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This paper presents an exploration of a specific type of a generalized multicomponent solution model, which appears to be first given by Saulov in the current explicit form. The assumptions of the underlying theory and a brief derivation of the main equation have been provided preliminarily for completeness and notational consistency. The resulting formulae for the Gibbs free energy of mixing and the chemical potentials are multivariate polynomials with physically meaningful coefficients and the mole fractions of the components as variables. With one additional assumption about the relative magnitudes of the solvent–solute and solute–solute interaction exchange energies, combining rules were obtained that express the mixed coefficients of the polynomial in terms of its pure coefficients. This was done by exploiting the mathematical structure of the asymmetric form of the solvent chemical potential equation. The combining rules allow one to calculate the thermodynamic properties of the solvent with multiple solutes from binary mixture data only (i.e., each solute with the solvent), and hence, are of practical importance. Furthermore, a connection was established between the osmotic virial coefficients derived in this work and the original osmotic virial coefficients of Hill found by employing a different procedure, illustrating the equivalency of what appears to be two different theories. A validation of the combining rules derived here has been provided in a separate paper where they were successfully used to predict the freezing points of ternary salt solutions of water. [ABSTRACT FROM AUTHOR]

A major limitation of amine-based post-combustion carbon capture technology is the necessity to regenerate amines at high temperatures, which dramatically increases operating costs. This paper concludes the effect of solvent choice as a possible route to modify the thermodynamics and kinetics characterizing the involved amine regeneration reactions and discusses whether these modifications can be economically beneficial. We report experimentally benchmarked computational chemistry calculations of monoethanolamine regeneration reactions employing aqueous and non-aqueous solvents with a wide range of dielectric constants. Unlike previous studies, our improved computational chemistry framework could accurately reproduce the right experimental activation energy of zwitterion formation. From the thermodynamics and kinetics of the predicted reactions, the use of non-aqueous solvents with small dielectric constants led to reductions in regeneration Gibbs free energies, activation barriers, and enthalpy changes. This can reduce energy consumption and give an opportunity to run desorption columns at relatively lower temperatures, thus offering the possibility of relying on low-grade waste heat as an energy input. [ABSTRACT FROM AUTHOR]

The study of the thermodynamics and structures of iron clusters has been carried on, focusing on small clusters and initial icosahedral and fcc-cuboctahedral structures. Two combined tools are used. First, energy intervals are explored by the Monte Carlo algorithm, called σ-mapping, detailed in the work of Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. In its flat histogram version, it provides the classical density of states, gp(Ep), in terms of the potential energy of the system. Second, the iron system is described by a potential which is called "corrected EAM" (cEAM), explained in the work of Basire et al. [J. Chem. Phys. 141, 104304 (2014), Paper II]. Small clusters from 3 to 12 atoms in their ground state have been compared first with published Density Functional Theory (DFT) calculations, giving a complete agreement of geometries. The series of 13, 55, 147, and 309 atom icosahedrons is shown to be the most stable form for the cEAM potential. However, the 147 atom cluster has a special behaviour, since decreasing the energy from the liquid zone leads to the irreversible trapping of the cluster in a reproducible amorphous state, 7.38 eV higher in energy than the icosahedron. This behaviour is not observed at the higher size of 309 atoms. The heat capacity of the 55, 147, and 309 atom clusters revealed a pronounced peak in the solid zone, related to a solid-solid transition, prior to the melting peak. The corresponding series of 13, 55, and 147 atom cuboctahedrons has been compared, underscoring the unstability towards the icosahedral structure. This unstability occurs clearly in several steps for the 147 atom cluster, with a sudden transformation at a transition state. This illustrates the concerted icosahedron-cuboctahedron transformation of Buckminster Fuller-Mackay, which is calculated for the cEAM potential. Two other clusters of initial fcc structures with 24 and 38 atoms have been studied, as well as a 302 atom cluster. Each one relaxes towards a more stable structure without regularity. The 38 atom cluster exhibits a nearly glassy relaxation, through a cascade of six metastable states of long life. This behaviour, as that of the 147 atom cluster towards the amorphous state, shows that difficulties to reach ergodicity in the lower half of the solid zone are related to particular features of the potential energy landscape, and not necessarily to a too large size of the system. Comparisons of the cEAM iron system with published results about Lennard-Jones systems and DFT calculations are made. The results of the previous clusters have been combined with that of Paper II to plot the cohesive energy Ec and the melting temperature Tm in terms of the cluster atom number Nat. The Nat1/3 linear dependence of the melting temperature (Pawlow law) is observed again for Nat > 150. In contrast, for Nat < 150, the curve diverges strongly from the Pawlow law, giving it an overall V-shape, with a linear increase of Tm when Nat goes from 55 to 13 atoms. Surprisingly, the 38 atom cluster is anomalously below the overall curve. [ABSTRACT FROM AUTHOR]

A model system of identical particles interacting via a hard-sphere potential is essential in condensed matter physics; it helps to understand in and out of equilibrium phenomena in complex fluids, such as colloidal dispersions. Yet, most of the fixed time-step algorithms to study the transport properties of those systems have drawbacks due to the mathematical nature of the interparticle potential. Because of this, mapping a hard-sphere potential onto a soft potential has been recently proposed [Báez et al., J. Chem. Phys. 149, 164907 (2018)]. More specifically, using the second virial coefficient criterion, one can set a route to estimate the parameters of the soft potential that accurately reproduces the thermodynamic properties of a monocomponent hard-sphere system. However, real colloidal dispersions are multicomponent or polydisperse, making it important to find an efficient way to extend the potential model for dealing with such kind of many-body systems. In this paper, we report on the extension and applicability of the second virial coefficient criterion to build a description that correctly captures the phenomenology of both multicomponent and polydisperse hard-sphere dispersions. To assess the accuracy of the continuous potentials, we compare the structure of soft polydisperse systems with their hard-core counterpart. We also contrast the structural and thermodynamic properties of soft binary mixtures with those obtained through mean-field approximations and the Ornstein–Zernike equation for the two-component hard-sphere dispersion. [ABSTRACT FROM AUTHOR]

