Electron transfer reaction in a polar solvent is modeled by a solute dipole surrounded by dipolar molecules with simple rotational dynamics posted on the three-dimensional distorted lattice sites. The interaction energy between the solute and solvent dipoles as a reaction coordinate is adopted and free energy landscapes are calculated by generating all possible states for a 26 dipolar system an...

The kinetics of folding-unfolding of a structurally diverse set of four proteins optimized for thermodynamic stability by rational redesign of surface charge-charge interactions is characterized experimentally. The folding rates are faster for designed variants compared with their wild-type proteins, whereas the unfolding rates are largely unaffected. A simple structure-based computational mode...

Energy landscapes provide a conceptual framework for structure prediction, and detailed understanding of their topological features is necessary to develop efficient methods exploration. The ability visualise these surfaces essential, but the high dimensionality corresponding configuration spaces makes this difficult. Here we present Stochastic Hyperspace Embedding Projection (SHEAP), method en...

Currently, the most common strategy when managing forests for biodiversity at the landscape scale is to maintain structural complexity within stands and provide a variety of seral stages across landscapes. Advances in ecological theory reveal that biodiversity at continental scales is strongly influenced by available energy (i.e., climate factors relating to heat and light and primary productiv...

Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we ...