Related papers: Reversibility, Water-Mediated Switching, and Direc…
Biological information processing often arises from mesoscopic molecular systems operating far from equilibrium, yet their complexity can make the underlying principles difficult to visualize. In this study, we introduce a macroscopic…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…
Recent theoretical advances have led to the creation of a unified phase diagram for the thermal glass and athermal jamming transitions. This diagram makes clear that, while related, the mode-coupling---or dynamic---glass transition is…
Active matter, whose motion is driven, and glasses, whose dynamics are arrested, seem to lie at opposite ends of the spectrum in nonequilibrium systems. In spite of this, both classes of systems exhibit a multitude of stable states that are…
Generative models show great promise for the inverse design of molecules and inorganic crystals, but remain largely ineffective within more complex structures such as amorphous materials. Here, we present a diffusion model that reliably…
2H NMR is used to study the mechanisms for the reorientation of protein hydration water. In the past, crossovers in temperature-dependent correlation times were reported at T_x1=225K (X1) and T_x2=200K (X2). We show that neither X1 nor X2…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by softening of the vibrational force constant by electrostatic and van der Waals forces…
We report that protein confinement within nanoscopic vesicular compartments corresponds to a liquid-liquid phase transition with the protein/water within vesicle lumen interacting very differently than in bulk. We show this effect leads to…
Thermodynamics and kinetics are thought to be linked in glass transitions. The quantitative predictions of -relaxation activation barriers provided by the theory of glasses based on random first order transitions are compared with…
Understanding the nature of glass transition, as well as precise estimation of the glass transition temperature for polymeric materials, remain open questions in both experimental and theoretical polymer sciences. We propose a data-driven…
The atomistic mechanisms occurring during the processes of aging and rejuvenation in glassy materials involve very small structural rearrangements that are extremely difficult to capture experimentally. Here we use in-situ X-ray diffraction…
Using molecular dynamics simulations, we study the slow dynamics of supercooled liquids confined in a random matrix of immobile obstacles. We study the dynamical crossover from glass-like to Lorentz-gas-like behavior in terms of the density…
A large number of water models exists for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient.…
The thermodynamics and dynamics of supercooled liquids correlate with their elasticity. In particular for covalent networks, the jump of specific heat is small and the liquid is {\it strong} near the threshold valence where the network…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
We present a modified version of our "sliding model", where chain arcs, between two contacts at the surface, may move if all the barriers along the arc are weaker than a certain threshold.An important advance of the revised model is that…
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of…
We introduce a system of bacteria confined to a finite 2D oil-water interface and driven on two distinct time scales by motility and by growth. The combined effect of activity on different time scales creates transitions between several…
The critical behaviour of the dynamical transition of glassy system is controlled by a Replica Symmetric action with n=1 replicas. The most divergent diagrams in the loop expansion correspond at all orders to the solutions of a stochastic…