Search

In this work we compare lattice and continuum versions of the same theory, as derived in the previous paper (Paper I), to predict the behavior of simple alkane mixtures. In the course of doing this we use characteristic parameters obtained for the pure alkane fluids; no fits of mixture properties are involved. Our two sets of predictions are tested against experimental data and against new Monte Carlo simulation results. The experimental properties of interest include mixed pressure-volume-temperature surfaces, as well as a variety of coexistence diagrams characterizing mixed system liquid-vapor equilibria. We contrast the performance of the lattice and continuum approaches and discuss the results in the context of underlying model approximations as derived in Paper I. [ABSTRACT FROM AUTHOR]

Electrochemical impedance spectroscopy (EIS) is a powerful characterization technique for the in-depth investigation of kinetic/transport parameters detection, reaction mechanism understanding, and degradation effects exploration in lithium-ion battery (LIB) systems. However, due to the lack of standardized criterion/paradigm, severe misinterpretations occur frequently during an EIS measurement. In this paper, the significance of instrumental accuracy is described and the character/principle of selection on the simulation model is illuminated/proposed, showing that an adequate precision device and an appropriate fitting model are a prerequisite for a correct EIS analysis. Moreover, the drawbacks of conventional two-electrode EIS experiments for typical coin-type cells are rigorously pointed out by comparison with the ideal three-electrode configuration, where the real impedance information of the cathode would be masked by the sum of both the anode film resistance response and the unavoidable inductive loop signal. The three-electrode case enables efficient accurate observations on individual electrodes, thus facilitating abundant and useful information acquisition. Consequently, devices with a sufficient accuracy, rational simulation models, and advanced three-electrode cells are distinctly illustrated as standardized criterion/paradigm for EIS characterizations, which are essentially important for electrode and interface modifications in LIBs. [ABSTRACT FROM AUTHOR]

This series of papers is devoted to identifying and explaining the properties of strongly correlating liquids, i.e., liquids with more than 90% correlation between their virial W and potential energy U fluctuations in the NVT ensemble. Paper IV [N. Gnan et al., J. Chem. Phys. 131, 234504 (2009)] showed that strongly correlating liquids have 'isomorphs,' which are curves in the phase diagram along which structure, dynamics, and some thermodynamic properties are invariant in reduced units. In the present paper, using the fact that reduced-unit radial distribution functions are isomorph invariant, we derive an expression for the shapes of isomorphs in the WU phase diagram of generalized Lennard-Jones systems of one or more types of particles. The isomorph shape depends only on the Lennard-Jones exponents; thus all isomorphs of standard Lennard-Jones systems (with exponents 12 and 6) can be scaled onto a single curve. Two applications are given. One tests the prediction that the solid-liquid coexistence curve follows an isomorph by comparing to recent simulations by Ahmed and Sadus [J. Chem. Phys. 131, 174504 (2009)]. Excellent agreement is found on the liquid side of the coexistence curve, whereas the agreement is less convincing on the solid side. A second application is the derivation of an approximate equation of state for generalized Lennard-Jones systems by combining the isomorph theory with the Rosenfeld-Tarazona expression for the temperature dependence of the potential energy on isochores. It is shown that the new equation of state agrees well with simulations. [ABSTRACT FROM AUTHOR]

In this paper we present a simulation study of water-like anomalies in core-softened system introduced in our previous papers. We investigate the anomalous regions for a system with the same functional form of the potential but with different parameters and show that the order of the region of anomalous diffusion and the region of density anomaly is inverted with increasing the width of the repulsive shoulder. [ABSTRACT FROM AUTHOR]

A new method of the stochastic simulation algorithm (SSA), named the Hashing-Leaping method (HLM), for exact simulations of a class of Markov jump processes, is presented in this paper. The HLM has a conditional constant computational cost per event, which is independent of the number of exponential clocks in the Markov process. The main idea of the HLM is to repeatedly implement a hash-table-like bucket sort algorithm for all times of occurrence covered by a time step with length t. This paper serves as an introduction to this new SSA method. We introduce the method, demonstrate its implementation, analyze its properties, and compare its performance with three other commonly used SSA methods in four examples. Our performance tests and CPU operation statistics show certain advantages of the HLM for large scale problems. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems, however, create the need for approximations to the standard MD methods and for uncertainty quantification and reliability assessment of those approximations. In this paper, we exploit the intrinsic two-scale nature ofMDto construct a class of large-scale dynamics approximations. The reliability of these methods is evaluated here by measuring the differences between full, classical MD simulations and those based on these large-scale approximations. Molecular dynamics evolutions are non-linear and chaotic, so the complete details of molecular evolutions cannot be accurately predicted even using full, classical MD simulations. This paper provides numerical results that demonstrate the existence of computationally efficient large-scale MD approximations which accurately model certain large-scale properties of the molecules: the energy, the linear and angular momenta, and other macroscopic features of molecular motions. [ABSTRACT FROM AUTHOR]

A diagrammatic kinetic theory of density fluctuations in simple dense liquids at long times, described in Paper I, is applied to a high density Lennard-Jones liquid to calculate various equilibrium time correlation functions. The calculation starts from the general theory and makes two approximations. (1) The general diagrammatic expression for an irreducible memory kernel is approximated using a one-loop approximation. (2) The generalized Enskog projected propagator, which is required for the calculation, is approximated using a simple kinetic model for the hard sphere memory function. The coherent intermediate scattering function (CISF), the longitudinal current correlation function (LCCF), the transverse current correlation function (TCCF), the incoherent intermediate scattering function (IISF), and the incoherent longitudinal current correlation function are calculated and compared with simulation results for the Lennard-Jones liquid at high density. The approximate theoretical results are in good agreement with the simulation data for the IISF for all wave vectors studied and for the CISF and LCCF for large wave vector. The approximate results are in poor agreement with the simulation data for the CISF, LCCF, and TCCF for small wave vectors because these functions are strongly affected by hydrodynamic fluctuations at small wave vector that are not well described by the simple kinetic model used. The possible implications of this approach for the study of liquids are discussed. [ABSTRACT FROM AUTHOR]

