Related papers: Water drives peptide conformational transitions
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in…
The extent to which biological interfaces affect the dynamics of water plays a key role in the exchange of matter and chemical interactions that are essential for life. The density and the mobility of water molecules depend on their…
Motivated by recent experiments, we theoretically analyze the flow past an obstacle of a one-dimensional "quantum fluid of light" which is resonantly driven, and exhibits bistability. The flow is found to abruptly change several times when…
We employ the Distance Matrix method to investigate metabasin dynamics in supercooled water. We find that the motion of the system consists in the exploration of a finite region of configuration space (enclosing several distinct local…
Using an activation mechanism reproducing facilitation, a dynamic phase transition triggered by a few active molecules was recently found in a supercooled model liquid. Prompted by this finding we investigate the presence of a similar…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
In molecular liquids such as water, time-delayed influences between microscopic or mesoscopic variables are typically probed using time-correlation functions, which are symmetric under detailed balance and therefore blind to dynamical…
Water molecules play an important role in providing unique environments for biological reactions on cell membranes. It is widely believed that water molecules form bridges that connect lipid molecules and stabilize cell membranes. Using…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Dynamic structuring of water is a key player in a large class of processes underlying biochemical and technological developments today, the latter often involving electric fields. However, the anisotropic coupling between the water…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…
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…
We present a fluid dynamics video which illustrates a kinetic-dominated phase change just prior to solidification inception for a static drop situated on a cold solid substrate. This metastable stage initiated from solid-vapor-liquid…
Water is vital for life, and without it biomolecules and cells cannot maintain their structures and functions. The remarkable properties of water originate from its ability to form hydrogen-bonding networks and dynamics, which the…
Water molecules confined between biological membranes exhibit a distinctive non-Gaussian displacement distribution, far different from bulk water. Here, we introduce a new transport equation for water molecules in the intermembrane space,…
We use numerical simulation to examine the possibility of a reversible liquid-liquid transition in supercooled water and related systems. In particular, for two atomistic models of water, we have computed free energies as functions of…
Isothermal-isobaric molecular dynamics simulations have been performed to examine a broad set of properties of the model water-1,2-dimethoxyethane (DME) mixture as a function of composition. The SPC-E and TIP4P-Ew water models and the…