One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution

Article Abstract:

A method to obtain a reaction coordinate whose potential of the mean force can reproduce the commitment probability distribution from the multidimensional surface is proposed. The usefulness of the method is examined, with dynamics in a two-dimensional system showing that the one-dimensional surface thus obtained can predict the existence of an intermediate and the occurrence of path switching without a priori knowledge of the morphology of the original surface.

Science & research, Research, Probabilities, Probability theory, Chemistry, Physical and theoretical, Physical chemistry, Switching theory

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A new twist on the helix-coil transition: A non-biological helix with protein-like intermediates and traps

Article Abstract:

The study on classical helix-coil picture, pPA folds via on-pathway intermediate states and can also be trapped in misfolded states in simple models for proteins is presented. Results show that quantitative characterization of pPA folding simulations finds a marked deviation from exponential kinetics.

Analysis, Biopolymers, Spectra

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Accurate and efficient corrections for missing dispersion interactions in molecular simulations

Article Abstract:

Study is conducted to obtain computed binding free energies that are independent of the Lennard-Jones cutoff.

Observations, Linear free energy relationship

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