Recent studies of active matter have stimulated interest in the driven self-assembly of complex structures. Phenomenological modeling of particular examples has yielded insight, but general thermodynamic principles unifying the rich diversity of behaviors observed have been elusive. Here, we study the stochastic search of a toy chemical space by a collection of reacting Brownian particles subje...

often in modeling the engineering optimization design problems, the value of objective function(s) is not clearly defined in terms of design variables. instead it is obtained by some numerical analysis such as fe structural analysis, fluid mechanic analysis, and thermodynamic analysis, etc. yet, the numerical analyses are considerably time consuming to obtain the final value of objective functi...

Allostery pervades macromolecular function and drives cooperative binding of ligands to macromolecules. To decipher the mechanisms of cooperative ligand binding it is necessary to define at a microscopic level the structural and thermodynamic consequences of binding of each ligand to its allosterically coupled site(s). However, dynamic sampling of alternative conformations (microstates) in allo...