Inferring a weighted elastic network from partial unfolding with coarse-grained simulations

A number of studies have demonstrated that simple elastic network models can reproduce experimental B-factors, providing insights into the structure-function properties of proteins. Here, we report a study on how to improve an elastic network model and explore its performance by predicting the experimental B-factors. Elastic network models are built on the experimental C coordinates, and they only take the pairs of C atoms within a given cutoff distance r(c) into account. These models describe the interactions by elastic springs with the same force constant. We have developed a method based on numerical simulations with a simple coarse-grained force field, to attribute weights to these spring constants. This method considers the time that two C atoms remain connected in the network during partial unfolding, establishing a means of measuring the strength of each link. We examined two different coarse-grained force fields and explored the computation of these weights by unfolding the native structures. Proteins 2014; 82:119-129. (c) 2013 Wiley Periodicals, Inc.

The influence of habitat homogenization on the trophic structure of fish fauna in tropical streams

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

S Q E D (4) and Q E D (4) on the Null-Plane

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The structure of non-abelian kinks

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

Temperature and storage period over spermatic parameters of jundia, Rhamdia quelen (Quoy & Gaimard, 1824)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Transformação de coordenadas com modelagem de distorções entre SAD69 e SIRGAS2000 com o uso de Thin-Plate Splines

Several countries have been passed by change processes in their fundamental geodesic structure with the focus on the adoption of geocentric reference systems. In Brazil, the adoption of the SIRGAS2000 evolves the coexistence of two realizations from the COrrego Alegre system, two realizations from the SAD69 system and one realization from the SIRGAS2000 system. To make use of products in the old reference systems, methods of coordinate transformation between the existent reference frames are necessary. So, in this paper one solution for the transformation between coordinates from different reference frames, based on Thin-Plate Splines (TPS), that allows the estimation of parameters from one linear transformation and also one non-linear model is presented. The TPS model was developed to work with tridimensional coordinates and in this paper the results and analysis are performed with simulated data and also with data from the official Brazilian Geodetic System (SGB). In the check points from SAD69 stations (realization of 1996 - SAD69/96), the values of RMSE obtained were of 78,2 mm in latitude and 67,5 mm in longitude, before the transformation to the SIRGAS2000. In the comparison between the TPS model and ProGriD (Brazilian software provided by IBGE), the statistical indicators were reduced in 97%, by using the TPS model. Based in the obtained results from real dataset, the TPS model appears to be promising, since it allows improving the quality of transformation process with simultaneous distortion modeling.

Automatic Orientation of Multi-Scale Terrestrial Images for 3D Reconstruction

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

Application of the PTT Model to Axisymmetric Free Surface Flows

This work is concerned with numerical simulation of axisymmetric viscoelastic free surface flows using the Phan-Thien-Tanner (PTT) constitutive equation. A finite difference technique for solving the governing equations for unsteady incompressible flows written in Cylindrical coordinates on a staggered grid is described. The fluid is modelled by a Marker-and-Cell type method and an accurate representation of the fluid surface is employed. The full free surface stress conditions are applied. The numerical method is verified by comparing numerical predictions of fully developed flow in a pipe with the corresponding analytic solutions. To demonstrate that the numerical method can simulate axisymmetric free surface flows governed by the PTT model, numerical results of the flow evolution of a drop impacting on a rigid dry plate are presented. In these simulations, the rheological effects of the parameters epsilon and xi are investigated.

Correlações lineares e espaciais entre atributos físico-químicos de solos de diferentes ambientes de produção de cana-de-açúcar no Noroeste do Estado de São Paulo

Pós-graduação em Agronomia - FEIS

Adubação corretiva de fósforo sobre o desempenho de variedades de cana-de-açúcar cultivadas em ambiente restritivo de cerrado

Pós-graduação em Agronomia - FEIS

Agroclimatic zoning of the state of Minas Gerais for the production of high quality soybean seeds

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

Gênese de solos coesos do leste maranhense: relação solo-paisagem

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

Understanding the Function of Conserved Variations in the Catalytic Loops of Fungal Glycoside Hydrolase Family 12

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

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

Reassessment of the potential applications of Eu3+-doped Y2O3 photoluminescent material in ceramic powder form

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