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In this work, we determine the dissociation line of the nitrogen (N2) hydrate by computer simulation using the TIP4P/Ice model for water and the TraPPE force field for N2. This work is the natural extension of Paper I, in which the dissociation temperature of the N2 hydrate has been obtained at 500, 1000, and 1500 bar [Algaba et al., J. Chem. Phys. 159, 224707 (2023)] using the solubility method and assuming single occupancy. We extend our previous study and determine the dissociation temperature of the N2 hydrate at different pressures, from 500 to 4500 bar, taking into account the single and double occupancy of the N2 molecules in the hydrate structure. We calculate the solubility of N2 in the aqueous solution as a function of temperature when it is in contact with a N2-rich liquid phase and when in contact with the hydrate phase with single and double occupancy via planar interfaces. Both curves intersect at a certain temperature that determines the dissociation temperature at a given pressure. We observe a negligible effect of occupancy on the dissociation temperature. Our findings are in very good agreement with the experimental data taken from the literature. We have also obtained the driving force for the nucleation of the hydrate as a function of temperature and occupancy at several pressures. As in the case of the dissociation line, the effect of occupancy on the driving force for nucleation is negligible. To the best of our knowledge, this is the first time that the effect of the occupancy on the driving force for nucleation of a hydrate that exhibits sII crystallographic structure is studied from computer simulation. [ABSTRACT FROM AUTHOR]

Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology. This paper reports a theoretical model and computer simulation of the ab initio folding of DNA inverted repeat sequences. The formulation is based on an all-atom conformational model of the sugar-phosphate backbone via chain closure, and it incorporates three major molecular-level driving forces—base stacking, counterion-induced backbone self-interactions, and base pairing—via separate analytical theories designed to capture and reproduce the effects of the solvent without requiring explicit water and ions in the simulation. To accelerate computational throughput, a mixed numerical/analytical algorithm for the calculation of the backbone conformational volume is incorporated into the Monte Carlo simulation, and special stochastic sampling techniques were employed to achieve the computational efficiency needed to fold nucleic acids from scratch. This paper describes implementation details, benchmark results, and the advantages and technical challenges with this approach. [ABSTRACT FROM AUTHOR]

Adding carbon nanoparticles into organic phase change materials (PCMs) such as paraffin is a common way to enhance their thermal conductivity and to improve the efficiency of heat storage devices. However, the sedimentation stability of such blends can be low due to aggregation of aromatic carbon nanoparticles in the aliphatic paraffin environment. In this paper, we explore whether this important issue can be resolved by the introduction of a polymer agent such as poly(3-hexylthiophene) (P3HT) into the paraffin–nanoparticle blends: P3HT could ensure the compatibility of aromatic carbon nanoparticles with aliphatic paraffin chains. We employed a combination of experimental and computational approaches to determine the impact of P3HT addition on the properties of organic PCMs composed of paraffin and carbon nanoparticles (asphaltenes). Our findings clearly show an increase in the sedimentation stability of paraffin–asphaltene blends, when P3HT is added, through a decrease in average size of asphaltene aggregates as well as in an increase of the blends' viscosity. We also witness the appearance of the yield strength and gel-like behavior of the mixtures. At the same time, the presence of P3HT in the blends has almost no effect on their thermophysical properties. This implies that all properties of the blends, which are critical for heat storage applications, are well preserved. Thus, we demonstrated that adding polyalkylthiophenes to paraffin–asphaltene mixtures led to significant improvement in the performance characteristics of these systems. Therefore, the polymer additives can serve as promising compatibilizers for organic PCMs composed of paraffins and asphaltenes and other types of carbon nanoparticles. [ABSTRACT FROM AUTHOR]

Can active forces be exploited to drive the consistent collapse of an active polymer into a folded structure? In this paper, we introduce and perform numerical simulations of a simple model of active colloidal folders and show that a judicious inclusion of active forces into a stiff colloidal chain can generate designable and reconfigurable two-dimensional folded structures. The key feature is to organize the forces perpendicular to the chain backbone according to specific patterns (sequences). We characterize the physical properties of this model and perform, using a number of numerical techniques, an in-depth statistical analysis of structure and dynamics of the emerging conformations. We discovered a number of interesting features, including the existence of a direct correspondence between the sequence of the active forces and the structure of folded conformations, and we discover the existence of an ensemble of highly mobile compact structures capable of moving from conformation to conformation. Finally, akin to protein design problems, we discuss a method that is capable of designing specific target folds by sampling over sequences of active forces. [ABSTRACT FROM AUTHOR]

The purpose of this paper is to investigate several analytical methods of solving first passage (FP) problem for the Rouse model, a simplest model of a polymer chain. We show that this problem has to be treated as a multi-dimensional Kramers' problem, which presents rich and unexpected behavior. We first perform direct and forward-flux sampling (FFS) simulations and measure the mean first-passage time t(z) for the free end to reach a certain distance z away from the origin. The results show that the mean FP time is getting faster if the Rouse chain is represented by more beads. Two scaling regimes of t(z) are observed, with transition between them varying as a function of chain length. We use these simulation results to test two theoretical approaches. One is a well known asymptotic theory valid in the limit of zero temperature. We show that this limit corresponds to fully extended chain when each chain segment is stretched, which is not particularly realistic. A new theory based on the well known Freidlin-Wentzell theory is proposed, where dynamics is projected onto the minimal action path. The new theory predicts both scaling regimes correctly, but fails to get the correct numerical prefactor in the first regime. Combining our theory with the FFS simulations leads us to a simple analytical expression valid for all extensions and chain lengths. One of the applications of polymer FP problem occurs in the context of branched polymer rheology. In this paper, we consider the arm-retraction mechanism in the tube model, which maps exactly on the model we have solved. The results are compared to the Milner-McLeish theory without constraint release, which is found to overestimate FP time by a factor of 10 or more. [ABSTRACT FROM AUTHOR]

