A two-phase model that unifies and extends the classical models of membrane transport.

Two models describe solvent transport through swollen, nonporous membranes. The pore-flow model, based on fluid mechanics, works for porous membranes, whereas the solution-diffusion model invokes molecular diffusion to treat nonporous membranes. Both approaches make valid arguments for swollen polymer membranes, but they disagree in their predictions of intramembrane pressure and concentration profiles. Using a fluid-solid model that treats the solvent and membrane matrix as separate phases, we show both classical models to be valid, to represent complementary approaches to the same phenomenon, and to make identical predictions. The fluid-solid model clarifies recent reverse osmosis measurements; provides a predictive and mechanistic basis for empirical high-pressure limiting flux phenomena, in quantitative agreement with classic measurements; and gives a framework to treat nonporous but mechanically heterogeneous membrane materials.

Free energies of crystals computed using Einstein crystal with fixed center of mass and differing spring constants.

Free energies of crystals computed using a center of mass constraint require a finite-size correction, as shown in previous work by Polson et al. [J. Chem. Phys. 112, 5339-5342 (2000)]. Their reference system is an Einstein crystal with equal spring constants. In this paper, we extend the work of Polson et al. [J. Chem. Phys. 112, 5339-5342 (2000)] to the case of differing spring constants. The generalization is convenient for constraining the center of mass in crystals with atoms of differing masses, and it helps to optimize the free energy calculations. To test the theory, we compare the free energies of LiI and NaCl crystals from calculations with differing spring constants to those computed using equal spring constants. Using these center of mass finite size corrections, we compute the true free energies of these crystals for different system sizes to eliminate the intrinsic finite-size effects. These calculations help demonstrate the size of these finite-size corrections relative to other contributions to the absolute free energy of the crystals.

Absolute chemical potentials for complex molecules in fluid phases: A centroid reference for predicting phase equilibria.

Solid-fluid phase equilibria are difficult to predict in simulations because bound degrees of freedom in the crystal phase must be converted to free translations and rotations in the fluid phase. Here, we avoid the solid-to-fluid transformation step by starting with chemical potentials for two reference systems, one for the fluid phase and one for the solid phase. For the solid, we start from the Einstein crystal and transform to the fully interacting molecular crystal. For the fluid phase, we introduce a new reference system, the "centroid," and then transform to gas phase molecules. We illustrate the new calculations by predicting the sublimation vapor pressure of succinic acid in the temperature range of 300 K-350 K.

Performing solvation free energy calculations in LAMMPS using the decoupling approach.

The decoupling approach to solvation free energy calculations requires scaling the interactions between the solute and the solution with all intramolecular interactions preserved. This paper reports a new procedure that makes it possible to these calculations in LAMMPS. The procedure is tested against built-in GROMACS capabilities. The model compounds chosen to test our methodology are ethanol and biphenyl. The LAMMPS and GROMACS results obtained are in good agreement with each other. This work should help perform solvation free energy calculations in LAMMPS and/or other molecular dynamics software having no built-in functions to implement the decoupling approach.

Ion dissolution mechanism and kinetics at kink sites on NaCl surfaces.

Desolvation barriers are present for solute-solvent exchange events, such as ligand binding to an enzyme active site, during protein folding, and at battery electrodes. For solution-grown crystals, desolvation at kink sites can be the rate-limiting step for growth. However, desolvation and the associated kinetic barriers are poorly understood. In this work, we use rare-event simulation techniques to investigate attachment/detachment events at kink sites of a NaCl crystal in water. We elucidate the desolvation mechanism and present an optimized reaction coordinate, which involves one solute collective variable and one solvent collective variable. The attachment/detachment pathways for Na+ and Cl- are qualitatively similar, with quantitative differences that we attribute to different ion sizes and solvent coordination. The attachment barriers primarily result from kink site desolvation, while detachment barriers largely result from breaking ion-crystal bonds. We compute ion detachment rates from kink sites and compare with results from an independent study. We anticipate that the reaction coordinate and desolvation mechanism identified in this work may be applicable to other alkali halides.

New Tricks of the Trade for Crystal Structure Refinement.

