Visualization of Protein Folding Funnels in Lattice Models

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

An introductory informatics theoretical framework, based on an integrable lattice model using quantized function algebras, for studying DNA-ionized gas interaction system

Usually we observe that Bio-physical systems or Bio-chemical systems are many a time based on nanoscale phenomenon in different host environments, which involve many particles can often not be solved explicitly. Instead a physicist, biologist or a chemist has to rely either on approximate or numerical methods. For a certain type of systems, called integrable in nature, there exist particular mathematical structures and symmetries which facilitate the exact and explicit description. Most integrable systems, we come across are low-dimensional, for instance, a one-dimensional chain of coupled atoms in DNA molecular system with a particular direction or exist as a vector in the environment. This theoretical research paper aims at bringing one of the pioneering ‘Reaction-Diffusion’ aspects of the DNA-plasma material system based on an integrable lattice model approach utilizing quantized functional algebras, to disseminate the new developments, initiate novel computational and design paradigms.

The Origin of Nonmonotonic Complex Behavior and the Effects of Nonnative Interactions on the Diffusive Properties of Protein Folding

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

The water factor in the protein-folding problem

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

Steric constraints as folding coadjuvant

Through the analyses of the Miyazawa-Jernigan matrix it has been shown that the hydrophobic effect generates the dominant driving force for protein folding. By using both lattice and off-lattice models, it is shown that hydrophobic-type potentials are indeed efficient in inducing the chain through nativelike configurations, but they fail to provide sufficient stability so as to keep the chain in the native state. However, through comparative Monte Carlo simulations, it is shown that hydrophobic potentials and steric constraints are two basic ingredients for the folding process. Specifically, it is shown that suitable pairwise steric constraints introduce strong changes on the configurational activity, whose main consequence is a huge increase in the overall stability condition of the native state; detailed analysis of the effects of steric constraints on the heat capacity and configurational activity are provided. The present results support the view that the folding problem of globular proteins can be approached as a process in which the mechanism to reach the native conformation and the requirements for the globule stability are uncoupled.

Estudo do coeficiente de difusão no enovelamento de proteínas na rede

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Termodinâmica do enovelamento de cadeias heteropoliméricas através do algoritmo de Wang-Landau

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Modelos de redes unidimensionais aplicados ao estudo termodinâmico do DNA

Pós-graduação em Biofísica Molecular - IBILCE

Visualização do funil de enovelamento de proteínas

Pós-graduação em Biofísica Molecular - IBILCE

Magnetism in spin models for depleted honeycomb-lattice iridates: Spin-glass order towards percolation

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

The Yang-Lee edge singularity in spin models on connected and non-connected rings

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Higher order Painleve equations and their symmetries via reductions of a class of integrable models

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

An ab initio study of oxygen vacancies and doping process of Nb and Cr atoms on TiO2 (110) surface models

We theoretically investigated how the formation of oxygen vacancies and the addition of niobium and chromium atoms as dopants modify the varistor properties of TiO2. The calculations were carried out at the HF level using a contracted basis set, developed by Huzinaga et al.. to represent the atomic centers on the (110) surface for the large (TiO2)(15) cluster model. The change of the values for the net atomic charges and band gap after oxygen vacancy formation and the presence of dopants in the lattice are analyzed and discussed. It is shown that the formation of oxygen vacancies decreases the band gap while an opposite effect is found when dopants are located in the reduced surface. The theoretical results are compared with available experimental data. A plausible explanation of the varistor behavior of this system is proposed. (C) 1997 John Wiley & Sons, Inc.

Toda and Volterra lattice equations from discrete symmetries of KP hierarchies

The discrete models of the Toda and Volterra chains are being constructed out of the continuum two-boson KP hierarchies. The main tool is the discrete symmetry preserving the Hamiltonian structure of the continuum models. The two-boson currents of KP hierarchy are being associated with sites of the corresponding chain by successive actions of discrete symmetry.

Analysis of Lattice Size, Energy Density and Denaturation for a One-Dimensional DNA Model

There are several mechanical models to describe the DNA phenomenology. In this work the DNA denaturation is stu- died under thermodynamical and dynamical point of view using the well known Peyrard-Bishop model. The thermody-namics analysis using the transfer integral operator method is briefly reviewed. In particular, the lattice size is discussed and a conjecture about the minimum energy to denaturation is proposed. In terms of the dynamical aspects of the model, the equations of motion for the system are integrated and the results determine the energy density where the denatura- tion occurs. The behavior of the lattice near the phase transition is analyzed. The relation between the thermodynamical and dynamical results is discussed.