyl esters, compounds with...
40 CFR 721.6100 - Phosphoric acid, C6-12-alkyl esters, compounds with 2-(dibutylamino) ethanol.
Code of Federal Regulations, 2010 CFR
2010-07-01
..., compounds with 2-(dibutylamino) ethanol. 721.6100 Section 721.6100 Protection of Environment ENVIRONMENTAL..., compounds with 2-(dibutylamino) ethanol. (a) Chemical substances and significant new uses subject to reporting. (1) The chemical substances identified as phosphoric acid, C6-12-alkyl esters, compounds with...
40 CFR 721.6100 - Phosphoric acid, C6-12-alkyl esters, compounds with 2-(dibutylamino) ethanol.
Code of Federal Regulations, 2012 CFR
2012-07-01
..., compounds with 2-(dibutylamino) ethanol. 721.6100 Section 721.6100 Protection of Environment ENVIRONMENTAL..., compounds with 2-(dibutylamino) ethanol. (a) Chemical substances and significant new uses subject to reporting. (1) The chemical substances identified as phosphoric acid, C6-12-alkyl esters, compounds with...
Hwang, Kao-Pin; Hsu, Yu-Lung; Hsieh, Tsung-Hsueh; Lin, Hsiao-Chuan; Yen, Ting-Yu; Wei, Hsiu-Mei; Lin, Hung-Chih; Chen, An-Chyi; Chow, Julie Chi; Huang, Li-Min
2014-05-01
This prospective study aimed to investigate the immune responses and safety of an influenza vaccine in vaccine-naïve infants aged 6-12 months, and was conducted from November 2010 to May 2011. Fifty-nine infants aged 6-12 months received two doses of trivalent inactivated influenza vaccine 4 weeks apart. Hemagglutination inhibition titers were measured 4 weeks after the two doses of study vaccine. Based on the assumption that a hemagglutination inhibition titer of 1:40 or greater against the antigen would be protective in adults, two doses of the study vaccine generated a protective immune response of 63.2% against influenza A(H1N1), 82.5% against influenza A(H3N2) and 38.6% against influenza B viruses in infants aged 6-12 months. The geometric mean fold rises against influenza type A and B viruses also met the European Medicines Agency criteria for flu vaccines. The solicited events within 7 days after vaccination were mild in intensity. No deaths or adverse events such as optic neuritis, cranial neuropathy, and brachial neuropathy or Guillain-Barre syndrome were reported. Two doses of inactivated influenza vaccine were well tolerated and induced a protective immune response against influenza in infants aged 6-12 months. PMID:24625341
Optimizing Noble Gas-Water Interactions via Monte Carlo Simulations.
Warr, Oliver; Ballentine, Chris J; Mu, Junju; Masters, Andrew
2015-11-12
In this work we present optimized noble gas-water Lennard-Jones 6-12 pair potentials for each noble gas. Given the significantly different atomic nature of water and the noble gases, the standard Lorentz-Berthelot mixing rules produce inaccurate unlike molecular interactions between these two species. Consequently, we find simulated Henry's coefficients deviate significantly from their experimental counterparts for the investigated thermodynamic range (293-353 K at 1 and 10 atm), due to a poor unlike potential well term (εij). Where εij is too high or low, so too is the strength of the resultant noble gas-water interaction. This observed inadequacy in using the Lorentz-Berthelot mixing rules is countered in this work by scaling εij for helium, neon, argon, and krypton by factors of 0.91, 0.8, 1.1, and 1.05, respectively, to reach a much improved agreement with experimental Henry's coefficients. Due to the highly sensitive nature of the xenon εij term, coupled with the reasonable agreement of the initial values, no scaling factor is applied for this noble gas. These resulting optimized pair potentials also accurately predict partitioning within a CO2-H2O binary phase system as well as diffusion coefficients in ambient water. This further supports the quality of these interaction potentials. Consequently, they can now form a well-grounded basis for the future molecular modeling of multiphase geological systems. PMID:26452070
NASA Astrophysics Data System (ADS)
Sadeghi, F.; Ansari, R.; Darvizeh, M.
2016-08-01
The present work aims to investigate the mechanical oscillatory behavior of ions, and in particular {Li+, Na+, Rb+} and {Cl-} ions, inside a cyclo[(- d-Ala- l-Ala)4-] peptide nanotube using the continuum approximation along with the 6-12 Lennard-Jones (LJ) potential function. Assuming that each peptide unit is comprised of an inner and an outer tube, the van der Waals (vdW) potential energy and interaction force between an ion and a cyclic peptide nanotube (CPN) are determined analytically. With respect to the present formulations, a detailed parametric study is conducted on the vdW potential energy and interaction force distributions by varying the number of peptide units. Employing the conservation of mechanical energy principle, a novel expression for precise evaluation of oscillation frequency is introduced. To verify the accuracy of the proposed frequency expression, the results obtained from energy equation are compared with the ones predicted through solving the equation of motion numerically. The effects of number of peptide units and initial conditions including initial separation distance and velocity on the oscillatory behavior of various ions inside CPNs are explored. Among the considered ions, {Cl-} ion is found to generate the highest frequency. According to the potential energy profile, one oscillatory zone for one peptide unit and different oscillatory zones for more than one peptide unit are observed. Numerical results indicate that optimal frequency decreases with increasing the number of peptide units and almost remains unchanged when the number of peptide units exceeds four.
NASA Astrophysics Data System (ADS)
Cuadros, F.; Mulero, A.; Faundez, C. A.
The Lennard-Jones attractive and repulsive contributions of intermolecular forces (as separated in the Weeks-Chandler-Andersen (WCA) theory) to the pressure and chemical potential of coexisting vapour and liquid phases are obtained by using an equation of state recently proposed by us. Some comments are given about the computer simulation results obtained by Plackov and Sadus (1997, Fluid Phase Equilib., 134, 77) using the McQuarrie-Katz separation of the intermolecular potential.
Molecular dynamics study of the stress singularity at a corner
NASA Astrophysics Data System (ADS)
Vafek, Oskar; Robbins, Mark O.
1999-11-01
Linear elasticity theory predicts a power-law singularity in the internal stress at the corner between dissimilar materials under a wide range of conditions. We have studied this singular region using molecular dynamics simulations with harmonic and Lennard-Jones interactions. For the harmonic potential the singularity is cut off by the discreteness of the lattice at a distance of one or two lattice constants from the corner. Anharmonicity leads to much longer range deviations for the Lennard-Jones potential, and plastic flow is observed in some cases. The prefactor of the singularity shows a power-law divergence with increasing system size. This implies that yield will always occur if the system is sufficiently large.
Solvation effects on the molecular 3s Rydberg state: AZAB/CYCLO octanes clustered with argon
NASA Astrophysics Data System (ADS)
Shang, Q. Y.; Moreno, P. O.; Li, S.; Bernstein, E. R.
1993-02-01
Two color, 1+1, mass resolved excitation spectroscopy (MRES) is used to obtain molecular Rydberg (3s←n) spectra of azabicyclo[2.2.2]octane (ABCO) and diazabicyclo[2.2.2]octane (DABCO) clustered with argon. Nozzle/laser timing delay studies are employed together with time-of-flight mass spectroscopy to identify cluster composition. Population depletion techniques are used to differentiate between clusters with the same mass, but different geometries. A Lennard-Jones 6-12 potential is used to model the intermolecular interactions and predict minimum energy cluster geometries and cluster binding energies. The experimental results are combined with the cluster geometry calculations to assign spectral features to specific cluster geometries. Three different excited state interactions are required to model the experimentally observed line shapes, spectral shifts, and cluster dissociation. The relationship between these model potentials and the cluster binding sites suggests that the form of the cluster intermolecular potential in the Rydberg excited state is dictated by the distance between the argon and chromophore atoms. A comparison of results for ABCO(Ar)1 and DABCO(Ar)1 leads to the conclusion that the nitrogen 3s Rydberg orbital in clusters of DABCO is delocalized.
Choudhury, Niharendu; Pettitt, Bernard M.
2005-05-15
We employ constant pressure molecular dynamics simulations to investigate the effects of solute size and solute-water dispersion interactions on the salvation behavior of nanoscopic hydrpophobic model solutes in water at normal temperature and pressure. The hydration behavior around a single planar atomic model solute as well as a pair of such solutes have been considered. The hydration water structure of a model nanoscopic solute with standard Lennard-Jones interaction is shown to be significantly different from that of their purely repulsive analogues. The density of water in the first salvation shell of a Lennard-Jones solute is much higher than that of bulk water and it remains almost unchanged with the increase of the solute dimensions from one to a few nanometers. On the other hand, for a purely repulsive analogue of the above model, solute hydration behavior shows a marked solute size dependence. The contact density of water in this case decreases with the increasing dimension of the solute. We also demonstrate the effect of solute-solvent attraction on the cavity formation in the inter solute region between two solutes with an inter solute separation of 6.8A, corresponding to the first solvent separated minimum in the free energy Profile as obtained in our earlier work.
Computer simulation of surface and film processes
NASA Technical Reports Server (NTRS)
Tiller, W. A.
1981-01-01
A molecular dynamics technique based upon Lennard-Jones type pair interactions is used to investigate time-dependent as well as equilibrium properties. The case study deals with systems containing Si and O atoms. In this case a more involved potential energy function (PEF) is employed and the system is simulated via a Monte-Carlo procedure. This furnishes the equilibrium properties of the system at its interfaces and surfaces as well as in the bulk.
Collision integrals for isotopic hydrogen molecules.
NASA Technical Reports Server (NTRS)
Brown, N. J.; Munn, R. J.
1972-01-01
The study was undertaken to determine the effects of reduced mass and differences in asymmetry on the collision integrals and thermal diffusion factors of isotopic hydrogen systems. Each system selected for study consisted of two diatoms, one in the j = 0 rotation state and the other in the j = 1 state. The molecules interacted with a Lennard-Jones type potential modified to include angular terms. A set of cross sections and collision integrals were obtained for each system.
NASA Astrophysics Data System (ADS)
Lynch, Gillian C.; Pettitt, B. Montgomery
1997-11-01
The extended system Hamiltonian for carrying out grand canonical ensemble molecular dynamics simulations is reformulated. This new Hamiltonian includes a generalized treatment of the reference state partition function of the total chemical potential that reproduces the ideal gas behavior and various previous partitionings of ideal and excess terms. Initial calculations are performed on a system of Lennard-Jones particles near the triple point and on liquid water at room temperature.
Analytical treatment of bosonic d-wave scattering in isotropic harmonic waveguides
NASA Astrophysics Data System (ADS)
Giannakeas, P.; Melezhik, V. S.; Schmelcher, P.
2012-04-01
We analyze d-wave resonances in atom-atom scattering in the presence of harmonic confinement by employing a higher-partial-wave pseudopotential. Analytical results for the scattering amplitude and transmission are obtained and compared to corresponding numerical ones, which employ the Lennard-Jones potential. Qualitative agreement is observed for weak confinement. For strong confinement the pseudopotential does not capture the s- and d-wave interference phenomena, yielding an asymmetric Fano profile for the transmission resonance.
Identification of structure in condensed matter with the topological cluster classification
NASA Astrophysics Data System (ADS)
Malins, Alex; Williams, Stephen R.; Eggers, Jens; Royall, C. Patrick
2013-12-01
We describe the topological cluster classification (TCC) algorithm. The TCC detects local structures with bond topologies similar to isolated clusters which minimise the potential energy for a number of monatomic and binary simple liquids with m ⩽ 13 particles. We detail a modified Voronoi bond detection method that optimizes the cluster detection. The method to identify each cluster is outlined, and a test example of Lennard-Jones liquid and crystal phases is considered and critically examined.
NASA Astrophysics Data System (ADS)
von Rudorff, Guido Falk; Wehmeyer, Christoph; Sebastiani, Daniel
2014-06-01
We adapt a swarm-intelligence-based optimization method (the artificial bee colony algorithm, ABC) to enhance its parallel scaling properties and to improve the escaping behavior from deep local minima. Specifically, we apply the approach to the geometry optimization of Lennard-Jones clusters. We illustrate the performance and the scaling properties of the parallelization scheme for several system sizes (5-20 particles). Our main findings are specific recommendations for ranges of the parameters of the ABC algorithm which yield maximal performance for Lennard-Jones clusters and Morse clusters. The suggested parameter ranges for these different interaction potentials turn out to be very similar; thus, we believe that our reported values are fairly general for the ABC algorithm applied to chemical optimization problems.
Venable, Richard M.; Luo, Yun; Gawrisch, Klaus; Roux, Benoît; Pastor, Richard W.
2013-01-01
Overbinding of ions to lipid head groups is a potentially serious artifact in simulations of charged lipid bilayers. In this study, the Lennard-Jones radii in the CHARMM force field for interactions of Na+ and lipid oxygen atoms of carboxyl, phosphate and ester groups were revised to match osmotic pressure data on sodium acetate, and electrophoresis data on palmitoyloleoyl phosphatidylcholine (POPC) vesicles. The new parameters were then validated by successfully reproducing previously published experimental NMR deuterium order parameters for dimyristoyl phosphatidylglycerol (DMPG) and newly obtained values for palmitoyloleoyl phosphatidylserine (POPS). Although the increases in Lennard-Jones diameters are only 0.02 to 0.12 Å, they are sufficient to reduce Na+ binding, and thereby increase surface areas per lipid by 5–10% compared with the unmodified parameters. PMID:23924441
Nonlinear dynamics of bi-layered graphene sheet, double-walled carbon nanotube and nanotube bundle
NASA Astrophysics Data System (ADS)
Gajbhiye, Sachin O.; Singh, S. P.
2016-05-01
Due to strong van der Waals (vdW) interactions, the graphene sheets and nanotubes stick to each other and form clusters of these corresponding nanostructures, viz. bi-layered graphene sheet (BLGS), double-walled carbon nanotube (DWCNT) and nanotube bundle (NB) or ropes. This research work is concerned with the study of nonlinear dynamics of BLGS, DWCNT and NB due to nonlinear interlayer vdW forces using multiscale atomistic finite element method. The energy between two adjacent carbon atoms is represented by the multibody interatomic Tersoff-Brenner potential, whereas the nonlinear interlayer vdW forces are represented by Lennard-Jones 6-12 potential function. The equivalent nonlinear material model of carbon-carbon bond is used to model it based on its force-deflection relation. Newmark's algorithm is used to solve the nonlinear matrix equation governing the motion of the BLGS, DWCNT and NB. An impulse and harmonic excitations are used to excite these nanostructures under cantilevered, bridged and clamped boundary conditions. The frequency responses of these nanostructures are computed, and the dominant resonant frequencies are identified. Along with the forced vibration of these structures, the eigenvalue extraction problem of armchair and zigzag NB is also considered. The natural frequencies and corresponding mode shapes are extracted for the different length and boundary conditions of the nanotube bundle.
Simulation optimization of spherical non-polar guest recognition by deep-cavity cavitands
NASA Astrophysics Data System (ADS)
Wanjari, Piyush P.; Gibb, Bruce C.; Ashbaugh, Henry S.
2013-12-01
Biomimetic deep-cavity cavitand hosts possess unique recognition and encapsulation properties that make them capable of selectively binding a range of non-polar guests within their hydrophobic pocket. Adamantane based derivatives which snuggly fit within the pocket of octa-acid deep cavity cavitands exhibit some of the strongest host binding. Here we explore the roles of guest size and attractiveness on optimizing guest binding to form 1:1 complexes with octa-acid cavitands in water. Specifically we simulate the water-mediated interactions of the cavitand with adamantane and a range of simple Lennard-Jones guests of varying diameter and attractive well-depth. Initial simulations performed with methane indicate hydrated methanes preferentially reside within the host pocket, although these guests frequently trade places with water and other methanes in bulk solution. The interaction strength of hydrophobic guests increases with increasing size from sizes slightly smaller than methane to Lennard-Jones guests comparable in size to adamantane. Over this guest size range the preferential guest binding location migrates from the bottom of the host pocket upwards. For guests larger than adamantane, however, binding becomes less favorable as the minimum in the potential-of-mean force shifts to the cavitand face around the portal. For a fixed guest diameter, the Lennard-Jones well-depth is found to systematically shift the guest-host potential-of-mean force to lower free energies, however, the optimal guest size is found to be insensitive to increasing well-depth. Ultimately our simulations show that adamantane lies within the optimal range of guest sizes with significant attractive interactions to match the most tightly bound Lennard-Jones guests studied.
Simulation optimization of spherical non-polar guest recognition by deep-cavity cavitands.
Wanjari, Piyush P; Gibb, Bruce C; Ashbaugh, Henry S
2013-12-21
Biomimetic deep-cavity cavitand hosts possess unique recognition and encapsulation properties that make them capable of selectively binding a range of non-polar guests within their hydrophobic pocket. Adamantane based derivatives which snuggly fit within the pocket of octa-acid deep cavity cavitands exhibit some of the strongest host binding. Here we explore the roles of guest size and attractiveness on optimizing guest binding to form 1:1 complexes with octa-acid cavitands in water. Specifically we simulate the water-mediated interactions of the cavitand with adamantane and a range of simple Lennard-Jones guests of varying diameter and attractive well-depth. Initial simulations performed with methane indicate hydrated methanes preferentially reside within the host pocket, although these guests frequently trade places with water and other methanes in bulk solution. The interaction strength of hydrophobic guests increases with increasing size from sizes slightly smaller than methane to Lennard-Jones guests comparable in size to adamantane. Over this guest size range the preferential guest binding location migrates from the bottom of the host pocket upwards. For guests larger than adamantane, however, binding becomes less favorable as the minimum in the potential-of-mean force shifts to the cavitand face around the portal. For a fixed guest diameter, the Lennard-Jones well-depth is found to systematically shift the guest-host potential-of-mean force to lower free energies, however, the optimal guest size is found to be insensitive to increasing well-depth. Ultimately our simulations show that adamantane lies within the optimal range of guest sizes with significant attractive interactions to match the most tightly bound Lennard-Jones guests studied. PMID:24359375
Energy behaviour for DNA translocation through graphene nanopores.
Alshehri, Mansoor H; Cox, Barry J; Hill, James M
2015-12-21
Nanoparticles have considerable promise for many applications in electronics, energy storage, bioscience and biotechnologies. Here we use applied mathematical modelling to exploit the basic principles of mechanics and the 6-12 Lennard-Jones potential function together with the continuum approach, which assumes that a discrete atomic structure can be replaced by an average constant atomic surface density of atoms that is assumed to be smeared over each molecule. We identify a circular hole in a graphene sheet as a nanopore and we consider the molecular interaction energy for both single-strand and double-strand DNA molecules assumed to move through the circular hole in a graphene sheet to determine the radius b of the hole that gives the minimum energy. By minimizing the interaction energy, we observe that the single-strand DNA and double-strand DNA molecules penetrate through a graphene nanopore when the pore radii b> 7.8Å and b> 12.7Å, respectively. Our results can be adopted to offer new applications in the atomic surface processes and electronic sensing. PMID:26449742
Oscillatory characteristics of metallic nanoparticles inside lipid nanotubes
NASA Astrophysics Data System (ADS)
Sadeghi, Fatemeh; Ansari, Reza; Darvizeh, Mansour
2015-12-01
This study is concerned with the oscillatory behavior of metallic nanoparticles, and in particular silver and gold nanoparticles, inside lipid nanotubes (LNTs) using the continuum approximation along with the 6-12 Lennard-Jones (LJ) potential function. The nanoparticle is modeled as a dense sphere and the LNT is assumed to be comprised of six layers including two head groups, two intermediate layers and two tail groups. To evaluate van der Waals (vdW) interactions, analytical expressions are first derived through undertaking surface and volume integrals which are then validated by a fully numerical scheme based on the differential quadrature (DQ) technique. Using the actual force distribution between the two interacting molecules, the equation of motion is directly solved utilizing the Runge-Kutta numerical integration scheme to arrive at the time history of displacement and velocity of the inner core. Also, a semi-analytical expression incorporating both geometrical parameters and initial conditions is introduced for the precise evaluation of oscillation frequency. A comprehensive study is conducted to gain an insight into the influences of nanoparticle radius, LNT length, head and tail group thicknesses and initial conditions on the oscillatory behavior of the metallic nanoparticles inside LNTs. It is found that the escape velocity and oscillation frequency of silver nanoparticles are higher than those of gold ones. It is further shown that the oscillation frequency is less affected by the tail group thickness when compared to the head group thickness.
NASA Astrophysics Data System (ADS)
Alshehri, Mansoor H.; Cox, Barry J.; Hill, James M.
2014-09-01
Fullerenes have attracted considerable attention in various areas of science and technology. Owing to their exceptional physical, chemical, and biological properties, they have many applications, particularly in cosmetic and medical products. Using the Lennard-Jones 6-12 potential function and the continuum approximation, which assumes that intermolecular interactions can be approximated by average atomic surface densities, we determine the binding energies of a C60 fullerene with respect to both single-strand and double-strand DNA molecules. We assume that all configurations are in a vacuum and that the C60 fullerene is initially at rest. Double integrals are performed to determine the interaction energy of the system. We find that the C60 fullerene binds to the double-strand DNA molecule, at either the major or minor grooves, with binding energies of -4.7 eV or -2.3 eV, respectively, and that the C60 molecule binds to the single-strand DNA molecule with a binding energy of -1.6 eV. Our results suggest that the C60 molecule is most likely to be linked to the major groove of the dsDNA molecule.
Modeling Composites of Multi-Walled Carbon Nanotubes in Polycarbonate
NASA Astrophysics Data System (ADS)
Jindal, Prashant; Goyal, Meenakshi; Kumar, Navin
2013-10-01
High strain rate experiments performed on multi-walled carbon nanotubes, polycarbonate composites (MWCNT-PC) have exhibited enhanced impact resistance under a dynamic strain rate of nearly 2500/s with composition of only 0.5 to 2.0% multi-walled carbon nanotubes (MWCNTs) in pure polycarbonate (PC). Similarly, hardness and elastic modulus under static loads resulted in a significant increase, depending upon the composition of MWCNTs in PC. The present work aims to analyze these results by correlating the data to fit expressions in generalizing the behavior of MWCNTs composition for MWCNT-PC composites under both static and impact loads. As a result, we found that an optimum composition of 2.1 weight % of MWCNTs exhibits maximum stress resistance within elastic range under strain rates of nearly 2500/s for MWCNT-PC composites. The composition of MWCNTs plays a crucial role in maximizing modification of static and dynamic impact-based mechanical properties of polycarbonates. Further, a simple model based on Lennard-Jones 6-12 atom-atom based potential is formulated and used to compute preliminary estimates of static properties of pure as well as composite PC with the aim to modify this in subsequent approaches.
Ab initio parameterization of YFF1, a universal force field for drug-design applications.
Yakovenko, Olexandr Ya; Li, Yvonne Y; Oliferenko, Alexander A; Vashchenko, Ganna M; Bdzhola, Volodymyr G; Jones, Steven J M
2012-02-01
The YFF1 is a new universal molecular mechanic force field designed for drug discovery purposes. The electrostatic part of YFF1 has already been parameterized to reproduce ab initio calculated dipole and quadrupole moments. Now we report a parameterization of the van der Waals interactions (vdW) for the same atom types that were previously defined. The 6-12 Lennard-Jones potential terms were parameterized against homodimerization energies calculated at the MP2/6-31 G level of theory. The Boys-Bernardi counterpoise correction was employed to account for the basis-set superposition error. As a source of structural information we used about 2,400 neutral compounds from the ZINC2007 database. About 6,600 homodimeric configurations were generated from this dataset. A special "closure" procedure was designed to accelerate the parameters fitting. As a result, dimerization energies of small organic compounds are reproduced with an average unsigned error of 1.1 kcal mol(-1). Although the primary goal of this work was to parameterize nonbonded interactions, bonded parameters were also derived, by fitting to PM6 semiempirically optimized geometries of approximately 20,000 compounds. PMID:21562826
Role of side-chain interactions on the formation of α -helices in model peptides
NASA Astrophysics Data System (ADS)
Mahmoudinobar, Farbod; Dias, Cristiano L.; Zangi, Ronen
2015-03-01
The role played by side-chain interactions on the formation of α -helices is studied using extensive all-atom molecular dynamics simulations of polyalanine-like peptides in explicit TIP4P water. The peptide is described by the OPLS-AA force field except for the Lennard-Jones interaction between Cβ-Cβ atoms, which is modified systematically. We identify values of the Lennard-Jones parameter that promote α -helix formation. To rationalize these results, potentials of mean force (PMF) between methane-like molecules that mimic side chains in our polyalanine-like peptides are computed. These PMF exhibit a complex distance dependence where global and local minima are separated by an energy barrier. We show that α -helix propensity correlates with values of these PMF at distances corresponding to Cβ-Cβ of i -i +3 and other nearest neighbors in the α -helix. In particular, the set of Lennard-Jones parameters that promote α -helices is characterized by PMF that exhibit a global minimum at distances corresponding to i -i +3 neighbors in α -helices. Implications of these results are discussed.
X-ray spectrum in the range (6-12) A emitted by laser-produced plasma of samarium
Louzon, Einat; Henis, Zohar; Levi, Izhak; Hurvitz, Gilad; Ehrlich, Yosi; Fraenkel, Moshe; Maman, Shlomo; Mandelbaum, Pinchas
2009-05-15
A detailed analysis of the x-ray spectrum emitted by laser-produced plasma of samarium (6-12 A) is presented, using ab initio calculations with the HULLAC relativistic code and isoelectronic considerations. Resonance 3d-nf (n=4 to 7), 3p-4d, 3d-4p, and 3p-4s transitions in Ni samarium ions and in neighboring ionization states (from Mn to Zn ions) were identified. The experiment results show changes in the fine details of the plasma spectrum for different laser intensities.
Jespersen, E; Rexen, C T; Franz, C; Møller, N C; Froberg, K; Wedderkopp, N
2015-04-01
The objectives of this prospective school cohort study were to describe the epidemiology of diagnosed musculoskeletal extremity injuries and to estimate the injury incidence rates in relation to different settings, different body regions and injury types. In all, 1259 schoolchildren, aged 6-12, were surveyed weekly during 2.5 years using a new method of automated mobile phone text messaging asking questions on the presence of any musculoskeletal problems. All injuries were clinically diagnosed. Physical activity was measured from text messaging and accelerometers. A total number of 1229 injuries were diagnosed; 180 injuries in the upper extremity and 1049 in the lower extremity, with an overall rate of 1.59 injuries per 1000 physical activity units [95% confidence interval (CI) 1.50-1.68]. Upper extremities accounted for a rate of 0.23 (95% CI 0.20-0.27) and lower extremities accounted for 1.36 (95% CI 1.27-1.44). This study has added a wide overall perspective to the area concerning incidence and incidence rates of musculoskeletal extremity injuries in schoolchildren aged 6-12 years, including severe and less severe, traumatic, and overuse injuries. The understanding of injury epidemiology in children is fundamental to the acknowledgement and insurance of the appropriate prevention and treatment. PMID:24472003
Lee, Aaron Y; Lee, Cecilia S; Butt, Thomas; Xing, Wen; Johnston, Robert L; Chakravarthy, Usha; Egan, Catherine; Akerele, Toks; McKibbin, Martin; Downey, Louise; Natha, Salim; Bailey, Clare; Khan, Rehna; Antcliff, Richard; Varma, Atul; Kumar, Vineeth; Tsaloumas, Marie; Mandal, Kaveri; Liew, Gerald; Keane, Pearse A; Sim, Dawn; Bunce, Catey; Tufail, Adnan
2015-01-01
Background/aims To study the effectiveness and clinical relevance of eyes treated with good (better than 6/12 or >70 Early Treatment Diabetic Retinopathy Study letters) visual acuity (VA) when initiating treatment with ranibizumab for neovascular age-related macular degeneration (nAMD) in the UK National Health Service. Currently eyes with VA better than (>) 6/12 are not routinely funded for therapy. Methods Multicentre national nAMD database study on patients treated 3–5 years prior to the analysis. Anonymised structured data were collected from 14 centres. The primary outcome was the mean VA at year 1, 2 and 3. Secondary measures included the number of clinic visits and injections. Results The study included 12 951 treatment-naive eyes of 11 135 patients receiving 92 976 ranibizumab treatment episodes. A total of 754 patients had baseline VA better than 6/12 and at least 1-year of follow up. Mean VA of first treated eyes with baseline VA>6/12 at year 1, 2, 3 were 6/10, 6/12, 6/15, respectively and those with baseline VA 6/12 to >6/24 were 6/15, 6/17, 6/20, respectively (p values <0.001 for comparing differences between 6/12 and 6/12–6/24 groups). For the second eyes with baseline VA>6/12, mean VA at year 1, 2, 3 were 6/9, 6/9, 6/10 and those with baseline VA 6/12 to >6/24 were 6/15, 6/15, 6/27, respectively (p values <0.001–0.005). There was no significant difference in the average number of clinic visits or injections between those with VA better and worse than 6/12. Conclusions All eyes with baseline VA>6/12 maintained better mean VA than the eyes with baseline VA 6/12 to >6/24 at all time points for at least 2 years. The significantly better visual outcome in patients who were treated with good baseline VA has implications on future policy regarding the treatment criteria for nAMD patients’ funding. PMID:25680619
Hg196 and the ``magical quartet'' of the extended Uν(6/12)⊗Uπ(6/4) supersymmetry
NASA Astrophysics Data System (ADS)
Bernards, C.; Heinze, S.; Jolie, J.; Albers, M.; Fransen, C.; Radeck, D.
