Dynamics of the deconfinement transition of quarks and gluons in a finite volume

We employ finite elements methods for the approximation of solutions of the Ginzburg-Landau equations describing the deconfinement transition in quantum chromodynamics. These methods seem appropriate for situations where the deconfining transition occurs over a finite volume as in relativistic heavy ion collisions. where in addition expansion of the system and flow of matter are important. Simulation results employing finite elements are presented for a Ginzburg-Landau equation based on a model free energy describing the deconfining transition in pure gauge SU(2) theory. Results for finite and infinite system are compared. (C) 2009 Elsevier B.V. All rights reserved.

A stability transition at mildly acidic pH in the alpha-hemolysin (alpha-toxin) from Staphylococcus aureus

The effects of mildly acidic conditions on the free energy of unfolding (Delta G(u)(buff)) of the pore-forming alpha-hemolysin (alpha HL) from Staphylococcus aureus were assessed between pH 5.0 and 7.5 by measuring intrinsic tryptophan fluorescence, circular dichroism and elution time in size exclusion chromatography during urea denaturation, Decreasing the pH from 7.0 to 5.0 reduced the calculated Delta G(u)(buff) from 8.9 to 4.2 kcal moI(-1), which correlates with an increased rate of pore formation previously observed over the same pH range, It is proposed that the lowered surface pH of biological membranes reduces the stability of alpha HL thereby modulating the rate of pore formation. (C) 1999 Federation of European Biochemical Societies.

Theoretical study of omeprazole behavior: Racemization barrier and decomposition reaction

omeprazole is a substituted benzimidazole which suppresses gastric-acid secretion by means of H+, K+-ATPase inhibition. It is an optically active drug with the sulfur of the sulfoxide being the chiral center. This pro-drug can be easily converted into its respective sulfenamide at low pH. In this work, omeprazole has been studied in relation to racemization barrier and decomposition reaction. Quantum chemistry coupled to PCA chemometric method were used to find all minimum energy structures. Conformational analysis and calculation of racemization barriers were carried out by PM3 semiempirical method (Gaussian 98). The average racemization energy barrier for all minimum energy structures (43.56 kcal mol(-1)) can be related to the velocity constant in Eyring's equation. The enormous half-life time at 100 degrees C (9.04 x 10(4) years) indicates that the process cannot be observed in human time scale. on the other hand, the difference of free energy change (Delta(Delta G) = -266.78 kcal mol(-1)) for the decomposition reaction shows that the process is favorable to the sulfenamide formation. The highly negative Delta(Delta G) obtained for the decomposition reaction shows that this process is extremely exothermic. This result explains why omeprazole decomposes and does not racemize. (C) 2008 Wiley Periodicals, Inc.

Coordinate and time-dependent diffusion dynamics in protein folding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Configuration-Dependent Diffusion Dynamics of Downhill and Two-State Protein Folding

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A mass-transportation approach to a one dimensional fluid mechanics model with nonlocal velocity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion. Including the configurational dependence will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory also will have to be modified quantitatively.

On the entropy operator for the general SU(1,1) TFD formulation

In this Letter, an entropy operator for the general unitary SU(1, 1) TFD formulation is proposed and used to lead a bosonic system from zero to finite temperature. Namely, considering the closed bosonic string as the target system, the entropy operator is used to construct the thermal vacuum. The behaviour of such a state under the breve conjugation rules is analyzed and it was shown that the breve conjugation does not affect the thermal effects. From this thermal vacuum the thermal energy, the entropy and the free energy of the closed bosonic string are calculated and the appropriated thermal distribution for the system is found after the free energy minimization. (C) 2004 Elsevier B.V. All rights reserved.

A path integral approach to the full Dicke model with dipole-dipole interaction

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Applicability of the linear delta expansion for the lambda phi(4) field theory at finite temperature in the symmetric and broken phases

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Thermal phase transitions for Dicke-type models in the ultrastrong-coupling limit

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Thermodynamic properties of water sorption of jackfruit (Artocarpus heterophyllus Lam.) as a function of moisture content

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Study of the enthalpy-entropy mechanism from water sorption of orange seeds (C. sinensis cv. Brazilian) for the use of agro-industrial residues as a possible source of vegetable oil production

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Depairing critical current density of a mesoscopic square superconductor

In the present paper we consider the vortex lattice properties of a square superconductor such as the vortex patterns, the Gibbs free energy, the magnetization, and the depairing critical current density. We show that this last quantity shows a matching effect, that is, it shows a discontinuous behavior as a function of the applied magnetic field.

Influence of strains and defects on ferroelectric and dielectric properties of thin-film barium-strontium titanates

Pristine, W and Mn 1% doped Ba(0.6)Sr(0.4)TiO(3) epitaxial thin films grown on the LaAlO(3) substrate were deposited by pulsed laser deposition (PLD). Dielectric and ferroelectric properties were determined by the capacitance measurements and X-ray diffraction was used to determine both residual elastic strains and defect-related inhomogeneous strains-by analyzing diffraction line shifts and line broadening, respectively. We found that both elastic and inhomogeneous strains are affected by doping. This strain correlates with the change in Curie-Weiss temperature and can qualitatively explain changes in dielectric loss. To explain the experimental findings, we model the dielectric and ferroelectric properties of interest in the framework of the Landau-Ginzburg-Devonshire thermodynamic theory. As expected, an, elastic-strain contribution due to the epilayer-substrate misfit has an important influence on the free-energy. However, additional terms that correspond to the defect-related inhomogeneous strain had to be introduced to fully explain the measurements.