Relative Entropy: Free Energy Associated with Equilibrium Fluctuations and Nonequilibrium Deviations

Using a one-dimensional macromolecule in aqueous solution as an illustration, we demonstrate that the relative entropy from information theory, $\sum_k p_k\ln(p_k/p_k^*)$, has a natural role in the energetics of equilibrium and nonequilibrium conformational fluctuations of the single molecule. It is identified as the free energy difference associated with a fluctuating density in equilibrium, and is associated with the distribution deviate from the equilibrium in nonequilibrium relaxation. This result can be generalized to any other isothermal macromolecular systems using the mathematical theories of large deviations and Markov processes, and at the same time provides the well-known mathematical results with an interesting physical interpretations.Comment: 5 page

Extended mapping and characteristics techniques for inverse aerodynamic design

Some ideas for using hodograph theory, mapping techniques and methods of characteristics to formulate typical aerodynamic design boundary value problems are developed. The inverse method of characteristics is shown to be a fast tool for design of transonic flow elements as well as supersonic flows with given shock waves

Stochastic Physics, Complex Systems and Biology

In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated equilibrium, spontaneous random "mutations" and "adaptations". On an evlutionary time scale it produces sustainable diversity among individuals in a homogeneous population rather than convergence as usually predicted by a deterministic dynamics. The emergent discrete states in such a system, i.e., attractors, have natural robustness against both internal and external perturbations. Phenotypic states of a biological cell, a mesoscopic nonlinear stochastic open biochemical system, could be understood through such a perspective.Comment: 10 page

Criticality and Continuity of Explosive Site Percolation in Random Networks

This Letter studies the critical point as well as the discontinuity of a class of explosive site percolation in Erd\"{o}s and R\'{e}nyi (ER) random network. The class of the percolation is implemented by introducing a best-of-m rule. Two major results are found: i). For any specific $m$, the critical percolation point scales with the average degree of the network while its exponent associated with $m$ is bounded by -1 and $\sim-0.5$. ii). Discontinuous percolation could occur on sparse networks if and only if $m$ approaches infinite. These results not only generalize some conclusions of ordinary percolation but also provide new insights to the network robustness.Comment: 5 pages, 5 figure