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Free energy calculations on solid phases are important for understanding the phase behavior of various systems. For periodic crystalline solids, the Einstein molecule method can be used to determine the free energy difference between the solid of interest and an ideal crystal for which the free energy can be found analytically. In this work, we show how this method is extensible to systems which are nonperiodic or periodic in some dimensions but not in others. This allows for the calculation of exact absolute free energies of finite-sized crystals having specific shapes and surface geometries. We demonstrate this using the fcc Lennard-Jones solid and also illustrate how surface contributions to free energies can easily be extracted from simulations of this solid in semi-infinite slab geometries. We have developed a software package which interfaces with the LAMMPS molecular dynamics code to perform these calculations. [ABSTRACT FROM AUTHOR]

Coarse-grained (CG) protein models in the structural biology literature have improved over the years from being simple tools to understand general folding and aggregation driving forces to capturing detailed structures achieved by actual folding sequences. Here, we ask whether such models can be developed systematically from recent advances in bottom-up coarse-graining methods without relying on bioinformatic data (e.g., protein data bank statistics). We use relative entropy coarse-graining to develop a hybrid CG but G o ¯ -like CG peptide model, hypothesizing that the landscape of proteinlike folds is encoded by the backbone interactions, while the sidechain interactions define which of these structures globally minimizes the free energy in a unique native fold. To construct a model capable of capturing varied secondary structures, we use a new extended ensemble relative entropy method to coarse-grain based on multiple reference atomistic simulations of short polypeptides with varied α and β character. Subsequently, we assess the CG model as a putative protein backbone forcefield by combining it with sidechain interactions based on native contacts but not incorporating native distances explicitly, unlike standard G o ¯ models. We test the model's ability to fold a range of proteins and find that it achieves high accuracy (∼2 Å root mean square deviation resolution for both short sequences and large globular proteins), suggesting the strong role that backbone conformational preferences play in defining the fold landscape. This model can be systematically extended to non-natural amino acids and nonprotein polymers and sets the stage for extensions to non-G o ¯ models with sequence-specific sidechain interactions. [ABSTRACT FROM AUTHOR]

The fluid phase diagram of trimer particles composed of one central attractive bead and two repulsive beads was determined as a function of simple geometric parameters using flat-histogram Monte Carlo methods. A variety of self-assembled structures were obtained including spherical micelle-like clusters, elongated clusters, and densely packed cylinders, depending on both the state conditions and shape of the trimer. Advanced simulation techniques were employed to determine transitions between self-assembled structures and macroscopic phases using thermodynamic and structural definitions. Simple changes in particle geometry yield dramatic changes in phase behavior, ranging from macroscopic fluid phase separation to molecular-scale self-assembly. In special cases, both self-assembled, elongated clusters and bulk fluid phase separation occur simultaneously. Our work suggests that tuning particle shape and interactions can yield superstructures with controlled architecture. [ABSTRACT FROM AUTHOR]

DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarsegrained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA-functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions. [ABSTRACT FROM AUTHOR]

We use discontinuous molecular dynamics and grand-canonical transition-matrix Monte Carlo simulations to explore how confinement between parallel hard walls modifies the relationships between packing fraction, self-diffusivity, partial molar excess entropy, and total excess entropy for binary hard-sphere mixtures. To accomplish this, we introduce an efficient algorithm to calculate partial molar excess entropies from the transition-matrix Monte Carlo simulation data. We find that the species-dependent self-diffusivities of confined fluids are very similar to those of the bulk mixture if compared at the same, appropriately defined, packing fraction up to intermediate values, but then deviate negatively from the bulk behavior at higher packing fractions. On the other hand, the relationships between self-diffusivity and partial molar excess entropy (or total excess entropy) observed in the bulk fluid are preserved under confinement even at relatively high packing fractions and for different mixture compositions. This suggests that the excess entropy, calculable from classical density functional theories of inhomogeneous fluids, can be used to predict some of the nontrivial dynamical behaviors of fluid mixtures in confined environments. [ABSTRACT FROM AUTHOR]

