Search results for "molecular dynamics"

Isomerization and disproportionation of m-xylene in a zeolite with 9- and 10-membered ring pores: Molecular dynamics and catalytic studies

2006

The unique pore topology of zeolite ITQ-13 with 9-membered ring (MR) channels intersected by perpendicular 10-MR channels and larger void space with 10-MR cross-sections was studied for meta-xylene isomerization and disproportionation. Product distribution was interpreted on the basis of pore topology and compared with zeolites with 12-MR (β), 10-MR, and intersecting 12-MR cavities (NU-87), as well as 10-MR (ZSM-5) zeolites. The presence of cavities allows more space for bulky intermediates and/or products and also provides room for molecules to drive consecutive reactions toward thermodynamic equilibrium. Channels, on the other hand, allow diffusion without trapping if their free diameters…

Conformational dynamics of active site loops 5, 6 and 7 of enzyme Triosephosphate Isomerase: A molecular dynamics study

2018

AbstractTriosephosphate Isomerase is a glycolytic enzyme catalyzing the interconversion of Dihydroxyacetone phosphate to Glyceraldehyde-3-phosphate. The active site is comprised of three distinct loops loop-6, loop-7 and loop-8. Based on loop-6 and loop-7 conformation we describe the enzyme as Open TIM and Closed TIM. Various NMR, X-ray crystallography and QM/MM simulation techniques have provided glimpses of individual events of what is essentially a dynamic process. We studied the conformational changes of two distinct loops (loop-6 and loop-7) enveloping the active site, in the presence of natural substrate, reaction intermediates and inhibitor molecules, by means of microsecond atomisti…

Enhanced Acid Dissociation at the Solid/Liquid Interface

2019

In this chapter we review some recent results from first principles molecular dynamics simulations which show how molecular properties, such as proton dissociation, can be influenced upon adsorption at a solid/liquid interface. In particular, we discuss in details the increased acidity of pyruvic acid at the quartz /water interface, which is of relevance for the chemistry of the atmosphere. Our simulations unveil the special role of the microsolvation at interface, as well as the role of the silanols in stabliziing the deprotonated form of the acid. The enhanced acidity at the hydrophilic quartz/water interface is at odd with what typically found at the water/air interface where acidity is …

ChemInform Abstract: Specific Heat of Amorphous Silica within the Harmonic Approximation.

2010

We investigate to what extent the specific heat of amorphous silica can be calculated within the harmonic approximation. For this we use molecular dynamics computer simulations to calculate, for a simple silica model (the BKS potential), the velocity autocorrelation function and hence an effective density of states g(ν). We find that the harmonic approximation is valid for temperatures below 300 K but starts to break down at higher temperatures. We show that, to obtain a reliable description of the low-frequency part of g(ν), i.e., where the boson peak is observed, it is essential to use large systems for the simulations and small cooling rates to quench the samples. We find that the calcul…

Understanding Acid Reaction and Diffusion in Chemically Amplified Photoresists: An Approach at the Molecular Level

2011

Acid diffusion in chemically amplified resist might limit the ultimate minimum half-pitch that can be achieved with high sensitivity resists unless diffusion length is reduced until new methods of sensitizing resists are found. Precise knowledge of molecular dynamics of resist materials and advanced techniques need to be developed actively for this issue. In this sense, computer simulations have become a valuable tool in terms of reducing time and costs. However, simulations are generally based on continuum or mesoscale models, which are unable to accurately predict variations at the molecular level. Deeper understanding and investigation of the coupled reaction-diffusion kinetics at the mo…

Influence of electronic and geometric properties on melting of sodium clusters

2004

Systematics of the melting transition for sodium clusters with 40-355 atoms has been studied with both ab initio and semiclassical molecular dynamics simulations. The melting temperatures obtained with an ab initio method for Na55 + and Na93 + correlate well with the experimental results. The semiclassically determined melting temperatures show similarities with the experimentally determined ones in the size region from 55 to 93 and near size 142, and the latent heat in the size region from 55 to 139, but not elsewhere in the size region studied. This indicates that the nonmonotonical melting behavior observed experimentally cannot be fully explained by geometrical effects. The semiclassica…

Single Particle Jumps in a Binary Lennard-Jones Glass

2002

ABSTRACTWe study a binary Lennard-Jones mixture below the glass transition with molecular dynamics (MD) simulations. To investigate the dynamics of the system we define single particle jumps via their single particle trajectories. We find two kinds of jumps: metastable jumps, where a particle jumps back and forth between two or more states, and real jumps, where a particle does not return to any of its former states. For both the real and metastable jumps we present as a function of temperature the number of jumps, jump size, time between jumps, and energy.

Computer simulations of SiO2 and GeO2

2004

Classical Molecular Dynamics (MD) simulations are used to study structural and dynamic properties of amorphous germania (GeO2) in comparison to those of silica (SiO2). The total structure factor, as obtained from these simulations, is in very good agreement with that of neutron scattering experiments, both for germania and silica. The tetrahedral network structure in silica and germania leads to a prepeak in the structure factor that appears at slightly smaller wavenumbers in GeO2 than in SiO2. At high temperatures the diffusion constants are very similar in both systems whereas at low temperatures diffusion is significantly faster in germania than in silica. We also outline the strategy fo…

Modelling Dislocation Patterns by Molecular Dynamics

1993

Elastic properties of CsCN

1983

The temperature dependence of the elastic constants of CsCN exhibiting the CsCl structure was measured with ultrasonic and neutron techniques. The room temperature values were found to bec11=18.8,c12=10.7 andc44=2.95 1010 dyn/cm2. The sound waves inT2g andEg symmetries exhibit anomalous temperature effects which are similar but definitively weaker than those in the NaCl type cyanides. In addition we measured the acoustic phonon dispersion along [100] and [110]. These results are compared with recent molecular dynamics calculations.