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.
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
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.
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.
Saddles on the potential energy landscape of a Lennard-Jones liquid
NASA Astrophysics Data System (ADS)
Broderix, Kurt; Bhattacharya, Kamal K.; Cavagna, Andrea; Zippelius, Annette; Giardina, Irene
2001-02-01
By means of molecular dynamics simulations, we study the stationary points of the potential energy in a Lennard-Jones liquid, giving a purely geometric characterization of the energy landscape of the system. We find a linear relation between the degree of instability of the stationary points and their potential energy, and we locate the energy where the instability vanishes. This threshold energy marks the border between saddle-dominated and minima-dominated regions of the energy landscape. The temperature where the potential energy of the Stillinger-Weber minima becomes equal to the threshold energy turns out to be very close to the mode-coupling transition temperature Tc.
Modified dust-acoustic waves in dusty plasma with Lennard-Jones potential
NASA Astrophysics Data System (ADS)
Qian, Y. Z.; Chen, H.; Yang, X. S.; Liu, S. Q.
2015-10-01
Dust-acoustic waves in a dusty plasma are investigated by solving the Vlasov equation including the effect of dust-dust interaction modeled by a Lennard-Jones-like potential. The latter contains a potential well and is applicable when thermionic or photo emission processes are important. It is shown that the excitation and linear dispersion of the dust-acoustic waves are strongly modified. In fact, the phase of the dust acoustic waves is shifted and a cut-off for the long-wavelength modes appears, leading to a purely growing 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.
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.
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
Wilson, D Scott; Lee, Lloyd L
2005-07-22
We explore the vapor-liquid phase behavior of binary mixtures of Lennard-Jones-type molecules where one component is supercritical, given the system temperature. We apply the self-consistency approach to the Ornstein-Zernike integral equations to obtain the correlation functions. The consistency checks include not only thermodynamic consistencies (pressure consistency and Gibbs-Duhem consistency), but also pointwise consistencies, such as the zero-separation theorems on the cavity functions. The consistencies are enforced via the bridge functions in the closure which contain adjustable parameters. The full solution requires the values of not only the monomer chemical potentials, but also the dimer chemical potentials present in the zero-separation theorems. These are evaluated by the direct chemical-potential formula [L. L. Lee, J. Chem. Phys. 97, 8606 (1992)] that does not require temperature nor density integration. In order to assess the integral equation accuracy, molecular-dynamics simulations are carried out alongside the states studied. The integral equation results compare well with simulation data. In phase calculations, it is important to have pressure consistency and valid chemical potentials, since the matching of phase boundaries requires the equality of the pressures and chemical potentials of both the liquid and vapor phases. The mixtures studied are methane-type and pentane-type molecules, both characterized by effective Lennard-Jones potentials. Calculations on one isotherm show that the integral equation approach yields valid answers as compared with the experimental data of Sage and Lacey. To study vapor-liquid phase behavior, it is necessary to use consistent theories; any inconsistencies, especially in pressure, will vitiate the phase boundary calculations.
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
Heffelfinger, G.S.; Lewitt, M.E.
1994-05-01
We present a new massively parallel decomposition for grand canonical Monte Carlo computer simulation (GCMC) suitable for short ranged fluids. Our spatial algorithm relies on the fact that for short-ranged fluids, molecules separated by a greater distance than the reach of the potential act independently, thus different processors can work concurrently in regions of the same system which are sufficiently far apart. Several parallelization issues unique to GCMC are addressed such as the handling of the three different types of Monte Carlo move used in GCMC: the displacement of a molecule, the creation of a molecule, and the destruction of a molecule. The decomposition is shown to scale with system size, making it especially useful for systems where the physical problem dictates the system size, for example, fluid behavior in mesopores.
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.
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. PMID:25362319
Density Functional Theory of Crystal Growth: Lennard-Jones Fluids
NASA Astrophysics Data System (ADS)
Shen, Yu Chen; Oxtoby, David
1996-03-01
We employ an extension of density functional theory to the dynamics of phase transitions in order to study the velocities of crystal growth and melting at planar undercooled and superheated crystal-melt interfaces. The free energy functional we use has a square-gradient form, with the parameters for a Lennard-Jones interaction potential determined by a modified weighted density approximation (MWDA) applied locally through the liquid-solid interface. We explore the role of the density change on freezing in crystal and melt growth, and discover a significant asymmetry between freezing and melting both close to and far from the equilibrium freezing point. The behavior of the superheated solid is governed by the close proximity of a spinodal, whereas in the undercooled liquid there is no evidence for a spinodal and the growth at large undercoolings is affected instead by the density deficit that appears in front of the growing interface.
Virial coefficients of Lennard-Jones mixtures
NASA Astrophysics Data System (ADS)
Schultz, Andrew J.; Kofke, David A.
2009-06-01
We report results of calculations of the second through sixth virial coefficients for four prototype Lennard-Jones (LJ) mixtures that have been the subject of previous studies in the literature. Values are reported for temperatures ranging from T =0.6 to T =10.0, where here the temperature is given units of the LJ energy parameter of one of the components. Thermodynamic stability of the mixtures is studied using the virial equation of state (VEOS) with the calculated coefficients, with particular focus on characterizing the vapor-liquid critical behavior of the mixtures. For three of the mixtures, vapor-liquid coexistence and critical data are available for comparison at only one temperature, while for the fourth we can compare to a critical line. We find that the VEOS provides a useful indication of the presence and location of critical behavior, although in some situations we find need to consider "near-miss" critical behavior, where the classical conditions of criticality are nearly but not exactly satisfied.
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.
Density functional theory of crystal growth: Lennard-Jones fluids
NASA Astrophysics Data System (ADS)
Shen, Yu Chen; Oxtoby, David W.
1996-03-01
We employ an extension of density functional theory to the dynamics of phase transitions in order to study the velocities of crystal growth and melting at planar undercooled and superheated crystal-melt interfaces. The free energy functional we use has a square-gradient form, with the parameters for a Lennard-Jones interaction potential determined by a modified weighted density approximation (MWDA) applied locally through the liquid-solid interface. We explore the role of the density change on freezing in crystal and melt growth, and discover a significant asymmetry between freezing and melting both close to and far from the equilibrium freezing point. The behavior of the superheated solid is governed by the close proximity of a spinodal, whereas in the undercooled liquid there is no evidence for a spinodal and the growth at large undercoolings is affected instead by the density deficit that appears in front of the growing interface. Comparisons are made with other density functional approaches and with computer simulations.
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.
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
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
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.
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.
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
Critical point estimation of the Lennard-Jones pure fluid and binary mixtures
NASA Astrophysics Data System (ADS)
Pérez-Pellitero, Javier; Ungerer, Philippe; Orkoulas, Gerassimos; Mackie, Allan D.
2006-08-01
The apparent critical point of the pure fluid and binary mixtures interacting with the Lennard-Jones potential has been calculated using Monte Carlo histogram reweighting techniques combined with either a fourth order cumulant calculation (Binder parameter) or a mixed-field study. By extrapolating these finite system size results through a finite size scaling analysis we estimate the infinite system size critical point. Excellent agreement is found between all methodologies as well as previous works, both for the pure fluid and the binary mixture studied. The combination of the proposed cumulant method with the use of finite size scaling is found to present advantages with respect to the mixed-field analysis since no matching to the Ising universal distribution is required while maintaining the same statistical efficiency. In addition, the accurate estimation of the finite critical point becomes straightforward while the scaling of density and composition is also possible and allows for the estimation of the line of critical points for a Lennard-Jones mixture.
Metastable Lennard-Jones fluids. III. Bulk viscosity.
Baidakov, Vladimir G; Protsenko, Sergey P
2014-09-21
The method of equilibrium molecular-dynamics simulation in combination with the Green-Kubo formula has been used to calculate the bulk viscosity of a Lennard-Jones fluid. Calculations have been made at temperatures 0.4 ≤ k(B)T/ɛ ≤ 2.0 and densities 0.0075 ≤ ρσ(3) ≤ 1.2 at 116 stable and 106 metastable states of liquid and gas. The depth of penetration into the region of metastable states was limited by spontaneous nucleation. In the region of stable states the data obtained are compared with the results of previous investigations. It has been established that the system transition across the lines of liquid-gas and liquid-crystal phase equilibrium and penetration into the metastable regions of liquid and gas are connected with increasing bulk viscosity. The behavior of bulk viscosity close to the spinodal of a superheated liquid and supersaturated vapor is discussed. PMID:25240360
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.
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.
Metastable Lennard-Jones fluids. III. Bulk viscosity.
Baidakov, Vladimir G; Protsenko, Sergey P
2014-09-21
The method of equilibrium molecular-dynamics simulation in combination with the Green-Kubo formula has been used to calculate the bulk viscosity of a Lennard-Jones fluid. Calculations have been made at temperatures 0.4 ≤ k(B)T/ɛ ≤ 2.0 and densities 0.0075 ≤ ρσ(3) ≤ 1.2 at 116 stable and 106 metastable states of liquid and gas. The depth of penetration into the region of metastable states was limited by spontaneous nucleation. In the region of stable states the data obtained are compared with the results of previous investigations. It has been established that the system transition across the lines of liquid-gas and liquid-crystal phase equilibrium and penetration into the metastable regions of liquid and gas are connected with increasing bulk viscosity. The behavior of bulk viscosity close to the spinodal of a superheated liquid and supersaturated vapor is discussed.
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.
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.
Nicolini, Paolo; Guàrdia, Elvira; Masia, Marco
2013-11-14
In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r(-6) term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations.
NASA Astrophysics Data System (ADS)
Nicolini, Paolo; Guàrdia, Elvira; Masia, Marco
2013-11-01
In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r-6 term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations.
Vacancy behavior in a compressed fcc Lennard-Jones crystal
Beeler, J.R. Jr.
1981-12-01
This computer experiment study concerns the determination of the stable vacancy configuration in a compressed fcc Lennard-Jones crystal and the migration of this defect in a compressed crystal. Isotropic and uniaxial compression stress conditions were studied. The isotropic and uniaxial compression magnitudes employed were 0.94 less than or equal to eta less than or equal to 1.5, and 1.0 less than or equal to eta less than or equal to 1.5, respectively. The site-centered vacancy (SCV) was the stable vacancy configuration whenever cubic symmetry was present. This includes all of the isotropic compression cases and the particular uniaxial compression case (eta = ..sqrt..2) that give a bcc structure. In addition, the SCV was the stable configuration for uniaxial compression eta < 1.29. The out-of-plane split vacancy (SV-OP) was the stable vacancy configuration for uniaxial compression 1.29 < eta less than or equal to 1.5 and was the saddle-point configuration for SCV migration when the SCV was the stable form. For eta > 1.20, the SV-OP is an extended defect and, therefore, a saddle point for SV-OP migration could not be determined. The mechanism for the transformation from the SCV to the SV-OP as the stable form at eta = 1.29 appears to be an alternating sign (101) and/or (011) shear process.
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
Metastable Lennard-Jones fluids. I. Shear viscosity.
Baidakov, Vladimir G; Protsenko, Sergey P; Kozlova, Zaliya R
2012-10-28
Molecular dynamics methods have been employed to calculate the coefficient of shear viscosity η(s)* of a Lennard-Jones fluid. Calculations have been performed in the range of reduced temperatures 0.4 ≤ k(B)T/ε ≤ 2.0 and densities 0.01 ≤ ρσ(3) ≤ 1.2. Values of η(s)* have been obtained for 217 states, 99 of which refer to metastable liquid and gas regions. The results of calculating η(s)* for thermodynamically stable states are in satisfactory agreement with the data of earlier investigations. An equation has been obtained which describes the temperature and density dependence of the coefficient of shear viscosity in stable and metastable regions of the phase diagram up to the boundaries of spontaneous nucleation. The behavior of the coefficient of shear viscosity close to the spinodal of a superheated liquid and supersaturated vapor is discussed and the applicability of the Stokes-Einstein relation at high supercoolings of the liquid phase is examined.
NASA Astrophysics Data System (ADS)
Polak, Wiesław Z.
2016-08-01
Simulated growth of four global-minimum Lennard-Jones clusters of sizes N = 561, 823, 850 and 923, representing multishell icosahedra and decahedron, always leads to formation of regular polyicosahedral clusters. Observation of cluster structure evolution revealed that new atoms form anti-Mackay islands spreading over the cluster surface by making strong island-island junctions at cluster edges. Analysis of potential energies of atoms composing different local structures shows that energy-driven preference for decahedral arrangement of several atoms initiating the junction of pentagonal symmetry on the cluster surface is responsible for kinetic effect in the cluster growth.
NASA Astrophysics Data System (ADS)
Ovchinnikov, M. N.; Kushtanova, G. G.
The redistribution of heat between two subsystems in the two-dimensional crystal consisting of particles interacting by means of the Lennard-Jones potential with argon parameters is considered in the frame of molecular dynamics method. Calculations of heat flux, its time derivative and kinetic temperature gradient showed that the characteristic relaxation times of the nonequilibrium flux within the nonlocal Cattaneo model at temperatures 10K < T < 40K are very small (τv <10-11s) and, comparable with the time of phonons free path.
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
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.
Cottin, X.; Monson, P.A.
1996-12-01
We consider the application of the cell theory to single component and binary Lennard-Jones solids. We calculate solid phase properties and solid{endash}fluid equilibrium using the cell theory for the solid phase and an equation of state for the fluid phase. In the single component case the thermodynamic properties as well as the solid{endash}fluid phase diagram predicted by the theory are in quite good agreement with Monte Carlo simulation results. The introduction of correlations between the motions of nearest neighbor particles into the cell theory in a fashion suggested by Barker significantly improves the agreement. For binary Lennard-Jones 12-6 mixtures the predictions of the theory are compared with experimental data for mixtures forming substitutionally disordered solid solutions involving argon, krypton and methane. The theory correctly predicts the form of the phase diagram but the quantitative predictions are quite sensitive to the choice of potential parameters. The shape of the phase diagram is similar to that for a hard sphere mixture with the same diameter ratio. {copyright} {ital 1996 American Institute of Physics.}
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.
Effect of Size Polydispersity on the Nature of Lennard-Jones Liquids.
Ingebrigtsen, Trond S; Tanaka, Hajime
2015-08-27
Polydisperse fluids are encountered everywhere in biological and industrial processes. These fluids naturally show a rich phenomenology exhibiting fractionation and shifts in critical point and freezing temperatures. We study here the effect of size polydispersity on the basic nature of Lennard-Jones (LJ) liquids, which represent most molecular liquids without hydrogen bonds, via two- and three-dimensional molecular dynamics computer simulations. A single-component liquid constituting spherical particles and interacting via the LJ potential is known to exhibit strong correlations between virial and potential energy equilibrium fluctuations at constant volume. This correlation significantly simplifies the physical description of the liquid, and these liquids are now known as Roskilde-simple (RS) liquids. We show that this simple nature of the single-component LJ liquid is preserved even for very high polydispersities (above 40% polydispersity for the studied uniform distribution). We also investigate isomorphs of moderately polydisperse LJ liquids. Isomorphs are curves in the phase diagram of RS liquids along which structure, dynamics, and some thermodynamic quantities are invariant in dimensionless units. We find that isomorphs are a good approximation even for polydisperse LJ liquids. The theory of isomorphs thus extends readily to size polydisperse fluids and can be used to improve even further the understanding of these intriguing systems. PMID:26069998
Widom line for the liquid-gas transition in Lennard-Jones system.
Brazhkin, V V; Fomin, Yu D; Lyapin, A G; Ryzhov, V N; Tsiok, E N
2011-12-01
The locus of extrema (ridges) for heat capacity, thermal expansion coefficient, compressibility, and density fluctuations for model particle systems with Lennard-Jones (LJ) potential in the supercritical region have been obtained. It was found that the ridges for different thermodynamic values virtually merge into a single Widom line at T < 1.1T(c) and P < 1.5P(c) and become practically completely smeared at T < 2.5T(c) and P < 10P(c), where T(c) and P(c) are the critical temperature and pressure. The ridge for heat capacity approaches close to critical isochore, whereas the lines of extrema for other values correspond to density decrease. The lines corresponding to the supercritical maxima for argon and neon are in good agreement with the computer simulation data for LJ fluid. The behavior of the ridges for LJ fluid, in turn, is close to that for the supercritical van der Waals fluid, which is indicative of a fairly universal behavior of the Widom line for a liquid-gas transition.
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)].
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
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.
Density functional theory for crystal-liquid interfaces of Lennard-Jones fluid.
Wang, Xin; Mi, Jianguo; Zhong, Chongli
2013-04-28
A density functional approach is presented to describe the crystal-liquid interfaces and crystal nucleations of Lennard-Jones fluid. Within the theoretical framework, the modified fundamental measure theory is applied to describe the free energy functional of hard sphere repulsion, and the weighted density method based on first order mean spherical approximation is used to describe the free energy contribution arising from the attractive interaction. The liquid-solid equilibria, density profiles within crystal cells and at liquid-solid interfaces, interfacial tensions, nucleation free energy barriers, and critical cluster sizes are calculated for face-centered-cubic and body-centered-cubic nucleus. Some results are in good agreement with available simulation data, indicating that the present model is quantitatively reliable in describing nucleation thermodynamics of Lennard-Jones fluid.
Density functional theory for crystal-liquid interfaces of Lennard-Jones fluid.
Wang, Xin; Mi, Jianguo; Zhong, Chongli
2013-04-28
A density functional approach is presented to describe the crystal-liquid interfaces and crystal nucleations of Lennard-Jones fluid. Within the theoretical framework, the modified fundamental measure theory is applied to describe the free energy functional of hard sphere repulsion, and the weighted density method based on first order mean spherical approximation is used to describe the free energy contribution arising from the attractive interaction. The liquid-solid equilibria, density profiles within crystal cells and at liquid-solid interfaces, interfacial tensions, nucleation free energy barriers, and critical cluster sizes are calculated for face-centered-cubic and body-centered-cubic nucleus. Some results are in good agreement with available simulation data, indicating that the present model is quantitatively reliable in describing nucleation thermodynamics of Lennard-Jones fluid. PMID:23635162
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
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.
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.
Effect of molecular flexibility of Lennard-Jones chains on vapor-liquid interfacial properties.
Blas, F J; Moreno-Ventas Bravo, A I; Algaba, J; Martínez-Ruiz, F J; MacDowell, L G
2014-03-21
We have determined the interfacial properties of short fully flexible chains formed from tangentially bonded Lennard-Jones monomeric units from direct simulation of the vapor-liquid interface. The results obtained are compared with those corresponding to rigid-linear chains formed from the same chain length, previously determined in the literature [F. J. Blas, A. I. M.-V. Bravo, J. M. Míguez, M. M. Piñeiro, and L. G. MacDowell, J. Chem. Phys. 137, 084706 (2012)]. The full long-range tails of the potential are accounted for by means of an improved version of the inhomogeneous long-range corrections of Janeček [J. Phys. Chem. B 129, 6264 (2006)] proposed recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2008)] valid for spherical as well as for rigid and flexible molecular systems. Three different model systems comprising of 3, 5, and 6 monomers per molecule are considered. The simulations are performed in the canonical ensemble, and the vapor-liquid interfacial tension is evaluated using the test-area method. In addition to the surface tension, we also obtained density profiles, coexistence densities, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the chain length and rigidity on these properties. According to our results, the main effect of increasing the chain length (at fixed temperature) is to sharpen the vapor-liquid interface and to increase the width of the biphasic coexistence region. As a result, the interfacial thickness decreases and the surface tension increases as the molecular chains get longer. Comparison between predictions for fully flexible and rigid-linear chains, formed by the same number of monomeric units, indicates that the main effects of increasing the flexibility, i.e., passing from a rigid-linear to a fully flexible chain, are: (a) to decrease the difference between the liquid and vapor densities; (b) to decrease the critical temperature and
Kunikeev, Sharif D; Kim, Kwang S
2012-11-01
The Monte Carlo (MC) estimates of thermal averages are usually functions of system control parameters λ, such as temperature, volume, and interaction couplings. Given the MC average at a set of prescribed control parameters λ{0}, the problem of analytic continuation of the MC data to λ values in the neighborhood of λ{0} is considered in both classic and quantum domains. The key result is the theorem that links the differential properties of thermal averages to the higher order cumulants. The theorem and analytic continuation formulas expressed via higher order cumulants are numerically tested on the classical Lennard-Jones cluster system of N=13, 55, and 147 neon particles.
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.
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)
Gruziel, Magdalena; Rudnicki, Witold R.; Lesyng, Bogdan
2008-02-01
In this study, the hydration of a model Lennard-Jones solute particle and the analytical approximations of the free energy of hydration as functions of solute microscopic parameters are analyzed. The control parameters of the solute particle are the charge, the Lennard-Jones diameter, and also the potential well depth. The obtained multivariate free energy functions of hydration were parametrized based on Metropolis Monte Carlo simulations in the extended NpT ensemble, and interpreted based on mesoscopic solvation models proposed by Gallicchio and Levy [J. Comput. Chem. 25, 479 (2004)], and Wagoner and Baker [Proc. Natl. Acad. Sci. U.S.A. 103, 8331 (2006)]. Regarding the charge and the solute diameter, the dependence of the free energy on these parameters is in qualitative agreement with former studies. The role of the third parameter, the potential well depth not previously considered, appeared to be significant for sufficiently precise bivariate solvation free energy fits. The free energy fits for cations and neutral solute particles were merged, resulting in a compact manifold of the free energy of solvation. The free energy of hydration for anions forms two separate manifolds, which most likely results from an abrupt change of the coordination number when changing the size of the anion particle.
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
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.
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.
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.
Mapping the phase diagram for neon to a quantum Lennard-Jones fluid using Gibbs ensemble simulations
NASA Astrophysics Data System (ADS)
Georgescu, IonuÅ£; 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 =hbar /(σ √{mɛ }). 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, ɛ = 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.
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
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
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
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
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
Tetrahedral global minimum for the 98-atom Lennard-Jones cluster.
Leary, R H; Doye, J P
1999-12-01
An unusual atomic cluster structure corresponding to the global minimum of the 98-atom Lennard-Jones cluster has been found using a variant of the basin-hopping global optimization algorithm. The structure has tetrahedral symmetry and an energy of -543.665 361 epsilon, which is 0.022 404 epsilon lower than the previous lowest-energy minimum. The LJ(98) structure is of particular interest because its tetrahedral symmetry establishes it as one of only three types of exception to the general pattern of icosahedral structural motifs for optimal LJ microclusters. Similar to the other exceptions the global minimum is difficult to find because it is at the bottom of a narrow funnel that only becomes thermodynamically most stable at low temperature. PMID:11970625
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.
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.
Theoretical scheme for the shear viscosity of Lennard-Jones fluids
NASA Astrophysics Data System (ADS)
Robles, M.; Uruchurtu, L. I.
2006-03-01
We use the shear viscosity expression from the Enskog theory of dense gases in a perturbative scheme for the Lennard-Jones (LJ) fluid. This perturbative scheme is formulated by combining the analytic rational function approximation method of Bravo Yuste and Santos [Phys. Rev. A 43, 5418 (1991)] for the radial distribution function of hard-sphere fluids and the well known Mansoori-Canfield/Rasaiah-Stell perturbation theory to determine an effective diameter for the LJ fluid. The scheme is reliable on a wide range of temperatures and densities, and is very accurate around the critical point. Using this information, we build an accurate empirical formula for the shear viscosity in the liquid phase, which fits the recent data [K. Meier et al., J. Chem. Phys. 121, 3671 (2004)] in the whole simulation range.
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
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
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.
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.
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.
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.
NASA Astrophysics Data System (ADS)
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 Tcr increases rapidly with density and approximately obeys a scaling relation valid for a reference system of particles interacting via a purely repulsive 1 /r18 potential.
Varanasi, Srinivasa R; Kumar, Parveen; Yashonath, S
2012-04-14
Investigations into the variation of self-diffusivity with solute radius, density, and degree of disorder of the host medium is explored. The system consists of a binary mixture of a relatively smaller sized solute, whose size is varied and a larger sized solvent interacting via Lennard-Jones potential. Calculations have been performed at three different reduced densities of 0.7, 0.8, and 0.933. These simulations show that diffusivity exhibits a maximum for some intermediate size of the solute when the solute diameter is varied. The maximum is found at the same size of the solute at all densities which is at variance with the prediction of the levitation effect. In order to understand this anomaly, additional simulations were carried out in which the degree of disorder has been varied while keeping the density constant. The results show that the diffusivity maximum gradually disappears with increase in disorder. Disorder has been characterized by means of the minimal spanning tree. Simulations have also been carried out in which the degree of disorder is constant and only the density is altered. The results from these simulations show that the maximum in diffusivity now shifts to larger distances with decrease in density. This is in agreement with the changes in void and neck distribution with density of the host medium. These results are in excellent agreement with the predictions of the levitation effect. They suggest that the effect of disorder is to shift the maximum in diffusivity towards smaller solute radius while that of the decrease in density is to shift it towards larger solute radius. Thus, in real systems where the degree of disorder is lower at higher density and vice versa, the effect due to density and disorder have opposing influences. These are confirmed by the changes seen in the velocity autocorrelation function, self part of the intermediate scattering function and activation energy.
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
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
A study of the static yield stress in a binary Lennard-Jones glass
NASA Astrophysics Data System (ADS)
Varnik, F.; Bocquet, L.; Barrat, J.-L.
2004-02-01
The stress-strain relations and the yield behavior of a model glass (a 80:20 binary Lennard-Jones mixture) [W. Kob and H. C. Andersen, Phys. Rev. E 52, 4134 (1995)] is studied by means of molecular dynamics simulations. In a previous paper [F. Varnik, L. Bocquet, J.-L. Barrat, and L. Berthier, Phys. Rev. Lett. 90, 095702 (2003)] it was shown that, at temperatures below the glass transition temperature, Tg, the model exhibits shear banding under imposed shear. It was also suggested that this behavior is closely related to the existence of a (static) yield stress (under applied stress, the system does not flow until the stress σ exceeds a threshold value σy). A thorough analysis of the static yield stress is presented via simulations under imposed stress. Furthermore, using steady shear simulations, the effect of physical aging, shear rate and temperature on the stress-strain relation is investigated. In particular, we find that the stress at the yield point (the "peak"-value of the stress-strain curve) exhibits a logarithmic dependence both on the imposed shear rate and on the "age" of the system in qualitative agreement with experiments on amorphous polymers [C. Ho Huu and T. Vu-Khanh, Theoretical and Applied Fracture Mechanics 40, 75 (2003); L. E. Govaert, H. G. H. van Melick, and H. E. H. Meijer, Polymer 42, 1271 (2001)] and on metallic glasses [W. L. Johnson, J. Lu, and M. D. Demetriou, Intermetallics 10, 1039 (2002)]. In addition to the very observation of the yield stress which is an important feature seen in experiments on complex systems like pastes, dense colloidal suspensions [F. Da Cruz, F. Chevoir, D. Bonn, and P. Coussot, Phys. Rev. E 66, 051305 (2002)] and foams [G. Debrégeas, H. Tabuteau, and J.-M. di Meglio, Phys. Rev. Lett. 87, 178305 (2001)], further links between our model and soft glassy materials are found. An example is the existence of hysteresis loops in the system response to a varying imposed stress. Finally, we measure the static yield
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.
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.
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.
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
NASA Astrophysics Data System (ADS)
Harris, Kenneth R.
2009-08-01
The fractional Stokes-Einstein (FSE) relation, (D /T)∝η-t, is shown to well correlate the molecular dynamics results of Meier et al. [J. Chem. Phys. 121, 3671 (2004); Meier et al.J. Chem. Phys. 121, 9526 (2004)] for the viscosity (η) and self-diffusion coefficient (D) of the Lennard-Jones fluid in the liquid and dense supercritical states, with the exponent t =(0.921±0.003). The Stokes-Einstein number n is viscosity dependent: ln n=const+(t -1)ln η. Molecular and ionic liquids for which high-pressure transport property data are available in the literature are shown to exhibit the same behavior with 0.79
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
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.
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
Nonequilibrium melting and crystallization of a model Lennard-Jones system.
