Biomedical subjects

Yves Lansac

Publications and source records attributed to Yves Lansac.

6 recordsLinked to original sources

PubMed2006

Discrete elastic model for two-dimensional melting.

We present a network model for the study of melting and liquid structure in two dimensions, the first in which the presence and energy of topological defects (dislocations and disclinations) and of geometrical defects (elemental voids) can be independently controlled. Interparticle interaction is via harmonic springs and control is achieved by Monte Carlo moves which springs can either be orientationally "flipped" between particles to generate topological defects, or can be "popped" in force-free shape, to generate geometrical defects. With the geometrical defects suppressed the transition to the liquid phase occurs via disclination unbinding, as described by the Kosterlitz-Thouless-Halperin-Nelson-Young model and found in soft potential two-dimensional (2D) systems, such as the dipole-dipole potential [H. H. von Grünberg, Phys. Rev. Lett. 93, 255703 (2004)]. By contrast, with topological defects suppressed, a disordering transition, the Glaser-Clark condensation of geometrical defects [M. A. Glaser and N. A. Clark, Adv. Chem. Phys. 83, 543 (1993); M. A. Glaser, (Springer-Verlag, Berlin, 1990), Vol. 52, p. 141], produces a state that accurately characterizes the local liquid structure and first-order melting observed in hard-potential 2D systems, such as hard disk and the Weeks-Chandler-Andersen (WCA) potentials (M. A. Glaser and co-workers, see above). Thus both the geometrical and topological defect systems play a role in melting. The present work introduces a system in which the relative roles of topological and geometrical defects and their interactions can be explored. We perform Monte Carlo simulations of this model in the isobaric-isothermal ensemble, and present the phase diagram as well as various thermodynamic, statistical, and structural quantities as a function of the relative populations of geometrical and topological defects. The model exhibits a rich phase behavior including hexagonal and square crystals, expanded crystal, dodecagonal quasicrystal, and isotropic liquid phases. In this system the geometrical defects effectively control the melting, reducing the solid-liquid transition temperature by a factor of relative to the topological-only case. The local structure of the dense liquid has been investigated and the results are compared to that from simulations of WCA systems.

Journal Article↗

PubMed2004

Phase behavior of polarizable spherocylinders in external fields.

Applied electric fields are known to induce significant changes in the properties of systems of polarizable molecules or particles. For rod-shaped molecules, the field-induced behavior can be rather surprising, as in the case of the negative electric birefringence of concentrated solutions of rodlike polyelectrolytes. We have investigated the interplay of shape anisotropy and field-induced anisotropy in molecular dynamics simulations of systems of polarizable soft spherocylinders in an electric field, in the limit of infinitely anisotropic polarizability, taking full account of mutual induction effects. We find a novel crystalline structure (K(2)) in the high-field limit, whose formation is driven by interactions between induced dipoles. For high pressures, the phase diagram exhibits a polar nematic phase between the hexagonal close-packed crystal phase and the K(2) phase. We also compare this system with an analogous system of spherocylinders with permanent electric dipoles and find that qualitatively similar behavior is obtained in the limit of strong coupling of the permanent dipoles to the external field.

Anisotropy↗

PubMed2004

Entropy-stabilized smectic C phase in a system of zigzag-shaped molecules.

We report Monte Carlo simulations of a system of rigid zigzag-shaped molecules that demonstrate that simple excluded-volume interactions are sufficient to produce a fluid tilted lamellar [smectic C (SmC)] liquid crystal phase. The molecules are composed of three rigidly linked hard spherocylinders arranged in a zigzag fashion. By varying the zigzag angle we have mapped out the whole phase diagram as a function of pressure and zigzag angle Psi. For Psi between 35 degrees and 80 degrees our model simulation exhibits the SmC phase. This is the first conclusive evidence where steric interactions arising out of molecular shape alone induce the occurrence of the SmC phase for a wide range of zigzag angles. For smaller Psi, a transition from tilted crystal to crystal is observed.

Journal Article↗

PubMed2003

Phase behavior of bent-core molecules.

Recently, a new class of smectic liquid crystal phases characterized by the spontaneous formation of macroscopic chiral domains from achiral bent-core molecules has been discovered. We have carried out Monte Carlo simulations of a minimal hard spherocylinder dimer model to investigate the role of excluded volume interactions in determining the phase behavior of bent-core materials and to probe the molecular origins of polar and chiral symmetry breaking. We present the phase diagram of hard spherocylinder dimers of length-diameter ratio of 5 as a function of pressure or density and dimer opening angle psi. With decreasing psi, a transition from a nonpolar to a polar smectic A phase is observed near psi=167 degrees, and the nematic phase becomes thermodynamically unstable for psi<135 degrees. Free energy calculations indicate that the antipolar smectic A (SmAP(A)) phase is more stable than the polar smectic A phase (SmAP(F)). No chiral smectic or biaxial nematic phases were found.

Journal Article↗

PubMed2002

Induced anticlinic ordering and nanophase segregation of bow-shaped molecules in a smectic solvent.

Recent experiments indicate that doping low concentrations of bent-core molecules into calamitic smectic solvents can induce anticlinic and biaxial smectic phases. We have carried out Monte Carlo simulations of mixtures of rodlike molecules (hard spherocylinders with length/breadth ratio L(rod)/D = 5) and bow-shaped molecules (hard spherocylinder dimers with length/breadth ratio L(ban)/D = 5 or 2.5 and opening angle psi). We find that a low concentration ( 3%) of L(ban)/D = 5 dimers induces anticlinic ( SmC(A)) ordering in an untilted smectic ( SmA) phase for 100 < or = psi < 150. For L(ban)/D = 2.5, no tilted phases are induced. However, with decreasing psi we observe a sharp transition from intralamellar nanophase segregation (bow-shaped molecules segregated within smectic layers) to interlamellar nanophase segregation (bow-shaped molecules concentrated between smectic layers) near psi = 130.

Journal Article↗

PubMed2002

Parallelizing a DNA simulation code for the Cray MTA-2.

The Cray MTA-2 (Multithreaded Architecture) is an unusual parallel supercomputer that promises ease of use and high performance. We describe our experience on the MTA-2 with a molecular dynamics code, SIMU-MD, that we are using to simulate the translocation of DNA through a nanopore in a silicon based ultrafast sequencer. Our sequencer is constructed using standard VLSI technology and consists of a nanopore surrounded by Field Effect Transistors (FETs). We propose to use the FETs to sense variations in charge as a DNA molecule translocates through the pore and thus differentiate between the four building block nucleotides of DNA. We were able to port SIMU-MD, a serial C code, to the MTA with only a modest effort and with good performance. Our porting process needed neither a parallelism support platform nor attention to the intimate details of parallel programming and interprocessor communication, as would have been the case with more conventional supercomputers.

Algorithms↗