Prediction of RNA secondary structure is a fundamental problem in computational structural biology. For several decades, free energy minimization has been the most popular method for prediction from a single sequence. In recent years, the McCaskill algorithm for computation of partition function and base-pair probabilities has become increasingly appreciated. This paradigm-shifting work has ins...

The second law of thermodynamics in nonextensive statistical mechanics is discussed in the quantum regime. Making use of the convexity property of the generalized relative entropy associated with the Tsallis entropy indexed by q, Clausius' inequality is shown to hold in the range q in (0, 2]. This restriction on the range of the entropic index, q, is purely quantum mechanical and there exists n...

Strongly nonlinear degrade-and-fire (DF) oscillations may emerge in genetic circuits having a delayed negative feedback loop as their core element. Here we study the synchronization of DF oscillators coupled through a common repressor field. For weak coupling, initially distinct oscillators remain desynchronized. For stronger coupling, oscillators can be forced to wait in the repressed state un...

Microcanonical thermodynamics [D. H. E. Gross, Microcanonical Thermodynamics, Phase Transitions in "Small" Systems (World Scientific, Singapore, 2001)] allows the application of statistical mechanics both to finite and even small systems and also to the largest, self-gravitating ones. However, one must reconsider the fundamental principles of statistical mechanics especially its key quantity, e...