The Asakura–Oosawa (AO) model of colloid–polymer mixtures has been extensively studied over the past several decades both via computer simulations and Density Functional Theory (DFT). At this point, its structural and thermodynamic properties both in the bulk and in contact with flat structureless walls are well understood. At the same time, the phase behavior of AO mixtures in spherical cavities and cylindrical pores, while thoroughly investigated by simulations, has not received a comparably detailed DFT treatment. In this paper, we use the DFT results for the AO model in the bulk and under planar confinement as a point of reference for studying its thermodynamic and structural properties in cavities and pores. The accuracy of the DFT approach is assessed by comparing its predictions with the available extensive simulation data; good overall agreement is generally found with some notable exceptions in the vicinity of wetting and drying transitions. The deviations of the phase behavior in confinement from the bulk phase diagram are analyzed using the Kelvin equation, which is seen to work reasonably well under moderate confinement, i.e., for sufficiently large radii of confining cavities and pores. [ABSTRACT FROM AUTHOR]

This paper studies physical aging by computer simulations of a 2:1 Kob–Andersen binary Lennard-Jones mixture, a system that is less prone to crystallization than the standard 4:1 composition. Starting from thermal-equilibrium states, the time evolution of the following four quantities is monitored by following up and down jumps in temperature: potential energy, virial, average squared force, and the Laplacian of the potential energy. Despite the fact that significantly larger temperature jumps are studied here than in typical similar experiments, to a good approximation, all four quantities conform to the single-parameter-aging scenario derived and validated for small jumps in experiments [T. Hecksher, N. B. Olsen, and J. C. Dyre, J. Chem. Phys. 142, 241103 (2015)]. As a further confirmation of single-parameter aging with a common material time for the four different quantities monitored, their relaxing parts are found to be almost identical for all temperature jumps. [ABSTRACT FROM AUTHOR]

The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of the scaling relationship was not possible due to the semi-empirical nature. In this second paper, an analytical excess entropy scaling relation is derived for bottom-up CG systems. At the single-site CG resolution, effective hard sphere systems are constructed that yield near-identical dynamical properties as the target CG systems by taking advantage of how hard sphere dynamics and excess entropy can be analytically expressed in terms of the liquid packing fraction. Inspired by classical equilibrium perturbation theories and recent advances in constructing hard sphere models for predicting activated dynamics of supercooled liquids, we propose a new approach for understanding the diffusion of molecular liquids in the normal regime using hard sphere reference fluids. The proposed "fluctuation matching" is designed to have the same amplitude of long wavelength density fluctuations (dimensionless compressibility) as the CG system. Utilizing the Enskog theory to derive an expression for hard sphere diffusion coefficients, a bridge between the CG dynamics and excess entropy is then established. The CG diffusion coefficient can be roughly estimated using various equations of the state, and an accurate prediction of accelerated CG dynamics at different temperatures is also possible in advance of running any CG simulation. By introducing another layer of coarsening, these findings provide a more rigorous method to assess excess entropy scaling and understand the accelerated CG dynamics of molecular fluids.

Phthalonitrile compounds with Si bridges were recently suggested for producing thermosetting polymer composites with reduced Tg and thus expanded processing range. The detailed experimental investigation of this class of phthalonitriles is still difficult due to development time and costs limitations and the need to take into account the structural changes during the crosslinking. In this paper, we try to overcome these limitations using computer simulations. We performed full-atomistic molecular dynamics simulations of various phthalonitrile compounds to understand the influence of molecular structure on the bulk glass temperature Tg. Two molecular properties affect Tg of the resulting bulk compound: the size of the residue and the length of the Si bridge. The larger residues lead to higher Tgs, while compounds with longer Si bridges have lower Tgs. We have also studied relaxation mechanisms involved in the classification of the samples. Two different factors influence the relaxation mechanisms: energetic, which is provided by the rigidity of molecules, and entropic, connected with the available volume of the conformational space of the monomer. [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 Papers I and II, we developed new shifted potential, gradient shifted force, and Taylor shifted force real-space methods for multipole interactions in condensed phase simulations. Here, we discuss the dielectric properties of fluids that emerge from simulations using these methods. Most electrostatic methods (including the Ewald sum) require correction to the conducting boundary fluctuation formula for the static dielectric constants, and we discuss the derivation of these corrections for the new real space methods. For quadrupolar fluids, the analogous material property is the quadrupolar susceptibility. As in the dipolar case, the fluctuation formula for the quadrupolar susceptibility has corrections that depend on the electrostatic method being utilized. One of the most important effects measured by both the static dielectric and quadrupolar susceptibility is the ability to screen charges embedded in the fluid. We use potentials of mean force between solvated ions to discuss how geometric factors can lead to distance-dependent screening in both quadrupolar and dipolar fluids. [ABSTRACT FROM AUTHOR]

Methanol as a basic liquid and the simplest alcohol is widely used in industry and scientific experiments. However, there are still no reliable data on the thermodynamic properties of methanol at high pressure. Here, we present an experimental and computational study of the thermodynamic properties of liquid methanol under high pressure up to 15 kbar, which significantly exceeds previously reported pressures. A temperature response to a small adiabatic change in pressure has been measured using a piston–cylinder apparatus. We have compared our experimental results with the literature data for lower pressures and NIST approximations. We find that all existing experimental data do not agree with each other and with our experiments. The NIST approximations are mainly based on low pressure data and appear to be unreliable in the high pressure region, giving even qualitatively wrong results. OPLS and COMPASS force field models have been used in the method of molecular dynamics. The agreement of molecular simulation with our experimental data is definitely unsatisfactory, which means that the most common computational models of methanol are not sufficiently good. We hope that these experimental data and approximations will help in developing better computational models. [ABSTRACT FROM AUTHOR]