Theoretical analysis and computer simulations (Monte Carlo and numerical integration of differential equations) indicate that the statistical effect of a small number of reacting molecules is affected by transfer of reagent molecules between nanoreactors (droplets in this study). As a model reaction, a simple reversible association A + B ⇆ C was chosen, which was studied previously without reagent transfer processes. For sufficiently fast exchange of reactant molecules and a sufficiently high number of nanoreactors, the studied systems virtually do not differ from large volume systems if overall kinetics and thermodynamics of the chemical process are concerned. However, if either reagent molecule exchange is not fast or the number of exchanging nanoreactors is low, then the stochastic effect is clearly visible, influencing the kinetics of reaching reaction equilibrium. In systems with a low number of nanoreactors, the apparent (average) equilibrium constant is affected as well. The distribution of reactant molecules in the nanoreactors is governed by stochastic processes, dependent on stochastic rate constants of all processes, chemical as well as physical (transfer of molecules outside and into droplets). When accumulation of reactant molecules in the continuous phase cannot be neglected, then the partition coefficients of reactants between the continuous and dispersed phases have to be taken into account. Distributions of reactant molecules described in the paper for systems composed of few nanoreactors can be especially important for some biochemical processes in living cells or devised corresponding artificial reactors. If the reactant molecules predominate in a continuous phase, then the kinetics and overall conversion of reversible association may be significantly affected by the presence of the dispersed phase and its catalytic behavior can be observed. It has been shown that Monte Carlo simulations, applying a devised simple algorithm, give reliable results, allowing theoretical studies of nanoscale-droplet systems. [ABSTRACT FROM AUTHOR]

We propose in this paper a theoretical model for fluid state thermodynamics based on modeling the fluctuation distributions and, hence, the corresponding moment generating functions providing the free energy of the system. Using the relatively simple and physically coherent gamma model for the fluctuation distributions, we obtain a complete theoretical equation of state, also giving insight into the statistical/molecular organization and phase or pseudo-phase transitions occurring under the sub- and super-critical conditions, respectively. Application to sub- and super-critical fluid water and a comparison with the experimental data show that this model provides an accurate description of fluid water thermodynamics, except close to the critical point region where limited but significant deviations from the experimental data occur. We obtain quantitative evidence of the correspondence between the sub- and super-critical thermodynamic behaviors, with the super-critical water pseudo-liquid and pseudo-gas phases being the evolution of the sub-critical water liquid and gas phases, respectively. Remarkably, according to our model, we find that for fluid water the minimal subsystem corresponding to either the liquid-like or the gas-like condition includes an infinite number of molecules in the sub-critical regime (providing the expected singularities due to macroscopic phase transitions) but only five molecules in the super-critical regime (coinciding with the minimal possible hydrogen-bonding cluster), thus suggesting that the super-critical regime be characterized by the coexistence of nanoscopic subsystems in either the pseudo-liquid or the pseudo-gas phase with each subsystem fluctuating between forming and disrupting the minimal hydrogen-bonding network. [ABSTRACT FROM AUTHOR]

The reasons for the sluggish kinetics of the hydrogen adsorption reaction in alkaline media remain a question still to be solved. This information is important to achieve a complete understanding of the mechanistic details that could lead to the production of key catalytic materials necessary for the development of a future hydrogen economy. For a better understanding of this reaction, it is important to acquire information about the thermodynamic parameters characteristic of the different steps in the reaction. Among these, the hydrogen adsorption is a key step in the process of hydrogen evolution. Although some debate still remains about the difference between adsorbed hydrogen in the underpotential deposition (UPD) region and at the overpotential deposition region, there is no doubt that understanding the former can help in the understanding of the latter. Making use of charge density measurements, we report on this paper a thermodynamic study of the hydrogen UPD process on Pt(111) in 0.05M NaOH over the range of temperatures from 283 ≤ T/K ≤ 313. The coulometric features corresponding to HUPD allow for the calculation of the hydrogen coverage and a fit to a Generalized Frumkin isotherm. From these values, different thermodynamic functions for the UPD reaction have been calculated: ΔGads, ΔSads, ΔHads, and the Pt–H bond energy. From extrapolation, a value of Δ S a d s ◦ = − 7.5 ± 4 J mol − 1 K − 1 was found, which is very close to 0, much lower than previously reported measurements both in acid and in alkaline solutions. Such value has an effect on the enthalpy and bond energy calculations, the latter having a decreasing tendency with pH and coverage. This tendency is completely different from the acidic systems and implies that the change in the thermodynamic functions due to the formation of the double layer and the reorganization of interfacial water has a strong influence on the process in high pH solutions. [ABSTRACT FROM AUTHOR]

In Paper I [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 139(23), 234104 (2013)], we showed that how a third-order Weeks-Chandler-Anderson (WCA) Thermodynamic Perturbation Theory and molecular simulation can be integrated to characterize the repulsive and dispersive contributions to the Helmholtz free energy for realistic molecular conformations. To this end, we focused on n-alkanes to develop a theory for fused and soft chains. In Paper II [A. F. Ghobadi and J. R. Elliott, J. Chem. Phys. 141(2), 024708 (2014)], we adapted the classical Density Functional Theory and studied the microstructure of the realistic molecular fluids in confined geometries and vapor-liquid interfaces. We demonstrated that a detailed consistency between molecular simulation and theory can be achieved for both bulk and inhomogeneous phases. In this paper, we extend the methodology to molecules with partial charges such as carbon dioxide, water, 1-alkanols, nitriles, and ethers. We show that the electrostatic interactions can be captured via an effective association potential in the framework of Statistical Associating Fluid Theory (SAFT). Implementation of the resulting association contribu¬tion in assessing the properties of these molecules at confined geometries and interfaces presents satisfactory agreement with molecular simulation and experimental data. For example, the predicted surface tension deviates less than 4% comparing to full potential simulations. Also, the theory, re¬ferred to as SAFT-γ WCA, is able to reproduce the specific orientation of hydrophilic head and hydrophobic tail of 1-alkanols at the vapor-liquid interface of water. [ABSTRACT FROM AUTHOR]

