Related papers: Protein structure, activity and thermal stability …
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Understanding the role of confinement while crystallizing nanocrystals is very relevant for predicting their structure and physical properties. With this aim we perform Langevin dynamics simulations of nanocrystals of the model system of…
Experiments in bulk water confirm the existence of two local arrangements of water molecules with different densities, but, because of inevitable freezing at low temperature $T$, can not ascertain whether the two arrangements separate in…
Water plays a key role in biological membrane transport. In ion channels and water-conducting pores (aquaporins), one dimensional confinement in conjunction with strong surface effects changes the physical behavior of water. In molecular…
Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Although wettability is a macroscopic manifestation of molecular-level forces, such as van der Waals (vdW) forces, the impact of nanoconfinement on material properties in reduced film thickness remains unexplored in predicting film…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
We consider the sedimentation of a colloidal gel under confinement in the direction of gravity. The confinement allows us to compare directly experiments and computer simulations, for the same system size in the vertical direction. The…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
Nanoconfinement effects on water dissociation and reactivity remain controversial, despite their importance to understand the aqueous chemistry at interfaces, pores, or aerosols. The pKw in confined environments has been assessed from…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Effect of confinement on the liquid-liquid transition of water are studied by simulations in the Gibbs ensemble. Upon cooling along the liquid-vapor coexistence curve, confined water undergoes transition from normal to strongly tetrahedral…
We study by molecular dynamics simulations the thermodynamics of an anomalous fluid confined in a slit pore with one wall structured and attractive and another unstructured and repulsive. We find that the phase diagram of the homogeneous…
The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density…
The influence of spatial confinement on the thermally excited stochastic cation dynamics of the room-temperature ionic liquid 1-N-butylpyridinium bis-((trifluoromethyl)sulfonyl)imide ([BuPy][Tf_2N]) inside porous carbide-derived carbons…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
Water confined in nanoscale cavities plays a crucial role in everyday phenomena in geology and biology, as well as technological applications at the water-energy nexus. However, even understanding the basic properties of nano-confined water…
We have studied phase behavior of hard gaussian overlap molecules with small anisotropic parameter confined in two plane parallel structureless hard walls. Our investigation based on standard constant-NPT Monte Carlo molecular simulation…