Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES). Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of pot...

We suggest and discuss a simple model of an ideal gas under the piston to gain an insight into the workings of the Jarzynski identity connecting the average exponential of the work over the nonequilibrium trajectories with the equilibrium free energy. We show that the identity is valid for our system, due to the very rapid molecules belonging to the tail of the Maxwell distribution. For the mos...

We present a statistical mechanics approach for the description of complex networks. We first define an energy and an entropy, associated with a degree distribution, which have a geometrical interpretation. Next we evaluate the distribution that extremizes the free energy of the network. We find two important limiting cases: a scale-free degree distribution and a finite-scale degree distributio...

Activities of many biological macromolecules involve large conformational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions...

We introduce a stability criterion for quantum statistical ensembles describing macroscopic systems. An ensemble is called "stable" when a small number of local measurements cannot significantly modify the probability distribution of the total energy of the system. We apply this criterion to lattices of spins-1/2, thereby showing that the canonical ensemble is nearly stable, whereas statistical...

The origin of protein folding thermodynamics is examined in terms of the energy landscape, employing an off-lattice protein model with scaled non-native attractions, which is continuously tunable between a Go-like model and a highly frustrated system. Extensive statistical temperature molecular dynamics simulations, combined with inherent structure analysis, reveal the intimate connection betwe...

In this article, the effect of the nonextensivity parameter on the energy fluctuations of nonextensive systems is studied in two different versions of the Tsallis statistical mechanics. Once a general expression has been reported for the energy fluctuations in the second version (Tsallis work in 1988), the energy fluctuations of an ideal gas and a harmonic oscillator are studied in the second a...