Search results for "Simulation."

Does glycosyl transfer involve an oxacarbenium intermediate? Computational simulation of the lifetime of the methoxymethyl cation in water

2011

2D free-energy surfaces for transfer of the methoxymethyl cation between two water molecules are constructed from molecular dynamics (MD) simulations in which these atoms are treated quantum-mechanically within a box of 1030 classical solvent water molecules at 300 K. This provides a simple model for glycosyl transfer in water. The AM1/TIP3P surfaces with 2D-spline corrections at either MPWB1K/6-31+G(d,p) or MP2/6-31+G(d,p) contain a shallow free-energy well corresponding to an oxacarbenium ion intermediate in a DN*AN mechanism. MD analysis at three temperatures leads to a classical estimate of the lifetime of the methoxymethyl cation in water; when quantum corrections for vibrational zero-…

Erratum: “Computing absolute free energies of disordered structures by molecular simulation” [J. Chem. Phys. 131, 231102 (2009)]

2011

Solute-induced Water Structure: Computer Simulation on a Model System

1988

Abstract Two series of Monte Carlo simulations have been carried out on a system consisting of 125 water molecules, one of which is kept fixed to simulate a water molecule whose mobility is restricted by a solute. The results are checked against similar simulations without restrictions, used as a control, and they show how the blocked molecule helps increase both the structural order and the connectivity of the hydrogen bond network. Cooperativity originating from proton polarizability of H-bonds and/or from many-body terms of interaction potentials cannot be involved since we use a rigid water model and ab initio pair potentials. The present findings are interpreted as indicative of a moti…

Study of percolation and clustering in supercritical water-CO2 mixtures

2008

The microscopic structure of supercritical water-CO(2) mixture is investigated by neutron diffraction experiments exploiting the isotopic HD substitution. The investigated water reach mixtures are in the liquidlike region of the phase diagram, according to the behavior of the radial distribution functions, yet a reduction of the average number of hydrogen bonds, compared to equivalent states of pure water, is found. As a consequence, the average dimension of water clusters is reduced and the system stays below the percolation threshold. These results, along with the shift of the main peaks of the site-site radial distribution functions, suggest that the excess volume in these supercritical …

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…

Direct Evidence of the Amino Acid Side Chain and Backbone Contributions to Protein Anharmonicity

2010

Elastic incoherent neutron scattering has been used to study the temperature dependence of the mean-square displacements of nonexchangeable hydrogen atoms in powders of a series of homomeric polypeptides (polyglycine, polyalanine, polyphenylalanine and polyisoleucine) in comparison with myoglobin at the same hydration level (h = 0.2). The aim of the work was to measure the dynamic behavior of different amino acid residues separately and assess the contribution of each type of side chain to the anharmonic dynamics of proteins. The results provide direct experimental evidence that the first anharmonic activation, at approximately 150 K, is largely due to methyl group rotations entering the ti…

Sensitivity of the Cherenkov Telescope Array to a dark matter signal from the Galactic centre

2021

Full list of authors: Acharyya, A.; Adam, R.; Adams, C.; Agudo, I.; Aguirre-Santaella, A.; Alfaro, R.; Alfaro, J.; Alispach, C.; Aloisio, R.; Alves Batista, R.; Amati, L.; Ambrosi, G.; Angüner, E. O.; Antonelli, L. A.; Aramo, C.; Araudo, A.; Armstrong, T.; Arqueros, F.; Asano, K.; Ascasíbar, Y. Ashley, M.; Balazs, C.; Ballester, O.; Baquero Larriva, A.; Barbosa Martins, V.; Barkov, M.; Barres de Almeida, U.; Barrio, J. A.; Bastieri, D.; Becerra, J.; Beck, G.; Becker Tjus, J.; Benbow, W.; Benito, M.; Berge, D.; Bernardini, E.; Bernlöhr, K.; Berti, A.; Bertucci, B.; Beshley, V.; Biasuzzi, B.; Biland, A.; Bissaldi, E.; Biteau, J.; Blanch, O.; Blazek, J.; Bocchino, F.; Boisson, C.; Bonneau Arbe…

Dynamics and risk assessment of pesticides in cucumber through field experiments and model simulation

2020

Abstract Pesticides are often applied multiple times during cucumber cultivation in China. In order to obtain the residue concentrations and subsequently human health risk assessment after pesticide multiple applications, plenty of field trials have been conducted, consuming a lot of labor force and funds. The application of kinetic models can address this problem to some extent by predicting the residue values of pesticides in cucumber. In this study, a dynamic model (dynamiCROP) was applied in combination with field experiments to investigate the distribution, translocation, and dissipation after the one-time application of seven pesticides in a cucumber-soil environment. Moreover, the re…

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…

Dynamics of Two Picophytoplankton Groups in Mediterranean Sea: Analysis of the Deep Chlorophyll Maximum by a Stochastic Advection-Reaction-Diffusion …

2013

A stochastic advection-reaction-diffusion model with terms of multiplicative white Gaussian noise, valid for weakly mixed waters, is studied to obtain the vertical stationary spatial distributions of two groups of picophytoplankton, i.e., picoeukaryotes and Prochlorococcus, which account about for 60% of total chlorophyll on average in Mediterranean Sea. By numerically solving the equations of the model, we analyze the one-dimensional spatio-temporal dynamics of the total picophytoplankton biomass and nutrient concentration along the water column at different depths. In particular, we integrate the equations over a time interval long enough, obtaining the steady spatial distributions for th…