2010-02-01
We present the results of a γγ angular correlation experiment investigating the nucleus Hg196 and compare these with a theoretical description of Hg196 within the Uν(6/12)⊗Uπ(6/4) extended supersymmetry. To populate excited Hg196 states, we used the Cologne FN Tandem accelerator inducing the reaction Pt194(α,2n)Hg196 and analyzed the γ decays of levels up to an excitation energy of 2.4 MeV with the HORUS cube spectrometer. The new results on this mercury isotope allow a comparison between the experimental data and the supersymmetrical predictions and show good agreement. This way we can add Hg196 as a fifth supermultiplet member to the so-called magical quartet consisting of Pt194,195 and Au195,196.
Back injuries in a cohort of schoolchildren aged 6-12: A 2.5-year prospective study.
Franz, C; Jespersen, E; Rexen, C T; Leboeuf-Yde, C; Wedderkopp, N
2016-08-01
The aims of this prospective school cohort study were to describe the epidemiology of diagnosed back pain in childhood, classified as either nontraumatic or traumatic back injury, and to estimate the association with physical activity in different settings. Over 2.5 years, 1240 children aged 6-12 years were surveyed weekly using mobile text messages to ask about the presence or absence of back pain. Pain was clinically diagnosed and injuries were classified using the International Classification of Diseases version 10. Physical activity data were obtained from text messages and accelerometers. Of the 315 back injuries diagnosed, 186 injuries were nontraumatic and 129 were traumatic. The incidence rate ratio was 1.5 for a nontraumatic back injury compared with a traumatic injury. The overall estimated back injury incidence rate was 0.20 per 1000 physical activity units (95% confidence interval 0.18-0.23). The back injury incidence rates were higher for sports when exposure per 1000 physical activity units was taken into consideration and especially children horse-riding had a 40 times higher risk of sustaining a traumatic back injury compared to the risk during non-organized leisure time physical activity. However, the reasonably low injury incidence rates support the recommendations of children continuously being physically active. PMID:26130046
Zhang, Shulan; Wu, Ziyan; Luo, Jing; Ding, Xuefeng; Hu, Chaojun; Li, Ping; Deng, Chuiwen; Zhang, Fengchun; Qian, Jiaming; Li, Yongzhe
2015-01-01
Abstract The need for reliable biomarkers for distinguishing Crohn disease (CD) from ulcerative colitis (UC) is increasing. This study aimed at evaluating the diagnostic potential of anti-GP2 antibodies as a biomarker in Chinese patients with CD. In addition, a variety of autoantibodies, including anti-saccharomyces cerevisiae antibodies (ASCA), perinuclear anti-neutrophil cytoplasmic antibodies (PANCA), anti-intestinal goblet cell autoantibodies (GAB), and anti-pancreatic autoantibodies (PAB), were evaluated. A total of 91 subjects were prospectively enrolled in this study, including 35 patients with CD, 35 patients with UC, 13 patients with non-IBD gastrointestinal diseases as disease controls (non-IBD DC), and 8 healthy controls (HC). The diagnosis of IBD was determined based on the Lennard-Jones criteria, and the clinical phenotypes of the IBD patients were determined based on the Montreal Classification. Anti-GP2 IgG antibodies were significantly elevated in patients with CD, compared with patients with UC (P = 0.0038), HC (P = 0.0055), and non-IBD DC (P = 0.0063). The prevalence of anti-GP2 IgG, anti-GP2 IgA and anti-GP2 IgA, or IgG antibodies in patients with CD was 40.0%, 37.1%, and 54.3%, respectively, which were higher than those in non-IBD DC (anti-GP2 IgG, 15.4%; anti-GP2 IgA, 7.7%; and anti-GP2 IgA or IgG, 23.1%) and those in patients with UC (anti-GP2 IgG, 11.4%; anti-GP2 IgA, 2.9%; and anti-GP2 IgA or IgG, 14.3%). For distinguishing CD from UC, the sensitivity, specificity, positive predictive value (PPV) and positive likelihood ratios (LR+) were 40%, 88.6%, 77.8%, and 3.51 for anti-GP2 IgG, 37.1%, 97.1%, 92.9%, and 13.0 for anti-GP2 IgA, and 54.3%, 85.3%, 79.2%, and 3.69 for anti-GP2 IgA or IgG. For CD diagnosis, the combination of anti-GP2 antibodies with ASCA IgA increased the sensitivity to 68.6% with moderate loss of specificity to 74.3%. Spearman's rank of order revealed a significantly positive correlation of anti-GP2 IgG with
NASA Astrophysics Data System (ADS)
Yajima, Hidenobu; Shlosman, Isaac; Romano-Díaz, Emilio; Nagamine, Kentaro
2015-07-01
We use high-resolution zoom-in cosmological simulations of galaxies of Romano-Díaz et al., post-processing them with a panchromatic three-dimensional radiation transfer code to obtain the galaxy UV luminosity function (LF) at z ≃ 6-12. The galaxies are followed in a rare, heavily overdense region within a ˜5σ density peak, which can host high-z quasars, and in an average density region, down to the stellar mass of Mstar ˜ 4 × 107 M⊙. We find that the overdense regions evolve at a substantially accelerated pace - the most massive galaxy has grown to Mstar ˜ 8.4 × 1010 M⊙ by z = 6.3, contains dust of Mdust ˜ 4.1 × 108 M⊙, and is associated with a very high star formation rate, SFR ˜ 745 M⊙ yr- 1. The attained SFR-Mstar correlation results in the specific SFR slowly increasing with Mstar. Most of the UV radiation in massive galaxies is absorbed by the dust, its escape fraction fesc is low, increasing slowly with time. Galaxies in the average region have less dust, and agree with the observed UV LF. The LF of the overdense region is substantially higher, and contains much brighter galaxies. The massive galaxies are bright in the infrared (IR) due to the dust thermal emission, with LIR ˜ 3.7 × 1012 L⊙ at z = 6.3, while LIR < 1011 L⊙ for the low-mass galaxies. Therefore, ALMA can probe massive galaxies in the overdense region up to z ˜ 10 with a reasonable integration time. The UV spectral properties of discy galaxies depend significantly upon the viewing angle. The stellar and dust masses of the most massive galaxy in the overdense region are comparable to those of the sub-millimetre galaxy found by Riechers et al. at z = 6.3, while the modelled SFR and the sub-millimetre flux fall slightly below the observed one. Statistical significance of these similarities and differences will only become clear with the upcoming ALMA observations.
Structure and stability of small Li2 +(X2Σ+ g )-Xen (n = 1-6) clusters
NASA Astrophysics Data System (ADS)
Saidi, Sameh; Ghanmi, Chedli; Berriche, Hamid
2014-04-01
We have studied the structure and stability of the Li2 +(X2Σ+ g )Xe n ( n = 1-6) clusters for special symmetry groups. The potential energy surfaces of these clusters, are described using an accurate ab initio approach based on non-empirical pseudopotential, parameterized l-dependent polarization potential and analytic potential forms for the Li+Xe and Xe-Xe interactions. The pseudopotential technique has reduced the number of active electrons of Li2 +(X2Σ+ g )-Xe n ( n = 1-6) clusters to only one electron, the Li valence electron. The core-core interactions for Li+Xe are included using accurate CCSD(T) potential fitted using the analytical form of Tang and Toennies. For the Xe-Xe potential interactions we have used the analytical form of Lennard Jones (LJ6 - 12). The potential energy surfaces of the Li2 +(X2Σ+ g )Xe n ( n = 1-6) clusters are performed for a fixed distance of the Li2 +(X2Σ+ g ) alkali dimer, its equilibrium distance. They are used to extract information on the stability of the Li2 +(X2Σ+ g Xe n ( n = 1-6) clusters. For each n, the stability of the different isomers is examined by comparing their potential energy surfaces. Moreover, we have determined the quantum energies ( D 0), the zero-point-energies (ZPE) and the ZPE%. To our best knowledge, there are neither experimental nor theoretical works realized for the Li2 +(X2Σ+ g Xe n ( n = 1-6) clusters, our results are presented for the first time.
ERIC Educational Resources Information Center
National Diffusion Network (DHEW/OE), Washington, DC.
This guide is correlated to the PASS (Priority Academic Student Skills) objectives for Oklahoma history in grades 6-12. The guide was developed to aid in the teaching of the PASS objectives by identifying primary sources, audiovisual materials, field trips and scholarly materials that relate to each objective. The guide is divided into seven…
Wei, Chunnan; Huang, Wenmin; Xing, Xiaoting; Dong, Shouliang
2010-09-01
[Tyr(6)]-gamma2-MSH(6-12) with a short effecting time of about 20 min is one of the most potent rMrgC receptor agonists. To possibly increase its potency and metabolic stability, a series of analogues were prepared by replacing the Tyr(6) residue with the non-canonical amino acids 3-(1-naphtyl)-L-alanine, 4-fluoro-L-phenylalanine, 4-methoxy-L-phenylalanine and 3-nitro-L-tyrosine. Dose-dependent nociceptive assays performed in conscious rats by intrathecal injection of the MSH peptides showed [Tyr(6)]-gamma2-MSH(6-12) hyperalgesic effects at low doses (5-20 nmol) and analgesia at high doses (100-200 nmol). This analgesic activity is fully reversed by the kyotorphin receptor-specific antagonist Leu-Arg. For the two analogues containing in position 6, 4-fluoro-L-phenylalanine and 3-nitro-L-tyrosine, a hyperalgesic activity was not observed, while the 3-(1-naphtyl)-L-alanine analogue at 10 nmol dose was found to induce hyperalgesia at a potency very similar to gamma2-MSH(6-12), but with longer duration of the effect. Finally, the 4-methoxy-L-phenylalanine analogue (0.5 nmol) showed greatly improved hyperalgesic activity and prolonged effects compared to the parent [Tyr(6)]-gamma2-MSH(6-12) compound. PMID:20629198
ERIC Educational Resources Information Center
Ekinci, Hatice
2014-01-01
This study was conducted in order to develop a valid and reliable scale that can be used in measuring self-efficacy of candidate music teachers in rendering piano education to children of 6-12 years. To this end, a pool of 51 items was created by using the literature, and taking the opinions of piano professors and piano instructors working with…
Interlayer correlation between two 4He monolayers adsorbed on both sides of α -graphyne
NASA Astrophysics Data System (ADS)
Ahn, Jeonghwan; Park, Sungjin; Lee, Hoonkyung; Kwon, Yongkyung
2015-07-01
Path-integral Monte Carlo calculations have been performed to study the 4He adsorption on both sides of a single α -graphyne sheet. For investigation of the interlayer correlation between the upper and the lower monolayers of 4He adatoms, the 4He-substrate interaction is described by the sum of the 4He-C interatomic pair potentials for which we use both Lennard-Jones and Yukawa-6 anisotropic potentials. When the lower 4He layer is a C4 /3 commensurate solid, the upper-layer 4He atoms are found to form a kagome lattice structure at a Mott-insulating density of 0.0706 Å-2 and a commensurate solid at an areal density of 0.0941 Å-2 for both substrate potentials. The correlation between upper- and lower-layer pseudospins, which were introduced in Kwon et al. [Phys. Rev. B 88, 201403(R) (2013)], 10.1103/PhysRevB.88.201403 for two degenerate configurations of three 4He atoms in a hexagonal cell, depends on the substrate potential used; with the substrate potential based on the anisotropic Yukawa-6 pair potentials, the Ising pseudospins of both 4He layers are found to be antiparallel to each other whereas the parallel and antiparallel pseudospin alignments between the two 4He layers are nearly degenerate with the Lennard-Jones potentials. This is attributed to the difference in the interlayer distance, which is ˜4 Å with the Yukawa-6 substrate potential but as large as ˜4.8 Å with the Lennard-Jones potential.
Elastic Scattering of Ultracold 133Cs and 85Rb Atoms in Triplet State
NASA Astrophysics Data System (ADS)
Sun, Jin-Feng; Hu, Qiu-Bo; Zhu, Zun-Lue; Wang, Xiao-Fei; Zhang, Ji-Cai
2007-06-01
Elastic scattering properties of the ultracold interaction for the triplet state of 133Cs and 85Rb atoms are studied using two kinds of potentials by the same phase Φ. One is the interpolation potential, and another is Lennard-Jones potential (LJ12,6). The radial Schrödinger equation is also solved using two computational methods, the semiclassical method (WKB), and the Numerov method. Our results are found to be in an excellent agreement with the more recent theoretical values. It shows that the two potentials and methods are applicable for studying ultracold collisions between the mixing alkali atoms.
Straight Talk about Risks: A Pre-K-12 Curriculum for Preventing Gun Violence. Grades 6-12.
ERIC Educational Resources Information Center
Center To Prevent Handgun Violence, Washington, DC.
Straight Talk about Risks (STAR) is a pre-kindergarten through grade 12 curriculum designed to reduce the potential for children and teens to be injured or killed in gunfire. STAR is based on sound prevention practice developed from a pilot project in Dade County (Florida). The flexible format allows activities to fit into a 3-week classroom unit…
Elastic scattering and total reaction cross sections for the B8, Be7, and Li6 +12C systems
NASA Astrophysics Data System (ADS)
Barioni, A.; Zamora, J. C.; Guimarães, V.; Paes, B.; Lubian, J.; Aguilera, E. F.; Kolata, J. J.; Roberts, A. L.; Becchetti, F. D.; Villano, A.; Ojaruega, M.; Jiang, H.
2011-07-01
Angular distributions for the elastic scattering of B8, Be7, and Li6 on a C12 target have been measured at Elab=25.8, 18.8, and 12.3 MeV, respectively. The analyses of these angular distributions have been performed in terms of the optical model using Woods-Saxon and double-folding type potentials. The effect of breakup in the elastic scattering of 8B+12C is investigated by performing coupled-channels calculations with the continuum discretized coupled-channel method and cluster-model folding potentials. Total reaction cross sections were deduced from the elastic-scattering analysis and compared with published data on elastic scattering of other weakly and tightly bound projectiles on C12, as a function of energy. With the exception of He4 and O16, the data can be described using a universal function for the reduced cross sections.
Effective protein-protein interaction from structure factor data of a lysozyme solution
Abramo, M. C.; Caccamo, C.; Costa, D.; Ruberto, R.; Wanderlingh, U.; Cavero, M.; Pellicane, G.
2013-08-07
We report the determination of an effective protein-protein central potential for a lysozyme solution, obtained from the direct inversion of the total structure factor of the system, as extracted from small angle neutron scattering. The inversion scheme rests on a hypernetted-chain relationship between the effective potential and the structural functions, and is preliminarily tested for the case of a Lennard-Jones interaction. The characteristics of our potential are discussed in comparison with current models of effective interactions in complex fluids. The phase behavior predictions are also investigated.
NASA Astrophysics Data System (ADS)
Benguria, R.; Dolbeault, J.; Monneau, R.
2009-01-01
We consider deformations in ℝ3 of an infinite linear chain of atoms where each atom interacts with all others through a two-body potential. We compute the effect of an external force applied to the chain. At equilibrium, the positions of the particles satisfy an Euler-Lagrange equation. For large classes of potentials, we prove that every solution is well approximated by the solution of a continuous model when applied forces and displacements of the atoms are small. We establish an error estimate between the discrete and the continuous solution based on a Harnack lemma of independent interest. Finally we apply our results to some Lennard-Jones potentials.
Colloids as model systems for liquid undercooled metals
NASA Astrophysics Data System (ADS)
Wette, Patrick; Klassen, Ina; Holland-Moritz, Dirk; Palberg, Thomas; Roth, Stephan V.; Herlach, Dieter M.
2009-01-01
Charged colloidal particles interact via a hard core Yukawa potential, while isotropic Lennard-Jones-like potentials are frequently used as pair potentials in metals. We present measurements of the structure factor of shear molten monodisperse colloids and molten metals using ultrasmall-angle x-ray scattering and elastic neutron scattering, respectively. In both systems data analysis gives evidence of fivefold-symmetric short-range order becoming more pronounced with increasing deviations from equilibrium. The experiments demonstrate that in both systems topological effects control ordering in the melt state.
Thermal motion in proteins: Large effects on the time-averaged interaction energies
NASA Astrophysics Data System (ADS)
Goethe, Martin; Fita, Ignacio; Rubi, J. Miguel
2016-03-01
As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.
ERIC Educational Resources Information Center
DiIorio, Colleen K.; Pluhar, Erika I.; Pines, Kathy; Jennings, Tanya
2006-01-01
In this article, we describe the Set the P.A.C.E.! (Parents And Children Empowered) curriculum designed for mothers of children 6-12 years of age. The development of the curriculum was part of a research study to test an intervention to enhance the mother's role in promoting resilience among 6- to 12-year-old children and to reduce the risk of…
NASA Astrophysics Data System (ADS)
Sadeghi, F.; Ansari, R.; Darvizeh, M.
2016-02-01
Research concerning the fabrication of nano-oscillators with operating frequency in the gigahertz (GHz) range has become a focal point in recent years. In this paper, a new type of GHz oscillators is introduced based on a C60 fullerene inside a cyclic peptide nanotube (CPN). To study the dynamic behavior of such nano-oscillators, using the continuum approximation in conjunction with the 6-12 Lennard-Jones (LJ) potential function, analytical expressions are derived to determine the van der Waals (vdW) potential energy and interaction force between the two interacting molecules. Employing Newton's second law, the equation of motion is solved numerically to arrive at the telescopic oscillatory motion of a C60 fullerene inside CPNs. It is shown that the fullerene molecule exhibits different kinds of oscillation inside peptide nanotubes which are sensitive to the system parameters. Furthermore, for the precise evaluation of the oscillation frequency, a novel semi-analytical expression is proposed based on the conservation of the mechanical energy principle. Numerical results are presented to comprehensively study the effects of the number of peptide units and initial conditions (initial separation distance and velocity) on the oscillatory behavior of C60 -CPN oscillators. It is found out that for peptide nanotubes comprised of one unit, the maximum achievable frequency is obtained when the inner core oscillates with respect to its preferred positions located outside the tube, while for other numbers of peptide units, such frequency is obtained when the inner core oscillates with respect to the preferred positions situated in the space between the two first or the two last units. It is further found out that four peptide units are sufficient to obtain the optimal frequency.
NASA Astrophysics Data System (ADS)
Kucukkal, Mustafa Umut
Molecular Dynamics (MD) is an effective method to study diverse systems to gain atomistic level details from the trajectories of particles in the system. MD require a potential which describes the interaction of the particles within the system, which is then used to solve Newton's equation of motion to obtain the trajectories of the particles. For an accurate simulation of a system, an appropriate potential should be used for the MD simulations. The Adaptive Interactive Reactive Empirical Bond Order (AIREBO) potential is a promising potential for MD simulations of systems involving bond breakage or formation [1, 2]. The AIREBO potential is a Tersoff-style bond order potential which adds LJ and torsional interactions to REBO potential developed by Brenner et al [3, 4]. Currently, the AIREBO potential is well parameterized to study carbonaceous and hydrocarbon systems. In the first part of this study, the AIREBO potential is used in MD simulations to study the welding of single wall carbon nanotubes (SWCNTs) through Ar bombardment. SWCNTs have unique electronic properties which make them an appropriate candidate to use in nanoscale transistor and nanocomputer studies. An optimum conductivity through SWCNTs is required for these applications in electronic devices and it is achieved by the bonding arrangements of the carbon atoms in the junction area. This spatial bonding between SWCNTs can be obtained by various experimental methods such as electron beam radiation, fast atom bombardment and chemical vapor deposition. This study focuses on simulating Ar bombardment over cross junction of two SWCNTs placed on an imaginary Lennard-Jones surface perpendicular to each other. The cross junction area of SWCNTs was bombarded with Ar atoms of various kinetic energies in microcanical ensemble which is followed by annealing at various temperatures. The main goal of this study is to find optimum conditions to obtain the highest number of connections between the SWCNTs and the
Theoretical studies of "stabilizing" behavior about carbon nanotubes under the electrostatic force.
Zhao, Hong-Wei; Hu, Li-Chun; Chang, Chun-Rui
2013-04-01
We study the dispersion and stability of carbon nanotube (CNT) suspensions under the electrostatic interactions. The potential energies of van der Waals (vdW) attractions between the CNT themselves are obtained on the continuum Lennard-Jones (LJ) model. The potential energies of electrostatic repulsions are based upon the Yukawa-segment model. We explore the overall interactions mediated by the vdW force and the electrostatic force between two identical, parallel CNTs. Consequently, we preliminarily confirm the accuracy and reliability of the electrostatic model. PMID:23763212
A calculation of the diffusion energies for adatoms on surfaces of F.C.C. metals
NASA Technical Reports Server (NTRS)
Halicioglu, T.; Pound, G. M.
1979-01-01
The activation energies for diffusion were determined for gold, platinum and iridium adatoms on plane and plane PT surfaces and were found to be in good agreement with the measurements reported by Bassett and Webber. The Lennard-Jones pair potentials were used to model the interatomic forces, and relaxation of the substrate atoms in near proximity to the adatom was considered in detail. The present calculations clarify the mechanism of the observed two-dimensional diffusion of platinum and iridium atoms on a plane PT surface. The results are compared with those obtained using Morse potential functions and different relaxation techniques.
Stoessel, J.P.; Wolynes, P.G.
1989-01-01
With analogy to the ''highly accurate'' summation of cluster diagrams for hard sphere fluids a la Carnahan-Starling, we present a simple, real space free energy density functional for arbitrary potential systems, based on the generalization of the second virial coefficient to inhomogeneous systems which, when applied to hard sphere, soft-sphere, and Lennard-Jones freezing, yield melting characteristics in remarkable agreement with experiment. Implications for the liquid-glass transition in all three potential systems are also presented. 45 refs., 7 figs., 1 tab.
One-dimensional models and thermomechanical properties of solids
NASA Astrophysics Data System (ADS)
de Gregorio, Paolo; Rondoni, Lamberto; Bonaldi, Michele; Conti, Livia
2011-12-01
We use open-ended chains of oscillators, like those introduced by Fermi, Pasta, and Ulam, to mimic thermomechanical properties of crystalline solids, such as thermal expansion and the change of elasticity and quality factors with temperature. We employ molecular dynamics and theoretical arguments, separately. Features of real solids are reproduced, such as the positiveness of the coefficient of thermal expansion and the decrease of the modulus of elasticity and of the quality factor with temperature. The results depend strongly on the interparticle potential at energy levels much higher than the average energy of the chain, with the Lennard-Jones potential yielding the most realistic cases.
Free energy evaluation in polymer translocation via Jarzynski equality
NASA Astrophysics Data System (ADS)
Mondaini, Felipe; Moriconi, L.
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.
Fractures in heterogeneous two-dimensional systems
NASA Astrophysics Data System (ADS)
Politi, Antonio; Zei, Maria
2001-05-01
A two-dimensional triangular lattice with bond disorder is used as a testing ground for fracture behavior in heterogeneous materials in strain-controlled conditions. Simulations are performed with two interaction potentials (harmonic and Lennard-Jones types) and different breaking thresholds. We study the strain range where the fracture progressively develops from the first to the last breakdown. Scaling properties with the lattice size are investigated: no qualitative difference is found between the two interaction potentials. Clustering properties of the broken bonds are also studied by grouping them into disjoint sets of connected bonds. Finally, the role of kinetic energy is analyzed by comparing overdamped with dissipationless dynamics.
Two-Dimensional Crystal Structure Formed by Two Components of DNA Nanoparticles on a Substrate
NASA Astrophysics Data System (ADS)
Katsuno, Hiroyasu; Maegawa, Yuya; Sato, Masahide
2016-07-01
We study the two-dimensional crystal structure of two components of DNA nanoparticles on a substrate by Brownian dynamics simulation. We use the Lennard-Jones potential as the interaction potential between particles and assume that the interaction length between different types of particles, σAB, is smaller than that between the same types of particles, σ. Two types of particles form an alloy structure. With decreasing σAB/σ, the crystal structure changes from a triangular lattice, to a square lattice, a honeycomb lattice, a rectangular lattice, and a triangular lattice.
Size dependence of cavity volume: a molecular dynamics study.
Patel, Nisha; Dubins, David N; Pomès, Régis; Chalikian, Tigran V
2012-02-01
Partial molar volume, V°, has been used as a tool to sample solute hydration for decades. The efficacy of volumetric investigations of hydration depends on our ability to reliably discriminate between the cavity, V(C), and interaction, V(I), contributions to the partial molar volume. The cavity volume, V(C), consists of the intrinsic volume, V(M), of a solute molecule and the thermal volume, V(T), with the latter representing the volume of the effective void created around the solute. In this work, we use molecular dynamics simulations in conjunction with the Kirkwood-Buff theory to compute the partial molar volumes for organic solutes of varying sizes in water. We perform our computations using the Lennard-Jones and Coulombic pair potentials as well as truncated potentials which contain only the Lennard-Jones but not the Coulombic contribution. The partial molar volume computed with the Lennard-Jones potentials in the absence of the Coulombic term nearly coincides with the cavity volume, V(C). We determine the thermal volume, V(T), for each compound by subtracting its van der Waals volume, V(W), from V(C). Finally, we apply the spherical approximation of solute geometry to evaluate the thickness of the thermal volume, δ. Our results reveal an increase in the thickness of thermal volume, δ, with an increase in the size of the solute. This finding may be related to dewetting of large nonpolar solutes and the concomitant increase in the compressibility of water of hydration. PMID:22133917
The influence of multiple frequency perturbations on particle chaotization in a cell
NASA Astrophysics Data System (ADS)
Guzev, M. A.; Izrailsky, Yu. G.; Koshel, K. V.; Dyskin, A. V.; Pasternak, E.
2015-06-01
We consider the onset of chaotic regimes in a phase space of a particle interacting with its neighbors by means of Lennard-Jones potential. It was shown, that in the case of a single frequency cell excitation, the chaotization onset is of a threshold type in both amplitude and frequency. We propose a way to form a global chaos based upon the use of multi-frequency external excitation. The numerical experiments and asymptotic analysis show that in this case the global chaotization starts at excitation amplitudes and frequencies far below their critical values for single-frequency excitation.
Amorphization in the vicinity of a grain boundary: A molecular-dynamics approach
NASA Astrophysics Data System (ADS)
Gutiérrez, Gonzalo; Kiwi, Miguel; Ramírez, Ricardo
1996-10-01
The dynamics of the melting process of a binary system (such as the one formed by Co and Zr) that contains a grain boundary is investigated by means of molecular dynamics using Lennard-Jones-type interatomic potentials. The evolution of the disordering sequence, as the temperature is increased, is quantitatively studied and graphically illustrated. It is found that the presence of the defect acts like a seed for the disordering, with the genesis of an intermediate amorphous phase. The latter is properly identified and characterized and constitutes an intermediate stage before the proper melting process sets in.
Three-dimensional "Mercedes-Benz" model for water.