Consider N independently diffusing particles that reversibly bind to a target. We study a problem recently introduced by Grebenkov of finding the first passage time (FPT) for K of the N particles to be simultaneously bound to the target. Since binding is reversible, bound particles may unbind before the requisite K particles bind to the target. This so-called "impatience" leads to a delicate temporal coupling between particles. Recent work found the mean of this FPT in the case that N = K = 2 in a one-dimensional spatial domain. In this paper, we approximate the full distribution of the FPT for any N ≥ K ≥ 1 in a broad class of domains in any space dimension. We prove that our approximation (i) is exact in the limit that the target and/or binding rate is small and (ii) is an upper bound in any parameter regime. Our approximation is analytically tractable and we give explicit formulas for its mean and distribution. These results reveal that the FPT can depend sensitively and nonlinearly on both K and N. The analysis is accompanied by detailed numerical simulations. [ABSTRACT FROM AUTHOR]

The development of colloidal particles that can become self-propelled when exposed to a source of light of a given frequency represents one of the most exciting new developments in the field of active matter. In this paper, we perform numerical simulations to explore several properties of crystalline colloidal aggregates in the presence of such external light fields. We show how permanent gaps of tunable size can be carved into these crystals as a result of a solid-gas transition that occurs above a threshold light intensity. We compare this phenomenon to that occurring in a parent system obtained by replacing self-propulsion with an effective temperature and discuss the main differences between the two setups. Finally, we show how moving the light field across a solid-fluid boundary allows us to transfer or transport the fluid component into or across the solid one. We discuss the dynamics of this process and set limits associated with its performance. [ABSTRACT FROM AUTHOR]

Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement results obtained for real materials. One of the examples is an intriguing problem within the density scaling idea that has attracted attention in recent decades due to its hallmarks of universality, i.e., the fact that the difference between the density scaling exponent and the exponent of the equation of state is observed for real materials, whereas it has not been reported for the model system. In this paper, we use new model molecules of simple but anisotropic architecture to study the effect of molecular anisotropy on the dynamic and thermodynamic properties of the system. We identify the applicable range of intermolecular interactions for a given physical process, and then we explain the reason for observed differences between the behavior of the model and real systems. It demonstrates that the new model systems open broad perspectives for simulation and theoretical research, for example, into unifying concepts in the glass transition physics. [ABSTRACT FROM AUTHOR]

Multi-configurational Ehrenfest (MCE) approaches, which are intended to remedy the lack of correlations in the standard mean-field Ehrenfest method, have been proposed as coherent-state based ansätze for quantum propagation [D. V. Shalashilin, J. Chem. Phys. 130, 244101 (2009)] and also as the classical limit of the variational Gaussian-based multiconfiguration time dependent Hartree (G-MCTDH) method [S. Römer and I. Burghardt, Mol. Phys. 111, 3618 (2013)]. In the present paper, we establish the formal connection between these schemes and assess the performance of MCE for a coherent-state representation of the classical-limit subsystem. As a representative model system, we address the ultrafast, coherent charge transfer dynamics in an oligothiophene-fullerene donor-acceptor complex described by a two-state linear vibronic coupling model. MCE calculations are compared with reference calculations performed with the MCTDH method, for 10–40 vibrational modes. Beyond a dimensionality of 10 modes, it is shown that the correct representation of electronic coherence depends crucially on the sampling of initially unoccupied Gaussians. [ABSTRACT FROM AUTHOR]

In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable. [ABSTRACT FROM AUTHOR]

Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a process that has broad implications in many research areas ranging from medicine to nanotechnology. As such, spontaneous nucleation of protein fibrils has received much attention in recent years with many theoretical and experimental studies focussing on the underlying physical principles. In this paper we make a step forward in this direction and explore the early time behaviour of filamentous protein growth in the context of nucleation theory. We first provide an overview of the thermodynamics and kinetics of spontaneous nucleation of protein filaments in the presence of one relevant degree of freedom, namely the cluster size. In this case, we review how key kinetic observables, such as the reaction order of spontaneous nucleation, are directly related to the physical size of the critical nucleus. We then focus on the increasingly prominent case of filament nucleation that includes a conformational conversion of the nucleating building-block as an additional slow step in the nucleation process. Using computer simulations, we study the concentration dependence of the nucleation rate. We find that, under these circumstances, the reaction order of spontaneous nucleation with respect to the free monomer does no longer relate to the overall physical size of the nucleating aggregate but rather to the portion of the aggregate that actively participates in the conformational conversion. Our results thus provide a novel interpretation of the common kinetic descriptors of protein filament formation, including the reaction order of the nucleation step or the scaling exponent of lag times, and put into perspective current theoretical descriptions of protein aggregation. [ABSTRACT FROM AUTHOR]

In a recent work, we developed a method [H. Takahashi et al., J. Chem. Phys. 143, 084104 (2015)] referred to as exchange-core function (ECF) approach, to compute exchange repulsion Eex between solute and solvent in the framework of the quantum mechanical (QM)/molecular mechanical (MM) method. The ECF, represented with a Slater function, plays an essential role in determining Eex on the basis of the overlap model. In the work of Takahashi et al. [J. Chem. Phys. 143, 084104 (2015)], it was demonstrated that our approach is successful in computing the hydrogen bond energies of minimal QM/MM systems including a cationic QM solute. We provide in this paper the extension of the ECF approach to the free energy calculation in condensed phase QM/MM systems by combining the ECF and the QM/MM-ER approach [H. Takahashi et al., J. Chem. Phys. 121, 3989 (2004)]. By virtue of the theory of solutions in energy representation, the free energy contribution δμex from the exchange repulsion was naturally formulated. We found that the ECF approach in combination with QM/MM-ER gives a substantial improvement on the calculation of the hydration free energy of a hydronium ion. This can be attributed to the fact that the ECF reasonably realizes the contraction of the electron density of the cation due to the deficit of an electron. [ABSTRACT FROM AUTHOR]

