Search results for "Molecular Dynamic"

Concurrent molecular dynamics simulation of spinodal phase transition on transputer arrays

1990

Abstract We describe a concurrent implementation on cost-effective transputer arrays of a molecular dynamics program to efficiently simulate physical systems consisting of thousands of mobile particles with an interaction range much shorter than the system dimensions. This program, which uses a geometric decomposition strategy and includes a distributed dynamic load balancer, has been extensively tested by simulating the two-dimensional spinodal phase separation of a large Lennard-Jones system.

Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry.

2017

When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control. However, designing cavity parameters to control chemistry requires a theoretical model wi…

Resolving the Benzophenone DNA-Photosensitization Mechanism at QM/MM Level

2015

International audience; Benzophenone, the parent of the diarylketone family, is a versatile compound commonly used as a UV blocker. It may also trigger triplet-based DNA photosensitization. Therefore, benzophenone is involved in DNA photodamage induction. In the absence of experimentally resolved structure, the mechanism of DNA damage production remains elusive. Employing a hybrid quantum mechanics/molecular mechanics approach, here we address the spin transfer mechanism between this drug and proximal thymine, that is, the DNA nucleobase most prone to suffer triplet damages.

Stringlike Cooperative Motion in a Supercooled Liquid

1998

Extensive molecular dynamics simulations are performed on a glass-forming Lennard-Jones mixture to determine the nature of the cooperative motions occurring in this model fragile liquid. We observe stringlike cooperative molecular motion (``strings'') at temperatures well above the glass transition. The mean length of the strings increases upon cooling, and the string length distribution is found to be nearly exponential.

Strategies for efficient field-free molecular alignment and its control

2008

Strategies using shaped laser fields to produce and control efficient field-free alignment are analyzed and compared. It is in particular shown that the strategy recently proposed using a shaped laser field combining an adiabatic ramp with a kick is superior to the bipulse strategy.

Multiconfigurational Quantum Chemistry Determinations of Absorption Cross Sections (σ) in the Gas Phase and Molar Extinction Coefficients (ε) in Aque…

2021

Theoretical determinations of absorption cross sections (σ) in the gas phase and molar extinction coefficients (e) in condensed phases (water solution, interfaces or surfaces, protein or nucleic acids embeddings, etc.) are of interest when rates of photochemical processes, J = ∫ ϕ(λ) σ(λ) I(λ) dλ, are needed, where ϕ(λ) and I(λ) are the quantum yield of the process and the irradiance of the light source, respectively, as functions of the wavelength λ. Efficient computational strategies based on single-reference quantum-chemistry methods have been developed enabling determinations of line shapes or, in some cases, achieving rovibrational resolution. Developments are however lacking for stron…

2020

Organisms use photo-receptors to react to light. The first step is usually the absorption of a photon by a prosthetic group embedded inside the photo-receptor, often a conjugated chromophore. The electronic changes in the chromophore induced by photo-absorption can trigger a cascade of structural or chemical transformations that culminate into a response to light. Understanding how these proteins have evolved to mediate their activation process has remained challenging because the required time and spacial resolutions are notoriously difficult to achieve experimentally. Therefore, mechanistic insights into photoreceptor activation have been predominantly obtained with computer simulations. …

Ionization potential of Al6 and Al7 as a function of temperature

1999

The temperature-depence of the ionization potential of Al6 and Al7 clusters is studied by using ab initio molecular dynamics. The threshold regions of theoretical photoionization efficiency curves are obtained from the calculated ionization potential distributions by integration and the determined ionization potentials are compared with the experimental ones. Two important effects, which complicate the determination of ionization potential from photoionization efficiency curves, are observed: the thermal tail effect and the isomerization. Also a link between the adiabatic ionization potential and the threshold of the photoionization efficiency curve is discussed. In the case of Al7, this of…

Flux expressions and NEMD perturbations for models of semi-flexible molecules

2001

We derive energy and momentum flux expressions, for systems composed of a general class of semi-flexible molecules, in the Ciccotti-Ferrario-Ryckaert linear constraint formalism. According to this formalism, the whole set of Cartesian coordinates is divided into basic (independent) and secondary (dependent) subsets. It is found that energy and momentum flux vectors have a simple and general expression using both basic and secondary coordinates. In the case of non-equilibrium molecular dynamics, we give general and simple heat and shear flow algorithms, deriving the dissipative fluxes in the space of all Cartesian coordinates. In comparison with previous derivations for some models of flexib…

Transition state ensemble optimization for reactions of arbitrary complexity.

2015

In the present work, we use Variational Transition State Theory (VTST) to develop a practical method for transition state ensemble optimization by looking for an optimal hyperplanar dividing surface in a space of meaningful trial collective variables. These might be interatomic distances, angles, electrostatic potentials, etc. Restrained molecular dynamics simulations are used to obtain on-the-fly estimates of ensemble averages that guide the variations of the hyperplane maximizing the transmission coefficient. A central result of our work is an expression that quantitatively estimates the importance of the coordinates used for the localization of the transition state ensemble. Starting fro…