Dias, Cristiano L; Ala-Nissila, Tapio; Grant, Martin; Karttunen, Mikko
2009-08-01
In this paper we introduce a three-dimensional version of the Mercedes-Benz model to describe water molecules. In this model van der Waals interactions and hydrogen bonds are given explicitly through a Lennard-Jones potential and a Gaussian orientation-dependent terms, respectively. At low temperature the model freezes forming Ice-I and it reproduces the main peaks of the experimental radial distribution function of water. In addition to these structural properties, the model also captures the thermodynamical anomalies of water: The anomalous density profile, the negative thermal expansivity, the large heat capacity, and the minimum in the isothermal compressibility. PMID:19673572
Three-dimensional ``Mercedes-Benz'' model for water
NASA Astrophysics Data System (ADS)
Dias, Cristiano L.; Ala-Nissila, Tapio; Grant, Martin; Karttunen, Mikko
2009-08-01
In this paper we introduce a three-dimensional version of the Mercedes-Benz model to describe water molecules. In this model van der Waals interactions and hydrogen bonds are given explicitly through a Lennard-Jones potential and a Gaussian orientation-dependent terms, respectively. At low temperature the model freezes forming Ice-I and it reproduces the main peaks of the experimental radial distribution function of water. In addition to these structural properties, the model also captures the thermodynamical anomalies of water: The anomalous density profile, the negative thermal expansivity, the large heat capacity, and the minimum in the isothermal compressibility.
Determining pressure-temperature phase diagrams of materials
NASA Astrophysics Data System (ADS)
Baldock, Robert J. N.; Pártay, Lívia B.; Bartók, Albert P.; Payne, Michael C.; Csányi, Gábor
2016-05-01
We extend the nested sampling algorithm to simulate materials under periodic boundary and constant pressure conditions, and show how it can be used to determine the complete equilibrium phase diagram for a given potential energy function, efficiently and in a highly automated fashion. The only inputs required are the composition and the desired pressure and temperature ranges, in particular, solid-solid phase transitions are recovered without any a priori knowledge about the structure of solid phases. We benchmark and showcase the algorithm on the periodic Lennard-Jones system, aluminum, and NiTi.
Viscosity of gaseous HFC-134a (1,1,1,2-tetrafluoroethane) under high pressures
Shibasaki-Kitakawa, N.; Takahashi, M.; Yokoyama, C.
1998-09-01
The viscosity of gaseous HFC-134a (1,1,1,2-tetrafluoroethane) was measured with an oscillating disk viscometer of the Maxwell type from 298.15 to 398.15 K at pressures up to 5.5 MPa. Intermolecular potential parameters for the Lennard-Jones 12-6 model were determined from the viscosity data at 0.1 MPa. The viscosity equation developed by Krauss et al. was applied to correlate the present viscosity data. In addition, the correlations proposed by Stiel and Thodos and by Lee and Thodos were tested for fitting the experimental viscosity data.
Theoretical evaluation of bulk viscosity: Expression for relaxation time
NASA Astrophysics Data System (ADS)
Hossein Mohammad Zaheri, Ali; Srivastava, Sunita; Tankeshwar, K.
2007-10-01
A theoretical calculation of bulk viscosity has been carried out by deriving an expression for the relaxation time which appears in the formula for bulk viscosity derived by Okumura and Yonezawa. The expression involved a pair distribution function and interaction potential. Numerical results have been obtained over a wide range of densities and temperatures for Lennard-Jones fluids. It is found that our results provide a good description of bulk viscosity as has been judged by comparing the results with nonequilibrium molecular dynamics results. In addition, our results demonstrate the importance of the multiparticle correlation function.
NASA Astrophysics Data System (ADS)
Yatsyshin, P.; Parry, A. O.; Kalliadasis, S.
2016-07-01
We study continuous interfacial transitions, analagous to two-dimensional complete wetting, associated with the first-order prewetting line, which can occur on steps, patterned walls, grooves and wedges, and which are sensitive to both the range of the intermolecular forces and interfacial fluctuation effects. These transitions compete with wetting, filling and condensation producing very rich phase diagrams even for relatively simple prototypical geometries. Using microscopic classical density functional theory to model systems with realistic Lennard-Jones fluid–fluid and fluid–substrate intermolecular potentials, we compute mean-field fluid density profiles, adsorption isotherms and phase diagrams for a variety of confining geometries.
Trillion-atom molecular dynamics becomes a reality
Kadau, Kai; Germann, Timothy C
2008-01-01
By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD{_}render.
Chaotic dynamics in dense fluids
Posch, H.A.; Hoover, W.G.
1987-09-01
We present calculations of the full spectra of Lyapunov exponents for 8- and 32-particle systems with periodic boundary conditions and interacting with the repulsive part of a Lennard-Jones potential both in equilibrium and nonequilibrium steady states. Lyapunov characteristic exponents lambda/sub n/ describe the mean exponential rates of divergence and convergence of neighbouring trajectories in phase-space. They are useful in characterizing the stochastic properties of a dynamical system. A new algorithm for their calculation is presented which incorporates ideas from control theory and constraint nonequilibrium molecular dynamics. 4 refs., 1 fig.
Modeling of gamma/gamma-prime phase equilibrium in the nickel-aluminum system
NASA Technical Reports Server (NTRS)
Sanchez, J. M.; Barefoot, J. R.; Jarrett, R. N.; Tien, J. K.
1984-01-01
A theoretical model is proposed for the determination of phase equilibrium in alloys, taking into consideration dissimilar lattice parameters. Volume-dependent pair interactions are introduced by means of phenomenological Lennard-Jones potentials and the configurational entropy of the system is treated in the tetrahedron approximation of the cluster variation method. The model is applied to the superalloy-relevant, nickel-rich, gamma/gamma-prime phase region of the Ni-Al phase diagram. The model predicts reasonable values for the lattice parameters and the enthalpy of formation as a function of composition, and the calculated phase diagram closely approximates the experimental diagram.
Theory of warm ionized gases: equation of state and kinetic Schottky anomaly.
Capolupo, A; Giampaolo, S M; Illuminati, F
2013-10-01
Based on accurate Lennard-Jones-type interaction potentials, we derive a closed set of state equations for the description of warm atomic gases in the presence of ionization processes. The specific heat is predicted to exhibit peaks in correspondence to single and multiple ionizations. Such kinetic analog in atomic gases of the Schottky anomaly in solids is enhanced at intermediate and low atomic densities. The case of adiabatic compression of noble gases is analyzed in detail and the implications on sonoluminescence are discussed. In particular, the predicted plasma electron density in a sonoluminescent bubble turns out to be in good agreement with the value measured in recent experiments. PMID:24229140
Solid-liquid phase transition in argon
NASA Technical Reports Server (NTRS)
Tsang, T.; Tang, H. T.
1978-01-01
Starting from the Lennard-Jones interatomic potential, a modified cell theory has been used to describe the solid-liquid phase transition in argon. The cell-size variations may be evaluated by a self-consistent condition. With the inclusion of cell-size variations, the transition temperature, the solid and liquid densities, and the liquid-phase radial-distribution functions have been calculated. These ab initio results are in satisfactory agreement with molecular-dynamics calculations as well as experimental data on argon.
NASA Astrophysics Data System (ADS)
Wang, Wei-Li; Miao, Gang; Li, Jian; Ma, Feng-Cai
2009-12-01
In order to study the collisional quantum interference (CQI) on rotational energy transfer in atom-diatom system, we have studied the relation of the integral interference angle and differential interference angle in Na + Na2 (A1 σ+u, v = 8 ~ b3п0u, v = 14) collision system. In this paper, based on the first-Born approximation of time-dependent perturbation theory and taking into accounts the anisotropic effect of Lennard-Jones interaction potentials, we present a theoretical model of collisional quantum interference in intramolecular rotational energy transfer, and a relationship between differential and integral interference angles.
Thermophysical properties of CF4/O2 and SF6/O2 gas mixtures
NASA Astrophysics Data System (ADS)
Damyanova, M.; Hohm, U.; Balabanova, E.; Barton, D.
2016-03-01
Fitting formulae are presented for the calculation of the second interaction virial coefficients, mixture viscosities and binary diffusion coefficients for CF4/O2 and SF6/O2 gas mixtures in the temperature range between 200 K and 1000 K. The data recommended are obtained from the isotropic (n-6) Lennard-Jones intermolecular interaction potentials of the pure substances by using the Hohm-Zarkova-Damyanova mixing rules. In general, a good agreement is observed between our results and the experimental and theoretical data found in the literature.
A computer simulation study of the ordered phases of some mesogenic fullerene derivatives
NASA Astrophysics Data System (ADS)
Sazonovas, Andrius; Orlandi, Silvia; Ricci, Matteo; Zannoni, Claudio; Gorecka, Ewa
2006-10-01
We present a Monte Carlo simulation study of the phase behaviour and molecular organization of a system of fullerene-based mesogens, represented by a three-site model composed of a fullerene sphere and two mesogenic moieties rigidly attached to it. It is shown that a combination of suitably modified Lennard-Jones and Gay-Berne attractive-repulsive potentials allows a satisfactory qualitative modeling of the interactions between the fullerene derivatives under investigation. Indeed, simulation results show that, despite the crude representation of the molecular structure, our model generates nematic and smectic phases, thus accounting qualitatively for the basic experimental observations on the class of compounds considered.
NASA Astrophysics Data System (ADS)
Ansari, R.; Ajori, S.
2016-05-01
In this paper, the oscillatory behavior of double-walled boron-nitride nanotubes is investigated based on the molecular dynamics (MD) simulations. The MD simulations are performed using the Lennard-Jones and Tersoff-like potential functions. The influences of friction between the walls of inner and outer tubes, flexibility, velocity and outer length-to-inner length ratio on the frequency of oscillations are studied. The results show that the flexibility increases the frequency during the simulation. Furthermore, it is observed that by increasing the initial velocity, the frequency decreases.
Thermal effects on van der Waals adhesive forces
NASA Astrophysics Data System (ADS)
Pinon, A. V.; Wierez-Kien, M.; Craciun, A. D.; Beyer, N.; Gallani, J. L.; Rastei, M. V.
2016-01-01
We present an experimental and theoretical study on how thermal energy alters van der Waals adhesion forces in nanoscale contacts stretched by mechanical probes. The force follows a distribution whose density function is an asymmetric bell-shaped curve presenting a temperature-dependent negative skewness. With increasing temperature the asymmetry increases whereas the most probable force value decreases. Using a 2-8 Lennard-Jones interaction potential within the reaction rate theory, we offer a theoretical framework permitting an evaluation of the microscopic parameters governing adhesion in a van der Waals nanocontact subjected to mechanical fluctuations.
Continuum modeling of breathing-like modes of spherical carbon onions
NASA Astrophysics Data System (ADS)
Ghavanloo, Esmaeal; Ahmad Fazelzadeh, S.
2015-08-01
In this letter, an analytical formulation is developed for predicting the breathing-like modes of spherical carbon onions consisting of an arbitrary number of layers. The spherical layers of the carbon onions are concentrically nested, and are coupled through van der Waals (vdW) forces between two adjacent layers. Lennard-Jones potential and continuum models are utilized to estimate the vdW interaction coefficients and the breathing-like modes of the carbon onions. The formulation is justified by a good agreement between the results given by the present model and available experimental and numerical data. Finally, numerical results are obtained for various carbon onions.
Negative Poisson's ratio materials via isotropic interactions.
Rechtsman, Mikael C; Stillinger, Frank H; Torquato, Salvatore
2008-08-22
We show that under tension a classical many-body system with only isotropic pair interactions in a crystalline state can, counterintuitively, have a negative Poisson's ratio, or auxetic behavior. We derive the conditions under which the triangular lattice in two dimensions and lattices with cubic symmetry in three dimensions exhibit a negative Poisson's ratio. In the former case, the simple Lennard-Jones potential can give rise to auxetic behavior. In the latter case, a negative Poisson's ratio can be exhibited even when the material is constrained to be elastically isotropic. PMID:18764632
Interaction of two substitutional impurity atoms in an hcp crystal
NASA Astrophysics Data System (ADS)
Belan, V. I.; Landau, A. I.
2010-04-01
Molecular dynamics computer simulation with a Lennard-Jones potential is used to investigate the interaction of two identical substitutional impurity atoms in an hcp crystal lattice. Different atomic radii of the impurities atoms, interaction energy of the atoms and the lattice atoms, and initial distances between the impurity atoms at zero temperature and pressure. It is found that in a number of cases for small distances between the impurity atoms not exceeding five interatomic distances these atoms attract one another contrary to the well-known laws of the continuum theory of elasticity. Good agreement between the computational results and the theory of elasticity obtains for short distances between impurity atoms.
Enthalpy of formation of Schottky defects in semiconductors
NASA Astrophysics Data System (ADS)
Gorichok, I. V.
2012-07-01
The enthalpy of formation of Schottky defects in crystals of II-VI, III-V, and IV-VI compounds has been calculated with the use of a method based on Mie-Lennard-Jones pair potentials, whose parameters have been determined from the experimental data on the Debye temperature, Grüneisen parameter, Poisson's ratio, elastic constants, and bulk modulus. The found values of the enthalpy of formation agree with the known literature data and can be used to calculate the density of these defects in the crystals.
Strain accommodation in inelastic deformation of glasses
NASA Astrophysics Data System (ADS)
Murali, P.; Ramamurty, U.; Shenoy, Vijay B.
2007-01-01
Motivated by recent experiments on metallic glasses, we examine the micromechanisms of strain accommodation including crystallization and void formation during inelastic deformation of glasses by employing molecular statics simulations. Our atomistic simulations with Lennard-Jones-like potentials suggests that a softer short range interaction between atoms favors crystallization. Compressive hydrostatic strain in the presence of a shear strain promotes crystallization whereas a tensile hydrostatic strain is found to induce voids. The deformation subsequent to the onset of crystallization includes partial reamorphization and recrystallization, suggesting important atomistic mechanisms of plastic dissipation in glasses.
Size-dependent elastic properties of crystalline polymers via a molecular mechanics model
NASA Astrophysics Data System (ADS)
Zhao, Junhua; Guo, Wanlin; Zhang, Zhiliang; Rabczuk, Timon
2011-12-01
An analytical molecular mechanics model is developed to obtain the size-dependent elastic properties of crystalline polyethylene. An effective "stick-spiral" model is adopted in the polymer chain. Explicit equations are derived from the Lennard-Jones potential function for the van der Waals force between any two polymer chains. By using the derived formulas, the nine size-dependent elastic constants are investigated systematically. The present analytical results are in reasonable agreement with those from present united-atom molecular dynamics simulations. The established analytical model provides an efficient route for mechanical characterization of crystalline polymers and related materials toward nanoelectromechanical applications.
Characteristic quantities and dimensional analysis
NASA Astrophysics Data System (ADS)
Grimvall, Göran
Phenomena in the physical sciences are described with quantities that have a numerical value and a dimension, i.e., a physical unit. Dimensional analysis is a powerful aspect of modeling and simulation. Characteristic quantities formed by a combination of model parameters can give new insights without detailed analytic or numerical calculations. Dimensional requirements lead to Buckingham's Π theorem - a general mathematical structure of all models in physics. These aspects are illustrated with many examples of modeling, e.g., an elastic beam on supports, wave propagation on a liquid surface, the Lennard-Jones potential for the interaction between atoms, the Lindemann melting rule, and saturation phenomena in electrical and thermal conduction.
Negative Poisson's Ratio Materials via Isotropic Interactions
NASA Astrophysics Data System (ADS)
Rechtsman, Mikael C.; Stillinger, Frank H.; Torquato, Salvatore
2008-08-01
We show that under tension a classical many-body system with only isotropic pair interactions in a crystalline state can, counterintuitively, have a negative Poisson’s ratio, or auxetic behavior. We derive the conditions under which the triangular lattice in two dimensions and lattices with cubic symmetry in three dimensions exhibit a negative Poisson’s ratio. In the former case, the simple Lennard-Jones potential can give rise to auxetic behavior. In the latter case, a negative Poisson’s ratio can be exhibited even when the material is constrained to be elastically isotropic.
Structural and elastic properties of fcc/fcc metallic multilayers: A molecular-dynamics study
NASA Astrophysics Data System (ADS)
Tȩcza, Grzegorz W.
1992-12-01
Interplanar and intraplanar spacings as well as the elastic constants of fcc/fcc metallic multilayers stacked along [001] were determined via variable-cell molecular-dynamics simulation in (HtN) and (EhN) ensembles at room temperature. Qualitative differences in the structural and elastic properties of the multilayers, simulated using various 12-6 Lennard-Jones potentials, were observed. The anomalous behavior of the elastic constants and the biaxial modulus was linked to the modulation wavelength dependence of various structural parameters. The importance of the fluctuation contributions for the calculation of the full elastic constants is demonstrated.
NASA Astrophysics Data System (ADS)
Zeppenfeld, P.; Büchel, M.; David, R.; Comsa, G.; Ramseyer, C.; Girardet, C.
1994-11-01
The phonon-dispersion curves for a xenon monolayer adsorbed on Cu(110) have been measured using inelastic He scattering. The size and geometry of the substrate unit cell introduces an anisotropic distortion of the xenon monolayer, which is reflected in a strong deformation of the phonon-dispersion curves with respect to the floating two-dimensional (2D) xenon layer. This effect is reproduced in a 2D phonon calculation, based on the Lennard-Jones Xe pair potential. In this way a microscopic relationship between lattice strain, force constants, and surface stress can be established.
Formation and structure of misfit dislocations
NASA Astrophysics Data System (ADS)
Nandedkar, A. S.; Srinivasan, G. R.; Murthy, C. S.
1991-03-01
We report here theoretical observations of the evolution of core structure of well-defined misfit dislocations arising from the spontaneous decomposition of highly strained coherent interfaces in a fcc bicrystal. We use a finely stepped energy-minimization technique and Lennard-Jones pair potential, which allowed Burgers-circuit construction and core-structure analysis. Simulations were made for (111) and (001) interfaces, which produced 60° and edge dislocations, respectively. The atomic configurations produced were consistent with those expected from the elasticity theory.
Temperature Dependence of Shock-Induced Plasticity: A Molecular Dynamics Approach
NASA Astrophysics Data System (ADS)
Hatano, Takahiro
2004-07-01
Molecular dynamics simulation on a fcc perfect crystal with the Lennard-Jones potential is performed in order to investigate temperature dependence of shock-induced plasticity. It is found that the critical piston velocity above which stacking faults emerge shifts downwards once the temperature exceeds approximately half the melting temperature. Also Hugoniot elastic limit is found to be a decreasing function of temperature, whereas the corresponding critical strain is insensitive to temperature. The discrepancy between the simulation and the experiments where Hugoniot elastic limit is a increasing function of temperature is discussed.
NASA Technical Reports Server (NTRS)
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.
A Compaction Model for Highly Porous Silica Powder.
NASA Astrophysics Data System (ADS)
Church, P. D.; Tsembelis, K.
2005-07-01
This paper describes research to develop an equation of state to describe the behaviour of a highly porous silica powder. It shows that whilst molecular modelling techniques can be readily applied to develop a description of a compact material the description of the compaction process is more problematic. An empirical model, based upon the Lennard-Jones potential, has been shown to be capable of describing the compaction process observed in simple experiments. This development and application of the model in the Eulerian hydrocode GRIM to reproduce experimental plate impact data over a wide range of impact velocities is described and the results compared with experimental data.
Room temperature synthesis and solid-state structure of Ni{sub 2}P{sub 2}O{sub 6}.12H{sub 2}O
Haag, J.M.; LeBret, G.C.; Cleary, D.A. . E-mail: cleary@gonzaga.edu; Twamley, B.
2005-04-15
The synthesis and crystal structure of Ni{sub 2}P{sub 2}O{sub 6}.12H{sub 2}O are reported. The compound was synthesized from aqueous solutions of nickel chloride and sodium hypodiphosphate at room temperature. The space group is orthorhombic, Pnnm. Unit cell dimensions are a=11.2418(5)A, b=18.5245(8)A, and c=7.3188(3)A, Z=4. The product is unstable with respect to dehydration above room temperature.
NASA Astrophysics Data System (ADS)
Nonnenmacher, E.; Brouant, P.; Mrozek, A.; Karolak-Wojciechowska, J.; Barbe, J.
2000-04-01
On the basis of structural similarities between various calcium channel antagonists (Verapamil or Diltiazem) a novel series of derivatives belonging to the dibenzodiazocinedione family were designed and synthesised to obtain drugs able to revert multidrug resistance (MDR). X-ray structure studies and conformational analysis of 5,11-dibenzyldibenzo[b,f][1,5]diazocine-6,12-dione were performed. Molecular modelling results have shown that observed reversal activity of this new derivative could refer to a thermodynamically limited concentration in a peculiar (extended) conformation.
AIREBO-M: A reactive model for hydrocarbons at extreme pressures
O’Connor, Thomas C. Robbins, Mark O.; Andzelm, Jan
2015-01-14
The Adaptive Intermolecular Reactive Empirical Bond Order potential (AIREBO) for hydrocarbons has been widely used to study dynamic bonding processes under ambient conditions. However, its intermolecular interactions are modeled by a Lennard-Jones (LJ) potential whose unphysically divergent power-law repulsion causes AIREBO to fail when applied to systems at high pressure. We present a modified potential, AIREBO-M, where we have replaced the singular Lennard-Jones potential with a Morse potential. We optimize the new functional form to improve intermolecular steric repulsions, while preserving the ambient thermodynamics of the original potentials as much as possible. The potential is fit to experimental measurements of the layer spacing of graphite up to 14 GPa and first principles calculations of steric interactions between small alkanes. To validate AIREBO-M’s accuracy and transferability, we apply it to a graphite bilayer and orthorhombic polyethylene. AIREBO-M gives bilayer compression consistent with quantum calculations, and it accurately reproduces the quasistatic and shock compression of orthorhombic polyethlyene up to at least 40 GPa.
Kang, Hongmei; Peng, Baoliang; Liang, Yanyan; Han, Xia; Liu, Honglai
2009-05-01
The interactions between negatively charged diblock polyelectrolyte PDMA(71)-b-PAA(59) and oppositely charged gemini surfactant hexylene-1,6-bis(dodecyldimethylammonium bromide) (12-6-12) in basic media were studied using dynamic light scattering, fluorescence spectroscopy, surface tension, and (1)H NMR. With increased addition of surfactant, the conformation of polyelectrolyte experienced changes from the initial unimer with open-extended PAA block, to the nano-scaled aggregates/complexes with a maximum hydrodynamic diameter (D(h)), and finally to the stable complexes with a smaller D(h). Accordingly, the value of D(h) during the whole process of increasing the surfactant concentration changed from 14-17 nm, to 184 nm, and to the final 70 nm, respectively. This transformation was driven by the electrostatic attractive/repulsive interactions, the hydrophobic interaction between hydrophobic surfactant tails, and the hydrophilicity of PDMA block. PMID:19217121
NASA Astrophysics Data System (ADS)
Bernards, C.; Heinze, S.; Jolie, J.; Fransen, C.; Linnemann, A.; Radeck, D.
2009-05-01
Using the Uν(6/12)⊗Uπ(6/4) extended supersymmetry, we constructed the energy spectrum and electromagnetic transition properties of the supermultiplet member Hg198 with two proton fermions coupled to a neutron boson core. Consistency between the supersymmetric interacting boson fermion fermion approximation (IBFFA) description and the F-spin symmetric interacting boson approximation (IBA-2) description is shown for this two-fermion-N-boson multiplet member. The data of a γγ angular correlation experiment using the HORUS cube γ-ray spectrometer—determining new multipole mixing ratios, level spins, γ transitions, and energy states—shows quite a good agreement, also for the low-energy part of the spectrum, when comparing theoretical predictions and experimental data. This is contrary to the usual assumption that a two-fermion-N-boson constellation should describe just the excited two-quasiparticle states.
Bernards, C.; Heinze, S.; Jolie, J.; Albers, M.; Fransen, C.; Radeck, D.
2010-02-15
We present the results of a {gamma}{gamma} angular correlation experiment investigating the nucleus {sup 196}Hg and compare these with a theoretical description of {sup 196}Hg within the U{sub {nu}}(6/12) x U{sub {pi}}(6/4) extended supersymmetry. To populate excited {sup 196}Hg states, we used the Cologne FN Tandem accelerator inducing the reaction {sup 194}Pt({alpha},2n){sup 196}Hg and analyzed the {gamma} decays of levels up to an excitation energy of 2.4 MeV with the HORUS cube spectrometer. The new results on this mercury isotope allow a comparison between the experimental data and the supersymmetrical predictions and show good agreement. This way we can add {sup 196}Hg as a fifth supermultiplet member to the so-called magical quartet consisting of {sup 194,195}Pt and {sup 195,196}Au.
Chevrier, Jonathan; Harley, Kim G.; Kogut, Katherine; Holland, Nina; Johnson, Caroline; Eskenazi, Brenda
2011-01-01
Although evidence suggests that maternal hypothyroidism and mild hypothyroxinemia during the first half of pregnancy alters fetal neurodevelopment among euthyroid offspring, little data are available from later in gestation. In this study, we measured free T4 using direct equilibrium dialysis, as well as total T4 and TSH in 287 pregnant women at 27 weeks' gestation. We also assessed cognition, memory, language, motor functioning, and behavior in their children at 6, 12, 24, and 60 months of age. Increasing maternal TSH was related to better performance on tests of cognition and language at 12 months but not at later ages. At 60 months, there was inconsistent evidence that higher TSH was related to improved attention. We found no convincing evidence that maternal TH during the second half of pregnancy was related to impaired child neurodevelopment. PMID:22132346
Mahantesha, Taranatha; Reddy, K M Parveen; Kumar, N H Praveen; Nara, Asha; Ashwin, Devasya; Buddiga, Vinutna
2015-01-01
Background: Dental caries is one of the most common health problems in the world. Probiotics are one the various preventive methods to reduce dental caries. The aim of this study is to compare the effectiveness of probiotic ice cream and drink on salivary Streptococcus mutans levels in children of 6-12 years age group. Materials and Methods: A three phase study was carried out in children (n = 50) of 6-12 years age with zero decayed missing filled teeth (dmft)/DMFT. They were randomly divided into two equal groups. Saliva samples were collected before the consumptions of probiotic ice cream and probiotic drink. Colony count obtained was recorded as baseline data. For both groups probiotic ice cream and drink was given randomly for 7 days and a washout period of 90 days were given and then the saliva samples were collected and colony counting was done. Results: Statistical analysis was performed using Student’s paired t-test and multiple comparisons by Tukey’s honest significant difference test which showed, there is a significant reduction in salivary S. mutans level in both groups after 7 days period. However, after washout period only probiotic ice cream showed reduction whereas drink did not. Also, there was no significant difference between probiotic ice cream and drink. Conclusion: Probiotic organisms definitely have a role in reducing the salivary S. mutans level and ice cream would be a better choice than drink. However, the prolonged use of the agents and their effects on caries is still to be determined. PMID:26435616
Giroux, Marie-Chantal; Santamaria, Raphael; Hélie, Pierre; Burns, Patrick; Beaudry, Francis; Vachon, Pascal
2015-01-01
The main objective of this study was to compare the physiological changes (withdrawal and corneal reflexes, respiratory and cardiac frequency, blood oxygen saturation, and rectal temperature) following intraperitoneal administration of ketamine (80 mg/kg) and xylazine (10 mg/kg) to 3-, 6-, 12- and 18-month-old male Sprague Dawley rats (n=6/age group). Plasma pharmacokinetics, liver metabolism, and blood biochemistry were examined for a limited number of animals to better explain anesthetic drug effects. Selected organs were collected for histopathology. The results for the withdrawal and corneal reflexes suggest a shorter duration and decreased depth of anesthesia with aging. Significant cardiac and respiratory depression, as well as decreased blood oxygen saturation, occurred in all age groups however, cardiac frequency was the most affected parameter with aging, since the 6-, 12-, and 18-month-old animals did not recuperate to normal values during recovery from anesthesia. Pharmacokinetic parameters (T1/2 and AUC) increased and drug clearance decreased with aging, which strongly suggests that drug exposure is associated with the physiological results. The findings for liver S9 fractions of 18-month-old rats compared with the other age groups suggest that following a normal ketamine anesthetic dose (80 mg/kg), drug metabolism is impaired, leading to a significant increase of drug exposure. In conclusion, age and related factors have a substantial effect on ketamine and xylazine availability, which is reflected by significant changes in pharmacokinetics and liver metabolism of these drugs, and this translates into shorter and less effective anesthesia with increasing age. PMID:26489361
The mean spherical approximation for a dipolar Yukawa fluid
NASA Astrophysics Data System (ADS)
Henderson, Douglas; Boda, Dezső; Szalai, István; Chan, Kwong-Yu
1999-04-01
The dipolar hard sphere fluid (DHSF) is a useful model of a polar fluid. However, the DHSF lacks a vapor-liquid transition due to the formation of chain-like structures. Such chains are not characteristic of real polar fluids. A more realistic model of a polar fluid is obtained by adding a Lennard-Jones potential to the intermolecular potential. Very similar results are obtained by adding a Yukawa potential, instead of the Lennard-Jones potential. We call this fluid the dipolar Yukawa fluid (DYF). We show that an analytical solution of the mean spherical approximation (MSA) can be obtained for the DYF. Thus, the DYF has many of the attractive features of the DHSF. We find that, within the MSA, the Yukawa potential modifies only the spherically averaged distribution function. Thus, although the thermodynamic properties of the DYF differ from those of the DHSF, the MSA dielectric constant of the DYF is the same as that of the DHSF. This result, and some other predictions, are tested by simulations and are found to be good approximations.