The process of bubble nucleation in a Lennard-Jones (LJ) liquid is studied by molecular dynamics (MD) simulation. The bubble nucleation rate J is determined by the mean life-time method at temperatures above that of the triple point in the region of negative pressures. The results of simulation are compared with classical nucleation theory (CNT) and modified classical nucleation theory (MCNT), in which the work of formation of a critical bubble is determined in the framework of the van der Waals-Cahn-Hilliard gradient theory (GT). It has been found that the values of J obtained in MD simulation systematically exceed the data of CNT, and this excess in the nucleation rate reaches 8-10 orders of magnitude close to the triple point temperature. The results of MCNT are in satisfactory agreement with the data of MD simulation. To describe the properties of vapor-phase nuclei in the framework of GT, an equation of state has been built up which describes stable, metastable and labile regions of LJ fluids. The surface tension of critical bubbles γ has been found from CNT and data of MD simulation as a function of the radius of curvature of the surface of tension R* The dependence γ(R*) has also been calculated from GT. The Tolman length has been determined, which is negative and in modulus equal to ≈(0.1 - 0.2)σ. The paper discusses the applicability of the Tolman formula to the description of the properties of critical nuclei in nucleation. [ABSTRACT FROM AUTHOR]

This paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the non-Markovian dynamics of the end-to-end vector and relies on the preaveraging of the mobility tensor (Zimm dynamics), is shown to reproduce very accurately the results of numerical simulations of the complete nonlinear dynamics. It is found that Markovian treatments based on a Wilemski-Fixman approximation significantly overestimate cyclization times (up to a factor 2), showing the importance of memory effects in the dynamics. In addition, this analysis provides scaling laws of the mean first cyclization time (MFCT) with the polymer size N and capture radius b, which are identical in both Markovian and non-Markovian approaches. In particular, it is found that the scaling of the MFCT for large N is given by T - N3/2ln(N/b²), which differs from the case of the Rouse dynamics where T - N². The extension to the case of the reaction kinetics of a monomer of a Zimm polymer with an external target in a confined volume is also presented. [ABSTRACT FROM AUTHOR]

Axial diffusion in a two-dimensional channel of smoothly varying geometry can be approximately described as one-dimensional diffusion in the entropy potential with position-dependent effective diffusivity by means of the modified Fick-Jacobs equation. In this paper, Brownian dynamics simulations are used to study the range of applicability of such a description, as well as the accuracy of the expressions for the effective diffusivity proposed by different researchers. [ABSTRACT FROM AUTHOR]

In this paper, we describe a new and fully coherent stochastic surface hopping method for simulating mixed quantum-classical systems. We illustrate the approach on the simple but unforgiving problem of quantum evolution of a two-state quantum system in the limit of unperturbed pure state dynamics and for dissipative evolution in the presence of both stationary and nonstationary random environments. We formulate our approach in the Liouville representation and describe the density matrix elements by ensembles of trajectories. Population dynamics are represented by stochastic surface hops for trajectories representing diagonal density matrix elements. These are combined with an unconventional coherent stochastic hopping algorithm for trajectories representing off-diagonal quantum coherences. The latter generalizes the binary (0,1) "probability" of a trajectory to be associated with a given state to allow integers that can be negative or greater than unity in magnitude. Unlike existing surface hopping methods, the dynamics of the ensembles are fully entangled, correctly capturing the coherent and nonlocal structure of quantum mechanics. [ABSTRACT FROM AUTHOR]

The paper addresses Brownian motion in the logarithmic potential with time-dependent strength, U(x, t) = g(t) log(x), subject to the absorbing boundary at the origin of coordinates. Such model can represent kinetics of diffusion-controlled reactions of charged molecules or escape of Brownian particles over a time-dependent entropic barrier at the end of a biological pore. We present a simple asymptotic theory which yields the long-time behavior of both the survival probability (first-passage properties) and the moments of the particle position (dynamics). The asymptotic survival probability, i.e., the probability that the particle will not hit the origin before a given time, is a functional of the potential strength. As such, it exhibits a rather varied behavior for different functions g(t). The latter can be grouped into three classes according to the regime of the asymptotic decay of the survival probability. We distinguish 1. the regular (power-law decay), 2. the marginal (power law times a slow function of time), and 3. the regime of enhanced absorption (decay faster than the power law, e.g., exponential). Results of the asymptotic theory show good agreement with numerical simulations. [ABSTRACT FROM AUTHOR]

Originally, the challenge of solving Kramers' turnover theory was limited to Ohmic friction, or equivalently, motion of the escaping particle governed by a Langevin equation. Mel'nikov and Meshkov [J. Chem. Phys. 85, 1018 (1986)] (MM) presented a solution valid for Ohmic friction. The turnover theory was derived more generally and for memory friction by Pollak, Grabert, and Hänggi [J. Chem. Phys. 91, 4073 (1989)] (PGH). Mel'nikov proceeded to also provide finite barrier corrections to his theory [Phys. Rev. E 48, 3271 (1993)]. Finite barrier corrections were derived only recently within the framework of PGH theory [E. Pollak and R. Ianconescu, J. Chem. Phys. 140, 154108 (2014)]. A comprehensive comparison betweenMMand PGH theories including finite barrier corrections and using Ohmic friction showed that the two methods gave quantitatively similar results and were in quantitative agreement with numerical simulation data. In the present paper, we extend the study of the turnover theories to exponential memory friction. By comparing with numerical simulation, we find that PGH theory is rather accurate, even in the strong friction long memory time limit, while MM theory fails. However, inclusion of finite barrier corrections to PGH theory leads to failure in this limit. The long memory time invalidates the fundamental assumption that consecutive traversals of the well are independent of each other. Why PGH theory without finite barrier corrections remains accurate is a puzzle. [ABSTRACT FROM AUTHOR]

