Related papers: Binding of thermalized and active membrane curvatu…
The buckling of thin elastic sheets is a classic mechanical instability that occurs over a wide range of scales. In the extreme limit of atomically thin membranes like graphene, thermal fluctuations can dramatically modify such mechanical…
The stability of a $\beta$-sheeted conformation and its transition into a random coil are studied with a 2D lattice biopolymer model. At low temperature and low external force, the polymer folds back and forth on itself and forms a…
Cell membranes interact with a myriad of curvature-active proteins that control membrane morphology and are responsible for mechanosensation and mechanotransduction. Some of these proteins, such as those containing BAR domains, are curved…
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is…
The dynamics of first order phase transitions are studied in the context of (3+1)-dimensional scalar field theories. Particular attention is paid to the question of quantifying the strength of the transition, and how `weak' and `strong'…
Homogeneous nucleation of a new phase near a second, continuous, transition, is considered. The continuous transition is in the metastable region associated with the first-order phase transition, one of whose coexisting phases is…
We demonstrate that absorbing phase transitions in one dimension may be induced by the dynamics of a single site. As an example we consider a one-dimensional model of diffusing particles, where a single site at the boundary evolves…
The interface of two solids in contact introduces a thermal boundary resistance (TBR), which is challenging to measure from experiments. Besides, if the interface is reactive, it can form an intermediate recrystallized or amorphous region,…
The assembly of curved protein rods on fluid membranes is studied using implicit-solvent meshless membrane simulations. As the rod curvature increases, the rods on a membrane tube assemble along the azimuthal direction first and…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
We consider membranes adhered through specific receptor-ligand bonds. Thermal undulations of the membrane induce effective interactions between adhesion sites. We derive an upper bound to the free energy that is independent of interaction…
We demonstrate the existence of topological phase transitions in interacting, symmetry-protected quantum matter at finite temperatures. Using a combined numerical and analytical approach, we study a one-dimensional Su-Schrieffer-Heeger…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
Within self-consistent field theory we study the phase behavior of a symmetrical binary AB polymer blend confined into a thin film. The film surfaces interact with the monomers via short range potentials. One surface attracts the A…
We investigated domain growth in switching processes between the low-spin and high-spin phases in thermally induced hysteresis loops of spin-crossover (SC) solids. Elastic interactions among the molecules induce effective long-range…
Some dimeric proteins first fold and then dimerize (three--state dimers) while others first dimerize and then fold (two--state dimers). Within the framework of a minimal lattice model, we can distinguish between sequences obeying to one or…
The interplay of phase separation and dynamical arrest can lead to the formation of gels and glasses, which is relevant for such diverse fields as hard and soft condensed matter physics, materials science, food engineering and…
We report a numerical simulation of the phase diagram of a simple model for membrane proteins constrained to move in a plane. In analogy with the corresponding three dimensional models, the liquid-gas transition becomes metastable as the…