Search results for " Simulation"
showing 10 items of 4034 documents
Dynamics of surface of lipid membranes: theoretical considerations and the ESR experiment.
2016
The effect of the surface layer of model membranes on their physical properties was discussed in this paper. The research involved a physical ESR experiment with the use of spin probes and computer simulation based on the Monte Carlo technique. Liposomes formed during the process of sonication of lecithin were scanned in an ESR spectrometer. The membrane surface layer model, represented by the system of electric dipoles arranged in rectangular or hexagonal matrices, was studied. The final states of computer simulations were presented as textures. It was found that in the gel phase some ordered domain structures are formed, while in the liquid–crystal phase we got complex textures comprising…
Effects of confinement and external fields on structure and transport in colloidal dispersions in reduced dimensionality
2012
In this work, we focus on low-dimensional colloidal model systems, via simulation studies and also some complementary experiments, in order to elucidate the interplay between phase behavior, geometric structures and transport properties. In particular, we try to investigate the (nonlinear!) response of these very soft colloidal systems to various perturbations: uniform and uniaxial pressure, laser fields, shear due to moving boundaries and randomly quenched disorder.We study ordering phenomena on surfaces or in monolayers by Monte Carlo computer simulations of binary hard-disk mixtures, the influence of a substrate being modeled by an external potential. Weak external fields allow a control…
Pressure effects on the vibrational properties of alpha-Bi2O3: an experimental and theoretical study
2014
We report an experimental and theoretical high-pressure study of the vibrational properties of synthetic monoclinic bismuth oxide (alpha-Bi2O3), also known as mineral bismite. The comparison of Raman scattering measurements and theoretical lattice-dynamics ab initio calculations is key to understanding the complex vibrational properties of bismite. On one hand, calculations help in the symmetry assignment of phonons and to discover the phonon interactions taking place in this low-symmetry compound, which shows considerable phonon anticrossings; and, on the other hand, measurements help to validate the accuracy of first-principles calculations relating to this compound. We have also studied …
Organometallic Oligomers Based on Bis(arylacetylide)bis(P-chirogenic phosphine)platinum(II) Complexes: Synthesis and Photonic Properties
2013
A series of P-chirogenic oligomers of the type (-C≡C-aryl-C≡C-PtL2-)n [L = (R)- and (S)-P(Ph)(iPr)(C17H35); aryl = 1,4-benzene, 2,1,3-benzothiadiazole] along the corresponding achiral analogues (L = PBu3) and model complexes PhC≡CPtL2C≡CPh were prepared from the ephedrine strategy and were fully characterized [(1)H, (31)P NMR; IR; small-angle X-ray scattering (SAXS); gel permeation chromatography (GPC); thermal gravimetric analysis (TGA); circular dichroism, UV-vis, and luminescence spectroscopy; photophysics, and degree of anisotropy measurements]. From the CD measurements, the chiral environment of the phosphine ligands is modestly felt by the aryl moieties. Concurrently, the TGA shows th…
Single-layer metal-on-metal islands driven by strong time-dependent forces
2012
Non-linear transport properties of single-layer metal-on-metal islands driven with strong static and time-dependent forces are studied. We apply a semi-empirical lattice model and use master equation and kinetic Monte Carlo simulation methods to compute observables such as the velocity and the diffusion coefficient. Two types of time-dependent driving are considered: a pulsed rotated field and an alternating field with a zero net force (electrophoretic ratchet). Small islands up to 12 atoms were studied in detail with the master equation method and larger ones with simulations. Results are presented mainly for a parametrization of Cu on Cu(001) surface, which has been the main system of int…
Motion, relaxation dynamics, and diffusion processes in two-dimensional colloidal crystals confined between walls
2012
The dynamical behavior of single-component two-dimensional colloidal crystals confined in a slit geometry is studied by Langevin dynamics simulation of a simple model. The colloids are modeled as pointlike particles, interacting with the repulsive part of the Lennard-Jones potential, and the fluid molecules in the colloidal suspension are not explicitly considered. Considering a crystalline strip of triangular lattice structure with n=30 rows, the (one-dimensional) walls confining the strip are chosen as two rigidly fixed crystalline rows at each side, commensurate with the lattice structure and, thus, stabilizing long-range order. The case when the spacing between the walls is incommensura…
2NH and 3OH are crucial structural requirements in sphingomyelin for sticholysin II binding and pore formation in bilayer membranes.
2013
AbstractSticholysin II (StnII) is a pore-forming toxin from the sea anemone Stichodactyla heliantus which belongs to the large actinoporin family. The toxin binds to sphingomyelin (SM) containing membranes, and shows high binding specificity for this lipid. In this study, we have examined the role of the hydrogen bonding groups of the SM long-chain base (i.e., the 2NH and the 3OH) for StnII recognition. We prepared methylated SM-analogs which had reduced hydrogen bonding capability from 2NH and 3OH. Both surface plasmon resonance experiments, and isothermal titration calorimetry measurements indicated that StnII failed to bind to bilayers containing methylated SM-analogs, whereas clear bind…
Flavonoids as noncompetitive inhibitors of Dengue virus NS2B-NS3 protease: Inhibition kinetics and docking studies
2014
NS2B-NS3 is a serine protease of the Dengue virus considered a key target in the search for new antiviral drugs. In this study flavonoids were found to be inhibitors of NS2B-NS3 proteases of the Dengue virus serotypes 2 and 3 with IC50 values ranging from 15 to 44 μM. Agathisflavone (1) and myricetin (4) turned out to be noncompetitive inhibitors of dengue virus serotype 2 NS2B-NS3 protease with Ki values of 11 and 4.7 μM, respectively. Docking studies propose a binding mode of the flavonoids in a specific allosteric binding site of the enzyme. Analysis of biomolecular interactions of quercetin (5) with NT647-NHS-labeled Dengue virus serotype 3 NS2B-NS3 protease by microscale thermophoresis…
Evidence for substrate binding-induced zwitterion formation in the catalytic Cys-His dyad of the SARS-CoV main protease.
2014
The coronavirus main protease (M(pro)) represents an attractive drug target for antiviral therapy of coronavirus (CoV) infections, including severe acute respiratory syndrome (SARS). The SARS-CoV M(pro) and related CoV proteases have several distinct features, such as an uncharged Cys-His catalytic dyad embedded in a chymotrypsin-like protease fold, that clearly separate these enzymes from archetypical cysteine proteases. To further characterize the catalytic system of CoV main proteases and to obtain information about improved inhibitors, we performed comprehensive simulations of the proton-transfer reactions in the SARS-CoV M(pro) active site that lead to the Cys(-)/His(+) zwitterionic st…
Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin.
2012
Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical ‘hot spots’ of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all as…