The so-called "raspberry" model refers to the hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of colloidal particles, originally developed by Lobaskin and Dünweg [New J. Phys. 6, 54 (2004)], wherein discrete surface points are used to achieve fluid-particle coupling. This technique has been used in many simulation studies on the behavior of colloids. However, there are fundamental questions with regards to the use of this model. In this paper, we examine the accuracy with which the raspberry method is able to reproduce Stokes-level hydrodynamic interactions when compared to analytic expressions for solid spheres in simple-cubic crystals. To this end, we consider the quality of numerical experiments that are traditionally used to establish these properties and we discuss their shortcomings. We show that there is a discrepancy between the translational and rotational mobility reproduced by the simple raspberry model and present a way to numerically remedy this problem by adding internal coupling points. Finally, we examine a non-convex shape, namely, a colloidal dumbbell, and show that the filled raspberry model replicates the desired hydrodynamic behavior in bulk for this more complicated shape. Our investigation is continued in de Graaf et al. [J. Chem. Phys. 143, 084108 (2015)], wherein we consider the raspberry model in the confining geometry of two parallel plates. [ABSTRACT FROM AUTHOR]

Stochastic simulation for in silico studies of large biochemical networks requires a great amount of computational time. We recently proposed a new exact simulation algorithm, called the rejectionbased stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)], to improve simulation performance by postponing and collapsing as much as possible the propensity updates. In this paper, we analyze the performance of this algorithm in detail, and improve it for simulating large-scale biochemical reaction networks. We also present a new algorithm, called simultaneous RSSA (SRSSA), which generates many independent trajectories simultaneously for the analysis of the biochemical behavior. SRSSA improves simulation performance by utilizing a single data structure across simulations to select reaction firings and forming trajectories. The memory requirement for building and storing the data structure is thus independent of the number of trajectories. The updating of the data structure when needed is performed collectively in a single operation across the simulations. The trajectories generated by SRSSA are exact and independent of each other by exploiting the rejection-based mechanism. We test our new improvement on real biological systems with a wide range of reaction networks to demonstrate its applicability and efficiency. [ABSTRACT FROM AUTHOR]

This paper considers laser-driven optimal control of an ensemble of non-interacting molecules whose dynamics lie in classical phase space. The molecules evolve independently under control to distinct final states. We consider a control landscape defined in terms of multi-target (MT) molecular states and analyze the landscape as a functional of the control field. The topology of the MT control landscape is assessed through its gradient and Hessian with respect to the control. Under particular assumptions, the MT control landscape is found to be free of traps that could hinder reaching the objective. The Hessian associated with an optimal control field is shown to have finite rank, indicating an inherent degree of robustness to control noise. Both the absence of traps and rank of the Hessian are shown to be analogous to the situation of specifying multiple targets for an ensemble of quantum states. Numerical simulations are presented to illustrate the classical landscape principles and further characterize the system behavior as the control field is optimized. [ABSTRACT FROM AUTHOR]

The functionality of many polymeric materials depends on their glass transition temperatures (Tg). In computer simulations, Tg is often calculated from the gradual change in macroscopic properties. Precise determination of this change depends on the fitting protocols. We previously proposed a robust data-driven approach to determine Tg from the molecular dynamics simulation data of a coarse-grained semiflexible polymer model. In contrast to the global macroscopic properties, our method relies on high-resolution microscopic details. Here, we demonstrate the generality of our approach by using various dimensionality reduction and clustering methods and apply it to an atomistic model of acrylic polymers. Our study reveals the explicit contribution of the side chain and backbone residues in influencing the determination of the glass transition temperature. [ABSTRACT FROM AUTHOR]

Asphaltenes represent a novel class of carbon nanofillers that are of potential interest for many applications, including polymer nanocomposites, solar cells, and domestic heat storage devices. In this work, we developed a realistic coarse-grained Martini model that was refined against the thermodynamic data extracted from atomistic simulations. This allowed us to explore the aggregation behavior of thousands of asphaltene molecules in liquid paraffin on a microsecond time scale. Our computational findings show that native asphaltenes with aliphatic side groups form small clusters that are uniformly distributed in paraffin. The chemical modification of asphaltenes via cutting off their aliphatic periphery changes their aggregation behavior: modified asphaltenes form extended stacks whose size increases with asphaltene concentration. At a certain large concentration (44 mol. %), the stacks of modified asphaltenes partly overlap, leading to the formation of large, disordered super-aggregates. Importantly, the size of such super-aggregates increases with the simulation box due to phase separation in the paraffin–asphaltene system. The mobility of native asphaltenes is systematically lower than that of their modified counterparts since the aliphatic side groups mix with paraffin chains, slowing down the diffusion of native asphaltenes. We also show that diffusion coefficients of asphaltenes are not very sensitive to the system size: enlarging the simulation box results in some increase in diffusion coefficients, with the effect being less pronounced at high asphaltene concentrations. Overall, our findings provide valuable insight into the aggregation behavior of asphaltenes on spatial and time scales that are normally beyond the scales accessible for atomistic simulations. [ABSTRACT FROM AUTHOR]

Forward flux sampling (FFS) is a path sampling technique widely used in computer simulations of crystal nucleation from the melt. In such studies, the order parameter underpinning the progress of the FFS algorithm is often the size of the largest crystalline nucleus. In this work, we investigate the effects of two computational aspects of FFS simulations, using the prototypical Lennard-Jones liquid as our computational test bed. First, we quantify the impact of the positioning of the liquid basin and first interface in the space of the order parameter. In particular, we demonstrate that these choices are key to ensuring the consistency of the FFS results. Second, we focus on the frequently encountered scenario where the population of crystalline nuclei is such that there are multiple clusters of size comparable to the largest one. We demonstrate the contribution of clusters other than the largest cluster to the initial flux; however, we also show that they can be safely ignored for the purposes of converging a full FFS calculation. We also investigate the impact of different clusters merging, a process that appears to be facilitated by substantial spatial correlations—at least at the supercooling considered here. Importantly, all of our results have been obtained as a function of system size, thus contributing to the ongoing discussion on the impact of finite size effects on simulations of crystal nucleation. Overall, this work either provides or justifies several practical guidelines for performing FFS simulations that can also be applied to more complex and/or computationally expensive models. [ABSTRACT FROM AUTHOR]

