Finding antipodal point grasps on irregularly shaped objects

Two-finger antipodal point grasping of arbitrarily shaped smooth 2-D and 3-D objects is considered. An object function is introduced that maps a finger contact space to the object surface. Conditions are developed to identify the feasible grasping region, F, in the finger contact space. A “grasping energy function”, E , is introduced which is proportional to the distance between two grasping points. The antipodal points correspond to critical points of E in F. Optimization and/or continuation techniques are used to find these critical points. In particular, global optimization techniques are applied to find the “maximal” or “minimal” grasp. Further, modeling techniques are introduced for representing 2-D and 3-D objects using B-spline curves and spherical product surfaces

Energetics of Protein-DNA Interactions

Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that theoretical models describe the macromolecular interaction energetics accurately. While several methods have been proposed, there has not been a careful comparison of how well the different methods are able to predict biologically important quantities such as the correct DNA binding sequence, total binding free energy, and free energy changes caused by DNA mutation. In addition to carrying out the comparison, we present two important theoretical models developed initially in protein folding that have not yet been tried on protein-DNA interactions. In the process, we find that the results of these knowledge-based potentials show a strong dependence on the interaction distance and the derivation method. Finally, we present a knowledge-based potential that gives comparable or superior results to the best of the other methods, including the molecular mechanics force field AMBER99

Inconsistency of Naive Dimensional Regularizations and Quantum Correction to Non-Abelian Chern-Simons-Matter Theory Revisited

We find the inconsistency of dimensional reduction and naive dimensional regularization in their applications to Chern-Simons type gauge theories. Further we adopt a consistent dimensional regularization to investigate the quantum correction to non-Abelian Chern-Simons term coupled with fermionic matter. Contrary to previous results, we find that not only the Chern-Simons coefficient receives quantum correction from spinor fields, but the spinor field also gets a finite quantum correction.Comment: 19 pages, RevTex, Feynman diagrams drawn by FEYNMAN routin

Accurate Reaction-Diffusion Operator Splitting on Tetrahedral Meshes for Parallel Stochastic Molecular Simulations

Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in sub-cellular models. This calls for parallel simulations that can take advantage of the power of modern supercomputers; however exact methods are known to be inherently serial. We introduce an operator splitting implementation for irregular grids with a novel method to improve accuracy, and demonstrate potential for scalable parallel simulations in an initial MPI version. We foresee that this groundwork will enable larger scale, whole-cell stochastic simulations in the near future.Comment: 33 pages, 10 figure

Determining the strange and antistrange quark distributions of the nucleon

The difference between the strange and antistrange quark distributions, \delta s(x)=s(x)-\sbar(x), and the combination of light quark sea and strange quark sea, \Delta (x)=\dbar(x)+\ubar(x)-s(x)-\sbar(x), are originated from non-perturbative processes, and can be calculated using non-perturbative models of the nucleon. We report calculations of $\delta s(x)$ and $\Delta(x)$ using the meson cloud model. Combining our calculations of $\Delta(x)$ with relatively well known light antiquark distributions obtained from global analysis of available experimental data, we estimate the total strange sea distributions of the nucleon.Comment: 4 pages, 3 figures; talk given by F.-G. at QNP0

Nuclear matter symmetry energy and the neutron skin thickness of heavy nuclei

Correlations between the thickness of the neutron skin in finite nuclei and the nuclear matter symmetry energy are studied in the Skyrme Hartree-Fock model. From the most recent analysis of the isospin diffusion data in heavy-ion collisions based on an isospin- and momentum-dependent transport model with in-medium nucleon-nucleon cross sections, a value of $L=88\pm 25$ MeV for the slope of the nuclear symmetry energy at saturation density is extracted, and this imposes stringent constraints on both the parameters in the Skyrme effective interactions and the neutron skin thickness of heavy nuclei. Predicted thickness of the neutron skin is $0.22\pm 0.04$ fm for $$Pb, $0.29\pm 0.04$ fm for $^{132}$Sn, and $0.22\pm 0.04$ fm for $$Sn.Comment: 6 pages, 4 figures, 1 table, revised version, to appear in PR

Further analysis of field effects on liquids and solidification

Numerical calculations of the magnitude of external field effects on liquids are presented to describe how external fields can influence the substructure of the field. Quantitative estimates of magnetic and gravitational effects are reported on melts of metals and semiconductors. The results are condensed in tables which contain the input data for calculation of the field effects on diffusion coefficient, solidification rate and for calculation of field forces on individual molecules in the melt