Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Sticking Probability on Zeolites
2006
The sticking coefficient, i.e., the probability that, on hitting the surface of a nanoporous particle (zeolite), a molecule shall be able to enter the intracrystalline space, is a key quantity for the application of such materials in heterogeneous catalysis and molecular sieving. On the basis of pulsed field gradient NMR diffusion measurements and molecular dynamics simulations, typical values of this probability are found to be close to one. They exceed previous estimates on the basis of IR uptake measurements by many orders of magnitude.
Physics of the nuclear pore complex: Theory, modeling and experiment
2021
Abstract The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular “nanomachine” known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the…
Structure and dynamics of amphiphilic Janus spheres and spherocylinders under shear.
2019
We study the structure formation and flow properties of colloidal dispersions comprised of Janus spheres, Janus spherocylinders, and their mixtures, using hybrid molecular dynamics simulations that take into account hydrodynamic interactions. We systematically vary the Janus balance and the shape anisotropy of the particles, and explore a range of colloid volume fractions in the liquid regime of the phase diagram. At rest, Janus spheres with small hydrophobic patches form spherical micelles for all investigated colloid concentrations. In contrast, Janus spheres with an entirely hydrophobic hemisphere aggregate to larger worm-like micelles and network-like structures. Janus spherocylinders e…
Hypoxia-Selective Dissociation Mechanism of a Nitroimidazole Nucleoside in a DNA Environment
2019
Photodynamic therapy is a promising approach to treat a variety of superficial tumors and other diseases. One of its major limitations arises from its dependence on molecular oxygen, which decreases the efficiency of the therapy in hypoxia conditions commonly developed by solid tumors. The present contribution reveals the molecular mechanism of a modified thymine bearing a nitroimidazole substituent, a photosensitizer able to produce highly harmful interstrand cross-links in the DNA double strand after irradiation selectively in absence of oxygen. The mechanism is resolved at a fully atomistic and electronic level relying on quantum mechanics (CASPT2, coupled-cluster, DFT, and TD-DFT method…
A comparative study of carboxy myoglobin in saccharide-water systems by molecular dynamics simulation.
2007
Results from room-temperature molecular dynamics simulation on a system containing carboxy-myoglobin, water, and maltose molecules are reported. Protein atomic fluctuations, protein−solvent and solvent−solvent hydrogen bonding have been analyzed and compared to the ones in trehalose−water and sucrose−water systems (Proteins 2005, 59, 291−302). Results help in rationalizing, at a molecular level, the effects of homologues disaccharides on protein structure/dynamics experimentally observed. Furthermore, the effectiveness of disaccharides in bioprotection in terms of peculiar protein−matrix coupling is also discussed.
In Silico Design, Synthesis and Biological Evaluation of Anticancer Arylsulfonamide Endowed with Anti-Telomerase Activity
2022
Telomerase, a reverse transcriptase enzyme involved in DNA synthesis, has a tangible role in tumor progression. Several studies have evidenced telomerase as a promising target for developing cancer therapeutics. The main reason is due to the overexpression of telomerase in cancer cells (85–90%) compared with normal cells where it is almost unexpressed. In this paper, we used a structure-based approach to design potential inhibitors of the telomerase active site. The MYSHAPE (Molecular dYnamics SHared PharmacophorE) approach and docking were used to screen an in-house library of 126 arylsulfonamide derivatives. Promising compounds were synthesized using classical and green methods. Com…
Computer simulation of disordering and premelting of low-index faces of copper.
1992
Molecular dynamics and the effective-medium theory have been applied to investigate the structure and dynamics of (110), (100), and (111) faces of copper in the whole temperature range from 0 K up to the bulk melting point, which has been determined to be 1240\ifmmode\pm\else\textpm\fi{}25 K. The observed order in the surface stability follows the order in the packing density. (110) disorders first via anharmonic effects (up to 700 K), then by vacancy-adatom formation and finally by premelting of the surface at about 1200 K. The (110) solid-melt interface is anisotropic and broadened, having a tendency to form small fluctuating (111) facets in equilibrium, which is suggested to be the atomi…
A molecular dynamics simulation study of the alpha-relaxation in a 1,4-polybutadiene melt as probed by the coherent dynamic structure factor.
2004
The dynamic coherent structure factor Scoh(q,t) for a 1,4-polybutadiene (PBD) melt has been investigated using atomistic molecular dynamics simulations. The relaxation of Scoh(q,t) at q = 1.44 angstroms(-1) and q = 2.72 angstroms(-1), corresponding to the first and second peaks in the static structure factor for PBD, was studied in detail over a wide range of temperature. It was found that time-temperature superposition holds for the alpha-relaxation for both q values over a wide temperature range and that the alpha-relaxation can be well described by a stretched (Kohlrauch-William-Watts) exponential with temperature independent but q dependent amplitude and stretching exponent. The alpha-r…
A Stereochemically Driven Supramolecular Polymerisation
2018
Anthracyclines self-assemble in water into dimers. In the presence of sufficiently high salt (NaCl) concentrations, solutions of the antibiotic doxorubicin, but not those of the closely related molecules daunomycin and epirubicin, turn into gels barely compatible with the presence of small oligomers. The use of spectroscopic, scattering, imaging and computational techniques, allowed light to be shed on the self-assembly process that triggered doxorubicin gelification. A complex picture emerged, with doxorubicin molecules assembled into long, highly chiral, supramolecular aggregates made of hundreds of units, showing redshifted fluorescence spectra, very short fluorescence lifetimes and smal…
On the use of reduced active space in CASSCF calculations
2014
Abstract The complete active space self-consistent field (CASSCF) method is one of the most used approaches to explore theoretically non-adiabatic photochemical processes in medium-size molecular systems. It is also frequently utilized in direct dynamics studies because this method offers a reliable description of the electronic state mixing in the regions of surface crossings (conical intersections). In this context, however, the large computational demand required to perform such on-the-fly molecular dynamics simulations using CASSCF as the electronic structure method means that only relatively small active space can be handled (typically not more than 10 electrons distributed in 10 orbit…