New method for the calculation of the pair correlation function. I

Predicting Solvation Free Energies from the Minnesota Solvation Database Using Classical Density Functional Theory Based on the PC-SAFT Equation of State

We critically assess the capabilities of classical density functional theory (DFT) based on the perturbed-chain statistical associating fluid theory (PC-SAFT) equation of state to predict the solvation free energies of small molecules in various hydrocarbon solvents. We compare DFT results with experimental data from the Minnesota solvation database and utilize statistical methods to analyze the accuracy of our approach, as well as its weaknesses. The mean absolute error of the solvation free energies is 3.7 kJ mol-1 for n-alkane solvents, ranging from pentane to hexadecane, with 473 solute-solvent systems. For solvents consisting of cyclic hydrocarbons (cyclohexane, benzene, toluene, and ethylbenzene) with 245 solute-solvent systems, we report a slightly larger mean absolute error of 4.2 kJ mol-1. We identify three possible sources of errors: (i) the neglect of solute-solvent and solvent-solvent Coulomb interactions, which limits the applicability of PC-SAFT DFT to nonpolar and weakly polar molecules; (ii) the solute's Lennard-Jones parameters supplied by the general AMBER force field, which are not parametrized toward solvation free energies; and (iii) the application of the Lorentz-Berthelot combining rules to the dispersive interactions between a segment of the PC-SAFT solvent and a Lennard-Jones interaction site of the solute. The approach is more accurate than standard implementations of phenomenological models in common chemistry software packages, which exhibit mean absolute errors larger than 9.12 kJ mol-1, even though newer phenomenological models achieve a mean absolute error of about 2 kJ mol-1. PC-SAFT DFT is more computationally efficient than state of the art explicit molecular simulations in combination with free energy perturbation methods. It is predictive with respect to solvation free energies, i.e., the input for the model is the (element-specific) molecular force field, the solute configuration from molecular dynamics simulations, and the (substance-specific) PC-SAFT parameters. The PC-SAFT parametrization uses pure-component data and does not require experimental solvation free energies. The PC-SAFT equation of state, without applying a DFT formalism, can also be used to calculate solvation free energies, provided that the PC-SAFT parameters for the solute are available. A large number of substances was recently parametrized by members of our group (Esper, T.; Bauer, G.; Rehner, P.; Gross, J. Ind. Eng. Chem. Res. 2023, 62), which enables a comparison to the DFT approach for 103 substances. Accurate results are obtained from the PC-SAFT equation of state with an MAE below 2.51 kJ mol-1. The DFT approach does not require PC-SAFT parameters for the solute and can be applied to all solutes that can be represented by the molecular force field.

Simulations and integral-equation theories for dipolar density interacting disks

Integral equation theories (IETs) based on the Ornstein-Zernike (OZ) relation can be used as an analytical tool to predict structural and thermodynamic properties and phase behavior of fluids with low numerical cost. However, there are no studies of the IETs for the dipolar density interaction potential in two-dimensional systems, a relevant interdomain interaction in lipid monolayers with phase coexistence. This repulsive interaction arises due to the excess dipole density of the domains, which are aligned perpendicular to the interface. This work studies the performance of three closures of the OZ equation for this novel system: Rogers-Young (RY), modified hypernetted chain (MHNC), and variational modified hypernetted chain (VMHNC). For the last two closures the bridge function of a reference system is required, with the hard disk being the most convenient reference system. Given that in two dimensions there is no analytical expressions for the hard disk correlation functions, two different approximations are proposed: one based on the Percus-Yevick (PY) approximation, and the other based on an extension of the hard spheres Verlet-Weis-Henderson-Grundke (LB) parametrization. The accuracy of the five approaches is evaluated by comparison of the pair correlation function and the structure factor with Monte Carlo simulation data. The results show that RY closure is satisfactory only for low-structured regimes. MHNC and VMHNC closures perform globally well, and there are no significant differences between them. However, the reference system in some cases affects their performance; when the pair correlation function serves as the measure, the LB-based closures quantitatively outperform the PY ones. From the point of view of its applicability, LB-based closures do not have a solution for all studied interaction strength parameters, and, in general, PY-based closures are numerically preferable.

