Effects of Trehalose on Lipid Membranes under Rapid Cooling using All-Atom and Coarse-Grained Molecular Simulations.

We investigate the effect of the cryopreservative α-α-trehalose on a model 1,2-dimyristoyl--glycero-3-phosphocholine (DMPC) lipid membrane undergoing cooling from 350 to 250 K using all-atom (AA) and coarse-grained (CG) molecular dynamics simulation. In the AA simulations, we find that the addition of trehalose alters the (liquid crystalline) to (ripple) phase transition, suppressing the major domain of the phase and increasing the degree of leaflet interdigitation (the minor domain) which yields a thinner membrane with a higher area per lipid. Calculation of dihedral angle distributions for the lipid tails shows a greater fraction of angles in the phase as trehalose concentration is increased, indicating that trehalose increases lipid disorder in the membrane.

Genetic Algorithm Approach for the Optimization of Protein Antifreeze Activity Using Molecular Simulations.

Antifreeze proteins (AFPs) are of much interest for their ability to inhibit ice growth at low concentrations. In this work, we present a genetic algorithm for the design of AFP mutants with improved antifreeze activity, measured as the predicted thermal hysteresis at a fixed concentration, Δ. Central to the algorithm is our recently developed neural network method for predicting Δ from molecular simulations [Kozuch et al.

Insights into Hydrophobic Ion Pairing from Molecular Simulation and Experiment.

Hydrophobic ion pairing (HIP) is the process by which a charged hydrophilic molecule of interest is electrostatically coupled with an oppositely charged hydrophobic counterion to produce a complex with greater hydrophobicity than the original molecule. This process is of interest in drug delivery, but a molecular-based mechanistic understanding is still incomplete. In this work, we used molecular simulation and experiment to study a model system of Polymyxin B (drug) and oleic acid (hydrophobic counterion).

Low temperature protein refolding suggested by molecular simulation.

The function of critical biological materials, such as proteins, is intrinsically tied to their structure, and this structure is in turn heavily dependent on the properties of the solvent, most commonly water or dilute aqueous solutions. As water is known to exhibit anomalous properties, especially at supercooled temperatures, it is natural to ask how these properties might impact the thermodynamics of protein folding. To investigate this question, we use molecular simulation to explore the behavior of a model miniprotein, Trp-cage, as low as 70 K below the freezing point of the solvent at ambient pressure.

Combined molecular dynamics and neural network method for predicting protein antifreeze activity.

Antifreeze proteins (AFPs) are a diverse class of proteins that depress the kinetically observable freezing point of water. AFPs have been of scientific interest for decades, but the lack of an accurate model for predicting AFP activity has hindered the logical design of novel antifreeze systems. To address this, we perform molecular dynamics simulation for a collection of well-studied AFPs.

Predicting the Flory-Huggins χ Parameter for Polymers with Stiffness Mismatch from Molecular Dynamics Simulations.

The Flory⁻Huggins χ parameter describes the excess free energy of mixing and governs phase behavior for polymer blends and block copolymers. For chemically-distinct nonpolar polymers, the value of χ is dominated by the mismatch in cohesive energy densities of the monomers. For blends of chemically-similar polymers, the entropic portion of χ, arising from non-ideal local packing, becomes more significant.

Large-scale synthesis and functionalization of hexagonal boron nitride nanosheets.

A simple and inexpensive method to functionalize hexagonal boron nitride (hBN) was achieved by using an acid mixture of phosphoric and sulphuric acid. This functionalization induced the exfoliation of the layered structure of hBN into monolayer to few-layer sheets where the sizes of the sheets were dependent on the parent hBN powder used. Exfoliated hBN was shown to be stable in solvents such as ethanol, acetone, deionized water and isopropyl alcohol, and this stability was linked to sulfur functionalization that was induced during the exfoliation process.