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.

Effect of dental finishing instruments on the surface roughness of composite resins as elucidated by atomic force microscopy

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Atomic radiative transitions in thermo field dynamics

In this work we rederive the Lamb-Retherford energy shift for an atomic electron in the presence of a thermal radiation. Using the Dalibard, Dupont-Roc and Cohen-Tannoudji (DDC) formalism, where physical observables are expressed as convolutions of suitable statistical functions, we construct the electromagnetic field propagator of thermo field dynamics in the Coulomb gauge in order to investigate finite temperature effects on the atomic energy levels. In the same context, we also analyze the problem of the ground state stability.

Quantum coherent tunneling between two atomic-molecular Bose-Einstein condensates

We study the quantum coherent tunneling dynamics of two weakly coupled atomic-molecular Bose-Einstein condensates (AMBEC). A weak link is supposed to be provided by a double-well trap. The regions of parameters where the macroscopic quantum localization of the relative atomic population occurs are revealed. The different dynamical regimes are found depending on the value of nonlinearity, namely, coupled oscillations of population imbalance of atomic and molecular condensate, including irregular oscillations regions, and macroscopic quantum self trapping regimes. Quantum means and quadrature variances are calculated for population of atomic and molecular condensates and the possibility of quadrature squeezing is shown via stochastic simulations within P-positive phase space representation method. Linear tunnel coupling between two AMBEC leads to correlations in quantum statistics.

Stability of atomic condensed systems with attractive two-body interactions

In the present report, we review recent investigations that we have conducted on the stability of atomic condensed systems, when the two-body interaction is attractive. In particular, the dynamics that occurs in the condensate due to nonconservative terms is considered in the context of an extension of the mean-field Gross-Pitaevskii approximation. Considering the relative intensity of the nonconservative parameters, chaotic and solitonic solutions are verified. Also discussed is the possibility of a liquid-gas phase transition in the presence of positive three-body elastic collisions.

Resonances in a trapped 3D Bose-Einstein condensate under periodically varying atomic scattering length

Nonlinear oscillations of a 3D radial symmetric Bose-Einstein condensate under periodic variation in time of the atomic scattering length have been studied. The time-dependent variational approach is used for the analysis of the characteristics of nonlinear resonances in the oscillations of the condensate. The bistability in oscillations of the BEC width is investigated. The dependence of the BEC collapse threshold on the drive amplitude and parameters of the condensate and trap is found. Predictions of the theory are confirmed by numerical simulations of the full Gross-Pitaevskii equation.

Atomic Bose-Einstein condensation with three-body interactions and collective excitations

The stability of a Bose-Einstein condensed state of trapped ultra-cold atoms is investigated under the assumption of an attractive two-body and a repulsive three-body interaction. The Ginzburg-Pitaevskii-Gross (GPG) nonlinear Schrodinger equation is extended to include an effective potential dependent on the square of the density and solved numerically for the s-wave. The lowest collective mode excitations are determined and their dependences on the number of atoms and on the strength of the three-body force are studied. The addition of three-body dynamics can allow the number of condensed atoms to increase considerably, even when the strength of the three-body force is very small compared with the strength of the two-body force. We study in detail the first-order liquid-gas phase transition for the condensed state, which can happen in a critical range of the effective three-body force parameter.

Symmetry analysis of an integrable reaction-diffusion equation

In this paper, we investigate the invariance and integrability properties of an integrable two-component reaction-diffusion equation. We perform Painleve analysis for both the reaction-diffusion equation modelled by a coupled nonlinear partial differential equations and its general similarity reduced ordinary differential equation and confirm its integrability. Further, we perform Lie symmetry analysis for this model. Interestingly our investigations reveals a rich variety of particular solutions, which have not been reported in the literature, for this model. (C) 2000 Elsevier B.V. Ltd. All rights reserved.

Mathematical models of generalized diffusion

We discuss in this paper equations describing processes involving non-linear and higher-order diffusion. We focus on a particular case (u(t) = 2 lambda (2)(uu(x))(x) + lambda (2)u(xxxx)), which is put into analogy with the KdV equation. A balance of nonlinearity and higher-order diffusion enables the existence of self-similar solutions, describing diffusive shocks. These shocks are continuous solutions with a discontinuous higher-order derivative at the shock front. We argue that they play a role analogous to the soliton solutions in the dispersive case. We also discuss several physical instances where such equations are relevant.

Four-fermion contact interactions at one-loop and the new atomic parity violation results.

We investigate the possibility that four-fermion contact interactions give rise to the observed deviation from the Standard Model prediction for the weak charge of cesium, through one-loop contributions. We show that the presence of loops involving the third generation quarks can explain such deviation.

A few-body treatment of low energy atomic collisions involving exotic particles

Faddeev-type equations are applied to three-charged particle systems. The rather satisfactory results are obtained for low energy e(+)H elastic scattering and muonic transfer reactions. The cross sections for antihydrogen formation from antiproton-positronium collisions are calculated using a six state model (Ps[1s2s2p], (H) over bar[1s2s2p]).

Dynamics of quasi-one-dimensional bright and vortex solitons of a dipolar Bose-Einstein condensate with repulsive atomic interaction

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

Dynamics of Bose-Einstein condensates with atomic pumping and dissipative processes

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

LARGE ATOMIC and NUCLEAR THREE-BODY SYSTEMS: SCATTERING and BINDING

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