Thermodynamic and kinetic modeling of electrocatalytic reactions using a first-principles approach

The computational modeling of electrochemical interfaces and their applications in electrocatalysis has attracted great attention in recent years. While tremendous progress has been made in this area, however, the accurate atomistic descriptions at the electrode/electrolyte interfaces remain a great challenge. The Computational Hydrogen Electrode (CHE) method and continuum modeling of the solvent and electrolyte interactions form the basis for most of these methodological developments. Several posterior corrections have been added to the CHE method to improve its accuracy and widen its applications. The most recently developed grand canonical potential approaches with the embedded diffuse layer models have shown considerable improvement in defining interfacial interactions at electrode/electrolyte interfaces over the state-of-the-art computational models for electrocatalysis. In this Review, we present an overview of these different computational models developed over the years to quantitatively probe the thermodynamics and kinetics of electrochemical reactions in the presence of an electrified catalyst surface under various electrochemical environments. We begin our discussion by giving a brief picture of the different continuum solvation approaches, implemented within the ab initio method to effectively model the solvent and electrolyte interactions. Next, we present the thermodynamic and kinetic modeling approaches to determine the activity and stability of the electrocatalysts. A few applications to these approaches are also discussed. We conclude by giving an outlook on the different machine learning models that have been integrated with the thermodynamic approaches to improve their efficiency and widen their applicability.

Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM)

The cell as a system of many components, governed by the laws of physics and chemistry drives molecular functions having an impact on the spatial organization of these systems and vice versa. Since the relationship between structure and function is an almost universal rule not only in biology, appropriate methods are required to parameterize the relationship between the structure and function of biomolecules and their networks, the mechanisms of the processes in which they are involved, and the mechanisms of regulation of these processes. Single molecule localization microscopy (SMLM), which we focus on here, offers a significant advantage for the quantitative parametrization of molecular organization: it provides matrices of coordinates of fluorescently labeled biomolecules that can be directly subjected to advanced mathematical analytical procedures without the need for laborious and sometimes misleading image processing. Here, we propose mathematical tools for comprehensive quantitative computer data analysis of SMLM point patterns that include Ripley distance frequency analysis, persistent homology analysis, persistent 'imaging', principal component analysis and co-localization analysis. The application of these methods is explained using artificial datasets simulating different, potentially possible and interpretatively important situations. Illustrative analyses of real complex biological SMLM data are presented to emphasize the applicability of the proposed algorithms. This manuscript demonstrated the extraction of features and parameters quantifying the influence of chromatin (re)organization on genome function, offering a novel approach to study chromatin architecture at the nanoscale. However, the ability to adapt the proposed algorithms to analyze essentially any molecular organizations, e.g., membrane receptors or protein trafficking in the cytosol, offers broad flexibility of use.

A long chain-induced depletion effect for abnormal grafting in the preparation of bimodal bidisperse polymer-grafted nanoparticles

One of the challenging problems in the research field of polymer nanocomposites is how to prepare nanocomposites with high grafting density and strong ability of dispersion at the same time. For nanocomposites composed of bimodal bidisperse polymer chains and nanoparticles, the above requirements can be met by rationally adjusting the ratio of long and short polymer chains. In this study, the process of grafting bimodal bidisperse polymer chains onto the surface of nanoparticles in a grafting-to manner was investigated via computer simulation and theoretical methods. Three grafting strategies were designed: first short then long (SL) system, both short and long (Both) system and first long then short (LS) system. An abnormal phenomenon for the Both system was found by analyzing the grafting density of long and short polymer chains on the surface of nanoparticles. We speculate that the reason for this anomalous phenomenon is the "depletion effect" brought about by the long chains in the Both system. We employ the Polymer Reference Interaction Site Model (PRISM) theory to investigate this anomaly in-depth. By comparing the radial distribution function (RDF) predicted by the PRISM theory with the RDF results obtained by the molecular dynamics (MD) simulation, we found that with the increase of the number of long chains in the system, the grafting density of short polymer chains on the nanoparticle surface showed an obvious upward trend. The "depletion effect" brought by long chains was the main reason for higher short chains' grafting density of the Both system compared to the SL system. Our findings provide effective guidance for the design of nanoparticle-grafted bimodal bidisperse polymer chains and provide a theoretical basis for experimentation and production of polymer nanocomposites with better performance.

