Cholesterol catalyzes unfolding in membrane-inserted motifs of the pore forming protein cytolysin A.

Plasma membrane-induced protein folding and conformational transitions play a central role in cellular homeostasis. Several transmembrane proteins are folded in the complex lipid milieu to acquire a specific structure and function. Bacterial pore forming toxins (PFTs) are proteins expressed by a large class of pathogenic bacteria that exploit the plasma membrane environment to efficiently undergo secondary structure changes, oligomerize, and form transmembrane pores.

Conformational Flexibility Is a Key Determinant for the Lytic Activity of the Pore-Forming Protein, Cytolysin A.

Several bacterial infections are mediated by pore-forming toxins (PFTs), a subclass of proteins that oligomerize on mammalian cell membranes forming lytic nanopores. Cytolysin A (ClyA), an α-PFT, undergoes a dramatic conformational change restructuring its two membrane-binding motifs (the β-tongue and the N-terminus helix), during pore formation. A complete molecular picture for this key transition and the driving force behind the secondary structure change upon membrane binding remain elusive.

Computing contact angles for oil-water-rock systems via thermodynamic integration.

Wettability of rock surfaces with respect to oil and water, which is characterized by the contact angle, is an important factor that determines the efficacy of enhanced oil recovery operations. Experimental determination of contact angles for oil-water-rock systems is expensive and time-consuming due to the extremely long times needed for the establishment of adsorption equilibrium at the liquid-solid interface. Hence, molecular simulations form an attractive tool for computing contact angles.

Finite temperature string method with umbrella sampling using path collective variables: application to secondary structure change in a protein.

The transition of an α-helix to a β-sheet in proteins is among the most complex conformational changes seen in biomolecular systems. Due to long time scales involved in the transition, it is challenging to study such protein conformational changes using direct molecular dynamics simulations. This limitation is typically overcome using an indirect approach wherein one computes the free energy landscape associated with the transition.

Modeling of effective interactions between ligand coated nanoparticles through symmetry functions.

Ligand coated nanoparticles are complex objects consisting of a metallic or semiconductor core with organic ligands grafted on their surface. These organic ligands provide stability to a nanoparticle suspension. In solutions, the effective interactions between such nanoparticles are mediated through a complex interplay of interactions between the nanoparticle cores, the surrounding ligands, and the solvent molecules.

Molecular Theory of Nucleation from Dilute Phases: Formulation and Application to Lennard-Jones Vapor.

In this Letter, we present a molecular theory of nucleation from dilute phases such as vapors or dilute solutions. The theory can model the nonclassical two-step crystal nucleation seen in many systems. When applied to study and analyze the crystal nucleation pathways from Lennard-Jones vapor, we find that prior explanations of the two-step mechanism based on lower barrier height for liquid nuclei is incomplete.

Computation of solid-fluid interfacial free energy in molecular systems using thermodynamic integration.

In this article, we present two methods based on thermodynamic integration for computing solid-fluid interfacial free energy for a molecular system. As a representative system, we choose two crystal polymorphs of orcinol (5-methylbenzene-1,3-diol) as the solid phase and chloroform and nitromethane as the liquid phase. The computed values of the interfacial free energy are then used in combination with the classical nucleation theory to predict solvent induced polymorph selectivity during crystallization of orcinol from solution.

Computation of the Dissociation Temperature of TBAB Semiclathrate in an Aqueous Solution Using Molecular Simulations.

Quaternary ammonium salts such as tetra--butyl ammonium bromide (TBAB) are known to form semiclathrate hydrates. Since they form at much milder conditions compared to gas hydrates, they have evoked much interest in development of new technologies for gas storage and gas separations. In this work, we present a method to compute the phase equilibrium of TBAB semiclathrate.

Modeling of many-body interactions between elastic spheres through symmetry functions.

Simple models for spherical particles with a soft shell have been shown to self-assemble into numerous crystal phases and even quasicrystals. However, most of these models rely on a simple pairwise interaction, which is usually a valid approximation only in the limit of small deformations, i.e.

Computational Study of Differences between Antifreeze Activity of Type-III Antifreeze Protein from Ocean Pout and Its Mutant.

