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.

Stability and collapse of a coupled Bose-Einstein condensate

The dynamics of a coupled Bose-Einstein condensate involving trapped atoms in two quantum states is studied using the time-dependent Gross-Pitaevskii equation including an interaction which can transform atoms from one state to the other. We find interesting oscillation of the number of atoms in each of the states. For all repulsive interactions, stable condensates are formed. When some of the atomic interactions are attractive, the possibility of collapse is studied by including an absorptive contact interaction and a quartic three-body recombination term. One or both components of the condensate may undergo collapse when one or more of the nonlinear terms are attractive in nature. (C) 2001 Elsevier B.V. B.V. 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.

Soliton-cuspon interaction for the Camassa-Holm equation

The interaction of different kinds of solitary waves of the Camassa-Holm equation is investigated. We consider soliton-soliton, soliton-cuspon and cuspon-cuspon interactions. The description of these solutions had previously been shown to be reducible to the solution of an algebraic equation. Here we give explicit examples, numerically solving these algebraic equations and plotting the corresponding solutions. Further, we show that the interaction is elastic and leads to a shift in the position of the solitons or cuspons. We give the analytical expressions for this shift and represent graphically the coupled soliton-cuspon, soliton-soliton and cuspon-cuspon interactions.

Macroscopic quantum tunneling and resonances in coupled Bose-Einstein condensates with oscillating atomic scattering length

We study the macroscopic quantum tunneling, self-trapping phenomena in two weakly coupled Bose-Einstein condensates with periodically time-varying atomic scattering length.The resonances in the oscillations of the atomic populations are investigated. We consider oscillations in the cases of macroscopic quantum tunneling and the self-trapping regimes. The existence of chaotic oscillations in the relative atomic population due to overlaps between nonlinear resonances is showed. We derive the whisker-type map for the problem and obtain the estimate for the critical amplitude of modulations leading to chaos. The diffusion coefficient for motion in the stochastic layer near separatrix is calculated. The analysis of the oscillations in the rapidly varying case shows the possibility of stabilization of the unstable pi-mode regime. (C) 2000 Published by Elsevier B.V. B.V. PACS: 03.75.Fi; 05.30.Jp.

Stable periodic waves in coupled Kuramoto-Sivashinsky-Korteweg-de Vries equations

Periodic waves are investigated in a system composed of a Kuramoto-Sivashinsky-Korteweg-de Vries (KS-KdV) equation linearly coupled to an extra linear dissipative one. The model describes, e.g., a two-layer liquid film flowing down an inclined plane. It has been recently shown that the system supports stable solitary pulses. We demonstrate that a perturbation analysis, based on the balance equation for the net field momentum, predicts the existence of stable cnoidal waves (CnWs) in the same system. It is found that the mean value u(0) of the wave field u in the main subsystem, but not the mean value of the extra field, affects the stability of the periodic waves. Three different areas can be distinguished inside the stability region in the parameter plane (L, u(0)), where L is the wave's period. In these areas, stable are, respectively, CnWs with positive velocity, constant solutions, and CnWs with negative velocity. Multistability, i.e., the coexistence of several attractors, including the waves with several maxima per period, appears at large value of L. The analytical predictions are completely confirmed by direct simulations. Stable waves are also found numerically in the limit of vanishing dispersion, when the KS-KdV equation goes over into the KS one.

Dissipative hydrodynamics coupled to chiral fields

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Nonlinear two-field models from orbit equation deformations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Influence of Ag additions on the activation energy for the reverse eutectoid reaction in Cu-Al alloys

The eutectoid transformation may be defined as a solid-state diffusion-controlled decomposition process of a high-temperature phase into a two-phase lamellar aggregate behind a migrating boundary on cooling below the eutectoid temperature. In substitutional solid solutions, the eutectoid reaction involves diffusion of the solute atoms either through the matrix or along the boundaries or ledges. The effect of Ag on the non-isothermal kinetics of the reverse eutectoid reaction in the Cu-9 mass%Al, Cu-10 mass%Al, and Cu-11 mass%Al alloys were studied using differential scanning calorimetry (DSC), X-ray diffraction (XRD), and scanning electron microscopy (SEM). The activation energy for this reaction was obtained using the Kissinger and Ozawa methods. The results indicated that Ag additions to Cu-Al alloys interfere on the reverse eutectoid reaction, increasing the activation energy values for the Cu-9 mass%Al and Cu-10 mass%Al alloys and decreasing these values for the Cu-11 mass%Al alloy for additions up to 6 mass%Ag. The changes in the activation energy were attributed to changes in the reaction solute and in Ag solubility due to the increase in Al content.

