Search results for "molecular dynamics"
showing 10 items of 1075 documents
Phase coexistence in finite van der Waals systems
1999
Phase coexistence in finite systems obeying van der Waals equation of state is studied by minimizing a model free energy function for a spherical liquid droplet and a gaseous phase around it. Phase diagrams are calculated for finite systems with a large range of sizes. According to this model, the highest temperature where a droplet and vapour can exist in equilibrium decreases as N −0.4, where N is the number of particles in the system. The model predicts higher equilibrium vapour pressures than molecular dynamics simulations.
The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part I: gas phase.
2014
The vibronic spectra of the green fluorescent protein chromophore analogues p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) and 3,5-tert-butyl-HBDI (35Bu) are similar in the vacuum, but very different in water or ethanol. To understand this difference, we have computed the vibrationally resolved solution spectra of these chromophores, using the polarizable continuum model (PCM) to account for solvent effects on the (harmonic) potential energy surfaces (PES). In agreement with experiment, we found that the vibrational progression increases with the polarity of the solvent, but we could neither reproduce the broadening, nor the large difference between the absorption spectra of HBDI and…
A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Rec…
2016
Molecular dynamics (MD) simulations can be used, prior to virtual screening, to add flexibility to proteins and study them in a dynamic way. Furthermore, the use of multiple crystal structures of the same protein containing different co-crystallized ligands can help elucidate the role of the ligand on a protein's active conformation, and then explore the most common interactions between small molecules and the receptor. In this work, we evaluated the contribution of the combined use of MD on crystal structures containing the same protein but different ligands to examine the crucial ligand-protein interactions within the complexes. The study was carried out on peroxisome proliferator-activat…
Aging Effects in a Lennard-Jones Glass
1997
Using molecular dynamics simulations we study the out of equilibrium dynamic correlations in a model glass-forming liquid. The system is quenched from a high temperature to a temperature below its glass transition temperature and the decay of the two-time intermediate scattering function C(t_w,t+t_w) is monitored for several values of the waiting time t_w after the quench. We find that C(t_w,t+t_w) shows a strong dependence on the waiting time, i.e. aging, depends on the temperature before the quench and, similar to the case of spin glasses, can be scaled onto a master curve.
Correction: “On-the-fly” coupled cluster path-integral molecular dynamics: impact of nuclear quantum effects on the protonated water dimer
2015
We present an accelerated ab initio path-integral molecular dynamics technique, where the interatomic forces are calculated “on-the-fly” by accurate coupled cluster electronic structure calculations. In this way not only dynamic electron correlation, but also the harmonic and anharmonic zero-point energy, as well as tunneling effects are explicitly taken into account. This method thus allows for very precise finite temperature quantum molecular dynamics simulations. The predictive power of this novel approach is illustrated on the example of the protonated water dimer, where the impact of nuclear quantum effects on its structure and the 1H magnetic shielding tensor are discussed in detail.
Iron’s Wake: The Performance of Quantum Mechanical-Derived Versus General-Purpose Force Fields Tested on a Luminescent Iron Complex
2020
Recently synthetized iron complexes have achieved long-lived excited states and stabilities which are comparable, or even superior, to their ruthenium analogues, thus representing an eco-friendly and cheaper alternative to those materials based on rare metals. Most of computational tools which could help unravel the origin of this large efficiency rely on ab-initio methods which are not able, however, to capture the nanosecond time scale underlying these photophysical processes and the influence of their realistic environment. Therefore, it exists an urgent need of developing new low-cost, but still accurate enough, computational methodologies capable to deal with the steady-state and trans…
Resonant activation in polymer translocation: new insights into the escape dynamics of molecules driven by an oscillating field
2010
The translocation of molecules across cellular membranes or through synthetic nanopores is strongly affected by thermal fluctuations. In this work we study how the dynamics of a polymer in a noisy environment changes when the translocation process is driven by an oscillating electric field. An improved version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics, by taking into account the harmonic interactions between adjacent monomers and the excluded-volume effect by introducing a Lennard–Jones potential between all beads. A bending recoil torque has also been included in our model. The polymer dynamics is simulated in a two-dimensional domain by num…
Adsorption of hydrogen isotopes in the zeolite NaX: Experiments and simulations
2017
Abstract Among the different methods to separate hydrogen isotopes one is based on the physisorption at low temperature (below 100 K) where quantum effects induce a particular behavior. In the present work, we study the adsorption of single H 2 and D 2 on the zeolite NaX by combining experiments (manometry) from 30 to 150 K and molecular dynamics simulations at 40 and 77 K. Simulations also include the adsorption analysis for T 2 . Adsorption on NaX membranes is simulated and quantum corrections are introduced by using the well-known Feynman–Hibbs approach into the interaction potentials. Experimental adsorption isotherms are reproduced by using the Toth equation and it is shown that the ad…
DISORDERING MECHANISMS OF THE Cu(110) SURFACE
1994
We review recent theoretical work on the various disordering mechanisms of the Cu(110) surface. In these studies the properties of the surface, from the onset of enhanced anharmonicity in surface vibrations up to bulk melting point T M , have been studied using molecular dynamics and lattice-gas Monte Carlo methods with many-body interactions derived from the effective medium theory. Well after the onset of enhanced out-of-plane surface vibrations, clustering of surface defects is found to induce a roughening transition at T≈0.81T M , and surface premelting is found to occur at T≈0.97T M . These results suggest, that these transitions can both appear at Cu(110). The general picture of diso…
Ab initio molecular dynamics studies of Au38(SR)24 isomers under heating
2019
Despite the great success in achieving monodispersity for a great number of monolayer-protected clusters, to date little is known about the dynamics of these ultra-small metal systems, their decomposition mechanisms, and the energy that separates their structural isomers. In this work, we use density functional theory (DFT) to calculate and compare the ground state energy and the Born-Oppenheimer molecular dynamics of two well-known Au 38 (SCH 2 CH 2 Ph) 24 nanocluster isomers. The aim is to shed light on the energy difference between the two clusters isomers and analyze their decomposition mechanisms triggered by high temperatures. The results demonstrate that the energy that separates the…