The antifreeze activity of a type-III antifreeze protein (AFP) expressed in ocean pout (Zoarces americanus) is compared with that of a specific mutant (T18N) using all-atom molecular dynamics simulations. The antifreeze activity of the mutant is only 10% of the wild-type AFP. The results from this simulation study revealed the following insights into the mechanism of antifreeze action by type-III AFPs.

Molecular simulation of homogeneous crystal nucleation of AB solid phase from a binary hard sphere mixture.

Co-crystal formation from fluid-mixtures is quite common in a large number of systems. The simplest systems that show co-crystal (also called substitutionally ordered solids) formation are binary hard sphere mixtures. In this work, we study the nucleation of AB type solid compounds using Monte Carlo molecular simulations in binary hard sphere mixtures with the size ratio of 0.

Enhancement of nucleation of protein crystals on nano-wrinkled surfaces.

The synthesis of high quality protein crystals is essential for determining their structure. Hence the development of strategies to facilitate the nucleation of protein crystals is of prime importance. Recently, Ghatak and Ghatak [Langmuir 2013, 29, 4373] reported heterogeneous nucleation of protein crystals on nano-wrinkled surfaces.

A Gibbs-ensemble based technique for Monte Carlo simulation of electric double layer capacitors (EDLC) at constant voltage.

Current methods for molecular simulations of Electric Double Layer Capacitors (EDLC) have both the electrodes and the electrolyte region in a single simulation box. This necessitates simulation of the electrode-electrolyte region interface. Typical capacitors have macroscopic dimensions where the fraction of the molecules at the electrode-electrolyte region interface is very low.

Determination of favorable inter-particle interactions for formation of substitutionally ordered solid phases from a binary mixture of oppositely charged colloidal suspensions.

The solid phase formed by a binary mixture of oppositely charged colloidal particles can be either substitutionally ordered or substitutionally disordered depending on the nature and strength of interactions among the particles. In this work, we use Monte Carlo molecular simulations along with the Gibbs-Duhem integration technique to map out the favorable inter-particle interactions for the formation of substitutionally ordered crystalline phases from a fluid phase. The inter-particle interactions are modeled using the hard core Yukawa potential but the method can be easily extended to other systems of interest.

Free energy barriers for homogeneous crystal nucleation in a eutectic system of binary hard spheres.

In this study, the free energy barriers for homogeneous crystal nucleation in a system that exhibits a eutectic point are computed using Monte Carlo simulations. The system studied is a binary hard sphere mixture with a diameter ratio of 0.85 between the smaller and larger hard spheres.

Methane and carbon dioxide adsorption on edge-functionalized graphene: a comparative DFT study.

With a view towards optimizing gas storage and separation in crystalline and disordered nanoporous carbon-based materials, we use ab initio density functional theory calculations to explore the effect of chemical functionalization on gas binding to exposed edges within model carbon nanostructures. We test the geometry, energetics, and charge distribution of in-plane and out-of-plane binding of CO(2) and CH(4) to model zigzag graphene nanoribbons edge-functionalized with COOH, OH, NH(2), H(2)PO(3), NO(2), and CH(3). Although different choices for the exchange-correlation functional lead to a spread of values for the binding energy, trends across the functional groups are largely preserved for each choice, as are the final orientations of the adsorbed gas molecules.

Effect of charge asymmetry and charge screening on structure of superlattices formed by oppositely charged colloidal particles.

Colloidal suspensions made up of oppositely charged particles have been shown to self-assemble into substitutionally ordered superlattices. For a given colloidal suspension, the structure of the superlattice formed from self-assembly depends on its composition, charges on the particles, and charge screening. In this study we have computed the pressure-composition phase diagrams of colloidal suspensions made up of binary mixtures of equal sized and oppositely charged particles interacting via hard core Yukawa potential for varying values of charge screening and charge asymmetry.

Theory of gas hydrates: effect of the approximation of rigid water lattice.

One of the assumptions of the van der Waals and Platteeuw theory for gas hydrates is that the host water lattice is rigid and not distorted by the presence of guest molecules. In this work, we study the effect of this approximation on the triple-point lines of the gas hydrates. We calculate the triple-point lines of methane and ethane hydrates via Monte Carlo molecular simulations and compare the simulation results with the predictions of van der Waals and Platteeuw theory.