Kramers [Physica 7, 284 (1940)], in his seminal paper, derived expressions for the rate of crossing a barrier in the underdamped limit of weak friction and the moderate to strong friction limit. The challenge of obtaining a uniform expression for the rate, valid for all damping strengths is known as Kramers turnover theory. Two different solutions have been presented. Mel'nikov and Meshkov [J. Chem. Phys. 85, 1018 (1986)] (MM) considered the motion of the particle, treating the friction as a perturbation parameter. Pollak, Grabert, and Hänggi [J. Chem. Phys. 91, 4073 (1989)] (PGH), considered the motion along the unstable mode which is separable from the bath in the barrier region. In practice, the two theories differ in the way an energy loss parameter is estimated. In this paper, we show that previous numerical attempts to resolve the quality of the two approaches were incomplete and that at least for a cubic potential with Ohmic friction, the quality of agreement of both expressions with numerical simulation is similar over a large range of friction strengths and temperatures. Mel'nikov [Phys. Rev. E 48, 3271 (1993)], in a later paper, improved his theory by introducing finite barrier corrections. In this paper we note that previous numerical tests of the finite barrier corrections were also incomplete. They did not employ the exact rate expression, but a harmonic approximation to it. The central part of this paper, is to include finite barrier corrections also within the PGH formalism. Tests on a cubic potential demonstrate that finite barrier corrections significantly improve the agreement of both MM and PGH theories when compared with numerical simulations. [ABSTRACT FROM AUTHOR]

In this second paper we exploit our thermodynamic partitioning cellular automaton (PCA) developed in Paper I [Pazzona et al., J. Chem. Phys. 131, 234703 (2009)] to study interacting molecules adsorbed in microporous materials. We present a mean-field theory of the single cell model at equilibrium followed by a detailed description of the procedure we propose to calculate the chemical potential in the canonical ensemble. Finally we use our approach to simulate transport properties starting from the parameterization devised by Ayappa [J. Chem. Phys. 111, 4736 (1999)] to reproduce the adsorption properties of xenon in zeolite NaA. We report how the correlations included in the PCA evolution rule affect the estimated self-diffusion coefficient. [ABSTRACT FROM AUTHOR]

Water is the most common liquid on the Earth. At the same time, it is the strangest liquid having numerous anomalous properties. For this reason, although water was investigated in numerous studies, many questions still remain unanswered. Even the thermodynamic properties of water at high pressures are unknown. In this paper, we present an experimental study of the thermodynamic properties of water up to a pressure of 12 kbar and a temperature of 473 K far above the range of pressures and temperatures in previous studies. We compare the experimental results to the results of computer simulations of two models of water (SPC/E and TIP4P) and show that the SPC/E model is not appropriate at high pressure, while the TIP4P model describes the equation of state of water, but fails to describe the heat capacity. [ABSTRACT FROM AUTHOR]

In the preceding paper by Stork and Tavan, [J. Chem. Phys. 126, 165105 (2007)], the authors have reformulated an electrostatic theory which treats proteins surrounded by dielectric solvent continua and approximately solves the associated Poisson equation [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)]. The resulting solution comprises analytical expressions for the electrostatic reaction field (RF) and potential, which are generated within the protein by the polarization of the surrounding continuum. Here the field and potential are represented in terms of Gaussian RF dipole densities localized at the protein atoms. Quite like in a polarizable force field, also the RF dipole at a given protein atom is induced by the partial charges and RF dipoles at the other atoms. Based on the reformulated theory, the authors have suggested expressions for the RF forces, which obey Newton’s third law. Previous continuum approaches, which were also built on solutions of the Poisson equation, used to violate the reactio principle required by this law, and thus were inapplicable to molecular dynamics (MD) simulations. In this paper, the authors suggest a set of techniques by which one can surmount the few remaining hurdles still hampering the application of the theory to MD simulations of soluble proteins and peptides. These techniques comprise the treatment of the RF dipoles within an extended Lagrangian approach and the optimization of the atomic RF polarizabilities. Using the well-studied conformational dynamics of alanine dipeptide as the simplest example, the authors demonstrate the remarkable accuracy and efficiency of the resulting RF-MD approach. [ABSTRACT FROM AUTHOR]

We use the extension of scaled particle theory presented in the accompanying paper [F. H. Stillinger et al., J. Chem. Phys. 125, 204504 (2006)] to calculate numerically the pair correlation function of the hard sphere fluid over the density range 0≤=ρσ3≤=0.96. Comparison with computer simulation results reveals that the new theory is able to capture accurately the fluid’s structure across the entire density range examined. The pressure predicted via the virial route is systematically lower than simulation results, while that obtained using the compressibility route is lower than simulation predictions for ρσ3≤=0.67 and higher than simulation predictions for ρσ3>=0.67. Numerical predictions are also presented for the surface tension and Tolman length of the hard sphere fluid [ABSTRACT FROM AUTHOR]

In an extensive computer simulation study, the transport coefficients of the Lennard-Jones model fluid were determined with high accuracy from equilibrium molecular-dynamics simulations. In the frame of time-correlation function theory, the generalized Einstein relations were employed to evaluate the transport coefficients. This third of a series of four papers presents the results for the bulk viscosity. With comprehensive simulation data at over 350 state points, the temperature and density dependences of the bulk viscosity are characterized in this work over a wide range of fluid states. The bulk viscosity exhibits a large critical enhancement similar to that known for the thermal conductivity, but it extends much farther into the supercritical region and can be observed even at 4.5 times the critical temperature. An investigation of the pressure-fluctuation autocorrelation functions shows that the enhancement is caused by extremely slowly decaying pressure fluctuations.© 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

