Monte Carlo thermodynamic and structural properties of the TIP4P water model: dependence on the computational conditions

Classical Monte Carlo simulations were carried out on the NPT ensemble at 25°C and 1 atm, aiming to investigate the ability of the TIP4P water model [Jorgensen, Chandrasekhar, Madura, Impey and Klein; J. Chem. Phys., 79 (1983) 926] to reproduce the newest structural picture of liquid water. The results were compared with recent neutron diffraction data [Soper; Bruni and Ricci; J. Chem. Phys., 106 (1997) 247]. The influence of the computational conditions on the thermodynamic and structural results obtained with this model was also analyzed. The findings were compared with the original ones from Jorgensen et al [above-cited reference plus Mol. Phys., 56 (1985) 1381]. It is notice that the thermodynamic results are dependent on the boundary conditions used, whereas the usual radial distribution functions g(O/O(r)) and g(O/H(r)) do not depend on them.

Simulation results and applications of an advection bounded scheme to practical flows

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

How C-terminal carboxyamidation alters the biological activity of peptides from the venom of the eumenine solitary wasp

Inflammatory peptides display different types of post-transcriptional modifications, such as C-terminal amidation, that alter their biological activity. Here we describe the structural and molecular dynamics features of the mast cell degranulating peptide, eumenine mastoparan-AF (EMP-AF-NH2), found in the venom of the solitary wasp, and of its carboxyl-free C-terminal form (EMP-AF-COO-) characterized by a reduced activity. Circular dichroism indicates that both peptides switch from a random coil conformation in water to a helical structure in TFE and SDS micelles. NMR data, in 30% TFE, reveal that the two peptides fold into an alpha-helix spanning most of their length, while they differ in terms of molecular rigidity. To understand the origins of the conformational flexibility observed in the case of EMP-AF-COO-, a 5 ns MD simulation was carried out for each peptide, in an explicit water/TFE environment. The results show that the two peptides differ in an H-bond between Leu14 NH2 and the backbone carbonyl of Ile11. The loss of that H-bond in EMP-AF-COO- leads to a significant modification of its structural dynamics. In fact, as evidenced by essential dynamics analysis, while EMP-AF-NH2 exists mainly as a rigid structure, EMP-AF-COO- presents two helical stretches that fluctuate in some sort of independent fashion. We conclude that the diverse biological activity of the two peptides is not simply due to the reduction of the net positive charge, as generally suggested, but also to a structural perturbation of the amphipathic alpha-helix that affects their ability to perturb the cell membrane.

Comparison between univariate and bivariate geostatistical models for estimating catch per unit of effort (cpue): A simulation study

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Crotacetin, a novel snake venom C-type lectin homolog of convulxin, exhibits an unpredictable antimicrobial activity

Snake venom (sv) C-type lectins encompass a group of hemorrhagic toxins that are capable of interfering with blood stasis. A very well-studied svC-type lectin is the heterodimeric toxin, convulxin (CVX), from the venom of South American rattlesnake Crotalus durissus terrificus. CVX is able to activate platelets and induce their aggregation by acting via p62/GPVI collagen receptor. By using polymerase chain reaction homology screening, we have cloned several cDNA precursors of CVX subunit homologs. One of them, named crotacetin (CTC) beta-subunit, predicts a polypeptide with a topology very similar to the tridimensional conformations of other subunits of CVX-like snake toxins, as determined by computational analysis. Using gel permeation and reverse-phase high-performance liquid chromatography, CTC was purified from C. durissus venoms. CTC can be isolated from the venom of several C. durissus subspecies, but its quantitative predominance is in the venom of C. durissus cascavella. Functional analysis indicates that CTC induces platelet aggregation, and, importantly, exhibits an antimicrobial activity against Gram-positive and -negative bacteria, comparable with CVX.

Statistics and kinetics of single-molecule electron transfer dynamics in complex environments: A simulation model study

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

Langevin simulation of scalar fields: Additive and multiplicative noises and lattice renormalization

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Numerical simulation of Ginzburg-Landau-Langevin equations

This work is concerned with non-equilibrium phenomena, with focus on the numerical simulation of the relaxation of non-conserved order parameters described by stochastic kinetic equations known as Ginzburg-Landau-Langevin (GLL) equations. We propose methods for solving numerically these type of equations, with additive and multiplicative noises. Illustrative applications of the methods are presented for different GLL equations, with emphasis on equations incorporating memory effects.

Some comments on the numerical simulation of self-synchronization of four non-ideal exciters

In this paper, self-synchronization of four non-ideal exciters is examined via numerical simulation. The mathematical model consists of four unbalanced direct Current motors with limited power supply mounted on a flexible Structural frame support. (c) 2004 Elsevier B.V. All rights reserved.