Accurate crystal structures and their experimental uncertainties, determined by X-ray diffraction/neutron diffraction techniques, are vital for crystal engineering studies, such as polymorph stability and crystal morphology calculations. Because of differences in crystal growth and data measurement conditions, crystallographic databases often contain multiple entries of varying quality of the same compound. The choice of the most reliable and best quality crystal structure from many very similar structures remains an unresolved problem, especially for nonexperts. In addition, while crystallographers can make use of some professional software (i.e., Materials Studio) for structure refinement, noncrystallographers may not have access to it. In the present paper, we propose a simple method to study the sensitivity of the crystal lattice energy to changes in the structural parameters, which creates a diagnostic tool to test the quality of crystal structure files and to improve the low-quality structures based on lattice energy distribution. Thus, noncrystallographers could take the proposed idea and program/optimize crystal structure by themselves. They can have their in-house program to determine the reliability of the selected crystal data and then use the best quality data or carry out structural optimization for low-quality data. The proposed method will benefit a broad cross-section of scientific researchers, especially those in solid-state and physical chemistry.

Energetic and entropic components of the Tolman length for mW and TIP4P/2005 water nanodroplets.

The surface free energy of a droplet is approximately γ(R)=γ(∞)(1-2δ/R), with R being the droplet radius and δ being the Tolman length. Here we use the mitosis method to compute δ=-0.56±0.1Å at 300 K for mW water, indicating that γ(R) increases as the droplet size decreases. The computed Tolman length agrees quite well with a previous study of TIP4P/2005 water. We also decompose the size-dependent surface free energy into energetic and entropic contributions for the mW and TIP4P/2005 force fields. Despite having similar Tolman lengths, the energy-entropy decompositions are very different for the two force fields. We discuss critical assumptions which lead to these findings and their relation to experiments on the nucleation of water droplets. We also discuss surface broken bonds and structural correlations as possible explanations for the energetic and entropic contributions.

Critical length of a one-dimensional nucleus.

One-dimensional (1D) nucleation is important in crystal growth, amyloid fibril formation, and supramolecular polymerization. The nucleation rate can be readily calculated, but there is no consensus on the critical length. In this work, we employ a splitting probability to derive an analytical expression for the critical length, which corresponds to a 50% survival probability. For a 1D nucleus on a crystal step, this critical length depends on the supersaturation (driving force) and is nearly independent of the kink (surface) energy.

Proteomic analysis reveals CACN-1 is a component of the spliceosome in Caenorhabditis elegans.

Cell migration is essential for embryonic development and tissue formation in all animals. cacn-1 is a conserved gene of unknown molecular function identified in a genome-wide screen for genes that regulate distal tip cell migration in the nematode worm Caenorhabditis elegans. In this study we take a proteomics approach to understand CACN-1 function. To isolate CACN-1-interacting proteins, we used an in vivo tandem-affinity purification strategy. Tandem-affinity purification-tagged CACN-1 complexes were isolated from C. elegans lysate, analyzed by mass spectrometry, and characterized bioinformatically. Results suggest significant interaction of CACN-1 with the C. elegans spliceosome. All of the identified interactors were screened for distal tip cell migration phenotypes using RNAi. Depletion of many of these factors led to distal tip cell migration defects, particularly a failure to stop migrating, a phenotype commonly seen in cacn-1 deficient animals. The results of this screen identify eight novel regulators of cell migration and suggest CACN-1 may participate in a protein network dedicated to high-fidelity gonad development. The composition of proteins comprising the CACN-1 network suggests that this critical developmental module may exert its influence through alternative splicing or other post-transcriptional gene regulation.

Size-Dependent Surface Free Energy and Tolman-Corrected Droplet Nucleation of TIP4P/2005 Water.

Classical nucleation theory is notoriously inaccurate when using the macroscopic surface free energy for a planar interface. We examine the size dependence of the surface free energy for TIP4P/2005 water nanodroplets (radii ranging from 0.7 to 1.6 nm) at 300 K with the mitosis method, that is, by reversibly splitting the droplets into two subclusters. We calculate the Tolman length to be -0.56 ± 0.09 Å, which indicates that the surface free energy of water droplets that we investigated is 5-11 mJ/m(2) greater than the planar surface free energy. We incorporate the computed Tolman length into a modified classical nucleation theory (δ-CNT) and obtain modified expressions for the critical nucleus size and barrier height. δ-CNT leads to excellent agreement with independently measured nucleation kinetics.

