Biomedical subjects

Claude Millot

Publications and source records attributed to Claude Millot.

5 recordsLinked to original sources

PubMed2005

Long-range electrostatic interactions in hybrid quantum and molecular mechanical dynamics using a lattice summation approach.

A method based on a lattice summation technique for treating long-range electrostatic interactions in hybrid quantum mechanics/molecular mechanics simulations is presented in this article. The quantum subsystem is studied at the semiempirical level, whereas the solvent is described by a two-body potential of molecular mechanics. Molecular dynamics simulations of a (quantum) chloride ion in (classical) water have been performed to test this technique. It is observed that the application of the lattice summations to solvent-solvent interactions as well as on solute-solvent ones has a significant effect on solvation energy and diffusion coefficient. Moreover, two schemes for the computation of the long-range contribution to the electrostatic interaction energy are investigated. The first one replaces the exact charge distribution of the quantum solute by a Mulliken charge distribution. The long-range electrostatic interactions are then calculated for this charge distribution that interacts with the solvent molecule charges. The second one is more accurate and involves a modified Fock operator containing long-range electron-charge interactions. It is shown here that both schemes lead to similar results, the method using Mulliken charges for the evaluation of long-range interactions being, however, much more computationally efficient.

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PubMed2005

Molecular simulation of the homogeneous crystal nucleation of carbon dioxide.

We report on a molecular simulation study of the homogeneous nucleation of CO2 in the supercooled liquid at low pressure (P = 5 MPa) and for degrees of supercooling ranging from 32% to 60%. In all cases, regardless of the degree of supercooling, the structure of the crystal nuclei is that of the Pa3 phase, the thermodynamically stable phase. For the more moderate degree of supercooling of 32%, the nucleation is an activated process and requires a method to sample states of high free energy. In this work, we apply a series of bias potentials, which promote the ordering of the centers of mass of the molecules and allow us to gradually grow crystal nuclei. The reliability of the results so obtained is assessed by studying the evolution of the nuclei in the absence of any bias potential, and by determining their probability of growth. We estimate that the size of the critical nucleus, for which the probability of growth is 0.5, is approximately 240 molecules. Throughout the nucleation process, the crystal nuclei clearly exhibit a Pa3 structure, in apparent contradiction with Ostwald's rule of stages. The other polymorphs have a much larger free energy. This makes their formation highly unlikely and accounts for the fact that the nucleation of CO2 proceeds directly in the stable Pa3 structure.

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PubMed2005

Atomistic simulation of the homogeneous nucleation and of the growth of N2 crystallites.

We report on a computer simulation study of the early stages of the crystallization of molecular nitrogen. First, we study how homogeneous nucleation takes place in supercooled liquid N(2) for a moderate degree of supercooling. Using the umbrella sampling technique, we determine the free energy barrier of formation for a critical nucleus of N(2). We show that, in accord with Ostwald's rule of stages, the structure of the critical nucleus is predominantly that of a metastable polymorph (alpha-N(2) for the state point investigated). We then monitor the evolution of several critical nuclei through a series of unbiased molecular dynamics trajectories. The growth of N(2) crystallites is accompanied by a structural evolution toward the stable polymorph beta-N(2). The microscopic mechanism underlying this evolution qualitatively differs from that reported previously. We do not observe any dissolution or reorganization of the alpha-like core of the nucleus. On the contrary, we show that alpha-like and beta-like blocks coexist in postcritical nuclei. We relate the structural evolution to a greater adsorption rate of beta-like molecules on the surface and show that this transition actually starts well within the precritical regime. We also carefully investigate the effect of the system size on the height of the free energy barrier of nucleation and on the structure and size of the critical nucleus.

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PubMed2004

Reorganization and growth of metastable alpha-N2 critical nuclei into stable beta-N2 crystals.

We report on results on the crystal nucleation and growth of nitrogen. Using molecular dynamics simulations, we show that while nucleation proceeds into the metastable alpha-phase (i.e., the crystalline phase associated with the lowest free energy barrier of formation), growth of the crystallite proceeds through a reorganization of the nucleus into the thermodynamically stable beta-phase.

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PubMed2003

OPEP: a tool for the optimal partitioning of electric properties.

OPEP is a suite of FORTRAN programs targeted at the optimal partitioning of molecular electric properties. It includes an interactive module for the construction of Cartesian grids of points, on which either the molecular electrostatic potential or the induction energy is mapped. The generation of distributed multipoles and polarizabilities is achieved using either the formalism of the normal equations of the least-squares problem, which restates the fitting procedure in terms of simple matrix operations, or a statistical approach, which provides a pictorial description of the distributed models of multipoles and polarizabilities, thereby allowing the pinpointing of pathological cases. Molecular symmetry is accounted for by means of local atomic frames, which are generated in an automated fashion. A Tcl/Tk graphical user interface wraps the suite of programs, thereby making OPEP a user-friendly package for building models of distributed multipoles and polarizabilities. OPEP is an open-source suite of programs distributed free of charge under the GNU general public license (GPL) at http://www.lctn.uhp-nancy.fr/Opep.

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