A framework for evaluating the performance of SMLM cluster analysis algorithms

Single-molecule localization microscopy (SMLM) generates data in the form of coordinates of localized fluorophores. Cluster analysis is an attractive route for extracting biologically meaningful information from such data and has been widely applied. Despite a range of cluster analysis algorithms, there exists no consensus framework for the evaluation of their performance. Here, we use a systematic approach based on two metrics to score the success of clustering algorithms in simulated conditions mimicking experimental data. We demonstrate the framework using seven diverse analysis algorithms: DBSCAN, ToMATo, KDE, FOCAL, CAML, ClusterViSu and SR-Tesseler. Given that the best performer depended on the underlying distribution of localizations, we demonstrate an analysis pipeline based on statistical similarity measures that enables the selection of the most appropriate algorithm, and the optimized analysis parameters for real SMLM data. We propose that these standard simulated conditions, metrics and analysis pipeline become the basis for future analysis algorithm development and evaluation.

Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins

Peripheral membrane-associated proteins are known to accumulate on the surface of biomembranes as a result of membrane-mediated interactions. For a pair of rotationally-symmetric curvature-inducing proteins, membrane mechanics at the low-temperature limit predicts pure repulsion. On the other hand, temperature-dependent entropic forces arise between pairs of stiff-binding proteins suppressing membrane fluctuations. These Casimir-like interactions have thus been suggested as candidates for attractive forces leading to aggregation. With dense assemblies of peripheral proteins on the membrane, both these abstractions encounter short-range and multi-body complications. Here, we make use of a particle-based membrane model augmented with flexible peripheral proteins to quantify purely membrane-mediated interactions and investigate their underlying nature. We introduce a continuous reaction coordinate corresponding to the progression of protein aggregation. We obtain free energy and entropy landscapes for different surface concentrations along this reaction coordinate. In parallel, we investigate time-dependent estimates of membrane entropy corresponding to membrane undulations and coarse-grained director field and how they change dynamically with protein aggregation. Congruent outcomes of the two approaches point to the conclusion that for low surface concentrations, interactions with an entropic nature may drive the aggregation. But at high concentrations, enthalpic contributions due to concerted membrane deformation by protein clusters are dominant.

Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy

Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.

Transport properties of a quasisymmetric binary nitrogen-oxygen mixture in the warm dense regime

Transport properties of mixtures in the warm dense matter (WDM) regime play an important role in natural astrophysics. However, a physical understanding of ionic transport properties in quasisymmetric liquid mixtures has remained elusive. Here, we present extensive ab initio molecular dynamics (AIMD) simulations on the ionic diffusion and viscosity of a quasisymmetric binary nitrogen-oxygen (N-O) mixture in a wide warm dense regime of 8-120 kK and 4.5-8.0 g/cm^{3}. Diffusion and viscosity of N-O mixtures with different compositions are obtained by using the Green-Kubo formula. Unlike asymmetric mixtures, the change of proportions in N-O mixtures slightly affects the viscosity and diffusion in the strong-coupling region. Furthermore, the AIMD results are used to build and verify a global pseudo-ion in jellium (PIJ) model for ionic transport calculations. The PIJ model succeeds in reproducing the transport properties of N-O mixtures where ionization has occurred, and provides a promising alternative approach to obtaining comparable results to AIMD simulations with relatively small computational costs. Our current results highlight the characteristic features of the quasisymmetric binary mixtures and demonstrate the applicability of the PIJ model in the WDM regime.

