Search results for "MD simulation"

Design and computer simulations of 2D MeX2 solid-state nanopores for DNA and protein detection analysis

2020

Solid-state nanopores (SSN) have emerged as versatile devices for biomolecule analysis. One of the most promising applications of SSN is DNA and protein sequencing, at a low cost and faster than the current standard methods. SSN sequencing is based on the measurement of ionic current variations when a biomolecule embedded in electrolyte is driven through a nanopore under an applied electric potential. As a biomolecule translocates through the nanopore, it occupies the pore volume and blocks the passage of ions. Hence, ultrafast monitoring of ionic flow during the passage of a biomolecule yields information about its structure and chemical properties. The size of the sensing region in SSN is…

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 …

Three-dimensional solvation structure of ethanol on carbonate minerals

2020

Calcite and magnesite are important mineral constituents of the earth’s crust. In aqueous environments, these carbonates typically expose their most stable cleavage plane, the (10.4) surface. It is known that these surfaces interact with a large variety of organic molecules, which can result in surface restructuring. This process is decisive for the formation of biominerals. With the development of 3D atomic force microscopy (AFM) it is now possible to image solid–liquid interfaces with unprecedented molecular resolution. However, the majority of 3D AFM studies have been focused on the arrangement of water at carbonate surfaces. Here, we present an analysis of the assembly of ethanol – an o…

H2 hitting on graphene supported palladium cluster: molecular dynamics simulations

2016

Dissociative adsorption of impinging gas-phase molecular hydrogen (H2) on a palladium cluster (Pd4) supported on defective graphene (C47) was studied by periodic density functional theory molecular dynamics simulations. The H2 on Pd4/C47 collision dynamics were investigated without any particular constraint, except for the Born–Oppenheimer approximation. The study, which had mostly method-testing aims, provided, anyway, valuable information about the collision kinetics of gas-phase molecular hydrogen. This was treated as an impacting projectile having different kinetic energy values. At lower kinetic energies, sticking was ruled by steering effects imputable to the Pd cluster that easily re…

Exploring the dynamics of AChBP unbound and bound to the Lobeline partial agonist

2012

Elucidating the catalytic reaction mechanism of orotate phosphoribosyltransferase by means of X-ray crystallography and computational simulations

2020

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Poly-sarcosine and poly(ethylene-glycol) interactions with proteins investigated using molecular dynamics simulations

2018

Nanoparticles coated with hydrophilic polymers often show a reduction in unspecific interactions with the biological environment, which improves their biocompatibility. The molecular determinants of this reduction are not very well understood yet, and their knowledge may help improving nanoparticle design. Here we address, using molecular dynamics simulations, the interactions of human serum albumin, the most abundant serum protein, with two promising hydrophilic polymers used for the coating of therapeutic nanoparticles, poly(ethylene-glycol) and poly-sarcosine. By simulating the protein immersed in a polymer-water mixture, we show that the two polymers have a very similar affinity for the…