We present molecular simulation data for viscosity, self-diffusivity, and the local structural ordering of (i) a hard-sphere fluid and (ii) a square-well fluid with short-range attractions. The latter fluid exhibits a region of dynamic anomalies in its phase diagram, where its mobility increases upon isochoric cooling, which is found to be a subset of a larger region of structural anomalies, in which its pair correlations strengthen upon isochoric heating. This “cascade of anomalies” qualitatively resembles that found in recent simulations of liquid water. The results for the hard-sphere and square-well systems also show that the breakdown of the Stokes–Einstein relation upon supercooling occurs for conditions where viscosity and self-diffusivity develop different couplings to the degree of pairwise structural ordering of the liquid. We discuss how these couplings reflect dynamic heterogeneities. Finally, we note that the simulation data suggest how repulsive and attractive glasses may generally be characterized by two distinct levels of short-range structural order. [ABSTRACT FROM AUTHOR]

We use grand canonical transition-matrix Monte Carlo and discontinuous molecular dynamics simulations to generate precise thermodynamic and kinetic data for the equilibrium hard-sphere fluid confined between smooth hard walls. These simulations show that the pronounced inhomogeneous structuring of the fluid normal to the confining walls, often the primary focus of density functional theory studies, has a negligible effect on many of its average properties over a surprisingly broad range of conditions. We present one consequence of this insensitivity to confinement: a simple analytical equation relating the average density of the confined fluid to that of the bulk fluid with equal activity. Nontrivial implications of confinement for average fluid properties do emerge in this system, but only when the fluid is both (i) dense and (ii) confined to a gap smaller than approximately three particle diameters. For this limited set of conditions, we find that “in-phase” oscillatory deviations in excess entropy and self-diffusivity (relative to the behavior of the bulk fluid at the same average density) occur as a function of gap size. These paired thermodynamic/kinetic deviations from bulk behavior appear to reflect the geometric packing frustration that arises when the confined space cannot naturally accommodate an integer number of particle layers. [ABSTRACT FROM AUTHOR]

Diffusivity, a measure for how rapidly a fluid self-mixes, shows an intimate, but seemingly fragmented, connection to thermodynamics. On one hand, the “configurational” contribution to entropy (related to the number of mechanically stable configurations that fluid molecules can adopt) has long been considered key for predicting supercooled liquid dynamics near the glass transition. On the other hand, the excess entropy (relative to ideal gas) provides a robust scaling for the diffusivity of fluids above the freezing point. Here we provide, to our knowledge, the first evidence that excess entropy also captures how supercooling a fluid modifies its diffusivity, suggesting that dynamics, from ideal gas to glass, is related to a single, standard thermodynamic quantity. [ABSTRACT FROM AUTHOR]

We calculate the pair diffusion coefficient D(r) as a function of the distance r between two hard sphere particles in a dense monodisperse fluid. The distance-dependent pair diffusion coefficient describes the hydrodynamic interactions between particles in a fluid that are central to theories of polymer and colloid dynamics. We determine D(r) from the propagators (Green's functions) of particle pairs obtained from molecular dynamics simulations. At distances exceeding ∼3 molecular diameters, the calculated pair diffusion coefficients are in excellent agreement with predictions from exact macroscopic hydrodynamic theory for large Brownian particles suspended in a solvent bath, as well as the Oseen approximation. However, the asymptotic 1/r distance dependence of D(r) associated with hydrodynamic effects emerges only after the pair distance dynamics has been followed for relatively long times, indicating non-negligible memory effects in the pair diffusion at short times. Deviations of the calculated D(r) from the hydrodynamic models at short distances r reflect the underlying many-body fluid structure, and are found to be correlated to differences in the local available volume. The procedure used here to determine the pair diffusion coefficients can also be used for single-particle diffusion in confinement with spherical symmetry. [ABSTRACT FROM AUTHOR]

A correction to the article "Relationship between thermodynamics and dynamics of supercooled liquids" that was published in the April 28, 2010 issue is presented.

Molecular dynamics simulations are used to study the occupancy and flow of water through nanotubes comprised of hydrophobic and hydrophilic atoms, which are arranged on a honeycomb lattice to mimic functionalized carbon nanotubes (CNTs). We consider single-file motion of TIP3P water through narrow channels of (6,6) CNTs with varying fractions (f) of hydrophilic atoms. Various arrangements of hydrophilic atoms are used to create heterogeneous nanotubes with separate hydrophobic/hydrophilic domains along the tube as well as random mixtures of the two types of atoms. The water occupancy inside the nanotube channel is found to vary nonlinearly as a function of f, and a small fraction of hydrophilic atoms (f ≈ 0.4) are sufficient to induce spontaneous and continuous filling of the nanotube. Interestingly, the average number of water molecules inside the channel and water flux through the nanotube are less sensitive to the specific arrangement of hydrophilic atoms than to the fraction, f, Two different regimes are observed for the water flux dependence on f - an approximately linear increase in flux as a function of f for f < 0.4, and almost no change in flux for higher f values, similar to the change in water occupancy. We are able to define an effective interaction strength between nanotube atoms and water's oxygen, based on a linear combination of interaction strengths between hydrophobic and hydrophilic nanotube atoms and water, that can quantitatively capture the observed behavior. [ABSTRACT FROM AUTHOR]