A large number of force fields have been proposed for describing the behavior of liquid water within classical atomistic simulations, particularly molecular dynamics. In the past two decades, models that incorporate molecular polarizability and even charge transfer have become more prevalent, in attempts to develop more accurate descriptions. These are frequently parameterized to reproduce the measured thermodynamics, phase behavior, and structure of water. On the other hand, the dynamics of water is rarely considered in the construction of these models, despite its importance in their ultimate applications. In this paper, we explore the structure and dynamics of polarizable and charge-transfer water models, with a focus on timescales that directly or indirectly relate to hydrogen bond (H-bond) making and breaking. Moreover, we use the recently developed fluctuation theory for dynamics to determine the temperature dependence of these properties to shed light on the driving forces. This approach provides key insight into the timescale activation energies through a rigorous decomposition into contributions from the different interactions, including polarization and charge transfer. The results show that charge transfer effects have a negligible effect on the activation energies. Furthermore, the same tension between electrostatic and van der Waals interactions that is found in fixed-charge water models also governs the behavior of polarizable models. The models are found to involve significant energy–entropy compensation, pointing to the importance of developing water models that accurately describe the temperature dependence of water structure and dynamics. [ABSTRACT FROM AUTHOR]

Confinement has been shown to contribute to the dynamics of small molecules within nanoscale hydrophobic or hydrophilic cavities. Enclosure within a confined space can also influence energy transfer pathways, such as the enhancement of fluorescence over thermal relaxation. In this paper, the effect of confinement on the thermodynamic properties and reaction kinetics of small hydrophobic molecules confined in a soft polymeric template is detailed. A quasi-elastic neutron scattering experiment identified a substantial decrease in translational diffusion of pyrrole after solubilization within a hydrophobic cavity. This decrease in mobility is due to pyrrole's closer packing and increased density under confinement vs the bulk liquid. The decreased mobility and increased density explain the spontaneous polymerization reaction of pyrrole observed within the cavity. The precise characterization of the polymerization kinetics under confinement found that the reaction is independent of pyrrole concentration, consistent with the close packing density. Kinetic data also show that confinement dimensionality finds a thermodynamic expression in the transition state entropy. The dynamics and kinetics experiments reported here offer rare empirical insight into the important influence that cavity geometry places on the reactions they host. [ABSTRACT FROM AUTHOR]

The first order curvature correction to the crystal-liquid interfacial free energy is calculated using a theoretical model based on the interfacial excess thermodynamic properties. The correction parameter (δ), which is analogous to the Tolman length at a liquid-vapor interface, is found to be 0.48 ± 0.05 for a Lennard-Jones (LJ) fluid. We show that this curvature correction is crucial in predicting the nucleation barrier when the size of the crystal nucleus is small. The thermodynamic driving force (Δμ) corresponding to available simulated nucleation conditions is also calculated by combining the simulated data with a classical density functional theory. In this paper, we show that the classical nucleation theory is capable of predicting the nucleation barrier with excellent agreement to the simulated results when the curvature correction to the interfacial free energy is accounted for. [ABSTRACT FROM AUTHOR]

Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms, by capturing the microscopic configurations of all the atoms. In this paper, we introduce a thermodynamic model that links macroscopic theories and atomicscale simulations and thus provide a simple and elegant framework for testing the limits of classical nucleation theory. [ABSTRACT FROM AUTHOR]

In this paper, we present a study of supercooled liquids interacting with the Lennard Jones potential and the corresponding purely repulsive (Weeks-Chandler-Andersen) potential, over a range of densities and temperatures, in order to understand the origin of their different dynamics in spite of their structures being similar. Using the configurational entropy as the thermodynamic marker via the Adam Gibbs relation, we show that the difference in the dynamics of these two systems at low temperatures can be explained from thermodynamics. At higher densities both the thermodynamical and dynamical difference between these model systems decrease, which is quantitatively demonstrated in this paper by calculating different parameters. The study also reveals the origin of the difference in pair entropy despite the similarity in the structure. Although the maximum difference in structure is obtained in the partial radial distribution function of the B type of particles, the rdf of AA pairs and AB pairs gives rise to the differences in the entropy and dynamics. This work supports the observation made in an earlier study [A. Banerjee et al., Phys. Rev. Lett. 113, 225701 (2014)] and shows that they are generic in nature, independent of density. [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 Paper I [O. Coquand and M. Sperl, J. Chem. Phys. 152, 124112 (2020)], we derived analytical expressions for the structure factor of the square-shoulder potential in a perturbative way around the high- and low-temperature regimes. Here, various physical properties of these solutions are derived. In particular, we investigate the large wave number sector and relate it to the contact values of the pair-correlation function. Then, the thermoelastic properties of the square-shoulder fluids are discussed. [ABSTRACT FROM AUTHOR]

Ionic microgel particles in a good solvent swell to an equilibrium size determined by a balance of electrostatic and elastic forces. When crowded, ionic microgels deswell owing to a redistribution of microions inside and outside the particles. The concentration-dependent deswelling affects the interactions between the microgels and, consequently, the suspension properties. We present a comprehensive theoretical study of crowding effects on thermodynamic, structural, and dynamic properties of weakly cross-linked ionic microgels in a good solvent. The microgels are modeled as microion- and solvent-permeable colloidal spheres with fixed charge uniformly distributed over the polymer gel backbone, whose elastic and solvent-interaction free energies are described using the Flory-Rehner theory. Two mean-field methods for calculating the crowding-dependent microgel radius are investigated and combined with calculations of the net microgel charge characterizing the electrostatic part of an effective microgel pair potential, with charge renormalization accounted for. Using this effective pair potential, thermodynamic and static suspension properties are calculated, including the osmotic pressure and microgel pair distribution function. The latter is used in our calculations of dynamic suspension properties, where we account for hydrodynamic interactions. Results for diffusion and rheological properties are presented over ranges of microgel concentration and charge. We show that deswelling mildly enhances self- diffusion and collective diffusion and the osmotic pressure, lowers the suspension viscosity, and significantly shifts the suspension crystallization point to higher concentrations. This paper presents a bottom-up approach to efficiently computing suspension properties of crowded ionic microgels using single-particle characteristics. [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]