This work considers the method of uniformization for continuous-time Markov chains in the context of chemical reaction networks. Previous work in the literature has shown that uniformization can be beneficial in the context of time-inhomogeneous models, such as chemical reaction networks incorporating extrinsic noise. This paper lays focus on the understanding of uniformization from the viewpoint of sample paths of chemical reaction networks. In particular, an efficient pathwise stochastic simulation algorithm for time-homogeneous models is presented which is complexity-wise equal to Gillespie's direct method. This new approach therefore enlarges the class of problems for which the uniformization approach forms a computationally attractive choice. Furthermore, as a new application of the uniformization method, we provide a novel variance reduction method for (raw) moment estimators of chemical reaction networks based upon the combination of stratification and uniformization. [ABSTRACT FROM AUTHOR]

The Adaptive Two-Regime Method (ATRM) is developed for hybrid (multiscale) stochastic simulation of reaction-diffusion problems. It efficiently couples detailed Brownian dynamics simulations with coarser lattice-based models. The ATRM is a generalization of the previously developed Two-Regime Method [Flegg et al., J. R. Soc., Interface 9, 859 (2012)] to multiscale problems which require a dynamic selection of regions where detailed Brownian dynamics simulation is used. Typical applications include a front propagation or spatio-temporal oscillations. In this paper, the ATRM is used for an in-depth study of front propagation in a stochastic reaction-diffusion system which has its mean-field model given in terms of the Fisher equation [R. Fisher, Ann. Eugen. 7, 355 (1937)]. It exhibits a travelling reaction front which is sensitive to stochastic fluctuations at the leading edge of the wavefront. Previous studies into stochastic effects on the Fisher wave propagation speed have focused on lattice-based models, but there has been limited progress using off-lattice (Brownian dynamics) models, which suffer due to their high computational cost, particularly at the high molecular numbers that are necessary to approach the Fisher mean-field model. By modelling only the wavefront itself with the off-lattice model, it is shown that the ATRM leads to the same Fisher wave results as purely off-lattice models, but at a fraction of the computational cost. The error analysis of the ATRM is also presented for a morphogen gradient model. [ABSTRACT FROM AUTHOR]

This paper proposes combining non-Boltzmann sampling with free energy perturbation to allow calculations of the free energy of hydration of a solute with both solute-water and water-water interactions with the nearest waters calculated by high-level quantum models. The method involves simulation of an approximate model of all interactions and uses both free energy perturbation and non-Boltzmann sampling to calculate the difference in energy between the approximate and quantum models. [ABSTRACT FROM AUTHOR]

In this paper, we report results of using enhanced sampling and blind selection techniques for high-accuracy protein structural refinement. By combining a parallel continuous simulated tempering (PCST) method, previously developed by Zang et al. [J. Chem. Phys. 141, 044113 (2014)], and the structure based model (SBM) as restraints, we refined 23 targets (18 from the refinement category of the CASP10 and 5 from that of CASP12). We also designed a novel model selection method to blindly select high-quality models from very long simulation trajectories. The combined use of PCST-SBM with the blind selection method yielded final models that are better than initial models. For Top-1 group, 7 out of 23 targets had better models (greater global distance test total scores) than the critical assessment of structure prediction participants. For Top-5 group, 10 out of 23 were better. Our results justify the crucial position of enhanced sampling in protein structure prediction and refinement and demonstrate that a considerable improvement of low-accuracy structures is achievable with current force fields. [ABSTRACT FROM AUTHOR]

Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis.With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed. [ABSTRACT FROM AUTHOR]

The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian dynamics or Green's function reaction dynamics, the RDME can be orders of magnitude faster if the lattice spacing can be chosen coarse enough. However, strongly diffusion-controlled reactions mandate a very fine mesh resolution for acceptable accuracy. It is common that reactions in the same model differ in their degree of diffusion control and therefore require different degrees of mesh resolution. This renders mesoscopic simulation inefficient for systems with multiscale properties. Mesoscopic-microscopic hybrid methods address this problem by resolving the most challenging reactions with a microscale, off-lattice simulation. However, all methods to date require manual partitioning of a system, effectively limiting their usefulness as "black-box" simulation codes. In this paper, we propose a hybrid simulation algorithm with automatic system partitioning based on indirect a priori error estimates.We demonstrate the accuracy and efficiency of the method on models of diffusion-controlled networks in 3D. [ABSTRACT FROM AUTHOR]

We formulate and apply a non-replica equilibrium theory for the fluid-glass transition, glass thermodynamic properties, and jamming of hard spheres in three and all higher spatial dimensions. Numerical predictions for the zero complexity glass transition and jamming packing fractions, and a 'densest' equilibrium glass, are made. The equilibrium glass equation of state is regarded as the practical continuation of its fluid analog up to jamming. The analysis provides a possible resolution to the inability of any fluid virial series re-summation based equation of state to capture jamming at a reasonable volume fraction. The numerical results are quantitatively compared with various simulation data for equilibrium hard sphere glasses in 3 to 12 dimensions. Although there are uncertainties in this comparison, the predicted zero complexity or configurational entropy and corresponding jamming packing fractions do agree well with two characteristic packing fractions deduced from the dynamic simulation data. The similarities and differences of our approach compared to the replica approach are discussed. The high dimensional scaling of the equilibrium glass transition and jamming volume fractions are also derived. The developments in this paper serve as input to Paper II [R. Jadrich and K. S. Schweizer, J. Chem. Phys. 139, 054502 (2013)] that constructs a self-consistent integral equation theory of the 3-dimensional hard sphere pair structure, in real and Fourier space, in the metastable regime up to jamming. The latter is employed as input to a microscopic dynamical theory of single particle activated barrier hopping. [ABSTRACT FROM AUTHOR]