Luo, Sheng-Nian; Strachan, Alejandro; Swift, Damian C
2004-06-22
Nonequilibrium melting and crystallization of a model Lennard-Jones system were investigated with molecular dynamics simulations to quantify the maximum superheating/supercooling at fixed pressure, and over-pressurization/over-depressurization at fixed temperature. The temperature and pressure hystereses were found to be equivalent with regard to the Gibbs free energy barrier for nucleation of liquid or solid. These results place upper bounds on hysteretic effects of solidification and melting in high heating- and strain-rate experiments such as shock wave loading and release. The authors also demonstrate that the equilibrium melting temperature at a given pressure can be obtained directly from temperatures at the maximum superheating and supercooling on the temperature hysteresis; this approach, called the hysteresis method, is a conceptually simple and computationally inexpensive alternative to solid-liquid coexistence simulation and thermodynamic integration methods, and should be regarded as a general method. We also found that the extent of maximum superheating/supercooling is weakly pressure dependent, and the solid-liquid interfacial energy increases with pressure. The Lindemann fractional root-mean-squared displacement of solid and liquid at equilibrium and extreme metastable states is quantified, and is predicted to remain constant (0.14) at high pressures for solid at the equilibrium melting temperature. PMID:15268198
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.
Surface tension of the two center Lennard-Jones plus point dipole fluid.
Werth, Stephan; Horsch, Martin; Hasse, Hans
2016-02-01
Molecular dynamics simulations are used for systematically studying the surface tension of the two center Lennard-Jones plus point dipole (2CLJD) model fluid. In a dimensionless representation, this model fluid has two parameters describing the elongation and the dipole moment. These parameters were varied in the entire range relevant for describing real fluids resulting in a grid of 38 individual models. For each model, the surface tension was determined at temperatures between 60% and 90% of the critical temperature. For completeness, the vapor pressure and the saturated densities were also determined. The latter results agree well with the literature data, whereas for the surface tension, only few data were previously available. From the present results, an empirical correlation for the surface tension of the 2CLJD model as a function of the model parameters is developed. The correlation is used to predict the surface tension of 46 2CLJD molecular models from the literature, which were adjusted to bulk properties, but not to interfacial properties. The results are compared to the experimental data. The molecular models overestimate the surface tension, and deviations between the predictions and experimental data are below 12% on average.
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.
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.
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
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
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.
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
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.
NASA Astrophysics Data System (ADS)
Munaò, Gianmarco; Costa, Dino; Caccamo, Carlo
2016-10-01
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.
NASA Astrophysics Data System (ADS)
Vorselaars, Bart
2015-03-01
Liquid free energies are computed by integration along a path from a reference system of known free energy, using a strong localization potential. A particular choice of localization pathway is introduced, convenient for use in molecular dynamics codes, and which achieves accurate results without the need to include the identity-swap or relocation Monte Carlo moves used in previous studies. Moreover, an adaptive timestep is introduced to attain the reference system. Furthermore, a center-of-mass correction that is different from previous studies and phase-independent is incorporated. The resulting scheme allows computation of both solid and liquid free energies with only minor differences in simulation protocol. This is used to re-visit solid-liquid equilibrium in a system of short semi-flexible Lennard-Jones chain molecules. The computed melting curve is demonstrated to be consistent with direct co-existence simulations and computed hysteresis loops, provided that an entropic term arising from unsampled solid states is included.
Georgescu, Ionuţ; Mandelshtam, Vladimir A
2012-10-14
The theory of self-consistent phonons (SCP) was originally developed to address the anharmonic effects in condensed matter systems. The method seeks a harmonic, temperature-dependent Hamiltonian that provides the "best fit" for the physical Hamiltonian, the "best fit" being defined as the one that optimizes the Helmholtz free energy at a fixed temperature. The present developments provide a scalable O(N) unified framework that accounts for anharmonic effects in a many-body system, when it is probed by either thermal (ℏ → 0) or quantum fluctuations (T → 0). In these important limits, the solution of the nonlinear SCP equations can be reached in a manner that requires only the multiplication of 3N × 3N matrices, with no need of diagonalization. For short range potentials, such as Lennard-Jones, the Hessian, and other related matrices are highly sparse, so that the scaling of the matrix multiplications can be reduced from O(N(3)) to ~O(N). We investigate the role of quantum effects by continuously varying the de-Boer quantum delocalization parameter Λ and report the N-Λ (T = 0), and also the classical N-T (Λ = 0) phase diagrams for sizes up to N ~ 10(4). Our results demonstrate that the harmonic approximation becomes inadequate already for such weakly quantum systems as neon clusters, or for classical systems much below the melting temperatures.
Li, Pengfei; Roberts, Benjamin P.; Chakravorty, Dhruva K.; Merz, Kenneth M.
2013-01-01
Metal ions play significant roles in biological systems. Accurate molecular dynamics (MD) simulations on these systems require a validated set of parameters. Although there are more detailed ways to model metal ions, the nonbonded model, which employs a 12-6 Lennard-Jones (LJ) term plus an electrostatic potential is still widely used in MD simulations today due to its simple form. However, LJ parameters have limited transferability due to different combining rules, various water models and diverse simulation methods. Recently, simulations employing a Particle Mesh Ewald (PME) treatment for long-range electrostatics have become more and more popular owing to their speed and accuracy. In the present work we have systematically designed LJ parameters for 24 +2 metal (M(II)) cations to reproduce different experimental properties appropriate for the Lorentz-Berthelot combining rules and PME simulations. We began by testing the transferability of currently available M(II) ion LJ parameters. The results showed that there are differences between simulations employing Ewald summation with other simulation methods and that it was necessary to design new parameters specific for PME based simulations. Employing the thermodynamic integration (TI) method and performing periodic boundary MD simulations employing PME, allowed for the systematic investigation of the LJ parameter space. Hydration free energies (HFEs), the ion-oxygen distance in the first solvation shell (IOD) and coordination numbers (CNs) were obtained for various combinations of the parameters of the LJ potential for four widely used water models (TIP3P, SPC/E, TIP4P and TIP4PEW). Results showed that the three simulated properties were highly correlated. Meanwhile, M(II) ions with the same parameters in different water models produce remarkably different HFEs but similar structural properties. It is difficult to reproduce various experimental values simultaneously because the nonbonded model underestimates the
Cohen, J.M.; Voter, A.F. , Los Alamos National Laboratory, Los Alamos, New Mexico 87545 )
1989-10-15
Surface self-diffusion constants have been calculated for the single component Lennard-Jones fcc(111) system using the dynamical corrections formalism for transition state theory (TST). At high temperatures, these results are found to be in agreement with previous molecular dynamics calculations. Over the extended temperature range in which this method is valid, deviations from Arrhenius behavior are observed. At lower temperatures, a noticeable contribution to the diffusion constant stems from trajectories in which the adatom recrosses the TST boundary, often due to a direction-reversing collision with the substrate atom on the far side of the binding site. This produces a dip in the dynamical correction factor centered around a reduced temperature of {ital T}=0.038. At higher temperatures, the expected multiple-jump effects are observed.
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.
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)
Palla, Pier Luca; Pierleoni, Carlo; Ciccotti, Giovanni
2008-08-01
Nonequilibrium molecular dynamics (NEMD) calculations of the bulk viscosity of the triple point Lennard-Jones fluid are performed with the aim of investigating the origin of the observed disagreement between Green-Kubo estimates and previous NEMD data. We show that a careful application of the Doll’s perturbation field, the dynamical NEMD method, the instantaneous form of the perturbation and the “subtraction technique” provides a NEMD estimate of the bulk viscosity at zero field in full agreement with the value obtained by the Green-Kubo formula. As previously reported for the shear viscosity, we find that the bulk viscosity exhibits a large linear regime with the field intensity.
Sumi, Tomonari; Maruyama, Yutaka; Mitsutake, Ayori; Koga, Kenichiro
2016-06-14
In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.
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.
Sumi, Tomonari; Maruyama, Yutaka; Mitsutake, Ayori; Koga, Kenichiro
2016-06-14
In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids. PMID:27305993
Ghosh, Satinath; Ghosh, Swapan K
2011-01-14
Density functional theory (DFT) with square gradient approximation for the free energy functional and a model density profile are used to obtain an analytical expression for the size-dependent free energy of formation of a liquid drop from the vapor through the process of homogeneous nucleation, without invoking the approximations used in classical nucleation theory (CNT). The density of the liquid drop in this work is not the same as the bulk liquid density but it corresponds to minimum free energy of formation of the liquid drop. The theory is applied to study the nucleation phenomena from supersaturated vapor of Lennard-Jones fluid. The barrier height predicted by this theory is significantly lower than the same in CNT which is rather high. The density at the center of the small liquid drop as obtained through optimization is less than the bulk density which is in agreement with other earlier works. Also proposed is a sharp interface limit of the proposed DFT of nucleation, which is as simple as CNT but with a modified barrier height and this modified classical nucleation theory, as we call it, is shown to lead to improved results.
The role of fcc tetrahedral subunits in the phase behavior of medium sized Lennard-Jones clusters.
Saika-Voivod, Ivan; Poon, Louis; Bowles, Richard K
2010-08-21
The free energy of a 600-atom Lennard-Jones cluster is calculated as a function of surface and bulk crystallinity in order to study the structural transformations that occur in the core of medium sized clusters. Within the order parameter range studied, we find the existence of two free energy minima at temperatures near freezing. One minimum, at low values of both bulk and surface order, belongs to the liquid phase. The second minimum exhibits a highly ordered core with a disordered surface and is related to structures containing a single fcc-tetrahedral subunit, with an edge length of seven atoms (l=7), located in the particle core. At lower temperatures, a third minimum appears at intermediate values of the bulk order parameter which is shown to be related to the formation of multiple l=6 tetrahedra in the core of the cluster. We also use molecular dynamics simulations to follow a series of nucleation events and find that the clusters freeze to structures containing l=5, 6, 7, and 8 sized tetrahedra as well as those containing no tetrahedral units. The structural correlations between bulk and surface order with the size of the tetrahedral units in the cluster core are examined. Finally, the relationships between the formation of fcc tetrahedral subunits in the core, the phase behavior of medium sized clusters and the nucleation of noncrystalline global structures such as icosahedra and decahedra are discussed.
Relaxation of surface tension in the free-surface boundary layer of simple Lennard-Jones liquids.
Lukyanov, A V; Likhtman, A E
2013-01-21
In this paper we use molecular dynamics to answer a classical question: how does the surface tension on a liquid/gas interface appear? After defining surface tension from the first principles and performing several consistency checks, we perform a dynamic experiment with a single simple liquid nanodroplet. At time zero, we remove all molecules of the interfacial layer, creating a fresh bare interface with the bulk arrangement of molecules. After that the system evolves towards equilibrium, and the expected surface tension is re-established. We found that the system relaxation consists of three distinct stages. First, the mechanical balance is quickly re-established. During this process the notion of surface tension is meaningless. In the second stage, the surface tension equilibrates, and the density profile broadens to a value which we call "intrinsic" interfacial width. During the third stage, the density profile continues to broaden due to capillary wave excitations, which does not however affect the surface tension. We have observed this scenario for monatomic Lennard-Jones (LJ) liquid as well as for binary LJ mixtures at different temperatures, monitoring a wide range of physical observables.
Galindo, A; Vega, C; Sanz, E; MacDowell, L G; de Miguel, E; Blas, F J
2004-02-22
The global phase behavior (i.e., vapor-liquid and fluid-solid equilibria) of rigid linear Lennard-Jones (LJ) chain molecules is studied. The phase diagrams for three-center and five-center rigid model molecules are obtained by computer simulation. The segment-segment bond lengths are L = sigma, so that models of tangent monomers are considered in this study. The vapor-liquid equilibrium conditions are obtained using the Gibbs ensemble Monte Carlo method and by performing isobaric-isothermal NPT calculations at zero pressure. The phase envelopes and critical conditions are compared with those of flexible LJ molecules of tangent segments. An increase in the critical temperature of linear rigid chains with respect to their flexible counterparts is observed. In the limit of infinitely long chains the critical temperature of linear rigid LJ chains of tangent segments seems to be higher than that of flexible LJ chains. The solid-fluid equilibrium is obtained by Gibbs-Duhem integration, and by performing NPT simulations at zero pressure. A stabilization of the solid phase, an increase in the triple-point temperature, and a widening of the transition region are observed for linear rigid chains when compared to flexible chains with the same number of segments. The triple-point temperature of linear rigid LJ chains increases dramatically with chain length. The results of this work suggest that the fluid-vapor transition could be metastable with respect to the fluid-solid transition for chains with more than six LJ monomer units.
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
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(c) = 2.5, 3, 4, and 5σ. In addition, we have also considered cutoff distances r(c) = 2.5 and 3σ in combination with the inhomogeneous long-range corrections proposed in this work. The normal and tangential microscopic components of the pressure tensor are obtained using the mechanical or virial route in combination with the recipe of Irving and Kirkwood, while the macroscopic components are calculated using the Volume Perturbation thermodynamic route proposed by de Miguel and Jackson [J. Chem. Phys. 125, 164109 (2006)]. The vapour-liquid interfacial tension is evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the Test-Area methodology. In addition to the pressure tensor and the surface tension, we also obtain density profiles, coexistence densities, vapour pressure, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the cutoff distance and the long-range corrections on these properties. According to our results, the main effect of increasing the cutoff distance (at fixed temperature) is to sharpen the vapour-liquid interface, to decrease the vapour pressure, and to increase the width of the biphasic coexistence region. As a result, the interfacial thickness
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.
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.
Mi, Jianguo; Tang, Yiping; Zhong, Chongli; Li, Yi-Gui
2006-04-14
The recently proposed first-order mean spherical approximation (FMSA) [Y. Tang, J. Chem. Phys. 121, 10605 (2004)] for inhomogeneous fluids is extended to study the phase behavior of nanoconfined Lennard-Jones fluids, which is consistent with the phase equilibria calculation of the corresponding bulk fluid. With a combination of fundamental measure theory, FMSA provides Helmholtz free energy and direct correlation function to formulate density functional theory, which implementation is as easy as the mean-field theory. Following previous success in predicting density profiles inside slit pores, this work is focused specially on the vapor-liquid equilibrium of the Lennard-Jones fluids inside these pores. It is found that outside the critical region FMSA predicts well the equilibrium diagram of slit pores with the sizes of 5.0, 7.5, and 10 molecular diameters by comparing with available computer simulation data. As a quantitative method, FMSA can be treated as an extension from its bulk calculation, while the mean-field theory is only qualitative, as its bulk version.
NASA Astrophysics Data System (ADS)
Abbaspour, Mohsen; Akbarzadeh, Hamed; Salemi, Sirous; Abroodi, Mousarreza
2016-11-01
By considering the anisotropic pressure tensor, two separate equations of state (EoS) as functions of the density, temperature, and carbon nanotube (CNT) diameter have been proposed for the radial and axial directions for the confined Lennard-Jones (LJ) fluid into (11,11), (12,10), and (19,0) CNTs from 120 to 600 K using molecular dynamics (MD) simulations. We have also investigated the effects of the pore size, pore loading, chirality, and temperature on some of the structural and dynamical properties of the confined LJ fluid into (11,11), (12,10), (19,0), and (19,19) CNTs such as the radial density profile and self-diffusion coefficient. We have also determined the EoS for the confined LJ fluid into double and triple walled CNTs.
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.
Ghosh, Satinath; Ghosh, Swapan K
2011-09-28
A double well type Helmholtz free energy density functional and a model density profile for a two phase vapor-liquid system are used to obtain the size-dependent interfacial properties of the vapor-liquid interface at coexistence condition along the lines of van der Waals and Cahn and Hilliard density functional formalism of the interface. The surface tension, temperature-density curve, density profile, and thickness of the interface of Lennard-Jones fluid droplet-vapor equilibrium, as predicted in this work are reported. The planar interfacial properties, obtained from consideration of large radius of the liquid drop, are in good agreement with the results of other earlier theories and experiments. The same free energy model has been tested by solving the equations numerically, and the results compare well with those from the use of model density profile. PMID:21974555
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)
Amadei, A.; Apol, M. E. F.; Chillemi, G.; Berendsen, H. J. C.; di Nola, A.
In this article we present an equation of state for fluids, based on the quasi-Gaussian entropy theory. The temperature dependence along isochores is described by a confined Gamma state, previously introduced, combined with a simple perturbation term. The 11 parameters occurring in the free energy and pressure expressions along the isochores are obtained from molecular dynamics simulation data. The equation of state has been parametrized for the Lennard-Jones fluid in the (reduced) density range 0-1.0 and (reduced) temperature range 1.0-20.0 using (partly new) NVT molecular dynamics simulation data. An excellent agreement for both energy and pressure was obtained. To test the ability to extrapolate to unknown state points, the parametrization was also performed on a smaller set of data in the temperature range 1.0-6.0. The results in the two cases are remarkably close, even in the high temperature range, and are often almost indistinguishable, in contrast to a pure empirical equation of state, like for example the modified Benedict-Webb-Rubin equation. The coexistence line agrees in general very well with Gibbs ensemble and NpT simulation results, and only very close to the critical point there are deviations. Our estimate of the critical point for both parametrizations is somewhat different from the best estimate based on Gibbs ensemble simulations, but is in excellent agreement with other estimates based on NVT simulations and integral equations.
NASA Astrophysics Data System (ADS)
Vogelsang, R.; Hoheisel, C.
1987-02-01
Molecular-dynamics (MD) calculations are reported for three thermodynamic states of a Lennard-Jones fluid. Systems of 2048 particles and 105 integration steps were used. The transverse current autocorrelation function, Ct(k,t), has been determined for wave vectors of the range 0.5<||k||σ<1.5. Ct(k,t) was fitted by hydrodynamic-type functions. The fits returned k-dependent decay times and shear viscosities which showed a systematic behavior as a function of k. Extrapolation to the hydrodynamic region at k=0 gave shear viscosity coefficients in good agreement with direct Green-Kubo results obtained in previous work. The two-exponential model fit for the memory function proposed by other authors does not provide a reasonable description of the MD results, as the fit parameters show no systematic wave-vector dependence, although the Ct(k,t) functions are somewhat better fitted. Similarly, the semiempirical interpolation formula for the decay time based on the viscoelastic concept proposed by Akcasu and Daniels fails to reproduce the correct k dependence for the wavelength range investigated herein.
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
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.
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
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.
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.
Baidakov, Vladimir G
2016-02-21
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. PMID:26896990
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.
NASA Astrophysics Data System (ADS)
Binder, Kurt; Block, Benjamin J.; Virnau, Peter; Tröster, Andreas
2012-12-01
As a rule, mean-field theories applied to a fluid that can undergo a transition from saturated vapor at density ρυ to a liquid at density ρℓ yield a van der Waals loop. For example, isotherms of the chemical potential μ(T ,ρ) as a function of the density ρ at a fixed temperature T less than the critical temperature Tc exhibit a maximum and a minimum. Metastable and unstable parts of the van der Waals loop can be eliminated by the Maxwell construction. Van der Waals loops and the corresponding double minimum potentials are mean-field artifacts. Simulations at fixed μ =μcoex for ρυ<ρ <ρℓ yield a loop, but for sufficiently large systems this loop does not resemble the van der Waals loop and reflects interfacial effects on phase coexistence due to finite size effects. In contrast to the van der Waals loop, all parts of the loop found in simulations are thermodynamically stable. The successive umbrella sampling algorithm is described as a convenient tool for seeing these effects. It is shown that the maximum of the loop is not the stability limit of a metastable vapor but signifies the droplet evaporation-condensation transition. The descending part of the loop contains information on Tolman-like corrections to the surface tension, rather than describing unstable states.
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.
A modified TIP3P water potential for simulation with Ewald summation
NASA Astrophysics Data System (ADS)
Price, Daniel J.; Brooks, Charles L.
2004-11-01
The charges and Lennard-Jones parameters of the TIP3P water potential have been modified to improve its performance under the common condition for molecular dynamics simulations of using Ewald summation in lieu of relatively short nonbonded truncation schemes. These parameters were optimized under the condition that the hydrogen atoms do not have Lennard-Jones parameters, thus making the model independent of the combining rules used for the calculation of nonbonded, heteroatomic interaction energies, and limiting the number of Lennard-Jones calculations required. Under these conditions, this model provides accurate density (ρ=0.997 g/ml) and heat of vaporization (ΔHvap=10.53 kcal/mol) at 25 °C and 1 atm, but also provides improved structure in the second peak of the O-O radial distribution function and improved values for the dielectric constant (ɛ0=89) and the diffusion coefficient (D=4.0×10-5 cm2/s) relative to the original parametrization. Like the original parameterization, however, this model does not show a temperature density maximum. Several similar models are considered with the additional constraint of trying to match the performance of the optimized potentials for liquid simulation atom force field to that obtained when using the simulation conditions under which it was originally designed, but no model was entirely satisfactory in reproducing the relative difference in free energies of hydration between the model compounds, phenol and benzene. Finally, a model that incorporates a long-range correction for truncated Lennard-Jones interactions is presented, which provides a very accurate dielectric constant (ɛ0=76), however, the improvement in this estimate is on the same order as the uncertainty in the calculation.
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.
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
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.
Chemical potential calculations in dense liquids using metadynamics
NASA Astrophysics Data System (ADS)
Perego, C.; Giberti, F.; Parrinello, M.
2016-07-01
The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to insert an extra particle in the system. In dense systems this method fails since the insertion probability is very low. In this paper we show that in a homogeneous fluid the insertion probability can be increased using metadynamics. We test our method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain efficiently converged results even when Widom's method fails.
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
NASA Astrophysics Data System (ADS)
Heyes, D. M.; Rickayzen, G.; Pieprzyk, S.; Brańka, A. C.
2016-08-01
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 ≃ 104 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.
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.
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.
Communication: Certifying the potential energy landscape
NASA Astrophysics Data System (ADS)
Mehta, Dhagash; Hauenstein, Jonathan D.; Wales, David J.
2013-05-01
It is highly desirable for numerical approximations to stationary points for a potential energy landscape to lie in the corresponding quadratic convergence basin. However, it is possible that an approximation may lie only in the linear convergence basin, or even in a chaotic region, and hence not converge to the actual stationary point when further optimization is attempted. Proving that a numerical approximation will quadratically converge to the associated stationary point is termed certification. Here, we apply Smale's α-theory to stationary points, providing a certification serving as a mathematical proof that the numerical approximation does indeed correspond to an actual stationary point, independent of the precision employed. As a practical example, employing recently developed certification algorithms, we show how the α-theory can be used to certify all the known minima and transition states of Lennard-Jones LJN atomic clusters for N = 7, …, 14.
Applicability of effective pair potentials for active Brownian particles.
Rein, Markus; Speck, Thomas
2016-09-01
We have performed a case study investigating a recently proposed scheme to obtain an effective pair potential for active Brownian particles (Farage et al., Phys. Rev. E 91, 042310 (2015)). Applying this scheme to the Lennard-Jones potential, numerical simulations of active Brownian particles are compared to simulations of passive Brownian particles interacting by the effective pair potential. Analyzing the static pair correlations, our results indicate a limited range of activity parameters (speed and orientational correlation time) for which we obtain quantitative, or even qualitative, agreement. Moreover, we find a qualitatively different behavior for the virial pressure even for small propulsion speeds. Combining these findings we conclude that beyond linear response active particles exhibit genuine non-equilibrium properties that cannot be captured by effective pair interaction alone. PMID:27628695
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.
Study of nanoscale damage evolution using embedded atom method potentials
NASA Astrophysics Data System (ADS)
Potirniche, Gabriel; Horstemeyer, Mark; Gullet, Phillip
2004-03-01
Damage evolution at nanoscale has been studied using embedded atom method (EAM) potentials based on molecular dynamics principles. The simulations were performed using WARP, a parallel computing atomistic stress simulator based on Lennard-Jones (LJ) potentials for Aluminum. By varying the number of atoms from a few hundred to a few hundred thousands, we analyzed void nucleation, growth and coalescence at increasing material length scale. Rectangular specimens with and without voids were subjected to uniaxial tension up to a total strain of 50rates. Uniaxial stress-strain curves, void-volume fraction evolution and stress triaxiality were monitored. The results indicated that nucleation process is highly dependent on the material length scale, while the void growth and void coalescence mechanisms were almost indifferent to the increasing length scale. Material length scale mostly affects dislocation nucleation mechanisms that lead to void formation. Strain rate also significantly influences the stress-strain response during plastic deformation at various length scales.
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)
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.
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.
Mie potentials for phase equilibria calculations: application to alkanes and perfluoroalkanes.
Potoff, Jeffrey J; Bernard-Brunel, Damien A
2009-11-01
Transferable united-atom force fields, based on n - 6 Lennard-Jones potentials, are presented for normal alkanes and perfluorocarbons. It is shown that by varying the repulsive exponent the range of the potential can be altered, leading to improved predictions of vapor pressures while also reproducing saturated liquid densities to high accuracy. Histogram-reweighting Monte Carlo simulations in the grand canonical ensemble are used to determine the vapor liquid coexistence curves, vapor pressures, heats of vaporization, and critical points for normal alkanes methane through tetradecane, and perfluorocarbons perfluoromethane through perfluorooctane. For all molecules studied, saturated liquid densities are reproduced to within 1% of experiment. Vapor pressures for normal alkanes and perfluorocarbons were predicted to within 3% and 6% of experiment, respectively. Calculations performed for binary mixture vapor-liquid equilibria for propane + pentane show excellent agreement with experiment, while slight deviations are observed for the ethane + perfluoroethane mixture.
A multiscale transport model for Lennard-Jones binary mixtures based on interfacial friction
NASA Astrophysics Data System (ADS)
Bhadauria, Ravi; Aluru, N. R.
2016-08-01
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.
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
Interaction forces between nanoparticles in Lennard-Jones (L-J) solvents
NASA Astrophysics Data System (ADS)
Sinha, Indrajit; Mukherjee, Ashim K.
2014-03-01
Molecular simulations, such as Monte Carlo (MC) and molecular dynamics (MD) have been recently used for understanding the forces between colloidal nanoparticles that determine the dispersion and stability of nanoparticle suspensions. Herein we review the current status of research in the area of nanoparticles immersed in L-J solvents. The first study by Shinto et al. used large smooth spheres to depict nanoparticles in L-J and soft sphere solvents. The nanoparticles were held fixed at a particular interparticle distance and only the solvents were allowed to equilibrate. Both Van-der-waals and solvation forces were computed at different but fixed interparticle separation. Later Qin and Fitchthorn improved on this model by considering the nanoparticles as collection of molecules, thus taking into the account the effect of surface roughness of nanoparticles. Although the inter particle distance was fixed, the rotation of such nanoparticles with respect to each other was also investigated. Recently, in keeping with the experimental situation, we modified this model by allowing the nanoparticles to move and rotate freely. Solvophilic, neutral and solvophobic interactions between the solvent atoms and those that make up the nanoparticles were modelled. While neutral and solvophobic nanoparticles coalesce even at intermediate distances, solvophilic nanoparticles are more stable in solution due to the formation of a solvent shield.
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.
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.
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...
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.
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.
Forte, Esther; Haslam, Andrew J; Jackson, George; Müller, Erich A
2014-09-28
The use of effective fluid-surface potentials, in which the full positional dependence is replaced by a dependence only on the distance from the surface of the solid, is common practice as a route to reduce the complexity of evaluating adsorption of fluids on substrates. Conceptually this is equivalent to replacing the detailed description of the discrete molecular nature by a coarse-grained description in which the solid is represented by a continuous (structureless) surface. These effective fluid-surface potentials are essential in the development of theories for surface adsorption, and they provide a means to reduce the computational cost associated with the molecular simulation of the system. The main purpose of the present contribution is to emphasise the necessity of using an adequate averaging procedure to obtain effective fluid-surface potentials. A simple unweighted average of the configurational energy is commonly employed, resulting in effective potentials that are temperature independent. We describe here a procedure to develop free-energy-averaged effective fluid-surface potentials retaining the important temperature dependence of the coarse-grained interaction between the particle and the surface. Although the approach is general in nature, we assess the merits of free-energy-averaged potentials for the adsorption of methane on graphene and graphite, making appropriate comparisons with the description obtained with the more traditional temperature-independent potentials. Additionally, we develop effective fluid-surface potentials for crystalline faces of monolayer and multilayer homogeneous and heterogeneous fcc lattices based on the Lennard-Jones (12-6) pair potential, and compute the corresponding adsorption isotherms of Lennard-Jones fluids on these surfaces using Grand Canonical Monte Carlo (GCMC) simulations. The adequacy of the two different options to obtain effective fluid-surface potentials (a free-energy-based versus a simple unweighted
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.