Macromolecular crowding in cells is recognized to have a significant impact on biological function, yet quantitative models for its effects are relatively undeveloped. The influence of crowding on protein-protein interactions is of particular interest, since these mediate many processes in the cell, including the self-assembly of larger complexes, recognition, and signaling. We use a residue-level coarse-grained model to investigate the effects of macromolecular crowding on the assembly of protein-protein complexes. Interactions between the proteins are treated using a fully transferable energy function, and interactions of protein residues with the spherical crowders are repulsive. We show that the binding free energy for two protein complexes, ubiquitin/UIM1 and cytochrome c/cytochrome c peroxidase, decreases modestly as the concentration of crowding agents increases. To obtain a quantitative description of the stabilizing effect, we map the aspherical individual proteins and protein complexes onto spheres whose radii are calculated from the crowder-excluded protein volumes. With this correspondence, we find that the change in the binding free energy due to crowding can be quantitatively described by the scaled particle theory model without any fitting parameters. The effects of a mixture of different-size crowders-as would be found in a real cell-are predicted by the same model with an additivity ansatz. We also obtain the remarkable result that crowding increases the fraction of specific complexes at the expense of nonspecific transient encounter complexes in a crowded environment. This result, due to the greater excluded volume of the nonspecific complexes, demonstrates that macromolecular crowding can have subtle functional effects beyond the relative stability of bound and unbound complexes. [ABSTRACT FROM AUTHOR]

Many thermodynamic and dynamic properties of water display unusual behavior at low enough temperatures. In a recent study, Yan et al. [Phys. Rev. Lett. 95, 130604 (2005)] identified a spherically symmetric two-scale potential that displays many of the same anomalous properties as water. More specifically, for select parametrizations of the potential, one finds that the regions where isothermal compression anomalously (i) decreases the fluid’s structural order, (ii) increases its translational self-diffusivity, and (iii) increases its entropy form nested domes in the temperature-density plane. These property relationships are similar to those found for more realistic models of water. In this work, the authors provide evidence that suggests that the anomalous regions specified above can all be linked through knowledge of the excess entropy. Specifically, the authors show how entropy scaling relationships developed by Rosenfeld [Phys. Rev. A 15, 2545 (1977)] can be used to describe the region of diffusivity anomalies and to predict the state conditions for which anomalous viscosity and thermal conductivity behavior might be found. [ABSTRACT FROM AUTHOR]

A correction to the article "Excess-entropy-based anomalies for a waterlike fluid" that appeared in a previous issue of this periodical is presented.

Förster resonance energy transfer (FRET) is a powerful tool for elucidating both structural and dynamic properties of unfolded or disordered biomolecules, especially in single-molecule experiments. However, the key observables, namely, the mean transfer efficiency and fluorescence lifetimes of the donor and acceptor chromophores, are averaged over a broad distribution of donor-acceptor distances. The inferred average properties of the ensemble therefore depend on the form of the model distribution chosen to describe the distance, as has been widely recognized. In addition, while the distribution for one type of polymer model may be appropriate for a chain under a given set of physico-chemical conditions, it may not be suitable for the same chain in a different environment so that even an apparently consistent application of the same model over all conditions may distort the apparent changes in chain dimensions with variation of temperature or solution composition. Here, we present an alternative and straightforward approach to determining ensemble properties from FRET data, in which the polymer scaling exponent is allowed to vary with solution conditions. In its simplest form, it requires either the mean FRET efficiency or fluorescence lifetime information. In order to test the accuracy of the method, we have utilized both synthetic FRET data from implicit and explicit solvent simulations for 30 different protein sequences, and experimental single-molecule FRET data for an intrinsically disordered and a denatured protein. In all cases, we find that the inferred radii of gyration are within 10% of the true values, thus providing higher accuracy than simpler polymer models. In addition, the scaling exponents obtained by our procedure are in good agreement with those determined directly from the molecular ensemble. Our approach can in principle be generalized to treating other ensemble-averaged functions of intramolecular distances from experimental data. [ABSTRACT FROM AUTHOR]