Revised Basin Hopping Monte Carlo Algorithm Applied for Nanoparticles
NASA Astrophysics Data System (ADS)
da Silva, Juarez L. F.; Rondina, Gustavo G.
2013-03-01
The Basin Hopping Monte Carlo (BHMC) algorithm has been very successful in obtaining the atomic structure of nanoparticles (NPs), however, its application for unbiased randomly initialized NPs have been restricted to few hundreds atoms employing empirical pair-potentials (EPP) and for small clusters employing first-principles interacting potentials based on density functional theory (DFT). In this talk, we will present our suggestions for bringing improvements to the the BHMC algorithm, which successfully extend its application for relatively large systems employing EPP and DFT potenticals. Using our implementation from scratch, we have found all the reported putative minimum energy configurations for Lennard-Jones and Sutton-Chen EPPs (N = 2 - 147, 200, 250, 300,..., 1000). We addressed also binary systems described by the Lennard-Jones or Sutton-Chen empirical potentials, and excellent results have been obtained. Finally, our revised BHMC implementation was combined with DFT potentials (FHI-AIMS), which was employed to study the atomic structure of Al clusters from 2 - 55 atoms in the neutral and charged states. Thus, our results indicate the our suggestions provide an important contribution to improve the quality of the BHMC results employing EPP or DFT potentials. We thank Sao Paulo Science Foundation (FAPESP)
NASA Astrophysics Data System (ADS)
Tovbin, Yu. K.; Zaitseva, E. S.; Rabinovich, A. B.
2016-01-01
The effect of internal motions of an adsorbate on the local characteristics of adsorption and layering phase diagrams are studied for structurally heterogeneous surfaces of slit-like pores. A molecular model describing adsorbate distributions inside slit-like pores, which is based on discrete distribution functions (lattice gas model), is used for the calculation. Molecular distributions are calculated by the Lennard-Jones potential (12-6) in a quasi-chemical approximation reflecting the effects of direct correlations of interacting particles and for the combined interaction of an adsorbate with walls in the average potential approximation (9-3) and the short-range Lennard-Jones potential for structurally heterogeneous surface areas. The conclusion is made that internal motions reflect the vibrational motion of molecules within a modified quasi-dimer model and a displacement of the adsorbate during its translational motion inside cells. It was found that the taking into account of internal motions decreases the critical temperature of adsorbate layering in slit-like pores.
Kashfi, Seyed Mansour; Khani Jeihooni, Ali; Rezaianzadeh, Abbas; Karimi, Shahnaz
2014-01-01
Background: Growth retardation in children is a result of nutritional ignorance, inappropriate care, and inadequate monitoring of growth monitoring. This study was performed to assess the effect of mothers education program based on the precede model on the mean weight of children (6-12 months) at health centers in Shiraz, Fars Province. Methods: This quasi experimental study was conducted on 120 mothers (60 in the experimental and 60 in the control group) with single child and exclusively on breast feeding who were cared by health centers in Shiraz, Fars province. The data were gathered through a questionnaire which included demographic characteristics, the components of the precede model (knowledge, attitude, enabling as well as reinforcing factors, and maternal function) and child weight. Educational intervention was performed during 6 sessions each of which lasted for 55 to 60 minutes. The questionnaire was completed by the experiment a land control group before and 4 months after the training program. Results: The results showed that the educational intervention program in the experimental group caused significant increase in the means of knowledge (p<0.001) and attitude scores (p<0.001). This study showed that enabling and reinforcing factors (and training sessions), performance score of mothers as well as weight of children among experimental group were significantly higher than control group (p=0.01). Conclusion: The results of this study can be used as a guideline prevents growth retardation in health centers and other related organizations. PMID:25664296
NASA Astrophysics Data System (ADS)
Mahata, Paritosh; Das, Sovan Lal
2014-12-01
Adsorption of proteins on membrane surfaces plays an important role in cell biological processes. In this work, we develop a two-dimensional fluid model for proteins. The protein molecules have been modeled as two-dimensional convex and soft particles. The Lennard-Jones potential for circular particles and Kihara (12,6) potential for elliptical particles with hard core have been used to model pairwise intermolecular interactions. The equation of state of the fluid model has been derived using Weeks-Chandler-Andersen decomposition and it involves three parameters, an attraction, a repulsion, and a size parameter, which depend on the shape and core size of the molecules. For validation of the model, a two-dimensional molecular dynamics simulation has been performed. Finally, the model has been applied to study the adsorption of proteins on a flat membrane. In comparison with the existing model of hard and convex particles for protein adsorption, our model predicts a higher packing fraction for the adsorption equilibria. Although the present work is based on Lennard-Jones-type interaction, it can be extended for other specific soft interactions between convex molecules. Thus the model has general applicability for any other two-dimensional adsorption systems of molecules with soft interaction.
Structural relaxation in atomic clusters: Master equation dynamics
NASA Astrophysics Data System (ADS)
Miller, Mark A.; Doye, Jonathan P. K.; Wales, David J.
1999-10-01
The role of the potential energy landscape in determining the relaxation dynamics of model clusters is studied using a master equation. Two types of energy landscape are examined: a single funnel, as exemplified by 13-atom Morse clusters, and the double funnel landscape of the 38-atom Lennard-Jones cluster. Interwell rate constants are calculated using Rice-Ramsperger-Kassel-Marcus theory within the harmonic approximation, but anharmonic model partition functions are also considered. Decreasing the range of the potential in the Morse clusters is shown to hinder relaxation toward the global minimum, and this effect is related to the concomitant changes in the energy landscape. The relaxation modes that emerge from the master equation are interpreted and analyzed to extract interfunnel rate constants for the Lennard-Jones cluster. Since this system is too large for a complete characterization of the energy landscape, the conditions under which the master equation can be applied to a limited database are explored. Connections are made to relaxation processes in proteins and structural glasses.
Onset of simple liquid behaviour in modified water models
Prasad, Saurav; Chakravarty, Charusita
2014-04-28
The transition to simple liquid behaviour is studied in a set of modified hybrid water models where the potential energy contribution of the Lennard-Jones dispersion-repulsion contribution is progressively enhanced relative to the electrostatic contribution. Characteristics of simple liquid behaviour that indicate the extent to which a given system can be mapped onto an inverse power law fluid are examined, including configurational energy-virial correlations, functional form of temperature dependence of the excess entropy along isochores, and thermodynamic and excess entropy scaling of diffusivities. As the Lennard-Jones contribution to the potential energy function increases, the strength of the configurational energy-virial correlations increases. The Rosenfeld-Tarazona temperature dependence of the excess entropy is found to hold for the range of state points studied here for all the hybrid models, regardless of the degree of correlating character. Thermodynamic scaling is found to hold for weakly polar fluids with a moderate degree of energy-virial correlations. Rosenfeld-scaling of transport properties is found not to be necessarily linked with the strength of energy-virial correlations but may hold for systems with poor thermodynamic scaling if diffusivities and excess entropies show correlated departures from the isomorph-invariant behaviour characteristic of approximate inverse power law fluids. The state-point dependence of the configurational energy-virial correlation coefficient and the implications for thermodynamic and excess entropy scalings are considered.
Simplicity of condensed matter at its core: Generic definition of a Roskilde-simple system
Schrøder, Thomas B. Dyre, Jeppe C.
2014-11-28
The isomorph theory is reformulated by defining Roskilde-simple systems by the property that the order of the potential energies of configurations at one density is maintained when these are scaled uniformly to a different density. If the potential energy as a function of all particle coordinates is denoted by U(R), this requirement translates into U(R{sub a}) < U(R{sub b}) ⇒ U(λR{sub a}) < U(λR{sub b}). Isomorphs remain curves in the thermodynamic phase diagram along which structure, dynamics, and excess entropy are invariant, implying that the phase diagram is effectively one-dimensional with respect to many reduced-unit properties. In contrast to the original formulation of the isomorph theory, however, the density-scaling exponent is not exclusively a function of density and the isochoric heat capacity is not an exact isomorph invariant. A prediction is given for the latter quantity's variation along the isomorphs. Molecular dynamics simulations of the Lennard-Jones and Lennard-Jones Gaussian systems validate the new approach.
Computer simulation of nucleation in a gas-saturated liquid
NASA Astrophysics Data System (ADS)
Protsenko, S. P.; Baidakov, V. G.; Teterin, A. S.; Zhdanov, E. R.
2007-03-01
Molecular dynamics methods have been used to investigate the kinetics of the liquid-gas phase transition in a two-component Lennard-Jones system at negative pressures and elastic stretches of the liquid to values close to spinodal ones. The molecular dynamics system consists of 2048 interacting particles with parameters of the Lennard-Jones potential for argon and neon. Density dependences of pressure and internal energy have been calculated for stable and metastable states of the mixture at a temperature T*≈0.7±0.01 and three values of the concentration. The location of mechanical and the diffusion spinodals has been determined. It has been established that a gas-saturated mixture retains its stability against finite variations of state variables up to stretches close to the values near the diffusion spinodal. The statistic laws of the process of destruction of the metastable state have been investigated. The lifetimes of the metastable phase have been determined. It is shown that owing to the small height of the potential barrier that separates the microheterogeneous from the homogeneous state a system of finite size has a possibility to make the reverse transition from the microheterogeneous into the homogeneous state. The lifetimes of the system in the microheterogeneous state, as well as the expectation times of the occurrence of a critical nucleus, are described by Poissonian distributions.
Analysis of Carbon Nanotubes and Graphene Nanoribbons with Folded Racket Shapes
NASA Astrophysics Data System (ADS)
Borum, Andy; Plaut, Raymond; Dillard, David
2011-10-01
When carbon nanotubes and graphene nanoribbons become long, they may self-fold and form tennis racket-like shapes. This phenomenon is analyzed in two ways by treating a nanotube or nanoribbon as an elastica. First, an approach from adhesion science is used, in which the two sides of the racket handle are assumed to be straight and bonded together with constant or no separation. New analytical results are obtained involving the shape, bending energy, and adhesion energy of the self-folded structures. These relations show that the dimensions of the racket loop are proportional to the square root of the flexural rigidity. The second analysis uses the Lennard-Jones potential to model the van der Waals forces between the two sides of the racket. A nanoribbon is considered, and the interatomic forces are integrated along the length and across the width of the nanoribbon. The resulting integro-differential equations are solved using the finite difference method. The racket handle is found to be in compression and the separation between the two sides of the racket handle decreases in the direction of the racket loop. The results for the Lennard-Jones model approximately satisfy the relationship between the dimensions and the flexural rigidity found using the adhesion model.
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
2016-08-01
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. PMID:27337546
Kadoura, Ahmad; Sun, Shuyu Salama, Amgad
2014-08-01
Accurate determination of thermodynamic properties of petroleum reservoir fluids is of great interest to many applications, especially in petroleum engineering and chemical engineering. Molecular simulation has many appealing features, especially its requirement of fewer tuned parameters but yet better predicting capability; however it is well known that molecular simulation is very CPU expensive, as compared to equation of state approaches. We have recently introduced an efficient thermodynamically consistent technique to regenerate rapidly Monte Carlo Markov Chains (MCMCs) at different thermodynamic conditions from the existing data points that have been pre-computed with expensive classical simulation. This technique can speed up the simulation more than a million times, making the regenerated molecular simulation almost as fast as equation of state approaches. In this paper, this technique is first briefly reviewed and then numerically investigated in its capability of predicting ensemble averages of primary quantities at different neighboring thermodynamic conditions to the original simulated MCMCs. Moreover, this extrapolation technique is extended to predict second derivative properties (e.g. heat capacity and fluid compressibility). The method works by reweighting and reconstructing generated MCMCs in canonical ensemble for Lennard-Jones particles. In this paper, system's potential energy, pressure, isochoric heat capacity and isothermal compressibility along isochors, isotherms and paths of changing temperature and density from the original simulated points were extrapolated. Finally, an optimized set of Lennard-Jones parameters (ε, σ) for single site models were proposed for methane, nitrogen and carbon monoxide.
NASA Astrophysics Data System (ADS)
Boned, C.; Galliero, G.; Bazile, J. P.; Magrini, W.
2013-09-01
Three recent physically based models (Lennard-Jones, free volume, thermodynamic scaling) for representing the viscosity of sulfur hexafluoride (SF6) are discussed together with two models (friction theory and Enskog 2σ) that have been recently applied to this fluid. The experimental database employed for adjustment (1562 data points) considers a large temperature (225.18 to 473.15 K) and pressure intervals (0.0264 to 51.21 MPa). The absolute average deviation is 3.8% for the Lennard-Jones model (one parameter), 1.7% for the free volume model (three parameters) and 1.5% for the thermodynamic scaling model (six parameters). Thus, it is shown that when physically based approaches are employed, a limited number of parameters is sufficient to represent accurately the shear viscosity of SF6. Furthermore it has been confirmed, using the thermodynamic scaling approach, that the repulsive steepness of the SF6 interaction potential is higher than usually found for fluids composed by non polar spherical molecule.
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, Jordan R.
2016-06-23
Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular 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, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, 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.« less
A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations.
Hédin, Florent; El Hage, Krystel; Meuwly, Markus
2016-08-22
The quality of atomistic simulations depends decisively on the accuracy of the underlying energy function (force field). Of particular importance for condensed-phase properties are nonbonded interactions, including the electrostatic and Lennard-Jones terms. Permanent atomic multipoles (MTPs) are an extension to common point-charge (PC) representations in atomistic simulations. MTPs are commonly determined from and fitted to an ab initio Electrostatic Potential (ESP), and Lennard-Jones (LJ) parameters are obtained from comparison of experimental and computed observables using molecular dynamics (MD) simulations. For this a set of thermodynamic observables such as density, heat of vaporization, and hydration free energy is chosen, to which the parametrization is fitted. The current work introduces a comprehensive computing environment (Fitting Wizard (FW)) for optimizing nonbonded interactions for atomistic force fields of different qualities. The FW supports fitting of standard PC-based force fields and more physically motivated multipolar (MTP) force fields. A broader study including 20 molecules ranging from N-methyl-acetamide and benzene to halogenated benzenes, phenols, anilines, and pyridines yields a root mean squared deviation for hydration free energies of 0.36 kcal/mol over a range of 8 kcal/mol. It is furthermore shown that PC-based force fields are not necessarily inferior compared to MTP parametrizations depending on the molecule considered. PMID:27438992
In silico prediction of drug solubility: 1. Free energy of hydration.
Westergren, Jan; Lindfors, Lennart; Höglund, Tobias; Lüder, Kai; Nordholm, Sture; Kjellander, Roland
2007-02-22
As a first step in the computational prediction of drug solubility the free energy of hydration, DeltaG*(vw) in TIP4P water has been computed for a data set of 48 drug molecules using the free energy of perturbation method and the optimized potential for liquid simulations all-atom force field. The simulations were performed in two steps, where first the Coulomb and then the Lennard-Jones interactions between the solute and the water molecules were scaled down from full to zero strength to provide physical understanding and simpler predictive models. The results have been interpreted using a theory assuming DeltaG*(vw) = A(MS)gamma + E(LJ) + E(C)/2 where A(MS) is the molecular surface area, gamma is the water-vapor surface tension, and E(LJ) and E(C) are the solute-water Lennard-Jones and Coulomb interaction energies, respectively. It was found that by a proper definition of the molecular surface area our results as well as several results from the literature were found to be in quantitative agreement using the macroscopic surface tension of TIP4P water. This is in contrast to the surface tension for water around a spherical cavity that previously has been shown to be dependent on the size of the cavity up to a radius of approximately 1 nm. The step of scaling down the electrostatic interaction can be represented by linear response theory. PMID:17266351
Entropy, local order, and the freezing transition in Morse liquids.
Chakraborty, Somendra Nath; Chakravarty, Charusita
2007-07-01
The behavior of the excess entropy of Morse and Lennard-Jones liquids is examined as a function of temperature, density, and the structural order metrics. The dominant pair correlation contribution to the excess entropy is estimated from simulation data for the radial distribution function. The pair correlation entropy (S2) of these simple liquids is shown to have a threshold value of (-3.5+/-0.3)kB at freezing. Moreover, S2 shows a T(-2/5) temperature dependence. The temperature dependence of the pair correlation entropy as well as the behavior at freezing closely correspond to earlier predictions, based on density functional theory, for the excess entropy of repulsive inverse power and Yukawa potentials [Rosenfeld, Phys. Rev. E 62, 7524 (2000)]. The correlation between the pair correlation entropy and the local translational and bond orientational order parameters is examined, and, in the case of the bond orientational order, is shown to be sensitive to the definition of the nearest neighbors. The order map between translational and bond orientational order for Morse liquids and solids shows a very similar pattern to that seen in Lennard-Jones-type systems. PMID:17677432
Vapor-liquid equilibria of alternative refrigerants by molecular dynamics simulations
Lisal, M.; Aim, K.; Budinsky, R.; Vacek, V.
1999-01-01
Alternative refrigerants HFC-152a (CHF{sub 2}CH{sub 3}), HFC-143a (CF{sub 3}CH{sub 3}), HFC-134a (CF{sub 3}CH{sub 2}F), and HCFC-142b (CF{sub 2}ClCH{sub 3}) are modeled as a dipolar two-center Lennard-Jones fluid. Potential parameters of the model are fitted to the critical temperature and vapor-liquid equilibrium data. The required vapor-liquid equilibrium data of the model fluid are computed by the Gibbs-Duhem integration for molecular elongations L = 0.505 and 0.67, and dipole moments {mu}{sup *2} = 0, 2, 4, 5, 6, 7, and 8. Critical properties of the model fluid are estimated from the law of rectilinear diameter and critical scaling relation. The vapor-liquid equilibrium data are presented by Wagner equations. Comparison of the vapor-liquid equilibrium data based on the dipolar two-center Lennard-Jones fluid with data from the REFPROP database shows good-to-excellent agreement for coexisting densities and vapor pressure.
Scaling of viscous dynamics in simple liquids: theory, simulation and experiment
NASA Astrophysics Data System (ADS)
Bøhling, L.; Ingebrigtsen, T. S.; Grzybowski, A.; Paluch, M.; Dyre, J. C.; Schrøder, T. B.
2012-11-01
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, and the prediction is shown to agree very well with simulations over large density changes. Our findings effectively reduce the problem of understanding the viscous slowing down from being a quest for a function of two variables to a search for a single-variable function.
Assessment of high-fidelity collision models in the direct simulation Monte Carlo method
NASA Astrophysics Data System (ADS)
Weaver, Andrew B.
Advances in computer technology over the decades has allowed for more complex physics to be modeled in the DSMC method. Beginning with the first paper on DSMC in 1963, 30,000 collision events per hour were simulated using a simple hard sphere model. Today, more than 10 billion collision events can be simulated per hour for the same problem. Many new and more physically realistic collision models such as the Lennard-Jones potential and the forced harmonic oscillator model have been introduced into DSMC. However, the fact that computer resources are more readily available and higher-fidelity models have been developed does not necessitate their usage. It is important to understand how such high-fidelity models affect the output quantities of interest in engineering applications. The effect of elastic and inelastic collision models on compressible Couette flow, ground-state atomic oxygen transport properties, and normal shock waves have therefore been investigated. Recommendations for variable soft sphere and Lennard-Jones model parameters are made based on a critical review of recent ab-initio calculations and experimental measurements of transport properties.
Neyt, Jean-Claude; Wender, Aurélie; Lachet, Véronique; Malfreyt, Patrice
2011-08-01
We report Monte Carlo simulations of the liquid-vapor interface of SO(2), O(2), N(2), and Ar to reproduce the dependence of the surface tension with the temperature. Whereas the coexisting densities, critical temperature, density, and pressure are very well reproduced by the two-phase simulations showing the same accuracy as the calculations performed using the Gibbs ensemble Monte Carlo technique (GEMC), the performance of the prediction of the variation of the surface tension with the temperature depends on the magnitude of the electrostatic and repulsive-dispersive interactions. The surface tension of SO(2) is very well reproduced, whereas the prediction of this property is less satisfactory for O(2) and N(2), for which the average intermolecular electrostatic interactions are several orders smaller than the dispersion interactions. For argon, we observe significant deviations from experiments. The representation of the surface tension of argon in reduced units shows that our calculations are in line with the existing surface tensions of the Lennard-Jones fluid in the literature. This underlines the difficulty of reproducing the temperature dependence of the surface tension of argon with interactions only modeled by the Lennard-Jones pair potential. PMID:21711018
NASA Technical Reports Server (NTRS)
Richards, P. G.; Buonsanto, M. J.; Reinisch, B. W.; Holt, J.; Fennelly, J. A.; Scali, J. L.; Comfort, R. H.; Germany, G. A.; Spann, J.; Brittnacher, M.
1999-01-01
Measurements from a network of digisondes and an incoherent scatter radar In Eastern North American For January 6-12, 1997 have been compared with the Field Line Interhemispheric Plasma (FLIP) model which now includes the effects of electric field convective. With the exception of Bermuda, the model reproduces the daytime electron density very well most of the time. As is typical behavior for winter solar minimum on magnetically undisturbed nights, the measurements at Millstone Hill show high electron temperatures before midnight followed by a rapid decay, which is accompanied by a pronounced density enhancement in the early morning hours. The FLIP model reproduces the nighttime density enhancement well, provided the model is constrained to follow the topside electron temperature and the flux tube is full. Similar density enhancements are seen at Goose Bay, Wallops Island and Bermuda. However, the peak height variation and auroral images indicate the density enhancements at Goose Bay are most likely due to particle precipitation. Contrary to previously published work we find that the nighttime density variation at Millstone Hill is driven by the temperature behavior and not the other way around. Thus, in both the data and model, the overall nighttime density is lowered and the enhancement does not occur if the temperature remains high all night. Our calculations show that convections of plasma from higher magnetic latitudes does not cause the observed density maximum but it may enhance the density maximum if over-full flux tubes are convected over the station. On the other had, convection of flux tubes with high temperatures and depleted densities may prevent the density maximum from occurring. Despite the success in modeling the nighttime density enhancements, there remain two unresolved problems. First, the measured density decays much faster than the modeled density near sunset at Millstone Hill and Goose Bay though not at lower latitude stations. Second, we
ERIC Educational Resources Information Center
Hutchison, Amy C.; Colwell, Jamie
2014-01-01
Digital tools have the potential to transform instruction and promote literacies outlined in the Common Core State Standards. Empirical research is examined to illustrate this potential in grades 6-12 instruction.
Enthalpy-Entropy Contributions to the Potential of Mean Force of Nanoscopic Hydrophobic Solutes
Choudhury, Niharendu; Pettitt, Bernard M.
2006-04-04
Entropic and enthalpic contributions to the hydrophobic interaction between nanoscopic hydrophobic solutes, modeled as graphene plates in water, have been calculated using molecular dynamics simulations in the isothermal-isobaric (NPT) ensemble with free energy perturbation methodology. We find the stabilizing contribution to the free energy of association (contact pair formation) to be the favorable entropic part, the enthalpic contribution being highly unfavorable. The desolvation barrier is dominated by the unfavorable enthalpic contribution, despite a fairly large favorable entropic compensation. The enthalpic contributions, incorporating the Lennard-Jones solute-solvent terms, largely determine the stability of the solvent separated configuration. We decompose the enthalpy into a direct solute-solute term, the solute-solvent interactions, and the remainder that contains pressure-volume work as well as contributions due to solvent reorganization. The enthalpic contribution due to changes in water-water interactions arising from solvent reorganization around the solute molecules is shown to have major contribution in the solvent induced enthalpy change.
ERIC Educational Resources Information Center
Ferraro, Jan; Houck, Bonnie; Klund, Sue; Hexum-Platzer, Sharon; Vortman-Smith, Jan
2006-01-01
The "Model Secondary (6-12) Plan for Reading Intervention and Development" has been designed to meet the cognitive needs of middle school through high school students whose reading performance ranges from those significantly below expectation through those reading at or above grade level. The reading needs of the population of students in need of…
Shen, Wei; Hao, Xiang; Shi, Yong; Tian, Wei-Sheng
2015-12-01
Herein we describe a synthesis of (6R,12R)-6,12-dimethylpentadecan-2-one (5), the female produced sex pheromone of banded cucumber beetle Diabrotica balteata Le Conte, from (R)-4-methyl-5-valerolactone, a methyl-branched chiron. PMID:26882689
Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample
NASA Technical Reports Server (NTRS)
Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)
2001-01-01
Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.
Boobbyer, D N; Goodford, P J; McWhinnie, P M; Wade, R C
1989-05-01
An empirical energy function designed to calculate the interaction energy of a chemical probe group, such as a carbonyl oxygen or an amine nitrogen atom, with a target molecule has been developed. This function is used to determine the sites where ligands, such as drugs, may bind to a chosen target molecule which may be a protein, a nucleic acid, a polysaccharide, or a small organic molecule. The energy function is composed of a Lennard-Jones, an electrostatic and a hydrogen-bonding term. The latter is dependent on the length and orientation of the hydrogen bond and also on the chemical nature of the hydrogen-bonding atoms. These terms have been formulated by fitting to experimental observations of hydrogen bonds in crystal structures. In the calculations, thermal motion of the hydrogen-bonding hydrogen atoms and lone-pair electrons may be taken into account. For example, in a alcoholic hydroxyl group, the hydrogen may rotate around the C-O bond at the observed tetrahedral angle. In a histidine residue, a hydrogen atom may be bonded to either of the two imidazole nitrogens and movement of this hydrogen will cause a redistribution of charge which is dependent on the nature of the probe group and the surrounding environment. The shape of some of the energy functions is demonstrated on molecules of pharmacological interest. PMID:2709375
Molecular dynamics simulation of benzene
NASA Astrophysics Data System (ADS)
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
NASA Astrophysics Data System (ADS)
Miyata, Tatsuhiko; Ikuta, Yasuhiro; Hirata, Fumio
2010-07-01
This article proposes a free energy calculation method based on the molecular dynamics simulation combined with the three dimensional reference interaction site model theory. This study employs the free energy perturbation (FEP) and the thermodynamic integration (TDI) along the coupling parameters to control the interaction potential. To illustrate the method, we applied it to a complex formation process in aqueous solutions between a crown ether molecule 18-Crown-6 (18C6) and a potassium ion as one of the simplest model systems. Two coupling parameters were introduced to switch the Lennard-Jones potential and the Coulomb potential separately. We tested two coupling procedures: one is a "sequential-coupling" to couple the Lennard-Jones interaction followed by the Coulomb coupling, and the other is a "mixed-coupling" to couple both the Lennard-Jones and the Coulomb interactions together as much as possible. The sequential-coupling both for FEP and TDI turned out to be accurate and easily handled since it was numerically well-behaved. Furthermore, it was found that the sequential-coupling had relatively small statistical errors. TDI along the mixed-coupling integral path was to be carried out carefully, paying attention to a numerical behavior of the integrand. The present model system exhibited a nonmonotonic behavior in the integrands for TDI along the mixed-coupling integral path and also showed a relatively large statistical error. A coincidence within a statistical error was obtained among the results of the free energy differences evaluated by FEP, TDI with the sequential-coupling, and TDI with the mixed-coupling. The last one is most attractive in terms of the computer power and is accurate enough if one uses a proper set of windows, taking the numerical behavior of the integrands into account. TDI along the sequential-coupling integral path would be the most convenient among the methods we tested, since it seemed to be well-balanced between the computational
Controlling the long-range corrections in atomistic Monte Carlo simulations of two-phase systems.