Chen, K.; Kaplan, T.; Mostoller, M.
1996-03-01
In 1995, North Americans installed $5 billion in efficiency equipment in their buildings in order to save money and conserve energy and water. But this covers only a small fraction of the existing cost-effective opportunities for energy savings investments. If all cost-effective efficiency investments were made in public and commercial buildings, the United States would save $20 billion per year on energy bills, create over 100,000 jobs, and significantly cut pollution. When firms invest in energy efficiency, they naturally want to know how much they have saved and how long their savings will last. If the installation had been made to generate energy, measurements would be trivial - install a meter. But to measure savings is a challenge, and requires both metering and a methodology, known as a measurement and verification protocol. To determine energy savings, the parties (the building owner, the installer and perhaps the financier) must first agree on the {open_quotes}base case{close_quotes} (what the building used before retrofit), and then must measure energy use after retrofit. They may want to adjust the savings for variations in the weather or changes in occupancy or work schedules. And they should keep up the measurements to ensure that their savings persist.
Dependance de la viscosité en fonction du taux de cisaillement dans un fluide de Lennard-Jones
NASA Astrophysics Data System (ADS)
Quentrec, B.
A l'aide de la théorie linéarisée de l'ordre local, nous calculons la fonction de mémoire du courant transverse. Nous trouvons que sa forme est la même que celle obtenue par Levesque, Verlet et Kurkijarvi par une simulation à l'équilibre de l'argon près du point triple (ρ* = 0,8442, T* = 0,722). Nous en déduisons les deux paramètres de la théorie, à savoir R le coefficient de couplage et τ la durée de vie de la structure locale. Nous calculons ensuite la viscosité dépendant du taux de cisaillement η(η(τ. Si nous prenons pour ces paramètres les valeurs données par la simulation à l'équilibre nous avons donc pour η() une expression sans paramètres ajustable. Lorsque nous comparons cette expression avec les valeurs expérimentales obtenues à partir de simulations numérique d'un écoulement de Couette, l'accord est satisfaisant.
Computer simulation of acetonitrile and methanol with ab initio-based pair potentials
NASA Astrophysics Data System (ADS)
Hloucha, M.; Sum, A. K.; Sandler, S. I.
2000-10-01
This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.
NASA Astrophysics Data System (ADS)
Kosevich, Yuriy A.; Savin, Alexander V.
2016-10-01
We provide molecular dynamics simulation of heat transport and energy diffusion in one-dimensional molecular chains with different interparticle pair potentials at zero and non-zero temperature. We model the thermal conductivity (TC) and energy diffusion (ED) in the chain of coupled rotators and in the Lennard-Jones chain either without or with the confining parabolic interparticle potential. The considered chains without the confining potential have normal TC and ED at non-zero temperature, while the corresponding chains with the confining potential are characterized by anomalous (diverging with the system length) TC and superdiffusion of energy. Similar effect is produced by the anharmonic quartic confining pair potential. We confirm in such a way that, surprisingly, the confining pair potential makes both heat transport and energy diffusion anomalous in one-dimensional phononic systems. We show that the normal TC is always accompanied by the normal ED in the thermalized anharmonic chains, while the superdiffusion of energy occurs in the thermalized chains with only anomalous heat transport.
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.
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
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)…
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…
Home Economics/Health Grades 6-12. Program Evaluation.
ERIC Educational Resources Information Center
Des Moines Public Schools, IA. Teaching and Learning Div.
Home economics programs are offered to students in grades 6-12 in the Des Moines INdependent Community School District (Iowa). Programs at the middle school level are exploratory, leading to occupational training in family and consumer science, child care, food service, and textile and fashion arts at the high school level. Health education…
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.
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.
Pair Potential That Reproduces the Shape of Isochrones in Molecular Liquids.
Veldhorst, Arno A; Schrøder, Thomas B; Dyre, Jeppe C
2016-08-18
Many liquids have curves (isomorphs) in their phase diagrams along which structure, dynamics, and some thermodynamic quantities are invariant in reduced units. A substantial part of their phase diagrams is thus effectively one dimensional. The shapes of these isomorphs are described by a material-dependent function of density, h(ρ), which for real liquids is well approximated by a power law, ρ(γ). However, in simulations, a power law is not adequate when density changes are large; typical models, such as Lennard-Jones liquids, show that γ(ρ) ≡ d ln h(ρ)/d ln ρ is a decreasing function of density. This article presents results from computer simulations using a new pair potential that diverges at a nonzero distance and can be tuned to give a more realistic shape of γ(ρ). Our results indicate that the finite size of molecules is an important factor to take into account when modeling liquids over a large density range.
Development of the Transferable Potentials for Phase Equilibria Model for Hydrogen Sulfide.
Shah, Mansi S; Tsapatsis, Michael; Siepmann, J Ilja
2015-06-11
The transferable potentials for phase equilibria force field is extended to hydrogen sulfide. The pure-component and binary vapor-liquid equilibria with methane and carbon dioxide and the liquid-phase relative permittivity are used for the parametrization of the Lennard-Jones (LJ) and Coulomb interactions, and models with three and four interaction sites are considered. For the three-site models, partial point charges are placed on the sites representing the three atoms, while the negative partial charge is moved to an off-atom site for the four-site models. The effect of molecular shape is probed using either only a single LJ interaction site on the sulfur atom or adding sites also on the hydrogen atoms. This procedure results in four distinct models, but only those with three LJ sites can accurately reproduce all properties considered for the parametrization. These two are further assessed for predictions of the liquid-phase structure, the lattice parameters and relative permittivity for the face-centered-cubic solid, and the triple point. An effective balance between LJ interactions and the dipolar and quadrupolar terms of the first-order electrostatic interactions is struck in order to obtain a four-site model that describes the condensed-phase properties and the phase equilibria with high accuracy. PMID:25981731
Pair Potential That Reproduces the Shape of Isochrones in Molecular Liquids.
Veldhorst, Arno A; Schrøder, Thomas B; Dyre, Jeppe C
2016-08-18
Many liquids have curves (isomorphs) in their phase diagrams along which structure, dynamics, and some thermodynamic quantities are invariant in reduced units. A substantial part of their phase diagrams is thus effectively one dimensional. The shapes of these isomorphs are described by a material-dependent function of density, h(ρ), which for real liquids is well approximated by a power law, ρ(γ). However, in simulations, a power law is not adequate when density changes are large; typical models, such as Lennard-Jones liquids, show that γ(ρ) ≡ d ln h(ρ)/d ln ρ is a decreasing function of density. This article presents results from computer simulations using a new pair potential that diverges at a nonzero distance and can be tuned to give a more realistic shape of γ(ρ). Our results indicate that the finite size of molecules is an important factor to take into account when modeling liquids over a large density range. PMID:27494438
Development of the Transferable Potentials for Phase Equilibria Model for Hydrogen Sulfide.
Shah, Mansi S; Tsapatsis, Michael; Siepmann, J Ilja
2015-06-11
The transferable potentials for phase equilibria force field is extended to hydrogen sulfide. The pure-component and binary vapor-liquid equilibria with methane and carbon dioxide and the liquid-phase relative permittivity are used for the parametrization of the Lennard-Jones (LJ) and Coulomb interactions, and models with three and four interaction sites are considered. For the three-site models, partial point charges are placed on the sites representing the three atoms, while the negative partial charge is moved to an off-atom site for the four-site models. The effect of molecular shape is probed using either only a single LJ interaction site on the sulfur atom or adding sites also on the hydrogen atoms. This procedure results in four distinct models, but only those with three LJ sites can accurately reproduce all properties considered for the parametrization. These two are further assessed for predictions of the liquid-phase structure, the lattice parameters and relative permittivity for the face-centered-cubic solid, and the triple point. An effective balance between LJ interactions and the dipolar and quadrupolar terms of the first-order electrostatic interactions is struck in order to obtain a four-site model that describes the condensed-phase properties and the phase equilibria with high accuracy.
Exponential repulsion improves structural predictability of molecular docking.
Bazgier, Václav; Berka, Karel; Otyepka, Michal; Banáš, Pavel
2016-10-30
Molecular docking is a powerful tool for theoretical prediction of the preferred conformation and orientation of small molecules within protein active sites. The obtained poses can be used for estimation of binding energies, which indicate the inhibition effect of designed inhibitors, and therefore might be used for in silico drug design. However, the evaluation of ligand binding affinity critically depends on successful prediction of the native binding mode. Contemporary docking methods are often based on scoring functions derived from molecular mechanical potentials. In such potentials, nonbonded interactions are typically represented by electrostatic interactions between atom-centered partial charges and standard 6-12 Lennard-Jones potential. Here, we present implementation and testing of a scoring function based on more physically justified exponential repulsion instead of the standard Lennard-Jones potential. We found that this scoring function significantly improved prediction of the native binding modes in proteins bearing narrow active sites such as serine proteases and kinases. © 2016 Wiley Periodicals, Inc. PMID:27620738
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
Do, D D; Do, H D
2004-12-01
Adsorption of ethylene and ethane on graphitized thermal carbon black and in slit pores whose walls are composed of graphene layers is studied in detail to investigate the packing efficiency, the two-dimensional critical temperature, and the variation of the isosteric heat of adsorption with loading and temperature. Here we used a Monte Carlo simulation method with a grand canonical Monte Carlo ensemble. A number of two-center Lennard-Jones (LJ) potential models are investigated to study the impact of the choice of potential models in the description of adsorption behavior. We chose two 2C-LJ potential models in our investigation of the (i) UA-TraPPE-LJ model of Martin and Siepmann for ethane and Wick et al. for ethylene and (ii) AUA4-LJ model of Ungerer et al. for ethane and Bourasseau et al. for ethylene. These models are used to study the adsorption of ethane and ethylene on graphitized thermal carbon black. It is found that the solid-fluid binary interaction parameter is a function of adsorbate and temperature, and the adsorption isotherms and heat of adsorption are well described by both the UA-TraPPE and AUA models, although the UA-TraPPE model performs slightly better. However, the local distributions predicted by these two models are slightly different. These two models are used to explore the two-dimensional condensation for the graphitized thermal carbon black, and these values are 110 K for ethylene and 120 K for ethane.
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
Paz-Borbón, Lauro Oliver; Mortimer-Jones, Thomas V; Johnston, Roy L; Posada-Amarillas, Alvaro; Barcaro, Giovanni; Fortunelli, Alessandro
2007-10-14
The energetics of 98 atom bimetallic Pd-Pt clusters are studied using a combination of: a genetic algorithm technique (to explore vast areas of the configurational space); a basin-hopping atom-exchange routine (to search for lowest-energy homotops at fixed composition); and a shell optimisation approach (to search for high symmetry isomers). The interatomic interactions between Pd and Pt are modelled by the Gupta many-body empirical potential. For most compositions, the putative global minima are found to have structures based on defective Marks decahedra, but in the composition range from Pd46Pt52 to Pd63Pt35, the Leary tetrahedron (LT)--a structure previously identified for 98 atom Lennard-Jones clusters--is consistently found as the most stable structure. Based on the excess energy stability criterion, Pd56Pt42 represents the most stable cluster across the entire composition range. This structure, a Td-symmetry LT, exhibits multi-layer segregation with an innermost core of Pd atoms, an intermediate layer of Pt atoms and an outermost Pd surface shell (Pd-Pt-Pd). The stability of the Leary tetrahedron is compared against other low-energy competing structural motifs: the Marks decahedron (Dh-M), a "quasi" tetrahedron (a closed-packed structure) and two other closed-packed structures. The stability of LT structures is rationalized in terms of their spherical shape and the large number of nearest neighbours.
Announcement: Sleep Awareness Week - March 6-12, 2016.
2016-03-01
Sleep Awareness Week, the National Sleep Foundation's annual campaign to educate the public about the importance of sleep in health and safety, will be observed March 6-12, 2016. The American Academy of Sleep Medicine and the Sleep Research Society recommend that adults aged 18-60 years sleep ≥7 hours each night to promote optimal health and well-being. However, 35% of U.S. adults report typically sleeping <7 hours Adults who do not get enough sleep on a regular basis are more likely to suffer from chronic conditions, such as obesity, high blood pressure, diabetes, and poor mental health.
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
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.
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.
Scattering of helium atoms by liquid helium
NASA Astrophysics Data System (ADS)
Goodman, Frank O.; Garcia, Nicolas
1986-04-01
We present results from a new He-liquid-He single-atom effective potential for scattering, obtained from an integration, over the region occupied by the liquid, of a standard Lennard-Jones 6-12 pairwise potential combined with a simple model of the pair-correlation function. The new potential is consistent with (a) the accepted internal energy (the negative of the latent heat) of liquid He, (b) the accepted long-range (-C3/z3 van der Waals) atom-surface interaction potential, and (c) the scattering (reflectivity) data of Edwards et al. Production of excitons (ripplons) at the surface is not necessary to interpret the data. The theory is unsymmetrized; that is, no account is taken of the fact that scattering among identical particles is being considered.
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, 2012 CFR
2012-07-01
... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Alcohols, C6-12, ethoxylated, reaction... 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...
40 CFR 721.524 - Alcohols, C6-12, ethoxylated, reaction product with maleic anhydride.
Code of Federal Regulations, 2010 CFR
2010-07-01
... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Alcohols, C6-12, ethoxylated, reaction... 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...
40 CFR 721.524 - Alcohols, C6-12, ethoxylated, reaction product with maleic anhydride.
Code of Federal Regulations, 2013 CFR
2013-07-01
... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Alcohols, C6-12, ethoxylated, reaction... 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...
40 CFR 721.524 - Alcohols, C6-12, ethoxylated, reaction product with maleic anhydride.
Code of Federal Regulations, 2011 CFR
2011-07-01
... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Alcohols, C6-12, ethoxylated, reaction... 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...
40 CFR 721.524 - Alcohols, C6-12, ethoxylated, reaction product with maleic anhydride.
Code of Federal Regulations, 2014 CFR
2014-07-01
... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Alcohols, C6-12, ethoxylated, reaction... 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...
Nanoparticle interaction potentials constructed by multiscale computation.
Lee, Cheng K; Hua, Chi C
2010-06-14
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 (SiO(2))(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 Si(6)O(12) 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 2alpha-alpha potential (alpha 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
Holtgrave, Jeremy C.; Wolf, Paul J.
2005-07-15
The broadening and shifting of spectral lines induced by collisions with the five noble gases in both the intercombination 5s{sup 2} {sup 1}S{sub 0}{yields}5s5p {sup 3}P{sub 1} system and the triplet 5s5p {sup 3}P{sub 0,1,2}{yields}5s6s {sup 3}S{sub 1} manifold of Sr are studied using tunable dye laser absorption spectroscopy. Cross sections for impact broadening and line shifting are determined from an examination of the spectral line profiles. These results are utilized in an analysis to compute difference potentials modeled by the Lennard-Jones (6-12) potential and the coefficients C{sub 6} and C{sub 12} derived from this analysis are reported.
Loeffler, Troy D; Chen, Bin
2013-12-21
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.
NASA Technical Reports Server (NTRS)
Gamache, Robert R.; Fischer, Jonathan
2001-01-01
Pressure-broadened half-widths and pressure-induced line shifts for the two most important bands of water vapor in the 0.7-micron region are determined using the complex Robert-Bonamy (CRB) formalism. The calculations are made with nitrogen and oxygen as the perturbing gas from which values for air as the perturbing gas are determined. The intermolecular potential is taken as a sum of electrostatic contributions and Lennard-Jones (6-12) atom-atom, and isotropic induction and dispersion components. The dynamics of the collision process are correct to second order in time. The calculated values are compared with published measurements and agreement is observed for both half-widths and line shifts. The temperature dependence of the half-width, which is necessary for reduction of remotely sensed data, is determined.
Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions.
Ballal, Deepti; Venkataraman, Pradeep; Fouad, Wael A; Cox, Kenneth R; Chapman, Walter G
2014-08-14
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 ε(W)/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-ε(W)/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. PMID:25134597
Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions.
Ballal, Deepti; Venkataraman, Pradeep; Fouad, Wael A; Cox, Kenneth R; Chapman, Walter G
2014-08-14
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 ε(W)/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-ε(W)/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.
Docherty, H; Galindo, A; Vega, C; Sanz, E
2006-08-21
We have obtained the excess chemical potential of methane in water, over a broad range of temperatures, from computer simulation. The methane molecules are described as simple Lennard-Jones interaction sites, while water is modeled by the recently proposed TIP4P/2005 model. We have observed that the experimental values of the chemical potential are not reproduced when using the Lorentz-Berthelot combining rules. However, we also noticed that the deviation is systematic, suggesting that this may be corrected. In fact, by introducing positive deviations from the energetic Lorentz-Berthelot rule to account indirectly for the polarization methane-water energy, we are able to describe accurately the excess chemical potential of methane in water. Thus, by using a model capable of describing accurately the density of pure water in a wide range of temperatures and by deviating from the Lorentz-Berthelot combining rules, it is possible to reproduce the properties of methane in water at infinite dilution. In addition, we have applied this methane-water potential to the study of the solid methane hydrate structure, commonly denoted as sI, and find that the model describes the experimental value of the unit cell of the hydrate with an error of about 0.2%. Moreover, we have considered the effect of the amount of methane contained in the hydrate. In doing so, we determine that the presence of methane increases slightly the value of the unit cell and decreases slightly the compressibility of the structure. We also note that the presence of methane increases greatly the range of pressures where the sI hydrate is mechanically stable. PMID:16942354
Docherty, H; Galindo, A; Vega, C; Sanz, E
2006-08-21
We have obtained the excess chemical potential of methane in water, over a broad range of temperatures, from computer simulation. The methane molecules are described as simple Lennard-Jones interaction sites, while water is modeled by the recently proposed TIP4P/2005 model. We have observed that the experimental values of the chemical potential are not reproduced when using the Lorentz-Berthelot combining rules. However, we also noticed that the deviation is systematic, suggesting that this may be corrected. In fact, by introducing positive deviations from the energetic Lorentz-Berthelot rule to account indirectly for the polarization methane-water energy, we are able to describe accurately the excess chemical potential of methane in water. Thus, by using a model capable of describing accurately the density of pure water in a wide range of temperatures and by deviating from the Lorentz-Berthelot combining rules, it is possible to reproduce the properties of methane in water at infinite dilution. In addition, we have applied this methane-water potential to the study of the solid methane hydrate structure, commonly denoted as sI, and find that the model describes the experimental value of the unit cell of the hydrate with an error of about 0.2%. Moreover, we have considered the effect of the amount of methane contained in the hydrate. In doing so, we determine that the presence of methane increases slightly the value of the unit cell and decreases slightly the compressibility of the structure. We also note that the presence of methane increases greatly the range of pressures where the sI hydrate is mechanically stable.
Chapela, Gustavo A; del Río, Fernando; Alejandre, José
2013-02-01
The liquid-vapor phase diagrams of equal size diameter σ binary mixtures of screened potentials have been reported for several ranges of interaction using Monte Carlo simulation methods [J. B. Caballero, A. M. Puertas, A. Ferńandez-Barbero, F. J. de las Nieves, J. M. Romero-Enrique, and L. F. Rull, J. Chem. Phys. 124, 054909 (2006); A. Fortini, A.-P. Hynninen, and M. Dijkstra, J. Chem. Phys. 125, 094502 (2006)]. Both works report controversial results about the stability of the phase diagram with the inverse Debye screening length κ. Caballero found stability for values of κσ up to 20 while Fortini reported stability for κσ up to 20 while Fortini reported stability for κσ ≤ 4. In this work a spinodal decomposition process where the liquid and vapor phases coexist through an interface in a slab geometry is used to obtain the phase equilibrium and surface properties using a discontinuous molecular dynamics simulations for mixtures of equal size particles carrying opposite charge and interacting with a mixture of attractive and repulsive Yukawa potentials at different values of κσ. An crude estimation of the triple point temperatures is also reported. The isothermal-isobaric method was also used to determine the phase stability using one phase simulations. We found that liquid-vapor coexistence is stable for values of κσ > 20 and that the critical temperatures have a maximum value at around κσ = 10, in agreement with Caballero et al. calculations. There also exists a controversy about the liquid-vapor envelope stability of the pure component attractive Yukawa model which is also discussed in the text. In addition, details about the equivalence between continuous and discontinuous molecular dynamics simulations are given, in the Appendix, for Yukawa and Lennard-Jones potentials.
NASA Astrophysics Data System (ADS)
Chapela, Gustavo A.; del Río, Fernando; Alejandre, José
2013-02-01
The liquid-vapor phase diagrams of equal size diameter σ binary mixtures of screened potentials have been reported for several ranges of interaction using Monte Carlo simulation methods [J. B. Caballero, A. M. Puertas, A. Ferńandez-Barbero, F. J. de las Nieves, J. M. Romero-Enrique, and L. F. Rull, J. Chem. Phys. 124, 054909 (2006), 10.1063/1.2159481; A. Fortini, A.-P. Hynninen, and M. Dijkstra, J. Chem. Phys. 125, 094502 (2006), 10.1063/1.2335453]. Both works report controversial results about the stability of the phase diagram with the inverse Debye screening length κ. Caballero found stability for values of κσ up to 20 while Fortini reported stability for κσ up to 20 while Fortini reported stability for κσ ⩽ 4. In this work a spinodal decomposition process where the liquid and vapor phases coexist through an interface in a slab geometry is used to obtain the phase equilibrium and surface properties using a discontinuous molecular dynamics simulations for mixtures of equal size particles carrying opposite charge and interacting with a mixture of attractive and repulsive Yukawa potentials at different values of κσ. An crude estimation of the triple point temperatures is also reported. The isothermal-isobaric method was also used to determine the phase stability using one phase simulations. We found that liquid-vapor coexistence is stable for values of κσ > 20 and that the critical temperatures have a maximum value at around κσ = 10, in agreement with Caballero et al. calculations. There also exists a controversy about the liquid-vapor envelope stability of the pure component attractive Yukawa model which is also discussed in the text. In addition, details about the equivalence between continuous and discontinuous molecular dynamics simulations are given, in the Appendix, for Yukawa and Lennard-Jones potentials.
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…
[Cr(III)8M(II)6](12+) Coordination Cubes (M(II)=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
2015-06-01
[Cr(III)8M(II)6](12+) (M(II) =Cu, Co) coordination cubes were constructed from a simple [Cr(III) L3 ] metalloligand and a "naked" M(II) 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.
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.
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.
Microcomputer Simulation of Real Gases--Part 1.
ERIC Educational Resources Information Center
Sperandeo-Mineo, R. M.; Tripi, G.
1987-01-01
Describes some simple computer programs designed to simulate the molecular dynamics of two-dimensional systems with a Lennard-Jones interaction potential. Discusses the use of the software in introductory physics courses at the high school and college level. (TW)
40 CFR 721.6100 - Phosphoric acid, C6-12-alkyl esters, compounds with 2-(dibutylamino) ethanol.
Code of Federal Regulations, 2011 CFR
2011-07-01
... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Phosphoric acid, C6-12-alkyl esters... Significant New Uses for Specific Chemical Substances § 721.6100 Phosphoric acid, C6-12-alkyl esters... 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
... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Phosphoric acid, C6-12-alkyl esters... Significant New Uses for Specific Chemical Substances § 721.6100 Phosphoric acid, C6-12-alkyl esters... 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
... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Phosphoric acid, C6-12-alkyl esters... Significant New Uses for Specific Chemical Substances § 721.6100 Phosphoric acid, C6-12-alkyl esters... 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
... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Phosphoric acid, C6-12-alkyl esters... Significant New Uses for Specific Chemical Substances § 721.6100 Phosphoric acid, C6-12-alkyl esters... 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, 2013 CFR
2013-07-01
... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Phosphoric acid, C6-12-alkyl esters... Significant New Uses for Specific Chemical Substances § 721.6100 Phosphoric acid, C6-12-alkyl esters... reporting. (1) The chemical substances identified as phosphoric acid, C6-12-alkyl esters, compounds with...
A corresponding-states framework for the description of the Mie family of intermolecular potentials
NASA Astrophysics Data System (ADS)
Ramrattan, N. S.; Avendaño, C.; Müller, E. A.; Galindo, A.
2015-05-01
The Mie (λr, λa) intermolecular pair potential has been suggested as an alternative to the traditional Lennard-Jones (12-6) potential for modelling real systems both via simulation and theory as its implementation leads to an accuracy and flexibility in the determination of thermophysical properties that cannot be obtained when potentials of fixed range are considered. An additional advantage of using variable-range potentials is noted in the development of coarse-grained models where, as the superatoms become larger, the effective potentials are seen to become softer. However, the larger number of parameters that characterise the Mie potential (λr, λa, σ, ɛ) can hinder a rational study of the particular effects that each individual parameter have on the observed thermodynamic properties and phase equilibria, and higher degeneracy of models is observed. Here a three-parameter corresponding states model is presented in which a cohesive third parameter α is proposed following a perturbation expansion and assuming a mean-field limit. It is shown that in this approximation the free energy of any two Mie systems sharing the same value of α will be the same. The parameter α is an explicit function of the repulsive and attractive exponents and consequently dictates the form of the intermolecular pair potential. Molecular dynamics simulations of a variety of Mie systems over a range of values of α are carried out and the solid-liquid, liquid-vapour and vapour-solid phase boundaries for the systems considered are presented. Using the simulation data, we confirm that systems of the same α exhibit conformal phase behaviour for the fluid-phase properties as well as for the solid-fluid boundary, although larger differences are noted in the solid region; these can be related to the approximations in the definition of the parameter. Furthermore, it is found that the temperature range over which the vapour-liquid envelope of a given Mie system is stable follows a linear
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…
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…
41 CFR 51-6.12 - Specification changes and similar actions.
Code of Federal Regulations, 2010 CFR
2010-07-01
...-PROCUREMENT PROCEDURES § 51-6.12 Specification changes and similar actions. (a) Contracting activities shall notify the nonprofit agency or agencies authorized to furnish a commodity on the Procurement List and the... Procurement List, including a change that involves the assignment of a new national stock number or...
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…
NASA Astrophysics Data System (ADS)
Parsafar, G. A.; Shokouhi, M.
A new hard-core potential model was recently used to calculate thermodynamic properties of some model fluids, including equilibrium properties, such as compressibility factor and internal energy. A Lennard-Jones (LJ) like potential has been used to modify the repulsive part of the potential. The modified potential contains five parameters, namely, α, R, ɛ, σ, and σHS. The parameter α is the tail of the attractive branch whose value changes from zero to one. In this work, we have chosen α = 1 to make the potential continuous at separation r = Rσ, where the parameter R is the well width. R lies in the range 1.2 to 2.5, and R = 1.3 was found to be the best value for all real gases studied. The parameter ɛ is the well depth of potential function, and σ is the separation at which the potential function is zero. σHS is the effective hard sphere diameter, which depends on temperature and an additional parameter. Using statistical mechanics along with the Boltzmann factor criterion (BFC) for the effective hard sphere diameter, an analytical expression has been derived for the reduced second virial coefficient in terms of the reduced temperature. Fitting experimental data to expression derived for the second virial coefficient, the potential parameters ɛ and σ are obtained. Since this potential is spherical (depending only on distance), three types of species are chosen, namely Ar and He (monoatomic), N2and O2 (diatomic), and methane (spherical molecule), to show how appropriate this potential model is for them. This model predicts an inversion temperature for the second virial coefficient (temperature at which the second virial coefficient pass through a maximum) at ILM0001, where T1 is the inversion temperature, and TB is the Boyle temperature. The predicted value is better than that of the L-J model (for which ILM0002). The maximum percentage deviation of the second virial coefficient is about 2%, except around the Boyle temperature. Then the transport
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
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
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.