Implicit Solvation Methods for Catalysis at Electrified Interfaces

Implicit solvation is an effective, highly coarse-grained approach in atomic-scale simulations to account for a surrounding liquid electrolyte on the level of a continuous polarizable medium. Originating in molecular chemistry with finite solutes, implicit solvation techniques are now increasingly used in the context of first-principles modeling of electrochemistry and electrocatalysis at extended (often metallic) electrodes. The prevalent ansatz to model the latter electrodes and the reactive surface chemistry at them through slabs in periodic boundary condition supercells brings its specific challenges. Foremost this concerns the difficulty of describing the entire double layer forming at the electrified solid–liquid interface (SLI) within supercell sizes tractable by commonly employed density functional theory (DFT). We review liquid solvation methodology from this specific application angle, highlighting in particular its use in the widespread ab initio thermodynamics approach to surface catalysis. Notably, implicit solvation can be employed to mimic a polarization of the electrode’s electronic density under the applied potential and the concomitant capacitive charging of the entire double layer beyond the limitations of the employed DFT supercell. Most critical for continuing advances of this effective methodology for the SLI context is the lack of pertinent (experimental or high-level theoretical) reference data needed for parametrization.

Probing the balance of Telechelic Polymers Bridging and Screened-Coulomb Interactions in Microemulsion System

The structural properties of neutral oil-in-water (O/W) microemulsions nanodroplets in the presence of telechelic polymers PEO modified with two hydrophobic end functions (PEO- 2m) were studied by Small-Angle Neutron Scattering (SANS). We show that the unknown attractive interaction introduced by the addition of PEO-2m, can could be balanced by a known repulsion interaction due to the addition of a cationic surfactant Cp +, which causes a progressive transformation of the bridges connecting the nanodroplets into loops. For this, we compute the structure factor S(q) with an effective pair potential, using the Ornstein Zernicke (OZ) integral equation approach with the Hypernetted Chain (HNC) closure relation. Generally, the agreement between the neutron scattering spectra and the numerical study is reasonable and allows a detailed description for each sample.

Interacting hard-sphere fluids in an external field

We present a method for studying equilibrium properties of interacting fluids in an arbitrary external field. The fluid is composed of monodisperse spherical particles with hard-core repulsion and additional interactions of arbitrary shape and limited range. Our method of analysis is exact in one dimension and provides demonstrably good approximations in higher dimensions. It can cope with homogeneous and inhomogeneous environments. We derive an equation for the pair distribution function. The solution, to be evaluated numerically, in general, or analytically for special cases, enters expressions for the entropy and free energy functionals. For some one-dimensional systems, our approach yields analytic solutions, reproducing available exact results from different approaches.

Structural and thermodynamic properties of hard-sphere fluids

This Perspective article provides an overview of some of our analytical approaches to the computation of the structural and thermodynamic properties of single-component and multicomponent hard-sphere fluids. For the structural properties, they yield a thermodynamically consistent formulation, thus improving and extending the known analytical results of the Percus-Yevick theory. Approximate expressions linking the equation of state of the single-component fluid to the one of the multicomponent mixtures are also discussed.

Coarse-graining strategy for modeling effective, highly diffusive fluids with reduced polydispersity: A dynamical study

We present a coarse-graining strategy for reducing the number of particle species in mixtures to achieve a simpler system with higher diffusion while preserving the total particle number and characteristic dynamic features. As a system of application, we chose the bidisperse Lennard-Jones-like mixture, discovered by Kob and Andersen [Phys. Rev. Lett. 73, 1376 (1994)], possessing a slow dynamics due to the fluid's multi-component character with its apparently unconventional choice for the pair potential of the type-A-type-B arrangement. We further established in a so-formed coarse-grained and temperature-independent monodisperse system an equilibrium structure with a radial distribution function resembling its mixture counterpart. This one-component system further possesses similar dynamic features such as glass transition temperature and critical exponents while subjected to Newtonian mechanics. This strategy may finally lead to the manufacturing of new nanoparticle/colloidal fluids by experimentally modeling only the outcoming effective pair potential(s) and no other macroscopic quantity.