The electrochemical thermodynamics of electrolytes in porous electrodes is qualitatively different from that in the bulk with planar electrodes when the pore size is comparable to the size of the electrolyte ions. In this paper, we discuss the thermodynamics of a two component electrolyte in a porous electrode by using Monte Carlo simulation. We show that electrolyte ions are selectively adsorbed in porous electrodes and the relative concentration of the two components significantly changes as a function of the applied voltage and the pore size. This selectivity is observed not only for the counterions but also for the coions. [ABSTRACT FROM AUTHOR]

The representability and transferability of effective pair potentials used in multiscale simulations of soft matter systems is ill understood. In this paper, we study liquid state systems composed of n-alkanes, the coarse-grained (CG) potential of which may be assumed pairwise additive and has been obtained using the conditional reversible work (CRW) method. The CRW method is a free-energy-based coarse-graining procedure, which, by means of performing the coarse graining at pair level, rigorously provides a pair potential that describes the interaction free energy between two mapped atom groups (beads) embedded in their respective chemical environments. The pairwise nature of the interactions combined with their dependence on the chemically bonded environment makes CRW potentials ideally suited in studies of chemical transferability. We report CRW potentials for hexane using a mapping scheme that merges two heavy atoms in one CG bead. It is shown that the model is chemically and thermodynamically transferable to alkanes of different chain lengths in the liquid phase at temperatures between the melting and the boiling point under atmospheric (1 atm) pressure conditions. It is further shown that CRW-CG potentials may be readily obtained from a single simulation of the liquid state using the free energy perturbation method, thereby providing a fast and versatile molecular coarse graining method for aliphatic molecules. [ABSTRACT FROM AUTHOR]

In this paper we investigate the solubility of a hard-sphere gas in a solvent modeled as an associating lattice gas. The solution phase diagram for solute at 5% is compared with the phase diagram of the original solute free model. Model properties are investigated both through Monte Carlo simulations and a cluster approximation. The model solubility is computed via simulations and is shown to exhibit a minimum as a function of temperature. The line of minimum solubility (TmS) coincides with the line of maximum density (TMD) for different solvent chemical potentials, in accordance with the literature on continuous realistic models and on the 'cavity' picture. [ABSTRACT FROM AUTHOR]

The multiscale coarse-graining (MS-CG) method is a method for constructing a coarse-grained (CG) model of a system using data obtained from molecular dynamics simulations of the corresponding atomically detailed model. The formal statistical mechanical derivation of the method shows that the potential energy function extracted from an MS-CG calculation is a variational approximation for the true potential of mean force of the CG sites, one that becomes exact in the limit that a complete basis set is used in the variational calculation if enough data are obtained from the atomistic simulations. Most applications of the MS-CG method have employed a representation for the nonbonded part of the CG potential that is a sum of all possible pair interactions. This approach, despite being quite successful for some CG models, is inadequate for some others. Here we propose a systematic method for including three body terms as well as two body terms in the nonbonded part of the CG potential energy. The current method is more general than a previous version presented in a recent paper of this series [L. Larini, L. Lu, and G. A. Voth, J. Chem. Phys. 132, 164107 (2010)], in the sense that it does not make any restrictive choices for the functional form of the three body potential. We use hierarchical multiresolution functions that are similar to wavelets to develop very flexible basis function expansions with both two and three body basis functions. The variational problem is solved by a numerical technique that is capable of automatically selecting an appropriate subset of basis functions from a large initial set. We apply the method to two very different coarse-grained models: a solvent free model of a two component solution made of identical Lennard-Jones particles and a one site model of SPC/E water where a site is placed at the center of mass of each water molecule. These calculations show that the inclusion of three body terms in the nonbonded CG potential can lead to significant improvement in the accuracy of CG potentials and hence of CG simulations. [ABSTRACT FROM AUTHOR]

We investigate the vibrational shift of beryllium oxide (BeO) in Xe matrix as well as in Ar matrix environments by mixed quantum-classical simulation and examine the origin of spectral shift in details. BeO is known to form strong chemical complex with single rare gas atom, and it is predicted from the gas phase calculations that vibrational frequencies are blueshifted by 78 cm-1 and 80 cm-1 upon formation of XeBeO and ArBeO, respectively. When the effects of other surrounding rare gas atoms are included by Monte Carlo simulations, it is found that the vibrational frequencies are redshifted by 21 cm-1 and 8 cm-1 from the isolated XeBeO and ArBeO complexes, respectively. The vibrational shift of XeBeO in Ar matrix is also calculated and compared with experimental data. In all simulations examined in this paper, the calculated vibrational frequency shifts from the isolated BeO molecule are in reasonable agreement with experimental values. The spectral shift due to the rare-gas-complex formation of RgBeO (Rg = Xe or Ar) is not negligible as seen in the previous studies, but it is shown in this paper that the effects of other surrounding rare gas atoms should be carefully taken into account for quantitative description of the spectral shifts and that these two effects are competing in vibrational spectroscopy of BeO in matrix environments. [ABSTRACT FROM AUTHOR]

In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials. Four rigid water models have been parameterized; the matching procedure has been used to assess the role of the ghost atom in TIP4P-like models and of electrostatic damping. In the former case, burying the negative charge inside the molecule allows to fit better the torques. In the latter, since short-range interactions are damped, a better fit of the forces is obtained. Overall, the best performing model is the one with a ghost atom and with electrostatic damping. The approach shown in this paper is of general validity and could be applied to any matching algorithm and to any level of coarse graining, also for non-rigid molecules. [ABSTRACT FROM AUTHOR]

