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

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

The Influence of Solutes on the Enthalpy/Entropy Change of the Actinomycin D Binding to DNA: Hydration, Energy Compensation and Long-Range Deformation on DNA

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

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.

Electromagnetic field at finite temperature: A first order approach

In this work we study the electromagnetic field at finite temperature via the massless DKP formalism. The constraint analysis is performed and the partition function for the theory is constructed and computed. When it is specialized to the spin 1 sector we obtain the well-known result for the thermodynamic equilibrium of the electromagnetic field. (c) 2006 Elsevier B.V. All rights reserved.

Limits of validity for a semiclassical mean-field two-fluid model for Bose-Einstein condensation thermodynamics

We reinvestigate the Bose-Einstein condensation (BEC) thermodynamics of a weakly interacting dilute Bose gas under the action of a trap using a semi-classical two-fluid mean-field model in order to find the domain of applicability of the model. Such a model is expected to break down once the condition of diluteness and weak interaction is violated. We find that this breakdown happens for values of coupling and density near the present experimental scenario of BEG. With the increase of the interaction coupling and density the model may lead to unphysical results for thermodynamic observables. (C) 2000 Published by Elsevier B.V. B.V, All rights reserved.

Quantum state density and critical temperature in M-theory

We discuss the asymptotic properties of quantum states density for fundamental p-branes which can yield a microscopic interpretation of the thermodynamic quantities in M-theory. The matching of the BPS part of spectrum for superstring and supermembrane gives the possibility of getting membrane's results via string calculations. In the weak coupling limit of M-theory, the critical behavior coincides with the first-order phase transition in the standard string theory at temperature less than the Hagedorn's temperature T-H. The critical temperature at large coupling constant is computed by considering M-theory on manifold with topology R-9 circle times T-2. Alternatively we argue that any finite temperature can be introduced in the framework of membrane thermodynamics.

A singular conformal spacetime

The infinite cosmological constant limit of the de Sitter solutions to Einstein's equation is studied. The corresponding spacetime is a singular, four-dimensional cone-space, transitive under proper conformal transformations, which constitutes a new example of maximally-symmetric spacetime. Grounded on its geometric and thermodynamic properties, some speculations are made in connection with the primordial universe. (c) 2005 Elsevier B.V. All rights reserved.

PP-wave light-cone free string field theory at finite temperature

In this paper, a real-time formulation of light-cone pp-wave string field theory at finite temperature is presented. This is achieved by developing the thermo field dynamics (TFD) formalism in a second quantized string scenario. The equilibrium thermodynamic quantities for a pp-wave ideal string gas are derived directly from expectation values on the second quantized string thermal vacuum. Also, we derive the real-time thermal pp-wave closed string propagator. In the flat space limit it is shown that this propagator can be written in terms of Theta functions, exactly as the zero temperature one. At the end, we show how superstrings interactions can be introduced, making this approach suitable to study the BMN dictionary at finite temperature.

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

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Podolsky electromagnetism at finite temperature: Implications on the Stefan-Boltzmann law

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Bekenstein bound in asymptotically free field theory

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)

Matsubara-Fradkin thermodynamical quantization of Podolsky electrodynamics

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effective Fokker-Planck equation for birhythmic modified van der Pol oscillator

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)