Perturbation approaches for describing dipolar fluids and electrolyte solutions

This work proposes perturbation approaches for describing dipolar fluids as well as model and aqueous electrolyte solutions. The electrostatic pair potentials are split into short- and long-ranged contributions, whereas a third order perturbation expansion is applied for the short-ranged potentials. This circumvents the problem of divergent correlation integrals. The dipolar perturbation terms are represented through a [2,1]-Padé approximation to resum the poorly convergent series. For the remaining charge-charge and charge-dipole contributions, we present a new approximant, which provides a (quasi)linear dependence of the Helmholtz energy. The underlying correlation integrals are adjusted to results from molecular simulations. The long-ranged contribution to the electrostatic interactions is treated through an analytic expression developed by Rodgers and Weeks [J. Chem. Phys. 131, 244108 (2010)]. Theoretical predictions of our perturbation theory are compared to results from a widely used integral equation theory, namely, the mean spherical approximation, and we find that our perturbation theory provides much more accurate results. Furthermore, the theory shows some quantities in rather good agreement with reference data, namely, Helmholtz energies, internal energies, and densities at higher densities of solutions. Limitations of the approach, however, are observed for several other partial molar quantities, such as the mean activity coefficient.

Molecular dynamics analysis of Mg2+ -dependent cleavage of a pistol ribozyme reveals a fail-safe secondary ion for catalysis

Pistol ribozymes comprise a class of small, self-cleaving RNAs discovered via comparative genomic analysis. Prior work in the field has probed the kinetics of the cleavage reaction, as well as the influence of various metal ion cofactors that accelerate the process. In the current study, we performed unbiased and unconstrained molecular dynamics simulations from two current high-resolution pistol crystal structures, and we analyzed trajectory data within the context of the currently accepted ribozyme mechanistic framework. Root-mean-squared deviations, radial distribution functions, and distributions of nucleophilic angle-of-attack reveal insights into the potential roles of three magnesium ions with respect to catalysis and overall conformational stability of the molecule. A series of simulation trajectories containing in silico mutations reveal the relatively flexible and partially interchangeable roles of two particular magnesium ions within solvated hydrogen-bonding distances from the catalytic center.

Analysis methods for interrogating spatial organisation of single molecule localisation microscopy data

Single-molecule localisation microscopy (SMLM) gives access to biological information below the diffraction limit, allowing nanoscale cellular structures to be probed. The data output is unlike that of conventional microscopy images, instead consisting of an array of molecular coordinates. These represent a spatial point pattern that attempts to approximate, as closely as possible, the underlying positions of the molecules of interest. Here, we review the analysis methods that can be used to extract biological insight from SMLM data, in particular for the application of quantifying nanoscale molecular clustering. We review how some of the common artefacts inherent in SMLM can corrupt the acquired data, and therefore, how the output of SMLM cluster analysis should be interpreted.

Determination of the Ion Temperature in a High-Energy-Density Plasma Using the Stark Effect

We present the experimental determination of the ion temperature in a neon-puff Z pinch. The diagnostic method is based on the effect of ion coupling on the Stark line shapes. It was found, in a profoundly explicit way, that at stagnation the ion thermal energy is small compared to the imploding-plasma kinetic energy, where most of the latter is converted to hydromotion. The method here described can be applied to other highly nonuniform and transient high-energy-density plasmas.

Uranyl Solvation by a Three-Dimensional Reference Interaction Site Model

We report an implementation of the three-dimensional reference interaction site model (3D RISM) that in particular addresses the treatment of the long-range Coulomb field of charged species, represented by point charges and/or a distributed charge density. A comparison of 1D and 3D results for atomic ions demonstrates a reasonable accuracy, even for a moderate size of the unit cell and a moderate grid resolution. In an application to uranyl complexes with 4-6 explicit aqua ligands and an implicit bulk solvent modeled by RISM, we show that the 3D technique is not susceptible to the deficiencies of the 1D technique exposed in our previous work [Li, Matveev, Krüger, Rösch, Comp. Theor. Chem. 2015, 1051, 151]. The 3D method eliminates the artificial superposition of explicit aqua ligands and the RISM medium and predicts essentially the same values for uranyl and uranyl-water bond lengths as a state-of-the-art polarizable continuum model. With the first solvation shell treated explicitly, the observables are nearly independent of the order of the closure relationship used when solving the set of integral equations for the various distribution functions. Furthermore, we calculated the activation barrier of water exchange with a hybrid approach that combines the 3D RISM model for the bulk aqueous solvent and a quantum mechanical description (at the level of electronic density functional theory) of uranyl interacting with explicitly represented water molecules. The calculated result agrees very well with experiment and the best theoretical estimates.

