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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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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, 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]

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]

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]

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]

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]

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]

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 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]

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]

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]

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]

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]

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]

Fluctuating hydrodynamics has been successfully combined with several computational methods to rapidly compute the correlated random velocities of Brownian particles. In the overdamped limit where both particle and fluid inertia are ignored, one must also account for a Brownian drift term in order to successfully update the particle positions. In this paper, we present an efficient computational method for the dynamic simulation of Brownian suspensions with fluctuating hydrodynamics that handles both computations and provides a similar approximation as Stokesian Dynamics for dilute and semidilute suspensions. This advancement relies on combining the fluctuating force-coupling method (FCM) with a new midpoint time-integration scheme we refer to as the drifter-corrector (DC). The DC resolves the drift term for fluctuating hydrodynamics-based methods at a minimal computational cost when constraints are imposed on the fluid flow to obtain the stresslet corrections to the particle hydrodynamic interactions. With the DC, this constraint needs only to be imposed once per time step, reducing the simulation cost to nearly that of a completely deterministic simulation. By performing a series of simulations, we show that the DC with fluctuating FCM is an effective and versatile approach as it reproduces both the equilibrium distribution and the evolution of particulate suspensions in periodic as well as bounded domains. In addition, we demonstrate that fluctuating FCM coupled with the DC provides an efficient and accurate method for large-scale dynamic simulation of colloidal dispersions and the study of processes such as colloidal gelation. [ABSTRACT FROM AUTHOR]

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency. [ABSTRACT FROM AUTHOR]

In this paper, the dynamical equation for polarization is derived. From this the dielectric response to a spatially varying electric field is analyzed showing a reduced response due to flux of polarization in the material. This flux is modeled as a diffusive process through linear constitutive relations between the flux and the gradient of the polarization. Comparison between the theory and molecular dynamics simulations confirms this effect. The effect is significant for small length scale electric field variations and the inclusion of the flux is thus important in nanoscale modeling of dielectric response. [ABSTRACT FROM AUTHOR]

This paper is devoted to particle transport in a tube formed by alternating wide and narrow sections, in the presence of an external biasing force. The focus is on the effective transport coefficients-- mobility and diffusivity, as functions of the biasing force and the geometric parameters of the tube. Dependences of the effective mobility and diffusivity on the tube geometric parameters are known in the limiting cases of no bias and strong bias. The approximations used to obtain these results are inapplicable at intermediate values of the biasing force. To bridge the two limits Brownian dynamics simulations were run to determine the transport coefficients at intermediate values of the force. The simulations were performed for a representative set of tube geometries over a wide range of the biasing force. They revealed that there is a range of the narrow section length, where the force dependence of the mobility has a maximum. In contrast, the diffusivity is a monotonically increasing function of the force. A simple formula is proposed, which reduces to the known dependences of the diffusivity on the tube geometric parameters in both limits of zero and strong bias. At intermediate values of the biasing force, the formula catches the diffusivity dependence on the narrow section length, if the radius of these sections is not too small. [ABSTRACT FROM AUTHOR]

Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement. [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]

Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)-glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898-915 (2011)]. These structures are stabilized by the short +N-H···O- bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm-1. It is caused by the asymmetric stretching vibrations of the +N-H···O- fragment. Result of the present paper suggests that infrared spectroscopy in the 2000-2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins. [ABSTRACT FROM AUTHOR]

In this paper, the surface tension and critical properties for the TIP4P/2005 and BLYPSP-4F models are reported. A clear dependence of surface tension on the van derWaals cutoff radius (rvdw) is shown when van der Waals interactions are modeled with a simple cutoff scheme. A linear extrapolation formula is proposed that can be used to determine the infinite rvdw surface tension through a few simulations with finite rvdw. A procedure for determining liquid and vapor densities is proposed that does not require fitting to a profile function. Although the critical temperature of water is also found to depend on the choice of rvdw, the dependence is weaker. We argue that a rvdw of 1.75 nm is a good compromise for water simulations when long-range van der Waals correction is not applied. Since the majority of computational programs do not support rigorous treatment of long-range dispersion, the establishment of a minimal acceptable rvdw is important for the simulation of a variety of inhomogeneous systems, such as water bubbles, and water in confined environments. The BLYPSP-4F model predicts room temperature surface tension marginally better than TIP4P/2005 but overestimates the critical temperature. This is expected since only liquid configurations were fit during the development of the BLYPSP-4F potential. The potential is expected to underestimate the stability of vapor and thus overestimate the region of stability for the liquid. [ABSTRACT FROM AUTHOR]

Recently, there has been a concerted effort to implement advanced classical potential energy surfaces by adding higher order multipoles to fixed point charge electrostatics in a bid to increase the accuracy of simulations of condensed phase systems. One major hurdle is the unwieldy nature of the expressions which in part has limited developers mostly to including only dipoles and quadrupoles. In this paper, we present a generalization of the Cartesian formulation of electrostatic multipolar interactions that enables the specification of an arbitrary order of multipoles. Specifically, we derive formulas for arbitrary order implementation of the particle mesh Ewald method and give a closed form formula for the stress tensor in the reciprocal space. In addition, we provide recurrence relations for common electrostatic potentials employed in molecular simulations, which allows for the generalization to arbitrary order and guarantees a computational cost that scales as O(p³) for Cartesian multipole interactions of order p. [ABSTRACT FROM AUTHOR]

