Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings

This paper compares 22 different similarity coefficients when they are used for searching databases of 2D fragment bit-strings. Experiments with the National Cancer Institute's AIDS and IDAlert databases show that the coefficients fall into several well-marked clusters, in which the members of a cluster will produce comparable rankings of a set of molecules. These clusters provide a basis for selecting combinations of coefficients for use in data fusion experiments. The results of these experiments provide a simple way of increasing the effectiveness of fragment-based similarity searching systems

Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings

This paper compares 22 different similarity coefficients when they are used for searching databases of 2D fragment bit-strings. Experiments with the National Cancer Institute's AIDS and IDAlert databases show that the coefficients fall into several well-marked clusters, in which the members of a cluster will produce comparable rankings of a set of molecules. These clusters provide a basis for selecting combinations of coefficients for use in data fusion experiments. The results of these experiments provide a simple way of increasing the effectiveness of fragment-based similarity searching systems

Nonequilibrium Dynamics of Charged Particles in an Electromagnetic Field: Causal and Stable Dynamics from 1/c Expansion of QED

We derive from a microscopic Hamiltonian a set of stochastic equations of motion for a system of spinless charged particles in an electromagnetic (EM) field based on a consistent application of a dimensionful 1/c expansion of quantum electrodynamics (QED). All relativistic corrections up to order 1/c^3 are captured by the dynamics, which includes electrostatic interactions (Coulomb), magnetostatic backreaction (Biot-Savart), dissipative backreaction (Abraham-Lorentz) and quantum field fluctuations at zero and finite temperatures. With self-consistent backreaction of the EM field included we show that this approach yields causal and runaway-free equations of motion, provides new insights into charged particle backreaction, and naturally leads to equations consistent with the (classical) Darwin Hamiltonian and has quantum operator ordering consistent with the Breit Hamiltonian. To order 1/c^3 the approach leads to a nonstandard mass renormalization which is associated with magnetostatic self-interactions, and no cutoff is required to prevent runaways. Our new results also show that the pathologies of the standard Abraham-Lorentz equations can be seen as a consequence of applying an inconsistent (i.e. incomplete, mixed-order) expansion in 1/c, if, from the start, the analysis is viewed as generating a low-energy effective theory rather than an exact solution. Finally, we show that the 1/c expansion within a Hamiltonian framework yields well-behaved noise and dissipation, in addition to the multiple-particle interactions.Comment: 17 pages, 2 figure

Geometry, thermodynamics, and finite-size corrections in the critical Potts model

We establish an intriguing connection between geometry and thermodynamics in the critical q-state Potts model on two-dimensional lattices, using the q-state bond-correlated percolation model (QBCPM) representation. We find that the number of clusters of the QBCPM has an energy-like singularity for q different from 1, which is reached and supported by exact results, numerical simulation, and scaling arguments. We also establish that the finite-size correction to the number of bonds, has no constant term and explains the divergence of related quantities as q --> 4, the multicritical point. Similar analyses are applicable to a variety of other systems.Comment: 12 pages, 6 figure

Gluon GPDs and Exclusive Photoproduction of a Quarkonium in Forward Region

Forward photoproduction of $J/\psi$ can be used to extract Generalized Parton Distributions(GPD's) of gluons. We analyze the process at twist-3 level and study relevant classifications of twist-3 gluon GPD's. At leading power or twist-2 level the produced $J/\psi$ is transversely polarized. We find that at twist-3 the produced $J/\psi$ is longitudinally polarized. Our study shows that in high energy limit the twist-3 amplitude is only suppressed by the inverse power of the heavy quark mass relatively to the twist-2 amplitude. This indicates that the power correction to the cross-section of unpolarized $J/\psi$ can have a sizeable effect. We have also derived the amplitude of the production of $h_c$ at twist-3, but the result contains end-point singularities. The production of other quarkonia has been briefly discussed.Comment: Discussions of results are adde

Detection of X-ray periodicity from a new eclipsing polar candidate XGPS-I J183251-100106

We report the results from a detailed analysis of an archival XMM-Newton observation of the X-ray source XGPS-I J183251-100106, which has been suggested as a promising magnetic cataclysmic variable candidate based on its optical properties. A single periodic signal of 1.5 hrs is detected from all EPIC cameras on board XMM-Newton. The phase-averaged X-ray spectrum can be well-modeled with a thermal bremsstrahlung of a temperature kT~50 keV. Both X-ray spectral and temporal behavior of this system suggest it as a eclipsing cataclysmic variable of AM Herculis (or polar) type.Comment: 15 pages, 6 figures, accepted for publication in Ap

Renormalization group approach to an Abelian sandpile model on planar lattices

One important step in the renormalization group (RG) approach to a lattice sandpile model is the exact enumeration of all possible toppling processes of sandpile dynamics inside a cell for RG transformations. Here we propose a computer algorithm to carry out such exact enumeration for cells of planar lattices in RG approach to Bak-Tang-Wiesenfeld sandpile model [Phys. Rev. Lett. {\bf 59}, 381 (1987)] and consider both the reduced-high RG equations proposed by Pietronero, Vespignani, and Zapperi (PVZ) [Phys. Rev. Lett. {\bf 72}, 1690 (1994)] and the real-height RG equations proposed by Ivashkevich [Phys. Rev. Lett. {\bf 76}, 3368 (1996)]. Using this algorithm we are able to carry out RG transformations more quickly with large cell size, e.g. $3 \times 3$ cell for the square (sq) lattice in PVZ RG equations, which is the largest cell size at the present, and find some mistakes in a previous paper [Phys. Rev. E {\bf 51}, 1711 (1995)]. For sq and plane triangular (pt) lattices, we obtain the only attractive fixed point for each lattice and calculate the avalanche exponent $\tau$ and the dynamical exponent $z$. Our results suggest that the increase of the cell size in the PVZ RG transformation does not lead to more accurate results. The implication of such result is discussed.Comment: 29 pages, 6 figure