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Transition path sampling: throwing ropes over rough mountain passes, in the dark.
This article reviews the concepts and methods of transition path sampling. These methods allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction
Membrane bending by protein–protein crowding
TLDR
A third general mechanism for bending fluid cellular membranes: protein–protein crowding is proposed, and it is found that even proteins unrelated to membrane curvature, such as green fluorescent protein (GFP), can bend membranes when sufficiently concentrated.
Transition Path Sampling
Often, the dynamics of complex condensed materials is characterized by the presence of a wide range of different time scales, complicating the study of such processes with computer simulations.
Drying-mediated self-assembly of nanoparticles
TLDR
A coarse-grained model of nanoparticle self-assembly that explicitly includes the dynamics of the evaporating solvent is presented, and the resulting guide for designing statistically patterned arrays of nanoparticles suggests the possibility of fabricating spontaneously organized nanoscale devices.
Ultrafast Hydrogen-Bond Dynamics in the Infrared Spectroscopy of Water
TLDR
Using simulations of an atomistic model of water, this work relates frequency fluctuations in the OH-stretching frequency of HOD in liquid D2O with femtosecond infrared spectroscopy to intermolecular dynamics.
The effects of dissolved halide anions on hydrogen bonding in liquid water.
TLDR
It is shown that changes in O-H vibrational spectra induced by the alkali halides in liquid water result instead from the actions of ions' electric fields on adjacent water molecules.
Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites
TLDR
It is demonstrated that Markov state models built from extensive computer simulations can identify prospective cryptic sites from the equilibrium fluctuations of three medically relevant proteins—β-lactamase, interleukin-2, and RNase H—even in the absence of any ligand.
Scaling of Hydrophobic Solvation Free Energies
We have calculated the free energy of solvation for hard sphere solutes, as large as 20 A in diameter, in two simple-point-charge models of water. These results were obtained using umbrella sampling
Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles.
TLDR
A "virtual-move" Monte Carlo algorithm for systems of pairwise-interacting particles that employs a size- and shape-dependent damping of cluster movements, motivated by collective hydrodynamic effects neglected in simple implementations of Brownian dynamics is introduced.
Size-dependent protein segregation at membrane interfaces.
TLDR
It is shown that size differences between binding and non-binding proteins can dramatically alter their organization at membrane interfaces in the absence of active contributions from the cytoskeleton, with as little as a ~5 nm increase in non- binding protein size driving its exclusion from the interface.
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