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

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

Particular solution for anomalous diffusion equation with source term

In literature the phenomenon of diffusion has been widely studied, however for nonextensive systems which are governed by a nonlinear stochastic dynamic, there are a few soluble models. The purpose of this study is to present the solution of the nonlinear Fokker-Planck equation for a model of potential with barrier considering a term of absorption. Systems of this nature can be observed in various chemical or biological processes and their solution enriches the studies of existing nonextensive systems.

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.

The Disk-Specimen Thickness Does Not Influence the Push-Out Bond Strength Results Between Fiber Post and Root Dentin

This study evaluated the effect of different thickness of disk-shaped specimens on the push-out bond strength test. Eighteen lower bovine teeth were sectioned (20mm) and prepared (15mm) with the same post system drill (Light Post (R) #1, Schaumburg, IL, Bisco, USA). The apical third of each specimen was embedded in a plastic matrix filled with an acrylic resin (Dencrilay (TM), Dencril, São Paulo, Brazil). The posts were cleaned with alcohol, silanated (ProSil (R), FGM, Joenville, SC, Brazil) and cemented with the RelyX (TM) U100 (3M ESPE, St. Paul, MN, USA). Each specimen was sectioned into three pieces of differing thicknesses (1, 2, and 4 mm). These disk-samples were allocated into 3 groups (n=18) and subjected to push-out testing. One-way ANOVA showed no influence of the specimen thickness on the results (p=0.842). No correlation was observed between thickness and push-out bond strength (Pearson Correlation, r(2)=0.0688; P=0.6209). The push-out bond strength test was not affected by the thickness of the disk-specimens.

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.

Anomalous diffusion of pions at RHIC

After pointing out the difference between normal and anomalous diffusion, we consider a hadron resonance cascade (HRC) model simulation for particle emission at RHIC and point out that rescattering in an expanding hadron resonance gas leads to a heavy tail in the source distribution. The results are compared to recent PHENIX measurements of the tail of the particle emitting source in Au+Au collisions at RHIC. In this context, we show how can one distinguish experimentally the anomalous diffusion of hadrons from a second order QCD phase transition.

A Short Note on Transverse Vibrations of a Shaft Carrying Two (or One) Disk Excited by a Nonideal Motor

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Blocking Radial Diffusion in a Double-Waved Hamiltonian Model

A non-twist Hamiltonian system perturbed by two waves with particular wave numbers can present Robust Tori, barriers created by the vanishing of the perturbing Hamiltonian at some defined positions. When Robust Tori exist, any trajectory in phase space passing close to them is blocked by emergent invariant curves that prevent the chaotic transport. We analyze the breaking up of the RT as well the transport dependence on the wave numbers and on the wave amplitudes. Moreover, we report the chaotic web formation in the phase space and how this pattern influences the transport.

Diffusion and interface controlled reactions in alpha-(Cu-Al-Ag) alloys

The isothermal kinetics of Ag precipitation was studied in Cu-Al-Ag alloys with concentrations ranging from 2 to 8 wt.%Al and 2 to 12 wt.%Ag, using scanning electron microscopy (SEM), X-ray energy dispersive spectroscopy (EDX) and microhardness measurements. The results indicated a change in the precipitates growing mechanism from diffusion to interface controlled process, probably due to a change in the nature of the interface with the Ag and Al enrichment of the precipitates. (C) 2006 Elsevier B.V. All rights reserved.

A label-free immunosensor based on recordable compact disk chip for early diagnostic of the dengue virus infection

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Tris-EDTA no teste de sensibilidade antimicrobiana in vitro em amostras de Pseudomonas aeruginosa

In vitro antimicrobial susceptibility of strains of Pseudomonas aeruginosa by standard diffusion disk test and a modified method, by the addition Tris-EDTA, was evaluated. Increase in sensitivity of agent using modified method was observed mainly in aminoglycosides (amikacin, gentamicin, tobramycin), quinolones (ofloxacin and norfloxacin) and cephalosporins (cefoperazone and ceftazidime) groups. by standard diffusion disk test and a modified method, by the addition Tris-EDTA, was evaluated. Increase in sensitivity of agent using modified method was observed mainly in aminoglycosides (amikacin, gentamicin, tobramycin), quinolones (ofloxacin and norfloxacin) and cephalosporins (cefoperazone and ceftazidime) groups.

Dimetilsulfóxido - DMSO no teste de sensibilidade microbiana in vitro em cepas de Rhodococcus equi isoladas de afecções pulmonares em potros

Comparou-se a sensibilidade microbiana in vitro de isolados de Rhodococcus equi pelo teste padrão de difusão com discos, com o modificado, pela adição de 5% de dimetilsulfóxido-DMSO. Observou-se aumento da sensibilidade do R. equi no teste com DMSO, frente a aminoglicosídeos (canamicina, amicacina, estreptomicina) e ao cloranfenicol, enquanto para a eritromicina e derivados ß-lactâmicos (penicilina G, cefalosporinas, amoxicilina, oxacilina), constatou-se redução da sensibilidade do agente.

Arrays of gold microelectrodes made from split integrated circuit chips

A simple and inexpensive way to fabricate arrays of gold microelectrodes is proposed. Integrated circuit chips are sawed through their middle, normal to the longest axis, leading to destruction of the silicon circuit and rupture of the gold wires that interconnect it with the external terminals. Polishing the resulting rough surface converts the tips of the wires embedded in the chip halves into arrays of gold microdisks of about 25 mu m diameter. The number of active microelectrodes (MEs), of an array depends on the number of pins in the chip, n, being typically (n/2)-4. These MEs can be used individually or externally interconnected in any combination. X-ray images of the chips and micrographs of the resulting surface of the polished arrays have revealed variable distances between neighbor MEs, which are, however, larger than 10 times the radius of the disks. This feature of the MEs prevents diffusional cross-talk between electrodes. The use of these microdisk electrodes for analytical purposes exhibits sigmoidal voltammograms, and chronoamperometric experiments confirm the nonlinear i vs. t(1/2) plots, typical for processes where radial diffusion prevails. Satisfactory uniformity was observed for the response of each electrode of an array, indicating similarity of geometry and disk areas. The potentialities of these MEs were demonstrated by the determination of cadmium at ppb levels using square wave voltammetry with preconcentration. Due to the relative ease with which these MEs can be manufactured and their good performance in (chemical) analysis, wide applications in electrochemistry and electroanalysis is envisioned.

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.