Determination of Glyphosate in Water Samples by Multi-pumping Flow System Coupled to a Liquid Waveguide Capillary Cell

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

NONLINEAR DIFFUSION PROCESS IN A BENARD SYSTEM AT THE CRITICAL-POINT FOR THE ONSET OF CONVECTION

The evolution equation governing surface perturbations of a shallow fluid heated from below at the critical Rayleigh number for the onset of convective motion, and with boundary conditions leading to zero critical wave number, is obtained. A solution for negative or cooling perturbations is explicitly exhibited, which shows that the system presents sharp propagating fronts.

On-line determination of Sb(III) and total Sb using baker's yeast immobilized on polyurethane foam and hydride generation inductively coupled plasma optical emission spectrometry

The yeast Saccharomyces cerevisiae was immobilized in cubes of polyurethane foam and the ability of this immobilized material to separate Sb(III) and Sb(V) was investigated. A method based on sequential determination of total Sb (after on-line reduction of Sb(V) to Sb(III) with thiourea) and Sb(Ill) (after on-line solid-liquid phase extraction) by hydride generation inductively coupled plasma optical emission spectrometry is proposed. A flow system assembled with solenoid valves was used to manage all stages of the process. The effects of pH, sample loading and elution flow rates on solid-liquid phase extraction of Sb(III) were evaluated. Also, the parameters related to online pre-reduction (reaction coil and flow rates) were optimized. Detection limits of 0.8 and 0.15 mu g L-1 were obtained for total Sb and Sb (III), respectively. The proposed method was applied to the analysis of river water and effluent samples. The results obtained for the determination of total Sb were in agreement with expected values, including the river water Standard Reference Material 1640 certified by the National Institute of Standards and Technology (NIST). Recoveries of Sb(III) and Sb(V) in spiked samples were between 81 19 and I I I 15% when 120 s of sample loading were used. (c) 2006 Elsevier B.V. All rights reserved.

Sintering mechanisms of ZrO2 center dot MgO with addition of TiO2 and CuO

Substitutions of Ti and Cu in ZrO2.MgO (Z), cause transformation from monoclinic (m) to cubic (c) and tetragonal (t). According to the vacancy model and solid Solution formation models, neither CuO nor TiO2 cause zirconia stabilization, which derives front other phenomena. Data analysis by TMA using the CRH (constant rate of heating) method shows a solid state reaction of ZrO2.MgO.TiO2 (Z.TiO2) demonstrating a dominant mechanism of volume diffusion (n = 1). However, the sintering of ZrO2.MgO.CuO (Z.CuO) shows a viscous flow mechanism (n = 0), a similar phenomena to that of by sintering of glass. Transformations, such as: CuO to Cu2O at 1000 degreesC, ZrO2 (m) to ZrO2 (t) at 1100 degreesC and Cu2O (s) to Cu2O (l) at 1230 degreesC cause successive rearrangements of microstructure inside of region I (sintering process) and lead to interpretation errors when the Bannister equation is used. (C) 2003 Elsevier Ltd and Techna Group S.r.l. All rights reserved.

A MODEL OF THE DEUTERON BASED ON A BREIT TYPE EQUATION

A relativistic treatment of the deuteron and its observables based on a two-body Dirac (Breit) equation, with phenomenological interactions, associated to one-boson exchanges with cutoff masses, is presented. The 16-component wave function for the deuteron (J(pi) = 1+) solution contains four independent radial functions which obey a system of four coupled differential equations of first order. This radial system is numerically integrated, from infinity to the origin, by fixing the value of the deuteron binding energy and using appropriate boundary conditions at infinity. Specific examples of mixtures containing scalar, pseudoscalar and vector like terms are discussed in some detail and several observables of the deuteron are calculated. Our treatment differs from more conventional ones in that nonrelativistic reductions of the order c-2 are not used.

Thermogravimetry (TG) applied to the study of the reaction of mercury with platinum-rhodium alloy

Thermogravimetry (TG) energy dispersive X-ray microanalysis (EDX), scanning electron microscopy (SEM), mapping surface, X-ray diffraction (XRD), inductively coupled plasma emission spectroscopy and atomic spectroscopy with cold vapor generation have been used to study the reaction of mercury with platinum-rhodium (Pt-Rh) alloy. The results suggest that, the electrodeposited Hg film reacts with Pt-Rh to form intermetallic compounds of different stability, when heated indicated by at least four weight loss steps. Intermetallic compounds as PtHg4 and PtHg2 was characterized by XRD. These intermetallic compound are the main product presents on the surface of the samples after remotion of the bulk mercury via thermal desorption techniques. (C) 2002 Elsevier B.V. B.V. All rights reserved.