Goujon, Florent; Ghoufi, Aziz; Malfreyt, Patrice; Tildesley, Dominic J
2015-10-13
The long-range correction to the surface tension can amount to up to 55% of the calculated value of the surface tension for cutoffs in the range of 2.1-6.4 σ. The calculation of the long-range corrections to the surface tension and to the configurational energy in two-phase systems remains an active area of research. In this work, we compare the long-range corrections methods proposed by Guo and Lu ( J. Chem. Phys. 1997 , 106 , 3688 - 3695 ) and Janeček ( J. Phys. Chem. B 2006 , 110 , 6264 - 6269 ) for the calculation of the surface tension and of the coexisting densities in Monte Carlo simulations of the truncated Lennard-Jones potential and the truncated and shifted Lennard-Jones potential models. These methods require an estimate of the long-range correction at each step in the Monte Carlo simulation. We apply the full version of the Guo and Lu method, which involves the calculation of a double integral that contains a series of density differences, and we compare these results with the simplified version of the method which is routinely used in two-phase simulations. We conclude that the cutoff dependencies of the surface tension and coexisting densities are identical for the full versions of Guo and Lu and Janeček methods. We show that it is possible to avoid applying the long-range correction at every step by using the truncated Lennard-Jones potential with a cutoff rc ≥ 5 σ. The long-range correction can then be applied at the end of the simulation. The limiting factor in the accurate calculation of this final correction is an accurate estimate of the coexisting densities. Link-cell simulations performed using a cutoff rc = 5.5 σ require twice as much computing time as those with a more typical cutoff of rc = 3.0 σ. The application of the Janeček correction increases the running time of the simulation by less than 10%, and it can be profitably applied with the shorter cutoff. PMID:26574249
Molecular dynamics study of the stability of methane structure H clathrate hydrates.
Alavi, Saman; Ripmeester, J A; Klug, D D
2007-03-28
Molecular dynamics simulations are used to study the stability of structure H (sH) methane clathrate hydrates in a 3 x 3 x 3 sH unit cell replica. Simulations are performed at experimental conditions of 300 K and 2 GPa for three methane intermolecular potentials. The five small cages of the sH unit cell are assigned methane guest occupancies of one and large cage guest occupancies of one to five are considered. Radial distribution functions, unit cell volumes, and configurational energies are studied as a function of large cage CH(4) occupancy. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies. Large cage occupancy of five is the most stable configuration for a Lennard-Jones united-atom potential and the Tse-Klein-McDonald potential parametrized for condensed methane phases and two for the most stable configuation for the Murad and Gubbins potential. PMID:17411153
Temperature and length scale dependence of solvophobic solvation in a single-site water-like liquid
NASA Astrophysics Data System (ADS)
Dowdle, John R.; Buldyrev, Sergey V.; Stanley, H. Eugene; Debenedetti, Pablo G.; Rossky, Peter J.
2013-02-01
The temperature and length scale dependence of solvation properties of spherical hard solvophobic solutes is investigated in the Jagla liquid, a simple liquid that consists of particles interacting via a spherically symmetric potential combining a hard core repulsion and a longer ranged soft core interaction, yet exhibits water-like anomalies. The results are compared with equivalent calculations for a model of a typical atomic liquid, the Lennard-Jones potential, and with predictions for hydrophobic solvation in water using the cavity equation of state and the extended simple point charge model. We find that the Jagla liquid captures the qualitative thermodynamic behavior of hydrophobic hydration as a function of temperature for both small and large length scale solutes. In particular, for both the Jagla liquid and water, we observe temperature-dependent enthalpy and entropy of solvation for all solute sizes as well as a negative solvation entropy for sufficiently small solutes at low temperature. This feature of water-like solvation is distinct from the strictly positive and temperature independent enthalpy and entropy of cavity solvation observed in the Lennard-Jones fluid. The results suggest that, compared to a simple liquid, it is the presence of a second thermally accessible repulsive energy scale, acting to increasingly favor larger separations for decreasing temperature, that is the essential characteristic of a liquid that favors low-density, open structures, and models hydrophobic hydration, and that it is the presence of this second energy scale that leads to the similarity in the behavior of water and the Jagla liquid. In addition, the Jagla liquid dewets surfaces of large radii of curvature less readily than the Lennard-Jones liquid, reflecting a greater flexibility or elasticity in the Jagla liquid structure than that of a typical liquid, a behavior also similar to that of water's hydrogen bonding network. The implications of the temperature and
Hydrophobicity and hydrogen-bonded network in liquid water
NASA Astrophysics Data System (ADS)
Li, Je-Luen; Wingreen, Ned; Tang, Chao; Car, Roberto
2004-03-01
Hydrophobicity is the main driving force behind numerous important biological processes at molecular level, including protein folding and the formation of biological membranes. Yet few experimental probes can measure the local water structure around a hydrophobic solute, and our understanding of the detailed structure of hydrophobic hydration has to rely on molecular dynamics simulation. As a model system, several groups studied two methane molecules in liquid water and obtained the potential of mean force using Lennard-Jones potential and various water models. However, hydrophobic effect critically depends on the description of hydrogen-bonded network, and classical simulations may not be sufficient to descirbe the forming and breaking of hydrogen bonds. In this work, we apply ab initio molecular dynamics simulations to study this model system. Besides the potential of mean force between 2 methanes in water, the role of the local water structure will be highlighted.
Exact quantum scattering calculations of transport properties for the H{sub 2}O–H system
Dagdigian, Paul J.; Alexander, Millard H.
2013-11-21
Transport properties for collisions of water with hydrogen atoms are computed by means of exact quantum scattering calculations. For this purpose, a potential energy surface (PES) was computed for the interaction of rigid H{sub 2}O, frozen at its equilibrium geometry, with a hydrogen atom, using a coupled-cluster method that includes all singles and doubles excitations, as well as perturbative contributions of connected triple excitations. To investigate the importance of the anisotropy of the PES on transport properties, calculations were performed with the full potential and with the spherical average of the PES. We also explored the determination of the spherical average of the PES from radial cuts in six directions parallel and perpendicular to the C{sub 2} axis of the molecule. Finally, the computed transport properties were compared with those computed with a Lennard-Jones 12-6 potential.
NASA Astrophysics Data System (ADS)
Qi, Kai; Liewehr, Benjamin; Koci, Tomas; Pattanasiri, Busara; Williams, Matthew; Bachmann, Michael
By means of advanced parallel-tempering replica-exchange Monte Carlo methods we systematically examine the effects of an asymmetric bond potential between the bonded monomers on the structural formations of an elastic flexible polymer model. Employing microcanonical inflection-point analysis and conformational analysis based on a suitable set of structural order parameters, we identify diverse structural phases in the low-temperature region of the microcanonical hyperphase diagram. In addition to the icosahedral phase occurring if the symmetry of the bonded interaction is broken by strong bonded Lennard-Jones potential, amorphous structures with bihexagonal cores appear for small values of the asymmetry control parameter in the bond potential. Another remarkable feature is the observation of the hierarchy of freezing transitions associated with the formation of the surface layer after nucleation.
Frequency dispersion of the viscoelastic properties of solutions of electrolytes
NASA Astrophysics Data System (ADS)
Odinaev, S.; Akdodov, D. M.; Sharifov, N. Sh.; Mirzoaminov, Kh.
2010-06-01
Analytical expressions obtained earlier are used to numerically calculate the dynamic coefficients of the bulk ην(ω) and shear η s (ω) viscosity and the corresponding modules of their bulk K(ω) and shear μ(ω) elasticity at a certain choice of the model of solution structure in an approximation of the osmotic solution theory. The potential energy of the interaction between ions Φ ab ( r) was taken as the sum of the Lennard-Jones potential and the generalized Debye potential, taking into account the configuration and size of ions. In this approximation, the viscoelastic properties of the NaCl water solution were numerically calculated over a wide interval of change in the thermodynamic parameters and frequency ranges. Satisfactory agreement with the literature experimental data was obtained.
Si-coated single-walled carbon nanotubes under axial loads: An atomistic simulation study
NASA Astrophysics Data System (ADS)
HaiYang, Song; XinWei, Zha
2007-04-01
The mechanical properties of the Si-coated imperfect (5, 5) single-walled carbon nanotube (SWCNT), the imperfect (5, 5) SWCNT and several perfect armchair SWCNTs under axial loads were investigated using molecular dynamics simulation. The interactions between atoms were modeled using the empirical Tersoff potential and the Tersoff-Brenner potential coupled with the Lennard-Jones potential. We get Young's modulus of the defective (5, 5) nanotube with and without the Si coating under axial tension 1107.92 and 1076.02 GPa, respectively. The results also show that the structure failure of the Si-coated imperfect (5, 5) SWCNT under axial compression occurs at a slightly higher strain than for the perfect (5, 5) SWCNT. Therefore, we can confirm the protective effect of Si as a coating material for defective SWCNTs. We also obtain the critical buckling strains of perfect SWCNTs.
NASA Astrophysics Data System (ADS)
Kluge, M. D.; Wolf, D.; Lutsko, J. F.; Phillpot, S. R.
1990-03-01
A new formalism for use in atomistic simulations to calculate the full local elastic-constant tensor in terms of local stresses and strains is presented. Results of simulations on a high-angle (001) twist grain boundary are illustrated, using both a Lennard-Jones potential for Cu and an embedded-atom potential for Au. The two conceptionally rather different potentials show similar anomalies in all elastic constants, confined to within a few lattice planes of the grain boundary, with an especially dramatic reduction in the resistance to shear parallel to the grain-boundary plane. It is found that the primary cause of the anomalies is the atomic disorder near the grain boundary, as evidenced by the slice-by-slice radial distribution functions for the inhomogeneous interface system.
Topics in the Physics of Disordered Media
NASA Astrophysics Data System (ADS)
Zhang, Xifeng
1995-01-01
In this dissertation, we study two independent problems: the numerical calculation of electrical and optical properties of binary composite materials and molecular dynamical simulation of diffusion properties of liquids. Using transfer-matrix algorithm, we calculated the linear and nonlinear electrical and optical properties of binary composite materials. The linear optical properties of a composite thin film, such as the percolation threshold and the surface-plasmon resonance frequency, are strongly affected by its dimensionality. The numerical results, calculated with transfer-matrix method, are compared with the predictions from the effective medium approximation and scaling theory as well. We found that the cross-over from 2D to 3D is very quick. A composite thin film starts to behave like bulk composite in many properties when its thickness is only several layers. For the nonlinear electrical and optical properties, we calculated the third order Kerr nonlinear susceptibility. The effective nonlinear susceptibility of certain composites can be enhanced by a huge factor over that of the nonlinear component in its bulk form. These composites include the composites of embedded fractals of proper size, the composites in which the critical component having the concentration near its percolation threshold, and the dielectric-metal composites with certain concentration (about 5%) of metal component, which give maximum enhancement for the frequencies around the surface-plasmon resonance. In the second part of this dissertation, we present our preliminary study on the diffusion properties of two kinds of liquids: Lennard-Jones liquids and liquid semi -conductors. For Lennard-Jones liquids, we study the temperature dependence of the diffusion constant. The numerical results are compared with experimental measurement. We also calculated the diffusion constant of different Lennard-Jones impurities and found some interesting effects. For the liquid semiconductors, we tried
Predicting the thermodynamic properties of gold nanoparticles using different force fields
NASA Astrophysics Data System (ADS)
Park, Yongjin
The objective of this research was to learn how to predict the thermodynamic properties of gold nanoparticles using computational tools. The lowest energy structures of gold nanoparticles of various sizes were determined and thermodynamic properties such as the free energy (F), internal energy (U), entropy (S), and specific heat (Cv) of the gold nanoparticles were investigated using a fully-atomistic Monte Carlo simulation method that utilizes a modified Wang-Landau algorithm. Eight well-known force fields for metallic systems were employed to model gold nanoparticles: the Lennard-Jones potential (LJ), the Lennard-Jones potential with Heinz's parameterization (LJH), the Gupta potential, the Sutton-Chen potential (SC), the Sutton-Chen potential with Pawluk's parameterization for small clusters (SCP), the Quantum Sutton-Chen potential (Q-SC), the Embedded Atom Method (EAM) by Cai and Ye, and the empirical potential for gold proposed by Olivier and coworkers (POT). Subsequently, we explored the accuracy of each force field in the description of the thermodynamic behavior of gold nanoparticles. The thermodynamic properties of gold nanoparticles were computed from the Density of States which was obtained as a result of the Monte Carlo simulation. Afterwards, the melting point of gold nanoparticles was determined from the behavior of the calculated thermodynamic properties and was compared with theory, experimental observations and other simulation results. The force fields employed predicted melting points of gold nanoparticles over a wide range of temperatures. A thorough comparison with the available experimental observations showed that the Quantum Sutton-Chen potential (Q-SC) correctly described the melting behavior of gold nanoparticles with sizes smaller than 1.3 nanometers.
Energetically favoured defects in dense packings of particles on spherical surfaces.
Paquay, Stefan; Kusumaatmaja, Halim; Wales, David J; Zandi, Roya; van der Schoot, Paul
2016-06-29
The dense packing of interacting particles on spheres has proved to be a useful model for virus capsids and colloidosomes. Indeed, icosahedral symmetry observed in virus capsids corresponds to potential energy minima that occur for magic numbers of, e.g., 12, 32 and 72 identical Lennard-Jones particles, for which the packing has exactly the minimum number of twelve five-fold defects. It is unclear, however, how stable these structures are against thermal agitation. We investigate this property by means of basin-hopping global optimisation and Langevin dynamics for particle numbers between ten and one hundred. An important measure is the number and type of point defects, that is, particles that do not have six nearest neighbours. We find that small icosahedral structures are the most robust against thermal fluctuations, exhibiting fewer excess defects and rearrangements for a wide temperature range. Furthermore, we provide evidence that excess defects appearing at low non-zero temperatures lower the potential energy at the expense of entropy. At higher temperatures defects are, as expected, thermally excited and thus entropically stabilised. If we replace the Lennard-Jones potential by a very short-ranged (Morse) potential, which is arguably more appropriate for colloids and virus capsid proteins, we find that the same particle numbers give a minimum in the potential energy, although for larger particle numbers these minima correspond to different packings. Furthermore, defects are more difficult to excite thermally for the short-ranged potential, suggesting that the short-ranged interaction further stabilises equilibrium structures. PMID:27263532
Coronene molecules in helium clusters: Quantum and classical studies of energies and configurations
Rodríguez-Cantano, Rocío; Pérez de Tudela, Ricardo; Bartolomei, Massimiliano; Hernández, Marta I.; Campos-Martínez, José; González-Lezana, Tomás Villarreal, Pablo; Hernández-Rojas, Javier; Bretón, José
2015-12-14
Coronene-doped helium clusters have been studied by means of classical and quantum mechanical (QM) methods using a recently developed He–C{sub 24}H{sub 12} global potential based on the use of optimized atom-bond improved Lennard-Jones functions. Equilibrium energies and geometries at global and local minima for systems with up to 69 He atoms were calculated by means of an evolutive algorithm and a basin-hopping approach and compared with results from path integral Monte Carlo (PIMC) calculations at 2 K. A detailed analysis performed for the smallest sizes shows that the precise localization of the He atoms forming the first solvation layer over the molecular substrate is affected by differences between relative potential minima. The comparison of the PIMC results with the predictions from the classical approaches and with diffusion Monte Carlo results allows to examine the importance of both the QM and thermal effects.
Thermal conductivity of simple liquids: Origin of temperature and packing fraction dependences
NASA Astrophysics Data System (ADS)
Ishii, Yoshiki; Sato, Keisuke; Salanne, Mathieu; Madden, Paul A.; Ohtori, Norikazu
2014-03-01
The origin of both weak temperature dependence and packing fraction dependence of T1/4η3/2 in the thermal conductivity of the simple Lennard-Jones (LJ) liquid is explored. In order to discuss the relative contributions from attractive or repulsive part of the interaction potential separately, the thermal conductivity of a series of Weeks-Chandler-Anderson (WCA) fluids is calculated by molecular dynamics simulations. The results show that the repulsive part plays the main role in the heat conduction, while the attractive part has no direct effect on the thermal conductivity for a given packing fraction. By investigating WCA fluids with potentials of varying softness, we explain the difference observed between the LJ liquids such as argon and Coulombic liquids such as NaCl.
NASA Astrophysics Data System (ADS)
Shimizu, Futoshi; Kimizuka, Hajime; Kaburaki, Hideo
2002-08-01
A new parallel computing environment, called as ``Parallel Molecular Dynamics Stencil'', has been developed to carry out a large-scale short-range molecular dynamics simulation of solids. The stencil is written in C language using MPI for parallelization and designed successfully to separate and conceal parts of the programs describing cutoff schemes and parallel algorithms for data communication. This has been made possible by introducing the concept of image atoms. Therefore, only a sequential programming of the force calculation routine is required for executing the stencil in parallel environment. Typical molecular dynamics routines, such as various ensembles, time integration methods, and empirical potentials, have been implemented in the stencil. In the presentation, the performance of the stencil on parallel computers of Hitachi, IBM, SGI, and PC-cluster using the models of Lennard-Jones and the EAM type potentials for fracture problem will be reported.
Long-range interaction of anisotropic systems
NASA Astrophysics Data System (ADS)
Zhang, J.-Y.; Schwingenschlögl, U.
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, \\varepsilon(D) \\propto -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 \\varepsilon(D) \\propto -D-4 .
Hubbard, L.M.; Miller, W.H.
1983-02-15
The semiclassical perturbation (SCP) approximation of Miller and Smith (Phys. Rev. A 17, 17 (1978)) is applied to the scattering of atoms and molecules from crystal surfaces. Specifically, diffraction of He from LiF, and diffraction and rotationally inelastic scattering of H/sub 2/ from LiF are treated, and the SCP model is seen to agree well with earlier coupled-channel and quantum sudden calculations. These tests of the SCP model are all for ''soft'' interaction potentials, e.g., of the Lennard-Jones Devonshire variety, but it is also shown that the model behaves correctly in the limit of an impulsive hard-wall potential function. The SCP picture thus appears to have a wide range of validity for describing the dynamics of gas-surface collisions.
Theoretical study of the nucleation/growth process of carbon clusters under pressure.
Pineau, N; Soulard, L; Los, J H; Fasolino, A
2008-07-14
We used molecular dynamics and the empirical potential for carbon LCBOPII to simulate the nucleation/growth process of carbon clusters both in vacuum and under pressure. In vacuum, our results show that the growth process is homogeneous and yields mainly sp(2) structures such as fullerenes. We used an argon gas and Lennard-Jones potentials to mimic the high pressures and temperatures reached during the detonation of carbon-rich explosives. We found that these extreme thermodynamic conditions do not affect substantially the topologies of the clusters formed in the process. However, our estimation of the growth rates under pressure are in much better agreement with the values estimated experimentally than our vacuum simulations. The formation of sp(3) carbon was negligible both in vacuum and under pressure which suggests that larger simulation times and cluster sizes are needed to allow the nucleation of nanodiamonds. PMID:18624553
Nonequilibrium study of the intrinsic free-energy profile across a liquid-vapour interface.
Braga, Carlos; Muscatello, Jordan; Lau, Gabriel; Müller, Erich A; Jackson, George
2016-01-28
We calculate an atomistically detailed free-energy profile across a heterogeneous system using a nonequilibrium approach. The path-integral formulation of Crooks fluctuation theorem is used in conjunction with the intrinsic sampling method to calculate the free-energy profile for the liquid-vapour interface of the Lennard-Jones fluid. Free-energy barriers are found corresponding to the atomic layering in the liquid phase as well as a barrier associated with the presence of an adsorbed layer as revealed by the intrinsic density profile. Our findings are in agreement with profiles calculated using Widom's potential distribution theorem applied to both the average and the intrinsic profiles as well as the literature values for the excess chemical potential. PMID:26827224
Coronene molecules in helium clusters: Quantum and classical studies of energies and configurations.
Rodríguez-Cantano, Rocío; Pérez de Tudela, Ricardo; Bartolomei, Massimiliano; Hernández, Marta I; Campos-Martínez, José; González-Lezana, Tomás; Villarreal, Pablo; Hernández-Rojas, Javier; Bretón, José
2015-12-14
Coronene-doped helium clusters have been studied by means of classical and quantum mechanical (QM) methods using a recently developed He-C24H12 global potential based on the use of optimized atom-bond improved Lennard-Jones functions. Equilibrium energies and geometries at global and local minima for systems with up to 69 He atoms were calculated by means of an evolutive algorithm and a basin-hopping approach and compared with results from path integral Monte Carlo (PIMC) calculations at 2 K. A detailed analysis performed for the smallest sizes shows that the precise localization of the He atoms forming the first solvation layer over the molecular substrate is affected by differences between relative potential minima. The comparison of the PIMC results with the predictions from the classical approaches and with diffusion Monte Carlo results allows to examine the importance of both the QM and thermal effects. PMID:26671374
Influence of carbon nanotube on the structure evolution of Ni-Cu alloy nanorod
NASA Astrophysics Data System (ADS)
Guo, J.-Y.; Xu, C.-X.; Yang, C.; Dai, J.; Li, Z.-H.
2011-02-01
A Monte Carlo method has been performed to simulate the structure evolution of Ni-Cu alloy nanorods encapsulated in the carbon nanotube and removed from the carbon nanotube. The Sutton-Chen many-body potential and Lennard-Jones potential are used to describe the metal-metal and metal-carbon interactions, respectively. The studies show that all Ni-Cu atoms in carbon nanotube are arranged in a series of concentric cylindrical layers even they have different fractions, and Cu atoms are apt to stay at the surface layers. If the carbon nanotube was removed, Ni-Cu alloy nanorod would turn into a cluster with nickel core and copper shell. The physical origin for such structure formation and evolution toward core-shell motifs are discussed. The bond pair analysis shows that the nanorods and clusters are amorphous structures dominated by the rhombohedral structure and mixed up with some local short-range order.
NASA Astrophysics Data System (ADS)
Gouriet, K.; Zhigilei, L. V.; Itina, T. E.
2009-03-01
Long-time evolution of nanoparticles produced by short laser interactions is investigated for different materials. To better understand the mechanisms of the nanoparticle formation at a microscopic level, we use molecular dynamics (MD) simulations to analyse the evolution of a cluster in the presence of a background gas with different parameters (density and temperature). In particular, we compare the simulation results obtained for materials with different interaction potentials (Morse, Lennard-Jones, and Embedded Atom Model). Attention is focused on the evaporation and condensation processes of a cluster with different size and initial temperature. As a result of the MD calculations, we determinate the influence of both cluster properties and background gas parameters on the nanoparticle evolution. The role of the interaction potential is discussed based on the results of the simulations.
NASA Astrophysics Data System (ADS)
Ghoufi, Aziz; Morineau, Denis; Lefort, Ronan; Malfreyt, Patrice
2011-01-01
Molecular simulations in the isothermal statistical ensembles require that the macroscopic thermal and mechanical equilibriums are respected and that the local values of these properties are constant at every point in the system. The thermal equilibrium in Monte Carlo simulations can be checked through the calculation of the configurational temperature, {k_BT_{conf}={< |nabla _r U({r}^N)|2>}/{< nabla _r{^2} U({r}^N) >}}, where nabla _r is the nabla operator of position vector r. As far as we know, T_{conf} was never calculated with the anisotropic Gay-Berne potential, whereas the calculation of T_{conf} is much more widespread with more common potentials (Lennard Jones, electrostatic, …). We establish here an operational expression of the macroscopic and local configurational temperatures, and we investigate locally the isotropic liquid phase, the liquid / vapor interface, and the isotropic-nematic transition by Monte Carlo simulations.
NASA Astrophysics Data System (ADS)
D'Alessandro, Marco
2011-10-01
We present a method for the evaluation of the interaction potential of an equilibrium classical system starting from the (partial) knowledge of its structure factor. The procedure is divided into two phases, both of which are based on the maximum entropy principle of information theory. First we determine the maximum entropy estimate of the radial distribution function constrained by the information contained in the structure factor. Next we invert the pair function and extract the interaction potential. The method is tested on a Lennard-Jones fluid at high density and the reliability of its results with respect to the missing information in the structure factor data are discussed. Finally, it is applied to the experimental data of liquid sodium at 100 ∘C.
Ghoufi, Aziz; Morineau, Denis; Lefort, Ronan; Malfreyt, Patrice
2011-01-21
Molecular simulations in the isothermal statistical ensembles require that the macroscopic thermal and mechanical equilibriums are respected and that the local values of these properties are constant at every point in the system. The thermal equilibrium in Monte Carlo simulations can be checked through the calculation of the configurational temperature, k(B)T(conf)=<|∇(r)U(r(N))|(2)>/<∇(r) (2)U(r(N))>, where ∇(r) is the nabla operator of position vector r. As far as we know, T(conf) was never calculated with the anisotropic Gay-Berne potential, whereas the calculation of T(conf) is much more widespread with more common potentials (Lennard Jones, electrostatic, ...). We establish here an operational expression of the macroscopic and local configurational temperatures, and we investigate locally the isotropic liquid phase, the liquid / vapor interface, and the isotropic-nematic transition by Monte Carlo simulations. PMID:21261339
NASA Astrophysics Data System (ADS)
Cuestas, Eloisa; Serra, Pablo
2016-03-01
The localization of the valence electron of H, Li and Na atoms enclosed by three different fullerene molecules is studied. The structure of the fullerene molecules is used to calculate the equilibrium position of the endohedrally atom as the minimum of the classical (N + 1)-body Lennard-Jones potential. Once the position of the guest atom is determined, the fullerene cavity is modeled by a short range attractive shell according to molecule symmetry, and the enclosed atom is modeled by an effective one-electron potential. In order to examine whether the endohedral compound is formed by a neutral atom inside a neutral fullerene molecule X@CN or if the valence electron of the encapsulated atom localizes in the fullerene giving rise to a state with the form X+@CN‑, we analyze the electronic density, the projections onto free atomic states and the weights of partial angular waves.
Accurate transport properties for H–CO and H–CO{sub 2}
Dagdigian, Paul J.
2015-08-07
Transport properties for collisions of hydrogen atoms with CO and CO{sub 2} have been computed by means of quantum scattering calculations. The carbon oxides are important species in hydrocarbon combustion. The following potential energy surfaces (PES’s) for the interaction of the molecule fixed in its equilibrium geometry were employed: for H–CO, the PES was taken from the work of Song et al. [J. Phys. Chem. A 117, 7571 (2013)], while the PES for H–CO{sub 2} was computed in this study by a restricted coupled cluster method that included single, double, and (perturbatively) triple excitations. The computed transport properties were found to be significantly different from those computed by the conventional approach that employs isotropic Lennard-Jones (12-6) potentials. The effect of using the presently computed accurate transport properties in 1-dimensional combustion simulations of methane-air flames was investigated.
Phonon instabilities in uniaxially compressed fcc metals as seen in molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Kimminau, Giles; Erhart, Paul; Bringa, Eduardo M.; Remington, Bruce; Wark, Justin S.
2010-03-01
We show that the generation of stacking faults in perfect face-centered-cubic (fcc) crystals, uniaxially compressed along [001], is due to transverse-acoustic phonon instabilities. The position in reciprocal space where the instability first manifests itself is not a point of high symmetry in the Brillouin zone. This model provides a useful explanation for the magnitude of the elastic limit, in addition to the affects of box size, temperature, and compression on the time scale for the generation of stacking faults. We observe this phenomenon in both simulations that use the Lennard-Jones potential and embedded atom potentials. Not only does this work provide fundamental insight into the microscopic response of the material but it also describes certain behavior seen in previous molecular dynamics simulations of single-crystal fcc metals shock compressed along the principal axis.
Adhesion effects in contact interaction of solids
NASA Astrophysics Data System (ADS)
Goryacheva, Irina; Makhovskaya, Yulya
2008-01-01
An approach to solving problems of the interaction of axisymmetric elastic bodies in the presence of adhesion is developed. The different natures of adhesion, i.e. capillary adhesion, or molecular adhesion described by the Lennard-Jones potential are examined. The effect of additional loading of the interacting bodies outside the contact zone is also investigated. The approach is based on the representation of the pressure outside the contact zone arising from adhesion by a step function. The analytical solution is obtained and is used to analyze the influence of the form of the adhesion interaction potential, of the surface energy of interacting bodies or the films covering the bodies, their shapes (parabolic, higher power exponential function), volume of liquid in the meniscus, density of contact spots, of elastic modulus and the Poisson ratio on the characteristics of the interaction of the bodies in the presence of adhesion. To cite this article: I. Goryacheva, Y. Makhovskaya, C. R. Mecanique 336 (2008).
