Related papers: Crowding effects on the structural transitions in …
Understand the nature of liquid structure and its evolution under different conditions is a major challenge in condensed physics and materials science. Here, we report a pressure-induced structure change spanning a wide pressure range in…
The theory of transition between $\alpha$-helix, $\beta$-sheet and random coil conformation of a protein is discussed through a simple model, that includes both short and long-range interactions. Besides the bonding parameter and helical…
Macromolecular crowding plays a crucial role in modulating protein dynamics in cellular and in vitro environments. Polymeric crowders such as dextran and Ficoll are known to induce entropic forces, including depletion interactions, that…
We give an overview exploring the role of kinetics in multicomponent mixtures. Compared to the most commonly studied binary (single species plus solvent) case, multicomponent fluids show a rich interplay between kinetics and thermodynamics…
The phase behavior of colloidal particles embedded in a binary fluid is influenced by wetting layers surrounding each particle. The free energy of the fluid film depends on its morphology, i.e., on size, shape and connectivity. Under rather…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
Metal films and other geometries of nanoscale thickness, when exposed to laser irradiation, melt and evolve as fluids as long as their temperature is sufficiently high. This evolution often leads to pattern formation, which may be…
We show how dynamic heterogeneities (DH), a hallmark of glass-forming materials, depend on chain flexibility and chain length in polymers. For highly flexible polymers, a relatively large number of monomers ($N_c\sim500$) undergo correlated…
Assemblies of purely repulsive and frictionless particles, such as emulsions or hard spheres, display very curious properties near their jamming transition, which occurs at the random close packing for mono-disperse spheres. Although such…
We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which…
The pressure induced bcc to hcp transition in Fe has been investigated via ab-initio electronic structure calculations. It is found by the disordered local moment (DLM) calculations that the temperature induced spin fluctuations result in…
We explore the impact of weak disorder on the dynamics of classical particles in a periodically oscillating lattice. It is demonstrated that the disorder induces a hopping process from diffusive to regular motion i.e. we observe the…
We have analyzed the equilibrium response of chain molecules to stretching. For a homogeneous sequence of monomers, the induced transition from compact globule to extended coil below the $\theta$-temperature is predicted to be sharp. For…
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-…
Using numerical simulations, we study the dynamical evolution of particles interacting via competing long-range repulsion and short-range attraction in two dimensions. The particles are compressed using a time-dependent quasi-one…
Force-driven translocation of a macromolecule through a nanopore is investigated by taking into account the monomer-pore friction as well as the "crowding" of monomers on the {\it trans} - side of the membrane which counterbalance the…
The densities of states are evaluated for very short chain molecules made up of overlapping monomers, using a model which has previously been shown to produce helical structure. The results of numerical calculations are presented for…
We study the model of a partially directed flexible or semi-flexible homopolymer on a square lattice, subject to an externally applied force, in a direction either parallel to, or perpendicular to the preferred direction. The polymer is…
The coil-globule transition of an energy polydisperse chain, a model heteropolymer system where the number of monomer species is as large as the total number of monomers, is studied by means of computer simulations. In this study, we…
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of…