Photo-induced electron detachment spectroscopy of anionic boron clusters, B4- and B5-, is theoretically investigated by performing electronic structure calculations and nuclear dynamics simulations. While the electronic potential energy surfaces (X1Ag, ã3B2u, b3B1u, Ã1B2u, c3B2g, and B1B2g of neutral B4 and X2B2, Ã2A1, B2B2, C2A1, D2B1, and E2A1 of neutral B5) and their coupling surfaces are constructed in this paper, the details of the nuclear dynamics on these electronic states are presented in Paper II. Electronic structure calculations are carried out at the complete active space self-consistent field - multi-reference configuration interaction level of theory employing the correlation consistent polarized valance triple zeta basis set. Using the calculated electronic structure data suitable vibronic Hamiltonians are constructed utilizing a diabatic electronic basis and displacement coordinates of the normal vibrational modes. The theoretical results are discussed in relation to those recorded in recent experiments. [ABSTRACT FROM AUTHOR]

The jet-cooled high resolution spectrum of the vibrationless Ã←X transition of the deuterated species of the methyl peroxy radical has been recently published in this journal (S. Wu, P. Dupré, P. Rupper, and T. A. Miller, J. Chem. Phys. 127, 224305 (2007)). The spectrum was analyzed using a rigid-rotor model with quadratic spin-rotation coupling. The analysis was based on the fit of ∼350 partially resolved line positions and was quite satisfactory. However, the full simulation of the spectral intensity clearly identifies a lack of ability to reproduce relatively small line clumps ('extra' lines) located between the two main central Q branches. This is indicating of an incomplete initial analysis. In the present paper we reanalyze this electronic transition by considering a reference-frame axis-switching resulting from the nuclear rearrangement associated to the electronic transition (spectra obtained at two different temperatures are considered). The potential energy hypersurfaces of the two electronic states are sufficiently dissimilar to induce changes in the molecule geometry, particularly, the angle COO⁁, which induces a rotation (∼1.7°) of the principal axes of inertia located in the molecule symmetry plane. The present analysis is supported by a global fitting of the spectrum intensity and gives rise to a slightly different set of molecular constants. Attention is paid to the wavefunction symmetry assignment of a non-orthorhombic molecule. Couplings due to the torsion of the methyl group are discussed in the following paper (P. Dupre, J. Chem. Phys. 134, 244309 (2011)). [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations were conducted to investigate the dynamic properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. The ring melts were found to diffuse faster than their linear counterparts, with both architectures approximately obeying a D ∼ N-2.4 scaling law for large N. The mean-square displacement of the center-of-mass of the rings follows a sub-diffusive behavior for times and distances beyond the ring extension g2>, neither compatible with the Rouse nor the reptation model. The rings relax stress much faster than linear polymers, and the zero-shear viscosity was found to vary as η0 ∼ N1.4 ± 0.2 which is much weaker than the N3.4 behavior of linear chains, not matching any commonly known model for polymer dynamics when compared to the observed mean-square displacements. These findings are discussed in view of the conformational properties of the rings presented in the preceding paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204904 (2011)]. [ABSTRACT FROM AUTHOR]

On the mesoscale, the molecular motion in a microporous material can be represented as a sequence of hops between different pore locations and from one pore to the other. On the same scale, the memory effects in the motion of a tagged particle are embedded in the displacement autocorrelation function (DACF), the discrete counterpart of the velocity autocorrelation function (VACF). In this paper, a mesoscopic hopping model, based on a lattice-gas automata dynamics, is presented for the coarse-grained modeling of the DACF in a microporous material under conditions of thermodynamic equilibrium. In our model, that we will refer to as central cell model, the motion of one tagged particle is mimicked through probabilistic hops from one location to the other in a small lattice of cells where all the other particles are indistinguishable; the cells closest to the one containing the tagged particle are simulated explicitly in the canonical ensemble, whereas the border cells are treated as mean-field cells in the grand-canonical ensemble. In the present paper, numerical simulation of the central cell model are shown to provide the same results as a traditional lattice-gas simulation. Along with this a mean-field theory of self-diffusion which incorporates time correlations is discussed. [ABSTRACT FROM AUTHOR]

In this paper we examine the phase behavior of the Weeks-Chandler-Andersen (WCA) potential with β[variant_greek_epsilon] = 40. Crystal nucleation in this model system was recently studied by Kawasaki and Tanaka [Proc. Natl. Acad. Sci. U.S.A. 107, 14036 (2010)], who argued that the computed nucleation rates agree well with experiment, a finding that contradicted earlier simulation results. Here we report an extensive numerical study of crystallization in the WCA model, using three totally different techniques (Brownian dynamics, umbrella sampling, and forward flux sampling). We find that all simulations yield essentially the same nucleation rates. However, these rates differ significantly from the values reported by Kawasaki and Tanaka and hence we argue that the huge discrepancy in nucleation rates between simulation and experiment persists. When we map the WCA model onto a hard-sphere system, we find good agreement between the present simulation results and those that had been obtained for hard spheres [L. Filion, M. Hermes, R. Ni, and M. Dijkstra, J. Chem. Phys. 133, 244115 (2010); S. Auer and D. Frenkel, Nature 409, 1020 (2001)]. [ABSTRACT FROM AUTHOR]