NASA Astrophysics Data System (ADS)
Vujić, Bojan; Lyubartsev, Alexander P.
2016-05-01
In this work we propose a new force field for modelling of adsorption of CO2, N2, O2 and Ar in all silica and Na+ exchanged Si-Al zeolites. The force field has a standard molecular-mechanical functional form with electrostatic and Lennard-Jones interactions satisfying Lorentz-Berthelot mixing rules and thus has a potential for further extension in terms of new molecular types. The parameters for the zeolite framework atom types are optimized by an iterative procedure minimizing the difference with experimental adsorption data for a number of different zeolite structures and Si:Al ratios. The new force field shows a good agreement with available experimental data including those not used in the optimization procedure, and which also shows a reasonable transferability within different zeolite topologies. We suggest a potential usage in screening of different zeolite structures for carbon capture and storage process, and more generally, for separation of other gases.
Nanostructured Composites: Effective Mechanical Property Determination of Nanotube Bundles
NASA Technical Reports Server (NTRS)
Saether, E.; Pipes, R. B.; Frankland, S. J. V.
2002-01-01
Carbon nanotubes naturally tend to form crystals in the form of hexagonally packed bundles or ropes that should exhibit a transversely isotropic constitutive behavior. Although the intratube axial stiffness is on the order of 1 TPa due to a strong network of delocalized bonds, the intertube cohesive strength is orders of magnitude less controlled by weak, nonbonding van der Waals interactions. An accurate determination of the effective mechanical properties of nanotube bundles is important to assess potential structural applications such as reinforcement in future composite material systems. A direct method for calculating effective material constants is developed in the present study. The Lennard-Jones potential is used to model the nonbonding cohesive forces. A complete set of transverse moduli are obtained and compared with existing data.
Transition saddle points and associated defects for a triaxially stretched FCC crystal
NASA Astrophysics Data System (ADS)
Delph, T. J.; Zimmerman, J. A.
2016-05-01
We demonstrate the use of a single-ended method for locating saddle points on the potential energy surface for a triaxially stretched FCC crystal governed by a Lennard-Jones potential. Single-ended methods require no prior knowledge of the defected state and are shown to have powerful advantages in this application, principally because the nature of the associated defects can be quite complicated and hence extremely difficult to predict ab initio. We find that while classical spherical cavitation occurs for high stretch values, for lower values the defect mode transitions to a non-spherical pattern without any apparent symmetries. This non-spherical mode plays the primary role in harmonic transition state theory predictions that are used to examine how instabilities vary with applied loading rate. Such a defect mode would be difficult to determine using double-ended methods for finding saddle points.
Accurate transport properties for H-CO and H-CO2
NASA Astrophysics Data System (ADS)
Dagdigian, Paul J.
2015-08-01
Transport properties for collisions of hydrogen atoms with CO and CO2 have been computed by means of quantum scattering calculations. The carbon oxides are important species in hydrocarbon combustion. The following potential energy surfaces (PES's) for the interaction of the molecule fixed in its equilibrium geometry were employed: for H-CO, the PES was taken from the work of Song et al. [J. Phys. Chem. A 117, 7571 (2013)], while the PES for H-CO2 was computed in this study by a restricted coupled cluster method that included single, double, and (perturbatively) triple excitations. The computed transport properties were found to be significantly different from those computed by the conventional approach that employs isotropic Lennard-Jones (12-6) potentials. The effect of using the presently computed accurate transport properties in 1-dimensional combustion simulations of methane-air flames was investigated.
NASA Astrophysics Data System (ADS)
Goldman, Saul
1981-10-01
A thermodynamic perturbation theory that derives from the work of Gray, Gubbins, and Stell is used to analyze the influence of the permanent dipole and quadrupole moments in water on a variety of thermodynamic functions that characterize hydrophobic solvation and hydrophobic interactions. The model used for water was a generalized Stockmayer potential. Experimental values were used for the dipole moment and for the three components of the quadrupole tensor of water, and the parameters for the Lennard-Jones part of this potential were taken from Finney et al.'s polarizable electropole model for water. This potential function involves reduced dipole and quadrupole moments that are shown to be within the range of validity of Stell's Padé approximant. Induced moments were not considered. The solute-solute and solute-solvent pair potential functions were taken to be the same as the Lennard-Jones part of the solvent-solvent pair potential function. The effects of three types of anisotropies, namely, dipole forces only, generalized quadrupole forces only, dipole-dipole plus generalized quadrupole-generalized quadrupole plus dipole-generalized quadrupole forces, are considered separately. Values obtained for the Henry's law constant, the heat of solution, the partial molal volume, and the partial molal heat capacity, at infinite dilution, are compared with ranges of experimental values for these quantities for the rare gases in water. The closeness of our results to those data, for our solvent with all the anisotropies simultaneously turned on, is, with the exception of the partial molal volume, remarkable good. The reason for this one failure is discussed. Most surprising perhaps was the result, again for the solvent with the most complicated anisotropy, that it was possible, over a restricted temperature range, to mimic the drop in the osmotic second virial coefficient that is found in real aqueous systems at ordinary temperatures. A physical explanation for this
Molecular Simulation of Solid-Fluid Phase Coexistence
NASA Astrophysics Data System (ADS)
Agrawal, Rupal
1995-01-01
A novel molecular simulation technique--Gibbs -Duhem integration method--provides the framework for the study of phase equilibria involving ordered phases, particularly solids. The technique allows coexistence to be determined by just one simulation, without ever attempting or performing particle insertions. This is achieved by thermodynamic integration along a path that coincides with the saturation line. This thesis aims at the development of simulation tools--in particular the Gibbs-Duhem technique--that can be used by researchers in molecular thermodynamics especially for the study of solids. The effect of both repulsive and attractive intermolecular forces on transitions involving two and three-phases for various model systems has been studied. We demonstrate how the Gibbs-Duhem integration technique may be modified to determine the phase diagram along a path in which the intermolecular potential itself varies. In particular, the method has been applied to evaluate solid-fluid coexistence for the inverse-power potential as a function of potential softness. Freezing into both fcc and bcc crystals has been investigated. The complete phase diagram for the Lennard-Jones model has also been determined and several semi-empirical 'melting rules' are examined in the light of these results. We also evaluate three-phase equilibria as a function of the intermolecular potential (a path that transforms the Lennard-Jones model into a square well model is defined). The first estimate of solid-liquid equilibrium for a square well model is also given. Solid-liquid-vapor triple point as a function of square well width has been computed. Isotropic -nematic transition for hard-ellipsoid mixtures as a model for liquid crystalline systems has also been studied. In addition, a thorough error analysis has been performed for the Gibbs-Duhem integration technique. We have also introduced a new simulation technique which is capable of determining the entire phase coexistence curve in a
An atomistic model of slip formation
NASA Technical Reports Server (NTRS)
Halicioglu, T.; Cooper, D. M.
1984-01-01
The results of an atomistic model for the simulation of the early stages of crack initiation in a two-dimensional triangular lattice are presented. In the current model, each particle in the system is treated discretely and assumed to be interacting with the surrounding particles via Lennard-Jones potentials. A uniaxial load (in incremental elongations) is applied to the rectangular two-dimensional slab in either the x or the y direction. After each incremental elongation the system is equilibrated using a static method. Initially, elastic behavior in the x and y directions is observed. Continued elongation results in plastic deformation. In lattices with point defects, the defects first move to the surface, creating vacancies which trigger plastic deformation.
First-order phase transitions in the real microcanonical ensemble
NASA Astrophysics Data System (ADS)
Schierz, Philipp; Zierenberg, Johannes; Janke, Wolfhard
2016-08-01
We present a simulation and data analysis technique to investigate first-order phase transitions and the associated transition barriers. The simulation technique is based on the real microcanonical ensemble where the sum of kinetic and potential energy is kept constant. The method is tested for the droplet condensation-evaporation transition in a Lennard-Jones system with up to 2048 particles at fixed density, using simple Metropolis-like sampling combined with a replica-exchange scheme. Our investigation of the microcanonical ensemble properties reveals that the associated transition barrier is significantly lower than in the canonical counterpart. Along the line of investigating the microcanonical ensemble behavior, we develop a framework for general ensemble evaluations. This framework is based on a clear separation between system-related and ensemble-related properties, which can be exploited to specifically tailor artificial ensembles suitable for first-order phase transitions.
NASA Astrophysics Data System (ADS)
Amelyushkin, I. A.; Stasenko, A. L.
2015-06-01
The principal aim of this work is to elaborate a robust physical model and the corresponding numerical code for prediction of the icing startup due to numerous water nanoparticles in the supercooled humid air. For this purpose, a scientified approach was used which is based not on the quantum-mechanics considerations but on the information about intermolecular potentials (especially, Lennard-Jones (LJ), etc.) tightly connected with the state equations of the corresponding specie (e. g., van der Waals for air and water and Mie-Grünaisen for circumfluent body). u In other words, the principal idea of this work is to adequately ascribe certain macroscopic characteristics of a water nanoparticle which may significantly differ from those indicated in physical reference books for bulk materials.
NASA Astrophysics Data System (ADS)
Kania, L.; Kamieńska-Trela, K.; Witanowski, M.
1984-06-01
The semiempirical molecular orbital CNDO/S-CI spectral parameterization is used in order to evaluate structural increments in UV spectra of a series of β-amino-α,β-un- saturated carbonyl compounds. For most of the compounds, theoretical values of con formational and configurational spectral effects are lower than the experimental ones. It is suggested that a substantial part of the discrepancy is associated with the neglect by the CNDO/S-CI approximation of the changes in the nonbonded interaction energies caused by conformational and configurational isomerizaticns. We show that the applica tion of due corrections based on simple electrostatic and van der Waals interactions according to the Lennard-Jones potentials leads to a good agreement in magnitude and sign between the experimental and theoretical increments.
Sub- and super-Maxwellian evaporation of simple gases from liquid water
NASA Astrophysics Data System (ADS)
Kann, Z. R.; Skinner, J. L.
2016-04-01
Non-Maxwellian evaporation of light atoms and molecules (particles) such as He and H2 from liquids has been observed experimentally. In this work, we use simulations to study systematically the evaporation of Lennard-Jones particles from liquid water. We find instances of sub- and super-Maxwellian evaporation, depending on the mass of the particle and the particle-water interaction strength. The observed trends are in qualitative agreement with experiment. We interpret these trends in terms of the potential of mean force and the effectiveness and frequency of collisions during the evaporation process. The angular distribution of evaporating particles is also analyzed, and it is shown that trends in the energy from velocity components tangential and normal to the liquid surface must be understood separately in order to interpret properly the angular distributions.
Sub- and super-Maxwellian evaporation of simple gases from liquid water.
Kann, Z R; Skinner, J L
2016-04-21
Non-Maxwellian evaporation of light atoms and molecules (particles) such as He and H2 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. PMID:27389228
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. PMID:22158949
Composition dependence of fluid thermophysical properties: Theory and modeling
Ely, J.F.
1993-03-29
Objectives are studies of equilibrium/nonequilibrium properties of asymmetric fluid mixtures through computer simulation (CS), development of predictive theories of mixture equilibrium properties, development and application of selection algorithm methodology for mixture equations of state, and use of theory to develop new engineering design models for fluid mixtures. Kirwood charging method CS of Lennard-Jones mixtures with large size ratios verified the Kirkwood-Buff/Baxter method of calculating chemical potentials. CS of n-butane showed that the rheology is not a function of system size. A modified stepwise regression algorithm was developed and applied to HFC R134a. An analytical expression was developed for conformal solution size correction for mixtures. The extended corresponding states theory (ECST) can be applied to systems having large polarity differences; an accurate representation was developed of bulk phase properties of water-hydrocarbon systems. It was found how to force ECST to reach the correct virial limit.
Composition dependence of fluid thermophysical properties: Theory and modeling. Progress report
Ely, J.F.
1993-03-29
Objectives are studies of equilibrium/nonequilibrium properties of asymmetric fluid mixtures through computer simulation (CS), development of predictive theories of mixture equilibrium properties, development and application of selection algorithm methodology for mixture equations of state, and use of theory to develop new engineering design models for fluid mixtures. Kirwood charging method CS of Lennard-Jones mixtures with large size ratios verified the Kirkwood-Buff/Baxter method of calculating chemical potentials. CS of n-butane showed that the rheology is not a function of system size. A modified stepwise regression algorithm was developed and applied to HFC R134a. An analytical expression was developed for conformal solution size correction for mixtures. The extended corresponding states theory (ECST) can be applied to systems having large polarity differences; an accurate representation was developed of bulk phase properties of water-hydrocarbon systems. It was found how to force ECST to reach the correct virial limit.
First-order phase transitions in the real microcanonical ensemble.
Schierz, Philipp; Zierenberg, Johannes; Janke, Wolfhard
2016-08-01
We present a simulation and data analysis technique to investigate first-order phase transitions and the associated transition barriers. The simulation technique is based on the real microcanonical ensemble where the sum of kinetic and potential energy is kept constant. The method is tested for the droplet condensation-evaporation transition in a Lennard-Jones system with up to 2048 particles at fixed density, using simple Metropolis-like sampling combined with a replica-exchange scheme. Our investigation of the microcanonical ensemble properties reveals that the associated transition barrier is significantly lower than in the canonical counterpart. Along the line of investigating the microcanonical ensemble behavior, we develop a framework for general ensemble evaluations. This framework is based on a clear separation between system-related and ensemble-related properties, which can be exploited to specifically tailor artificial ensembles suitable for first-order phase transitions. PMID:27627238
Takae, Kyohei; Onuki, Akira
2014-02-01
Using molecular dynamics simulation with an angle-dependent Lennard-Jones potential, we study orientational glass with quadrupolar symmetry in mixtures of elliptic particles and circular impurities in two dimensions. With a mild aspect ratio (= 1.23) and a mild size ratio (= 1.2), we realize a plastic crystal at relatively high temperature T. With further lowering T, we find a structural phase transition for very small impurity concentration c and pinned disordered orientations for not small c. The ellipses are anchored by the impurities in the planar alignment. With increasing c, the orientation domains composed of isosceles triangles gradually become smaller, resulting in orientational glass with crystal order. In our simulation, the impurity distribution becomes heterogeneous during quenching from liquid, which then produces rotational dynamic heterogeneities. We also examine rheology in orientational glass to predict a shape memory effect and a superelasticity effect, where a large fraction of the strain is due to collective orientation changes. PMID:25353473
Density scaling and quasiuniversality of flow-event statistics for athermal plastic flows.
Lerner, Edan; Bailey, Nicholas P; Dyre, Jeppe C
2014-11-01
Athermal steady-state plastic flows were simulated for the Kob-Andersen binary Lennard-Jones system and its repulsive version in which the sign of the attractive terms is changed to a plus. Properties evaluated include the distributions of energy drops, stress drops, and strain intervals between the flow events. We show that simulations at a single density in conjunction with an equilibrium-liquid simulation at the same density allow one to predict the plastic flow-event statistics at other densities. This is done by applying the recently established "hidden scale invariance" of simple liquids to the glass phase. The resulting scaling of flow-event properties reveals quasiuniversality, i.e., that the probability distributions of energy drops, stress drops, and strain intervals in properly reduced units are virtually independent of the microscopic pair potentials. PMID:25493793
The non-equilibrium charge screening effects in diffusion-driven systems with pattern formation
NASA Astrophysics Data System (ADS)
Kuzovkov, V. N.; Kotomin, E. A.; de la Cruz, M. Olvera
2011-07-01
The effects of non-equilibrium charge screening in mixtures of oppositely charged interacting molecules on surfaces are analyzed in a closed system. The dynamics of charge screening and the strong deviation from the standard Debye-Hückel theory are demonstrated via a new formalism based on computing radial distribution functions suited for analyzing both short-range and long-range spacial ordering effects. At long distances the inhomogeneous molecular distribution is limited by diffusion, whereas at short distances (of the order of several coordination spheres) by a balance of short-range (Lennard-Jones) and long-range (Coulomb) interactions. The non-equilibrium charge screening effects in transient pattern formation are further quantified. It is demonstrated that the use of screened potentials, in the spirit of the Debye-Hückel theory, leads to qualitatively incorrect results.
Vitrification of a monatomic simple liquid in two dimensions
NASA Astrophysics Data System (ADS)
Odagaki, Takashi; Mizuguchi, Tomoko
2011-03-01
We investigate vitrification and crystallization process of a monatomic system by molecular dynamics simulation, where atoms interact via Lennard-Jones-Gauss potential. We first determine the time-temperature-transformation diagram by observing the crystallization time of the rapidly quenched state from the melt. The crystallization time becomes shortest at a certain temperature T*. The glassy state at low temperatures is shown to be fairly long-lived. In order to examine atomic mechanism of the crystallization, we introduce a modified incoherent intermediate scattering function which measures the structural correlation to a target structure. We show that the crystallization above and below T* take different paths. We also determine the free energy landscape (FEL) and show that the atomic dynamics is consistent with the FEL picture of the glass transition. This work was partially supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Science, Sports and Culture.
NASA Astrophysics Data System (ADS)
Pandey, Ras; Farmer, Barry
2010-03-01
HIV-1 protease (1DIFA) consists of two polypeptide chains, each monomer with 99 residues where two aspartic acid residues (Asp^25) form the active catalytic site. The conformation and dynamics of the protein chain (with 198 residues) are investigated on a cubic lattice where empty sites represent effective solvent. Specificities of residues are captured via an interaction matrix (residue-residue, residue-solvent) of the Lennard-Jones potential. We examine global properties such as the variation of the root mean square displacement and radius of gyration with the time steps for a range of solvent interaction strength. Local quantities include energy and mobility profiles of residues to understand the active segments (useful in proteolysis). The hydrophobic residues possess higher energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. We find that the radius of gyration of the protein collapses (globular structure) in a narrow range of solvent interaction strength.
Huš, Matej; Urbic, Tomaz; Munaò, Gianmarco
2014-10-28
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.
(H2)2 mole-fraction altitude profile in the atmosphere of Jupiter: A computational study
NASA Astrophysics Data System (ADS)
Slanina, Z.; Kim, S. J.; Fox, K.
1994-02-01
The mole fraction x2 of (H2)2 in equilibrium mixture with H2 under the atmospheric conditions of Jupiter is evaluated from the dimerization equilibrium constant calculated by quantum-chemical treatments and also from the Lennard-Jones potential. The treatments are of an ab initio type with the second and fourth order Moller-Plesset perturbation techniques and a basis set superposition error evaluation. The computed dimerization equilibrium constant is combined with observed height profiles of temperature and pressure. In six treatments considered it is found that the mole fraction decreases with increasing height. Various approximations suggest the dimeric mole fraction at the Jupiter 1 atm pressure level between 0.04 and 1.06%.
Interaction field modeling of mini-UAV swarm
NASA Astrophysics Data System (ADS)
Liou, William W.; Ro, Kapseong; Szu, Harold
2006-05-01
A behavior-based, simple interaction model inspired by molecular interaction field depicted by the Lennard-Jones function is examined for the averaged interaction in swarming. The modeled kinematic equation of motion contains only one variable, instead of a multiple state variable dependence a more complete dynamics entails. The model assumes a spatial distribution of the potential associate with the swarm. The model has been applied to examine the formation of swarm and the results are reported. The modeling can be reflected in an equilibrium theory for the operation of a swarm of mini-UAVs pioneered by Szu, where every member serves the mission while exploiting other's loss, resulting in a zero-sum game among the team members.
Space-time properties of Gram-Schmidt vectors in classical Hamiltonian evolution.
Green, Jason R; Jellinek, Julius; Berry, R Stephen
2009-12-01
Not all tangent space directions play equivalent roles in the local chaotic motions of classical Hamiltonian many-body systems. These directions are numerically represented by basis sets of mutually orthogonal Gram-Schmidt vectors, whose statistical properties may depend on the chosen phase space-time domain of a trajectory. We examine the degree of stability and localization of Gram-Schmidt vector sets simulated with trajectories of a model three-atom Lennard-Jones cluster. Distributions of finite-time Lyapunov exponent and inverse participation ratio spectra formed from short-time histories reveal that ergodicity begins to emerge on different time scales for trajectories spanning different phase-space regions, in a narrow range of total energy and history length. Over a range of history lengths, the most localized directions were typically the most unstable and corresponded to atomic configurations near potential landscape saddles. PMID:20365252
NASA Astrophysics Data System (ADS)
Masnoon, Ahmed Shafkat; Bipasha, Ferdaushi Alam; Morshed, A. K. M. M.
2016-07-01
The effect of nanoparticles decoration on the thermal conductivity of a nanowire is studied using Non Equilibrium Molecular Dynamics (NEMD) simulation. The simulation was conducted using simplified molecular model with Lennard-Jones potential. Argon-like solid was used as the material for both the nanowire and nanoparticles. Nanoparticles were placed on the surface of the nanowire and also embedded inside the structure. Non-equilibrium molecular dynamics simulation was conducted by imposing temperature gradient along the length of the nanowire and thermal conductivity of the nanowire was calculated. Nanowire without any nanoparticles was used as the baseline data. Due to presence of nanoparticles thermal conductivity of the nanowire was observed to decrease and up to 40% reduction in thermal conductivity was observed. With the increase in number of the nanoparticles, thermal conductivity was observed to decrease; however size of nanoparticles has little effect.
Correlation between spatial heterogeneity and local dynamics
NASA Astrophysics Data System (ADS)
Bhatia, Ritwik; Medvedev, Grigori; Corti, David; Caruthers, James
2003-03-01
Spatially correlated dynamic heterogeneity has been observed in binary Lennard-Jones mixtures [1]; however, the properites that cause the dynamic heterogeneity are not completely understood. In order to investigate the origin of the dynamic heterogeneity, we have examined the correlation of various thermodynamic properties in the region surrounding the mobile particles. Specifically, the simulation box is divided into a number of sub-volumes and the autocorrelation functions of the density, potential energy and thermal energy are determioned for each sub-volume. A comparison of autocorrelation functions of the sub-volumes containing a large number of mobile particles to sub-volumes containing no mobile particles is reported. [1] Donati et. al., Phys Rev E. v60, n3, p3107, 1999.
(H2)2 mole-fraction altitude profile in the atmosphere of Jupiter: A computational study
NASA Technical Reports Server (NTRS)
Slanina, Zdenek; Kim, Sang J.; Fox, Kenneth
1994-01-01
The mole fraction x(sub 2) of (H2)2 in equilibrium mixture with H2 under the atmospheric conditions of Jupiter is evaluated from the dimerization equilibrium constant calculated by quantum-chemical treatments and also from the Lennard-Jones potential. The treatments are of an ab initio type with the second and fourth order Moller-Plesset perturbation techniques and a basis set superposition error evaluation. The computed dimerization equilibrium constant is combined with observed height profiles of temperature and pressure. In six treatments considered it is found that the mole fraction decreases with increasing height. Various approximations suggest the dimeric mole fraction at the Jupiter 1 atm pressure level between 0.04 and 1.06%.
NASA Astrophysics Data System (ADS)
Chushak, Y.; Travesset, A.
2005-12-01
Multiblock polymers in aqueous solution, where one or several blocks are hydrophobic, exhibit a rich variety of phases and states of aggregation. In this paper, we investigate a pentablock system ABCBA, where the B block is always hydrophilic and the A and C blocks have varying degrees of hydrophobicity depending on external conditions. We report coarse-grained molecular-dynamics simulations where the solvent is included explicitly and monomers interact via a 6-9 Lennard Jones potential function. The hydrophobic interaction is modeled by tuning the parameter controlling the strength of the interaction between the hydrophobic monomers and the solvent. We investigate the structure and morphology of the micelles for two concrete situations representing changes in temperature and the pH level. The simulated system is directly relevant to a recently synthesized pentablock system consisting of a triblock Pluronic® with an added pH-sensitive end group [B. C. Anderson et al., Macromolecules 36, 1670 (2003)].
Sodium Chloride, NaCl/ϵ: New Force Field.
Fuentes-Azcatl, Raúl; Barbosa, Marcia C
2016-03-10
A new computational model for sodium chloride, the NaCl/ϵ, is proposed. The force field employed for the description of the NaCl is based on a set of radial particle-particle pair potentials involving Lennard-Jones (LJ) and Coulombic forces. The parametrization is obtained by fitting the density of the crystal and the density and the dielectric constant of the mixture of the salt with water at a diluted solution. Our model shows good agreement with the experimental values for the density and for the surface tension of the pure system, and for the density, the viscosity, the diffusion, and the dielectric constant for the mixture with water at various molal concentrations. The NaCl/ϵ together with the water TIP4P/ϵ models provide a good approximation for studying electrolyte solutions. PMID:26890321
Stochastic stick-slip nanoscale friction on oxide surfaces.
Craciun, A D; Gallani, J L; Rastei, M V
2016-02-01
The force needed to move a nanometer-scale contact on various oxide surfaces has been studied using an atomic force microscope and theoretical modeling. Force-distance traces unveil a stick-slip movement with erratic slip events separated by several nanometers. A linear scaling of friction force with normal load along with low pull-off forces reveals dispersive adhesive interactions at the interface. We model our findings by considering a variable Lennard-Jones-like interaction potential, which accounts for slip-induced variation of the effective contact area. The model explains the formation and fluctuation of stick-slip phases and provides guidelines for predicting transitions from stick-slip to continuous sliding on oxide surfaces. PMID:26751769
Crystal structures and freezing of dipolar fluids.
Groh, B; Dietrich, S
2001-02-01
We investigate the crystal structure of classical systems of spherical particles with an embedded point dipole at T=0. The ferroelectric ground state energy is calculated using generalizations of the Ewald summation technique. Due to the reduced symmetry compared to the nonpolar case the crystals are never strictly cubic. For the Stockmayer (i.e., Lennard-Jones plus dipolar) interaction three phases are found upon increasing the dipole moment: hexagonal, body-centered orthorhombic, and body-centered tetragonal. An even richer phase diagram arises for dipolar soft spheres with a purely repulsive inverse power law potential approximately r(-n). A crossover between qualitatively different sequences of phases occurs near the exponent n=12. The results are applicable to electro- and magnetorheological fluids. In addition to the exact ground state analysis we study freezing of the Stockmayer fluid by density-functional theory. PMID:11308482
Loading-unloading of an elastic-plastic adhesive spherical microcontact.
Kadin, Y; Kligerman, Y; Etsion, I
2008-05-01
A numerical solution is presented for a single load-unload cycle of an adhesive contact between an elastic-plastic sphere and a rigid flat. The interacting forces between the sphere and the flat are obtained through connecting nonlinear spring elements having force-displacement behavior that obeys the Lennard-Jones potential. Kinematic, rather than isotropic, hardening is assumed for the sphere material to account for possible secondary plastification during the unloading. The well-known Tabor parameter and a plasticity parameter are shown to be the two main dimensionless parameters governing the problem. The effects of these two parameters on the load-approach curves, on the plastically deformed sphere profiles, and on the plastic strain fields inside the sphere are presented, showing different modes of separation during the unloading. PMID:18275967
Liquid crystal nanodroplets in solution
NASA Astrophysics Data System (ADS)
Brown, W. Michael; Petersen, Matt K.; Plimpton, Steven J.; Grest, Gary S.
2009-01-01
The aggregation of liquid crystal nanodroplets from a homogeneous solution is studied by molecular dynamics simulations. The liquid crystal particles are modeled as elongated ellipsoidal Gay-Berne particles while the solvent is modeled as spherical Lennard-Jones particles. Extending previous studies of Berardi et al. [J. Chem. Phys. 126, 044905 (2007)], we find that liquid crystal nanodroplets are not stable and that after sufficiently long times the nanodroplets always aggregate into a single large droplet. Results describing the droplet shape and orientation for different temperatures and shear rates are presented. The implementation of the Gay-Berne potential for biaxial ellipsoidal particles in a parallel molecular dynamics code is also briefly discussed.
Liquid crystal nanodroplets in solution.
Brown, W Michael; Petersen, Matt K; Plimpton, Steven J; Grest, Gary S
2009-01-28
The aggregation of liquid crystal nanodroplets from a homogeneous solution is studied by molecular dynamics simulations. The liquid crystal particles are modeled as elongated ellipsoidal Gay-Berne particles while the solvent is modeled as spherical Lennard-Jones particles. Extending previous studies of Berardi et al. [J. Chem. Phys. 126, 044905 (2007)], we find that liquid crystal nanodroplets are not stable and that after sufficiently long times the nanodroplets always aggregate into a single large droplet. Results describing the droplet shape and orientation for different temperatures and shear rates are presented. The implementation of the Gay-Berne potential for biaxial ellipsoidal particles in a parallel molecular dynamics code is also briefly discussed. PMID:19191407
Cluster pair correlation function of simple fluids: energetic connectivity criteria.
