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.

Mechanochemical synthesis of ceramic powders with perovskite structure

The mechanical activation is one of the most effective method for obtaining highly disperse system due to mechanical action stress fields form in solids during milling procedure. This effect results in changes of free energy, leading to release of heat, formation of a new surface, formation of different crystal lattice defects and initiation of solid-state chemical reaction. The accumulated deformation energy determines irreversible changes of crystal structure and consequently microstructure resulting in the change of their properties. Mechanochemical processing route has been developed recently for the production of intermetallic and alloy compounds. The intrinsic advantage of this process is that the solid-state reaction is activated due to mechanical energy instead of the temperature. It was shown that the chemical reactivity of starting materials could be improved significantly after mechanochemical activation and, subsequently, the calcination temperature was reduced. Besides, it was apparent that the mechanochemical treatment could enhance the reactivity of constituent oxides; however, the sintering process could not be avoided to develop the desired ceramics. A novel mechanochemical technique for synthesis of fine-grained perovskite structured powders has shown that it is possible to form perovskite at room temperature. The effect of milling on the formation of perovskite structure of barium titanate (BT), lead titanate (PT), PZT, PZN, magnesium niobate (PMN) and LM ceramic materials was analyzed. The dielectric properties of sintered ceramics are comparable with those prepared by other methods in the literature. (C) 2003 Elsevier B.V. B.V. All rights reserved.

NOLEN-SCHIFFER ANOMALY AND RHO(0)-OMEGA MIXING

The Nolen-Schiffer anomaly is the long standing discrepancy between theory and experiment of binding energy differences of mirror nuclei. It appears that the anomaly is largely explained by the charge symmetry breaking force generated by the rho(0)-omega mixing. In this paper I discuss the effect of the rho(0)-omega mixing to the binding energy differences in relativistic models of the nucleus. I also discuss the issue of momentum dependence of rho(0)-omega mixing amplitude and present an alternative explanation of the anomaly based on the partial restoration of chiral symmetry in the nucleus.

Temperature-dependent vortex motion in a square mesoscopic superconducting cylinder: Ginzburg-Landau calculations

In this work we investigate the dynamics of vortices in a square mesoscopic superconductor. As time evolves we show how the vortices are nucleated into the sample to form a multivortex, single vortex, and giant vortex states. We illustrate how the vortices move around at the transition fields before they accommodate into an equilibrium configuration. We also calculate the magnetization and the free energy as functions of the applied magnetic field for several values of temperature. In addition, we evaluate the upper critical field.

Electric characterization of a hybrid composite based on POMA/P(VDF- TrFE)/Zn2SiO4 : Mn using impedance spectroscopy

Understanding the microscopic origin of the dielectric properties of disordered materials has been a challenge for many years, especially in the case of samples with more than one phase. For polar dielectrics, for instance, the Lepienski approach has indicated that the random free energy barrier model of Dyre must be extended. Here we analyse the dielectric properties of a polymer blend made up with the semiconducting poly(o-methoxyaniline) and poly( vinylidene fluoride-trifluorethylene) POMA/P(VDF-TrFE), and of a hybrid composite of POMA/P(VDF-TrFE)/Zn2SiO4:Mn. For the blend, the Lepienski model, which takes into account the rotation or stretching of electric dipoles, provided excellent fitting to the ac impedance data. Because two phases had to be assumed for the hybrid composite, we had to extend the Lepienski model to fit the data, by incorporating a second transport mechanism. The two mechanisms were associated with the electronic transport in the polymeric matrix and with transport at the interfaces between Zn2SiO4: Mn microparticles and the polymeric matrix, with the relative importance of the interfacial component increasing with the percentage of Zn2SiO4: Mn in the composite. The analysis of impedance data at various temperatures led to a prediction of the theoretical model of a change in morphology at 190 +/- 40 K, and this was confirmed experimentally with a differential scanning calorimetry experiment.