Growth mechanism of octahedron-like BaMoO4 microcrystals processed in microwave-hydrothermal: Experimental observations and computational modeling

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Electrochemical genosensors for the detection of Bonamia parasite. Selection of single strand-DNA (ssDNA) probes by simulation of the secondary structure folding

A post-PCR nucleic acid work by comparing experimental data, from electrochemical genosensors, and bioinformatics data, derived from the simulation of the secondary structure folding and prediction of hybridisation reaction, was carried out in order to rationalize the selection of ssDNA probes for the detection of two Bonamia species, B. exitiosa and B. ostreae, parasites of Ostrea edulis.Six ssDNA probes (from 11 to 25 bases in length, 2 thiolated and 4 biotinylated) were selected within different regions of B. ostreae and B. exitiosa PCR amplicons (300 and 304 bases, respectively) with the aim to discriminate between these parasite species. ssDNA amplicons and probes were analyzed separately using the "Mfold Web Server" simulating the secondary structure folding behaviour. The hybridisation of amplicon-probe was predicted by means of "Dinamelt Web Server". The results were evaluated considering the number of hydrogen bonds broken and formed in the simulated folding and hybridisation process, variance in gaps for each sequence and number of available bases. In the experimental part, thermally denatured PCR products were captured at the sensor interface via sandwich hybridisation with surface-tethered probes (thiolated probes) and biotinylated signalling probes. A convergence between analytical signals and simulated results was observed, indicating the possibility to use bioinformatic data for ssDNA probes selection to be incorporated in genosensors. (C) 2011 Elsevier B.V. All rights reserved.

Re-examination of the anion derivatives of isoflavones by radical fragmentation in negative electrospray ionization tandem mass spectrometry: experimental and computational studies

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

Modelagem matemática aplicada ao controle biológico de Ceratitis capitata Wiedemann (Diptera: Tephritidae) por Diachasmimorpha longicaudata Ashmed (Hymenoptera: Braconidae) em Citrus

O modelo matemático apresentado tem como objetivos: (1) simular as dinâmicas populacionais de um sistema hospedeiro parasitóide de três níveis tróficos composto pelas populações de mosca-do-mediterrâneo Ceratitis capitata (Wiedemann), vespa braconídea parasitóide Diachasmimorpha longicaudata (Ashmed) e frutos cítricos; (2) auxiliar no melhor entendimento dos principais fatores biológicos e ecológicos que regem as interações populacionais e (3) colaborar com programas mais eficientes de controle biológico para o sistema em questão. A metodologia empregada baseou-se na formulação de sistemas de equações de diferenças que descrevessem os processos de interação do sistema trófico. Posteriormente, foram elaboradas resoluções numéricas desses sistemas de equações e sua representação gráfica, utilizando-se o programa computacional Matlab, versão 6.1. Os dados biológicos e ecológicos necessários para a formulação das equações matemáticas foram fornecidos por especialistas em controle de C. capitata e retirados da literatura referente ao controle biológico das moscas-das-frutas em plantações de citros no Brasil, principalmente através da utilização de vespas parasitóides, como D. longicaudata. Os resultados obtidos nas simulações sugerem que o modelo proposto descreve adequadamente o sistema ecológico em questão e permite entender melhor suas principais características biológicas e ecológicas. em conseqüência pode auxiliar na escolha do modo e momento para liberação da vespa parasitóide para o controle mais efetivo de C. capitata.

Simulation of the energy performance of maize production integrated to pig farming

Foi avaliado o desempenho energético da suinocultura integrada à produção de milho em grão em sistema de plantio direto mecanizado. Nesta concepção de integração proposta, os dejetos suínos são utilizados como fertilizantes na produção de milho. O sistema foi delimitado envolvendo as atividades associadas ao manejo dos suínos e de produção do milho (manejo do solo, cultivo e colheita). O período de análise considerado foi de um ano, o que possibilita a produção de três lotes de suínos e duas safras de milho. Para avaliar o desempenho energético, foram criados três indicadores: eficiência energética, eficiência de uso de fontes não renováveis e o custo de energia não renovável para a produção de proteína. As entradas energéticas são compostas pelos insumos e pela infraestrutura, utilizados na criação dos suínos e na produção de milho, e pela radiação solar incidente no agrossistema. Já as saídas são representadas pelos seus produtos (suínos terminados e o milho). Os resultados obtidos nas simulações apontam que a integração melhora o desempenho energético das granjas suinícolas, aumentando a eficiência energética (186%) e a eficiência não renovável (352%), além de reduzir o custo de energia não renovável para a produção de proteína (‑58%).