Pugnaloni, Luis A; Zarragoicoechea, Guillermo J; Vericat, Fernando
2006-11-21
We consider the clustering of Lennard-Jones particles by using an energetic connectivity criterion proposed long ago by Hill [J. Chem. Phys. 32, 617 (1955)] for the bond between pairs of particles. The criterion establishes that two particles are bonded (directly connected) if their relative kinetic energy is less than minus their relative potential energy. Thus, in general, it depends on the direction as well as on the magnitude of the velocities and positions of the particles. An integral equation for the pair connectedness function, proposed by two of the authors [Phys. Rev. E 61, R6067 (2000)], is solved for this criterion and the results are compared with those obtained from molecular dynamics simulations and from a connectedness Percus-Yevick-type integral equation for a velocity-averaged version of Hill's energetic criterion. PMID:17129128
Long-ranged solvation forces in a fluid with short-ranged interactions
NASA Astrophysics Data System (ADS)
Pertsin, Alexander J.; Grunze, Michael
2003-05-01
The grand canonical Monte Carlo technique is used to calculate the solvation force and interfacial tension in a simple Lennard-Jones fluid confined between two solid walls. Emphasis is placed on large wall-to-wall separations, where the oscillations of density and solvation force due to layering effects have decayed. Despite the short range of the fluid-fluid and fluid-wall interaction potentials used, the solvation force shows an unsuspectedly long-ranged behavior, remaining quite perceptible up to a separation of 100 molecular diameters. It is also found that the sign of the solvation force at large separations is not uniquely determined by the sign of the interfacial tension: The walls that are "philic" with respect to the constrained fluid may well exhibit both repulsive and attractive solvation forces.
Simple Molecular Reactive Force Field for Metal-Organic Synthesis.
Andrejevic, Jovana; Stevenson, James; Clancy, Paulette
2016-02-01
For colloidal quantum dots to transition from research laboratories to deployment as optical and electronic products, there will be a need to scale-up their production to large-scale manufacturing processes. This demand increases the need to understand their formation via a molecular representation of the nucleation of lead sulfide (PbS) quantum dot systems passivated by lead oleate complexes. We demonstrate the effectiveness of a new type of reactive potential, custom-made for this system, that is drawn from simple Morse, Lennard-Jones, and Coulombic components, which can reproduce reactions across a broad range of PbS quantum dot sizes with good accuracy. We validate the capability of this model to capture reactive systems by comparison to ab initio calculations for a reaction between two dots. PMID:26745239
Niiyama, Tomoaki; Shimizu, Yasushi; Kobayashi, Taizo R; Okushima, Teruaki; Ikeda, Kensuke S
2009-05-01
We investigate numerically and analytically the effects of conservation of total translational and angular momentum on the distribution of kinetic energy among particles in microcanonical particle systems with small number of degrees of freedom, specifically microclusters. Molecular dynamics simulations of microclusters with constant total energy and momenta, using Lennard-Jones, Morse, and Coulomb plus Born-Mayer-type potentials, show that the distribution of kinetic energy among particles can be inhomogeneous and depend on particle mass and position even in thermal equilibrium. Statistical analysis using a microcanonical measure taking into account of the additional conserved quantities gives theoretical expressions for kinetic energy as a function of the mass and position of a particle with only O(1/N;{2}) deviation from the Maxwell-Boltzmann distribution. These expressions fit numerical results well. Finally, we propose an intuitive interpretation for the inhomogeneity of the kinetic energy distributions. PMID:19518410
Structure factor and rheology of chain molecules from molecular dynamics
NASA Astrophysics Data System (ADS)
Castrejón-González, Omar; Castillo-Tejas, Jorge; Manero, Octavio; Alvarado, Juan F. J.
2013-05-01
Equilibrium and non-equilibrium molecular dynamics were performed to determine the relationship between the static structure factor, the molecular conformation, and the rheological properties of chain molecules. A spring-monomer model with Finitely Extensible Nonlinear Elastic and Lennard-Jones force field potentials was used to describe chain molecules. The equations of motion were solved for shear flow with SLLOD equations of motion integrated with Verlet's algorithm. A multiple time scale algorithm extended to non-equilibrium situations was used as the integration method. Concentric circular patterns in the structure factor were obtained, indicating an isotropic Newtonian behavior. Under simple shear flow, some peaks in the structure factor were emerged corresponding to an anisotropic pattern as chains aligned along the flow direction. Pure chain molecules and chain molecules in solution displayed shear-thinning regions. Power-law and Carreau-Yasuda models were used to adjust the generated data. Results are in qualitative agreement with rheological and light scattering experiments.
Cyclic loading of an elastic-plastic adhesive spherical microcontact
NASA Astrophysics Data System (ADS)
Kadin, Y.; Kligerman, Y.; Etsion, I.
2008-10-01
A previous study of a single load-unload cycle of an adhesive contact between an elastic-plastic microscopic sphere and a rigid flat is extended here for several load-unload cycles. The interacting forces between the sphere and the flat obey the Lennard-Jones potential. Kinematic hardening is assumed for the sphere material to account for possible plastic shakedown, and the difference between kinematic and isotropic hardenings is discussed. The main goal of the current work is to investigate the evolution of the load-approach curves for the elastic-plastic spherical contact during its cyclic loading-unloading. These curves are presented for different physical conditions, represented by three main dimensionless parameters, which affect the behavior of the elastic-plastic adhesive contact. A transition value of the Tabor parameter is found, below which the load-approach curves are always continuous and jump-in and jump-out instabilities are not expected.
Distribution of Thermally Activated Plastic Events in a Flowing Glass
NASA Astrophysics Data System (ADS)
Rodney, David; Schuh, Christopher
2009-06-01
The potential energy landscape of a flowing metallic glass is revealed using the activation-relaxation technique. For a two-dimensional Lennard-Jones system initially deformed into a steady-state condition through quasistatic shear, the distribution of activation energies is shown to contain a large fraction of low-energy barriers, consistent with a highly nonequilibrium flow state. The distribution of plastic strains has a fundamentally different shape than that obtained during quasistatic simulations, exhibiting a peak at finite strain and, after elastic unloading, a nonzero mean plastic strain that evidences a polarization of the flow state. No significant correlation is found between the activation energy of a plastic event and its associated plastic strain.
Jump-in induced plastic yield onset of approaching microcontacts in the presence of adhesion
NASA Astrophysics Data System (ADS)
Kadin, Y.; Kligerman, Y.; Etsion, I.
2008-01-01
Approach between two deformable microbodies in the presence of adhesion is sometimes accompanied by discontinuous change of the surface profile at the narrow region near their summits (jump-in phenomenon). Previous studies of adhesive spherical contact showed that neck formation during jump-in always involves onset of local plastic yield near the edge of the contact zone. The current paper reveals that pure elastic jump-in is also feasible. The solution is based on a Lennard-Jones potential in combination with the von Mises yield criterion. The theoretical strength rather than the engineering yield strength of the material is used and the sufficient condition for jump-in induced onset of plastic yield under this extreme strength is discussed.
Characteristic quantities and dimensional analysis
NASA Astrophysics Data System (ADS)
Grimvall, Göran
2008-04-01
Phenomena in the physical sciences are described with quantities that have a numerical value and a dimension, i.e., a physical unit. Dimensional analysis is a powerful aspect of modeling and simulation. Characteristic quantities formed by a combination of model parameters can give new insights without detailed analytic or numerical calculations. Dimensional requirements lead to Buckingham’s Π theorem—a general mathematical structure of all models in physics. These aspects are illustrated with many examples of modeling, e.g., an elastic beam on supports, wave propagation on a liquid surface, the Lennard-Jones potential for the interaction between atoms, the Lindemann melting rule, and saturation phenomena in electrical and thermal conduction.
Prediction of radial breathing-like modes of double-walled carbon nanotubes with arbitrary chirality
NASA Astrophysics Data System (ADS)
Ghavanloo, Esmaeal; Fazelzadeh, S. Ahmad
2014-10-01
The radial breathing-like modes (RBLMs) of double-walled carbon nanotubes (DWCNTs) with arbitrary chirality are investigated by a simple analytical model. For this purpose, DWCNT is considered as double concentric elastic thin cylindrical shells, which are coupled through van der Waals (vdW) forces between two adjacent tubes. Lennard-Jones potential and a molecular mechanics model are used to calculate the vdW forces and to predict the mechanical properties, respectively. The validity of these theoretical results is confirmed through the comparison of the experimental results. Finally, a new approach is proposed to determine the diameters and the chiral indices of the inner and outer tubes of the DWCNTs with high precision.
Anomalous sound propagation and slow kinetics in dynamically compressed amorphous carbon
NASA Astrophysics Data System (ADS)
Reed, Evan J.; Maiti, Amitesh; Fried, Laurence E.
2010-01-01
We have performed molecular-dynamics simulations of dynamic compression waves propagating through amorphous carbon using the Tersoff potential and find that a variety of dynamic compression features appear for two different initial densities. These features include steady elastic shocks, steady chemically reactive shocks, unsteady elastic waves, and unsteady chemically reactive waves. We show how these features can be distinguished by analyzing time-dependent propagation speeds, time-dependent sound speeds, and comparison to multiscale shock technique (MSST) simulations. Understanding such features is a key challenge in quasi-isentropic experiments involving phase transformations. In addition to direct simulations of dynamic compression, we employ the MSST and find agreement with the direct method for this system for the shocks observed. We show how the MSST can be extended to include explicit material viscosity and demonstrate on an amorphous Lennard-Jones system.
Characteristic quantities and dimensional analysis
NASA Astrophysics Data System (ADS)
Grimvall, Göran
Phenomena in the physical sciences are described with quantities that have a numerical value and a dimension, i.e., a physical unit. Dimensional analysis is a powerful aspect of modeling and simulation. Characteristic quantities formed by a combination of model parameters can give new insights without detailed analytic or numerical calculations. Dimensional requirements lead to Buckingham's Π theorem—a general mathematical structure of all models in physics. These aspects are illustrated with many examples of modeling, e.g., an elastic beam on supports, wave propagation on a liquid surface, the Lennard-Jones potential for the interaction between atoms, the Lindemann melting rule, and saturation phenomena in electrical and thermal conduction.
NASA Astrophysics Data System (ADS)
Flores-Ruiz, Hugo M.; Naumis, Gerardo G.
2009-10-01
Using molecular dynamics at constant pressure, the relationship between the excess of low frequency vibrational modes (known as the boson peak) and the glass transition is investigated for a truncated Lennard-Jones potential. It is observed that the quadratic mean displacement is enhanced by such modes, as predicted using a harmonic Hamiltonian for metastable states. As a result, glasses loose mechanical stability at lower temperatures than the corresponding crystal, since the Lindemann criteria are observed, as is also deduced from density functional theory. Finally, we found that the average force and elastic constant are reduced in the glass due to such excess of modes. The ratio between average elastic constants can be approximated using the 2/3 rule between melting and glass transition temperatures.
An atomistic J-integral at finite temperature based on Hardy estimates of continuum fields
NASA Astrophysics Data System (ADS)
Jones, R. E.; Zimmerman, J. A.; Oswald, J.; Belytschko, T.
2011-01-01
In this work we apply a material-frame, kernel-based estimator of continuum fields to atomic data in order to estimate the J-integral for the analysis of an atomically sharp crack at finite temperatures. Instead of the potential energy appropriate for zero temperature calculations, we employ the quasi-harmonic free energy as an estimator of the Helmholtz free energy required by the Eshelby stress in isothermal conditions. We employ the simplest of the quasi-harmonic models, the local harmonic model of LeSar and co-workers, and verify that it is adequate for correction of the zero temperature J-integral expression for various deformation states for our Lennard-Jones test material. We show that this method has the properties of: consistency among the energy, stress and deformation fields; path independence of the contour integrals of the Eshelby stress; and excellent correlation with linear elastic fracture mechanics theory.
Quick and accurate estimation of the elastic constants using the minimum image method
NASA Astrophysics Data System (ADS)
Tretiakov, Konstantin V.; Wojciechowski, Krzysztof W.
2015-04-01
A method for determining the elastic properties using the minimum image method (MIM) is proposed and tested on a model system of particles interacting by the Lennard-Jones (LJ) potential. The elastic constants of the LJ system are determined in the thermodynamic limit, N → ∞, using the Monte Carlo (MC) method in the NVT and NPT ensembles. The simulation results show that when determining the elastic constants, the contribution of long-range interactions cannot be ignored, because that would lead to erroneous results. In addition, the simulations have revealed that the inclusion of further interactions of each particle with all its minimum image neighbors even in case of small systems leads to results which are very close to the values of elastic constants in the thermodynamic limit. This enables one for a quick and accurate estimation of the elastic constants using very small samples.
Mechanics of physisorption on elastomer surface
NASA Astrophysics Data System (ADS)
He, L. H.
2010-09-01
Mechanical aspects of physisorption on elastomeric substrates are studied via a continuum model in combination with the Lennard-Jones potential. In light of the incompressibility of elastomers, it is shown that the presence of a zero-dimensional adsorbate gives rise to a distributed force on the surface of the substrate. The induced surface deformation is determined, and the adsorption force and energy which depend on the substrate stiffness are derived. The results are then used to examine mutual interaction between two like adsorbates with small spacing, showing complicated attraction and repulsion arising from elastic deformation of the substrate. The dipole and quadruple moments of an adsorbate are also calculated, and the multipole approximation is adopted to quantify the interaction when the two adsorbates are separated remotely.
NASA Astrophysics Data System (ADS)
Asenjo, Daniel; Lund, Fernando; Poblete, Simón; Soto, Rodrigo; Sotomayor, Marcos
2011-05-01
A molecular dynamics study of a two-dimensional system of particles interacting through a Lennard-Jones pairwise potential is performed at a fixed temperature and vanishing external pressure. As the temperature is increased, a solid-to-liquid transition occurs. When the melting temperature Tc is approached from below, there is a proliferation of dislocation pairs and the elastic constant approaches the value predicted by the KTHNY theory. In addition, as Tc is approached from above, the relaxation time increases, consistent with an approach to criticality. However, simulations fail to produce a stable hexatic phase using systems with up to 90,000 particles. A significant jump in enthalpy at Tc is observed, consistent with either a first order or a continuous transition. The role of external pressure is discussed.
A multiscale modeling approach to adhesive contact
NASA Astrophysics Data System (ADS)
Fan, KangQi; Wang, WeiDong; Zhu, YingMin; Zhang, XiuYan
2011-09-01
In order to model the adhesive contact across different length scales, a multiscale approach is developed and used to study the adhesive contact behaviors between a rigid cylinder and an elastic face-centered cubic (FCC) substrate. The approach combines an atomistic treatment of the interfacial region with an elastic mechanics method description of the continuum region. The two regions are connected by a coupling region where nodes of the continuum region are refined to atoms of the atomistic region. Moreover, the elastic constants of FCC crystals are obtained directly from the Lennard-Jones potential to describe the elastic response characteristics of the continuum region, which ensures the consistency of material proprieties between atomistic and continuum regions. The multiscale approach is examined by comparing it with the pure MD simulation, and the results indicate that the multiscale modeling approach agrees well with the MD method in studying the adhesive contact behaviors.
Local structural excitations in model glass systems under applied load
NASA Astrophysics Data System (ADS)
Swayamjyoti, S.; Löffler, J. F.; Derlet, P. M.
2016-04-01
The potential-energy landscape of a model binary Lennard-Jones structural glass is investigated as a function of applied external strain, in terms of how local structural excitations (LSEs) respond to the load. Using the activation relaxation technique and nudged elastic band methods, the evolving structure and barrier energy of such LSEs are studied in detail. For the case of a tensile/compressive strain, the LSE barrier energies generally decrease/increase, whereas under pure shear, it may either increase or decrease resulting in a broadening of the barrier energy distribution. It is found that how a particular LSE responds to an applied strain is strongly controlled by the LSE's far-field internal stress signature prior to loading.
Diffusion on strained surfaces
NASA Astrophysics Data System (ADS)
Schroeder, M.; Wolf, D. E.
1997-03-01
The change of diffusion kinetics when elastic fields are present is discussed for diffusion on (001) surfaces of simple cubic, fcc and bcc lattices. All particles interact pairwise with a Lennard-Jones potential. The simple cubic lattice was stabilized by an anisotropic prefactor. It is found that generically compressive strain enhances diffusion whereas tensile strain increases the activation barrier. An approximately linear dependence of the barrier in a wide range of misfits is found. In heteroepitaxy, diffusion on top of large clusters is inhomogeneous and anisotropic. The kinetics close to edges and centers of islands are remarkably different. In many cases changes of binding energies are small compared to those of saddle point energies. Thermodynamic arguments (minimization of free energy) are not appropriate to describe diffusion on strained surfaces in these cases.
Shape transition and dislocation nucleation in strained epitaxial islands
NASA Astrophysics Data System (ADS)
Trushin, Oleg; Granato, Enzo; Ying, See Chen; Jalkanen, Jari; Ala-Nissila, Tapio
2004-03-01
We study numerically the equilibrium shape and dislocation nucleation of strained epitaxial islands with a two-dimensional atomistic model, using interatomic potentials of Lennard-Jones type. Relaxation processes from coherent to incoherent states for different transition paths are studied using a systematic saddle point and transition path search based on the Nudged Elastic Band method. We obtain the phase diagram for island shapes, as a function of island size and lattice misfit with the substrate, as well the energy barrier for first order shape transitions. The minimum energy barrier and transition path for dislocation nucleation is also obtained for different island shapes. It is found that dislocations can nucleate spontaneously at the edges of the adsorbate-substrate interface above a critical size.
NASA Astrophysics Data System (ADS)
Hoheisel, C.; Vogelsang, R.; Schoen, M.
1987-01-01
The vectorization of FORTRAN programmes for the computation of the forces in molecular dynamics (MD) calculations are described. For systems containing linear molecules, two equivalent MD methods can be used: the Singer method and the constraints method. The FORTRAN vector code is presented and discussed for both methods. A comparison of computational times on the CYBER 205 is presented. For the two-centre Lennard-Jones potential, the constraints algorithm becomes increasingly less efficient than the Singer algorithm when executed on the CYBER 205. The reason for this is the difference in the neighbour-list which is made for the centre of each molecule in the Singer method and for each site in the molecule in the constraints method. Both programmes run about a factor of 15 faster on the Cyber 205 than on the conventional computer Cyber 175, for 108 or 256 linear molecules.
Density scaling and quasiuniversality of flow-event statistics for athermal plastic flows
NASA Astrophysics Data System (ADS)
Lerner, Edan; Bailey, Nicholas P.; Dyre, Jeppe C.
2014-11-01
Athermal steady-state plastic flows were simulated for the Kob-Andersen binary Lennard-Jones system and its repulsive version in which the sign of the attractive terms is changed to a plus. Properties evaluated include the distributions of energy drops, stress drops, and strain intervals between the flow events. We show that simulations at a single density in conjunction with an equilibrium-liquid simulation at the same density allow one to predict the plastic flow-event statistics at other densities. This is done by applying the recently established "hidden scale invariance" of simple liquids to the glass phase. The resulting scaling of flow-event properties reveals quasiuniversality, i.e., that the probability distributions of energy drops, stress drops, and strain intervals in properly reduced units are virtually independent of the microscopic pair potentials.
Cell model and elastic moduli of disordered solids - Low temperature limit
NASA Technical Reports Server (NTRS)
Peng, S. T. J.; Landel, R. F.; Moacanin, J.; Simha, Robert; Papazoglou, Elisabeth
1987-01-01
The cell theory has been previously employed to compute the equation of state of a disordered condensed system. It is now generalized to include anisotropic stresses. The condition of affine deformation is adopted, transforming an orginally spherical into an ellipsoidal cell. With a Lennard-Jones n-m potential between nonbonded centers, the formal expression for the deformational free energy is derived. It is to be evaluated in the limit of the linear elastic range. Since the bulk modulus in this limit is already known, it is convenient to consider a uniaxial deformation. To begin with, restrictions are made to the low-temperature limit in the absence of entropy contributions. Young's modulus and Poisson's ratio then follow.
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
Bernards, C.; Heinze, S.; Jolie, J.; Fransen, C.; Linnemann, A.; Radeck, D.
2009-05-15
Using the U{sub {nu}}(6/12) x U{sub {pi}}(6/4) extended supersymmetry, we constructed the energy spectrum and electromagnetic transition properties of the supermultiplet member {sup 198}Hg with two proton fermions coupled to a neutron boson core. Consistency between the supersymmetric interacting boson fermion fermion approximation (IBFFA) description and the F-spin symmetric interacting boson approximation (IBA-2) description is shown for this two-fermion-N-boson multiplet member. The data of a {gamma}{gamma} angular correlation experiment using the HORUS cube {gamma}-ray spectrometer--determining new multipole mixing ratios, level spins, {gamma} transitions, and energy states--shows quite a good agreement, also for the low-energy part of the spectrum, when comparing theoretical predictions and experimental data. This is contrary to the usual assumption that a two-fermion-N-boson constellation should describe just the excited two-quasiparticle states.
A new intermolecular potential for simulations of methanol: The OPLS/2016 model
NASA Astrophysics Data System (ADS)
Gonzalez-Salgado, D.; Vega, C.
2016-07-01
In this work, a new rigid-nonpolarizable model of methanol is proposed. The model has three sites, located at the same positions as those used in the OPLS model previously proposed by Jorgensen [J. Phys. Chem. 90, 1276 (1986)]. However, partial charges and the values of the Lennard-Jones parameters were modified by fitting to an adequately selected set of target properties including solid-fluid experimental data. The new model was denoted as OPLS/2016. The overall performance of this model was evaluated and compared to that obtained with other popular models of methanol using a similar test to that recently proposed for water models. In the test, a certain numerical score is given to each model. It was found that the OPLS/2016 obtained the highest score (7.4 of a maximum of 10) followed by L1 (6.6), L2 (6.4), OPLS (5.8), and H1 (3.5) models. The improvement of OPLS/2016 with respect to L1 and L2 is mainly due to an improvement in the description of fluid-solid equilibria (the melting point is only 14 K higher than the experimental value). In addition, it was found that no methanol model was able to reproduce the static dielectric constant and the isobaric heat capacity, whereas the better global performance was found for models that reproduce the vaporization enthalpy once the so-called polarization term is included. Similar conclusions were suggested previously in the analysis of water models and are confirmed here for methanol.
A new intermolecular potential for simulations of methanol: The OPLS/2016 model.
Gonzalez-Salgado, D; Vega, C
2016-07-21
In this work, a new rigid-nonpolarizable model of methanol is proposed. The model has three sites, located at the same positions as those used in the OPLS model previously proposed by Jorgensen [J. Phys. Chem. 90, 1276 (1986)]. However, partial charges and the values of the Lennard-Jones parameters were modified by fitting to an adequately selected set of target properties including solid-fluid experimental data. The new model was denoted as OPLS/2016. The overall performance of this model was evaluated and compared to that obtained with other popular models of methanol using a similar test to that recently proposed for water models. In the test, a certain numerical score is given to each model. It was found that the OPLS/2016 obtained the highest score (7.4 of a maximum of 10) followed by L1 (6.6), L2 (6.4), OPLS (5.8), and H1 (3.5) models. The improvement of OPLS/2016 with respect to L1 and L2 is mainly due to an improvement in the description of fluid-solid equilibria (the melting point is only 14 K higher than the experimental value). In addition, it was found that no methanol model was able to reproduce the static dielectric constant and the isobaric heat capacity, whereas the better global performance was found for models that reproduce the vaporization enthalpy once the so-called polarization term is included. Similar conclusions were suggested previously in the analysis of water models and are confirmed here for methanol. PMID:27448897
Grzybowski, A; Koperwas, K; Paluch, M
2014-01-28
In this paper, based on the effective intermolecular potential with well separated density and configuration contributions and the definition of the isothermal bulk modulus, we derive two similar equations of state dedicated to describe volumetric data of supercooled liquids studied in the extremely wide pressure range related to the density range, which is extremely wide in comparison with the experimental range reached so far in pressure-volume-temperature measurements of glass-forming liquids. Both the equations comply with the generalized density scaling law of molecular dynamics versus h(ρ)/T at different densities ρ and temperatures T, where the scaling exponent can be in general only a density function γ(ρ) = d ln h/d ln ρ as recently argued by the theory of isomorphs. We successfully verify these equations of state by using data obtained from molecular dynamics simulations of the Kob-Andersen binary Lennard-Jones liquid. As a very important result, we find that the one-parameter density function h(ρ) analytically formulated in the case of this prototypical model of supercooled liquid, which implies the one-parameter density function γ(ρ), is able to scale the structural relaxation times with the value of this function parameter determined by fitting the volumetric simulation data to the equations of state. We also show that these equations of state properly describe the pressure dependences of the isothermal bulk modulus and the configurational isothermal bulk modulus in the extremely wide pressure range investigated by the computer simulations. Moreover, we discuss the possible forms of the density functions h(ρ) and γ(ρ) for real glass formers, which are suggested to be different from those valid for the model of supercooled liquid based on the Lennard-Jones intermolecular potential. PMID:25669550
Deterministic numerical solutions of the Boltzmann equation using the fast spectral method
NASA Astrophysics Data System (ADS)
Wu, Lei; White, Craig; Scanlon, Thomas J.; Reese, Jason M.; Zhang, Yonghao
2013-10-01
The Boltzmann equation describes the dynamics of rarefied gas flows, but the multidimensional nature of its collision operator poses a real challenge for its numerical solution. In this paper, the fast spectral method [36], originally developed by Mouhot and Pareschi for the numerical approximation of the collision operator, is extended to deal with other collision kernels, such as those corresponding to the soft, Lennard-Jones, and rigid attracting potentials. The accuracy of the fast spectral method is checked by comparing our numerical solutions of the space-homogeneous Boltzmann equation with the exact Bobylev-Krook-Wu solutions for a gas of Maxwell molecules. It is found that the accuracy is improved by replacing the trapezoidal rule with Gauss-Legendre quadrature in the calculation of the kernel mode, and the conservation of momentum and energy are ensured by the Lagrangian multiplier method without loss of spectral accuracy. The relax-to-equilibrium processes of different collision kernels with the same value of shear viscosity are then compared; the numerical results indicate that different forms of the collision kernels can be used as long as the shear viscosity (not only the value, but also its temperature dependence) is recovered. An iteration scheme is employed to obtain stationary solutions of the space-inhomogeneous Boltzmann equation, where the numerical errors decay exponentially. Four classical benchmarking problems are investigated: the normal shock wave, and the planar Fourier/Couette/force-driven Poiseuille flows. For normal shock waves, our numerical results are compared with a finite difference solution of the Boltzmann equation for hard sphere molecules, experimental data, and molecular dynamics simulation of argon using the realistic Lennard-Jones potential. For planar Fourier/Couette/force-driven Poiseuille flows, our results are compared with the direct simulation Monte Carlo method. Excellent agreements are observed in all test cases
Electro-osmosis in a nanometer-scale channel studied by atomistic simulation
NASA Astrophysics Data System (ADS)
Freund, Jonathan B.
2002-02-01
An atomistic simulation of an electro-osmotic flow in a 65.3 Å-wide channel is performed to study its physical details and evaluate continuum models. The working fluid is a 0.01 M solution (at midchannel) of Cl- in water. For simplicity and computational efficiency, only negatively charged ions are included. The water is modeled by the SPC/E potential and the Cl- are modeled as point charges plus an established Lennard-Jones potential. The channel walls are fixed lattices of positively charged Lennard-Jones atoms. In one case an appropriate fraction of the wall atoms is given elementary charges; for comparison, another case is simulated with uniformly distributed partial charges on the wall atoms. For the distributed elementary charge case the Cl- concentration at the wall is 80 percent higher than predicted by the Poisson-Boltzmann theory. It is over 100 percent higher for the uniformly charged wall case. In both cases, the waters in the 10 Å closest to the walls are preferentially oriented. Their respective orientations are similar except in the first monolayer. However, the effect of this orientational bias on the permittivity and subsequently the Cl- distribution is shown to be minor by Monte Carlo simulations, which predict an ion distribution in agreement with the dynamic simulation using only ɛ=80 to model the water. Computed, one-dimensional self-diffusivities of the waters match accepted values greater than 10 Å from the walls, but decay significantly close to the walls. The decay is not monotonic for the wall-normal diffusivity. The atoms near the walls are not fixed in a Stern layer, as typically assumed in models, but the viscosity is found to increase by over a factor of 6 in the 10 Å closest to the wall.