In this paper, we examine the behaviour of basic autocatalytic feedback modules involving a species catalyzing its own production, either directly or indirectly. We first perform a systematic study of the autocatalytic feedback module in isolation, examining the effect of different factors, showing how this module is capable of exhibiting monostable threshold and bistable switch-like behaviour. We then study the behaviour of this module embedded in different kinds of basic networks includ-ing (essentially) irreversible cycles, open and closed reversible chains, and networks with additional feedback. We study the behaviour of the networks deterministically and also stochastically, using simulations, analytical work, and bifurcation analysis. We find that (i) there are significant differ-ences between the behaviour of this module in isolation and in a network: thresholds may be altered or destroyed and bistability may be destroyed or even induced, even when the ambient network is simple. The global characteristics and topology of this network and the position of the module in the ambient network can play important and unexpected roles. (ii) There can be important differences between the deterministic and stochastic dynamics of the module embedded in networks, which may be accentuated by the ambient network. This provides new insights into the functioning of such en-zymatic modules individually and as part of networks, with relevance to other enzymatic signalling modules as well. [ABSTRACT FROM AUTHOR]

The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes, the precise structure of complexes of DNA and H-NS proteins is still not well understood. In particular, it is not clear whether the structure of DNA/H-NS complexes in the living cell is similar to that of complexes deposited on mica surfaces, which may be observed by AFM microscopy. A coarse-grained model, which helps getting more insight into this question, is described and analyzed in the present paper. This model is able of describing both the bridging of bacterial DNA by H-NS in the bulk and the deposition and equilibration of the complex on a charged surface. Simulations performed with the model reveal that a slight attraction between DNA and the charged surface is sufficient to let DNA/H-NS complexes reorganize from 3D coils to planar plasmids bridged by H-NS proteins similar to those observed by AFM microscopy. They furthermore highlight the antagonistic effects of the interactions between DNA and the surface. Indeed, increasing these interactions slows down the equilibration of naked plasmids on the surface but, on the other hand, enables a faster equilibration of DNA/H-NS complexes. Based on the distribution of the lifetimes of H-NS bridges and the time evolution of the number of trans-binding protein dimers during equilibration of the complexes on the surface, it is argued that the decrease of the equilibration time of the complex upon increase of the interaction strength between DNA and the surface is ascribable to the associated decrease of the probability to form new bridges between DNA and the proteins. [ABSTRACT FROM AUTHOR]

Understanding and controlling the transportation of water molecules across carbon nanotube (CNT) is of great importance in bio-nanotechnology. In this paper, we systematically investigate the water transporting behaviors (i.e., water flow rate) inside the CNT in the presence of lipid membranes by using all atom molecular dynamic simulations. Our results show that the hydrophilicity of CNT as well as membrane thickness can have important impacts on the water flow rate. Interestingly, since the membrane thickness is temperature-dependent, the water flow rate can exhibit thermo-responsive behaviors. Further, we also provide insights into the effect of CNT on lipid membranes. It is found that all CNTs can increase the lipid tail order parameters and thicken the membrane at 320 K; while these effects are not obvious at 290 K. Importantly, we observe that the CNT with specific hydrophobicity has the least effect on membranes. The present study may give some useful advice on future experimental design of novel devices and sensors. [ABSTRACT FROM AUTHOR]

In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2-3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard- Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent. [ABSTRACT FROM AUTHOR]

In this paper we investigate the adsorption of various probe molecules in order to characterize the porous structure of a series of pillared interlayered clays (PILC). To that aim, volumetric and microcalorimetric adsorption experiments were performed on various Zr PILC samples using nitrogen, toluene, and mesitylene as probe molecules. For one of the samples, neutron scattering experiments were also performed using toluene as adsorbate. Various structural models are proposed and tested by means of a comprehensive computer simulation study, using both geometric and percolation analysis in combination with Grand Canonical Monte Carlo simulations in order to model the volumetric and microcalorimetric isotherms. On the basis of this analysis, we propose a series of structural models that aim at accounting for the adsorption experimental behavior, and make possible a microscopic interpretation of the role played by the different interactions and steric effects in the adsorption processes in these rather complex disordered microporous systems. [ABSTRACT FROM AUTHOR]

Combining simulation and model theories, this paper analyses the impact of pair dynamics on the intermolecular nuclear Overhauser effect (NOE) in liquids. For the first time, we give a distance resolved NOE. When applied to the ionic liquid 1-ethyl-3-methyl-imidazolium tetrafluoroborate the NOE turns out to be of long-range nature. This behaviour translates to the experimentally measured cross- and longitudinal relaxation rates.We were able to calculate the heteronuclear NOE from simulation data, despite the high computational effort.Model theories are computationally less demanding and cover the complete frequency range of the respective spectral density function, they are usually based on a very simple pair distribution function and the solution of the diffusion equation. In order to model the simulated data sufficiently, these simplifications in structure and dynamics have to be generalised considerably. [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]