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
An Experimental Trial of Adaptive Programming in Drug Court: Outcomes at 6, 12 and 18 Months
Marlowe, Douglas B.; Festinger, David S.; Dugosh, Karen L.; Benasutti, Kathleen M.; Fox, Gloria; Harron, Ashley
2013-01-01
Objectives Test whether an adaptive program improves outcomes in drug court by adjusting the schedule of court hearings and clinical case-management sessions pursuant to a priori performance criteria. Methods Consenting participants in a misdemeanor drug court were randomly assigned to the adaptive program (n = 62) or to a baseline-matching condition (n = 63) in which they attended court hearings based on the results of a criminal risk assessment. Outcome measures were re-arrest rates at 18 months post-entry to the drug court and urine drug test results and structured interview results at 6 and 12 months post-entry. Results Although previously published analyses revealed significantly fewer positive drug tests for participants in the adaptive condition during the first 18 weeks of drug court, current analyses indicate the effects converged during the ensuing year. Between-group differences in new arrest rates, urine drug test results and self-reported psychosocial problems were small and non-statistically significant at 6, 12 and 18 months post-entry. A non-significant trend (p = .10) suggests there may have been a small residual impact (Cramer's ν = .15) on new misdemeanor arrests after 18 months. Conclusions Adaptive programming shows promise for enhancing short-term outcomes in drug courts; however, additional efforts are needed to extend the effects beyond the first 4 to 6 months of enrollment. PMID:25346652
Müller, Erich A; Mejía, Andrés
2011-11-10
Canonical ensemble molecular dynamics (MD) simulations are reported which compute both the vapor-liquid equilibrium properties (vapor pressure and liquid and vapor densities) and the interfacial properties (density profiles, interfacial tensions, entropy and enthalpy of surface formation) of four long-chained n-alkanes: n-decane (n-C(10)), n-eicosane (n-C(20)), n-hexacontane (n-C(60)), and n-decacontane (n-C(100)). Three of the most commonly employed united-atom (UA) force fields for alkanes (SKS: Smit, B.; Karaborni, S.; Siepmann, J. I. J. Chem. Phys. 1995,102, 2126-2140; J. Chem. Phys. 1998,109, 352; NERD: Nath, S. K.; Escobedo, F. A.; de Pablo, J. J. J. Chem. Phys. 1998, 108, 9905-9911; and TraPPE: Martin M. G.; Siepmann, J. I. J. Phys. Chem. B1998, 102, 2569-2577.) are critically appraised. The computed results have been compared to the available experimental data and those fitted using the square gradient theory (SGT). In the latter approach, the Lennard-Jones chain equation of state (EoS), appropriately parametrized for long hydrocarbons, is used to model the homogeneous bulk phase Helmholtz energy. The MD results for phase equilibria of n-decane and n-eicosane exhibit sensible agreement both to the experimental data and EoS correlation for all potentials tested, with the TraPPE potential showing the lowest deviations. However, as the molecular chain increases to n-hexacontane and n-decacontane, the reliability of the UA potentials decreases, showing notorious subpredictions of both saturated liquid density and vapor pressure. Based on the recommended data and EoS results for the heaviest hydrocarbons, it is possible to attest, that in this extreme, the TraPPE potential shows the lowest liquid density deviations. The low absolute values of the vapor pressure preclude the discrimination among the three UA potentials studied. On the other hand, interfacial properties are very sensitive to the type of UA potential thus allowing a differentiation of the
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
Chaotic dynamics near steep transition states
NASA Astrophysics Data System (ADS)
Green, Jason R.; Hofer, Thomas S.; Wales, David J.; Berry, R. Stephen
2012-08-01
Classical molecular motion near potential energy saddles can be more or less chaotic relative to motion near minima. The relative degree of chaos depends on the extent of coupling between the degrees of freedom and on the curvature of the potential energy landscape. Here, we explore these effects using constant energy molecular dynamics simulations and independent criteria associated with locally chaotic behavior - namely, the constancy of the local mode action and the magnitude of finite-time Lyapunov exponents. These criteria reconcile the chaotic basins and relatively ordered saddles of the Lennard-Jones trimer, with the chaotic saddles and ordered basins for reactive, all-atom H2O described by the Garofalini H2O potential. By modifying the Garofalini and Lennard-Jones models we separate the compounding effects of nonlinear three-body interactions and steep reaction path curvature on the local degree of chaos near saddles and minima.
Fluid-solid transition in simple systems using density functional theory.
Bharadwaj, Atul S; Singh, Yashwant
2015-09-28
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. PMID:26429020
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.
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.
ERIC Educational Resources Information Center
Brightwell, D. Shelby; Dugas, Edmond A.
This study focused on all teachers, in the public schools of Louisiana in grades 6-12, who taught health and physical education at least 50 percent of the time. A 53 percent return was obtained, which represented 917 teachers in 381 schools. Responses were received from all 64 parishes and the two city school systems in the state. The study…
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.
ERIC Educational Resources Information Center
Stanford Univ., CA. Stanford Program on International and Cross Cultural Education.
This unit, developed for grades 6-12, is designed to help students grasp what life is like in a highland village in Guatemala. It is intended that students develop skills in geography and begin to discuss such ideas as rural poverty, migration to urban centers, land distribution, and agricultural methods. The unit involves the use of a set of…
Interfacial dynamnics at sliding Ta/Al interfaces
NASA Astrophysics Data System (ADS)
Hammerberg, J. E.; Ravelo, R.; Holian, B. L.; Germann, T. C.; Olson, C. J.
2002-03-01
We present results of large-scale MD simulations of sliding Al(100)/Ta(100) interfaces at high shearing velocties. The Ta and Al interactions are modeled using EAM potentials. We discuss the structural evolution near the interface and compare our results with known 2-dimensional simulations which make use of Lennard-Jones potentials but in similar scaled-velocity regimes, namely, 0.01
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.
Molecular dynamic simulation of Copper and Platinum nanoparticles Poiseuille flow in a nanochannels
NASA Astrophysics Data System (ADS)
Toghraie, Davood; Mokhtari, Majid; Afrand, Masoud
2016-10-01
In this paper, simulation of Poiseuille flow within nanochannel containing Copper and Platinum particles has been performed using molecular dynamic (MD). In this simulation LAMMPS code is used to simulate three-dimensional Poiseuille flow. The atomic interaction is governed by the modified Lennard-Jones potential. To study the wall effects on the surface tension and density profile, we placed two solid walls, one at the bottom boundary and the other at the top boundary. For solid-liquid interactions, the modified Lennard-Jones potential function was used. Velocity profiles and distribution of temperature and density have been obtained, and agglutination of nanoparticles has been discussed. It has also shown that with more particles, less time is required for the particles to fuse or agglutinate. Also, we can conclude that the agglutination time in nanochannel with Copper particles is faster that in Platinum nanoparticles. Finally, it is demonstrated that using nanoparticles raises thermal conduction in the channel.
Design parameters for carbon nanobottles to absorb and store methane.
Lee, Richard K F; Hill, James M
2011-08-01
We investigate the internal mechanics for methane storage in a nanobottle, which is assumed to comprise a metallofullerene located inside a carbon nanobottle, which is constructed from a half-fullerene as the base, and two nanotubes which are joined by a nanocone. The interaction potential energy for the metallofullerene is obtained from the 6-12 Lennard-Jones potential and the continuum approximation, which assumes that a discrete atomic structure can be replaced by an average atomic surface density. This potential energy shows that the metallofullerene has two minimum energy positions, which are located close to the neck of the bottle and at the base of the nanobottle, and therefore it may be used as a bottle-stopper to open or to close the nanobottle. At the neck of the bottle, the encapsulated metallofullerene closes the nanobottle, and by applying an external electrical force, the metallofullerene can overcome the energy barrier of the nanotube, and pass from the neck of the nanobottle to the base so that the nanobottle is open. For methane storage, the metallofullerene serves the dual purposes of opening and closing the nanobottle, as well as an attractor for the methane gas. The analytical formulation gives rise to a rapid computational capacity, and enables the direct determination of the optimal dimensions necessary to ensure the correct working function of the nanobottle, and specific ranges for the critical parameters are formulated. PMID:22103096
Molecular dynamics simulations of carbon nanotube-based gears
NASA Astrophysics Data System (ADS)
Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn
1997-09-01
We use a molecular dynamics simulation to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with 0957-4484/8/3/001/img1. Brenner's reactive hydrocarbon potential is used to model interatomic forces within each molecular gear. A Lennard - Jones 6 - 12 potential or the Buckingham 0957-4484/8/3/001/img2 potential plus electrostatic interaction terms are used for intermolecular interactions between gears. A number of gear and gear/shaft configurations are simulated on parallel computers. One gear is powered by forcing the atoms near the end of the nanotube to rotate, and a second gear is allowed to rotate by keeping the atoms near the end of its nanotube constrained to a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. Results suggest that these gears can operate at up to 50 - 100 GHz in a vacuum at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering the temperature and/or rotation rate.
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.
Effect of partial charge parametrization on the fluid phase behavior of hydrogen sulfide.
Kamath, Ganesh; Lubna, Nusrat; Potoff, Jeffrey J
2005-09-22
The effect of partial charge parametrization on the fluid phase behavior of hydrogen sulfide is investigated with grand canonical histogram reweighting Monte Carlo simulations. Four potential models, based on a Lennard-Jones + point charge functional form, are developed. It is shown that Lennard-Jones parameters can be tuned such that partial charges for the sulfur atom in the range -0.40 < q(s) < -0.252 will lead to an accurate reproduction of experimental vapor-liquid equilibria. Each of the parameter sets developed in this work are used to predict the pressure composition behavior H2S-n-pentane at 377.6 K. While the mixture calculation provides a means of reducing the number of candidate parameter sets, multiple parameter sets were found to yield an excellent reproduction of both the pure component and mixture phase behavior.
Self-learning metabasin escape algorithm for supercooled liquids.
Cao, Penghui; Li, Minghai; Heugle, Ravi J; Park, Harold S; Lin, Xi
2012-07-01
A generic history-penalized metabasin escape algorithm that contains no predetermined parameters is presented in this work. The spatial location and volume of imposed penalty functions in the configurational space are determined in self-learning processes as the 3N-dimensional potential energy surface is sampled. The computational efficiency is demonstrated using a binary Lennard-Jones liquid supercooled below the glass transition temperature, which shows an O(10(3)) reduction in the quadratic scaling coefficient of the overall computational cost as compared to the previous algorithm implementation. Furthermore, the metabasin sizes of supercooled liquids are obtained as a natural consequence of determining the self-learned penalty function width distributions. In the case of a bulk binary Lennard-Jones liquid at a fixed density of 1.2, typical metabasins are found to contain about 148 particles while having a correlation length of 3.09 when the system temperature drops below the glass transition temperature.
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.
Phase transitions of methane using molecular dynamics simulations
NASA Astrophysics Data System (ADS)
El-Sheikh, S. M.; Barakat, K.; Salem, N. M.
2006-03-01
Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.
Phase transitions of methane using molecular dynamics simulations.
El-Sheikh, S M; Barakat, K; Salem, N M
2006-03-28
Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4 under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256 molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.
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.
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.
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.
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
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.
Molecular dynamics simulations of thermal resistance at the liquid-solid interface.
Kim, Bo Hung; Beskok, Ali; Cagin, Tahir
2008-11-01
Heat conduction between parallel plates separated by a thin layer of liquid Argon is investigated using three-dimensional molecular dynamics (MD) simulations employing 6-12 Lennard-Jones potential interactions. Channel walls are maintained at specific temperatures using a recently developed interactive thermal wall model. Heat flux and temperature distribution in nanochannels are calculated for channel heights varying from 12.96 to 3.24 nm. Fourier law of heat conduction is verified for the smallest channel, while the thermal conductivity obtained from Fourier law is verified using the predictions of Green-Kubo theory. Temperature jumps at the liquid/solid interface, corresponding to the well known Kapitza resistance, are observed. Using systematic studies thermal resistance length at the interface is characterized as a function of the surface wettability, thermal oscillation frequency, wall temperature, thermal gradient, and channel height. An empirical model for the thermal resistance length, which could be used as the jump coefficient of a Navier boundary condition, is developed. Temperature distribution in nanochannels is predicted using analytical solution of continuum heat conduction equation subjected to the new temperature jump condition. Analytical predictions are verified using MD simulations.
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)
Monge, Josue Roberto
The goal of our scattering experiments is to derive the distribution the differential cross-section and elucidate the dynamics of a bimolecular collision via pure rotational spectroscopy. We have explored the use of a data reduction model to directly transform rotational line shapes into the differential cross section and speed distribution of a reactive bimolecular collision. This inversion technique, known as Fourier Transform Doppler Spectroscopy (FTDS), initially developed by James Kinsey, deconvolves the velocity information contained in one-dimensional Doppler Profiles to construct the non-thermal, state-selective three-dimensional velocity distribution. By employing an expansion in classical orthogonal polynomials, the integral transform in FTDS can be simplified into a set of purely algebraic expressions technique; i.e. the Taatjes method. In this investigation, we extend the Taatjes method for general use in recovering asymmetric velocity distributions. We have also constructed a hypothetical asymmetric distribution from adiabatic scattering in Argon-Argon to test the general method. The angle- and speed-components of the sample distribution were derived classically from a Lennard-Jones 6-12 potential, with collisions at 60 meV, and mapped onto Radon space to generate a set of discrete Doppler profiles. The sample distribution was reconstructed from these profiles using FTDS. Both distributions were compared along with derived total cross sections for the Argon--Argon system. This study serves as a template for constructing velocity distributions from bimolecular scattering experiments using the FTDS inversion technique.
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.
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
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
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…
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…
Van der Waals interaction between two crossed carbon nanotubes.
Zhbanov, Alexander I; Pogorelov, Evgeny G; Chang, Yia-Chung
2010-10-26
The analytical expressions for the van der Waals potential energy and force between two crossed carbon nanotubes are presented. The Lennard-Jones potential between pairs of carbon atoms and the smeared-out approximation suggested by L. A. Girifalco (J. Phys. Chem. 1992, 96, 858) were used. The exact formula is expressed in terms of rational and elliptical functions. The potential and force for carbon nanotubes were calculated. The uniform potential curves for single- and multiwall nanotubes were plotted. The equilibrium distance, maximal attractive force, and potential energy have been evaluated. PMID:20863127
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.
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.
Effective protein-protein interaction from structure factor data of a lysozyme solution
NASA Astrophysics Data System (ADS)
Abramo, M. C.; Caccamo, C.; Cavero, M.; Costa, D.; Pellicane, G.; Ruberto, R.; Wanderlingh, U.
2013-08-01
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.
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…
A computer simulation study of racemic mixtures
NASA Astrophysics Data System (ADS)
Largo, J.; Vega, C.; MacDowell, L. G.; Solana, J. R.
A simple model for a chiral molecule is proposed. The model consists of a central atom bonded to four different atoms in tetrahedral coordination. Two different potentials were used to describe the pair potentials between atoms: the hard sphere potential and the Lennard-Jones potential. For both the hard sphere and the Lennard-Jones chiral models, computer simulations have been performed for the pure enantiomers and also for the racemic mixture. The racemic mixture consisted of an equimolar mixture of the two optically active enantiomers. It is found that the equations of state are the same, within statistical uncertainty, for the pure enantiomer fluid and for the racemic mixture. Only at high pressures does the racemic mixture seem to have a higher density, for a given pressure, than the pure enantiomer. Concering the structure, no difference is found in the site-site correlation functions between like and unlike molecules in the racemic mixture either at low or at high densities. However, small differences are found for the site-site correlations of the pure enantiomer and those of the racemic mixtures. In the Lennard-Jones model, similar conclusions are drawn. The extension of Wertheim's first-order perturbation theory, denoted bonded hard sphere theory (ARCHER, A. L., and JACKSON, G., 1991, Molec. Phys. , 73 , 881; AMOS, M. D., and JACKSON, G., 1992, J. chem. Phys. , 96 , 4604), successfully reproduces the simulation results for the hard chiral model. Virial coefficients of the hard chiral model up to the fourth have also been evaluated. Again, no differences are found between virial coefficients of the pure fluid and of the racemic mixture. All the results of this work illustrate the quasi-ideal behaviour of racemic mixtures in the fluid phase.
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.
Two-dimensional discrete model for DNA dynamics: Longitudinal wave propagation and denaturation
NASA Astrophysics Data System (ADS)
Muto, V.; Lomdahl, P. S.; Christiansen, P. L.
1990-12-01
In this paper, a simple, two-dimensional model of the deoxyribonucleic acid (DNA) is presented. In the model the two polynucleotide strands are linked together through the hydrogen bonds. The phosphodiester bridges in the backbone are described by the anharmonic potential of Toda kind, while the hydrogen bonds are described by the Lennard-Jones potential. Longitudinal wave propagation on ring-shaped DNA molecules is investigated. The model predicts a significant increase in the lifetime of the open states of the hydrogen bonds at physiological temperatures. Thus anharmonicity may play a role in DNA denaturation.
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.
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.
Comparison of methods for improving the 1/N expansion
NASA Astrophysics Data System (ADS)
Varshni, Y. P.
1989-08-01
The recently proposed method by Papp [Phys. Rev. A 36, 3550 (1987); 38, 2158 (1988)] for determining the shift parameter in the shifted 1/N expansion method has been applied in three approximations to calculate the eigenenergies for the static screened Coulomb potential (SSCP) and Lennard-Jones 12-6 potential. The results are compared with those obtained by the method of Imbo et al. [Phys. Rev. D 29, 1669 (1984)] and the exact values. For the SSCP, comparison is also made with the results obtained by two methods proposed by Doren and Herschbach [Phys. Rev. A 34, 2654 (1986); 34, 2665 (1986)].
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
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
Rondina, Gustavo G; Da Silva, Juarez L F
2013-09-23
Suggestions for improving the Basin-Hopping Monte Carlo (BHMC) algorithm for unbiased global optimization of clusters and nanoparticles are presented. The traditional basin-hopping exploration scheme with Monte Carlo sampling is improved by bringing together novel strategies and techniques employed in different global optimization methods, however, with the care of keeping the underlying algorithm of BHMC unchanged. The improvements include a total of eleven local and nonlocal trial operators tailored for clusters and nanoparticles that allow an efficient exploration of the potential energy surface, two different strategies (static and dynamic) of operator selection, and a filter operator to handle unphysical solutions. In order to assess the efficiency of our strategies, we applied our implementation to several classes of systems, including Lennard-Jones and Sutton-Chen clusters with up to 147 and 148 atoms, respectively, a set of Lennard-Jones nanoparticles with sizes ranging from 200 to 1500 atoms, binary Lennard-Jones clusters with up to 100 atoms, (AgPd)55 alloy clusters described by the Sutton-Chen potential, and aluminum clusters with up to 30 atoms described within the density functional theory framework. Using unbiased global search our implementation was able to reproduce successfully the great majority of all published results for the systems considered and in many cases with more efficiency than the standard BHMC. We were also able to locate previously unknown global minimum structures for some of the systems considered. This revised BHMC method is a valuable tool for aiding theoretical investigations leading to a better understanding of atomic structures of clusters and nanoparticles. PMID:23957311
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.
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.
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.
Park, T.; Rettich, T.R.; Battino, R.; Emmerich, W.
1987-04-01
The binary gaseous diffusion coefficients for cyclooctane and trans-1,2-dimethylcyclohexane diffusing into helium, argon, methane, and sulfur hexafluoride were measured at about 313.15, 328.15, and 343.15K and atmospheric pressure by the capillary tube method of Stefan. The experimental results are compared with diffusion coefficients calculated via the first-order Chapman-Enskog approximation. For the gases, effective Lennard-Jones pair potential parameters were taken from recent literature; for the liquids they were obtained from an extended corresponding-states correlation.
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.
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.
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.
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.
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.
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.
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.
Zhou, Xin; Jiang, Yi; Kremer, Kurt; Ziock, Hans; Rasmussen, Steen
2006-09-01
We develop a generalized hyperdynamics method that is able to simulate slow dynamics in atomistic general (both energy- and entropy-dominated) systems. We show that a few functionals of the pair correlation function, involving two-body entropy, form a low-dimensional collective space, which is a good approximation that is able to distinguish stable and transitional conformations. A bias potential, which raises the energy in stable regions, is constructed on the fly. We examine the slow nucleation processes of a Lennard-Jones gas and show that our method can generate correct long-time dynamics without prior knowledge.
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 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.
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.
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
Percolation of clusters with a residence time in the bond definition: Integral equation theory.
Zarragoicoechea, Guillermo J; Pugnaloni, Luis A; Lado, Fred; Lomba, Enrique; Vericat, Fernando
2005-03-01
We consider the clustering and percolation of continuum systems whose particles interact via the Lennard-Jones pair potential. A cluster definition is used according to which two particles are considered directly connected (bonded) at time t if they remain within a distance d, the connectivity distance, during at least a time of duration tau, the residence time. An integral equation for the corresponding pair connectedness function, recently proposed by two of the authors [Phys. Rev. E 61, R6067 (2000)], is solved using the orthogonal polynomial approach developed by another of the authors [Phys. Rev. E 55, 426 (1997)]. We compare our results with those obtained by molecular dynamics simulations.
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.
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
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.
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
Martini straight: Boosting performance using a shorter cutoff and GPUs
NASA Astrophysics Data System (ADS)
de Jong, Djurre H.; Baoukina, Svetlana; Ingólfsson, Helgi I.; Marrink, Siewert J.
2016-02-01
In molecular dynamics simulations, sufficient sampling is of key importance and a continuous challenge in the field. The coarse grain Martini force field has been widely used to enhance sampling. In its original implementation, this force field applied a shifted Lennard-Jones potential for the non-bonded van der Waals interactions, to avoid problems related to a relatively short cutoff. Here we investigate the use of a straight cutoff Lennard-Jones potential with potential modifiers. Together with a Verlet neighbor search algorithm, the modified potential allows the use of GPUs to accelerate the computations in Gromacs. We find that this alternative potential has little influence on most of the properties studied, including partitioning free energies, bulk liquid properties and bilayer properties. At the same time, energy conservation is kept within reasonable bounds. We conclude that the newly proposed straight cutoff approach is a viable alternative to the standard shifted potentials used in Martini, offering significant speedup even in the absence of GPUs.
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.
Fernandez Santos, Jorge R; Ruiz, Jonatan R; Gonzalez-Montesinos, Jose Luis; Castro-Piñero, Jose
2016-05-01
The aim of this study was to analyze the reliability and the validity of the handgrip, basketball throw and pushups tests in children aged 6-12 years. One hundred and eighty healthy children (82 girls) agreed to participate in this study. All the upper body muscular fitness tests were performed twice (7 days apart) whereas the 1 repetition maximum (1RM) bench press test was performed 2 days after the first session of testing. All the tests showed a high reproducibility (ICC > 0.9) except the push-ups test (intertrial difference = 0.77 ± 2.38, p < .001 and the percentage error = 9%). The handgrip test showed the highest association with 1RM bench press test (r = .79, p < .01; R2 = .621). In conclusion the handgrip and basketball throw tests are shown as reliable and valid tests to assess upper body muscular strength in children. More studies are needed to assess the validity and the reliability of the upper body muscular endurance tests in children.
Computer simulation of nucleation in a gas-saturated liquid.
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* approximately 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.
Simplicity of condensed matter at its core: generic definition of a Roskilde-simple system.
Schrøder, Thomas B; Dyre, Jeppe C
2014-11-28
The isomorph theory is reformulated by defining Roskilde-simple systems by the property that the order of the potential energies of configurations at one density is maintained when these are scaled uniformly to a different density. If the potential energy as a function of all particle coordinates is denoted by U(R), this requirement translates into U(Ra) < U(Rb) ⇒ U(λRa) < U(λRb). Isomorphs remain curves in the thermodynamic phase diagram along which structure, dynamics, and excess entropy are invariant, implying that the phase diagram is effectively one-dimensional with respect to many reduced-unit properties. In contrast to the original formulation of the isomorph theory, however, the density-scaling exponent is not exclusively a function of density and the isochoric heat capacity is not an exact isomorph invariant. A prediction is given for the latter quantity's variation along the isomorphs. Molecular dynamics simulations of the Lennard-Jones and Lennard-Jones Gaussian systems validate the new approach.
Blowing bubbles in Lennard-Jonesium along the saturation curve.
Ashbaugh, Henry S
2009-05-28
Extensive molecular simulations of the Lennard-Jones fluid have been performed to determine its liquid-vapor coexistence properties and solvent contact densities with cavities up to ten times the diameter of the solvent from the triple point to the critical point. These simulations are analyzed using a revised scaled-particle theory [H. S. Ashbaugh and L. R. Pratt, Rev. Mod. Phys. 78, 159 (2006)] to evaluate the thermodynamics of cavity solvation and curvature dependent interfacial properties along the saturation curve. While the thermodynamic signatures of cavity solvation are distinct from those in water, exhibiting a chemical potential dominated by a large temperature independent enthalpy, the solvent dewets cavities of increasing size similar with water near coexistence. The interfacial tension for forming a liquid-wall interface is found to be consistently greater than the liquid-vapor surface tension of the Lennard-Jones fluid by up to 10% and potentially reflects the suppression of high amplitude fluctuations at the cavity surface. The first-order curvature correction for the surface tension is negative and appears to diverge to negative infinity at temperatures approaching the critical point. Our results point to the success of the revised scaled-particle theory at bridging molecular and macroscopic descriptions of cavity solvation.
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.
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
NASA Astrophysics Data System (ADS)
Schrøder, Thomas B.; Dyre, Jeppe C.
2014-11-01
The isomorph theory is reformulated by defining Roskilde-simple systems by the property that the order of the potential energies of configurations at one density is maintained when these are scaled uniformly to a different density. If the potential energy as a function of all particle coordinates is denoted by U(R), this requirement translates into U(Ra) < U(Rb) ⇒ U(λRa) < U(λRb). Isomorphs remain curves in the thermodynamic phase diagram along which structure, dynamics, and excess entropy are invariant, implying that the phase diagram is effectively one-dimensional with respect to many reduced-unit properties. In contrast to the original formulation of the isomorph theory, however, the density-scaling exponent is not exclusively a function of density and the isochoric heat capacity is not an exact isomorph invariant. A prediction is given for the latter quantity's variation along the isomorphs. Molecular dynamics simulations of the Lennard-Jones and Lennard-Jones Gaussian systems validate the new approach.
Hanson, Nicholas Buck; Kachin, Kevin; Berger, Jan
2016-01-01
Background Obesity is the leading cause of preventable death costing the health care system billions of dollars. Combining self-monitoring technology with personalized behavior change strategies results in clinically significant weight loss. However, there is a lack of real-world outcomes in commercial weight-loss program research. Objective Retrofit is a personalized weight management and disease-prevention solution. This study aimed to report Retrofit’s weight-loss outcomes at 6, 12, and 24 months and characterize behaviors, age, and sex of high-performing participants who achieved weight loss of 10% or greater at 12 months. Methods A retrospective analysis was performed from 2011 to 2014 using 2720 participants enrolled in a Retrofit weight-loss program. Participants had a starting body mass index (BMI) of >25 kg/m² and were at least 18 years of age. Weight measurements were assessed at 6, 12, and 24 months in the program to evaluate change in body weight, BMI, and percentage of participants who achieved 5% or greater weight loss. A secondary analysis characterized high-performing participants who lost ≥10% of their starting weight (n=238). Characterized behaviors were evaluated, including self-monitoring through weigh-ins, number of days wearing an activity tracker, daily step count average, and engagement through coaching conversations via Web-based messages, and number of coaching sessions attended. Results Average weight loss at 6 months was −5.55% for male and −4.86% for female participants. Male and female participants had an average weight loss of −6.28% and −5.37% at 12 months, respectively. Average weight loss at 24 months was −5.03% and −3.15% for males and females, respectively. Behaviors of high-performing participants were assessed at 12 months. Number of weigh-ins were greater in high-performing male (197.3 times vs 165.4 times, P=.001) and female participants (222 times vs 167 times, P<.001) compared with remaining participants
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
Test of a new heat-flow equation for dense-fluid shock waves.
Holian, Brad Lee; Mareschal, Michel; Ravelo, Ramon
2010-09-21
Using a recently proposed equation for the heat-flux vector that goes beyond Fourier's Law of heat conduction, we model shockwave propagation in the dense Lennard-Jones fluid. Disequilibrium among the three components of temperature, namely, the difference between the kinetic temperature in the direction of a planar shock wave and those in the transverse directions, particularly in the region near the shock front, gives rise to a new transport (equilibration) mechanism not seen in usual one-dimensional heat-flow situations. The modification of the heat-flow equation was tested earlier for the case of strong shock waves in the ideal gas, which had been studied in the past and compared to Navier-Stokes-Fourier solutions. Now, the Lennard-Jones fluid, whose equation of state and transport properties have been determined from independent calculations, allows us to study the case where potential, as well as kinetic contributions are important. The new heat-flow treatment improves the agreement with nonequilibrium molecular-dynamics simulations under strong shock wave conditions, compared to Navier-Stokes.
