Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

The stationary points of a potential energy surface provide a convenient framework for
coarse-graining calculations of thermodynamics and kinetics. Thermodynamic properties …

The framework of transition path theory (TPT) is developed in the context of continuous-time
Markov chains on discrete state-spaces. Under assumption of ergodicity, TPT singles out …

Theself-assembly of the soluble peptide Aβ into Alzheimer's disease amyloid is believed to
involve a conformational change. Hence the solution conformation of Aβ is of significant …

The plastic network model (PNM) is used to generate a conformational change pathway for
Escherichia coli adenylate kinase based on two crystal structures, namely that of an open …

Characterizing protein–protein association quantitatively has been a long standing
challenge for computer simulations. Here, a theoretical framework is put forth that addresses …

An improved and simplified version of the finite temperature string (FTS) method [W. E, W.
Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109, 6688 (2005)] is proposed. Like the …

Soft condensed matter physics, which emerged as a distinct branch of physics in the 1990s,
studies complex fluids: liquids in which structures with length scale between the molecular …

Milestoning is a procedure to compute the time evolution of complicated processes such as
barrier crossing events or long diffusive transitions between predefined states. Milestoning …

The discrete path sampling approach is applied to analyse the dynamics of several atomic
and molecular clusters. Permutational isomerization rates are first calculated for icosahedral …