Related papers: Protein folding, anisotropic collapse and blue pha…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
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…
We examine dense self-gravitating stellar systems dominated by a central potential, such as nuclear star clusters hosting a central supermassive black hole. Different dynamical properties of these systems evolve on vastly different…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
The chiral phase transition at a certain critical temperature is a restoration mechanism of the chiral symmetry, broken by the nonzero mass of quarks and mesons. The transition can be studied through several models, among which are the…
We discuss the relation between the emergence of new phases with broken symmetry within the framework of simple models of biopolymers. We start with a classic model for a chain molecule of spherical beads tethered together, with the steric…
A model of dipolar dimer liquid (DDL) on a two-dimensional lattice has been proposed. We found that at high density and low temperature, it has a partially ordered phase which we called glacia phase. The glacia phase transition can be…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a…
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…
The pressure-temperature phase diagram of a one-component system, with particles interacting through a spherically symmetric pair potential in two dimensions is studied. The interaction consists of a hard core plus an additional repulsion…
Despite their considerable practical and biological applications, the link between molecular properties, assembly conditions and self-organized structure in confined polymer solutions remains elusive. Here, we explore the lyotropic nematic…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
Freezing of charged colloids on square or triangular two-dimensional periodic substrates has been recently shown to realize a rich variety of orientational orders. We propose a theoretical framework to analyze the corresponding structures.…
Partially phase-separated liquid-crystal/polymer dispersions display highly fibrillar domain morphologies that are dramatically different from the typical structures found in isotropic mixtures. To explain this, we numerically explore the…
We study the viscoelasticity of an active solution of polar biofilaments and motor proteins. Using a molecular model, we derive the constitutive equations for the stress tensor in the isotropic phase and in phases with liquid crystalline…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
We present a Bethe approximation to study lattice models of linear polymers. The approach is variational in nature and based on the cluster variation method (CVM). We focus on a model with $(i)$ a nearest neighbor attractive energy…
We review the theory of second--order (ferro--)elastic phase transitions, where the order parameter consists of a certain linear combination of strain tensor components, and the accompanying soft mode is an acoustic phonon. In…