Trotter's theorem forms the theoretical basis of most modern molecular dynamics. In essence this theorem states that a time displacement operator (a Lie operator) constructed by exponentiating a sum of noncommuting operators can be approximated by a product of single operators provided the time interval is 'very small.' In theory 'very small' implies infinitesimally small (at which point the approximate product becomes exact), while in practical analysis a finite time interval is divided into several small subintervals or steps. It follows, therefore, that the larger the number of steps the better the approximation to the exact time displacement operator. The question therefore arises: How many steps are sufficient? For bounded operators, standard theorems are available to provide the answer. In this paper we show that a very simple combinatorial formula can be derived which allows the computation of the global differences (as a function of the number of steps) between the Taylor coefficients of the exact time displacement operator and an approximate one constructed by using a finite number of steps. The formula holds for both bounded and nonbounded operators and shows, quantitatively, what is qualitatively expected-that the error decreases with increasing number of steps. Furthermore, the formula applies irrespective of the complexity of the system, boundary conditions, or the thermodynamic ensemble employed for averaging the initial conditions. The analysis yields explicit expressions for the Taylor coefficients which are then used to compute the errors. In the case of the algorithmically based practical numerical simulations in which fixed, albeit small, steps are repeatedly applied, the rise in the number of steps does not reduce the size of the steps but increases the total time of interest. The combinatorial formula shows that, here, the errors diverge. Furthermore, this work can be used to supplement other efforts such as the use of shadow Hamiltonians where the truncation of the series expansion of the latter will produce errors in the higher order propagator moments. [ABSTRACT FROM AUTHOR]

Tau leaping methods enable efficient simulation of discrete stochastic chemical systems. Stiff stochastic systems are particularly challenging since implicit methods, which are good for stiffness, result in noninteger states. The occurrence of negative states is also a common problem in tau leaping. In this paper, we introduce the implicit Minkowski-Weyl tau (IMW-τ) methods. Two updating schemes of the IMW-τ methods are presented: implicit Minkowski-Weyl sequential (IMW-S) and implicit Minkowski-Weyl parallel (IMW-P). The main desirable feature of these methods is that they are designed for stiff stochastic systems with molecular copy numbers ranging from small to large and that they produce integer states without rounding. This is accomplished by the use of a split step where the first part is implicit and computes the mean update while the second part is explicit and generates a random update with the mean computed in the first part. We illustrate the IMW-S and IMW-P methods by some numerical examples, and compare them with existing tau methods. For most cases, the IMW-S and IMW-P methods perform favorably. [ABSTRACT FROM AUTHOR]

In the present paper, we report a molecular dynamics simulation of two-dimensional Lennard-Jones system with a simple square start configuration. Mean square displacement was computed showing interesting dependence on high pressure conditions in short time scale, corresponding to an abrupt restructurization. This paper is the first to report the qualitative and quantitative details of this phenomenon. [ABSTRACT FROM AUTHOR]

Attempts to simulate crystal growth of ice from liquid water and to provide a consistent microscopic description of this process have been challenging tasks. In this paper we have adapted our previously developed molecular dynamics simulation methodology to enable the investigation of steady-state directional crystal growth/melting of ice. Specifically, we examine ice/water systems of the (001), (110), and (111) faces of ice Ic and the (0001), [formula], and [formula] faces of ice Ih, where the TIP4P, TIP4P-Ew, and SPC/E water models have been utilized. The influence of different growth/melting conditions (temperature gradients and growth velocities) is investigated. Profile functions of properties of interest across the interface are obtained from nonequilibrium steady-state simulations and provide consistent descriptions of ice/water interfaces. The widths of the various crystallographic faces are found to increase in the apparent order Ic111, Ih0001 < [formula] < [formula] < Ic001 < Ic110. The observed growth rates were in agreement with experimental values and the possible dependence on the various faces is explored. The melting temperatures obtained with the present methodology for the different models are in good agreement with estimates from other work. [ABSTRACT FROM AUTHOR]

Over the last number of years several simulation methods have been introduced to study rare events such as nucleation. In this paper we examine the crystal nucleation rate of hard spheres using three such numerical techniques: molecular dynamics, forward flux sampling, and a Bennett-Chandler-type theory where the nucleation barrier is determined using umbrella sampling simulations. The resulting nucleation rates are compared with the experimental rates of Harland and van Megen [Phys. Rev. E 55, 3054 (1997)], Sinn et al. [Prog. Colloid Polym. Sci. 118, 266 (2001)], Schätzel and Ackerson [Phys. Rev. E 48, 3766 (1993)], and the predicted rates for monodisperse and 5% polydisperse hard spheres of Auer and Frenkel [Nature 409, 1020 (2001)]. When the rates are examined in units of the long-time diffusion coefficient, we find agreement between all the theoretically predicted nucleation rates, however, the experimental results display a markedly different behavior for low supersaturation. Additionally, we examined the precritical nuclei arising in the molecular dynamics, forward flux sampling, and umbrella sampling simulations. The structure of the nuclei appears independent of the simulation method, and in all cases, the nuclei contains on average significantly more face-centered-cubic ordered particles than hexagonal-close-packed ordered particles. [ABSTRACT FROM AUTHOR]

We use the bond fluctuation model (BFM) to study the pore-blockade times of a translocating polymer of length N in two dimensions, in the absence of external forces on the polymer (i.e., unbiased translocation) and hydrodynamic interactions (i.e., the polymer is a Rouse polymer), through a narrow pore. Earlier studies using the BFM concluded that the pore-blockade time scales with polymer length as τd∼Nβ, with β=1+2ν, whereas some recent studies using different polymer models produce results consistent with β=2+ν, originally predicted by us. Here ν is the Flory exponent of the polymer; ν=0.75 in 2D. In this paper we show that for the BFM if the simulations are extended to longer polymers, the purported scaling τd∼N1+2ν ceases to hold. We characterize the finite-size effects, and study the mobility of individual monomers in the BFM. In particular, we find that in the BFM, in the vicinity of the pore the individual monomeric mobilities are heavily suppressed in the direction perpendicular to the membrane. After a modification of the BFM which counters this suppression (but possibly introduces other artifacts in the dynamics), the apparent exponent β increases significantly. Our conclusion is that BFM simulations do not rule out our theoretical prediction for unbiased translocation, namely, β=2+ν. [ABSTRACT FROM AUTHOR]