The lattice cluster theory (LCT) for semiflexible linear telechelic melts, developed in Paper I, is applied to examine the influence of chain stiffness on the average degree of self-assembly and the basic thermodynamic properties of linear telechelic polymer melts. Our calculations imply that chain stiffness promotes self-assembly of linear telechelic polymer melts that assemble on cooling when either polymer volume fraction f or temperature T is high, but opposes self-assembly when both f and T are sufficiently low. This allows us to identify a boundary line in the f-T plane that separates two regions of qualitatively different influence of chain stiffness on self-assembly. The enthalpy and entropy of self-assembly are usually treated as adjustable parameters in classical Flory-Huggins type theories for the equilibrium self-assembly of polymers, but they are demonstrated here to strongly depend on chain stiffness. Moreover, illustrative calculations for the dependence of the entropy density of linear telechelic polymer melts on chain stiffness demonstrate the importance of including semiflexibility within the LCT when exploring the nature of glass formation in models of linear telechelic polymer melts. [ABSTRACT FROM AUTHOR]

In this paper, a new theory is developed for the self-assembly of associating molecules confined to a single spatial dimension, but allowed to explore all orientation angles. The interplay of the anisotropy of the pair potential and the low dimensional space results in orientationally ordered associated clusters. This local order enhances association due to a decrease in orientational entropy. Unlike bulk 3D fluids which are orientationally homogeneous, association in 1D necessitates the self-consistent calculation of the orientational distribution function. To test the new theory, Monte Carlo simulations are performed and the theory is found to be accurate. It is also shown that the traditional treatment in first order perturbation theory fails to accurately describe this system. The theory developed in this paper may be used as a tool to study hydrogen bonding of molecules in 1D zeolites as well as the hydrogen bonding of molecules in carbon nanotubes. [ABSTRACT FROM AUTHOR]

The thermodynamics of iron clusters of various sizes, from 76 to 2452 atoms, typical of the catalyst particles used for carbon nanotubes growth, has been explored by a flat histogram Monte Carlo (MC) algorithm (called the a -mapping), developed by Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. This method provides the classical density of states, gp(Ep) in the configurational space, in terms of the potential energy of the system, with good and well controlled convergence properties, particularly in the melting phase transition zone which is of interest in this work. To describe the system, an iron potential has been implemented, called "corrected EAM" (cEAM), which approximates the MEAM potential of Lee et al. [Phys. Rev. B 64, 184102 (2001)] with an accuracy better than 3 meV/at, and a five times larger computational speed. The main simplification concerns the angular dependence of the potential, with a small impact on accuracy, while the screening coefficients Sij are exactly computed with a fast algorithm. With this potential, ergodic explorations of the clusters can be performed efficiently in a reasonable computing time, at least in the upper half of the solid zone and above. Problems of ergodicity exist in the lower half of the solid zone but routes to overcome them are discussed. The solid-liquid (melting) phase transition temperature Tm is plotted in terms of -- 1/3 the cluster atom number Nat. The standard Nat -1/3 <150, a strong divergence is observed compared to the Pawlow law. The melting transition, which begins at the surface, is stated by a Lindemann-Berry index and an atomic density analysis. Several new features are obtained for the thermodynamics of cEAM clusters, compared to the Rydberg pair potential clusters studied in Paper I. [ABSTRACT FROM AUTHOR]at <150, a strong divergence is observed compared to the Pawlow law. The melting transition, which begins at the surface, is stated by a Lindemann-Berry index and an atomic density analysis. Several new features are obtained for the thermodynamics of cEAM clusters, compared to the Rydberg pair potential clusters studied in Paper I. [ABSTRACT FROM AUTHOR]

In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = sY between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats sY. We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction. [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]

A good understanding and determination of colloidal interactions is paramount to comprehend and model the thermodynamic and structural properties of colloidal suspensions. In concentrated aqueous suspensions of colloids with a titratable surface charge, this determination is, however, complicated by the density dependence of the effective pair potential due to both the many-body interactions and the charge regulation of the colloids. In addition, colloids generally present a size distribution which results in a virtually infinite combination of colloid pairs. In this paper, we develop two methods and describe the corresponding algorithms to solve this problem for arbitrary size distributions. An implementation in Nim is also provided. The methods, inspired by the seminal work of Torres et al., [J. Chem. Phys. 128, 154906 (2008)] are based on a generalization of the cell and renormalized jellium models to polydisperse suspensions of spherical colloids with a charge regulating boundary condition. The latter is described by the one-pK-Stern model. The predictions of the models are confronted to the equations of state of various commercially available silica dispersions. The renormalized Yukawa parameters (effective charges and screening lengths) are also calculated. The importance of size and charge polydispersity as well as the validity of these two models is discussed in light of the results. [ABSTRACT FROM AUTHOR]

We propose to couple a state-resolved rovibrational coarse-grain model to a stochastic particle method for simulating internal energy excitation and dissociation of a molecular gas. A coarse-grained model for a rovibrational reaction mechanism of an ab initio database developed at the NASA Ames Research Center for the N2–N system is modified based on variably spaced energy bins. The thermodynamic properties of the modified coarse-grained model allow us to closely match those obtained with the full set of rovibrational levels over a wide temperature range, while using a number of bins significantly smaller than the complete mechanism. The chemical-kinetic behavior of equally and variably spaced bin formulations is compared by simulating internal energy excitation and dissociation of nitrogen in an adiabatic, isochoric reactor. We find that the variably spaced formulation is better suited for reproducing the dynamics of the full database at conditions of interest in the Earth atmospheric entry. Also in this paper, we discuss the details of our particle method implementation for the uniform rovibrational collisional bin model and describe changes to the Direct Simulation Monte Carlo (DSMC) collision algorithm, which become necessary to accommodate our state-resolved reaction mechanism for excitation and dissociation reactions. The DSMC code is then verified against equivalent master equation calculations. In these simulations, state-resolved cross sections are used in analytical form. These cross sections verify micro-reversibility relations for the rovibrational bins and allow for fast execution of the DSMC code. In our verification calculations, we obtain very close agreement for the concentrations profiles of N and N2, as well as the translational and rovibrational mode temperatures obtained independently through both methods. In addition to macroscopic moments, we compare discrete internal energy populations predicted at selected time steps via DSMC and the master equations. We observe good agreement between the two sets of results within the limits imposed by statistical scatter, which is inherent to particle-based DSMC solutions. As future work, the rovibrational coarse-grain model coupled to the particle method will allow us to study 3D reentry flow configurations. [ABSTRACT FROM AUTHOR]

