Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Predicting Skin Permeability by Means of Computational Approaches: Reliability and Caveats in Pharmaceutical Studies
2019
The skin is the main barrier between the internal body environment and the external one. The characteristics of this barrier and its properties are able to modify and affect drug delivery and chemical toxicity parameters. Therefore, it is not surprising that permeability of many different compounds has been measured through several in vitro and in vivo techniques. Moreover, many different in silico approaches have been used to identify the correlation between the structure of the permeants and their permeability, to reproduce the skin behavior, and to predict the ability of specific chemicals to permeate this barrier. A significant number of issues, like interlaboratory variability, experim…
Measurement of branching fractions and charge asymmetries for exclusive B decays to charmonium
2005
We report measurements of branching fractions and charge asymmetries of exclusive decays of neutral and charged B mesons into two-body final states containing a charmonium state and a light strange meson. The charmonium mesons considered are J/Psi, Psi(2S) and Chi_c1, and the light meson is either K or K*. We use a sample of about 124 million BBbar events collected with the BABAR detector at the PEP-II storage ring at the Stanford Linear Accelerator Center.
Study of the different polymorphs of alumina and transitional phases appearing in the first oxidation stage of aluminium : simulation at the atomic s…
2014
The goal of this work is to develop a new SMTB-Q potential in order to study the early stages of the oxidation of aluminium by molecular dynamics (MD).Our potential is able to model different alumina polymorphs as well as transitions from the amorphous state to a crystalline phase. Our approach couples a covalent term with the charge. It uses Rapp_ and Goddard scheme for the electrostatic part and the model of alternating network developed by C. Noguera for the covalent part.The SMTB-Q potential was validated with a Monte Carlo approach. This study shows that the potential SMTB-Q gives satisfactory results for the Al-O bonding in different atomic configurations. The bonding results from the…
On the origin of controlled anisotropic growth of monodisperse gold nanobipyramids
2021
We elucidate the crucial role of the cetyl trimethylammonium bromide (CTAB) surfactant in the anisotropic growth mechanism of gold nano-bipyramids, nano-objects with remarkable optical properties and high tunability. Atomistic molecular dynamics simulations predict different surface coverages of the CTAB (positively charged) heads and their (bromide) counterions as function of the gold exposed surfaces. High concentration of CTAB surfactant promotes formation of gold nanograins in solution that work as precursors for the smooth anisotropic growth of more elongated nano-bipyramidal objects. Nanobipyramids feature higher index facets with respect to nanorods, allowing higher CTAB coverages th…
Structure of the 5′ untranslated region in SARS-CoV-2 genome and its specific recognition by innate immune systemviathe human oligoadenylate synthase…
2022
2′-5′-Oligoadenylate synthetase 1 (OAS1) is one of the key enzymes driving the innate immune system response to SARS-CoV-2 infection whose activity has been related to COVID-19 severity. OAS1 is a sensor of endogenous RNA that triggers the 2′-5′-oligoadenylate/RNase L pathway. Upon SARS-CoV-2 infection, OAS1 is responsible for the recognition of viral RNA and has been shown to possess a particularly high sensitivity for the 5′-untranslated (5′-UTR) RNA region, which is organized in a double-strand stem loop motif (SL1). Here we report the structure of the SL1/OAS1 complex also rationalizing the high affinity for OAS1.
Micelles, Rods, Liposomes, and Other Supramolecular Surfactant Aggregates: Computational Approaches
2017
Surfactants are an interesting class of compounds characterized by the segregation of polar and apolar domains in the same molecule. This peculiarity makes possible a whole series of microscopic and macroscopic effects. Among their features, their ability to segregate particles (fluids or entire domains) and to reduce the surface/interfacial tension is the utmost important. The interest in the chemistry of surfactants never weakened; instead, waves of increasing interest have occurred every time a new field of application of these molecules has been discovered. All these special characteristics depend largely on the ability of surfactants to self-assemble and constitute supramolecular struc…
Effect of ion exchange capacity and water uptake on hydroxide transport in PSU-TMA membranes: A DFT and molecular dynamics study
2020
Abstract Anion Exchange Membranes (AEMs) are nowadays used in a very wide range of different applications, from electrodialytic systems for water treatment, to Fuel Cells for energy generation. In many of these cases, the AEM is in contact with water molecules, either in aqueous or gas phase, which can strongly interact with the AEM polymer, thus affecting membrane properties. The role of water in fully swollen AEM and its effect on the diffusion of hydroxide is the focus of this work. Density Functional Theory (DFT) based calculations were merged with Molecular Dynamics (MD) simulations coming to a more accurate description of the ionic exchange capacity effect on the hydroxide ion diffusi…
Rational design of allosteric modulators of the aromatase enzyme: An unprecedented therapeutic strategy to fight breast cancer.
2019
Estrogens play a key role in cellular proliferation of estrogen-receptor-positive (ER+) breast cancers (BCs). Suppression of estrogen production by competitive inhibitors of the enzyme aromatase (AIs) is currently one of the most effective therapies against ER + BC. Yet, the development of acquired resistance, after prolonged treatments with AIs, represents a clinical major concern. Serendipitous findings indicate that aromatase may be non-competitively inhibited by clinically employed drugs and/or industrial chemicals. Here, by performing in silico screening on two putative allosteric sites, molecular dynamics and free energy simulations, supported by enzymatic and cell-based assays, we id…
Ionization and Dissociation Dynamic of H2 Molecule Driven by a Laser Field
2007
We study the single and double ionization yields and the dissociation dynamics of a onedimensional two-electron molecule exposed to an intense laser pulse. The double ionization yields are systematically investigated for both fixed and moveable nuclei. At low intensities the ionization curves have a power law shape, followed by a knee profile for higher intensities. A temporal correlation between the nuclear motion and the electron ionization shows that the nuclear motion deeply affects the ionization yield.
Quantitative Analysis of the Interactions of Metal Complexes and Amphiphilic Systems: Calorimetric, Spectroscopic and Theoretical Aspects.
2022
Metals and metal-based compounds have many implications in biological systems. They are involved in cellular functions, employed in the formation of metal-based drugs and present as pollutants in aqueous systems, with toxic effects for living organisms. Amphiphilic molecules also play important roles in the above bio-related fields as models of membranes, nanocarriers for drug delivery and bioremediating agents. Despite the interest in complex systems involving both metal species and surfactant aggregates, there is still insufficient knowledge regarding the quantitative aspects at the basis of their binding interactions, which are crucial for extensive comprehension of their behavior in sol…