WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets.

BackgroundSharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software.ResultsWe here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages.ConclusionsWith these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called "Smiley2png 1.0") can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu

Viscous fingering in liquid crystals: Anisotropy and morphological transitions

We show that a minimal model for viscous fingering with a nematic liquid crystal in which anisotropy is considered to enter through two different viscosities in two perpendicular directions can be mapped to a two-fold anisotropy in the surface tension. We numerically integrate the dynamics of the resulting problem with the phase-field approach to find and characterize a transition between tip-splitting and side-branching as a function of both anisotropy and dimensionless surface tension. This anisotropy dependence could explain the experimentally observed (reentrant) transition as temperature and applied pressure are varied. Our observations are also consistent with previous experimental evidence in viscous fingering within an etched cell and simulations of solidification.Comment: 12 pages, 3 figures. Submitted to PR

Orbital Kondo effect in Cobalt-Benzene sandwich molecules

We study a Co-benzene sandwich molecule bridging the tips of a Cu nanocontact as a realistic model of correlated molecular transport. To this end we employ a recently developed method for calculating the correlated electronic structure and transport properties of nanoscopic conductors. When the molecule is slightly compressed by the tips of the nanocontact the dynamic correlations originating from the strongly interacting Co 3d shell give rise to an orbital Kondo effect while the usual spin Kondo effect is suppressed due to Hund's rule coupling. This non-trivial Kondo effect produces a sharp and temperature-dependent Abrikosov-Suhl resonance in the spectral function at the Fermi level and a corresponding Fano line shape in the low bias conductance

Aggregation Patterns in Stressed Bacteria

We study the formation of spot patterns seen in a variety of bacterial species when the bacteria are subjected to oxidative stress due to hazardous byproducts of respiration. Our approach consists of coupling the cell density field to a chemoattractant concentration as well as to nutrient and waste fields. The latter serves as a triggering field for emission of chemoattractant. Important elements in the proposed model include the propagation of a front of motile bacteria radially outward form an initial site, a Turing instability of the uniformly dense state and a reduction of motility for cells sufficiently far behind the front. The wide variety of patterns seen in the experiments is explained as being due the variation of the details of the initiation of the chemoattractant emission as well as the transition to a non-motile phase.Comment: 4 pages, REVTeX with 4 postscript figures (uuencoded) Figures 1a and 1b are available from the authors; paper submitted to PRL

Localized basis sets for unbound electrons in nanoelectronics

It is shown how unbound electron wave functions can be expanded in a suitably chosen localized basis sets for any desired range of energies. In particular, we focus on the use of gaussian basis sets, commonly used in first-principles codes. The possible usefulness of these basis sets in a first-principles description of field emission or scanning tunneling microscopy at large bias is illustrated by studying a simpler related phenomenon: The lifetime of an electron in a H atom subjected to a strong electric field.Comment: 6 pages, 5 figures, accepted by J. Chem. Phys. (http://jcp.aip.org/

SM(2,4k) fermionic characters and restricted jagged partitions

A derivation of the basis of states for the $SM(2,4k)$ superconformal minimal models is presented. It relies on a general hypothesis concerning the role of the null field of dimension $2k-1/2$. The basis is expressed solely in terms of $G_r$ modes and it takes the form of simple exclusion conditions (being thus a quasi-particle-type basis). Its elements are in correspondence with $(2k-1)$-restricted jagged partitions. The generating functions of the latter provide novel fermionic forms for the characters of the irreducible representations in both Ramond and Neveu-Schwarz sectors.Comment: 12 page

New path description for the M(k+1,2k+3) models and the dual Z_k graded parafermions

We present a new path description for the states of the non-unitary M(k+1,2k+3) models. This description differs from the one induced by the Forrester-Baxter solution, in terms of configuration sums, of their restricted-solid-on-solid model. The proposed path representation is actually very similar to the one underlying the unitary minimal models M(k+1,k+2), with an analogous Fermi-gas interpretation. This interpretation leads to fermionic expressions for the finitized M(k+1,2k+3) characters, whose infinite-length limit represent new fermionic characters for the irreducible modules. The M(k+1,2k+3) models are also shown to be related to the Z_k graded parafermions via a (q to 1/q) duality transformation.Comment: 43 pages (minor typo corrected and minor rewording in the introduction

Novel type of phase transition in a system of self-driven particles

A simple model with a novel type of dynamics is introduced in order to investigate the emergence of self-ordered motion in systems of particles with biologically motivated interaction. In our model particles are driven with a constant absolute velocity and at each time step assume the average direction of motion of the particles in their neighborhood with some random perturbation ($\eta$) added. We present numerical evidence that this model results in a kinetic phase transition from no transport (zero average velocity, $| {\bf v}_a | =0$) to finite net transport through spontaneous symmetry breaking of the rotational symmetry. The transition is continuous since $| {\bf v}_a |$ is found to scale as $(\eta_c-\eta)^\beta$ with $\beta\simeq 0.45$