Equation of state for five-dimensional hyperspheres from the chemical-potential route

We use the Percus-Yevick approach in the chemical-potential route to evaluate the equation of state of hard hyperspheres in five dimensions. The evaluation requires the derivation of an analytical expression for the contact value of the pair distribution function between particles of the bulk fluid and a solute particle with arbitrary size. The equation of state is compared with those obtained from the conventional virial and compressibility thermodynamic routes and the associated virial coefficients are computed. The pressure calculated from all routes is exact up to third density order, but it deviates with respect to simulation data as density increases, the compressibility and the chemical-potential routes exhibiting smaller deviations than the virial route. Accurate linear interpolations between the compressibility route and either the chemical-potential route or the virial one are constructed.

Computation of virial coefficients from integral equations

A polynomial-time method of computing the virial coefficients from an integral equation framework is presented. The method computes the truncated density expansions of the correlation functions by series transformations, and then extracts the virial coefficients from the density components. As an application, the method was used in a hybrid-closure integral equation with a set of self-consistent conditions, which produced reasonably accurate virial coefficients for the hard-sphere fluid and Gaussian model in high dimensions.

Correctness of certain integral equation theories for core-softened fluids

Integral equation approaches, based on the Ornstein-Zernike equation, provide a fast way to calculate phase diagrams and thermodynamic properties of systems as opposed to time-consuming and computationally expensive computer simulations. However, when employing integral equations it is necessary to introduce simplifications. The Ornstein-Zernike equation merely relates two unknown functions h(r) and c(r), and another relation (closer) between these two functions is needed. The later function cannot be obtained in a closed form and it is always in some approximations. Various approximations exist with each of its own advantages and disadvantages. In this work we extensively tested hyper-netted chain, Percus-Yevick, Kovalenko-Hirata, and Rogers-Young closure on an interaction model with core-softened potential. Convergence domain was established for each method. We calculated pair distribution functions, pressure, and excess energy. Results were compared with Monte Carlo simulation results and literature data from molecular dynamics simulations.

Variational approach for nonpolar solvation analysis

Solvation analysis is one of the most important tasks in chemical and biological modeling. Implicit solvent models are some of the most popular approaches. However, commonly used implicit solvent models rely on unphysical definitions of solvent-solute boundaries. Based on differential geometry, the present work defines the solvent-solute boundary via the variation of the nonpolar solvation free energy. The solvation free energy functional of the system is constructed based on a continuum description of the solvent and the discrete description of the solute, which are dynamically coupled by the solvent-solute boundaries via van der Waals interactions. The first variation of the energy functional gives rise to the governing Laplace-Beltrami equation. The present model predictions of the nonpolar solvation energies are in an excellent agreement with experimental data, which supports the validity of the proposed nonpolar solvation model.

Equation of state beyond the radius of convergence of the virial expansion

The well-known problem of the virial expansion low-density limitation is considered within Mayer's cluster expansion method. The expression for the configuration integral and the corresponding equation of state are presented based on this approach but not limited by the convergence radius of the series for density and activity. When taking into account any number of irreducible integrals at the thermodynamic limit, this equation of state demonstrates the exact coincidence with the virial one inside the domain of its convergence but specifies the condensation process directly outside that domain. Thus, the assumption of some researchers that the condensation should appear in the domain where the proof of the virial expansion is limited may now be regarded as confirmed, exclusively using the classical Gibbs statistics.