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
A molecular model for H(2) interactions in aliphatic and aromatic hydrocarbons.
Figueroa-Gerstenmaier, Susana; Giudice, Simona; Cavallo, Luigi; Milano, Giuseppe
2009-05-28
A model for molecular hydrogen interacting with aliphatic and aromatic hydrocarbons is presented. The model has been derived using ab initio techniques and molecular dynamics simulations. In particular, quadrupole moments of hydrogen, and variation on energy with intermolecular distance of different conformations for the hydrogen-benzene couple were calculated using the Møller-Plesset method. Hydrogen was modelled using a two-centre Lennard-Jones potential plus electrostatic interactions. Lennard-Jones parameters were optimized on the basis of a correct reproduction of experimental data of hydrogen solubility in benzene and cyclohexane, calculated using the test particle insertion method. Different sets of parameters for specific interactions (hydrogen-aliphatic and hydrogen-aromatic systems) were considered avoiding the simple use of Lorentz-Berthelot combining rules. Additionally, structural and thermodynamic properties of hydrogen-benzene, hydrogen-cyclohexane and hydrogen in an equimolar mixture of benzene-cyclohexane at different low concentrations of hydrogen were investigated by means of molecular dynamics simulations. Electrostatic charges were taken from ab initio quantum mechanical calculations but after careful analysis of the calculated properties, their irrelevance was evidenced. Moreover, Coulombic interactions make simulations more expensive and, therefore, we do not recommend their inclusion in the modelling of hydrogen-aliphatic and aromatic interactions. PMID:19440622
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.
Test of a new heat-flow equation for dense-fluid shock waves.
Holian, Brad Lee; Mareschal, Michel; Ravelo, Ramon
2010-09-21
Using a recently proposed equation for the heat-flux vector that goes beyond Fourier's Law of heat conduction, we model shockwave propagation in the dense Lennard-Jones fluid. Disequilibrium among the three components of temperature, namely, the difference between the kinetic temperature in the direction of a planar shock wave and those in the transverse directions, particularly in the region near the shock front, gives rise to a new transport (equilibration) mechanism not seen in usual one-dimensional heat-flow situations. The modification of the heat-flow equation was tested earlier for the case of strong shock waves in the ideal gas, which had been studied in the past and compared to Navier-Stokes-Fourier solutions. Now, the Lennard-Jones fluid, whose equation of state and transport properties have been determined from independent calculations, allows us to study the case where potential, as well as kinetic contributions are important. The new heat-flow treatment improves the agreement with nonequilibrium molecular-dynamics simulations under strong shock wave conditions, compared to Navier-Stokes. PMID:20866140
Filippini, G; Bourasseau, E; Ghoufi, A; Goujon, F; Malfreyt, P
2014-08-28
Microscopic Monte Carlo simulations of liquid sheets of copper and tin have been performed in order to study the dependence of the surface tension on the thickness of the sheet. It results that the surface tension is constant with the thickness as long as the sheet remains in one piece. When the sheet is getting thinner, holes start to appear, and the calculated surface tension rapidly decreases with thickness until the sheet becomes totally unstable and forms a cylinder. We assume here that this decrease is not due to a confinement effect as proposed by Werth et al. [Physica A 392, 2359 (2013)] on Lennard-Jones systems, but to the appearance of holes that reduces the energy cost of the surface modification. We also show in this work that a link can be established between the stability of the sheet and the local fluctuations of the surface position, which directly depends on the value of the surface tension. Finally, we complete this study by investigating systems interacting through different forms of Lennard-Jones potentials to check if similar conclusions can be drawn.
NASA Astrophysics Data System (ADS)
Filippini, G.; Bourasseau, E.; Ghoufi, A.; Goujon, F.; Malfreyt, P.
2014-08-01
Microscopic Monte Carlo simulations of liquid sheets of copper and tin have been performed in order to study the dependence of the surface tension on the thickness of the sheet. It results that the surface tension is constant with the thickness as long as the sheet remains in one piece. When the sheet is getting thinner, holes start to appear, and the calculated surface tension rapidly decreases with thickness until the sheet becomes totally unstable and forms a cylinder. We assume here that this decrease is not due to a confinement effect as proposed by Werth et al. [Physica A 392, 2359 (2013)] on Lennard-Jones systems, but to the appearance of holes that reduces the energy cost of the surface modification. We also show in this work that a link can be established between the stability of the sheet and the local fluctuations of the surface position, which directly depends on the value of the surface tension. Finally, we complete this study by investigating systems interacting through different forms of Lennard-Jones potentials to check if similar conclusions can be drawn.
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.
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.
Scanning the potential energy surface of iron clusters: A novel search strategy
NASA Astrophysics Data System (ADS)
Bobadova-Parvanova, P.; Jackson, K. A.; Srinivas, S.; Horoi, M.; Köhler, C.; Seifert, G.
2002-03-01
A new methodology for finding the low-energy structures of transition metal clusters is developed. A two-step strategy of successive density functional tight binding (DFTB) and density functional theory (DFT) investigations is employed. The cluster configuration space is impartially searched for candidate ground-state structures using a new single-parent genetic algorithm [I. Rata et al., Phys. Rev. Lett. 85, 546 (2000)] combined with DFTB. Separate searches are conducted for different total spin states. The ten lowest energy structures for each spin state in DFTB are optimized further at a first-principles level in DFT, yielding the optimal structures and optimal spin states for the clusters. The methodology is applied to investigate the structures of Fe4, Fe7, Fe10, and Fe19 clusters. Our results demonstrate the applicability of DFTB as an efficient tool in generating the possible candidates for the ground state and higher energy structures of iron clusters. Trends in the physical properties of iron clusters are also studied by approximating the structures of iron clusters in the size range n=2-26 by Lennard-Jones-type structures. We find that the magnetic moment of the clusters remains in the vicinity of 3μB/atom over this entire size range.
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…
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.
Waterlike features, liquid-crystal phase and self-assembly in Janus dumbbells
NASA Astrophysics Data System (ADS)
Bordin, José Rafael
2016-10-01
We explore the phase diagram of Janus nanoparticles using Molecular Dynamics simulations. Each monomer in the dimer has distinct characteristics. One type of monomer interacts by a Lennard Jones potential, while the other type interacts through a two length scale potential. Previous studies for the monomeric system using this specific two length scale potential do not indicate the presence of waterlike anomalies. However, our results show that the combination of two length scales potential and LJ potential in the Janus nanoparticle will lead to thermodynamic and dynamic anomalies. The self-assembly properties were also explored. We observe distinct kinds of self-assembled structures and a liquid-crystal phase. This result indicates that it is possible to create Janus nanoparticles with waterlike features using monomers without anomalous behavior. The anomalies and structures are explained with the two length scale potential characteristics.
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
Free energy cost of forming an interface between a crystal and its frozen version
NASA Astrophysics Data System (ADS)
Benjamin, Ronald; Horbach, Jürgen
2015-10-01
Using a thermodynamic integration scheme, we compute the free energy cost per unit area, γ , of forming an interface between a crystal and a frozen structured wall, formed by particles frozen into the same equilibrium structure as the crystal. Even though the structure and potential energy of the crystalline phase in the vicinity of the wall is the same as in the bulk, γ has a nonzero value and increases with increasing density of the crystal and the wall. Investigating the effect of several interaction potentials between the particles, we observe a positive γ at all crystalline densities if the potential is purely repulsive. For models with attractive interactions, such as the Lennard-Jones potential, a negative value for γ is obtained at low densities. A qualitative explanation for the change of sign of γ when going from repulsive to attractive interactions, at low crystal densities, is suggested.
Characterizing molecular motion in H2O and H3O+ with dynamical instability statistics
NASA Astrophysics Data System (ADS)
Green, Jason R.; Hofer, Thomas S.; Berry, R. Stephen; Wales, David J.
2011-11-01
Sets of finite-time Lyapunov exponents characterize the stability and instability of classically chaotic dynamical trajectories. Here we show that their sample distributions can contain subpopulations identifying different types of dynamics. In small isolated molecules these dynamics correspond to distinct elementary motions, such as isomerizations. Exponents are calculated from constant total energy molecular dynamics simulations of H2O and H3O+, modelled with a classical, reactive, all-atom potential. Over a range of total energy, exponent distributions for these systems reveal that phase space exploration is more chaotic near saddles corresponding to isomerization and less chaotic near potential energy minima. This finding contrasts with previous results for Lennard-Jones clusters, and is explained in terms of the potential energy landscape.
Extension of the JCZ product species database
Hobbs, M.L.; Baer, M.R.; McGee, B.C.
1998-09-01
A database has been created for use with the Jacobs-Cowperthwaite-Zwisler-3 equation-of-state (JCZ3-EOS) to determine thermochemical equilibrium states for energetic materials. The JCZ3-EOS uses the exponential 6 intermolecular potential function to describe interactions between molecules. Product species are characterized by r{sup *}, the radius of the minimum pair potential energy, and {var_epsilon}/{kappa}, the well depth energy normalized by Boltzmann`s constant. These parameters constitute the JCZS (S for Sandia) database describing 750 gases listed in the JANNAF tables and were obtained by using literature values of the Lennard-Jones potential, a corresponding states theory, pure liquid shock Hugoniot data, and fit values to an empirical EOS. Detonation velocities predicted with the JCZS database for a wide variety of explosives are in good agreement with data. Improved predictions of low density explosives is attributed to a better description of molecular interactions at intermediate pressures.
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.
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
Energetically favoured defects in dense packings of particles on spherical surfaces
NASA Astrophysics Data System (ADS)
Paquay, Stefan; Kusumaatmaja, Halim; Wales, David J.; Zandi, Roya; van der Schoot, Paul
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.
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.
Universal curves for the van der Waals interaction between single-walled carbon nanotubes.
Pogorelov, Evgeny G; Zhbanov, Alexander I; Chang, Yia-Chung; Yang, Sung
2012-01-17
We report very simple and accurate algebraic expressions for the van der Waals (VDW) potentials and the forces between two parallel and crossed carbon nanotubes. The Lennard-Jones potential for two carbon atoms and the method of the smeared-out approximation suggested by Girifalco were used. It is found that the interaction between parallel and crossed tubes is described by two universal curves for parallel and crossed configurations that do not depend on the van der Waals constants, the angle between tubes, and the surface density of atoms and their nature but only on the dimensionless distance. The explicit functions for equilibrium VDW distances, well depths, and maximal attractive forces have been given. These results may be used as a guide for the analysis of experimental data to investigate the interaction between nanotubes of various natures. PMID:22129302
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.
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.
Gas viscosity of difluoromethane from 298.15 to 423.15 K and up to 10 MPa
Takahashi, Mitsuo; Shibasaki-Kitakawa, N.; Yokoyama, Chiaki; Takahashi, Shinji
1995-07-01
Chlorodifluoromethane (HCFC-22) has been used mostly as a refrigerant for air-conditioning systems, but it is scheduled to be phased out by 2030 due to its ozone depletion properties. Difluoromethane (HFC-32) has no ozone depletion potential (ODP) since there are no chlorine atoms in the molecule and has been considered as a substitute for HCFC-22. The gas viscosity of difluoromethane was measured using an oscillating disk viscometer of the Maxwell type from 298.15 to 423.15 K at pressures up to 10 MPa. The results were fitted to an empirical equation as a function of temperature and density. Intermolecular force constants of the Lennard-Jones 12-6 potential were determined. In addition, the experimental density was compared with the calculated values from various equations of state previously reported.
NASA Astrophysics Data System (ADS)
Wu, Xia; Wu, Genhua
2014-08-01
Geometrical optimization of atomic clusters is performed by a development of adaptive immune optimization algorithm (AIOA) with dynamic lattice searching (DLS) operation (AIOA-DLS method). By a cycle of construction and searching of the dynamic lattice (DL), DLS algorithm rapidly makes the clusters more regular and greatly reduces the potential energy. DLS can thus be used as an operation acting on the new individuals after mutation operation in AIOA to improve the performance of the AIOA. The AIOA-DLS method combines the merit of evolutionary algorithm and idea of dynamic lattice. The performance of the proposed method is investigated in the optimization of Lennard-Jones clusters within 250 atoms and silver clusters described by many-body Gupta potential within 150 atoms. Results reported in the literature are reproduced, and the motif of Ag61 cluster is found to be stacking-fault face-centered cubic, whose energy is lower than that of previously obtained icosahedron.
Modeling Shear Banding in Amorphous Solids, from Atomistic to Continuum
NASA Astrophysics Data System (ADS)
Alix-Williams, Darius; Falk, Michael
Molecular dynamics simulations of strain localization are carried out using different materials systems and interatomic potentials including CuZr modeled via the embedded-atom method (EAM), amorphous Si modeled using Stillinger-Weber (SW) and a binary Lennard-Jones (LJ) system. Quench schedules and strain rates are varied. Different systems exhibit marked similarities in plastic behavior. Systematic differences between systems are analyzed in the context of Shear Transformation Zone (STZ) theory in the effort to develop a generalized constitutive framework for plasticity in glasses. Effective temperature inferred from the potential energy is explored as a local coarse-grained measure of the degree of disorder. This research is supported by National Science Foundation Award 1408685.
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.
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.
NASA Astrophysics Data System (ADS)
Legon, A. C.; Millen, D. J.; North, Hazel M.
1987-03-01
The zero-point and equilibrium dissociation energies (D0 and De) of the hydrogen-bonded dimers CH3CN-HF and HCCCN-HF are determined experimentally on the basis of absolute intensity measurements of selected rotational transitions. A Stark-modulated microwave spectrometer is employed with the cooled absorption cell described by Legon et al. (1980). The results are presented in tables and analyzed. Energies determined are D0 = 26.1(0.6) kJ/mol and De = 29.0(0.9) kJ/mol for CH3CN-HF and D0 = 20.4(0.7) kJ/mol and De = 23.4(0.9) kJ/mol for HCCCN-HF. Theoretical De values calculated using the Morse potential function are found to be in much better agreement with the experimental results than those calculated with the Lennard-Jones potential function.
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.
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.
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.
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.
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.
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.
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)
Farrell, James D.; Lines, Christabel; Shepherd, James J.; Chakrabarti, Dwaipayan; Miller, Mark A.; Wales, David J.
Clusters of spherical particles with isotropic attraction favour compact structures that maximise the number of energetically optimal nearest-neighbour interactions. In contrast, dipolar interactions lead to the formation of chains with a low coordination number. When both isotropic and dipolar interactions are present, the competition between them can lead to intricate knot, link and coil structures. Here, we investigate how these structures may self-organise and interconvert in clusters bound by the Stockmayer potential (Lennard-Jones plus point dipole). We map out the low-lying region of the energy landscape using disconnectivity graphs to follow how it evolves as the strength of the dipolar interactions increases. From comprehensive surveys of isomerisation pathways, we identify a number of rearrangement mechanisms that allow the topology of chain-like structures to interconvert.
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.
Damage in materials following ablation by ultrashort laser pulses: A molecular-dynamics study
Bouilly, Delphine; Perez, Danny; Lewis, Laurent J.
2007-11-01
The formation of craters following femtosecond- and picosecond-pulse laser ablation in the thermal regime is studied using a generic two-dimensional numerical model based on molecular-dynamics simulations and the Lennard-Jones potential. Femtosecond pulses are found to produce very clean craters through a combination of etching of the walls and the formation of a very thin heat affected zone. Our simulations also indicate that dislocations are emitted continuously during all of the ablation process (i.e., for hundreds of ps). For picosecond pulses, we observe much thicker heat affected zones which result from melting and recrystallization following the absorption of the light. In this case also, continuous emission of dislocations--though fewer in number--takes place throughout the ablation process.
Thermodynamic curvature for attractive and repulsive intermolecular forces.
May, Helge-Otmar; Mausbach, Peter; Ruppeiner, George
2013-09-01
The thermodynamic curvature scalar R for the Lennard-Jones system is evaluated in phase space, including vapor, liquid, and solid state. We paid special attention to the investigation of R along vapor-liquid, liquid-solid, and vapor-solid equilibria. Because R is a measure of interaction strength, we traced out the line R=0 dividing the phase space into regions with effectively attractive (R<0) or repulsive (R>0) interactions. Furthermore, we analyzed the dependence of R on the strength of attraction applying a perturbation ansatz proposed by Weeks-Chandler-Anderson. Our results show clearly a transition from R>0 (for poorly repulsive interaction) to R<0 when loading attraction in the intermolecular potential.
Dimensional strategies and the minimization problem: Barrier-avoiding algorithms
Faken, D.B.; Voter, A.F.; Freeman, D.L.; Doll, J.D.
1999-11-25
In the present paper the authors examine the role of dimensionality in the minimization problem. Since it has such a powerful influence on the topology of the associated potential energy landscape, the authors argue that it may prove useful to alter the dimensionality of the space of the original minimization problem. The general idea is explored in the context of finding the minimum energy geometries of Lennard-Jones clusters. It is shown that it is possible to locate barrier-free, high-dimensional pathways that connect local, three-dimensional cluster minima. The performance of the resulting, barrier-avoiding minimization algorithm is examined for clusters containing as many as 55 atoms.
Interface characteristics of nanorope reinforced polymer composites
NASA Astrophysics Data System (ADS)
Ahmed, Khondaker S.; Keng, Ang K.
2013-09-01
A shear-lag model is proposed to obtain interface characteristics of nanorope reinforced polymer composites using representative volume element (RVE) concept. In the axisymmetric RVE, the nanorope is modelled as a closed-packed cylindrical lattice consisting seven single-walled carbon nanotubes. In the model, rope is considered to be perfectly bonded with the polymer resin where the nanotubes are assumed to be chemically non-bonded with each other in the rope system. Since, nanotubes are considered to be non-bonded in the nanorope there must exist a van der Waals interaction in terms of Lennard-Jones potential. A separate model is also proposed to determine the cohesive stress caused by this interaction. Closed form analytical solutions are derived for stress components of rope, resin and individual carbon nanotubes in the rope system. Parametric study has also been conducted to investigate the influences of key composite factors involved at both perfectly bonded and non-bonded interfaces.
A free-energy surface exploration algorithm for supercooled liquids and amorphous solids
NASA Astrophysics Data System (ADS)
Lewis, Kirk D.; Shin, Yongwoo; Lin, Xi; BU Team
2014-03-01
Efficient exploration of the multidimensional free-energy surfaces (FES) of supercooled liquids and amorphous solids at low temperatures is extremely challenging. The recently developed autonomous basin-climbing (ABC) algorithm (JCP 130: 224504, 2009) allows the sluggish system to self-explore the multidimensional potential energy surface (PES) and climb out of deep energy basins through a series of collective activation and relaxation events. In this work, we present a new FES exploration algorithm that enforces an explicit temperature dependence on the ABC trajectories. The explicit temperature dependence is achieved by introducing an ensemble of walkers to collectively maintain the detailed balance criteria among all the relevant energy basins. Using this new algorithm, the metabasin correlation length of a binary Lennard-Jones supercooled liquid is identified at the glass transition temperature.
Mathematical model for drug molecules encapsulated in lipid nanotube
NASA Astrophysics Data System (ADS)
Putthikorn, Sasipim; Baowan, Duangkamon
2016-11-01
Lipid nanotube is considered as a nanocontainer for drug and gene delivery. It is important to understand a basic idea of the encapsulation process. In this paper, we use the Lennard-Jones potential function and the continuous approximation to explain the energy behaviour of three hollow shapes of Doxorubicin (DOX) clusters that are a sphere, a cylinder, and an ellipsoid interacting with the lipid nanotube. On assuming that the surface areas of the three structures are equal, we can find the minimum size of the lipid nanotube that encapsulates DOX inside by determining the suction energy. Moreover, we find that a long cylindrical drug provides the largest suction energy among other structures studied here due to the perfect fit between the cylindrical drug and the cylindrical tube. This investigation is the first step to develop the design of nanocapsule for medical application.
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.
Molecular simulation of the salting out effect in the system H2S-H2O-NaCl.
Vorholz, Johannes; Maurer, Gerd
2008-12-28
The reduction of the solubility of a gas due to the presence of ionic species in a solvent is called "salting-out". The "salting-out" of hydrogen sulfide by sodium chloride in water was predicted by Gibbs ensemble Monte Carlo simulation at temperatures between 373 and 423 K and at salt molalities up to 10 mol kg(-1). The intermolecular interactions were modeled by combining Lennard-Jones potentials with Coulomb interactions. Several force fields were examined. The interactions between unlike species were estimated using two common combining rules without any adjustable parameters for the dispersion interaction. The simulations predict the "salting-out" of hydrogen sulfide by sodium chloride in aqueous solutions in an at least qualitative, partly in a quantitative manner. PMID:19060969
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.
Selectivity in the inelastic rotational scattering of hydrogen molecules from graphite
NASA Astrophysics Data System (ADS)
Rutigliano, Maria; Pirani, Fernando
2016-11-01
The inelastic scattering of hydrogen molecules in well-defined roto-vibrational states, impinging a graphite surface from sub-thermal up to hyper-thermal collision energies, has been investigated by using a new Potential Energy Surface, formulated in terms of a recently proposed Improved Lennard Jones model, suitable to describe non-covalent interactions in the full space of the configurations. The collision dynamics is studied by a semiclassical method. The focus has been on behaviour of molecules initially in low-medium lying roto-vibrational states, for which, under the assumed conditions, initial vibrational state is in general preserved during the collision. For the rotational relaxation, some selectivities in the final state formation have been characterized. They are emerging especially at low collision energies, where the scattering is manly driven by the attractive forces controlling the physical adsorption. The rotational and vibrational accommodation coefficients have been evaluated and found to be in agreement with those reported in literature.
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.
Molecular simulation of the salting out effect in the system H2S-H2O-NaCl.
Vorholz, Johannes; Maurer, Gerd
2008-12-28
The reduction of the solubility of a gas due to the presence of ionic species in a solvent is called "salting-out". The "salting-out" of hydrogen sulfide by sodium chloride in water was predicted by Gibbs ensemble Monte Carlo simulation at temperatures between 373 and 423 K and at salt molalities up to 10 mol kg(-1). The intermolecular interactions were modeled by combining Lennard-Jones potentials with Coulomb interactions. Several force fields were examined. The interactions between unlike species were estimated using two common combining rules without any adjustable parameters for the dispersion interaction. The simulations predict the "salting-out" of hydrogen sulfide by sodium chloride in aqueous solutions in an at least qualitative, partly in a quantitative manner.
(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%.
Origins of thermal conductivity changes in strained crystals
NASA Astrophysics Data System (ADS)
Parrish, Kevin D.; Jain, Ankit; Larkin, Jason M.; Saidi, Wissam A.; McGaughey, Alan J. H.
2014-12-01
The strain-dependent phonon properties and thermal conductivities of a soft system [Lennard-Jones (LJ) argon] and a stiff system (silicon modeled using first-principles calculations) are predicted using lattice dynamics calculations and the Boltzmann transport equation. As is commonly assumed for materials under isotropic strain, the thermal conductivity of LJ argon decreases monotonically as the system moves from compression into tension. The reduction in thermal conductivity is attributed to decreases in both the phonon lifetimes and group velocities. The thermal conductivity of silicon, however, is constant in compression and only begins to decrease once the system is put in tension. The silicon lifetimes show an anomalous behavior, whereby they increase as the system moves from compression into tension, which is explained by examining the potential energy surface felt by an atom. The results emphasize the need to separately consider the harmonic and anharmonic effects of strain on material stiffness, phonon properties, and thermal conductivity.
AMBER-ii: New Combining Rules and Force Field for Perfluoroalkanes.
Nikitin, Alexei; Milchevskiy, Yury; Lyubartsev, Alexander
2015-11-19
A molecular mechanics force field of the AMBER/OPLS family for perfluoroalkanes, noble gases, and their mixtures with alkanes has been proposed. We had to abandon the traditional Lorentz-Berthelot combining rules for the Lennard-Jones potential to be able to uniformly describe these substance classes and their mixtures. Instead, the Waldman-Hagler rules developed for noble gases were used for all of these elements except hydrogen. Hydrogen is considered to be a particular substance to which the usual Lorentz-Berthelot rules are applied. The proposed rules have little effect on the organic chemistry of H, C, N, and O elements but make it compliant with the chemistry of heavy elements. Because of assigning a relatively high partial charge of -0.37e to fluorine atoms, the new force field reproduces the mutual insolubility of higher liquid alkanes and perfluoroalkanes. PMID:26498002
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
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.
Stability of monatomic and diatomic quasicrystals and the influence of noise
NASA Astrophysics Data System (ADS)
Roth, J.; Schilling, R.; Trebin, H.-R.
1990-02-01
The stability of quasicrystals endowed with atomic Lennard-Jones-like pair potentials was investigated with use of the method of steepest descent. Starting from two- and three-dimensional Penrose patterns, the basic units were decorated in various fashions with one or two sorts of atoms. In accord with previous studies, all monatomic two-dimensional quasicrystals decay to a hexagonal periodic crystal with defects; diatomic systems remain stable when the relative size of the atoms is suitably chosen. In three dimensions, the monatomic quasicrystalline unit-sphere packing was proven stable as well as the structure of truncated icosahedra, even if in the initial configuration the atoms were displaced statistically up to 7% and 25%, respectively, of the edge length (noise). A series of decorations (among them one involving Mackay icosahedra) relaxed to the amorphous state. In these transitions the atoms arrange in families of Fibonacci planes whose separations scale down to atomic distances in a self-similar fashion.
Hybrid Monte Carlo with non-uniform step size.
Holzgräfe, Christian; Bhattacherjee, Arnab; Irbäck, Anders
2014-01-28
The Hybrid Monte Carlo method offers a rigorous and potentially efficient approach to the simulation of dense systems, by combining numerical integration of Newton's equations of motion with a Metropolis accept-or-reject step. The Metropolis step corrects for sampling errors caused by the discretization of the equations of motion. The integration is usually performed using a uniform step size. Here, we present simulations of the Lennard-Jones system showing that the use of smaller time steps in the tails of each integration trajectory can reduce errors in energy. The acceptance rate is 10-15 percentage points higher in these runs, compared to simulations with the same trajectory length and the same number of integration steps but a uniform step size. We observe similar effects for the harmonic oscillator and a coarse-grained peptide model, indicating generality of the approach.
Tchouar, N; Ould-Kaddour, F; Levesque, D
2004-10-15
The properties of liquid methane, liquid neon, and gas helium are calculated at low temperatures over a large range of pressure from the classical molecular-dynamics simulations. The molecular interactions are represented by the Lennard-Jones pair potentials supplemented by quantum corrections following the Feynman-Hibbs approach. The equations of state, diffusion, and shear viscosity coefficients are determined for neon at 45 K, helium at 80 K, and methane at 110 K. A comparison is made with the existing experimental data and for thermodynamical quantities, with results computed from quantum numerical simulations when they are available. The theoretical variation of the viscosity coefficient with pressure is in good agreement with the experimental data when the quantum corrections are taken into account, thus reducing considerably the 60% discrepancy between the simulations and experiments in the absence of these corrections.
Polymer-attractive spherical cage system
NASA Astrophysics Data System (ADS)
Arkın, Handan; Janke, Wolfhard
2013-01-01
We analyze the structural behavior of a single polymer chain inside an attractive sphere. Our model is composed of a coarse-grained polymer governed by Lennard-Jones interactions of the monomers and an attractive sphere potential which follows by integrating the monomer-monomer interaction over the (inner) surface of the sphere. By means of extensive multicanonical Monte Carlo simulations it is shown that the system exhibits a rich phase diagram in the adsorption strength-temperature ( ɛ - T) plane ranging from highly ordered and compact to extended and random coil structures and from desorbed to partially or even completely adsorbed conformations. These findings are identified with different energetic and structural observables. The resulting phase diagram in the ɛ - T plane is compared with that for a polymer adsorbing to a plane, attractive substrate obtained previously by Möddel, Bachmann, and one of the authors.
Adsorption-induced changes of the structure of the tethered chain layers in a simple fluid.
