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We have carried out a detailed study of the chemical bonding for two room-temperature stable platinum silicide phases, tetragonal alpha-Pt_2Si and orthorhombic PtSi. An analysis of the valence electronic charge density reveals surprising…
In suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in…
In a previous work a model was proposed for the phase transitions of crystals with localized magnetic moments which at low temperature have a "conical" arrangement that at higher T transforms into a more symmetrical structure (depending on…
Long linear polymers in dilute solutions are known to undergo a collapse transition from a random coil (expand itself) to a compact ball (fold itself up) when the temperature is lowered, or the solvent quality deteriorates. A natural model…
This paper reviews recent Monte Carlo simulation studies of the glassy behavior in thin polymer films. The simulations employ a version of the bond-fluctuation lattice model, in which the glass transition is driven by the competition…
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…
The power of polymorphism in carbon is vividly manifested by the numerous applications of carbon-based nano-materials. Ranging from environmental issues to biomedical applications, it has the potential to address many of today's dire…
We use complete enumeration and Monte Carlo techniques to study two-dimensional self-avoiding polymer chains with quenched ``charges'' $\pm 1$. The interaction of charges at neighboring lattice sites is described by $q_i q_j$. We find that…
Many critical biological processes, like wound healing, require confluent cell monolayers/bulk tissues to transition from a jammed solid-like to a fluid-like state. Although numerical studies anticipate changes in the cell shape alone can…
A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…
The thermodynamic behavior of collapse transition in a fully flexible coarse-grained model of energy polydisperse polymer (EPP), a statistical model of random heteropolymer, is investigated in an implicit solvent by means of molecular…
We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the…
We investigate the structural and topological properties of hydrophobic homopolymer chains in aqueous solutions using molecular dynamics simulations and circuit topology (CT) analysis. By combining geometric observables, such as radius of…
The beta polytope $P_{n,d}^\beta$ is the convex hull of $n$ i.i.d. random points distributed in the unit ball of $\mathbb{R}^d$ according to a density proportional to $(1-\lVert{x}\rVert^2)^{\beta}$ if $\beta>-1$ (in particular, $\beta=0$…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
We study the dynamic structure factor of fluctuating elastic thin sheets subject to conservative (athermal) random forcing. In Steinbock, Katzav & Boudaoud, Phys. Rev. Research 4, 033096 (2022), the static structure factor of such a sheet…
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this…
We propose a new and effective means for designing stable and fast-folding polypeptide sequences using a cumulant expansion of the molecular partition function. This method is unique in that $T_{Z}$, the ``cumulant design temperature''…
A ring polymer in a confining space may exhibit at least two phases, namely an expanded (or solvent-rich phase) if its concentration is small, or a collapsed (or polymer-rich phase) when it is concentrated and compressed. These phases are…