The solid-solid and melting transitions that occur in Lennard-Jones LJn clusters have been both fascinating and challenging for the computational physics community over the last several decades. A number of attempts to extend these studies to the quantum case have also been made. Particularly interesting is the exploration of the parallel between the thermally induced and quantum-induced transitions. Yet, both numerically accurate and systematic studies of the latter are still lacking. In this paper, we apply the diffusion Monte Carlo method to the especially difficult case of LJ38. Starting with the truncated octahedral global minimum configuration, as the de Boer quantum delocalization parameterΛincreases, the system undergoes two consecutive solid-solid transitions, switching to anti-Mackay configurations. At sufficiently large values of Λ, the cluster is completely "melted" which is manifested by delocalization of the ground statewavefunction over a very large number of minima that represent several structural motifs. [ABSTRACT FROM AUTHOR]

Fluctuating hydrodynamics (FHD) provides a framework for modeling microscopic fluctuations in a manner consistent with statistical mechanics and nonequilibrium thermodynamics. This paper presents an FHD formulation for isothermal reactive incompressible liquid mixtures with stochastic chemistry. Fluctuating multispecies mass diffusion is formulated using a Maxwell–Stefan description without assuming a dilute solution, and momentum dynamics is described by a stochastic Navier–Stokes equation for the fluid velocity. We consider a thermodynamically consistent generalization for the law of mass action for non-dilute mixtures and use it in the chemical master equation (CME) to model reactions as a Poisson process. The FHD approach provides remarkable computational efficiency over traditional reaction-diffusion master equation methods when the number of reactive molecules is large, while also retaining accuracy even when there are as few as ten reactive molecules per hydrodynamic cell. We present a numerical algorithm to solve the coupled FHD and CME equations and validate it on both equilibrium and nonequilibrium problems. We simulate a diffusively driven gravitational instability in the presence of an acid-base neutralization reaction, starting from a perfectly flat interface. We demonstrate that the coupling between velocity and concentration fluctuations dominates the initial growth of the instability. [ABSTRACT FROM AUTHOR]

The numerical computation of chemical potential in dense non-homogeneous fluids is a key problem in the study of confined fluid thermodynamics. To this day, several methods have been proposed; however, there is still need for a robust technique, capable of obtaining accurate estimates at large average densities. A widely established technique is the Widom insertion method, which computes the chemical potential by sampling the energy of insertion of a test particle. Non-homogeneity is accounted for by assigning a density dependent weight to the insertion points. However, in dense systems, the poor sampling of the insertion energy is a source of inefficiency, hampering a reliable convergence. We have recently presented a new technique for the chemical potential calculation in homogeneous fluids. This novel method enhances the sampling of the insertion energy via well-tempered metadynamics, reaching accurate estimates at very large densities. In this paper, we extend the technique to the case of non-homogeneous fluids. The method is successfully tested on a confined Lennard-Jones fluid. In particular, we show that, thanks to the improved sampling, our technique does not suffer from a systematic error that affects the classic Widom method for non-homogeneous fluids, providing a precise and accurate result. [ABSTRACT FROM AUTHOR]

We extend the vibronic exciton theory introduced in our previous work to study singlet fission dynamics, in particular addressing recent indications of the importance of vibronic coupling in this process. A microscopic and non-perturbative treatment of electronic and selected vibrational degrees of freedom in combination with Redfield theory allows us to dynamically consider clusters of molecules under conditions close to those in molecular crystals that exhibit fission. Using bulk pentacene as a concrete example, our results identify a number of factors that render fission rapid and effective. Strong coupling to high-frequency Holstein modes generates resonances between the photo-prepared singlet and product triplet states. We furthermore find the large number of triplet combinations associated with bulk periodic systems to be critical to the fission process under such vibronically resonant conditions. In addition, we present results including, in an approximate manner, the effects of Peierls coupling, indicating that this factor can both enhance and suppress fission depending on its interplay with vibronic resonance and thermodynamics. [ABSTRACT FROM AUTHOR]

Attempts to establish an absolute single-ion hydration free energy scale have followed multiple strategies. Two central themes consist of (1) employing bulk pair thermodynamic data and an underlying interfacial-potential-free model to partition the hydration free energy into individual contributions [Marcus, Latimer, and tetraphenyl-arsonium/tetraphenyl-borate (TATB) methods] or (2) utilizing bulk thermodynamic and cluster data to estimate the free energy to insert a proton into water, including in principle an interfacial potential contribution [the cluster pair approximation (CPA)]. While the results for the hydration free energy of the proton agree remarkably well between the three approaches in the first category, the value differs from the CPA result by roughly +10 kcal/mol, implying a value for the effective electrochemical surface potential of water of −0.4 V. This paper provides a computational re-analysis of the TATB method for single-ion free energies using quasichemical theory. A previous study indicated a significant discrepancy between the free energies of hydration for the TA cation and the TB anion. We show that the main contribution to this large computed difference is an electrostatic artifact arising from modeling interactions in periodic boundaries. No attempt is made here to develop more accurate models for the local ion/solvent interactions that may lead to further small free energy differences between the TA and TB ions, but the results clarify the primary importance of interfacial potential effects for analysis of the various free energy scales. Results are also presented, related to the TATB assumption in the organic solvents dimethyl sulfoxide and 1,2-dichloroethane. [ABSTRACT FROM AUTHOR]

