Biomolecular dynamics: order–disorder transitions and energy landscapes
While the energy landscape theory of protein folding is now a widely accepted view for
understanding how relatively weak molecular interactions lead to rapid and cooperative …
understanding how relatively weak molecular interactions lead to rapid and cooperative …
SMOG 2: a versatile software package for generating structure-based models
Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven
to be an effective means of capturing the functionally important long-time and large-length …
to be an effective means of capturing the functionally important long-time and large-length …
Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy
Internal friction, which reflects the “roughness” of the energy landscape, plays an important
role for proteins by modulating the dynamics of their folding and other conformational …
role for proteins by modulating the dynamics of their folding and other conformational …
What protein folding teaches us about biological function and molecular machines
Protein folding was the first area of molecular biology for which a systematic statistical–
mechanical analysis of dynamics was developed. As a result, folding is described as a …
mechanical analysis of dynamics was developed. As a result, folding is described as a …
Diffusion models of protein folding
In theory and in the analysis of experiments, protein folding is often described as diffusion
along a single coordinate. We explore here the application of a one-dimensional diffusion …
along a single coordinate. We explore here the application of a one-dimensional diffusion …
The many faces of structure-based potentials: from protein folding landscapes to structural characterization of complex biomolecules
Structural biology techniques, such as nuclear magnetic resonance (NMR), x-ray
crystallography, and cryogenic electron microscopy (cryo-EM), have provided extraordinary …
crystallography, and cryogenic electron microscopy (cryo-EM), have provided extraordinary …
Microscopic aspects of Stretched Exponential Relaxation (SER) in homogeneous molecular and network glasses and polymers
JC Phillips - Journal of Non-Crystalline Solids, 2011 - Elsevier
The “diffusion to traps” model quantitatively explains “magic” stretching fractions β (Tg) for a
wide variety of relaxation experiments (nearly 50 altogether) on microscopically …
wide variety of relaxation experiments (nearly 50 altogether) on microscopically …
[HTML][HTML] Supersymmetric quantum mechanics method for the Fokker–Planck equation with applications to protein folding dynamics
This work developed analytical methods to explore the kinetics of the time-dependent
probability distributions over thermodynamic free energy profiles of protein folding and …
probability distributions over thermodynamic free energy profiles of protein folding and …
Reduced model captures Mg2+-RNA interaction free energy of riboswitches
The stability of RNA tertiary structures depends heavily on Mg 2+. The Mg 2+-RNA
interaction free energy that stabilizes an RNA structure can be computed experimentally …
interaction free energy that stabilizes an RNA structure can be computed experimentally …
[HTML][HTML] Diffusion of tRNA inside the ribosome is position-dependent
In recent years, there has been a growing interest to quantify the energy landscape that
governs ribosome dynamics. However, in order to quantitatively integrate theoretical …
governs ribosome dynamics. However, in order to quantitatively integrate theoretical …