Related papers: Depth dependent dynamics in the hydration shell of…
There is a long-standing question about the molecular configuration of interfacial water molecules in the proximity of solid surfaces, particularly carbon atoms which play a crucial role in electrochemistry and biology. In this study, the…
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…
Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed…
2H NMR spin-lattice relaxation and line-shape analyses are performed to study the temperature-dependent dynamics of water in the hydration shells of myoglobin, elastin, and collagen.
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
1. Role of inter-domain water clusters in large-scale dynamics of proteins; 2. Description of large-scale dynamics of proteins based on generalized Stokes-Einstein and Eyring-Polany equation; 3. Dynamic model of protein-ligand complexes…
The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out many other tasks in the cell. We…
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…
We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or…
One of the most promising applications in nanoscience is the design of new materials to improve water permeability and selectivity of nanoporous membranes. Understanding the molecular architecture behind these fascinating structures and how…
Experiments in bulk water confirm the existence of two local arrangements of water molecules with different densities, but, because of inevitable freezing at low temperature $T$, can not ascertain whether the two arrangements separate in…
Particles diffusing near interfaces face anisotropic resistance to motion due to hydrodynamic interactions. While this has been extensively studied near \textit{hard} interfaces since the works of Lorentz and Brenner, our understanding of…
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
We have investigated the dynamics of liquid water confined in mesostructured porous silica (MCM-41) and periodic mesoporous organosilicas (PMOs) by incoherent quasielastic neutron scattering experiments. The effect of tuning the…
Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes formidable computational bottle-necks in approaches that…
We study a strongly interacting dense hard-sphere system confined between two parallel plates by event-driven molecular dynamics simulations to address the fundamental question of the nature of the 3D to 2D crossover. As the fluid becomes…
We develop theory and computational methods to investigate particle inclusions embedded within curved lipid bilayer membranes. We consider the case of spherical lipid vesicles where inclusion particles are coupled through (i) intramembrane…