This paper derives and discusses the configuration-space Langevin equation describing a physically aging R-simple system and the corresponding Smoluchowski equation. Externally controlled thermodynamic variables like temperature, density, and pressure enter the description via the single parameter Ts/T, in which T is the bath temperature and Ts is the "systemic" temperature defined at any time t as the thermodynamic equilibrium temperature of the state point with density p(t) and potential energy U(t). In equilibrium, Ts ≌ T with fluctuations that vanish in the thermodynamic limit. In contrast to Tool's fictive temperature and other effective temperatures in glass science, the systemic temperature is defined for any configuration with a well-defined density, even if it is not close to equilibrium. Density and systemic temperature define an aging phase diagram, in which the aging system traces out a curve. Predictions are discussed for aging following various densitytemperature and pressure-temperature jumps from one equilibrium state to another, as well as for a few other scenarios. The proposed theory implies that R-simple glass-forming liquids are characterized by the dynamic Prigogine-Defay ratio being equal to unity. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules, but they are limited by the time scale barrier. That is, we may not obtain properties' efficiently because we need to run microseconds or longer simulations using femtosecond time steps. To overcome this time scale barrier, we can use the weighted ensemble (WE) method, a powerful enhanced sampling method that efficiently samples thermodynamic and kinetic properties. However, the WE method requires an appropriate partitioning of phase space into discrete macrostates, which can be problematic when we have a high-dimensional collective space or when little is known a priori about the molecular system. Hence, we developed a new WE-based method, called the "Concurrent Adaptive Sampling (CAS) algorithm," to tackle these issues. The CAS algorithm is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective variables and adaptive macrostates to enhance the sampling in the high-dimensional space. This is especially useful for systems in which we do not know what the right reaction coordinates are, in which case we can use many collective variables to sample conformations and pathways. In addition, a clustering technique based on the committor function is used to accelerate sampling the slowest process in the molecular system. In this paper, we introduce the new method and show results from two-dimensional models and bio-molecules, specifically penta-alanine and a triazine trimer. [ABSTRACT FROM AUTHOR]

It has been extensively demonstrated through first principles quantum mechanics calculations that water exhibits strong hydrogen bond cooperativity. Equations of state developed from statistical mechanics typically assume pairwise additivity, meaning they cannot account for these 3-body and higher cooperative effects. In this paper, we extend a second order thermodynamic perturbation theory to correct for hydrogen bond cooperativity in 4 site water. We demonstrate that the theory predicts hydrogen bonding structure consistent spectroscopy, neutron diffraction, and molecular simulation data. Finally, we implement the approach into a general equation of state for water. [ABSTRACT FROM AUTHOR]

In the present paper we examine the risk-sensitive and sampling issues associated with the problem of calculating generalized averages. By combining thermodynamic integration, stationary phase Monte Carlo, and infinite swapping techniques, we develop an approach for such problems and explore its utility for a prototypical class of applications. [ABSTRACT FROM AUTHOR]

The aim of this paper is to decide which of the two possible thermodynamic expressions for the cooperativity length in glass forming liquids is the correct one. In the derivation of these two expressions, the occurrence of temperature fluctuations in the considered nanoscale subsystems is either included or neglected. Consequently, our analysis gives also an answer to the widely discussed problem whether temperature fluctuations have to be generally accounted for in thermodynamics or not. To this end, the characteristic length-scales at equal times and temperatures for propylene glycol were determined independently from AC calorimetry in both the above specified ways and from quasielastic neutron scattering (QENS), and compared. The result shows that the cooperative length determined from QENS coincides most consistently with the cooperativity length determined from AC calorimetry measurements for the case that the effect of temperature fluctuations is incorporated in the description. This conclusion indicates that--accounting for temperature fluctuations--the characteristic length can be derived by thermodynamic considerations from the specific parameters of the liquid at glass transition and that temperature does fluctuate in small systems. [ABSTRACT FROM AUTHOR]

The paper aims at a comparison of techniques based on the kinetic Monte Carlo (kMC) and the conventional Metropolis Monte Carlo (MC) methods as applied to the hard-sphere (HS) fluid and solid. In the case of the kMC, an alternative representation of the chemical potential is explored [E. A. Ustinov and D. D. Do, J. Colloid Interface Sci. 366, 216 (2012)], which does not require any external procedure like the Widom test particle insertion method. A direct evaluation of the chemical potential of the fluid and solid without thermodynamic integration is achieved by molecular simulation in an elongated box with an external potential imposed on the system in order to reduce the particle density in the vicinity of the box ends. The existence of rarefied zones allows one to determine the chemical potential of the crystalline phase and substantially increases its accuracy for the disordered dense phase in the central zone of the simulation box. This method is applicable to both the Metropolis MC and the kMC, but in the latter case, the chemical potential is determined with higher accuracy at the same conditions and the number of MC steps. Thermodynamic functions of the disordered fluid and crystalline face-centered cubic (FCC) phase for the hard-sphere system have been evaluated with the kinetic MC and the standard MC coupled with the Widom procedure over a wide range of density. The melting transition parameters have been determined by the point of intersection of the pressure-chemical potential curves for the disordered HS fluid and FCC crystal using the Gibbs-Duhem equation as a constraint. A detailed thermodynamic analysis of the hardsphere fluid has provided a rigorous verification of the approach, which can be extended to more complex systems. [ABSTRACT FROM AUTHOR]

The extent to which solvent-mediated effective interactions between nanoparticles can be predicted based on structure and associated thermodynamic estimators for bulk solvents and for solvation of single and pairs of nanoparticles is studied here. As a test of the approach, we analyse the strategy for creating temperature-independent solvent environments using a series of homologous chain fluids as solvents, as suggested by an experimental paper [M. I. Bodnarchuk et al., J. Am. Chem. Soc. 132, 11967 (2010)]. Our conclusions are based on molecular dynamics simulations of Au140(SC10H21)62 nanoparticles in n-alkane solvents, specifically hexane, octane, decane and dodecane, using the TraPPE-UA potential to model the alkanes and alkylthiols. The 140-atom gold core of the nanocrystal is held rigid in a truncated octahedral geometry and the gold-thiolate interaction is modeled using a Morse potential. The experimental observation was that the structural and rheological properties of n-alkane solvents are constant over a temperature range determined by equivalent solvent vapour pressures. We show that this is a consequence of the fact that long chain alkane liquids behave to a good approximation as simple liquids formed by packing of monomeric methyl/methylene units. Over the corresponding temperature range (233-361 K), the solvation environment is approximately constant at the single and pair nanoparticle levels under good solvent conditions. However, quantitative variations of the order of 10%-20% do exist in various quantities, such as molar volume of solute at infinite dilution, entropy of solvation, and onset distance for soft repulsions. In the opposite limit of a poor solvent, represented by vacuum in this study, the effective interactions between nanoparticles are no longer temperature-independent with attractive interactions increasing by up to 50% on decreasing the temperature from 361 K to 290 K, accompanied by an increase in emergent anisotropy due to correlation of mass dipoles on the two nanoparticles. One expects therefore that during self-assembly using solvent evaporation, temperature can be used as a structure-directing factor as long as good solvent conditions are maintained. It also suggests that disordered configurations may emerge as solvent quality decreases due to increasing role of short-range attractions and ligand fluctuation-driven anisotropy. The possibilities of using structural estimators of various thermodynamic quantities to analyse the interplay of ligand fluctuations and solvent quality in self-assembly as well as to design solvation environments are discussed. [ABSTRACT FROM AUTHOR]