Explicit and implicit size effects in computer simulations result from considering systems with a fixed number of particles and periodic boundary conditions, respectively. We investigate these effects in the relation D*(L) = A(L) exp(α(L)s2(L)) between reduced self-diffusion coefficient D*(L) and two-body excess entropy s2(L) for prototypical simple-liquid systems of linear size L. To this aim, we introduce and validate a finite-size two-body excess entropy integral equation. Our analytical arguments and simulation results show that s2(L) exhibits a linear scaling with 1/L. Since D*(L) displays a similar behavior, we show that the parameters A(L) and α(L) are also linearly proportional to 1/L. By extrapolating to the thermodynamic limit, we report the coefficients A∞ = 0.048 ± 0.001 and α∞ = 1.000 ± 0.013 that agree well with the universal values available in the literature [M. Dzugutov, Nature 381, 137–139 (1996)]. Finally, we find a power law relation between the scaling coefficients for D*(L) and s2(L), suggesting a constant viscosity-to-entropy ratio. [ABSTRACT FROM AUTHOR]

We investigate the effect of pressure on the carbon dioxide (CO2) hydrate–water interfacial free energy along its dissociation line using advanced computer simulation techniques. In previous works, we have determined the interfacial energy of the hydrate at 400 bars using the TIP4P/Ice and TraPPE molecular models for water and CO2, respectively, in combination with two different extensions of the Mold Integration technique [J. Colloid Interface Sci. 623, 354 (2022) and J. Chem. Phys. 157, 134709 (2022)]. Results obtained from computer simulation, 29(2) and 30(2) mJ/m2, are found to be in excellent agreement with the only two measurements that exist in the literature, 28(6) mJ/m2 determined by Uchida et al. [J. Phys. Chem. B 106, 8202 (2002)] and 30(3) mJ/m2 determined by Anderson et al. [J. Phys. Chem. B 107, 3507 (2002)]. Since the experiments do not allow to obtain the variation of the interfacial energy along the dissociation line of the hydrate, we extend our previous studies to quantify the effect of pressure on the interfacial energy at different pressures. Our results suggest that there exists a correlation between the interfacial free energy values and the pressure, i.e., it decreases with the pressure between 100 and 1000 bars. We expect that the combination of reliable molecular models and advanced simulation techniques could help to improve our knowledge of the thermodynamic parameters that control the interfacial free energy of hydrates from a molecular perspective. [ABSTRACT FROM AUTHOR]

Desorption of a self-propelling filament from an attractive surface is studied by computer simulations and the influence of activity, chain length, and chain rigidity is explored. For the flexible filament, we find three scaling regimes of desorption time vs activity with various scaling exponents. At low activity, the scaling law results from the spiral-like detachment kinetics. And at high activity, by theoretical analysis, the desorption is reminiscent of the escaping mechanism of a super-diffusive blob from a potential well at a short time scale. Additionally, the desorption time decreases first and then increases with chain length at low activity, since it is hard to form a spiral for short filaments due to the limited volume repulsion. For high activities, the desorption time approximately scales with chain length, with a scaling exponent ∼ 0.5 , which can be explained by the theory and numerically fitting scaling law between the end-to-end distance of the "globule-like" filament and chain length. Furthermore, a non-monotonic behavior is observed between the desorption time and the chain stiffness. Desorption time slightly decreases first and then rapidly increases with stiffness due to the opposed effects of increasing rigidity on headiing-up time and leaving-away time. In contrast to traditional polymers, the scaling behavior suggests unique desorption characteristics of active polymers. [ABSTRACT FROM AUTHOR]

Self-assembly of chiral particles with an L-shape is explored by Monte-Carlo computer simulations in two spatial dimensions. For sufficiently high packing densities in confinement, a carpet-like texture emerges due to the interlocking of L-shaped particles, resembling a distorted smectic liquid crystalline layer pattern. From the positions of either of the two axes of the particles, two different types of layers can be extracted, which form distinct but complementary entangled networks. These coarse-grained network structures are then analyzed from a topological point of view. We propose a global charge conservation law by using an analogy to uniaxial smectics and show that the individual network topology can be steered by both confinement and particle geometry. Our topological analysis provides a general classification framework for applications to other intertwined dual networks. [ABSTRACT FROM AUTHOR]

The stochastic simulation algorithm has been used to generate exact trajectories of biochemical reaction networks. For each simulation step, the simulation selects a reaction and its firing time according to a probability that is proportional to the reaction propensity. We investigate in this paper new efficient formulations of the stochastic simulation algorithm to improve its computational efficiency. We examine the selection of the next reaction firing and reduce its computational cost by reusing the computation in the previous step. For biochemical reactions with delays, we present a new method for computing the firing time of the next reaction. The principle for computing the firing time of our approach is based on recycling of random numbers. Our new approach for generating the firing time of the next reaction is not only computationally efficient but also easy to implement. We further analyze and reduce the number of propensity updates when a delayed reaction occurred. We demonstrate the applicability of our improvements by experimenting with concrete biological models.

