Search results for "Computer simulation"
showing 10 items of 1054 documents
Mapping the network of pathways of CO diffusion in myoglobin.
2010
The pathways of diffusion of a CO molecule inside a myoglobin protein and toward the solvent are investigated. Specifically, the three-dimensional potential of mean force (PMF or free energy) of the CO molecule position inside the protein is calculated by using the single-sweep method in concert with fully resolved atomistic simulations in explicit solvent. The results are interpreted under the assumption that the diffusion of the ligand can be modeled as a navigation on the PMF in which the ligand hops between the PMF local minima following the minimum free energy paths (MFEPs) with rates set by the free energy barriers that need to be crossed. Here, all the local minima of the PMF, the MF…
New fitting scheme to obtain effective potential from Car-Parrinello molecular dynamics simulations: Application to silica
2008
A fitting scheme is proposed to obtain effective potentials from Car-Parrinello molecular dynamics (CPMD) simulations. It is used to parameterize a new pair potential for silica. MD simulations with this new potential are done to determine structural and dynamic properties and to compare these properties to those obtained from CPMD and a MD simulation using the so-called BKS potential. The new potential reproduces accurately the liquid structure generated by the CPMD trajectories, the experimental activation energies for the self-diffusion constants and the experimental density of amorphous silica. Also lattice parameters and elastic constants of alpha-quartz are well-reproduced, showing th…
Interactions between T-2 toxin and its metabolites in HepG2 cells and in silico approach
2021
Abstract The T-2 toxin (T-2) is commonly metabolized to HT-2 toxin (HT-2), Neosolaniol (NEO), T2-triol and T2-tetraol and they can modify the toxicity of T-2. In this study, T-2 and its modified forms were evaluated by in vitro and in silico methods. The in vitro cytotoxicity individually was evaluated by MTT and Total Protein Content (PC) assays in human hepatocarcinoma (HepG2) cells. The order of IC50 was T-2 tetraol > T-2 triol > NEO > T-2 = HT-2. The T-2 and HT-2 evidenced the highest cytotoxic effect in HepG2 cells individually. No differences were observed in binary combinations tested and the two mycotoxins in the mixture tested individually. The T-2+HT-2 combination showed the highe…
Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction.
2006
Chalcone isomerase catalyzes the transformation of chalcones to flavanones. We present a computational study of the rate-limiting chemical step, an intramolecular Michael addition of a 2'-oxyanion to the alpha,beta-double bound. By using quantum mechanical/molecular mechanical hybrid methods we traced the free-energy profiles associated with the reaction of two different substrates (chalcone and 6'-deoxychalcone) in two different conformations of the active site that are described in the different crystallographic structures available. We have obtained significant differences (about 4 kcal/mol) in the free-energy barriers calculated for the two active sites. According to our results, the ac…
Prediction of acute toxicity of organophosphorus pesticides using topological indices
2007
Topological indices were used in the prediction of the acute toxicity (intraperitoneal and oral LD(50)) of organophosphorus pesticides on rats. Models with six variables for the prediction of LD(50)-i.p. (r = 0.849, Q(2) = 0.613) and eight variables for LD(50)-oral (r = 0.906, Q(2) = 0.701) were selected. External group and cross-validation by use of leave-n-out tests were also performed in order to assess the stability and the prediction performance of the selected topological models.
Assessment of a single-acquisition imaging sequence for oxygen-sensitive (3)He-MRI.
2001
MRI of the lungs using hyperpolarized helium-3 (3He) allows the determination of intrapulmonary oxygen partial pressures (pO2). The need to separate competing processes of signal loss has hitherto required two different imaging series during two different breathing maneuvers. In this work, a new imaging strategy to measure pO2 by a single series of consecutive scans is presented. The feasibility of the method is demonstrated in three healthy human volunteers. Maps and histograms of intrapulmonary pO2 are calculated. Changes in the oxygen concentration of the inhaled gas mixture are well reproduced in the histograms. Monte Carlo (MC) simulations of the temporal evolution of 3He hyperpolariza…
Quantum chemical simulation of excited states of chlorophylls, bacteriochlorophylls and their complexes
2006
The present review describes the use of quantum chemical methods in estimation of structures and electronic transition energies of photosynthetic pigments in vacuum, in solution and imbedded in proteins. Monomeric Mg-porphyrins, chlorophylls and bacteriochlorophylls and their solvent 1:1 and 1:2 complexes were studied. Calculations were performed for Mg-porphyrin, Mg-chlorin, Mg-bacteriochlorin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), d and bacteriochlorophylls a, b, c, d, e, f, g, h, plus several homologues. Geometries were optimised with PM3, PM3/CISD, PM5, ab initio HF (6-31G*/6-311G**) and density functional B3LYP (6-31G*/6-311G**) methods. Spectroscopic transition energ…
Automatic detection of large dense-core vesicles in secretory cells and statistical analysis of their intracellular distribution.
2010
Analyzing the morphological appearance and the spatial distribution of large dense-core vesicles (granules) in the cell cytoplasm is central to the understanding of regulated exocytosis. This paper is concerned with the automatic detection of granules and the statistical analysis of their spatial locations in different cell groups. We model the locations of granules of a given cell as a realization of a finite spatial point process and the point patterns associated with the cell groups as replicated point patterns of different spatial point processes. First, an algorithm to segment the granules using electron microscopy images is proposed. Second, the relative locations of the granules with…
Combined effect of solvent content, temperature and pH on the chromatographic behaviour of ionisable compounds. III: Considerations about robustness
2009
Abstract We previously reported a model able to predict the retention time of ionisable compounds as a function of the solvent content, temperature and pH [J. Chromatogr. A 1163 (2007) 49]. The model was applied further, developing an optimisation of the resolution based on the peak purity concept [J. Chromatogr. A 1193 (2008) 117]. However, we left aside an important issue: we did not consider incidental overlaps caused by shifts in the predicted peak positions, owing either to uncertainties in the source data, modelling errors, or the practical implementation in the chromatograph of the optimal mobile phase (or any other). These shifts can ruin the predicted separation, since they can eas…
A theoretical plate model accounting for slow kinetics in chromatographic elution.
2011
The chromatographic elution has been studied from different perspectives. However, in spite of the simplicity and evident deficiencies of the plate model proposed by Martin and Synge, it has served as a basis for the characterization of columns up-to-date. This approach envisions the chromatographic column as an arbitrary number of theoretical plates, each of them consisting of identical repeating portions of mobile phase and stationary phase. Solutes partition between both phases, reaching the equilibrium. Mobile phase transference between the theoretical plates is assumed to be infinitesimally stepwise (or continuous), giving rise to the mixing of the solutions in adjacent plates. This yi…