This paper investigates the conformational and scaling properties of long linear polymer chains. These investigations are done with the aid of Monte Carlo (MC) and molecular dynamics (MD) simulations. Chain lengths that comprise several orders of magnitude to reduce errors of finite size scaling, including the effect of solvent quality, ranging from the athermal limit over the θ-transition to the collapsed state of chains are investigated. Also the effect of polydispersity on linear chains is included which is an important issue in the real fabrication of polymers. A detailed account of the hybrid MD and MC simulation model and the exploited numerical methods is given. Many results of chain properties in the extrapolated limit of infinite chain lengths are documented and universal properties of the chains within their universality class are given. An example of the difference between scaling exponents observed in actual solvents and those observed in the extremes of “good solvents” and “θ-solvents” in simulations is provided by comparing simulation results with experimental data on low density polyethylene. This paper is concluded with an outlook on the extension of this study to branched chain systems of many different branching types. [ABSTRACT FROM AUTHOR]

A method to sum over logarithmic potential in two-dimensions (2D) and Coulomb potential in three dimensions (3D) with periodic boundary conditions in all directions is given. We consider the most general form of unit cells, the rhombic cell in 2D and the triclinic cell in 3D. For the 3D case, this paper presents a generalization of Sperb’s work [R. Sperb, Mol. Simulation 22, 199 (1999)]. The expressions derived in this work converge extremely fast in all region of the simulation cell. We also obtain results for slab geometry. Furthermore, self-energies for both 2D as well as 3D cases are derived. Our general formulas can be employed to obtain Madelung constants for periodic structures. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We compare the predictions of the mean field, the two site multiple scattering, and the simple mode coupling approximation developed in the previous paper for the dynamics of a tagged particle in an excluded volume lattice gas with the results of computer simulations. The tagged particle has a transition rate of γ while the background particles have transition rates of αγ. We consider the tracer diffusion coefficient and the incoherent intermediate scattering function (IISF) for low, intermediate, and high concentrations of particles and for simple square and cubic lattices. In general, the approximate kinetic theories are more accurate in predicting simulations results at low concentrations, high dimensions, and large α. For the tracer diffusion coefficient, the mean field approximation is the least accurate, the two site multiple scattering approximation is more accurate, and the simple mode coupling approximation is the most accurate; all three approximate theories overestimate the simulation results. For the IISF, the mean field approximation is quantitatively accurate in the limit of small concentration and large α but in general decays too quickly. The two site multiple scattering approximation is quantitatively accurate at low and intermediate concentrations for large wave vectors; it is always more accurate than the mean field approximation and always decays more quickly than the simulation results. The simple mode coupling approximation is the most accurate of the three approximations in most cases and especially so for small wave vectors, high concentration, and small α; unfortunately, its predictions are not quantitatively accurate in these highly nonmean field regimes. We discuss the implications of these results for developing diagrammatic kinetic theories. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are used to calculate the surface tension γ and study the structural properties of the liquid–vapor interface of the simple molten salt KI. The focus of the present paper is the effect on the calculated surface tension of different terms in the interionic potential and of the way that long-ranged interactions are treated. Specifically, we analyze the dependence of γ on: (a) boundary conditions employed in the Ewald summations of Coulomb interactions; (b) truncation of dispersion interactions; (c) inclusion of polarization effects. Our results show that (a) the use of vacuum boundary conditions in the direction perpendicular to the interface helps to maintain the mechanical equilibrium of the interface; (b) an Ewald summation of dispersion interactions is necessary to avoid substantial truncation effects; (c) polarization tends to decrease γ by significant amounts, and improves the agreement with experiment. In all cases, a reduction of γ comes with a corresponding increase of the interfacial width. As a structural indicator, the tangential pair distribution functions at the interface are compared with those of the bulk liquid. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Sets of atoms collectively behaving as rigid bodies are often used in molecular dynamics to model entire molecules or parts thereof. This is a coarse-graining strategy that eliminates degrees of freedom and supposedly admits larger time steps without abandoning the atomistic character of a model. In this paper, we rely on a particular factorization of the rotation matrix to simplify the mechanical formulation of systems containing rigid bodies. We then propose a new derivation for the exact solution of torque-free rotations, which are employed as part of a symplectic numerical integration scheme for rigid-body dynamics. We also review methods for calculating pressure in systems of rigid bodies with pairwise-additive potentials and periodic boundary conditions. Finally, simulations of liquid phases, with special focus on water, are employed to analyze the numerical aspects of the proposed methodology. Our results show that energy drift is avoided for time step sizes up to 5 fs, but only if a proper smoothing is applied to the interatomic potentials. Despite this, the effects of discretization errors are relevant, even for smaller time steps. These errors induce, for instance, a systematic failure of the expected equipartition of kinetic energy between translational and rotational degrees of freedom. [ABSTRACT FROM AUTHOR]

Morphology of symmetric ABCD tetrablock quaterpolymers in melt was studied by the Monte Carlo (MC) simulation, where the volume fractions of the block chains, f, kept the relationships of fA = fD and fB = fC, and the volume fraction of the two mid-blocks φ was defined as φ = fB + fC. Previous self-consistent field theory for ABCD reported morphological change including several structures; however, the scope was limited within a two-dimensional system. To the contrary, in this paper, MC simulations were carried out in three dimensions with changing the φ value finely, which resulted in finding a tetracontinuous structure in the range of 0.625 ⩽ φ ⩽ 0.75. Moreover the tetracontinuous structure has been found to be the gyroid structure, and the mean curvature of the B/C interface is nearly zero. We concluded that the B/C interface must be the Schoen gyroid surface, one of three-dimensional periodic minimal surfaces. The geometrical nature of the A/B interface should be equivalent to that of the C/D interface, and they stand as level surfaces to the Schoen gyroid surface. [ABSTRACT FROM AUTHOR]

