Related papers: Reversibility, Water-Mediated Switching, and Direc…
Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the…
Clarification of the detailed mechanisms involved in the DNA polymorphism is an important challenge for computational molecular biophysics. This paper reports about reversible A/B transitions in DNA observed in silico in a simulated…
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…
Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [PNAS 103, 9012 (2006)] suggested that anomalies near 220 K observed by quasi-elastic…
Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast ($\sim$ pico-nanosecond, ps-ns) and small-amplitude ($\sim$ \AA )…
We study the glass transition by exploring a broad class of kinetic rules that can significantly modify the normal dynamics of super-cooled liquids, while maintaining thermal equilibrium. Beyond the usual dynamics of liquids, this class…
Non-reversing relaxation enthalpies (DHnr) at glass transitions Tg(x) in the PxGexSe1-2x ternary display a wide, sharp and deep global minimum (~0) in the 0.09 < x < 0.145 range, within which Tg becomes thermally reversing. In the…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
A molecular dynamics simulation of SPC/E water confined in a Silica pore is presented. The pore has been constructed to reproduce the average properties of a pore of Vycor glass. Due to the confinement and to the presence of a strong…
Bacterial assemblies exhibit rich collective behaviors that control their biological functions, making them a relevant object of study from an active matter physics perspective. Dense bacterial suspensions self-organize into distinct…
Glass forming liquids exhibit a rich phenomenology upon confinement. This is often related to the effects arising from wall-fluid interactions. Here we focus on the interesting limit where the separation of the confining walls becomes of…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
We consider the stationary state of a fluid comprised of inelastic hard spheres or disks under the influence of a random, momentum-conserving external force. Starting from the microscopic description of the dynamics, we derive a nonlinear…
We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…
The Boltzmann distribution of a protein provides a roadmap to all of its functional states. Normalizing flows are a promising tool for modeling this distribution, but current methods are intractable for typical pharmacological targets; they…
A mode-coupling theory for the slow single-particle dynamics in fluids adsorbed in disordered porous media is derived, which complements previous work on the collective dynamics [V. Krakoviack, Phys. Rev. E 75, 031503 (2007)]. Its…
The axiomatic theory of ideally glassy networks, which has proved effective in describing phase diagrams and many properties of chalcogenide, oxide, and even molecular glasses, is here broadened to describe both geometrical properties, such…
Single particle dynamics of water confined in a nanopore is studied through Computer Molecular Dynamics. The pore is modeled to represent the average properties of a pore of Vycor glass. Dynamics is analyzed at different hydration levels…
We develop a transferable machine learning model which predicts structural relaxation from amorphous supercooled liquid structures. The trained networks are able to predict dynamic heterogeneity across a broad range of temperatures and time…