Homogeneous shear flow of a hard-sphere fluid: Analytic solutions

Recently, a solution for collision-free trajectories in an N particle thermostatted hard-sphere system undergoing homogeneous shear (the so-called "Sllod" equations of motion) led to a kinetic theory of dilute hard-sphere gases under shear. However, a solution for collisions, necessary for a complete theory at higher densities, has been missing. We present an analytic solution to this problem, which provides surprising insights into the mechanical aspects of thermostatting a system in an external field. The equivalence of constant temperature and constant energy ensembles in the thermodynamic limit in equilibrium, the conditions for the nature of heat exchange with the environment (entropy creation and reduction) in the system, and the condition for appearance of the artificial string phase follow from our solution

The QCD Phase Structure at High Baryon Density

We consider the possibility that color deconfinement and chiral symmetry restoration do not coincide in dense baryonic matter at low temperature. As a consequence, a state of massive "constituent" quarks would exist as an intermediate phase between confined nuclear matter and the plasma of deconfined massless quarks and gluons. We discuss the properties of this state and its relation to the recently proposed quarkyonic matter.Comment: 17 pages, 9 figure

Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure

The phase diagram of hadronic matter

Castorina P, Redlich K, Satz H. The phase diagram of hadronic matter. EUROPEAN PHYSICAL JOURNAL C. 2009;59(1):67-73.We interpret the phase structure of hadronic matter in terms of the basic dynamical and geometrical features of hadrons. Increasing the density of constituents of finite spatial extension, by increasing the temperature T or the baryochemical potential mu, eventually "fills the box" and eliminates the physical vacuum. We determine the corresponding transition as a function of T and mu through percolation theory. At low baryon density, this means a fusion of overlapping mesonic bags to one large bag, while at high baryon density, hard-core repulsion restricts the spatial mobility of baryons. As a consequence, there are two distinct limiting regimes for hadronic matter. We compare our results to those from effective chiral model studies