Integral equations in the study of polar and ionic interaction site fluids

In this review article we consider some of the current integral equation approaches and application to model polar liquid mixtures. We consider the use of multidimensional integral equations and in particular progress on the theory and applications of three dimensional integral equations. The IEs we consider may be derived from equilibrium statistical mechanical expressions incorporating a classical Hamiltonian description of the system. We give example including salt solutions, inhomogeneous solutions and systems including proteins and nucleic acids.

Polymorphism, crystal nucleation and growth in the phase-field crystal model in 2D and 3D

We apply a simple dynamical density functional theory, the phase-field crystal (PFC) model of overdamped conservative dynamics, to address polymorphism, crystal nucleation, and crystal growth in the diffusion-controlled limit. We refine the phase diagram for 3D, and determine the line free energy in 2D and the height of the nucleation barrier in 2D and 3D for homogeneous and heterogeneous nucleation by solving the respective Euler-Lagrange (EL) equations. We demonstrate that, in the PFC model, the body-centered cubic (bcc), the face-centered cubic (fcc), and the hexagonal close-packed structures (hcp) compete, while the simple cubic structure is unstable, and that phase preference can be tuned by changing the model parameters: close to the critical point the bcc structure is stable, while far from the critical point the fcc prevails, with an hcp stability domain in between. We note that with increasing distance from the critical point the equilibrium shapes vary from the sphere to specific faceted shapes: rhombic dodecahedron (bcc), truncated octahedron (fcc), and hexagonal prism (hcp). Solving the equation of motion of the PFC model supplied with conserved noise, solidification starts with the nucleation of an amorphous precursor phase, into which the stable crystalline phase nucleates. The growth rate is found to be time dependent and anisotropic; this anisotropy depends on the driving force. We show that due to the diffusion-controlled growth mechanism, which is especially relevant for crystal aggregation in colloidal systems, dendritic growth structures evolve in large-scale isothermal single-component PFC simulations. An oscillatory effective pair potential resembling those for model glass formers has been evaluated from structural data of the amorphous phase obtained by instantaneous quenching. Finally, we present results for eutectic solidification in a binary PFC model.

Fundamental theory of statistical particle dynamics

We present a fundamental theory for the kinetics of systems of classical particles. The theory represents a unification of kinetic theory, Brownian motion, and field theory. It is self-consistent and is the dynamic generalization of the functional theory of fluids in equilibrium. This gives one a powerful tool for investigating the existence of ergodic-nonergodic transitions near the liquid-glass transition.

Entropic flows, crowding effects, and stability of asymmetric proteins

The study of the excluded-volume effects on protein stability and reactions or the stability of colloidal suspensions is an active area of research. Using hard-disk collisional dynamics we investigate whether the presence of a crowding agent can induce a shape change from a nonspherical molecule to a spherical one. We show the averaged density profiles and velocity field of hard-disk crowders with an interior noncircular convex shape as a boundary condition. The density profile is not axially symmetric, consistent with other hard-potential experiments with asymmetry. However, more interestingly, the averaged velocity field was found to have a nonzero curl, implying a region of vorticity without a thermal gradient, advective field, or other motivating potential. To explain the occurrence of the vortices, a theoretical model is provided based on angular momentum of hard disks at contact. All these results, as well as difference in pressure along the axes, support the fact that as the packing fraction of the crowder rises, increasing force is exerted on an asymmetric molecule toward a symmetric one.

Ion structure in warm dense matter: benchmarking solutions of hypernetted-chain equations by first-principle simulations

We investigate the microscopic structure of strongly coupled ions in warm dense matter using ab initio simulations and hypernetted chain (HNC) equations. We demonstrate that an approximate treatment of quantum effects by weak pseudopotentials fails to describe the highly degenerate electrons in warm dense matter correctly. However, one-component HNC calculations for the ions agree well with first-principles simulations if a linearly screened Coulomb potential is used. These HNC results can be further improved by adding a short-range repulsion that accounts for bound electrons. Examples are given for recently studied light elements, lithium and beryllium, and for aluminum where the extra short-range repulsion is essential.

