A method to find low energy paths in macromolecules is described. It can be applied either to determine paths between two given energy minimum conformations, or to explore low energy paths departing from one energy minimized conformation. The principle of the method consists in carrying out energy minimizations or molecular dynamics simulations with root mean square distance constraints with re...

We examine the recently-proposed scheme W. Kohn, Phys. Rev. Lett. 76, 3168 (1996)] for performing linear-scaling calculations within density-functional theory by direct minimization with respect to the single-particle density-matrix using a penalty-functional to exactly enforce the idempotency constraint. We show that such methods are incompatible with standard minimization algorithms (using co...

We derive sufficient conditions for the uniqueness of loopy belief propagation fixed points. These conditions depend on both the structure of the graph and the strength of the potentials and naturally extend those for convexity of the Bethe free energy. We compare them with (a strengthened version of) conditions derived elsewhere for pairwise potentials. We discuss possible implications for con...

Mixtures of Lennard-Jones and Stockmayer molecules provide a convenient model system which can be used to study the effects of composition and polarity in polar/non-polar mixtures. The structure and phase behaviour of such mixtures are currently topics of great interest Eli. Since the Stockmayer potential, qSs, is obtained from the usual Lennard-Jones potential, ~buj, by the sole addition of a ...

A thermodynamical minimum principle valid for photon radiation is shown to hold for arbitrary geometries. It is successfully extended to neutrinos, in the zero mass and chemical potential case, following a parallel development of photon and neutrino statistics. This minimum principle stems more from that of Planck than that of classical Onsager-Prigogine irreversible thermodynamics. Its extensi...

The adhesion of Acidithiobacillus ferrooxidans bacterial cells have been assessed by following the thermodynamic and extended DLVO theoretical approaches. Surface potential, interfacial tension and contact angle parameters that are necessary for the calculation of free energy of adhesion have been determined experimentally. The Hamaker constant involved in the Lifshitz-van der Waals interaction...

Molecular dynamics simulations are used to calculate the free energy of methane association in water, using the polarizable fluctuating charge model that treats the charges on atomic sites as dynamical variables. Compared with previous studies using nonpolarizable potentials, the inclusion of polarizability leads only to small differences in the methane pair potential of mean force. This is in ...

This work presents a procedure to optimize the molecular geometry at the Hartree-Fock level, based on a global optimization method—the Generalized Simulated Annealing. The main characteristic of this methodology is that, at least in principle, it enables the mapping of the energy hypersurface as to guarantee the achievement of the absolute minimum. This method does not use expansions of the ene...