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We address the problem of inverse polymer swelling. This phenomenon, in which a collapsed polymer chain swells upon decreasing temperature, can be observed experimentally in so-called thermoreversible homopolymers in aqueous solution, and…
We present a theoretical derivation of a rheology for dense granular flow, based on the process of inelastic collapse of neighboring particles. This collapse creates regions of correlated motion, which control the viscous behavior of the…
Inelastic collapse is found in a two-dimensional system of inelastic hard disks confined between two walls which act as an energy source. As the coefficient of restitution is lowered, there is a transition between a state containing small…
The swelling equilibrium of Olympic gels, which are composed of entangled cyclic polymers, is studied by Monte Carlo Simulations. In contrast to chemically crosslinked polymer networks, we observe that Olympic gels made of chains with a…
The nucleation of crystals from the liquid melt is often characterized by a competition between different crystalline structures or polymorphs, and can result in nuclei with heterogeneous compositions. These mixed-phase nuclei can display…
Urea denatures proteins due to its strong tendency to dehydrate the first solvation shell via urea-residue preferential binding. However, even after extensive experimental and computational investigations, the influence of urea on the…
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins.…
We study the Brownian dynamics of flexible and semiflexible polymer chains densely grafted on a flat substrate, upon rapid quenching of the system when the quality of solvent becomes poor and chains attempt collapse into a globular state.…
We study the problem of adsorption and collapse transition of a linear polymer chain situated in a fractal container represented by a 4-simplex lattice and interacting with a surface adsorbed linear polymer chain. The adsorbed chain…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
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…
We investigate the evolution of a system of colloidal particles, trapped at a fluid interface and interacting via capillary attraction, as function of the range of the capillary interaction and temperature. We address the collapse of an…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
We present numerical simulations of the evolution of low-mass, isothermal, molecular cores which are subjected to an increase in external pressure $P\xt$. If $P\xt$ increases very slowly, the core approaches instability quite…
We investigate the collapse kinetics of charged polymers (polyelectrolytes) induced by counterion condensation using coarse-grained molecular dynamics simulations. Under good solvent conditions, polyelectrolytes above the critical charge…
Effects of size and charge asymmetry between oppositely charged ions or particles on spatial inhomogeneities are studied for a large range of charge and size ratios. We perform a stability analysis of the primitive model (PM) of ionic…
We investigated the dynamics of a binary mixture confined within van der Waals (vdW) walls using molecular dynamics simulations. We discovered a novel phenomenon named perpendicular separations of two phases (PSTP). In the initial stage,…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
Dispersed colloidal particles within a suspension can aggregate and spontaneously self-organize into a robust, percolating structure known as a gel. These network-like structures are prevalent in nature and play a critical role in many…