Hyperfluorescent intensity maxima during protein unfolding titrations are often taken as a sign for a thermodynamic folding intermediate. Here we explore another possibility: that hyperfluorescence could be the signature of a "pretransition" conformationally loosened native state. To model such native states, we study mutants of a fluorescent ubiquitin variant, placing cavities at various dista...

Our recent quasi-two-dimensional thermodynamic description of thin liquid films stabilized by colloidal particles is generalized to describe nonuniform equilibrium states of films in external potentials and nonequilibrium transport processes produced in the film by gradients of thermodynamic forces. Using a Monte Carlo simulation method, we have determined equilibrium equations of state for a f...

Abstract Using thermodynamic perturbation theory, we derive a simple formalism for treating intrinsic anharmonic effects in solids. In this formalism, the central quantity is the intrinsic anharmonicity parameter a, which can be derived from vibrational spectroscopy or computer simulation. Advantages of our approach include (1) correct lowand high-temperature behaviour, (2) analyticity of all t...

Compounds formed by exchanging one of the resveratrol hydroxy groups to methoxy or formyl groups are biologically important. Quantum chemical DFT calculations were applied for the simulation of some of their properties. Their optimized structures and charge distributions were computed. Based on the calculated vibrational force constants and optimized molecular structure infrared and Raman spect...

The ST2 interaction potential has been used in a large number of simulation studies to explore the possibility of a liquid-liquid phase transition (LLPT) in supercooled water. Using umbrella sampling Monte Carlo simulations of ST2 water, we evaluate the free energy of formation of small ice nuclei in the supercooled liquid in the vicinity of the Widom line, the region above the critical tempera...

In this paper we introduce efficient thermodynamically consistent techniques to extrapolate and interpolate normalized Canonical NVT ensemble averages for Lennard-Jones (L-J) fluids at different thermodynamic conditions from expensively simulated data points. This leads to a significant speed up in generating intensive data. Preliminary results show promising applicability in oil and gas modell...