In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo (KMC). Sensitivity analysis for stochastic systems is typically based on approximating continuous derivatives with respect to model parameters by the mean value of samples from a finite difference scheme. Instead of using independent samples the proposed algorithm reduces the variance of the estimator by developing a strongly correlated-"coupled"- stochastic process for both the perturbed and unperturbed stochastic processes, defined in a common state space. The novelty of our construction is that the new coupled process depends on the targeted observables, e.g., coverage, Hamiltonian, spatial correlations, surface roughness, etc., hence we refer to the proposed method as goal-oriented sensitivity analysis. In particular, the rates of the coupled Continuous Time Markov Chain are obtained as solutions to a goal-oriented optimization problem, depending on the observable of interest, by considering the minimization functional of the corresponding variance. We show that this functional can be used as a diagnostic tool for the design and evaluation of different classes of couplings. Furthermore, the resulting KMC sensitivity algorithm has an easy implementation that is based on the Bortz-Kalos-Lebowitz algorithm's philosophy, where events are divided in classes depending on level sets of the observable of interest. Finally, we demonstrate in several examples including adsorption, desorption, and diffusion Kinetic Monte Carlo that for the same confidence interval and observable, the proposed goal-oriented algorithm can be two orders of magnitude faster than existing coupling algorithms for spatial KMC such as the Common Random Number approach. We also provide a complete implementation of the proposed sensitivity analysis algorithms, including various spatial KMC examples, in a supplementary MATLAB source code. [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]

We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with 109 atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent statistics for cluster properties over a wide range of cluster sizes. The nucleation rates, cluster growth rates, and size distributions are presented in Diemand et al. [J. Chem. Phys. 139, 74309 (2013)], while this paper analyses the properties of the clusters. We explore the cluster temperatures, density profiles, potential energies, and shapes. A thorough understanding of the properties of the clusters is crucial to the formulation of nucleation models. Significant latent heat is retained by stable clusters, by as much as ΔkT = 0.1ϵ for clusters with size i = 100. We find that the clusters deviate remarkably from spherical-with ellipsoidal axis ratios for critical cluster sizes typically within b/c = 0.7 ± 0.05 and a/c = 0.5 ± 0.05. We examine cluster spin angular momentum, and find that it plays a negligible role in the cluster dynamics. The interfaces of large, stable clusters are thinner than planar equilibrium interfaces by 10%-30%. At the critical cluster size, the cluster central densities are between 5% and 30% lower than the bulk liquid expectations. These lower densities imply larger-than-expected surface areas, which increase the energy cost to form a surface, which lowers nucleation rates. [ABSTRACT FROM AUTHOR]

Polymer field theory has emerged as a powerful tool for describing the equilibrium phase behavior of complex polymer formulations, particularly when one is interested in the thermodynamics of dense polymer melts and solutions where the polymer chains can be accurately described using Gaussian models. However, there are many systems of interest where polymer field theory cannot be applied in such a straightforward manner, such as polymer nanocomposites. Current approaches for incorporating nanoparticles have been restricted to the mean-field level and often require approximations where it is unclear how to improve their accuracy. In this paper, we present a unified framework that enables the description of polymer nanocomposites using a field theoretic approach. This method enables straightforward simulations of the fully fluctuating field theory for polymer formulations containing spherical or anisotropic nanoparticles. We demonstrate our approach captures the correlations between particle positions, present results for spherical and cylindrical nanoparticles, and we explore the effect of the numerical parameters on the performance of our approach. [ABSTRACT FROM AUTHOR]

Molecular mechanisms of the steady-state growth of the chain folded lamella and the cold crystallization across the glass transition temperature Tg are investigated by molecular dynamics simulation for a system of long polyethylene (PE)-like polymers made of 512 united atoms C512. The present paper aims to reconsider results of our previous simulations for short PE-like polymers C100 by carrying out very long simulations up to 1 μs for more realistic systems of much longer chains, thereby to establish the firm molecular image of chain-folded crystallization and clarify the specific molecular process of cold crystallization. We observe that the chain-folded lamella shows fast thickening-growth keeping marked tapered growth front. Despite the fast growth in much longer chains, the fold-surface is found to be predominantly of adjacent-reentry. Detailed inspections of the molecular pathway give an insightful image that can explain the apparently contradicting results. In addition, the fold-structure with specific spatial heterogeneity is found to give rise to heterogeneous mobility within the crystalline region. On the other hand, investigations of the cold crystallization during slow heating of the glassy film across Tg is found to give a granular texture made of small crystallites. The crystallites are found to nucleate preferentially near the free surfaces having lower Tg, and to be dominantly edge-on showing a definite tendency to orient their chain axes parallel to the free surface. [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]