The recent theoretical prediction by Maimbourg and Kurchan [e-print arXiv:1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2,3,4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized by high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly. [ABSTRACT FROM AUTHOR]

The formation of core/shell structures in hydrogels upon interaction with surfactants is a well-known phenomenon, but whether they are equilibrium states or not is still under debate. This paper presents an equilibrium theory of phase coexistence in hydrogels meant to answer the question of the stability of core/shell separation. The theory suggests that core/shell separation caused by surfactants can indeed be thermodynamically stable if the amount of added surfactant is not too large, but that the exact phase behaviour is governed by both the volume and concentration of the added surfactant solution. [ABSTRACT FROM AUTHOR]

Coarse-grained models are useful tools to investigate the structural and thermodynamic properties of biomolecules. They are obtained by merging several atoms into one interaction site. Such simplified models try to capture as much as possible information of the original biomolecular system in all-atom representation but the resulting parameters of these coarse-grained force fields still need further optimization. In this paper, a force field optimization method, which is based on maximum-likelihood fitting of the simulated to the experimental conformational ensembles and least-squares fitting of the simulated to the experimental heat-capacity curves, is applied to optimize the Nucleic Acid united-RESidue 2-point (NARES-2P) model for coarse-grained simulations of nucleic acids recently developed in our laboratory. The optimized NARES-2P force field reproduces the structural and thermodynamic data of small DNA molecules much better than the original force field. [ABSTRACT FROM AUTHOR]

Standard Flory-Huggins (FH) theory is utilized to describe the enigmatic cosolvency and cononsolvency phenomena for systems of polymers dissolved in mixed solvents. In particular, phase boundaries (specifically upper critical solution temperature spinodals) are calculated for solutions of homopolymers B in pure solvents and in binary mixtures of small molecule liquids A and C. The miscibility (or immiscibility) patterns for the ternary systems are classified in terms of the FH binary interaction parameters {Xαβ} and the ratio r = øA/øC of the concentrations øA and øC of the two solvents. The trends in miscibility are compared to those observed for blends of random copolymers (AxC1-x) with homopolymers (B) and to those deduced for A/B/C solutions of polymers B in liquid mixtures of small molecules A and C that associate into polymeric clusters {ApCq}i, (i = 1,2, ..., ∞). Although the classic FH theory is able to explain cosolvency and cononsolvency phenomena, the theory does not include a consideration of the mutual association of the solvent molecules and the competitive association between the solvent molecules and the polymer. These interactions can be incorporated in refinements of the FH theory, and the present paper provides a foundation for such extensions for modeling the rich thermodynamics of polymers in mixed solvents. [ABSTRACT FROM AUTHOR]

Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achieve this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute. [ABSTRACT FROM AUTHOR]

In this paper, we define and experimentally verify thermodynamic characteristics of the liquid-glass transition, taking into account a kinetic origin of the process. Using the density scaling law and the four-point measure of the dynamic heterogeneity of molecular dynamics of glass forming liquids, we investigate contributions of enthalpy, temperature, and density fluctuations to spatially heterogeneous molecular dynamics at the liquid-glass transition, finding an equation for the pressure coefficient of the glass transition temperature, dTg/dp. This equation combined with our previous formula for dTg/dp, derived solely from the density scaling criterion, implies a relationship among thermodynamic coefficients at Tg. Since this relationship and both the equations for dTg/dp are very well validated using experimental data at Tg, they are promising alternatives to the classical Prigogine-Defay ratio and both the Ehrenfest equations in case of the liquid-glass transition. [ABSTRACT FROM AUTHOR]

In this paper, we present an improved method for obtaining unbiased estimates of the free energy difference between two thermodynamic states using the work distribution measured in nonequilibrium driven experiments connecting these states. The method is based on the assumption that any observed work distribution is given by a mixture of Gaussian distributions, whose normal components are identical in either direction of the nonequilibrium process, with weights regulated by the Crooks theorem. Using the prototypical example for the driven unfolding/folding of deca-alanine, we show that the predicted behavior of the forward and reverse work distributions, assuming a combination of only two Gaussian components with Crooks derived weights, explains surprisingly well the striking asymmetry in the observed distributions at fast pulling speeds. The proposed methodology opens the way for a perfectly parallel implementation of Jarzynski-based free energy calculations in complex systems. [ABSTRACT FROM AUTHOR]

Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics (MD) simulation approaches appropriate for the study of complex systems. This paper examines the use of two common truncated Lennard-Jones (Weeks-Chandler-Andersen (WCA)) potentials to describe a pair of colloidal particles in a thermal bath of depletants. The shifted-WCA model is the steeper of the two repulsive potentials considered, while the combinatorial-WCA model is the softer. It is found that the depletion-induced well depth for the combinatorial-WCA model is significantly deeper than the shifted-WCA model because the resulting overlap of the colloids yields extra accessible volume for depletants. For both shifted- and combinatorial-WCA simulations, the second virial coefficients and pair potentials between colloids are demonstrated to be well approximated by the Morphometric Thermodynamics (MT) model. This agreement suggests that the presence of depletants can be accurately modelled in MD simulations by implicitly including them through simple, analytical MT forms for depletion-induced interactions. Although both WCA potentials are found to be effective generic coarse-grained simulation approaches for studying depletion effects in complicated soft matter systems, combinatorial-WCA is the more efficient approach as depletion effects are enhanced at lower depletant densities. The findings indicate that for soft matter systems that are better modelled by potentials with some compressibility, predictions from hard-sphere systems could greatly underestimate the magnitude of depletion effects at a given depletant density. [ABSTRACT FROM AUTHOR]