Borówko, M; Sokołowski, S; Staszewski, T
2014-06-21
We use density functional theory to study the influence of fluid adsorption on the structure of grafted chain layer. The chains are modeled as freely jointed spheres. The chain segments and spherical molecules of the fluid interact via the Lennard-Jones potential. The fluid molecules are attracted by the substrate. We calculate the excess adsorption isotherms, the average height of tethered chains, and the force acting on selected segments of the chains. The parameters that were varied include the length of grafted chains, the grafting density, the parameters characterizing fluid-chain and fluid-surface interactions, the bulk fluid density, and temperature. We show that depending on the density of the bulk fluid the height of the bonded layer increases, remains constant, or decreases with increasing temperature.
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.
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.
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
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.
Direct calculation of solid-liquid equilibria from density-of-states Monte Carlo simulations.
Mastny, Ethan A; de Pablo, Juan J
2005-03-22
A density-of-states Monte Carlo method is proposed for simulations of solid-liquid phase equilibria. A modified Wang-Landau density-of-states sampling approach is used to perform a random walk in regions of potential energy and volume relevant to solid-liquid equilibrium. The method provides a direct estimate of the relative density of states [Omega(U,V)] and thus the relative free energy within these regions, which is subsequently used to determine portions of the melting curve over wide ranges of pressure and temperature. The validity and usefulness of the method are demonstrated by performing crystallization simulations for the Lennard-Jones fluid and for NaCl.
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
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.
Communication: Thermodynamic analysis of critical conditions of polymer adsorption
Cimino, R.; Neimark, A. V.; Rasmussen, C. J.
2013-11-28
Polymer adsorption to solid surfaces is a ubiquitous phenomenon, which has attracted long-lasting attention. Dependent on the competition between the polymer-solid adsorption and polymer-solvent solvation interactions, a chain may assume either 3d solvated conformation when adsorption is weak or 2d adsorbed conformation when adsorption is strong. The transition between these conformations occurring upon variation of adsorption strength is quite sharp, and in the limit of “infinite” chain length, can be treated as a critical phenomenon. We suggest a novel thermodynamic definition of the critical conditions of polymer adsorption from the equality of incremental chemical potentials of adsorbed and free chains. We show with the example of freely jointed Lennard-Jones chains tethered to an adsorbing surface that this new definition provides a link between thermodynamic and geometrical features of adsorbed chains and is in line with classical scaling relationships for the fraction of adsorbed monomers, chain radii of gyration, and free energy.
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.
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
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.
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.
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.
New theories for smectic and nematic liquid crystalline polymers
Dowell, F.
1987-01-01
A summary of results from new statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with LCPs is presented. Thermodynamic and molecular ordering properties (including odd-even effects) have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories have been used to design new LCPs and new solvents and to predict and explain properties.
Dowell, F.
1987-01-01
A summary of predictions and explanations from statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with backbone LCPs are presented. Trends in the thermodynamic and molecular ordering properties have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. The theoretical results are found to be in good agreement with existing experimental data. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories can be used to design new LCPs and new solvents as well as to predict and explain properties. 27 refs., 4 tabs.
Mognetti, B M; Virnau, P; Yelash, L; Paul, W; Binder, K; Müller, M; MacDowell, L G
2009-03-28
In this paper we investigate the phase diagram of pure dipolar substances and their mixtures with short alkanes, using grand canonical Monte Carlo simulations of simplified coarse-grained models. Recently, an efficient coarse-grained model for simple quadrupolar molecules, based on a Lennard-Jones (LJ) interaction plus a spherically averaged quadrupolar potential, has been shown to be successful in predicting single-component and mixture phase diagrams. Motivated by these results, we investigate the phase diagrams of simple dipolar molecules (and their mixtures with alkanes) using a spherically averaged potential. First, we test the model on pure components. A generalized (state-dependent) mapping procedure allows us to recycle Monte Carlo results of the simple Lennard-Jones (LJ) potential. Considering ammonia, nitrous oxide, and hydrogen sulfide, we generally observe improvements in the single-component phase diagram compared to a pure LJ description, but also some discrepancies in the coexistence pressure near the critical point and in the liquid branch of the coexistence densities well below criticality. In addition, we present results for mixtures. We consider mixtures of ammonia (NH3) with methane (CH4), nonane (C9H20) and hexadecane (C16H34)--for which experimental results are available--and compare the predictions from this modeling ansatz with predictions from simple LJ models. We also present results for the hydrogen sulfide-pentane mixture (H2S and C5H12) for which big discrepancies between simulations and experiments are present. Possible explanations for these discrepancies and limitations of the modeling are discussed.
Isomorph invariance of the structure and dynamics of classical crystals
NASA Astrophysics Data System (ADS)
Albrechtsen, Dan E.; Olsen, Andreas E.; Pedersen, Ulf R.; Schrøder, Thomas B.; Dyre, Jeppe C.
2014-09-01
This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics of a defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnström binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles interacting via the Buckingham pair potential and via a purely repulsive pair potential diverging at a finite separation, an ortho-terphenyl molecular model crystal, and SPC/E hexagonal ice. Except for NaCl and ice, the crystals simulated all have isomorphs. Based on previous simulations of liquid models, we conjecture that crystalline solids with isomorphs include most or all formed by atoms or molecules interacting via metallic or van der Waals forces, whereas covalently bonded or hydrogen-bonded crystals are not expected to have isomorphs; crystals of ions or dipolar molecules constitute a limiting case for which isomorphs are only expected when the Coulomb interactions are relatively weak. We briefly discuss the consequences of the findings for theories of melting and crystallization.
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.
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.
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)
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.
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
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.
Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model.
Li, Pengfei; Song, Lin Frank; Merz, Kenneth M
2015-04-14
Monovalent ions play fundamental roles in many biological processes in organisms. Modeling these ions in molecular simulations continues to be a challenging problem. The 12-6 Lennard-Jones (LJ) nonbonded model is widely used to model monovalent ions in classical molecular dynamics simulations. A lot of parameterization efforts have been reported for these ions with a number of experimental end points. However, some reported parameter sets do not have a good balance between the two Lennard-Jones parameters (the van der Waals (VDW) radius and potential well depth), which affects their transferability. In the present work, via the use of a noble gas curve we fitted in former work (J. Chem. Theory Comput. 2013, 9, 2733), we reoptimized the 12-6 LJ parameters for 15 monovalent ions (11 positive and 4 negative ions) for three extensively used water models (TIP3P, SPC/E, and TIP4P(EW)). Since the 12-6 LJ nonbonded model performs poorly in some instances for these ions, we have also parameterized the 12-6-4 LJ-type nonbonded model (J. Chem. Theory Comput. 2014, 10, 289) using the same three water models. The three derived parameter sets focused on reproducing the hydration free energies (the HFE set) and the ion-oxygen distance (the IOD set) using the 12-6 LJ nonbonded model and the 12-6-4 LJ-type nonbonded model (the 12-6-4 set) overall give improved results. In particular, the final parameter sets showed better agreement with quantum mechanically calculated VDW radii and improved transferability to ion-pair solutions when compared to previous parameter sets. PMID:26574374
Updated Principle of Corresponding States
ERIC Educational Resources Information Center
Ben-Amotz, Dor; Gift, Alan D.; Levine, R. D.
2004-01-01
The rule of corresponding states, which shows the connection between the thermodynamic properties of various liquids is re-examined. The overall likeness is observed by using an updated scaling technique of Lennard-Jones corresponding states (LJ-CS).
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
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.
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
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
Computational studies on intermolecular interactions in solvation
NASA Astrophysics Data System (ADS)
Song, Weiping
This thesis presents the results of computational studies of intermolecular interactions in various contexts. We first investigated the relation between solute-solvent intermolecular interactions and local density augmentation in supercritical solvation. The phenomenon of interest is the excess density that exists in the neighborhood of an attractive solute in a supercritical solvent in the vicinity of the critical point. In Chapter 2, we examined the ability of various measures of the strength of solute-solvent interactions, calculated from all-atom potential functions, to correlate the extent of local density augmentation in both experimental and model solvents. The Gibbs Ensemble Monte Carlo (GEMC) method enables us to calculate phase equilibrium in pure substances and mixtures. It provides a convenient way to test and develop model potentials. In Chapter 3 we present some methodological aspects of such calculations, the issues related to approach to critical points and finite-size effects and applications to simple fluids. Chapter 4 then describes a simplified 2-site potential model for simulating supercritical fluoroform. The GEMC method was used to simulate the vapor-liquid coexistence curve of the model fluid and the dynamic properties were studied by performing NVT molecular dynamics (MD) simulations. The results show that despite its simplicity, this model is able to reproduce many important properties of supercritical fluoroform, making it useful in molecular simulations of supercritical solvation. In the above two studies, the intermolecular interactions are described by a sum of pair-wise additive Lennard-Jones + Coulomb terms. The standard Lorentz-Berthelot combining rules (geometric mean rule for well depth and arithmetic mean rule for collision diameter) are commonly applied to account for the unlike pair Lennard-Jones parameters. In Chapter 5, we examined the applicability of the combining rules for modeling alkane-perfluoroalkane interactions. It
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
Multipole Algorithms for Molecular Dynamics Simulation on High Performance Computers.
NASA Astrophysics Data System (ADS)
Elliott, William Dewey
1995-01-01
A fundamental problem in modeling large molecular systems with molecular dynamics (MD) simulations is the underlying N-body problem of computing the interactions between all pairs of N atoms. The simplest algorithm to compute pair-wise atomic interactions scales in runtime {cal O}(N^2), making it impractical for interesting biomolecular systems, which can contain millions of atoms. Recently, several algorithms have become available that solve the N-body problem by computing the effects of all pair-wise interactions while scaling in runtime less than {cal O}(N^2). One algorithm, which scales {cal O}(N) for a uniform distribution of particles, is called the Greengard-Rokhlin Fast Multipole Algorithm (FMA). This work describes an FMA-like algorithm called the Molecular Dynamics Multipole Algorithm (MDMA). The algorithm contains several features that are new to N-body algorithms. MDMA uses new, efficient series expansion equations to compute general 1/r^{n } potentials to arbitrary accuracy. In particular, the 1/r Coulomb potential and the 1/r^6 portion of the Lennard-Jones potential are implemented. The new equations are based on multivariate Taylor series expansions. In addition, MDMA uses a cell-to-cell interaction region of cells that is closely tied to worst case error bounds. The worst case error bounds for MDMA are derived in this work also. These bounds apply to other multipole algorithms as well. Several implementation enhancements are described which apply to MDMA as well as other N-body algorithms such as FMA and tree codes. The mathematics of the cell -to-cell interactions are converted to the Fourier domain for reduced operation count and faster computation. A relative indexing scheme was devised to locate cells in the interaction region which allows efficient pre-computation of redundant information and prestorage of much of the cell-to-cell interaction. Also, MDMA was integrated into the MD program SIgMA to demonstrate the performance of the program over
Accurate statistical associating fluid theory for chain molecules formed from Mie segments
NASA Astrophysics Data System (ADS)
Lafitte, Thomas; Apostolakou, Anastasia; Avendaño, Carlos; Galindo, Amparo; Adjiman, Claire S.; Müller, Erich A.; Jackson, George
2013-10-01
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
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.
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
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
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
NASA Astrophysics Data System (ADS)
Teich-McGoldrick, Stephanie Leah
extension of NMA to finite temperature systems was developed without having to couple to slower simulations. Using the Lennard-Jones model, kinetic energy was introduced into the system by randomly displacing particles in a crystal. Temperature was related to these displacements through the equipartition theorem. Upon comparison with published work on the Lennard-Jones spinodal, we determined that NMA reasonably predicts the limit of mechanical stability at low temperatures, but overestimates it at higher temperatures.
Social Science Performance Descriptors, Grades 6-12.
ERIC Educational Resources Information Center
Best, Tom; Bettis, Norman; Carlson, Richard; Dempsey, Joanne; Greene, Matt; Gunn, Will; Kahl, Colleen; McBride, Lawrence W.; Miller, Arlan; Schrand, Jim; Walk, Fred
The Illinois Learning Standards are state content standards that describe what students should know and be able to achieve in grades K-12. The challenge for the 2000-2001 school year was to produce performance standards that would indicate how well students should perform to meet the state standards. The performance standards describe how well…
Calculation of liquid water-hydrate-methane vapor phase equilibria from molecular simulations.
Jensen, Lars; Thomsen, Kaj; von Solms, Nicolas; Wierzchowski, Scott; Walsh, Matthew R; Koh, Carolyn A; Sloan, E Dendy; Wu, David T; Sum, Amadeu K
2010-05-01
Monte Carlo simulation methods for determining fluid- and crystal-phase chemical potentials are used for the first time to calculate liquid water-methane hydrate-methane vapor phase equilibria from knowledge of atomistic interaction potentials alone. The water and methane molecules are modeled using the TIP4P/ice potential and a united-atom Lennard-Jones potential, respectively. The equilibrium calculation method for this system has three components, (i) thermodynamic integration from a supercritical ideal gas to obtain the fluid-phase chemical potentials, (ii) calculation of the chemical potential of the zero-occupancy hydrate system using thermodynamic integration from an Einstein crystal reference state, and (iii) thermodynamic integration to obtain the water and guest molecules' chemical potentials as a function of the hydrate occupancy. The three-phase equilibrium curve is calculated for pressures ranging from 20 to 500 bar and is shown to follow the Clapeyron behavior, in agreement with experiment; coexistence temperatures differ from the latter by 4-16 K in the pressure range studied. The enthalpy of dissociation extracted from the calculated P-T curve is within 2% of the experimental value at corresponding conditions. While computationally intensive, simulations such as these are essential to map the thermodynamically stable conditions for hydrate systems.
Quantum and classical simulations of molecular clusters
NASA Astrophysics Data System (ADS)
Dong, Xiao
to a fast discovery of accessible topological paths towards the global minimum. The ATMC can be readily linked to systems described by classical model potentials or systems described quantum mechanically. Serial and parallel versions of the ATMC have been implemented and applied for the structural optimization of classical Lennard-Jones nanoclusters and Morse nanoclusters, and tight-binding calcium nanoclusters, crystallization of infinite Lennard-Jones liquid, and optimization of the folding process leading to the native state of a polypeptide chain.
NASA Astrophysics Data System (ADS)
Hennad, A.; Eichwald, O.; Yousfi, M.; Lamrous, O.
1997-09-01
This paper is devoted to the determination of the differential and integral collision cross sections needed for the calculation of the transport coefficient of ions in weakly ionized gases. In the case of Ar^+/Ar system and for energy interval varying up to 100 eV, the cross sections are obtained from the interaction potential of polarization for low energies and of Lennard-Jones for higher energies. The calculation method of the collision cross sections based on the classical mechanics has been first validated from comparisons of measured and calculated differential cross sections. Then, these cross sections have been used in a Monte-Carlo code for simulation of the transport of Ar^+ ions in Ar gas at room temperature (300 K). The obtained transport coefficients (ion mobility, drift velocity and diffusion coefficient) are in good agreement with the drift tube measurements given in the literature thus confirming the validity of the method of collision cross section calculation. Cet article est consacré à la détermination des sections efficaces différentielles et intégrales ion-atome nécessaires au calcul des coefficients de transport des ions dans les gaz faiblement ionisés. Dans le cas du système Ar^+/Ar et pour des intervalles d'énergie allant jusqu'à quelques dizaines d'eV, les sections efficaces sont obtenues à partir des potentiels d'interaction de polarisation pour les faibles énergies et de Lennard-Jones pour les énergies plus élevées. La méthode de calcul des sections efficaces basée sur la mécanique classique a d'abord été validée par comparaison des sections efficaces différentielles mesurées et calculées. Ensuite, ces sections efficaces ont été utilisées dans un code de simulation statistique de Monte-Carlo du transport des ions Ar^+ dans l'Argon à la température ambiante (300 K). Les coefficients de transport (vitesse de dérive, mobilité ionique et coefficient de diffusion) obtenus sont en bon accord avec les mesures de
Universal scaling laws for homogeneous dislocation nucleation during nano-indentation
NASA Astrophysics Data System (ADS)
Garg, Akanksha; Maloney, Craig E.
2016-10-01
We perform atomistic simulations to study the mechanism of homogeneous dislocation nucleation in two dimensional (2D) hexagonal crystals during nanoindentation with a circular indenter of radius R. We study both a realistic embedded atom method (EAM) potential for Al in addition to simple pair-wise potentials: Lennard-Jones, Morse, and Hookean springs. The nucleation process is governed by the vanishing of the energy associated with a single energy eigenmode. The critical eigenmode, or dislocation embryo, is found to be localized along a line (or plane in 3D) of atoms with a lateral extent, ξ, at some depth, Y*, below the surface. For all interatomic potentials, the scaled critical load, Fc / R, and scaled critical contact length, Cc / R, decrease to R-independent values in the limit of large R. However, ξ / R and Y* / R display non-trivial scaling with R despite the R independence of Fc / R and Cc / R. We show that although both the interaction potential and the orientation of the lattice affect the prefactors in the scaling relations, all the scaling laws are robust. Furthermore, we show that a stability criterion proposed by Van Vliet et al. based on the minimum eigenvalue, Λ, of the local acoustic tensor predicts the location, orientation, and polarization of the dislocation embryo with a high degree of accuracy for all potentials and crystallographic orientations. However, we also show that, for all crystallographic orientations and interaction potentials, Λ erroneously indicates instability before the true instability occurs.
Dependence of the fragility of a glass former on the softness of interparticle interactions.
Sengupta, Shiladitya; Vasconcelos, Filipe; Affouard, Frédéric; Sastry, Srikanth
2011-11-21
We study the influence of the softness of the interparticle interactions on the fragility of a glass former by considering three model binary mixture glass formers. The interaction potential between particles is a modified Lennard-Jones type potential, with the repulsive part of the potential varying with an inverse power q of the interparticle distance, and the attractive part varying with an inverse power p. We consider the combinations (12,11) (model I), (12,6) (model II), and (8,5) (model III) for (q,p) such that the interaction potential becomes softer from model I to III. We evaluate the kinetic fragilities from the temperature variation of diffusion coefficients and relaxation times, and a thermodynamic fragility from the temperature variation of the configurational entropy. We find that the kinetic fragility increases with increasing softness of the potential, consistent with previous results for these model systems, but at variance with the thermodynamic fragility, which decreases with increasing softness of the interactions, as well as expectations from earlier results. We rationalize our results by considering the full form of the Adam-Gibbs relation, which requires, in addition to the temperature dependence of the configurational entropy, knowledge of the high temperature activation energies in order to determine fragility. We show that consideration of the scaling of the high temperature activation energy with the liquid density, analyzed in recent studies, provides a partial rationalization of the observed behavior.
An EQT-cDFT approach to determine thermodynamic properties of confined fluids.
Mashayak, S Y; Motevaselian, M H; Aluru, N R
2015-06-28
We present a continuum-based approach to predict the structure and thermodynamic properties of confined fluids at multiple length-scales, ranging from a few angstroms to macro-meters. The continuum approach is based on the empirical potential-based quasi-continuum theory (EQT) and classical density functional theory (cDFT). EQT is a simple and fast approach to predict inhomogeneous density and potential profiles of confined fluids. We use EQT potentials to construct a grand potential functional for cDFT. The EQT-cDFT-based grand potential can be used to predict various thermodynamic properties of confined fluids. In this work, we demonstrate the EQT-cDFT approach by simulating Lennard-Jones fluids, namely, methane and argon, confined inside slit-like channels of graphene. We show that the EQT-cDFT can accurately predict the structure and thermodynamic properties, such as density profiles, adsorption, local pressure tensor, surface tension, and solvation force, of confined fluids as compared to the molecular dynamics simulation results.
NASA Technical Reports Server (NTRS)
Oh, B. K.; Kim, S. K.
1974-01-01
A model of helium adsorption on an argon crystal is built up from the premise that local adsorption predominates in the first layer and nonlocal adsorption in the second. Application of the virial expansion theorem to the second layer gives a series in which the first term represents the motion of a single molecule in the external potential field and the second a two-body interaction under this field. The thermodynamic functions of the adsorbed phase are calculated ab initio, the gas-solid interaction potential being derived from lattice summation and the partition function from an appropriate choice of a site-spacing polynomial to describe the periodic potential. The mutual interaction of adsorbed molecules is calculated with a two-dimensional Lennard-Jones potential. The second virial coefficient is calculated and its dependence on temperature and choice of potential is studied. It is found that the second virial coefficient is very well approximated by a two-dimensional gas in free space. The adsorption isotherm, isosteric heat, and specific heat are obtained and compared with the results of Ross and Steele, giving excellent agreement.
Molecular dynamics studies of material property effects on thermal boundary conductance.
Zhou, X W; Jones, R E; Duda, J C; Hopkins, P E
2013-07-14
Thermal boundary resistance (inverse of conductance) between different material layers can dominate the overall thermal resistance in nanostructures and therefore impact the performance of the thermal property limiting nano devices. Because relationships between material properties and thermal boundary conductance have not been fully understood, optimum devices cannot be developed through a rational selection of materials. Here we develop generic interatomic potentials to enable material properties to be continuously varied in extremely large molecular dynamics simulations to explore the dependence of thermal boundary conductance on the characteristic properties of materials such as atomic mass, stiffness, and interfacial crystallography. To ensure that our study is not biased to a particular model, we employ different types of interatomic potentials. In particular, both a Stillinger-Weber potential and a hybrid embedded-atom-method + Stillinger-Weber potential are used to study metal-on-semiconductor compound interfaces, and the results are analyzed considering previous work based upon a Lennard-Jones (LJ) potential. These studies, therefore, reliably provide new understanding of interfacial transport phenomena particularly in terms of effects of material properties on thermal boundary conductance. Our most important finding is that thermal boundary conductance increases with the overlap of the vibrational spectra between metal modes and the acoustic modes of the semiconductor compound, and increasing the metal stiffness causes a continuous shift of the metal modes. As a result, the maximum thermal boundary conductance occurs at an intermediate metal stiffness (best matched to the semiconductor stiffness) that maximizes the overlap of the vibrational modes.
NASA Astrophysics Data System (ADS)
Fuentes-Herrera, M.; Moreno-Razo, J. A.; Guzmán, O.; López-Lemus, J.; Ibarra-Tandi, B.
2016-06-01
Molecular simulations in the canonical and isothermal-isobaric ensembles were performed to study the effect of varying the shape of the intermolecular potential on the phase diagram, critical, and interfacial properties of model fluids. The molecular interactions were modeled by the Approximate Non-Conformal (ANC) theory potentials. Unlike the Lennard-Jones or Morse potentials, the ANC interactions incorporate parameters (called softnesses) that modulate the steepness of the potential in their repulsive and attractive parts independently. This feature allowed us to separate unambiguously the role of each region of the potential on setting the thermophysical properties. In particular, we found positive linear correlation between all critical coordinates and the attractive and repulsive softness, except for the critical density and the attractive softness which are negatively correlated. Moreover, we found that the physical properties related to phase coexistence (such as span of the liquid phase between the critical and triple points, variations in the P-T vaporization curve, interface width, and surface tension) are more sensitive to changes in the attractive softness than to the repulsive one. Understanding the different roles of attractive and repulsive forces on phase coexistence may contribute to developing more accurate models of liquids and their mixtures.
Solving integral equations for binary and ternary systems
NASA Astrophysics Data System (ADS)
Nader Lotfollahi, Mohammad; Modarress, Hamid
2002-02-01
Solving integral equations is an effective approach to obtain the radial distribution function (RDF) of multicomponent mixtures. In this work, by extending Gillan's approach [M. J. Gillan, Mol. Phys. 38(6), 1781 (1979)], the integral equation was solved by numerical method and was applied to both binary and ternary mixtures. The Lennard-Jones (LJ) potential function was used to express the pair molecular interactions in calculating the RDF and chemical potential. This allowed a comparison with available simulation data, on the RDF and the chemical potential, since the simulation data have been reported for the LJ potential function. The RDF and the chemical potential results indicated good agreement with the simulation data. The calculations were extended to the ternary system and the RDFs for carbon dioxide-octane-naphthalene were obtained. The numerical method used in solving integral equation was rapidly convergent and not sensitive to the first estimation. The method proposed in this work can be easily extended to more than the three-component systems.
An EQT-cDFT approach to determine thermodynamic properties of confined fluids
Mashayak, S. Y.; Motevaselian, M. H.; Aluru, N. R.
2015-06-28
We present a continuum-based approach to predict the structure and thermodynamic properties of confined fluids at multiple length-scales, ranging from a few angstroms to macro-meters. The continuum approach is based on the empirical potential-based quasi-continuum theory (EQT) and classical density functional theory (cDFT). EQT is a simple and fast approach to predict inhomogeneous density and potential profiles of confined fluids. We use EQT potentials to construct a grand potential functional for cDFT. The EQT-cDFT-based grand potential can be used to predict various thermodynamic properties of confined fluids. In this work, we demonstrate the EQT-cDFT approach by simulating Lennard-Jones fluids, namely, methane and argon, confined inside slit-like channels of graphene. We show that the EQT-cDFT can accurately predict the structure and thermodynamic properties, such as density profiles, adsorption, local pressure tensor, surface tension, and solvation force, of confined fluids as compared to the molecular dynamics simulation results.
Computer simulation of liquid-vapor coexistence of confined quantum fluids
NASA Astrophysics Data System (ADS)
Trejos, Víctor M.; Gil-Villegas, Alejandro; Martinez, Alejandro
2013-11-01
The liquid-vapor coexistence (LV) of bulk and confined quantum fluids has been studied by Monte Carlo computer simulation for particles interacting via a semiclassical effective pair potential Veff(r) = VLJ + VQ, where VLJ is the Lennard-Jones 12-6 potential (LJ) and VQ is the first-order Wigner-Kirkwood (WK-1) quantum potential, that depends on β = 1/kT and de Boer's quantumness parameter Λ = h/σ √{mɛ }, where k and h are the Boltzmann's and Planck's constants, respectively, m is the particle's mass, T is the temperature of the system, and σ and ɛ are the LJ potential parameters. The non-conformal properties of the system of particles interacting via the effective pair potential Veff(r) are due to Λ, since the LV phase diagram is modified by varying Λ. We found that the WK-1 system gives an accurate description of the LV coexistence for bulk phases of several quantum fluids, obtained by the Gibbs Ensemble Monte Carlo method (GEMC). Confinement effects were introduced using the Canonical Ensemble (NVT) to simulate quantum fluids contained within parallel hard walls separated by a distance Lp, within the range 2σ ⩽ Lp ⩽ 6σ. The critical temperature of the system is reduced by decreasing Lp and increasing Λ, and the liquid-vapor transition is not longer observed for Lp/σ < 2, in contrast to what has been observed for the classical system.
Exponential 6 parameterization for the JCZ3-EOS
McGee, B.C.; Hobbs, M.L.; Baer, M.R.
1998-07-01
A database has been created for use with the Jacobs-Cowperthwaite-Zwisler-3 equation-of-state (JCZ3-EOS) to determine thermochemical equilibrium for detonation and expansion states of energetic materials. The JCZ3-EOS uses the exponential 6 intermolecular potential function to describe interactions between molecules. All product species are characterized by r*, the radius of the minimum pair potential energy, and {var_epsilon}/k, the well depth energy normalized by Boltzmann`s constant. These parameters constitute the JCZS (S for Sandia) EOS database describing 750 gases (including all the gases in the JANNAF tables), and have been obtained by using Lennard-Jones potential parameters, a corresponding states theory, pure liquid shock Hugoniot data, and fit values using an empirical EOS. This database can be used with the CHEETAH 1.40 or CHEETAH 2.0 interface to the TIGER computer program that predicts the equilibrium state of gas- and condensed-phase product species. The large JCZS-EOS database permits intermolecular potential based equilibrium calculations of energetic materials with complex elemental composition.
ABCluster: the artificial bee colony algorithm for cluster global optimization.
Zhang, Jun; Dolg, Michael
2015-10-01
Global optimization of cluster geometries is of fundamental importance in chemistry and an interesting problem in applied mathematics. In this work, we introduce a relatively new swarm intelligence algorithm, i.e. the artificial bee colony (ABC) algorithm proposed in 2005, to this field. It is inspired by the foraging behavior of a bee colony, and only three parameters are needed to control it. We applied it to several potential functions of quite different nature, i.e., the Coulomb-Born-Mayer, Lennard-Jones, Morse, Z and Gupta potentials. The benchmarks reveal that for long-ranged potentials the ABC algorithm is very efficient in locating the global minimum, while for short-ranged ones it is sometimes trapped into a local minimum funnel on a potential energy surface of large clusters. We have released an efficient, user-friendly, and free program "ABCluster" to realize the ABC algorithm. It is a black-box program for non-experts as well as experts and might become a useful tool for chemists to study clusters. PMID:26327507
Collective behavior of penetrable self-propelled rods in two dimensions.