Simple smectic A liquid crystal phases with different types of prescribed orientational distribution functions have been simulated and compared in order to study the possibility to distinguish between the Maier-Saupe type and cone-like orientational distributions using the popular method of Davidson et al. [J. Phys. II 5, 113 (1995)]. This method has been used to extract the orientational distribution functions from simulated diffraction patterns, and the results have been compared with actual distribution functions which have been prescribed during simulations. It has been shown that it is indeed possible to distinguish between these two qualitatively different types of orientational distribution already from the shape of the 2D diffraction pattern. Moreover, typical experimental diffraction patterns for "de Vries"-type smectic liquid crystals appear to be close to the ones which have been simulated using the prescribed Maier-Saupe orientational distribution function. [ABSTRACT FROM AUTHOR]

We investigate the spatial correlations of microscopic stresses in soft particulate gels using 2D and 3D numerical simulations. We use a recently developed theoretical framework predicting the analytical form of stress–stress correlations in amorphous assemblies of athermal grains that acquire rigidity under an external load. These correlations exhibit a pinch-point singularity in Fourier space. This leads to long-range correlations and strong anisotropy in real space, which are at the origin of force-chains in granular solids. Our analysis of the model particulate gels at low particle volume fractions demonstrates that stress–stress correlations in these soft materials have characteristics very similar to those in granular solids and can be used to identify force chains. We show that the stress–stress correlations can distinguish floppy from rigid gel networks and that the intensity patterns reflect changes in shear moduli and network topology, due to the emergence of rigid structures during solidification. [ABSTRACT FROM AUTHOR]

Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca(2+) ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein's conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding are treated implicitly within the grand canonical ensemble. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca(2+) with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop's structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.

Line tension in wetting processes is of high scientific and technological relevance, but its understanding remains vague, mainly because it is difficult to determine. A widely used method to extract line tension relies on the variation of a droplet's contact angle with the droplet's size. Such an approach yields the apparent line tension, which is an effective parameter that factors in numerous contributions to the finite-size dependence, thus masking the actual line tension in terms of the excess free energy of the three-phase contact line. Based on our recent computer simulation study, we investigate how small amounts of nonionic surfactants, such as surface-active impurities, contribute to the apparent line tension in aqueous droplets. When depositing polydisperse droplets, their different surface area-to-volume ratios can result in different final bulk concentrations of surfactants, different excess adsorptions to the interfaces, and, consequently, different contact angles. We show that already trace amounts of longer-chained surfactants in a pre-contaminated liquid are enough to affect measurements of the apparent line tension. Our analysis quantifies to what extent "background" impurities, inevitably present in all kinds of experimental settings, limit the resolution of line tension measurements, which is crucial for avoiding data misinterpretation. [ABSTRACT FROM AUTHOR]

We employ all-atom well-tempered metadynamics simulations to study the mechanistic details of both the early stages of nucleation and crystal decomposition for the benchmark metal–organic framework (MOF) ZIF-8. To do so, we developed and validated a force field that reliably models the modes of coordination bonds via a Morse potential functional form and employs cationic and anionic dummy atoms to capture coordination symmetry. We also explored a set of physically relevant collective variables and carefully selected an appropriate subset for our problem at hand. After a rapid increase of the Zn–N connectivity, we observe the evaporation of small clusters in favor of a few large clusters, which leads to the formation of an amorphous highly connected aggregate. Zn (MIm) 4 2 − and Zn (MIm) 3 − complexes are observed with lifetimes in the order of a few picoseconds, while larger structures, such as four-, five-, and six-membered rings, have substantially longer lifetimes of a few nanoseconds. The free ligands act as "templating agents" for the formation of sodalite cages. ZIF-8 crystal decomposition results in the formation of a vitreous phase. Our findings contribute to a fundamental understanding of MOF's synthesis that paves the way to controlling synthesis products. Furthermore, our developed force field and methodology can be applied to model solution processes that require coordination bond reactivity for other ZIFs besides ZIF-8. [ABSTRACT FROM AUTHOR]

We develop an accurate, highly efficient, and scalable random batch Ewald (RBE) method to conduct molecular dynamics simulations in the isothermal–isobaric ensemble (the NPT ensemble) for charged particles in a periodic box. After discretizing the Langevin equations of motion derived using suitable Lagrangians, the RBE method builds the mini-batch strategy into the Fourier space in the Ewald summation for the pressure and forces such that the computational cost is reduced to O (N) per time step. We implement the method in the Large-scale Atomic/Molecular Massively Parallel Simulator package and report accurate simulation results for both dynamical quantities and statistics for equilibrium for typical systems including all-atom bulk water and a semi-isotropic membrane system. Numerical simulations on massive supercomputing cluster are also performed to show promising central processing unit efficiency of the RBE. [ABSTRACT FROM AUTHOR]

The growth pattern and nucleation rate of carbon dioxide hydrate critically depend on the precise value of the hydrate–water interfacial free energy. There exist in the literature only two independent experimental measurements of this thermodynamic magnitude: one obtained by Uchida et al. [J. Phys. Chem. B 106, 8202 (2002)], 28(6) mJ/m2, and the other by Anderson and co-workers [J. Phys. Chem. B 107, 3507 (2003)], 30(3) mJ/m2. Recently, Algaba et al. [J. Colloid Interface Sci. 623, 354 (2022)] have extended the mold integration method proposed by Espinosa and co-workers [J. Chem. Phys. 141, 134709 (2014)] to deal with the CO2 hydrate–water interfacial free energy (mold integration–guest or MI-H). Computer simulations predict a value of 29(2) mJ/m2, in excellent agreement with experimental data. The method is based on the use of a mold of attractive wells located at the crystallographic positions of the oxygen atoms of water molecules in equilibrium hydrate structures to induce the formation of a thin hydrate slab in the liquid phase at coexistence conditions. We propose here a new implementation of the mold integration technique using a mold of attractive wells located now at the crystallographic positions of the carbon atoms of the CO2 molecules in the equilibrium hydrate structure. We find that the new mold integration–guest methodology, which does not introduce positional or orientational information of the water molecules in the hydrate phase, is able to induce the formation of CO2 hydrates in an efficient way. More importantly, this new version of the method predicts a CO2 hydrate–water interfacial energy value of 30(2) mJ/m2, in excellent agreement with experimental data, which is also fully consistent with the results obtained using the previous methodology. [ABSTRACT FROM AUTHOR]

