The formation of amyloid fibrils is a complex phenomenon that remains poorly understood at
the atomic scale. Herein, we perform extended unbiased all-atom simulations in explicit …

Here, we perform all-atom molecular dynamics simulations in explicit solvent to study the
aggregation of amphipathic peptides into amyloid-like fibrils. We use large simulation boxes …

GRADE is an open-source software package that identifies clathrate hydrate structures
given the atomic coordinates of oxygen atoms of water. These structures are commonly …

We study the stability of globular proteins as a function of temperature and pressure through
NPT simulations of a coarse-grained model. We reproduce the elliptical stability of proteins …

In this study, we investigate interactions of extended conformations of homodimeric peptides
made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains …

The density, diffusion, and structural anomalies of the simple two-dimensional model of
water were determined by Monte Carlo simulations. The rose model was used which is a …

Hydrophobic interactions are responsible for water-driven processes such as protein folding
and self-assembly of biomolecules. Microscopic theories and molecular simulations have …

We developed an analytical theory for studying of rotational degrees of freedom of a simple
model of liquid water. Wertheim's integral equation theory (IET) for associative liquids was …

Clathrate hydrate forms when a hydrophobic molecule is entrapped inside a water cage or
cavity. Although biomolecular structures also have hydrophobic patches, clathrate-like water …

We have developed an analytical theory for a simple model of liquid water. We apply
Wertheim's thermodynamic perturbation theory (TPT) and integral equation theory (IET) for …