2006/01/01 by John D. Chodera, William C. Swope, Jed W. Pitera +1 · 2 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Physics and Astronomy · #Biological system #Computer science #Dynamics (music) #Folding (DSP implementation) #Markov chain #Mass Spectrometry Techniques and Applications #Microsecond #Molecular dynamics #Physics #Protein Structure and Dynamics #Protein dynamics #Protein folding #Quantum mechanics #Relaxation (psychology) #Simple (philosophy) #Spectroscopy and Quantum Chemical Studies #Statistical physics #Time evolution
paper · doi:10.1137/06065146x
openalex publication_date 2006/01/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/09
Protein folding involves physical timescales—microseconds to seconds—that are too long to be studied directly by straightforward molecular dynamics simulation, where the fundamental timestep is constrained to femtoseconds. Here we show how the long‐time statistical dynamics of a simple solvated biomolecular system can be well described by a discrete‐state Markov chain model constructed from trajectories that are an order of magnitude shorter than the longest relaxation times of the system. This suggests that such models, appropriately constructed from short molecular dynamics simulations, may have utility in the study of long‐time conformational dynamics.