In this paper and in a companion paper [M. E. Tuckerman and M. Parrinello, J. Chem. Phys. 101, 1316 (1994)] the problem of integrating the equations of motion in Car–Parrinello simulations is addressed. In this paper, new techniques for treating the constraint problem based on the velocity Verlet integrator and the Gaussian dynamics are presented. Questions of adiabaticity and temperature control are discussed, and it is shown how to combine the new techniques with the recently developed Nosé–Hoover chain thermostat method. All new techniques are described using the formalism of operator factorizations applied to the classical Liouville propagator. In the companion paper, the formalism and application of multiple time scale methodology in Car–Parrinello simulations are discussed. [ABSTRACT FROM AUTHOR]

In this paper, we present a new canonical replica exchange molecular dynamics (REMD) simulation method with normal pressure for all replicas (REMD-NV(p)T). This method is suitable for systems for which conventional constant NPT-setups are difficult to implement. In this implementation, each replica has an individual volume, with normal pressure maintained for each replica in the simulation. We derive a novel exchange term and validate this method on the structural properties of SPC/E water and dialanine (Ala2) in the bulk and in the presence of a graphene layer. Compared to conventional constant NPT-REMD and NVT-REMD simulations, we find that the structural properties of our new method are in good agreement with simulations in the NPT-ensemble at all temperatures. The structural properties of the systems considered are affected by high pressures at elevated temperatures in the constant NVT-ensemble, an effect that our method corrects for. Unprojected distributions reveal that essential motions of the peptide are affected by the presence of the barostat in the NPT implementation but that the dynamical eigenmodes of the NV(p)T method are in close quantitative agreement with the NVT-ensemble. [ABSTRACT FROM AUTHOR]

Postcollision multifragmentation which we have recently observed experimentally in C-60-surface impact is the phenomenon of a delayed multiparticle breakup of a highly collisionally vibrationally excited large molecule/cluster (the precursor species) into several polyatomic fragments, after leaving the surface. In this paper, we show that the molecular dynamics simulations of near-grazing C60 collisions with a gold surface at 300 eV impact energy (very similar to the experimental conditions) successfully reproduce the experimentally observed characteristics of the postcollision multifragmentation process. The calculated mass resolved kinetic energy distributions and the time dependent yield curves of the Cn fragments revealed a precursor mediated, velocity correlated, delayed fragmentation event along the outgoing trajectory, far away from the surface. Most of the large fragments (n = 5) are formed within a time window of 2-20 ps after leaving the surface, corresponding to the vertical distances of 3-30 nm from the surface. Analysis of delay times and actual time duration for multifragmentation reveal that a large part can be described as simultaneous postcollision (delayed) multifragmentation events. The delayed nature of the event seems to be due to an early sequence of structural transformations of the precursor. [ABSTRACT FROM AUTHOR]

Stochastic simulation of large biochemical reaction networks is often computationally expensive due to the disparate reaction rates and high variability of population of chemical species. An approach to accelerate the simulation is to allow multiple reaction firings before performing update by assuming that reaction propensities are changing of a negligible amount during a time interval. Species with small population in the firings of fast reactions significantly affect both performance and accuracy of this simulation approach. It is even worse when these small population species are involved in a large number of reactions. We present in this paper a new approximate algorithm to cope with this problem. It is based on bounding the acceptance probability of a reaction selected by the exact rejection-based simulation algorithm, which employs propensity bounds of reactions and the rejection-based mechanism to select next reaction firings. The reaction is ensured to be selected to fire with an acceptance rate greater than a predefined probability in which the selection becomes exact if the probability is set to one. Our new algorithm improves the computational cost for selecting the next reaction firing and reduces the updating the propensities of reactions. [ABSTRACT FROM AUTHOR]

The Jarzynski relation (and its variants) has provided a route to the experimental evaluation of equilibrium free energy changes based on measurements conducted under arbitrary non-equilibrium conditions. Schroeder and co-workers [Soft Matter 10, 2178 (2014) and J. Chem. Phys. 141, 174903 (2014)] have recently exploited this fact to determine the elastic properties of model DNA from simulations and experiments of chain extension under elongational flow, bypassing the need to make these measurements mechanically using sophisticated optical trapping techniques. In this paper, motivated by these observations, we investigate chain elasticity analytically, using the Jarzynski relation and a finitely extensible nonlinear elastic-type Rouse model within a path integral formalism to calculate (essentially exactly) both the flow-induced free energy change between chain conformations of definite average end-to-end distance, as well as the force-extension curve that follows from it. This curve, based on a new analytic expression, matches the trends in the corresponding curve obtained from a model of chain stretching developed by Marko and Siggia [Macromolecules 28, 8759 (1995)], which itself is in very satisfactory agreement with the numerical and experimental data from the work of Schroeder et al. [ABSTRACT FROM AUTHOR]

Electronic structure calculations of atomistic systems based on density functional theory involve solving the Poisson equation. In this paper, we present a plane-wave based algorithm for solving the generalized Poisson equation subject to periodic or homogeneous Neumann conditions on the boundaries of the simulation cell and Dirichlet type conditions imposed at arbitrary subdomains. In this way, source, drain, and gate voltages can be imposed across atomistic models of electronic devices. Dirichlet conditions are enforced as constraints in a variational framework giving rise to a saddle point problem. The resulting system of equations is then solved using a stationary iterative method in which the generalized Poisson operator is preconditioned with the standard Laplace operator. The solver can make use of any sufficiently smooth function modelling the dielectric constant, including density dependent dielectric continuum models. For all the boundary conditions, consistent derivatives are available and molecular dynamics simulations can be performed. The convergence behaviour of the scheme is investigated and its capabilities are demonstrated. [ABSTRACT FROM AUTHOR]