Search results for "molecular dynamics"
showing 10 items of 1075 documents
Linear Dimensions of Adsorbed Semiflexible Polymers: What can be learned about their persistence length?
2019
Conformations of partially or fully adsorbed semiflexible polymer chains are studied varying both contour length $L$, chain stiffness, $\ensuremath{\kappa}$, and the strength of the adsorption potential over a wide range. Molecular dynamics simulations show that partially adsorbed chains (with ``tails,'' surface attached ``trains,'' and ``loops'') are not described by the Kratky-Porod wormlike chain model. The crossover of the persistence length from its three-dimensional value (${\ensuremath{\ell}}_{p}$) to the enhanced value in two dimensions ($2{\ensuremath{\ell}}_{p}$) is analyzed, and excluded volume effects are identified for $L\ensuremath{\gg}{\ensuremath{\ell}}_{p}$. Consequences fo…
Dynamics of Dense Polymers: A Molecular Dynamics Approach
1988
The physics of polymeric materials[1, 2] is one of the most challenging problems in condensed matter physics today. It is a problem of great interest both from a fundamental viewpoint and for their various technical applications. In addition to theortical and experimental approaches, computer simulations[3–11] have played an important role in our present understanding of polymers. For static properties Monte Carlo methods have been widely used and give excellent results for static critical exponents. To investigate dynamic properties three different methods — Monte Carlo (MC)[3–7], molecular dynamics (MD)[8, 9] and Brownian dynamics methods[10] — have been used. Detailed microscopic dynamic…
NOISE EFFECTS IN POLYMER DYNAMICS
2008
The study of the noise induced effects on the dynamics of a chain molecule crossing a potential barrier, in the presence of a metastable state, is presented. A two-dimensional stochastic version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics and to take into account the interactions between adjacent monomers. We obtain a nonmonotonic behavior of the mean first passage time and its standard deviation, of the polymer centre of inertia, with the noise intensity. These findings reveal a noise induced effect on the mean crossing time. The role of the polymer length is also investigated.
Probing ultrafast thermalization with field-free molecular alignment
2012
International audience; The rotation-translation thermalization of CO2 gas is investigated 500 ps after its preheating by a nonresonant short and intense laser pulse. The temperature of thermalization is optically determined with two additional short laser pulses enabling a field-free molecular alignment process and its probing, respectively. The measurements are performed for various intensities of the preheat pulse, leading to the observation of different temperatures which are in very good agreement with classical molecular dynamics simulations. The results can be regarded as a step towards real-time tracking of ultrafast relaxation pathways in molecular motion.
Coherent Light Harvesting through Strong Coupling to Confined Light
2018
When photoactive molecules interact strongly with confined light modes, new hybrid light–matter states may form: the polaritons. These polaritons are coherent superpositions of excitations of the molecules and of the cavity photon. Recently, polaritons were shown to mediate energy transfer between chromophores at distances beyond the Forster limit. Here we explore the potential of strong coupling for light-harvesting applications by means of atomistic molecular dynamics simulations of mixtures of photoreactive and non-photo-reactive molecules strongly coupled to a single confined light mode. These molecules are spatially separated and present at different concentrations. Our simulations sug…
Molecular correlation functions for uniaxial ellipsoids in the isotropic state
2006
We perform event-driven molecular dynamics simulations of a system composed by uniaxial hard ellipsoids for different values of the aspect-ratio and packing fraction . We compare the molecular orientational-dependent structure factors previously calculated within the Percus-Yevick approximation with the numerical results. The agreement between theoretical and numerical results is rather satisfactory. We also show that, for specific orientational quantities, the molecular structure factors are sensitive to the particle shape and can be used to distinguish prolate from oblate ellipsoids. A first-order theoretical expansion around the spherical shape and a geometrical analysis of the configura…
Event-Driven Simulation of the Dynamics of Hard Ellipsoids
2008
We introduce a novel algorithm to perform event-driven simulations of hard rigid bodies of arbitrary shape, that relies on the evaluation of the geometric distance. In the case of a monodisperse system of uniaxial hard ellipsoids,we perform molecular dynamics simulations varying the aspect-ratio X0 and the packing fraction phi. We evaluate the translational Dtrans and the rotational Drot diffusion coefficient and the associated isodiffusivity lines in the phi-X0 plane. We observe a decoupling of the translational and rotational dynamics which generates an almost perpendicular crossing of the Dtrans and Drot isodiffusivity lines. While the self intermediate scattering function exhibits stret…
Influence of Confining Walls on the Dynamics of Supercooled Simple Liquids
2003
The relaxation dynamics of supercooled liquids in the bulk shows many features that are not seen in the dynamics of liquids at elevated temperatures, such as a very slow decay of the time-correlation functions, stretching, etc. The dynamics of liquids that are close to a surface (free space, confining wall, etc.) is even more complex in that the stretching is increased and in that there is evidence for the presence of multiple time scales. In this paper we review some results of recent molecular dynamics computer simulations in which we investigated the dynamics of a simple glass forming liquid in the vicinity of a wall. Two types of walls axe studied: A rough one and a smooth one. We find …
Molecular dynamics study of phase separation kinetics in thin films.
2005
We use molecular dynamics to simulate experiments where a symmetric binary fluid mixture (AB), confined between walls that preferentially attract one component (A), is quenched from the one-phase region into the miscibility gap. Surface enrichment occurs during the early stages, yielding a B-rich mixture in the film center with well-defined A-rich droplets. The droplet size grows with time as l(t) proportional t(2/3) after a transient regime. The present atomistic model is also compared to mesoscopic coarse-grained models for this problem.
The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
2015
Fibrinogen is a serum multi-chain protein which, when activated, aggregates to form fibrin, one of the main components of a blood clot. Fibrinolysis controls blood clot dissolution through the action of the enzyme plasmin, which cleaves fibrin at specific locations. Although the main biochemical factors involved in fibrin formation and lysis have been identified, a clear mechanistic picture of how these processes take place is not available yet. This picture would be instrumental, for example, for the design of improved thrombolytic or anti-haemorrhagic strategies, as well as, materials with improved biocompatibility. Here, we present extensive molecular dynamics simulations of fibrinogen w…