We investigate the process of the second harmonic generation by plasmonic nano-antennas that exhibit Fano-like resonances. A rigorous fully vectorial Maxwell-hydrodynamics approach is employed to directly calculate the second order susceptibilities as a function of the pump frequency, considering a periodic array of nanodolmens comprised of three Au nanorods. The results of the numerical simulations demonstrate a noticeable enhancement of the second harmonic efficiency by the antisymmetric mode. Additionally, a simple analytical model based on two coupled nonlinear oscillators is proposed. It is shown that the second order optical response can be significantly enhanced at the frequency of the antisymmetric normal mode, thus supporting our numerical results. [ABSTRACT FROM AUTHOR]

Non-Maxwellian evaporation of light atoms and molecules (particles) such as He and H2 from liquids has been observed experimentally. In this work, we use simulations to study systematically the evaporation of Lennard-Jones particles from liquid water. We find instances of sub- and super-Maxwellian evaporation, depending on the mass of the particle and the particle-water interaction strength. The observed trends are in qualitative agreement with experiment. We interpret these trends in terms of the potential of mean force and the effectiveness and frequency of collisions during the evaporation process. The angular distribution of evaporating particles is also analyzed, and it is shown that trends in the energy from velocity components tangential and normal to the liquid surface must be understood separately in order to interpret properly the angular distributions. [ABSTRACT FROM AUTHOR]

The liquidus temperature curve that characterizes the boundary between the liquid methanol/water mixture and its coexistence with ice Ih is determined using the direct-coexistence method. Several methanol concentrations and pressures of 0.1, 50, and 100 MPa are considered. In this study, we used the TIP4P/Ice model for water and two different models for methanol: OPLS and OPLS/2016, using the geometric rule for the Lennard-Jones cross interactions. We compared our simulation results with available experimental data and found that this combination of models reproduces the liquidus curve for methanol mole fractions reasonably well, up to xm = 0.3 at p = 0.1 MPa. The freezing point depression of these mixtures is calculated and compared to experimental results. We also analyzed the effect of pressure on the liquidus curve and found that both models also reproduce the experimental decrease of the liquidus temperatures as the pressure increases qualitatively well. [ABSTRACT FROM AUTHOR]

While many physical processes are non-equilibrium in nature, the theory and modeling of such phenomena lag behind theoretical treatments of equilibrium systems. The diversity of powerful theoretical tools available to describe equilibrium systems has inspired strategies that map non-equilibrium systems onto equivalent equilibrium analogs so that interrogation with standard statistical mechanical approaches is possible. In this work, we revisit the mapping from the non-equilibrium random sequential addition process onto an equilibrium multi-component mixture via the replica method, allowing for theoretical predictions of non-equilibrium structural quantities. We validate the above approach by comparing the theoretical predictions to numerical simulations of random sequential addition. [ABSTRACT FROM AUTHOR]

By combining interface-pinning simulations with numerical integration of the Clausius–Clapeyron equation, we accurately determine the melting-line coexistence pressure and fluid/crystal densities of the Weeks–Chandler–Andersen system, covering four decades of temperature. The data are used for comparing the melting-line predictions of the Boltzmann, Andersen–Weeks–Chandler, Barker–Henderson, and Stillinger hard-sphere approximations. The Andersen–Weeks–Chandler and Barker–Henderson theories give the most accurate predictions, and they both work excellently in the zero-temperature limit for which analytical expressions are derived here. [ABSTRACT FROM AUTHOR]

A new heteronuclear decoupling pulse sequence is introduced, dubbed ROtor-Synchronized Phase-Alternated Cycles (ROSPAC). It is based on a partial refocusing of the coherences (spin operator products or cross-terms) [Filip et al., J. Mag. Reson. 176, 2 (2005)] responsible for transverse spin-polarization dephasing, on the irradiation of a large pattern of radio-frequencies, and on a significant minimization of the cross-effects implying 1H chemical-shift anisotropy. Decoupling efficiency is analyzed by numerical simulations and experiments and compared to that of established decoupling sequences [swept-frequency two-pulse phase-modulated (TPPM), TPPM, small phase incremental alternation (SPINAL), refocused Continuous-wave (CWApa), and Rotor-Synchronized Hahn-Echo pulse train (RS-HEPT)]. It was found that ROSPAC offers good 1H offset robustness for a large range of chemical shifts and low radio-frequency (RF) powers, and performs very well in the ultra-fast magic-angle spinning (MAS) regime, where it is almost independent from RF power and permits it to avoid rotary-resonance recoupling conditions (v1 = nvr, n = 1, 2). It has the advantage that only the pulse lengths require optimization and has a low duty cycle in the pulsed decoupling regime. The efficiency of the decoupling sequence is demonstrated on a model microcrystalline sample of the model protein domain GB1 at 100 kHz MAS at 18.8 T. [ABSTRACT FROM AUTHOR]

The hydration free energy (HFE) is a crucially important physical quantity to discuss various chemical processes in aqueous solutions. Although an explicit-solvent computation with molecular dynamics (MD) simulations is a preferable treatment of the HFE, huge computational load has been inevitable for large, complex solutes like proteins. In the present paper, we propose an efficient computation method for the HFE. In our method, the HFE is computed as a sum of 〈UUV〉/2 (〈UUV〉 is the ensemble average of the sum of pair interaction energy between solute and water molecule) and the water reorganization term mainly reflecting the excluded volume effect. Since 〈UUV〉 can readily be computed through a MD of the system composed of solute and water, an efficient computation of the latter term leads to a reduction of computational load. We demonstrate that the water reorganization term can quantitatively be calculated using the morphometric approach (MA) which expresses the term as the linear combinations of the four geometric measures of a solute and the corresponding coefficients determined with the energy representation (ER) method. Since the MA enables us to finish the computation of the solvent reorganization term in less than 0.1 s once the coefficients are determined, the use of the MA enables us to provide an efficient computation of the HFE even for large, complex solutes. Through the applications, we find that our method has almost the same quantitative performance as the ER method with substantial reduction of the computational load.