Abkenar, Masoud; Marx, Kristian; Auth, Thorsten; Gompper, Gerhard
2013-12-01
Collective behavior of self-propelled particles is observed on a microscale for swimmers such as sperm and bacteria as well as for protein filaments in motility assays. The properties of such systems depend both on their dimensionality and the interactions between their particles. We introduce a model for self-propelled rods in two dimensions that interact via a separation-shifted Lennard-Jones potential. Due to the finite potential barrier, the rods are able to cross. This model allows us to efficiently simulate systems of self-propelled rods that effectively move in two dimensions but can occasionally escape to the third dimension in order to pass each other. Our quasi-two-dimensional self-propelled particles describe a class of active systems that encompasses microswimmers close to a wall and filaments propelled on a substrate. Using Monte Carlo simulations, we first determine the isotropic-nematic transition for passive rods. Using Brownian dynamics simulations, we characterize cluster formation of self-propelled rods as a function of propulsion strength, noise, and energy barrier. Contrary to rods with an infinite potential barrier, an increase of the propulsion strength does not only favor alignment but also effectively decreases the potential barrier that prevents crossing of rods. We thus find a clustering window with a maximum cluster size at medium propulsion strengths.
Molecular dynamics simulations of shock waves in cis-1,4-polybutadiene melts
NASA Astrophysics Data System (ADS)
He, Lan; Sewell, Thomas D.; Thompson, Donald L.
2013-10-01
Molecular dynamics simulations of supported shock waves in monodisperse melts of cis-1,4-polybutadiene initially at atmospheric pressure and T = 413 K were performed to study the shock-induced structural changes and post-shock relaxation. Simulations were performed for Rankine-Hugoniot shock pressures between 7.22 GPa and 8.26 GPa using the united-atom force field due to Smith and Paul [G. D. Smith and W. Paul, J. Phys. Chem. A 102, 1200 (1998)] for systems composed of chains containing 32, 64, or 128 united atoms. The sensitivity of the results to the non-bonded interaction potential was studied by comparing results obtained using the Lennard-Jones 12-6 potential from the original Smith and Paul force field to ones obtained when the 12-6 potential was replaced by the Buckingham exponential-6 potential. Several structural and mechanical properties were studied as functions of distance (time) behind the shock front. Bulk relaxation was characterized by calculating profiles of temperature, density, and principal and shear stress. Microscopic shock-induced structural rearrangement and relaxation were studied by calculating the ratio of Cartesian components of the mean-squared radius of gyration to corresponding values for the equilibrated material; dihedral angle distributions; and the distribution of, and second Legendre polynomial order parameter for, the angle formed by covalent bond vectors and the shock propagation direction.
Molecular dynamics study of mechanical properties of carbon nanotube reinforced aluminum composites
NASA Astrophysics Data System (ADS)
Srivastava, Ashish Kumar; Mokhalingam, A.; Singh, Akhileshwar; Kumar, Dinesh
2016-05-01
Atomistic simulations were conducted to estimate the effect of the carbon nanotube (CNT) reinforcement on the mechanical behavior of CNT-reinforced aluminum (Al) nanocomposite. The periodic system of CNT-Al nanocomposite was built and simulated using molecular dynamics (MD) software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The mechanical properties of the nanocomposite were investigated by the application of uniaxial load on one end of the representative volume element (RVE) and fixing the other end. The interactions between the atoms of Al were modeled using embedded atom method (EAM) potentials, whereas Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential was used for the interactions among carbon atoms and these pair potentials are coupled with the Lennard-Jones (LJ) potential. The results show that the incorporation of CNT into the Al matrix can increase the Young's modulus of the nanocomposite substantially. In the present case, i.e. for approximately 9 with % reinforcement of CNT can increase the axial Young's modulus of the Al matrix up to 77 % as compared to pure Al.
Computer simulations of the Adsorption of Xenon onto a C60 monolayer on Ag (111)
NASA Astrophysics Data System (ADS)
Gatica, Silvina; Cole, Milton; Diehl, Renee
2007-03-01
We performed Grand Canonical Monte Carlo simulations to study the adsorption of Xenon on a substrate composed of C60 molecules placed on top of a Ag(111) surface. The C60 molecules form a commensurate structure at a distance of 0.227 nm above the Ag surface. The interaction potential between the Xe atoms and the substrate has two contributions: from the C60 molecules and from the Ag atoms. In the simulations, the interaction with the Ag surface was computed using an ab initio van der Waals potential, varying as 1/d^3. The interaction between the Xe atoms and each C60 molecule was computed using a potential previously developed by Hernandez et.al. (E. S. Hernandez, M. W. Cole and M. Boninsegni, ``Wetting of spherical surfaces by quantum fluids'', J. Low Temp. Phys. 134, 309-314 (2004)), who integrated the Lennard Jones interaction over the surface of a spherical buckyball. The total potential has especially attractive 3-fold sites, positioned 0.4 nm above the point between each three buckyballs. The low coverage uptake populates those sites, and then continues forming a monolayer. The adsorption isotherms show several steps, typical of substrates that have distinct adsorption sites. We compare the results with the experimental data.
Chowdhury, Sanjib Chandra; Okabe, Tomonaga; Nishikawa, Masaaki
2010-02-01
We investigate the effects of the vacancy defects (i.e., missing atoms) in carbon nanotubes (CNTs) on the interfacial shear strength (ISS) of the CNT-polyethylene composite with the molecular dynamics simulation. In the simulation, the crystalline polyethylene matrix is set up in a hexagonal array with the polymer chains parallel to the CNT axis. Vacancy defects in the CNT are introduced by removing the corresponding atoms from the pristine CNT (i.e., CNT without any defect). Three patterns of vacancy defects with three different sizes are considered. Two types of interfaces, with and without cross-links between the CNT and the matrix are also considered here. Polyethylene chains are used as cross-links between the CNT and the matrix. The Brenner potential is used for the carbon-carbon interaction in the CNT, while the polymer is modeled by a united-atom potential. The nonbonded van der Waals interaction between the CNT and the polymer matrix and within the polymer matrix itself is modeled with the Lennard-Jones potential. To determine the ISS, we conduct the CNT pull-out from the polymer matrix and the ISS has been estimated with the change of total potential energy of the CNT-polymer system. The simulation results reveal that the vacancy defects significantly influence the ISS. Moreover, the simulation clarifies that CNT breakage occurs during the pull-out process for large size vacancy defect which ultimately reduces the reinforcement. PMID:20352712
Adsorption of Hydrogen Molecules on Carbon Nanotubes Using Quantum Chemistry and Molecular Dynamics.
Faginas-Lago, N; Yeni, D; Huarte, F; Wang, Y; Alcamí, M; Martin, F
2016-08-18
Physisorption and storage of molecular hydrogen on single-walled carbon nanotube (SWCNT) of various diameters and chiralities are studied by means of classical molecular dynamics (MD) simulations and a force field validated using DFT-D2 and CCSD(T) calculations. A nonrigid carbon nanotube model is implemented with stretching (C-C) and valence angle potentials (C-C-C) formulated as Morse and Harmonic cosine potentials, respectively. Our results evidence that the standard Lennard-Jones potential fails to describe the H2-H2 binding energies. Therefore, our simulations make use of a potential that contains two-body term with parameters obtained from fitting CCSD(T)/CBS binding energies. From our MD simulations, we have analyzed the interaction energies, radial distribution functions, gravimetric densities (% wt), and the distances of the adsorbed H2 layers to the three zigzag type of nanotubes (5,0), (10,0), and (15,0) at 100 and 300 K. PMID:27467122
Relationships between Depression and High Intellectual Potential.
Weismann-Arcache, Catherine; Tordjman, Sylvie
2012-01-01
This paper proposes to analyse the relationships between depression and high intellectual potential through a multidisciplinary and original approach. Based on their respective experience in psychology and child psychiatry, the authors will focus their analysis on creative potential. First, relationships between creativity (literary, artistic, or scientific creativity) and melancholy ("melancholy" comes from the Greek words for "black" ("melas") and "bile" ("khole")) will be examined from antiquity to modern times. Aristotle introduced a quantitative factor, asserting that levels of melancholy and black bile are positively correlated; however, under a given threshold of black bile, it can give rise to an exceptional being. Second, the case study of Blaise Pascal (scientific and philosophical creativity associated with major depressive episodes from childhood) will be presented and discussed. This case study sheds light on the paradoxical role of depression in the overinvestment in intellectual and creative spheres as well as on the impact of traumatic events on high intellectual potential. Third, observations will be reported based on a study conducted on 100 children with high intellectual potential (6-12 years old). Finally, based on these different levels of analysis, it appears that heterogeneity of mental functioning in children with high intellectual potential is at the center of the creative process and it has related psychological vulnerability.
The critical compressibility factor value: Associative fluids and liquid alkali metals
Kulinskii, V. L.
2014-08-07
We show how to obtain the critical compressibility factor Z{sub c} for simple and associative Lennard-Jones fluids using the critical characteristics of the Ising model on different lattices. The results show that low values of critical compressibility factor are correlated with the associative properties of fluids in critical region and can be obtained on the basis of the results for the Ising model on lattices with more than one atom per cell. An explanation for the results on the critical point line of the Lennard-Jones fluids and liquid metals is proposed within the global isomorphism approach.
Nanodroplet impact onto solid platinum surface: Spreading and bouncing
NASA Astrophysics Data System (ADS)
Lussier, Daniel; Ventikos, Yiannis
2009-11-01
The impact of droplets onto solid surfaces is found in a huge variety of natural and technological applications, from rain drops splashing on the pavement, to material manufacturing by molten droplet deposition. Taking inspiration from existing microfluidic technologies (i.e. lab-on-chip), there is increasing interest in the use of nanodroplets (D < 100 nm) for a number of applications such as drug delivery and semiconductor device manufacturing. However, as the size of the droplet is reduced into the nanoscale, the direct use of previously obtained macroscopic results is not guaranteed. At the nanoscale, important effects due to the molecular nature of the fluid, thermal fluctuations and reduced dimensionality can play a critical role in determining system dynamics. In this paper we present the results of large-scale, fully atomistic, three-dimensional molecular dynamics (MD) simulation of an argon nanodroplet (D = 18 nm, 54 000 atoms) impact onto a solid platinum surface, using the LAMMPS software package. The fluid argon is modeled using the well-known Lennard-Jones (LJ) potential, while the embedded-atom model (EAM) potential is used for the solid platinum. By varying both the impact velocities (10-1000 m/s) and the wettability of the solid surface a wide range of impact behaviors is observed, from smooth spreading, to bouncing recoil, pointing towards a wide array of potential applications.
Zheng, Zheng
2013-01-01
We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the PDB. Forty-nine types of atomic pairwise interactions were derived using this method, which we call the knowledge-based and empirical combined scoring algorithm (KECSA). Two validation benchmarks were introduced to test the performance of KECSA. The first validation benchmark included two test sets that address the training-set and enthalpy/entropy of KECSA The second validation benchmark suite included two large-scale and five small-scale test sets to compare the reproducibility of KECSA with respect to two empirical score functions previously developed in our laboratory (LISA and LISA+), as well as to other well-known scoring methods. Validation results illustrate that KECSA shows improved performance in all test sets when compared with other scoring methods especially in its ability to minimize the RMSE. LISA and LISA+ displayed similar performance using the correlation coefficient and Kendall τ as the metric of quality for some of the small test sets. Further pathways for improvement are discussed which would KECSA more sensitive to subtle changes in ligand structure. PMID:23560465
Atomistic clustering-ordering and high-strain deformation of an Al0.1CrCoFeNi high-entropy alloy
Sharma, Aayush; Singh, Prashant; Johnson, Duane D.; Liaw, Peter K.; Balasubramanian, Ganesh
2016-08-08
Here, computational investigations of structural, chemical, and deformation behavior in high-entropy alloys (HEAs), which possess notable mechanical strength, have been limited due to the absence of applicable force fields. To extend investigations, we propose a set of intermolecular potential parameters for a quinary Al-Cr-Co-Fe-Ni alloy, using the available ternary Embedded Atom Method and Lennard-Jones potential in classical molecular-dynamics simulations. The simulation results are validated by a comparison to first-principles Korringa-Kohn-Rostoker (KKR) - Coherent Potential Approximation (CPA) [KKR-CPA] calculations for the HEA structural properties (lattice constants and bulk moduli), relative stability, pair probabilities, and high-temperature short-range ordering. The simulation (MD)-derived propertiesmore » are in quantitative agreement with KKR-CPA calculations (first-principles) and experiments. We study AlxCrCoFeNi for Al ranging from 0 ≤ x ≤2 mole fractions, and find that the HEA shows large chemical clustering over a wide temperature range for x < 0.5. At various temperatures high-strain compression promotes atomistic rearrangements in Al0.1CrCoFeNi, resulting in a clustering-to-ordering transition that is absent for tensile loading. Large fluctuations under stress, and at higher temperatures, are attributed to the thermo-plastic instability in Al0.1CrCoFeNi.« less
Atomistic clustering-ordering and high-strain deformation of an Al0.1CrCoFeNi high-entropy alloy
NASA Astrophysics Data System (ADS)
Sharma, Aayush; Singh, Prashant; Johnson, Duane D.; Liaw, Peter K.; Balasubramanian, Ganesh
2016-08-01
Computational investigations of structural, chemical, and deformation behavior in high-entropy alloys (HEAs), which possess notable mechanical strength, have been limited due to the absence of applicable force fields. To extend investigations, we propose a set of intermolecular potential parameters for a quinary Al-Cr-Co-Fe-Ni alloy, using the available ternary Embedded Atom Method and Lennard-Jones potential in classical molecular-dynamics simulations. The simulation results are validated by a comparison to first-principles Korringa-Kohn-Rostoker (KKR) - Coherent Potential Approximation (CPA) [KKR-CPA] calculations for the HEA structural properties (lattice constants and bulk moduli), relative stability, pair probabilities, and high-temperature short-range ordering. The simulation (MD)-derived properties are in quantitative agreement with KKR-CPA calculations (first-principles) and experiments. We study AlxCrCoFeNi for Al ranging from 0 ≤ x ≤2 mole fractions, and find that the HEA shows large chemical clustering over a wide temperature range for x < 0.5. At various temperatures high-strain compression promotes atomistic rearrangements in Al0.1CrCoFeNi, resulting in a clustering-to-ordering transition that is absent for tensile loading. Large fluctuations under stress, and at higher temperatures, are attributed to the thermo-plastic instability in Al0.1CrCoFeNi.
Atomistic clustering-ordering and high-strain deformation of an Al0.1CrCoFeNi high-entropy alloy.
Sharma, Aayush; Singh, Prashant; Johnson, Duane D; Liaw, Peter K; Balasubramanian, Ganesh
2016-01-01
Computational investigations of structural, chemical, and deformation behavior in high-entropy alloys (HEAs), which possess notable mechanical strength, have been limited due to the absence of applicable force fields. To extend investigations, we propose a set of intermolecular potential parameters for a quinary Al-Cr-Co-Fe-Ni alloy, using the available ternary Embedded Atom Method and Lennard-Jones potential in classical molecular-dynamics simulations. The simulation results are validated by a comparison to first-principles Korringa-Kohn-Rostoker (KKR) - Coherent Potential Approximation (CPA) [KKR-CPA] calculations for the HEA structural properties (lattice constants and bulk moduli), relative stability, pair probabilities, and high-temperature short-range ordering. The simulation (MD)-derived properties are in quantitative agreement with KKR-CPA calculations (first-principles) and experiments. We study AlxCrCoFeNi for Al ranging from 0 ≤ x ≤2 mole fractions, and find that the HEA shows large chemical clustering over a wide temperature range for x < 0.5. At various temperatures high-strain compression promotes atomistic rearrangements in Al0.1CrCoFeNi, resulting in a clustering-to-ordering transition that is absent for tensile loading. Large fluctuations under stress, and at higher temperatures, are attributed to the thermo-plastic instability in Al0.1CrCoFeNi. PMID:27498807
Ustinov, E A
2015-02-21
This paper presents a refined technique to describe two-dimensional phase transitions in dense fluids adsorbed on a crystalline surface. Prediction of parameters of 2D liquid-solid equilibrium is known to be an extremely challenging problem, which is mainly due to a small difference in thermodynamic functions of coexisting phases and lack of accuracy of numerical experiments in case of their high density. This is a serious limitation of various attempts to circumvent this problem. To improve this situation, a new methodology based on the kinetic Monte Carlo method was applied. The methodology involves analysis of equilibrium gas-liquid and gas-solid systems undergoing an external potential, which allows gradual shifting parameters of the phase coexistence. The interrelation of the chemical potential and tangential pressure for each system is then treated with the Gibbs-Duhem equation to obtain the point of intersection corresponding to the liquid/solid-solid equilibrium coexistence. The methodology is demonstrated on the krypton-graphite system below and above the 2D critical temperature. Using experimental data on the liquid-solid and the commensurate-incommensurate transitions in the krypton monolayer derived from adsorption isotherms, the Kr-graphite Lennard-Jones parameters have been corrected resulting in a higher periodic potential modulation.
Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics
2016-01-01
We compare the performance of five magnesium (Mg2+) ion models in simulations of an RNA stem loop which has an experimentally determined divalent ion dependent conformational shift. We show that despite their differences in parametrization and resulting van der Waals terms, including differences in the functional form of the nonbonded potential, when the RNA adopts its folded conformation, all models behave similarly across ten independent microsecond length simulations with each ion model. However, when the entire structure ensemble is accounted for, chelation of Mg2+ to RNA is seen in three of the five models, most egregiously and likely artifactual in simulations using a 12-6-4 model for the Lennard-Jones potential. Despite the simple nature of the fixed point-charge and van der Waals sphere models employed, and with the exception of the likely oversampled directed chelation of the 12-6-4 potential models, RNA–Mg2+ interactions via first shell water molecules are surprisingly well described by modern parameters, allowing us to observe the spontaneous conformational shift from Mg2+ free RNA to Mg2+ associated RNA structure in unrestrained molecular dynamics simulations. PMID:27294370
Desgranges, Caroline; Huber, Landon; Delhommelle, Jerome
2016-07-01
We determine the impact of the Friedel oscillations on the phase behavior, critical properties, and thermodynamic contours in films [two dimensions (2D)] and bulk phases [three dimensions (3D)]. Using expanded Wang-Landau simulations, we calculate the grand-canonical partition function and, in turn, the thermodynamic properties of systems modeled with a linear combination of the Lennard-Jones and Dzugutov potentials, weighted by a parameter X (0
NASA Astrophysics Data System (ADS)
Wang, Gang; Wu, Nanhua; Chen, Jionghua; Wang, Jinjian; Shao, Jingling; Zhu, Xiaolei; Lu, Xiaohua; Guo, Lucun
2016-11-01
The thermodynamic and kinetic behaviors of gold nanoparticles confined between two-layer graphene nanosheets (two-layer-GNSs) are examined and investigated during heating and cooling processes via molecular dynamics (MD) simulation technique. An EAM potential is applied to represent the gold-gold interactions while a Lennard-Jones (L-J) potential is used to describe the gold-GNS interactions. The MD melting temperature of 1345 K for bulk gold is close to the experimental value (1337 K), confirming that the EAM potential used to describe gold-gold interactions is reliable. On the other hand, the melting temperatures of gold clusters supported on graphite bilayer are corrected to the corresponding experimental values by adjusting the εAu-C value. Therefore, the subsequent results from current work are reliable. The gold nanoparticles confined within two-layer GNSs exhibit face center cubic structures, which is similar to those of free gold clusters and bulk gold. The melting points, heats of fusion, and heat capacities of the confined gold nanoparticles are predicted based on the plots of total energies against temperature. The density distribution perpendicular to GNS suggests that the freezing of confined gold nanoparticles starts from outermost layers. The confined gold clusters exhibit layering phenomenon even in liquid state. The transition of order-disorder in each layer is an essential characteristic in structure for the freezing phase transition of the confined gold clusters. Additionally, some vital kinetic data are obtained in terms of classical nucleation theory.
Bailey, Nicholas P.; Bøhling, Lasse; Veldhorst, Arno A.; Schrøder, Thomas B.; Dyre, Jeppe C.
2013-11-14
We derive exact results for the rate of change of thermodynamic quantities, in particular, the configurational specific heat at constant volume, C{sub V}, along configurational adiabats (curves of constant excess entropy S{sub ex}). Such curves are designated isomorphs for so-called Roskilde liquids, in view of the invariance of various structural and dynamical quantities along them. The slope of the isomorphs in a double logarithmic representation of the density-temperature phase diagram, γ, can be interpreted as one third of an effective inverse power-law potential exponent. We show that in liquids where γ increases (decreases) with density, the contours of C{sub V} have smaller (larger) slope than configurational adiabats. We clarify also the connection between γ and the pair potential. A fluctuation formula for the slope of the C{sub V}-contours is derived. The theoretical results are supported with data from computer simulations of two systems, the Lennard-Jones fluid, and the Girifalco fluid. The sign of dγ/dρ is thus a third key parameter in characterizing Roskilde liquids, after γ and the virial-potential energy correlation coefficient R. To go beyond isomorph theory we compare invariance of a dynamical quantity, the self-diffusion coefficient, along adiabats and C{sub V}-contours, finding it more invariant along adiabats.
Bailey, Nicholas P; Bøhling, Lasse; Veldhorst, Arno A; Schrøder, Thomas B; Dyre, Jeppe C
2013-11-14
We derive exact results for the rate of change of thermodynamic quantities, in particular, the configurational specific heat at constant volume, CV, along configurational adiabats (curves of constant excess entropy Sex). Such curves are designated isomorphs for so-called Roskilde liquids, in view of the invariance of various structural and dynamical quantities along them. The slope of the isomorphs in a double logarithmic representation of the density-temperature phase diagram, γ, can be interpreted as one third of an effective inverse power-law potential exponent. We show that in liquids where γ increases (decreases) with density, the contours of CV have smaller (larger) slope than configurational adiabats. We clarify also the connection between γ and the pair potential. A fluctuation formula for the slope of the CV-contours is derived. The theoretical results are supported with data from computer simulations of two systems, the Lennard-Jones fluid, and the Girifalco fluid. The sign of dγ∕dρ is thus a third key parameter in characterizing Roskilde liquids, after γ and the virial-potential energy correlation coefficient R. To go beyond isomorph theory we compare invariance of a dynamical quantity, the self-diffusion coefficient, along adiabats and CV-contours, finding it more invariant along adiabats.
Atomistic clustering-ordering and high-strain deformation of an Al0.1CrCoFeNi high-entropy alloy
Sharma, Aayush; Singh, Prashant; Johnson, Duane D.; Liaw, Peter K.; Balasubramanian, Ganesh
2016-01-01
Computational investigations of structural, chemical, and deformation behavior in high-entropy alloys (HEAs), which possess notable mechanical strength, have been limited due to the absence of applicable force fields. To extend investigations, we propose a set of intermolecular potential parameters for a quinary Al-Cr-Co-Fe-Ni alloy, using the available ternary Embedded Atom Method and Lennard-Jones potential in classical molecular-dynamics simulations. The simulation results are validated by a comparison to first-principles Korringa-Kohn-Rostoker (KKR) - Coherent Potential Approximation (CPA) [KKR-CPA] calculations for the HEA structural properties (lattice constants and bulk moduli), relative stability, pair probabilities, and high-temperature short-range ordering. The simulation (MD)-derived properties are in quantitative agreement with KKR-CPA calculations (first-principles) and experiments. We study AlxCrCoFeNi for Al ranging from 0 ≤ x ≤2 mole fractions, and find that the HEA shows large chemical clustering over a wide temperature range for x < 0.5. At various temperatures high-strain compression promotes atomistic rearrangements in Al0.1CrCoFeNi, resulting in a clustering-to-ordering transition that is absent for tensile loading. Large fluctuations under stress, and at higher temperatures, are attributed to the thermo-plastic instability in Al0.1CrCoFeNi. PMID:27498807
Multibody expansion of particle interactions: How many-body is a particular element in a cluster
NASA Astrophysics Data System (ADS)
Carrasco, Sebastián; Varas, Alejandro; Rogan, José; Kiwi, Miguel; Valdivia, Juan Alejandro
2016-08-01
The particle-particle interaction potential of an N -atom cluster is expanded in n -body contributions. The expansion allows us to determine the magnitude of each one of the n -body terms, and consequently quantifies how n -body a potential really is. This way we obtain bounds for the relative error due to truncation, a feature that could be applicable in several contexts like the search of minimal energy cluster conformations, to obtain adequate seeds for further ab initio refinement, or to speed up molecular dynamics computations. We develop the formalism, and test the procedure numerically for the Lennard-Jones, Murrel-Motram, Gupta, and Sutton-Chen potentials. The contributions of the n -body terms for Ag, Al, Au, Co, Cu, Fe, Ir, Ni, Pb, Pd, Pt, and Rh clusters are computed up to n =9 ; they show that the importance and magnitude of the n >2 interaction terms depend on the particular element. The relevance of the n -body corrections as a function of cluster size is also explored for N ≤50 , and for a linear chain of N ≤1000 atoms.
Transport Properties of a Rarefied Ch4-N2 Gas Mixture
NASA Astrophysics Data System (ADS)
Fokin, L. R.; Kalashnikov, A. N.
2016-01-01
The area of application of the rarefied neutral methane-nitrogen gas mixture is considered. Experimental data on the transport properties of this mixture and its components were analyzed and generalized on the basis of molecular-kinetic theory relations with the use of the potentials of pair uniform and cross interactions of CH4 and N2 molecules. The parameters of three spherical symmetric three-parameter m-6 Lennard-Jones interaction potentials with a repulsive branch of varying rigidity were determined with the use of the nonlinear weight method of least squares. Tables of reference data on the viscosity of the indicated mixture and the coefficients of interdiffusion of its components were calculated for the concentration range 0-1 at temperatures 100-1150 K. Estimates of the confidential errors in determining the properties of this mixture have been made with the use of the error matrix of parameters of the indicated potentials. The results of calculations were compared with the corresponding reference data obtained earlier for the CH4-N2 gas mixture.
NASA Astrophysics Data System (ADS)
Desgranges, Caroline; Huber, Landon; Delhommelle, Jerome
2016-07-01
We determine the impact of the Friedel oscillations on the phase behavior, critical properties, and thermodynamic contours in films [two dimensions (2 D )] and bulk phases [three dimensions (3 D )]. Using expanded Wang-Landau simulations, we calculate the grand-canonical partition function and, in turn, the thermodynamic properties of systems modeled with a linear combination of the Lennard-Jones and Dzugutov potentials, weighted by a parameter X (0
Can we approach the gas-liquid critical point using slab simulations of two coexisting phases?
NASA Astrophysics Data System (ADS)
Goujon, Florent; Ghoufi, Aziz; Malfreyt, Patrice; Tildesley, Dominic J.
2016-09-01
In this paper, we demonstrate that it is possible to approach the gas-liquid critical point of the Lennard-Jones fluid by performing simulations in a slab geometry using a cut-off potential. In the slab simulation geometry, it is essential to apply an accurate tail correction to the potential energy, applied during the course of the simulation, to study the properties of states close to the critical point. Using the Janeček slab-based method developed for two-phase Monte Carlo simulations [J. Janec̆ek, J. Chem. Phys. 131, 6264 (2006)], the coexisting densities and surface tension in the critical region are reported as a function of the cutoff distance in the intermolecular potential. The results obtained using slab simulations are compared with those obtained using grand canonical Monte Carlo simulations of isotropic systems and the finite-size scaling techniques. There is a good agreement between these two approaches. The two-phase simulations can be used in approaching the critical point for temperatures up to 0.97 TC ∗ (T∗ = 1.26). The critical-point exponents describing the dependence of the density, surface tension, and interfacial thickness on the temperature are calculated near the critical point.