Homogeneous nucleation of methane hydrates: unrealistic under realistic conditions.

Methane hydrates are ice-like inclusion compounds with importance to the oil and natural gas industry, global climate change, and gas transportation and storage. The molecular mechanism by which these compounds form under conditions relevant to industry and nature remains mysterious. To understand the mechanism of methane hydrate nucleation from supersaturated aqueous solutions, we performed simulations at controlled and realistic supersaturation. We found that critical nuclei are extremely large and that homogeneous nucleation rates are extremely low. Our findings suggest that nucleation of methane hydrates under these realistic conditions cannot occur by a homogeneous mechanism.

Multisite models to determine the distribution of kink sites adjacent to low-energy edges.

Kink sites play a critical role in crystal growth. The incorporation of a growth unit into a kink site (1) maintains the free energy of the edge constant and (2) creates another site with the same properties. These properties allow growth through successive incorporation events to proceed in a self-sustaining manner such that the equilibrium spacing between kinks is maintained on average. Traditionally the distributions of kink sites have been determined using a single-site model whereby the probabilities of encountering a kink site adjacent to an edge and encountering a disturbance along an edge are assumed equivalent. In this paper, we develop multisite models that determine the probabilities of encountering kink sites; with the requirement that they obey both properties necessary for growth through successive self-sustaining incorporation events. The probabilities determined using the multisite models diverge significantly from the single-site model for edges with intermolecular interactions ≲6k(b)T between successive molecules. The implications of these findings for the development of predictive crystal shape models and experimental analysis are discussed.

Communication: Bubbles, crystals, and laser-induced nucleation.

Short intense laser pulses of visible and infrared light can dramatically accelerate crystal nucleation from transparent solutions; previous studies invoke mechanisms that are only applicable for nucleation of ordered phases or high dielectric phases. However, we show that similar laser pulses induce CO(2) bubble nucleation in carbonated water. Additionally, in water that is cosupersaturated with argon and glycine, argon bubbles escaping from the water can induce crystal nucleation without a laser. Our findings suggest a possible link between laser-induced nucleation of bubbles and crystals.

A simulation test of the optical Kerr mechanism for laser-induced nucleation.

Recent experiments have demonstrated that intense, nanosecond laser pulses can induce crystal nucleation from supersaturated solutions that are transparent at the incident wavelengths, a phenomenon termed nonphotochemical laser-induced nucleation (NPLIN). Previous work has proposed that this effect is due to the alignment of solute molecules in solution due to the electric field of the applied laser light, promoting crystalline order. We have used simulations of NPLIN to examine how an orientational bias in solution affects nucleation with Monte Carlo simulations of a Potts lattice gas model. We examine this effect within both a classical, one-step nucleation framework as well as in the context of two-step nucleation. Our results indicate that an orientational bias can reduce the free energy barrier to nucleation within the one-step picture as well as promote the crystallization of amorphous precritical nuclei (the rate-determining step in the two-step picture). However, these effects are only present with field strengths that are much greater than those used in experiments.

Estimating diffusivity along a reaction coordinate in the high friction limit: Insights on pulse times in laser-induced nucleation.

In the high friction limit of Kramers' theory, the diffusion coefficient for motion along the reaction coordinate is a crucial parameter in determining reaction rates from mean first passage times. The Einstein relation between mean squared displacement, time, and diffusivity is inaccurate at short times because of ballistic motion and inaccurate at long times because trajectories drift away from maxima in the potential of mean force. Starting from the Smoluchowski equation for a downward parabolic barrier, we show how drift induced by the potential of mean force can be included in estimating the diffusivity. A modified relation between mean squared displacement, time, and diffusivity now also includes a dependence on the barrier curvature. The new relation provides the diffusivity at the top of the barrier from a linear regression that is analogous to the procedure commonly used with Einstein's relation. The new approach has particular advantages over previous approaches when evaluations of the reaction coordinate are costly or when the reaction coordinate cannot be differentiated to compute restraining forces or velocities. We use the new method to study the dynamics of barrier crossing in a Potts lattice gas model of nucleation from solution. Our analysis shows that some current hypotheses about laser-induced nucleation mechanisms lead to a nonzero threshold laser pulse duration below which a laser pulse will not affect nucleation. We therefore propose experiments that might be used to test these hypotheses.