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We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by…
The reaction-diffusion waves of proteins are known to be involved in fundamental cellular functions, such as cell migration, cell division, and vesicular transportation. In some of these phenomena, pattern formation on the membranes is…
We study quench dynamics of the Bose-Hubbard model by exact diagonalization. Initially the system is at thermal equilibrium and of a finite temperature. The system is then quenched by changing the on-site interaction strength $U$ suddenly.…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilised sucrose exhibited steadily increasing absorption with…
Two dimensional crystalline membranes in isotropic embedding space exhibit a flat phase with anomalous elasticity, relevant e.g., for graphene. Here we study their thermal fluctuations in the absence of exact rotational invariance in the…
We use a coarse grained molecular model of supported lipid bilayers to study the formation of adhesion domains. We find that this process is a first order phase transition, triggered by a combination of pairwise short range attractive…
The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer…
Experimental observations suggest that proteins follow different pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the SH3 domain over a broad range of temperatures, and identify…
The relation between thermal fluctuations and the mechanical response of a free membrane has been explored in great detail, both theoretically and experimentally. However, understanding this relationship for membranes, locally pinned by…
We propose a model describing the phase behavior of two-component membranes consisting of binary mixtures of electrically charged and neutral lipids. We take into account the structural phase transition (main-transition) of the hydrocarbon…
Despite their significance in biology and materials science, the dynamics of multicomponent vesicles under shear flow remain poorly understood because of their nonlinear and strongly coupled nature, especially regarding the role of membrane…
Recent single-molecule force measurements on single-domain proteins have highlighted a three-state folding mechanism where a stabilized intermediate state (I) is observed on the folding trajectory between the stretched state and the native…
We use molecular dynamics to study the vibrations of a thermally fluctuating two-dimensional elastic membrane clamped at both ends. We directly extract the eigenmodes from resonant peaks in the frequency domain of the time-dependent height…
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
We introduce and study the behavior of a tethered membrane of non-zero thickness embedded in three dimensions subject to an effective self-attraction induced by hydrophobicity arising from the tendency to minimize the area exposed to a…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
The Zeroth Law of Thermodynamics states that if two systems are in thermal equilibrium with a third one, then they are also in equilibrium with each other. This study explores not only the final state of thermal equilibrium between ideal…
The adhesion of biological membranes is controlled by various types of receptor and ligand molecules. In this letter, we present a statistical-mechanical model for membranes that interact via receptor/ligand bonds of two different lengths.…