Any solid surface is intrinsically rough on the microscopic scale. In this paper, we study the effect of this roughness on the wetting properties of hydrophilic substrates. Macroscopic arguments, such as those leading to the well-known Wenzel's law, predict that surface roughness should amplify the wetting properties of such adsorbents. We use a fundamental measure density functional theory to demonstrate the opposite effect from roughness for microscopically corrugated surfaces, i.e., wetting is hindered. Based on three independent analyses we show that microscopic surface corrugation increases the wetting temperature or even makes the surface hydrophobic. Since for macroscopically corrugated surfaces the solid texture does indeed amplify wetting there must exist a crossover between two length-scale regimes that are distinguished by opposite response on surface roughening. This demonstrates how deceptive can be efforts to extend the thermodynamical laws beyond their macroscopic territory. [ABSTRACT FROM AUTHOR]

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterionmediated free energy conclusively directs folding into a compact structure. [ABSTRACT FROM AUTHOR]

A classical molecular dynamics simulation was conducted for a system composed of fluid molecules between two planar solid surfaces, and whose interactions are described by the 12-6 Lennard-Jones form. This paper presents a general description of the pressure components and interfacial tension at a fluid-solid interface obtained by the perturbative method on the basis of statistical thermodynamics, proposes a method to consider the pressure components tangential to an interface which are affected by interactions with solid atoms, and applies this method to the calculation system. The description of the perturbative method is extended to subsystems, and the local pressure components and interfacial tension at a liquid-solid interface are obtained and examined in one- and two-dimensions. The results are compared with those obtained by two alternative methods: (a) an evaluation of the intermolecular force acting on a plane, and (b) the conventional method based on the virial expression. The accuracy of the numerical results is examined through the comparison of the results obtained by each method. The calculated local pressure components and interfacial tension of the fluid at a liquid-solid interface agreed well with the results of the two alternative methods at each local position in one dimension. In two dimensions, the results showed a characteristic profile of the tangential pressure component which depended on the direction tangential to the liquid-solid interface, which agreed with that obtained by the evaluation of the intermolecular force acting on a plane in the present study. Such good agreement suggests that the perturbative method on the basis of statistical thermodynamics used in this study is valid to obtain the local pressure components and interfacial tension at a liquid-solid interface. [ABSTRACT FROM AUTHOR]

In this paper, we have demonstrated that resonant activation (RA) is possible even in a thermodynamically closed system where the particle experiences a random force and a spatio-temporal frictional coefficient from the thermal bath. For this stochastic process, we have observed a hallmark of RA phenomena in terms of a turnover behavior of the barrier-crossing rate as a function of noise correlation time at a fixed noise variance. Variance can be fixed either by changing temperature or damping strength as a function of noise correlation time. Our another observation is that the barrier crossing rate passes through a maximum with increase in coupling strength of the multiplicative noise. If the damping strength is appreciably large, then the maximum may disappear. Finally, we compare simulation results with the analytical calculation. It shows that there is a good agreement between analytical and numerical results. [ABSTRACT FROM AUTHOR]

We develop a physically based equation of state that describes Mie ν-6 fluids with an accuracy comparable to that of state-of-the-art empirical models. The equation of state is developed within the framework of the uv-theory [T. van Westen and J. Gross, J. Chem. Phys. 155, 244501 (2021)], which is modified by incorporating the third virial coefficient B3 in the low-density description of the model. The new model interpolates between a first-order Weeks–Chandler–Andersen (WCA) perturbation theory at high densities and a modified first-order WCA theory that recovers the virial expansion up to B3 at low densities. A new algebraic equation for the third virial coefficient of Mie ν-6 fluids is developed—other inputs are taken from previous work. Predicted thermodynamic properties and phase equilibria are compared to a comprehensive database of molecular simulation results from the literature, including Mie fluids of repulsive exponents 9 ≤ ν ≤ 48. The new equation of state is applicable to states with densities up to ρ * ( T * ) ⪅ 1.1 + 0.12 T * and temperatures T* > 0.3. For the Lennard-Jones fluid (ν = 12), the performance of the model is comparable to that of the best empirical equations of state available. As compared to empirical models, the physical basis of the new model provides several advantages, however: (1) the new model is applicable to Mie fluids of repulsive exponents 9 ≤ ν ≤ 48 instead of only ν = 12, (2) the model leads to a better description of the meta-stable and unstable region (which is important for describing interfacial properties by classical density functional theory), and (3) being a first-order perturbation theory, the new model (potentially) allows an easier and more rigorous extension to non-spherical (chain) fluids and mixtures. [ABSTRACT FROM AUTHOR]

Pressure-induced perturbation of a protein structure leading to its folding–unfolding mechanism is an important yet not fully understood phenomenon. The key point here is the role of water and its coupling with protein conformations as a function of pressure. In the current work, using extensive molecular dynamics simulation at 298 K, we systematically examine the coupling between protein conformations and water structures of pressures of 0.001, 5, 10, 15, 20 kbar, starting from (partially) unfolded structures of the protein Bovine Pancreatic Trypsin Inhibitor (BPTI). We also calculate localized thermodynamics at those pressures as a function of protein–water distance. Our findings show that both protein-specific and generic effects of pressure are operating. In particular, we found that (1) the amount of increase in water density near the protein depends on the protein structural heterogeneity; (2) the intra-protein hydrogen bond decreases with pressure, while the water–water hydrogen bond per water in the first solvation shell (FSS) increases; protein–water hydrogen bonds also found to increase with pressure, (3) with pressure hydrogen bonds of waters in the FSS getting twisted; and (4) water's tetrahedrality in the FSS decreases with pressure, but it is dependent on the local environment. Thermodynamically, at higher pressure, the structural perturbation of BPTI is due to the pressure–volume work, while the entropy decreases with the increase of pressure due to the higher translational and rotational rigidity of waters in the FSS. The local and subtle effects of pressure, found in this work, are likely to be typical of pressure-induced protein structure perturbation. [ABSTRACT FROM AUTHOR]