Structure and energetics guide dynamic behaviour in a T = 3 icosahedral virus capsid.

Although virus capsids appear as rigid, symmetric particles in experimentally determined structures; biochemical studies suggest a significant degree of structural flexibility in the particles. We carried out all-atom simulations on the icosahedral capsid of an insect virus, Flock House Virus, which show intriguing differences in the degree of flexibility of quasi-equivalent capsid subunits consistent with previously described biological behaviour. The flexibility of all the β and γ subunits of the protein and RNA fragments is analysed and compared.

The Operating Cycle of NO Adsorption and Desorption in Pd-Chabazite for Passive NO Adsorbers.

Pd-doped chabazite (Pd/CHA) offers unique opportunities to adsorb and desorb NO in the target temperature range for application as a passive NO adsorber (PNA). The ability of Pd/CHA to trap NO emissions at low temperatures (<200 °C) is facilitated by the binding of NO species at various Pd sites available in the CHA framework. Density functional theory (DFT) simulations are performed to understand Pd speciation in CHA and the interaction of NO with Pd/CHA to explain the mechanisms of NO adsorption, oxidation, and desorption processes.

Optimizing String Method's Reproducibility Using Generalized Solute Tempering Replica Exchange.

Obtaining accurate and reproducible free energies from molecular simulations is somewhat tricky due to incomplete knowledge of crucial slow degrees of freedom leading to hidden barriers that can stymie sampling. Employing a sufficiently large number of collective variables (CV) and ensuring ergodic sampling in orthogonal CV space, perhaps via tempering methods, can reduce these issues to some extent. For complex systems with high-dimensional free energy landscapes, both these approaches become computationally expensive.

Mapping saddles and minima on free energy surfaces using multiple climbing strings.

Locating saddle points on free energy surfaces is key in characterizing multistate transition events in complicated molecular-scale systems. Because these saddle points represent transition states, determining minimum free energy pathways to these saddles and measuring their free energies relative to their connected minima are further necessary, for instance, to estimate transition rates. In this work, we propose a new multistring version of the climbing string method in collective variables to locate all saddles and corresponding pathways on free energy surfaces.

Capillary evaporation of the ionic liquid [EMIM][BF] in nanoscale solvophobic confinement.

Solvent density fluctuations play a crucial role in liquid-vapor transitions in solvophobic confinement and can also be important for understanding solvation of polar and apolar solutes. In the case of ionic liquids (ILs), density fluctuations can be used to understand important processes in the context of nanoscale aggregation and colloidal self-assemblies. In this article, we explore the nature of density fluctuations associated with capillary evaporation of the IL 1-ethyl-3-methylimidazolium tetrafluoroborate ([EMIM][BF]) in the confined region of model solvophobic nanoscale sheets by using molecular dynamics simulations combined with non-Boltzmann sampling techniques.

Molecular dynamics study of nanoscale organization and hydrogen bonding in binary mixtures of butylammonium nitrate ionic liquid and primary alcohols.

Molecular dynamics simulations are utilized here to explore the nanoscale morphology and the nature of hydrogen bonding in the equimolar mixtures of butylammonium nitrate protic ionic liquid with ethanol, propanol, and butanol. The X-ray scattering experimental study of Greaves et al. [Phys.

Stress-Strain Relationships in Hydroxyl Substituted Polyethylene.

Stress-strain relationships in semicrystalline hydroxylated polyethylene are studied using all-atom molecular dynamics simulations. Chain sizes ranging from 50 to 2000 carbons are gradually cooled from melt in order to obtain semicrystalline samples for pure, 4%, and 8% hydroxylated chains. Local orientational order of the polymer backbone and hydrogen bonding behavior is studied.

Effective interactions between nanoparticles: Creating temperature-independent solvation environments for self-assembly.

The extent to which solvent-mediated effective interactions between nanoparticles can be predicted based on structure and associated thermodynamic estimators for bulk solvents and for solvation of single and pairs of nanoparticles is studied here. As a test of the approach, we analyse the strategy for creating temperature-independent solvent environments using a series of homologous chain fluids as solvents, as suggested by an experimental paper [M. I.