Coordinate and time-dependent diffusion dynamics in protein folding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

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.

Position-dependent noncommutativity in quantum mechanics

The model of the position-dependent noncommutativity in quantum mechanics is proposed. We start with given commutation relations between the operators of coordinates [(x) over cap (i), (x) over cap (j)] = omega(ij) ((x) over cap), and construct the complete algebra of commutation relations, including the operators of momenta. The constructed algebra is a deformation of a standard Heisenberg algebra and obeys the Jacobi identity. The key point of our construction is a proposed first-order Lagrangian, which after quantization reproduces the desired commutation relations. Also we study the possibility to localize the noncommutativity.

Mean Motion in Stochastic Plasmas With a Space-Dependent Diffusion Coefficient

Radial transport in the tokamap, which has been proposed as a simple model for the motion in a stochastic plasma, is investigated. A theory for previous numerical findings is presented. The new results are stimulated by the fact that the radial diffusion coefficients is space-dependent. The space-dependence of the transport coefficient has several interesting effects which have not been elucidated so far. Among the new findings are the analytical predictions for the scaling of the mean radial displacement with time and the relation between the Fokker-Planck diffusion coefficient and the diffusion coefficient from the mean square displacement. The applicability to other systems is also discussed. (c) 2009 WILEY-VCH GmbH & Co. KGaA, Weinheim

Position-dependent effective mass Dirac equations with PT-symmetric and non-PT-symmetric potentials

We present a new procedure to construct the one-dimensional non-Hermitian imaginary potential with a real energy spectrum in the context of the position-dependent effective mass Dirac equation with the vector-coupling scheme in 1 + 1 dimensions. In the first example, we consider a case for which the mass distribution combines linear and inversely linear forms, the Dirac problem with a PT-symmetric potential is mapped into the exactly solvable Schrodinger-like equation problem with the isotonic oscillator by using the local scaling of the wavefunction. In the second example, we take a mass distribution with smooth step shape, the Dirac problem with a non-PT-symmetric imaginary potential is mapped into the exactly solvable Schrodinger-like equation problem with the Rosen-Morse potential. The real relativistic energy levels and corresponding wavefunctions for the bound states are obtained in terms of the supersymmetric quantum mechanics approach and the function analysis method.

On the Dirac equation with PT-symmetric potentials in the presence of position-dependent mass

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Extension of PT-symmetric quantum mechanics to the Dirac theory with position-dependent mass

We present a new method to construct the exactly solvable PT-symmetric potentials within the framework of the position-dependent effective mass Dirac equation with the vector potential coupling scheme in 1 + 1 dimensions. In order to illustrate the procedure, we produce three PT-symmetric potentials as examples, which are PT-symmetric harmonic oscillator-like potential, PT-symmetric potential with the form of a linear potential plus an inversely linear potential, and PT-symmetric kink-like potential, respectively. The real relativistic energy levels and corresponding spinor components for the bound states are obtained by using the basic concepts of the supersymmetric quantum mechanics formalism and function analysis method. (C) 2007 Elsevier B.V. All rights reserved.

Two-dimensional position-dependent massive particles in the presence of magnetic fields

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Wigner distribution for a class of isospectral position-dependent mass systems

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)

On the solutions of the position-dependent effective mass Schrodinger equation of a nonlinear oscillator related with the isotonic oscillator

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Remarks on supersymmetry of quantum systems with position-dependent effective masses

We apply the supersymmetry approach to one-dimensional quantum systems with spatially dependent mass, by including their ordering ambiguities dependence. In this way we extend the results recently reported in the literature. Furthermore, we point out a connection between these systems and others with constant masses. This is done through convenient transformations in the coordinates and wave functions.

Pressure field in a tube with a general and arbitrary time- and position-dependent gas source

In this article we present analytical and numerical results for a pressure profile along the axis of a tube with a general and arbitrary time- and position-dependent gas source. The model is able to determine the pressure values along the tube, once the pumping speed at each extremity and the gas sources are specified. The time evolution of the pressure along a tube is presented for situations commonly found in high-vacuum applications, such as particle accelerators, colliders, storage rings, and synchrotron light sources. (C) 2004 American Vacuum Society.

Amphiphilic planar membranes in ionic equilibrium: a study of pH position-dependent values

The pH values near a planar dissociating membrane are studied under a mean field approximation using the Poisson-Boltzmann equation and its linear form. The equations are solved in planar symmetry with the consideration that the charge density on the dissociating membrane surface results from an equilibrium process with the neighboring electrolyte. Results for the membrane dissociation degree are presented as a function of the electrolyte ionic strength and membrane surface charge density. Our calculations indicate that pH values have an appreciable variation within 2 nm from the membrane. It is shown that the dissociation process is enhanced due to the presence of bivalent ions and that pH values acquire better stability than in an electrolyte containing univalent ions.