Structure of a protein (H2AX): a comparative study with knowledge-based interactions
NASA Astrophysics Data System (ADS)
Fritsche, Miriam; Heermann, Dieter; Farmer, Barry; Pandey, Ras
2013-03-01
The structural and conformational properties of the histone protein H2AX (with143 residues) is studied by a coarse-grained model as a function of temperature (T). Three knowledge-based phenomenological interactions (MJ, BT, and BFKV) are used as input to a generalized Lennard-Jones potential for residue-residue interactions. Large-scale Monte Carlo simulations are performed to identify similarity and differences in the equilibrium structures with these potentials. Multi-scale structures of the protein are examined by a detailed analysis of their structure functions. We find that the radius of gyration (Rg) of H2AX depends non-monotonically on temperature with a maximum at a characteristic value Tc, a common feature to each interaction. The characteristic temperature and the range of non-monotonic thermal response and decay pattern are, however, sensitive to interactions. A comparison of the structural properties emerging from three potentials will be presented in this talk. This work is supported by Air Force Research Laboratory.
Neumann, Martin; Zoppi, Marco
2002-03-01
We have performed extensive path integral Monte Carlo simulations of liquid and solid neon, in order to derive the kinetic energy as well as the single-particle and pair distribution functions of neon atoms in the condensed phases. From the single-particle distribution function n(r) one can derive the momentum distribution and thus obtain an independent estimate of the kinetic energy. The simulations have been carried out using mostly the semiempirical HFD-C2 pair potential by Aziz et al. [R. A. Aziz, W. J. Meath, and A. R. Allnatt, Chem. Phys. 79, 295 (1983)], but, in a few cases, we have also used the Lennard-Jones potential. The differences between the potentials, as measured by the properties investigated, are not very large, especially when compared with the actual precision of the experimental data. The simulation results have been compared with all the experimental information that is available from neutron scattering. The overall agreement with the experiments is very good.
Carbyne fiber synthesis within evaporating metallic liquid carbon
Cannella, Christopher B.; Goldman, Nir
2015-07-09
Carbyne (e.g., linear chains of sp-bonded carbon) has been the subject of intense research focus due to its presence in astrophysical bodies, as well as its potential for use as a nanoelectronic device and superhard material. In this work, we discuss the formation of carbyne fiber bundles over a nanosecond time scale in laser pulse melting studies, using a previously determined density functional tight binding model for carbon coupled with a new correction for the dispersion energy. We determine our dispersion energy model by optimizing a modified Lennard-Jones potential to an experimentally determined equation of state for graphite, yielding excellent results for the bulk modulus and density under ambient conditions. We then simulate previous experiments by heating graphite to high temperature, followed by expanding the ensuing liquid phase to low density. Our results indicate that the initial, hot liquid phase mainly consists of sp2-bonded carbon atoms, which form a system of sp-bonded strands bound together via dispersion interactions upon achieving low density and temperature. Lastly, the high computational efficiency of our approach allows for direct comparison with experiments that span a wide range of thermodynamic conditions and can help determine parameters for synthesis of carbon-based materials with potentially exotic properties.
Carbyne fiber synthesis within evaporating metallic liquid carbon
Cannella, Christopher B.; Goldman, Nir
2015-07-09
Carbyne (e.g., linear chains of sp-bonded carbon) has been the subject of intense research focus due to its presence in astrophysical bodies, as well as its potential for use as a nanoelectronic device and superhard material. In this work, we discuss the formation of carbyne fiber bundles over a nanosecond time scale in laser pulse melting studies, using a previously determined density functional tight binding model for carbon coupled with a new correction for the dispersion energy. We determine our dispersion energy model by optimizing a modified Lennard-Jones potential to an experimentally determined equation of state for graphite, yielding excellentmore » results for the bulk modulus and density under ambient conditions. We then simulate previous experiments by heating graphite to high temperature, followed by expanding the ensuing liquid phase to low density. Our results indicate that the initial, hot liquid phase mainly consists of sp2-bonded carbon atoms, which form a system of sp-bonded strands bound together via dispersion interactions upon achieving low density and temperature. Lastly, the high computational efficiency of our approach allows for direct comparison with experiments that span a wide range of thermodynamic conditions and can help determine parameters for synthesis of carbon-based materials with potentially exotic properties.« less
2012-01-01
Comparisons are made among Molecular Dynamics (MD), Classical Density Functional Theory (c-DFT), and Poisson–Boltzmann (PB) modeling of the electric double layer (EDL) for the nonprimitive three component model (3CM) in which the two ion species and solvent molecules are all of finite size. Unlike previous comparisons between c-DFT and Monte Carlo (MC), the present 3CM incorporates Lennard-Jones interactions rather than hard-sphere and hard-wall repulsions. c-DFT and MD results are compared over normalized surface charges ranging from 0.2 to 1.75 and bulk ion concentrations from 10 mM to 1 M. Agreement between the two, assessed by electric surface potential and ion density profiles, is found to be quite good. Wall potentials predicted by PB begin to depart significantly from c-DFT and MD for charge densities exceeding 0.3. Successive layers are observed to charge in a sequential manner such that the solvent becomes fully excluded from each layer before the onset of the next layer. Ultimately, this layer filling phenomenon results in fluid structures, Debye lengths, and electric surface potentials vastly different from the classical PB predictions. PMID:23316120
Properties of solvate shells and the mobility of ions, according to molecular dynamics data
NASA Astrophysics Data System (ADS)
Lankin, A. V.; Norman, G. E.; Orekhov, M. A.
2016-05-01
The solvate shells of an ion, its velocity autocorrelation function, and diffusion coefficient D are found, and the interrelations between them are analyzed. A single ion in the system of atoms of a liquid is considered a model system. The interaction between the ion and atoms of the liquid is described by polarization potential U( r); the interaction between atoms of the liquid alone is described by the Lennard-Jones potential. A classical molecular dynamics method is used. Five solvate shells around the ion are found, and the lifetimes of atoms on each shell are calculated. It is found that the velocity autocorrelation function is of a vibrating nature. The spectrum of the autocorrelator and the frequency of cluster vibrations in a linear approximation are compared. Dependences D on parameters of potential U( r) are found. No dependence D on the ion mass is found; this is explained by solvation. The Einstein-Stokes formula and the HSK approximation are used in discussing the results. It is shown that at small radii of the ion, dependence D on parameters U( r) is described by such a model. When the ion radius is increased, the deviation from this dependence and an increase in D are observed. The results are compared to experimental mobilities of O 2 - and Ar 2 + ions in liquid argon.
Ustinov, E A
2015-02-21
This paper presents a refined technique to describe two-dimensional phase transitions in dense fluids adsorbed on a crystalline surface. Prediction of parameters of 2D liquid-solid equilibrium is known to be an extremely challenging problem, which is mainly due to a small difference in thermodynamic functions of coexisting phases and lack of accuracy of numerical experiments in case of their high density. This is a serious limitation of various attempts to circumvent this problem. To improve this situation, a new methodology based on the kinetic Monte Carlo method was applied. The methodology involves analysis of equilibrium gas-liquid and gas-solid systems undergoing an external potential, which allows gradual shifting parameters of the phase coexistence. The interrelation of the chemical potential and tangential pressure for each system is then treated with the Gibbs-Duhem equation to obtain the point of intersection corresponding to the liquid/solid-solid equilibrium coexistence. The methodology is demonstrated on the krypton-graphite system below and above the 2D critical temperature. Using experimental data on the liquid-solid and the commensurate-incommensurate transitions in the krypton monolayer derived from adsorption isotherms, the Kr-graphite Lennard-Jones parameters have been corrected resulting in a higher periodic potential modulation. PMID:25702018
Strain-rate dependent shear viscosity of the Gaussian core model fluid.
Ahmed, Alauddin; Mausbach, Peter; Sadus, Richard J
2009-12-14
Nonequilibrium molecular dynamics simulations are reported for the shear viscosity of the Gaussian core model (GCM) fluid over a wide range of densities, temperatures and strain rates. A transition from Newtonian and non-Newtonian behavior is observed in all cases for sufficiently high strain rates. On the high-density side of the solid region where re-entrant melting occurs, the shear viscosity decreases significantly when the density is increased at constant temperature and Newtonian behavior persists until very high strain rates. This behavior, which is attributed to particle overlap, is in contrast to the monotonic increase in shear viscosity with density observed for the Lennard-Jones potential. Contrary to the behavior of normal fluids, the viscosity is observed to increase with increasing temperatures at high densities. This reflects a peculiarity of the GCM, namely the approach to the "infinite-density ideal-gas limit." The behavior is also consistent with viscosity measurements of cationic surfactant solutions. In contrast to other potentials, the shear viscosities for the Gaussian core potential at low to moderate strain rates are obtained with modest statistical uncertainties. Zero shear viscosities extrapolated from the nonequilibrium simulations are in good agreement with equilibrium Green-Kubo calculations.
Desgranges, Caroline; Huber, Landon; Delhommelle, Jerome
2016-07-01
We determine the impact of the Friedel oscillations on the phase behavior, critical properties, and thermodynamic contours in films [two dimensions (2D)] and bulk phases [three dimensions (3D)]. Using expanded Wang-Landau simulations, we calculate the grand-canonical partition function and, in turn, the thermodynamic properties of systems modeled with a linear combination of the Lennard-Jones and Dzugutov potentials, weighted by a parameter X (0
Modelling of 'sub-atomic' contrast resulting from back-bonding on Si(111)-7×7.
Sweetman, Adam; Jarvis, Samuel P; Rashid, Mohammad A
2016-01-01
It has recently been shown that 'sub-atomic' contrast can be observed during NC-AFM imaging of the Si(111)-7×7 substrate with a passivated tip, resulting in triangular shaped atoms [Sweetman et al. Nano Lett. 2014, 14, 2265]. The symmetry of the features, and the well-established nature of the dangling bond structure of the silicon adatom means that in this instance the contrast cannot arise from the orbital structure of the atoms, and it was suggested by simple symmetry arguments that the contrast could only arise from the backbonding symmetry of the surface adatoms. However, no modelling of the system has been performed in order to understand the precise origin of the contrast. In this paper we provide a detailed explanation for 'sub-atomic' contrast observed on Si(111)-7×7 using a simple model based on Lennard-Jones potentials, coupled with a flexible tip, as proposed by Hapala et al. [Phys. Rev. B 2014, 90, 085421] in the context of interpreting sub-molecular contrast. Our results show a striking similarity to experimental results, and demonstrate how 'sub-atomic' contrast can arise from a flexible tip exploring an asymmetric potential created due to the positioning of the surrounding surface atoms.
Chemical Dynamics Simulations of Intermolecular Energy Transfer: Azulene + N2 Collisions.
Kim, Hyunsik; Paul, Amit K; Pratihar, Subha; Hase, William L
2016-07-14
Chemical dynamics simulations were performed to investigate collisional energy transfer from highly vibrationally excited azulene (Az*) in a N2 bath. The intermolecular potential between Az and N2, used for the simulations, was determined from MP2/6-31+G* ab initio calculations. Az* is prepared with an 87.5 kcal/mol excitation energy by using quantum microcanonical sampling, including its 95.7 kcal/mol zero-point energy. The average energy of Az* versus time, obtained from the simulations, shows different rates of Az* deactivation depending on the N2 bath density. Using the N2 bath density and Lennard-Jones collision number, the average energy transfer per collision ⟨ΔEc⟩ was obtained for Az* as it is collisionally relaxed. By comparing ⟨ΔEc⟩ versus the bath density, the single collision limiting density was found for energy transfer. The resulting ⟨ΔEc⟩, for an 87.5 kcal/mol excitation energy, is 0.30 ± 0.01 and 0.32 ± 0.01 kcal/mol for harmonic and anharmonic Az potentials, respectively. For comparison, the experimental value is 0.57 ± 0.11 kcal/mol. During Az* relaxation there is no appreciable energy transfer to Az translation and rotation, and the energy transfer is to the N2 bath. PMID:27182630
Dib, R F A; Ould-Kaddour, F; Levesque, D
2006-07-01
Numerous theoretical and numerical works have been devoted to the study of the algebraic decrease at large times of the velocity autocorrelation function of particles in a fluid. The derivation of this behavior, the so-called long-time tail, generally based on linearized hydrodynamics, makes no reference to any specific characteristic of the particle interactions. However, in the literature doubts have been expressed about the possibility that by numerical simulations the long-time tail can be observed in the whole fluid phase domain of systems in which the particles interact by soft-core and attractive pair potentials. In this work, extensive and accurate molecular-dynamics simulations establish that the predicted long-time tail of the velocity autocorrelation function exists in a low-density fluid of particles interacting by a soft-repulsive potential and near the liquid-gas critical point of a Lennard-Jones system. These results contribute to the confirmation that the algebraic decay of the velocity autocorrelation function is universal in these fluid systems.
NASA Astrophysics Data System (ADS)
Espinosa, J. R.; Vega, C.; Sanz, E.
2014-10-01
The interfacial free energy between a crystal and a fluid, γcf, is a highly relevant parameter in phenomena such as wetting or crystal nucleation and growth. Due to the difficulty of measuring γcf experimentally, computer simulations are often used to study the crystal-fluid interface. Here, we present a novel simulation methodology for the calculation of γcf. The methodology consists in using a mold composed of potential energy wells to induce the formation of a crystal slab in the fluid at coexistence conditions. This induction is done along a reversible pathway along which the free energy difference between the initial and the final states is obtained by means of thermodynamic integration. The structure of the mold is given by that of the crystal lattice planes, which allows to easily obtain the free energy for different crystal orientations. The method is validated by calculating γcf for previously studied systems, namely, the hard spheres and the Lennard-Jones systems. Our results for the latter show that the method is accurate enough to deal with the anisotropy of γcf with respect to the crystal orientation. We also calculate γcf for a recently proposed continuous version of the hard sphere potential and obtain the same γcf as for the pure hard sphere system. The method can be implemented both in Monte Carlo and Molecular Dynamics. In fact, we show that it can be easily used in combination with the popular Molecular Dynamics package GROMACS.
New contact measures for the protein docking problem
Lenhof, H.P.
1997-12-01
We have developed and implemented a parallel distributed algorithm for the rigid-body protein docking problem. The algorithm is based on a new fitness function for evaluating the surface matching of a given conformation. The fitness function is defined as the weighted sum of two contact measures, the geometric contact measure and the chemical contact measure. The geometric contact measure measures the {open_quotes}size{close_quotes} of the contact area of two molecules. It is a potential function that counts the {open_quotes}van der Waals contacts{close_quotes} between the atoms of the two molecules (the algorithm does not compute the Lennard-Jones potential). The chemical contact measure is also based on the {open_quotes}van der Waals contacts{close_quotes} principle: We consider all atoms pairs that have a {open_quotes}van der Waals{close_quotes} contact, but instead of adding a constant for each pair (a, b), we add a {open_quotes}chemical weight{close_quotes} that depends on the atom pair (a, b). We tested our docking algorithm with a test set that contains the test examples of Norel et al. and Fischer et al. and compared the results of our docking algorithm with the results of Norel et al., Fischer et al. and Meyer et al. In 32 of 35 test examples the best conformation with respect to the fitness function was an approximation of the real conformation. 37 refs., 6 figs., 4 tabs.
Modelling of ‘sub-atomic’ contrast resulting from back-bonding on Si(111)-7×7
Jarvis, Samuel P; Rashid, Mohammad A
2016-01-01
Summary It has recently been shown that ‘sub-atomic’ contrast can be observed during NC-AFM imaging of the Si(111)-7×7 substrate with a passivated tip, resulting in triangular shaped atoms [Sweetman et al. Nano Lett. 2014, 14, 2265]. The symmetry of the features, and the well-established nature of the dangling bond structure of the silicon adatom means that in this instance the contrast cannot arise from the orbital structure of the atoms, and it was suggested by simple symmetry arguments that the contrast could only arise from the backbonding symmetry of the surface adatoms. However, no modelling of the system has been performed in order to understand the precise origin of the contrast. In this paper we provide a detailed explanation for ‘sub-atomic’ contrast observed on Si(111)-7×7 using a simple model based on Lennard-Jones potentials, coupled with a flexible tip, as proposed by Hapala et al. [Phys. Rev. B 2014, 90, 085421] in the context of interpreting sub-molecular contrast. Our results show a striking similarity to experimental results, and demonstrate how ‘sub-atomic’ contrast can arise from a flexible tip exploring an asymmetric potential created due to the positioning of the surrounding surface atoms. PMID:27547610
Computer simulation of the mechanical properties of metamaterials
NASA Astrophysics Data System (ADS)
Gerasimov, R. A.; Eremeyev, V. A.; Petrova, T. O.; Egorov, V. I.; Maksimova, O. G.; Maksimov, A. V.
2016-08-01
For a hybrid discrete-continual model describing a system which consists of a substrate and polymer coating, we provide computer simulation of its mechanical properties for various levels of deformations. For the substrate, we apply the elastic model with the Hooke law while for the polymeric coating, we use a discrete model. Here we use the Stockmayer potential which is a Lennard-Jones potential with additional term which describes the dipole interactions between neighbour segments of polymer chains, that is Keesom energy. Using Monte-Carlo method with Metropolis algorithm for a given temperature the equilibrium state is determined. We obtain dependencies of the energy, force, bending moment and Young's modulus for various levels of deformations and for different values of temperature. We show that for the increase of the deformations level the influence of surface coating on the considered material parameters is less pronounced. We provide comparison of obtained results with experimental data on deformations of crystalline polymers (gutta-percha, etc.)
Trajectory study of supercollision relaxation in highly vibrationally excited pyrazine and CO2.
Li, Ziman; Sansom, Rebecca; Bonella, Sara; Coker, David F; Mullin, Amy S
2005-09-01
Classical trajectory calculations were performed to simulate state-resolved energy transfer experiments of highly vibrationally excited pyrazine (E(vib) = 37,900 cm(-1)) and CO(2), which were conducted using a high-resolution transient infrared absorption spectrometer. The goal here is to use classical trajectories to simulate the supercollision energy transfer pathway wherein large amounts of energy are transferred in single collisions in order to compare with experimental results. In the trajectory calculations, Newton's laws of motion are used for the molecular motion, isolated molecules are treated as collections of harmonic oscillators, and intermolecular potentials are formed by pairwise Lennard-Jones potentials. The calculations qualitatively reproduce the observed energy partitioning in the scattered CO(2) molecules and show that the relative partitioning between bath rotation and translation is dependent on the moment of inertia of the bath molecule. The simulations show that the low-frequency modes of the vibrationally excited pyrazine contribute most to the strong collisions. The majority of collisions lead to small DeltaE values and primarily involve single encounters between the energy donor and acceptor. The large DeltaE exchanges result from both single impulsive encounters and chattering collisions that involve multiple encounters.
Sum Rule Constraints and the Quality of Approximate Kubo-Transformed Correlation Functions.
Hernández de la Peña, Lisandro
2016-02-11
In this work, a general protocol for evaluating the quality of approximate Kubo correlation functions of nontrivial systems in many dimensions is discussed. We first note that the generalized deconvolution of the Kubo transformed correlation function onto a time correlation function at a given value τ in imaginary time, such that 0 < τ < βℏ, leads to a series of sum rules applicable to the nth derivative of the Kubo function and whose iterative extension allows us to link derivatives of different order in the corresponding correlation functions. We focus on the case when τ = βℏ/2, for which all deconvolution kernels become real valued functions and their asymptotic behavior at long times exhibits a polynomial divergence. It is then shown that thermally symmetrized static averages, and the averages of the corresponding time derivatives, are ideally suited to investigate the quality of approximate Kubo correlation functions at successively larger (and up to arbitrarily long) times. This overall strategy is illustrated analytically for a harmonic system and numerically for a multidimensional double-well potential and a Lennard-Jones fluid. The analysis includes an assessment of RPMD position autocorrelation results as a function of the number of dimensions in a double-well potential and of the RPMD velocity autocorrelation function of liquid neon at 30 K.
Lattice thermal conductivity of multi-component alloys
Caro, Magdalena; Béland, Laurent K.; Samolyuk, German D.; Stoller, Roger E.; Caro, Alfredo
2015-06-12
High entropy alloys (HEA) have unique properties including the potential to be radiation tolerant. These materials with extreme disorder could resist damage because disorder, stabilized by entropy, is the equilibrium thermodynamic state. Disorder also reduces electron and phonon conductivity keeping the damage energy longer at the deposition locations, eventually favoring defect recombination. In the short time-scales related to thermal spikes induced by collision cascades, phonons become the relevant energy carrier. In this paper, we perform a systematic study of phonon thermal conductivity in multiple component solid solutions represented by Lennard-Jones (LJ) potentials. We explore the conditions that minimize phonon mean free path via extreme alloy complexity, by varying the composition and the elements (differing in mass, atomic radii, and cohesive energy). We show that alloy complexity can be tailored to modify the scattering mechanisms that control energy transport in the phonon subsystem. Finally, our analysis provides a qualitative guidance for the selection criteria used in the design of HEA alloys with low phonon thermal conductivity.
NASA Astrophysics Data System (ADS)
Keten, Sinan; Xia, Wenjie; Hsu, David
2015-03-01
We present a systematic, two-bead per monomer coarse graining strategy that simulates the thermomechanical behavior of polymers several hundred times faster than all-atom MD (Hsu et al. JCTC, 2014). The predictive capability of the technique is illustrated here for 5 different methacrylate monomers and polystyrene stereoisomers. The approach involves optimization of analytical bonded potentials from atomistic bonded distributions to emulate local structure, as validated by chain end-to-end length and the radius of gyration comparisons with experiments and random coil theory. Nonbonded Lennard-Jones potentials are tuned to reproduce the elastic modulus (E) and glass transition temperature (Tg) at a single thermodynamic state. Density-corrected parameters capture temperature-modulus dependence in the 150-600 K range. Flory-Fox constants of the CG models are commensurate with all atomistic and experimental results, even though all calibrations are done at a single molecular weight. Finally, we further demonstrate the predictive capabilities of the models by examining thin film nanoconfinement effects for different polymers, film thicknesses, interfacial energies, and molecular weights. Our technique, called thermomechanically consistent coarse graining (TCCG), is demonstrated, using polystyrene and poly(methylmethacrylate) as universal benchmarks, to be a robust and effective technique to understand the thermomechanical behavior of polymers thin films and nanocomposites.
Diffusion coefficient of krypton atoms in helium gas at low and moderate temperatures
NASA Astrophysics Data System (ADS)
Bouazza, M. T.; Bouledroua, M.
In the present work, using the Chapman-Enskog method for dilute gases, the diffusion coefficients of ground krypton atoms in a very weakly ionized helium buffer gas are revisited. The calculations are carried out quantum mechanically in the range of low and moderate temperatures. The 1 Σ+ potential-energy curve via which Kr approaches He is constructed from the most recent ab initio energy points. The reliable data points used in the construction are smoothly connected to adequate long- and short-range forms. The calculations of the classical second virial coefficients and the Boyle temperature of the helium-krypton mixture are also discussed. These coefficients and their variations in terms of temperature are analysed by adopting the constructed HeKr potential and the Lennard-Jones form that fits it. The diffusion and elastic cross sections are also explored and the resonance features they exhibit are closely examined. The variation law of the diffusion coefficients with temperature is determined for typical values of density and pressure. The coefficients show excellent agreement with the available experimental data; the discrepancies do not exceed 5%.
Lattice thermal conductivity of multi-component alloys
Caro, Magdalena; Béland, Laurent K.; Samolyuk, German D.; Stoller, Roger E.; Caro, Alfredo
2015-06-12
High entropy alloys (HEA) have unique properties including the potential to be radiation tolerant. These materials with extreme disorder could resist damage because disorder, stabilized by entropy, is the equilibrium thermodynamic state. Disorder also reduces electron and phonon conductivity keeping the damage energy longer at the deposition locations, eventually favoring defect recombination. In the short time-scales related to thermal spikes induced by collision cascades, phonons become the relevant energy carrier. In this paper, we perform a systematic study of phonon thermal conductivity in multiple component solid solutions represented by Lennard-Jones (LJ) potentials. We explore the conditions that minimize phonon meanmore » free path via extreme alloy complexity, by varying the composition and the elements (differing in mass, atomic radii, and cohesive energy). We show that alloy complexity can be tailored to modify the scattering mechanisms that control energy transport in the phonon subsystem. Finally, our analysis provides a qualitative guidance for the selection criteria used in the design of HEA alloys with low phonon thermal conductivity.« less
Density Functional Approximation for Non-Hard Sphere Fluids Subjected to External Fields
NASA Astrophysics Data System (ADS)
Zhou, Shiqi
A theoretical way is proposed, by which any hard sphere density functional approximation (DFA) can be applied to non-hard sphere fluids for the calculation of density profile in the framework of density functional theory (DFT). Used as examples, the present formalism is combined respectively with two recently proposed hard sphere DFAs to predict the density profile of Lennard-Jones (LJ) fluid, hard core square well (SW) fluid and penetrable potenial fluid subjected to diverse external fields. Extensive comparison between theoretical predictions and corresponding simulation results shows that the present theoretical way, when combined with an accurate hard sphere DFA, can perform well for calculating the density profile of the non-uniform fluids of the above mentioned potentials. Concretely speaking, for LJ and hard core SW fluid, even a less accurate FEDFA is sufficient, while for extreme potential such as the penetrable potenial, a more accurate adjustable parameter free version of LTDFA is needed to combine with the present theoretical way to predict density profile satisfactorily. The advantage of the proposed theoretical way is that the resultant DFA is applicable to both subcritical and supercritical temperature cases, thereby overcoming the disadvantages of previous two categories of DFT approach.
Attenuation of shock waves propagating through nano-structured porous materials
NASA Astrophysics Data System (ADS)
Al-Qananwah, Ahmad K.; Koplik, Joel; Andreopoulos, Yiannis
2013-07-01
Porous materials have long been known to be effective in energy absorption and shock wave attenuation. These properties make them attractive in blast mitigation strategies. Nano-structured materials have an even greater potential for blast mitigation because of their high surface-to-volume ratio, a geometric parameter which substantially attenuates shock wave propagation. A molecular dynamics approach was used to explore the effects of this remarkable property on the behavior of traveling shocks impacting on solid materials. The computational setup included a moving piston, a gas region and a target solid wall with and without a porous structure. The gas and porous solid were modeled by Lennard-Jones-like and effective atom potentials, respectively. The shock wave is resolved in space and time and its reflection from a solid wall is gradual, due to the wave's finite thickness, and entails a self-interaction as the reflected wave travels through the incoming incident wave. Cases investigated include a free standing porous structure, a porous structure attached to a wall and porous structures with graded porosity. The effects of pore shape and orientation have been also documented. The results indicate that placing a nano-porous material layer in front of the target wall reduced the stress magnitude and the energy deposited inside the solid by about 30 percent, while at the same time substantially decreasing the loading rate.
Fröhlich, Markus G; Sewell, Thomas D; Thompson, Donald L
2014-01-14
The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s(-1), yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ∼0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude. PMID:24437906
NASA Astrophysics Data System (ADS)
Fröhlich, Markus G.; Sewell, Thomas D.; Thompson, Donald L.
2014-01-01
The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s-1, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ˜0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.
Fröhlich, Markus G. E-mail: ThompsonDon@missouri.edu; Sewell, Thomas D. Thompson, Donald L. E-mail: ThompsonDon@missouri.edu
2014-01-14
The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s{sup −1}, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ∼0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.
Modelling of 'sub-atomic' contrast resulting from back-bonding on Si(111)-7×7.
Sweetman, Adam; Jarvis, Samuel P; Rashid, Mohammad A
2016-01-01
It has recently been shown that 'sub-atomic' contrast can be observed during NC-AFM imaging of the Si(111)-7×7 substrate with a passivated tip, resulting in triangular shaped atoms [Sweetman et al. Nano Lett. 2014, 14, 2265]. The symmetry of the features, and the well-established nature of the dangling bond structure of the silicon adatom means that in this instance the contrast cannot arise from the orbital structure of the atoms, and it was suggested by simple symmetry arguments that the contrast could only arise from the backbonding symmetry of the surface adatoms. However, no modelling of the system has been performed in order to understand the precise origin of the contrast. In this paper we provide a detailed explanation for 'sub-atomic' contrast observed on Si(111)-7×7 using a simple model based on Lennard-Jones potentials, coupled with a flexible tip, as proposed by Hapala et al. [Phys. Rev. B 2014, 90, 085421] in the context of interpreting sub-molecular contrast. Our results show a striking similarity to experimental results, and demonstrate how 'sub-atomic' contrast can arise from a flexible tip exploring an asymmetric potential created due to the positioning of the surrounding surface atoms. PMID:27547610