Probing the kinetics of single molecule protein folding

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments ( for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier. The ratio between first-passage-time moments is proposed to be a good variable to quantitatively probe these kinetic changes. The temperature-dependent kinetics is consistent with the strange kinetics found in folding dynamics experiments. The potential applications of the current results to single-molecule protein folding are discussed.

SAXS study of monodispersed silica nanospheres obtained by an amino acid route

Spherical silica nanoparticles were prepared using a basic amino acid catalysis route and the kinetics of the particles growth was investigated by small angle X-ray scattering (SAXS). L-arginine was used in the polar aqueous phase as the basic catalyst whereas the tetraethylorthosilicate (TEOS) was dissolved in the cyclohexane oil phase as the silicate monomer source. The SAXS measurements were taken in the aqueous phase at different reaction times. A high degree of monodispersity was clearly evidenced for the spherical nanoparticles as a result of the pronounced high-order oscillations observed in the SAXS curves. The SAXS data show that the particles number density remains unchanged since both the particle size as well as the volume fraction gradually increase. This process was discussed based on a reaction-controlled addition of monomer species at the surface of the growing particles. Consequently, the monodispersed spherical nanoparticles radius can as such be finely tuned from 7 to 12 nm by varying the reaction time. (C) 2010 Elsevier B.V. All rights reserved.

Application of a bounded upwinding scheme to complex fluid dynamics problems

This paper is concerned with an overview of upwinding schemes, and further nonlinear applications of a recently introduced high resolution upwind differencing scheme, namely the ADBQUICKEST [V.G. Ferreira, F.A. Kurokawa, R.A.B. Queiroz, M.K. Kaibara, C.M. Oishi, J.A.Cuminato, A.F. Castelo, M.F. Tomé, S. McKee, assessment of a high-order finite difference upwind scheme for the simulation of convection-diffusion problems, International Journal for Numerical Methods in Fluids 60 (2009) 1-26]. The ADBQUICKEST scheme is a new TVD version of the QUICKEST [B.P. Leonard, A stable and accurate convective modeling procedure based on quadratic upstream interpolation, Computer Methods in Applied Mechanics and Engineering 19 (1979) 59-98] for solving nonlinear balance laws. The scheme is based on the concept of NV and TVD formalisms and satisfies a convective boundedness criterion. The accuracy of the scheme is compared with other popularly used convective upwinding schemes (see, for example, Roe (1985) [19], Van Leer (1974) [18] and Arora & Roe (1997) [17]) for solving nonlinear conservation laws (for example, Buckley-Leverett, shallow water and Euler equations). The ADBQUICKEST scheme is then used to solve six types of fluid flow problems of increasing complexity: namely, 2D aerosol filtration by fibrous filters; axisymmetric flow in a tubular membrane; 2D two-phase flow in a fluidized bed; 2D compressible Orszag-Tang MHD vortex; axisymmetric jet onto a flat surface at low Reynolds number and full 3D incompressible flows involving moving free surfaces. The numerical simulations indicate that this convective upwinding scheme is a good generic alternative for solving complex fluid dynamics problems. © 2012.

Solução numérica das equações de Navier-Stokes em um canal-tipo estenose usando métodos compactos e não compacos de alta ordem

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Determinação de órbitas com o GPS através de mínimos quadrados recursivo com rotações de Givens

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

Verificação da formação de complexos protéicos nos telômeros de L. amazonensis

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Desenvolvimento de um método numérico para simular escoamentos viscoelásticos axissimétricos com superfícies livres: Modelo PTT

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

Controle ativo de vibrações em estruturas espaciais tipo treliças usando controladores IMSC

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Parâmetros genéticos para produção de leite e persistência de lactações múltiplas na raça Gir

Pós-graduação em Genética e Melhoramento Animal - FCAV

Técnica para dedução do modelo algébrico PTT, aplicações e análises numéricas em escoamentos bidimensionais

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

Metabolic profiling by ultra-performance liquid chromatography-mass spectrometry and parallel factor analysis for the determination of disease biomarkers in Eucalyptus

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

A smooth evolutionary structural optimization procedure applied to plane stress problem

Topological optimization problems based on stress criteria are solved using two techniques in this paper. The first technique is the conventional Evolutionary Structural Optimization (ESO), which is known as hard kill, because the material is discretely removed; that is, the elements under low stress that are being inefficiently utilized have their constitutive matrix has suddenly reduced. The second technique, proposed in a previous paper, is a variant of the ESO procedure and is called Smooth ESO (SESO), which is based on the philosophy that if an element is not really necessary for the structure, its contribution to the structural stiffness will gradually diminish until it no longer influences the structure; its removal is thus performed smoothly. This procedure is known as "soft-kill"; that is, not all of the elements removed from the structure using the ESO criterion are discarded. Thus, the elements returned to the structure must provide a good conditioning system that will be resolved in the next iteration, and they are considered important to the optimization process. To evaluate elasticity problems numerically, finite element analysis is applied, but instead of using conventional quadrilateral finite elements, a plane-stress triangular finite element was implemented with high-order modes for solving complex geometric problems. A number of typical examples demonstrate that the proposed approach is effective for solving problems of bi-dimensional elasticity. (C) 2014 Elsevier Ltd. All rights reserved.

The influence of self-weight of elastic 2D structures in topology optimization via numerical technique Smooth Evolutionary Structural Optimization (SESO)

This paper deals with topology optimization in plane elastic-linear problems considering the influence of the self weight in efforts in structural elements. For this purpose it is used a numerical technique called SESO (Smooth ESO), which is based on the procedure for progressive decrease of the inefficient stiffness element contribution at lower stresses until he has no more influence. The SESO is applied with the finite element method and is utilized a triangular finite element and high order. This paper extends the technique SESO for application its self weight where the program, in computing the volume and specific weight, automatically generates a concentrated equivalent force to each node of the element. The evaluation is finalized with the definition of a model of strut-and-tie resulting in regions of stress concentration. Examples are presented with optimum topology structures obtaining optimal settings. (C) 2012 CIMNE (Universitat Politecnica de Catalunya). Published by Elsevier Espana, S.L.U. All rights reserved.

Compressible modes in a square lid-driven cavity

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Performance characteristics of high performance liquid chromatography, first order derivative UV spectrophotometry and bioassay for fluconazole determination in capsules

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