Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
A molecular dynamics study of structure, stability and fragmentation patterns of sodium bis(2-ethylhexyl)sulfosuccinate positively charged aggregates…
2011
Positively charged supramolecular aggregates formed in vacuo by n AOTNa (sodium bis(2-ethylhexyl)sulfosuccinate) molecules and n(c) additional sodium ions, i.e. [AOT(n)Na(n+n(c))](n(c)), have been investigated by molecular dynamics (MD) simulations for n = 1-20 and n(c) = 0-5. Statistical analysis of physical quantities like gyration radii, atomic B-factors and moment of inertia tensors provides detailed information on their structural and dynamical properties. Even for n(c) = 5, all stable aggregates show a reverse micelle-like structure with an internal solid-like core including sodium counterions and surfactant polar heads surrounded by an external layer consisting of the surfactant alky…
Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs**
2021
Abstract We present the results of classical and QM/MM simulations for the inhibition of SARS‐CoV‐2 3CL protease by a hydroxymethylketone inhibitor, PF‐00835231. In the noncovalent complex the carbonyl oxygen atom of the warhead is placed in the oxyanion hole formed by residues 143 to 145, while P1–P3 groups are accommodated in the active site with interactions similar to those observed for the peptide substrate. According to alchemical free energy calculations, the P1′ hydroxymethyl group also contributes to the binding free energy. Covalent inhibition of the enzyme is triggered by the proton transfer from Cys145 to His41. This step is followed by the nucleophilic attack of the Sγ atom on …
Frictional Forces between Strongly Compressed, Nonentangled Polymer Brushes: Molecular Dynamics Simulations and Scaling Theory
2010
By means of molecular dynamics simulations and scaling theory we study the response of opposing polymer brushes to constant shear motion under good solvent conditions. Model systems that contain explicit solvent molecules (Lennard-Jones dimers) are compared to solvent-free systems while varying of the distance between the grafted layers and their molecular parameters, chain length and grafting density. Our study reveals a power-law dependence of macroscopic transport properties on the Weissenberg number, W, beyond linear response. For instance, we find that the kinetic friction constant scales as μ ∼ W0.57 for large values of W. We develop a scaling theory that describes our data and previo…
A variable charge molecular dynamics study of the initial stage of nickel oxidation
2010
Abstract The oxidation of nickel single crystals is investigated by using variable charge molecular dynamics. The simulations are performed on three nickel low-index surfaces ((1 0 0), (1 1 0) and (1 1 1)) at temperatures between 300 K and 950 K. The results show that the shape of the oxidation kinetics is independent of the crystallographic orientation and the temperature under the present conditions. The oxide thin film grows according to an island growth mode, this initial stage of oxidation can be divided in three steps: (i) the dissociative chemisorption step (ii) the oxide island nucleation and (iii) the lateral growth of the island. The first step is slowdown/speedup by the surface o…
Towards a deeper understanding of the inhibition mechanism of a new 1,2,3-triazole derivative for mild steel corrosion in the hydrochloric acid solut…
2020
Abstract The corrosion inhibition effect of a new synthesized heterocycle 1,2,3-triazole, namely(1-p-tolyl-1H-1,2,3-triazol-4-yl) methanol (TTM) was studied in 1 M hydrochloric acid solution by using both experimental and theoretical techniques. The inhibitory action of the TTM was investigated by potentiodynamic polarization (PDP) at various temperatures (298–333 K). PDP experiments revealed that the TTM behaved as mixed type inhibitor by decreasing both anodic and cathodic corrosion densities. Electrochemical impedance spectroscopy (EIS) measurements confirmed that the studied inhibitor can suppress mild steel corrosion effectively in acidic solution with an inhibition efficiency of 90% a…
Stratification Dynamics in Drying Colloidal Mixtures
2017
Stratification in binary colloidal mixtures was investigated using implicit-solvent molecular dynamics simulations. For large particle size ratios and film Péclet numbers greater than unity, smaller colloids migrated to the top of the film, while big colloids were pushed to the bottom, creating an "inverted" stratification. This peculiar behavior was observed in recent simulations and experiments conducted by Fortini et al. [ Phys. Rev. Lett. 2016 , 116 , 118301 ]. To rationalize this behavior, particle size ratios and drying rates spanning qualitatively different Péclet number regimes were systematically studied, and the dynamics of the inverted stratification were quantified in detail. Th…
Temperature-dependent EXAFS study of the local structure and lattice dynamics in cubic Y2O3
2016
The local structure and lattice dynamics in cubic Y2O3were studied at the YK-edge by X-ray absorption spectroscopy in the temperature range from 300 to 1273 K. The temperature dependence of the extended X-ray absorption fine structure was successfully interpreted using classical molecular dynamics and a novel reverse Monte Carlo method, coupled with the evolutionary algorithm. The obtained results allowed the temperature dependence of the yttria atomic structure to be followed up to ∼6 Å and to validate two force-field models.
Mossbauer spectroscopic studies on the molecular dynamics of organotin(IV) polymers
1981
Abstract Linear organotin(IV) polymers with tin appended to the polymer chain or inserted into the polymer backbone have been characterized by Mossbauer spectroscopy. The lattice dynamics of three representative examples of these classes, as well as of a cross-linked organotin(IV) polymer, have been investigated by temperature-dependent Mossbauer spectroscopy. It has been shown that parameters associated with polymers having low interchain interactions practically correspond to those of molecular, non-coupled, solids.
Spatial correlations of mobility and immobility in a glass-forming Lennard-Jones liquid
1998
Using extensive molecular dynamics simulations of an equilibrium, glass-forming Lennard-Jones mixture, we characterize in detail the local atomic motions. We show that spatial correlations exist among particles undergoing extremely large (``mobile'') or extremely small (``immobile'') displacements over a suitably chosen time interval. The immobile particles form the cores of relatively compact clusters, while the mobile particles move cooperatively and form quasi-one-dimensional, stringlike clusters. The strength and length scale of the correlations between mobile particles are found to grow strongly with decreasing temperature, and the mean cluster size appears to diverge near the mode-cou…
Growing length scales in a supercooled liquid close to an interface
2002
We present the results of molecular dynamics computer simulations of a simple glass former close to an interface between the liquid and the frozen amorphous phase of the same material. By investigating F_s(q,z,t), the incoherent intermediate scattering function for particles that have a distance z from the wall, we show that the relaxation dynamics of the particles close to the wall is much slower than the one for particles far away from the wall. For small z the typical relaxation time for F_s(q,z,t) increases like exp(Delta/(z-z_p)), where Delta and z_p are constants. We use the location of the crossover from this law to the bulk behavior to define a first length scale tilde{z}. A differe…