NASA Astrophysics Data System (ADS)
Collell, Julien; Galliero, Guillaume
2014-05-01
The multi-component diffusive mass transport is generally quantified by means of the Maxwell-Stefan diffusion coefficients when using molecular simulations. These coefficients can be related to the Fick diffusion coefficients using the thermodynamic correction factor matrix, which requires to run several simulations to estimate all the elements of the matrix. In a recent work, Schnell et al. ["Thermodynamics of small systems embedded in a reservoir: A detailed analysis of finite size effects," Mol. Phys. 110, 1069-1079 (2012)] developed an approach to determine the full matrix of thermodynamic factors from a single simulation in bulk. This approach relies on finite size effects of small systems on the density fluctuations. We present here an extension of their work for inhomogeneous Lennard Jones fluids confined in slit pores. We first verified this extension by cross validating the results obtained from this approach with the results obtained from the simulated adsorption isotherms, which allows to determine the thermodynamic factor in porous medium. We then studied the effects of the pore width (from 1 to 15 molecular sizes), of the solid-fluid interaction potential (Lennard Jones 9-3, hard wall potential) and of the reduced fluid density (from 0.1 to 0.7 at a reduced temperature T* = 2) on the thermodynamic factor. The deviation of the thermodynamic factor compared to its equivalent bulk value decreases when increasing the pore width and becomes insignificant for reduced pore width above 15. We also found that the thermodynamic factor is sensitive to the magnitude of the fluid-fluid and solid-fluid interactions, which softens or exacerbates the density fluctuations.
Collell, Julien; Galliero, Guillaume
2014-05-21
The multi-component diffusive mass transport is generally quantified by means of the Maxwell-Stefan diffusion coefficients when using molecular simulations. These coefficients can be related to the Fick diffusion coefficients using the thermodynamic correction factor matrix, which requires to run several simulations to estimate all the elements of the matrix. In a recent work, Schnell et al. [“Thermodynamics of small systems embedded in a reservoir: A detailed analysis of finite size effects,” Mol. Phys. 110, 1069–1079 (2012)] developed an approach to determine the full matrix of thermodynamic factors from a single simulation in bulk. This approach relies on finite size effects of small systems on the density fluctuations. We present here an extension of their work for inhomogeneous Lennard Jones fluids confined in slit pores. We first verified this extension by cross validating the results obtained from this approach with the results obtained from the simulated adsorption isotherms, which allows to determine the thermodynamic factor in porous medium. We then studied the effects of the pore width (from 1 to 15 molecular sizes), of the solid-fluid interaction potential (Lennard Jones 9-3, hard wall potential) and of the reduced fluid density (from 0.1 to 0.7 at a reduced temperature T* = 2) on the thermodynamic factor. The deviation of the thermodynamic factor compared to its equivalent bulk value decreases when increasing the pore width and becomes insignificant for reduced pore width above 15. We also found that the thermodynamic factor is sensitive to the magnitude of the fluid-fluid and solid-fluid interactions, which softens or exacerbates the density fluctuations.
NASA Astrophysics Data System (ADS)
Blas, Felipe J.; Mendiboure, Bruno
2013-04-01
We extend the well-known Test-Area methodology of Gloor et al. [J. Chem. Phys. 123, 134703 (2005)], 10.1063/1.2038827, originally proposed to evaluate the surface tension of planar fluid-fluid interfaces along a computer simulation in the canonical ensemble, to deal with the solid-fluid interfacial tension of systems adsorbed on cylindrical pores. The common method used to evaluate the solid-fluid interfacial tension invokes the mechanical relation in terms of the tangential and normal components of the pressure tensor relative to the interface. Unfortunately, this procedure is difficult to implement in the case of cylindrical geometry, and particularly complex in case of nonspherical molecules. Following the original work of Gloor et al., we perform free-energy perturbations due to virtual changes in the solid-fluid surface. In this particular case, the radius and length of the cylindrical pore are varied to ensure constant-volume virtual changes of the solid-fluid surface area along the simulation. We apply the modified methodology for determining the interfacial tension of a system of spherical Lennard-Jones molecules adsorbed inside cylindrical pores that interact with fluid molecules through the generalized 10-4-3 Steele potential recently proposed by Siderius and Gelb [J. Chem. Phys. 135, 084703 (2011)], 10.1063/1.3626804. We analyze the effect of pore diameter, density of adsorbed molecules, and fluid-fluid cutoff distance of the Lennard-Jones intermolecular potential on the solid-fluid interfacial tension. This extension, as the original Test-Area formulation, offers clear advantages over the classical mechanical route of computational efficiency, easy of implementation, and generality.
Force distribution for double-walled carbon nanotubes and gigahertz oscillators
NASA Astrophysics Data System (ADS)
Baowan, Duangkamon; Hill, James M.
2007-09-01
Advances in nanotechnology have led to the creation of many nano-scale devices and carbon nanotubes are representative materials to construct these devices. Double-walled carbon nanotubes with the inner tube oscillating can be used as gigahertz oscillators and form the basis of possible nano-electronic devices that might be instrumental in the micro-computer industry which are predominantly based on electron transport phenomena. There are many experiments and molecular dynamical simulations which show that a wave is generated on the outer cylinder as a result of the oscillation of the inner carbon nanotube and that the frequency of this wave is also in the gigahertz range. As a preliminary to analyze and model such devices, it is necessary to estimate accurately the resultant force distribution due to the inter-atomic interactions. Here we determine some new analytical expressions for the van der Waals force using the Lennard Jones potential for general lengths of the inner and outer tubes. These expressions are utilized together with Newton’s second law to determine the motion of an oscillating inner tube, assuming that any frictional effects may be neglected. An idealized and much simplified representation of the Lennard Jones force is used to determine a simple formula for the oscillation frequency resulting from an initial extrusion of the inner tube. This simple formula is entirely consistent with the existing known behavior of the frequency and predicts a maximum oscillation frequency occurring when the extrusion length is (L 2 L 1)/2 where L 1 and L 2 are the respective half-lengths of the inner and outer tubes (L 1 < L 2).
Coccé, Mariela C; Mardin, Balca R; Bens, Susanne; Stütz, Adrian M; Lubieniecki, Fabiana; Vater, Inga; Korbel, Jan O; Siebert, Reiner; Alonso, Cristina N; Gallego, Marta S
2016-09-01
Congenital gliobastoma multiforme (GBM) is rare and little is known about the molecular defects underlying the initiation and progression of this tumor type. We present a case of congenital GBM analyzed by conventional cytogenetics, fluorescence in situ hybridization, array comparative genomic hybridization and next generation sequencing. On cytogenetic analysis we detected a reciprocal translocation t(6;12)(q21;q24.3). By sequencing, the translocation was shown to form a fusion between the 5' region of ZCCHC8 and the 3' region of ROS1. RT-PCR analyses confirmed the existence of an in-frame fusion transcript with ZCCHC8 exons 1-3 joined to ROS1 exons 36-43. In addition to the ZCCHC8-ROS1 fusion, we detected a deletion in the short arm of chromosome 9, including homozygous loss of the CDKN2A/2B locus in 9p21.3 and heterozygous deletion of the HAUS6 gene in 9p22.1. The latter encodes a protein involved in faithful chromosome segregation by regulating microtubule nucleation and its deletion might be associated with the marked subclonal changes of ploidy observed in the tumor. This report adds the ZCCHC8-ROS1 fusion as oncogenic driver in GBM and supports the role of ROS1 activation in the pathogenesis of a subset of GBM. © 2016 Wiley Periodicals, Inc. PMID:27121553
Iwatsuki, Satoshi; Ichiyama, Atsushi; Tanooka, Syogo; Toyama, Mari; Katagiri, Kosuke; Kawahata, Masatoshi; Yamaguchi, Kentaro; Danjo, Hiroshi; Chayama, Kenji
2016-08-01
N-Substituted-9-aza-3,6,12,15-tetrathiaheptadecanes having Ph-C-N frameworks (N-R-ATH; R = benzyl (N-Bn-ATH), 4-nitrobenzyl (N-NO2Bn-ATH), and diphenylmethyl (N-Ph2CH-ATH)) were synthesized, and their Ag(i) complexes were structurally characterized. X-Ray crystal structure analyses of [Ag(N-R-ATH)](BF4) (R = Bn and Ph2CH) revealed monomeric tetra-S-coordinated complex cation structures without the N-coordination, and a benzene ring of the N-R group covered over the amine nitrogen atom. The precise extraction analyses of a Ag(i) ion with ATH derivatives (L = N-R-ATHs and N-H-ATH) associated with the (1)H NMR analyses of the [Ag(L)](+) complexes in polar and non-polar solvents revealed that the introduction of the N-substituent significantly enhanced the extractability of Ag(+), due to the "hydrophobic cover" effect by the Ph-C-N framework in the [Ag(N-R-ATH)](+) complexes. PMID:27435308
KE, Vijayaprasad; Taranath, Mahanthesh; Ramagoni, Naveen Kumar; Nara, Asha; Sarpangala, Mythri
2015-01-01
Introduction: To evaluate the caries risk based on the salivary levels of streptococcus mutans in children of 6-12 years of age group before and after consuming probiotic ice-cream containing Bifidobacterium lactis Bb-12 and Lactobacillus acidophilus La-5. Materials and Methods: A double blind, placebo controlled trial was carried out in 60 children aged between 6 to 12 years with zero decayed, missing, and filled teeth (DMFT). They were randomly divided into two equal groups. Saliva sample were collected before the consumption of ice-cream and Streptococcus mutans count was calculated and recorded as baseline data. For the next seven days both the groups were given ice creams marked as A and B. Saliva samples were collected after ice-cream consumption at the end of study period and also after a washout period of 30 days and again after six months. Samples were inoculated and colonies were counted. Results: On statistical evaluation by students paired t-test, probiotic ice-cream brought significant reduction in the Streptococcus mutans count after seven days of ice-cream ingestion (p<0.001) and also after 30 d of washout period (p<0.001). There was no significant reduction (p=0.076) by normal ice-cream consumption. After six months of the study period in both the groups the salivary levels of Streptococcus mutans was similar to the baseline. Conclusion: Probiotic ice-cream containing Bifidobacterium lactis Bb-12 and Lactobacillus acidophilus La-5 can cause reduction in caries causative organism. The dosage of the probiotic organisms for the long term or synergetic effect on the oral health are still needed to be explored. PMID:25859515
A t(6;12)(q23;p13) results in the fusion of ETV6 to a novel gene, STL, in a B-cell ALL cell line.
Suto, Y; Sato, Y; Smith, S D; Rowley, J D; Bohlander, S K
1997-04-01
ETV6 (TEL) is rearranged in various types of hematologic malignancies. The B-cell precursor acute lymphoblastic leukemia (ALL) cell line SUP-B2 has a t(6;12)(q23;p13) involving ETV6 at 12p13 and a submicroscopic deletion of the other ETV6 allele. The reciprocal translocation results in the fusion of ETV6 to a previously unknown gene at 6q23, which we named STL (six-twelve leukemia gene). Both reciprocal fusion transcripts can be detected: On the der(6) chromosome, the ETV6/STL mRNA shows an apparently out of frame fusion of ETV6 at nucleotide 187 to STL, which would result in the addition of 14 amino acids to the first 54 amino acids of ETV6. On the der(12) chromosome three different variants of the STL/ETV6 fusion mRNA could be detected; variable size segments were inserted at the breakpoint between STL and ETV6 exon 3. One of these variants could give rise to a protein in which the first 54 amino acids of ETV6 are replaced by 12 amino acids from one of the STL short open reading frames. Sequence analysis of a 1.4 kb STL cDNA clone from a skeletal muscle library revealed no long open reading frames. This cell line will be very useful in studying the different mechanisms by which alterations of ETV6 contribute to leukemogenesis and in testing the hypothesis that ETV6 might act as a tumor suppressor gene. PMID:9087565
NASA Astrophysics Data System (ADS)
Cohen, E.
2013-12-01
The mass extinction event at the Cretaceous-Paleogene (K-Pg) boundary was the result of a bolide impact, and is popularly known for the extinction of the dinosaurs, but is also one of the largest Paleogene mass extinctions identified. In addition, it was followed by a period of drastic changes in ecological conditions, including a complete alteration of the global carbon cycle; the root cause of this change is still debated. Little information is known regarding changes in the nitrogen cycle during these periods of mass extinction and recovery. Given the importance of the nitrogen cycle to primary production and its relationship to the redox state of the local environment, determining changes in the nitrogen cycle will provide important information as to the processes of global mass extinction and the subsequent recovery. Data from the JOIDES Resolution is used to introduce students to authentic data analysis. Students are asked to analyze if standards are consistent, is there anomalous data, how are significant figures used, and how consistent is the method which then, in turn effects data collection. Students are provided data from one core sample and asked to represent the data using technology. Students use Infograms, a technology which not only includes graphs but also visuals and texts in order to represent information in a meaningful way. Students create correlation between the data of nitrogen isotopes, foraminifera, oxygen isotopes, age of the earth and depth of collections. The lesson aligned to standards for students' grade 6-12 were created to support the content surrounding: National Science Education Content Standards: Standard A: Science as Inquiry Standard D: Earth and Space Science Ocean Literacy Essential Principles: 3. The ocean is a major influence on weather and climate 7. The ocean is largely unexplored.
NASA Astrophysics Data System (ADS)
Cohen, E.; Quan, T. M.
2012-12-01
The mass extinction event at the Cretaceous-Paleogene (K-Pg) boundary was the result of a bolide impact, and is popularly known for the extinction of the dinosaurs, but is also one of the largest Paleogene mass extinctions identified. In addition, it was followed by a period of drastic changes in ecological conditions, including a complete alteration of the global carbon cycle; the root cause of this change is still debated. Little information is known regarding changes in the nitrogen cycle during these periods of mass extinction and recovery. Given the importance of the nitrogen cycle to primary production and its relationship to the redox state of the local environment, determining changes in the nitrogen cycle will provide important information as to the processes of global mass extinction and the subsequent recovery. Three lessons for students' grade 6-12 were created to support the content surrounding: National Science Education Content Standards: Standard A: Science as Inquiry Standard D: Earth and Space Science Ocean Literacy Essential Principles: 3. The ocean is a major influence on weather and climate 7. The ocean is largely unexplored In the Nature of Science activity, students sequence a series of photographs to illustrate the scientific process of one scientist, Dr. Tracy Quan, of Oklahoma State University as she uses deep sea core data obtained by the JOIDES Resolution research vessel to investigate the climate during the mass extinction that took place ~ 65 million years ago. By reading the information contained on each card and studying the pictures, students learn that science is a dynamic, non-linear, and creative process. Students do not have to create the exact order Dr. Quan uses as her scientific process, but they need to justify their reasoning for placing the pictures in the order they did. The activity begins with a photo of the JOIDES Resolution and ends during a presentation at a scientific conference. There are 21 other photo cards
Path Integral representation of quantum particles in fluids: Convergence of observables
NASA Astrophysics Data System (ADS)
Reese, Terrebce; Miller, Bruce
2015-03-01
In previous work the Path Integral Monte Carlo (PIMC) technique was used to simulate a low mass quantum particle (qp) in a dense Lennard-Jones 6-12 fluid having the thermodynamic properties of Xenon. Because of the difference in thermal wavelengths between the qp and the fluid molecules, the fluid molecules can be treated classically. This combination of using quantum mechanics for the qp and classical mechanics for the fluid molecules is known as a hybrid model. In the path integral formulation the qp is represented as a closed chain of P classical particles where the quantum uncertainty in the position of the qp is manifested by the finite spread of the polymer chain. The PIMC technique allows standard classical Monte Carlo techniques to be used to compute quantum mechanical equilibrium values like the ortho-Positronium pick-off decay rate. Here we compare the convergence of PIMC for different thermodynamic states, including one near the liquid-vapor critical point of the fluid. We employ the correlation function of the iterated quantum observables to estimate the number of statistically independent configurations in a run and provide an estimate of the standard error.
Rapid insights from remote sensing in the geosciences
NASA Astrophysics Data System (ADS)
Plaza, Antonio
2015-03-01
The growing availability of capacity computing for atomistic materials modeling has encouraged the use of high-accuracy computationally intensive interatomic potentials, such as SNAP. These potentials also happen to scale well on petascale computing platforms. SNAP has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The computational cost per atom is much greater than that of simpler potentials such as Lennard-Jones or EAM, while the communication cost remains modest. We discuss a variety of strategies for implementing SNAP in the LAMMPS molecular dynamics package. We present scaling results obtained running SNAP on three different classes of machine: a conventional Intel Xeon CPU cluster; the Titan GPU-based system; and the combined Sequoia and Vulcan BlueGene/Q. The growing availability of capacity computing for atomistic materials modeling has encouraged the use of high-accuracy computationally intensive interatomic potentials, such as SNAP. These potentials also happen to scale well on petascale computing platforms. SNAP has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The computational cost per atom is much greater than that of simpler potentials such as Lennard-Jones or EAM, while the
Exact quantum scattering calculation of transport properties for free radicals: OH(X2Π)-helium
NASA Astrophysics Data System (ADS)
Dagdigian, Paul J.; Alexander, Millard H.
2012-09-01
Transport properties for OH-He are computed through quantum scattering calculations using the ab initio potential energy surfaces determined by Lee et al. [J. Chem. Phys. 113, 5736 (2000), 10.1063/1.1290605]. To gauge the importance of the open-shell character of OH and the anisotropy of the potential on the transport properties, including the collision integrals Ω(1,1) and Ω(2,2), as well as the diffusion coefficient, calculations were performed with the full potential, with the difference potential Vdif set to zero, and with only the spherical average of the potential. Slight differences (3%-5%) in the computed diffusion coefficient were found between the values obtained using the full potential and the truncated potentials. The computed diffusion coefficients were compared to recent experimental measurements and those computed with a Lennard-Jones (LJ) 12-6 potential. The values obtained with the full potential were slightly higher than the experimental values. The LJ 12-6 potential was found to underestimate the variation in temperature as compared to that obtained using the full OH-He ab initio potential.
NASA Astrophysics Data System (ADS)
Li, Wu-Xiong; Keyes, T.
1999-09-01
The pure translation (TR) imaginary-frequency (or unstable) instantaneous normal modes (INM), which we have proposed as representative of barrier crossing and diffusion, are obtained for seven densities and eight temperatures of supercooled and near-melting liquid CS2 via computer simulation. The self-diffusion constant D, with a range of over two decades, has been determined previously for these 56 states [Li and Keyes, J. Chem. Phys. 111, 328 (1999)], allowing a comprehensive test of the relation of INM to diffusion. INM theory is reviewed and extended. At each density Arrhenius T-dependence is found for the fraction fu of unstable modes, for the product <ω>ufu of the fraction times the averaged unstable frequency, and for D. The T-dependence of D is captured very accurately by fu at higher densities and by <ω>ufu at lower densities. Since the T-dependence of <ω>u is weak at high density, the formula D∝<ω>ufu provides a good representation at all densities; it is derived for the case of low-friction barrier crossing. Density-dependent activation energies determined by Arrhenius fits to <ω>ufu are in excellent agreement with those found from D. Thus, activation energies may be obtained with INM, requiring far less computational effort than an accurate simulation of D in supercooled liquids. Im-ω densities of states, <ρuTR(ω,T)>, are fit to the function a(T)ω exp[-(a2(T)ω/√T )a3(T)]. The strong T-dependence of D, absent in Lennard-Jones (LJ) liquids, arises from the multiplicative factor a(T); its activation energy is determined by the inflection-point energy on barriers to diffusion. Values of the exponent a3(T) somewhat greater than 2.0 suggest that liquid CS2 is nonfragile in the extended Angell-Kivelson scheme for the available states. A striking contrast is revealed between CS2 and LJ; a3→2 at low-T in CS2 and at high-T in LJ. The INM interpretation is that barrier height fluctuations in CS2 are negligible at low-T but grow with increasing T
Accurate statistical associating fluid theory for chain molecules formed from Mie segments.
Lafitte, Thomas; Apostolakou, Anastasia; Avendaño, Carlos; Galindo, Amparo; Adjiman, Claire S; Müller, Erich A; Jackson, George
2013-10-21
A highly accurate equation of state (EOS) for chain molecules formed from spherical segments interacting through Mie potentials (i.e., a generalized Lennard-Jones form with variable repulsive and attractive exponents) is presented. The quality of the theoretical description of the vapour-liquid equilibria (coexistence densities and vapour pressures) and the second-derivative thermophysical properties (heat capacities, isobaric thermal expansivities, and speed of sound) are critically assessed by comparison with molecular simulation and with experimental data of representative real substances. Our new EOS represents a notable improvement with respect to previous versions of the statistical associating fluid theory for variable range interactions (SAFT-VR) of the generic Mie form. The approach makes rigorous use of the Barker and Henderson high-temperature perturbation expansion up to third order in the free energy of the monomer Mie system. The radial distribution function of the reference monomer fluid, which is a prerequisite for the representation of the properties of the fluid of Mie chains within a Wertheim first-order thermodynamic perturbation theory (TPT1), is calculated from a second-order expansion. The resulting SAFT-VR Mie EOS can now be applied to molecular fluids characterized by a broad range of interactions spanning from soft to very repulsive and short-ranged Mie potentials. A good representation of the corresponding molecular-simulation data is achieved for model monomer and chain fluids. When applied to the particular case of the ubiquitous Lennard-Jones potential, our rigorous description of the thermodynamic properties is of equivalent quality to that obtained with the empirical EOSs for LJ monomer (EOS of Johnson et al.) and LJ chain (soft-SAFT) fluids. A key feature of our reformulated SAFT-VR approach is the greatly enhanced accuracy in the near-critical region for chain molecules. This attribute, combined with the accurate modeling of second
First-principles binary diffusion coefficients for H, H₂, and four normal alkanes + N₂.
Jasper, Ahren W; Kamarchik, Eugene; Miller, James A; Klippenstein, Stephen J
2014-09-28
Collision integrals related to binary (dilute gas) diffusion are calculated classically for six species colliding with N2. The most detailed calculations make no assumptions regarding the complexity of the potential energy surface, and the resulting classical collision integrals are in excellent agreement with previous semiclassical results for H + N2 and H2 + N2 and with recent experimental results for CnH(2n+2) + N2, n = 2-4. The detailed classical results are used to test the accuracy of three simplifying assumptions typically made when calculating collision integrals: (1) approximating the intermolecular potential as isotropic, (2) neglecting the internal structure of the colliders (i.e., neglecting inelasticity), and (3) employing unphysical R(-12) repulsive interactions. The effect of anisotropy is found to be negligible for H + N2 and H2 + N2 (in agreement with previous quantum mechanical and semiclassical results for systems involving atomic and diatomic species) but is more significant for larger species at low temperatures. For example, the neglect of anisotropy decreases the diffusion coefficient for butane + N2 by 15% at 300 K. The neglect of inelasticity, in contrast, introduces only very small errors. Approximating the repulsive wall as an unphysical R(-12) interaction is a significant source of error at all temperatures for the weakly interacting systems H + N2 and H2 + N2, with errors as large as 40%. For the normal alkanes in N2, which feature stronger interactions, the 12/6 Lennard-Jones approximation is found to be accurate, particularly at temperatures above ∼700 K where it predicts the full-dimensional result to within 5% (although with somewhat different temperature dependence). Overall, the typical practical approach of assuming isotropic 12/6 Lennard-Jones interactions is confirmed to be suitable for combustion applications except for weakly interacting systems, such as H + N2. For these systems, anisotropy and inelasticity can safely be
First-principles binary diffusion coefficients for H, H2, and four normal alkanes + N2
NASA Astrophysics Data System (ADS)
Jasper, Ahren W.; Kamarchik, Eugene; Miller, James A.; Klippenstein, Stephen J.
2014-09-01
Collision integrals related to binary (dilute gas) diffusion are calculated classically for six species colliding with N2. The most detailed calculations make no assumptions regarding the complexity of the potential energy surface, and the resulting classical collision integrals are in excellent agreement with previous semiclassical results for H + N2 and H2 + N2 and with recent experimental results for CnH2n+2 + N2, n = 2-4. The detailed classical results are used to test the accuracy of three simplifying assumptions typically made when calculating collision integrals: (1) approximating the intermolecular potential as isotropic, (2) neglecting the internal structure of the colliders (i.e., neglecting inelasticity), and (3) employing unphysical R-12 repulsive interactions. The effect of anisotropy is found to be negligible for H + N2 and H2 + N2 (in agreement with previous quantum mechanical and semiclassical results for systems involving atomic and diatomic species) but is more significant for larger species at low temperatures. For example, the neglect of anisotropy decreases the diffusion coefficient for butane + N2 by 15% at 300 K. The neglect of inelasticity, in contrast, introduces only very small errors. Approximating the repulsive wall as an unphysical R-12 interaction is a significant source of error at all temperatures for the weakly interacting systems H + N2 and H2 + N2, with errors as large as 40%. For the normal alkanes in N2, which feature stronger interactions, the 12/6 Lennard-Jones approximation is found to be accurate, particularly at temperatures above ˜700 K where it predicts the full-dimensional result to within 5% (although with somewhat different temperature dependence). Overall, the typical practical approach of assuming isotropic 12/6 Lennard-Jones interactions is confirmed to be suitable for combustion applications except for weakly interacting systems, such as H + N2. For these systems, anisotropy and inelasticity can safely be
Tappura, K
2001-08-15
An adjustable-barrier dihedral angle potential was added as an extension to a novel, previously presented soft-core potential to study its contribution to the efficacy of the search of the conformational space in molecular dynamics. As opposed to the conventional soft-core potential functions, the leading principle in the design of the new soft-core potential, as well as of its extension, the soft-core and adjustable-barrier dihedral angle (SCADA) potential (referred as the SCADA potential), was to maintain the main equilibrium properties of the original force field. This qualifies the methods for a variety of a priori modeling problems without need for additional restraints typically required with the conventional soft-core potentials. In the present study, the different potential energy functions are applied to the problem of predicting loop conformations in proteins. Comparison of the performance of the soft-core and SCADA potential showed that the main hurdles for the efficient sampling of the conformational space of (loops in) proteins are related to the high-energy barriers caused by the Lennard-Jones and Coulombic energy terms, and not to the rotational barriers, although the conformational search can be further enhanced by lowering the rotational barriers of the dihedral angles. Finally, different evaluation methods were studied and a few promising criteria found to distinguish the near-native loop conformations from the wrong ones. PMID:11455590
NASA Astrophysics Data System (ADS)
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
NASA Astrophysics Data System (ADS)
Dinpajooh, Mohammadhasan; Bai, Peng; Allan, Douglas A.; Siepmann, J. Ilja
2015-09-01
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 Tc = 1.3128 ± 0.0016, ρc = 0.316 ± 0.004, and pc = 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 ≤ ρt ≤ 0.336) agree to within the statistical uncertainties. For simulations with tail corrections, data obtained using rcut = 3.5σ yield Tc and pc that are higher by 0.2% and 1.4% than simulations with rcut = 5 and 8σ but still with overlapping 95% confidence intervals. In contrast, GEMC simulations with a truncated and shifted potential show that rcut = 8σ is insufficient to obtain accurate results. Additional GEMC simulations for hard-core square-well particles with various ranges of the
Dinpajooh, Mohammadhasan; Bai, Peng; Allan, Douglas A.; Siepmann, J. Ilja
2015-09-21
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{sub c} = 1.3128 ± 0.0016, ρ{sub c} = 0.316 ± 0.004, and p{sub 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{sub t} ≤ 0.336) agree to within the statistical uncertainties. For simulations with tail corrections, data obtained using r{sub cut} = 3.5σ yield T{sub c} and p{sub c} that are higher by 0.2% and 1.4% than simulations with r{sub cut} = 5 and 8σ but still with overlapping 95% confidence intervals. In contrast, GEMC simulations with a truncated and shifted potential show that r{sub cut} = 8σ is insufficient to obtain accurate results. Additional GEMC simulations for hard