On the influence of spatial correlations on sound propagation in concentrated solutions of rigid particles

In a previous paper [J. Acoust. Soc. Am. 121, 3386-3387 (2007)], a self-consistent effective medium theory has been used to account for hydrodynamic interactions between neighboring rigid particles, which considerably affect the sound propagation in concentrated solutions. However, spatial correlations were completely left out in this model. They correspond to the fact that the presence of one particle at a given position locally affects the location of the other ones. In the present work, the importance of such correlations is demonstrated within a certain frequency range and particle concentration. For that purpose, spatial correlations are integrated in our two-phase formulation by using a closure scheme similar to the one introduced by Spelt et al. [''Attenuation of sound in concentrated suspensions theory and experiments," J. Fluid Mech. 430, 51-86 (2001)]. Then, the effect is shown through a careful comparison of the results obtained with this model, the ones obtained with different self-consistent approximations and the experiments performed by Hipp et al. ["Acoustical characterization of concentrated suspensions and emulsions. 2. Experimental validation," Langmuir, 18, 391-404 (2002)]. With the present formulation, an excellent agreement is reached for all frequencies (within the limit of the long wavelength regime) and for concentrations up to 30% without any adjustable parameter.

Structure of strongly coupled multicomponent plasmas

We investigate the short-range structure in strongly coupled fluidlike plasmas using the hypernetted chain approach generalized to multicomponent systems. Good agreement with numerical simulations validates this method for the parameters considered. We found a strong mutual impact on the spatial arrangement for systems with multiple ion species which is most clearly pronounced in the static structure factor. Quantum pseudopotentials were used to mimic diffraction and exchange effects in dense electron-ion systems. We demonstrate that the different kinds of pseudopotentials proposed lead to large differences in both the pair distributions and structure factors. Large discrepancies were also found in the predicted ion feature of the x-ray scattering signal, illustrating the need for comparison with full quantum calculations or experimental verification.

Structural anomalies of fluids: origins in second and higher coordination shells

Compressing or cooling a fluid typically enhances its static interparticle correlations. However, there are notable exceptions. Isothermal compression can reduce the translational order of fluids that exhibit anomalous waterlike trends in their thermodynamic and transport properties, while isochoric cooling (or strengthening of attractive interactions) can have a similar effect on fluids of particles with short-range attractions. Recent simulation studies by Yan [Phys. Rev. E 76, 051201 (2007)] on the former type of system and Krekelberg [J. Chem. Phys. 127, 044502 (2007)] on the latter provide examples where such structural anomalies can be related to specific changes in second and more distant coordination shells of the radial distribution function. Here, we confirm the generality of this microscopic picture through analysis, via molecular simulation and integral equation theory, of coordination shell contributions to the two-body excess entropy for several related model fluids which incorporate different levels of molecular resolution. The results suggest that integral equation theory can be an effective and computationally inexpensive tool for assessing, based on the pair potential alone, whether new model systems are good candidates for exhibiting structural (and hence thermodynamic and transport) anomalies.

Pair-distribution functions of two-temperature two-mass systems: comparison of molecular dynamics, classical-map hypernetted chain, quantum Monte Carlo, and Kohn-Sham calculations for dense hydrogen

Two-temperature, two-mass quasiequilibrium plasmas may occur in electron-ion plasmas, nuclear-matter, as well as in electron-hole condensed-matter systems. Dense two-temperature hydrogen plasmas straddle the difficult partially degenerate regime of electron densities and temperatures which are important in astrophysics, in inertial-confinement fusion research, and other areas of warm dense-matter physics. Results from quantum Monte Carlo (QMC) are used to benchmark the procedures used in classical molecular-dynamics simulations and hypernetted chain (HNC) and classical-map HNC (CHNC) methods to derive electron-electron and electron-proton pair-distribution functions. Where QMC is not available, we used Kohn-Sham results as the reference calculation. Then, nonequilibrium molecular dynamics for two-temperature, two-mass plasmas are used to obtain pair distribution functions without specifying the interspecies cross temperature. Using these results, the correct HNC and CHNC procedures for the evaluation of pair-distribution functions in two-temperature two-mass two-component charged fluids are established and results for a mass ratio of 1:5, typical of electron-hole fluids, are presented.