By using a thermal Finite Energy QCD Sum Rule, we are able to establish the temperature dependence of the gωρπ(T) strong coupling. It turns out that this coupling decreases as a function of temperature, vanishing at the critical temperature. This corresponds to a possible deconfining phenomenological signal. This result, together with the Vector Meson Dominance (VMD) expression for the amplitud...

We analyze the recent NA48 data for the reaction K L → π 0 γγ with and without the assumption of vector meson dominance (VMD). We find that the data is well described by a three-parameter expression inspired by O(p 6) chiral perturbation theory. We also find that it is impossible to fit the shape of the decay distribution and the overall rate simultaneously if one imposes the VMD constraints on...

The possible impact of hydrophobic lectin nanoparticles on the prognosis and progression of Alzheimer's disease (AD) and cancers was investigated by Visual Molecular Dynamics (VMD) computer modeling programs available from the Beckmann Advanced Research Institute at the University of Illinois at Urbana. Our results indicate the possibility of impeding pathological aggregation of certain protein...

The possible impact of hydrophobic lectin nanoparticles on the prognosis and progression of Alzheimer's disease (AD) and cancers was investigated by Visual Molecular Dynamics (VMD) computer modeling programs available from the Beckmann Advanced Research Institute at the University of Illinois at Urbana. Our results indicate the possibility of impeding pathological aggregation of certain protein...

SUMMARY The volume of an internal protein pocket is fundamental to ligand accessibility. Few programs that compute such volumes manage dynamic data from molecular dynamics (MD) simulations. Limited performance often prohibits analysis of large datasets. We present Epock, an efficient command-line tool that calculates pocket volumes from MD trajectories. A plugin for the VMD program provides a g...

After describing the SU(2) linear sigma model (LσM), we dynamically generate it using the B.W. Lee null tadpole sum (characterizing the true vacuum) together with the dimensional regularization lemma. Next we generate the chiral-limiting (CL) nonstrange and strange constituent quark masses m̂ = 325.7 MeV; ms = 486 MeV away from the CL. Finally, we study vector meson dominance (VMD) and the pion,...

Reading and manipulating molecular structure data is a standard task in every molecular visualization and analysis program, but is rarely available in a form readily accessible to the user. Instead, the development of new methods for analysis, display, and interaction is often achieved by writing a new program, rather than building on pre-existing software. We present the Tcl-based script langu...

The time evolution of structure factors (SF) in the disordering process of an initially phase-separated lattice depends crucially on the microscopic disordering mechanism, such as Kawasaki dynamics (KD) or vacancy-mediated disordering (VMD). Monte Carlo simulations show unexpected "dips" in the SFs. A phenomenological model is introduced to explain the dips in the odd SFs, and an analytical sol...

Based on the previous studies of RNA nanorings, in this contribution we computationally analyze the structure and properties of RNA nanotubes, where we focus on nanotubes consisting of up to five nanorings of around 20nm in diameter. We have developed a molecular dynamics (MD) method and implemented it by using the NAMD and VMD packages in a high-performance computing environment to study the s...

I review results on the shift of the ρ meson mass at nonzero temperature in a gauged linear sigma model, under the assumption of strict vector meson