Search results for "molecular dynamics"
showing 10 items of 1075 documents
Molecular mode-coupling theory for supercooled liquids: application to water.
1999
We present mode-coupling equations for the description of the slow dynamics observed in supercooled molecular liquids close to the glass transition. The mode-coupling theory (MCT) originally formulated to study the slow relaxation in simple atomic liquids, and then extended to the analysis of liquids composed by linear molecules, is here generalized to systems of arbitrarily shaped, rigid molecules. We compare the predictions of the theory for the $q$-vector dependence of the molecular nonergodicity parameters, calculated by solving numerically the molecular MCT equations in two different approximation schemes, with ``exact'' results calculated from a molecular dynamics simulation of superc…
Sum Frequency Generation Spectra from Velocity–Velocity Correlation Functions
2017
We developed an expression for the calculation of the sum frequency generation spectra (SFG) of water interfaces that is based on the projection of the atomic velocities on the local normal modes. Our approach permits one to obtain the SFG signal from suitable velocity-velocity correlation functions, reducing the computational cost to that of the accumulation of a molecular dynamics trajectory, and therefore cutting the overhead costs associated with the explicit calculation of the dipole moment and polarizability tensor. Our method permits to interpret the peaks in the spectrum in terms of local modes, also including the bending region. The results for the water-air interface, obtained usi…
Simple Microscopic Theory of Amontons' Laws for Static Friction
2001
A microscopic theory for the ubiquitous phenomenon of static friction is presented. Interactions between two surfaces are modeled by an energy penalty that increases exponentially with the degree of surface overlap. The resulting static friction is proportional to load, in accordance with Amontons' laws. However the friction coefficient between bare surfaces vanishes as the area of individual contacts grows, except in the rare case of commensurate surfaces. An area independent friction coefficient is obtained for any surface geometry when an adsorbed layer of mobile atoms is introduced between the surfaces. The predictions from our simple analytic model are confirmed by atomistically detail…
Simulation of surface-controlled phase separation in slit pores: Diffusive Ginzburg-Landau kinetics versus Molecular Dynamics
2008
The phase separation kinetics of binary fluids in constrained geometry is a challenge for computer simulation, since nontrivial structure formation occurs extending from the atomic scale up to mesoscopic scales, and a very large range of time needs to be considered. One line of attack to this problem is to try nevertheless standard Molecular Dynamics (MD), another approach is to coarse-grain the model to apply a time-dependent nonlinear Ginzburg–Landau equation that is numerically integrated. For a symmetric binary mixture confined between two parallel walls that prefer one species, both approaches are applied and compared to each other. There occurs a nontrivial interplay between the forma…
Memory expansion for diffusion coefficients
1998
We present a memory expansion for macroscopic transport coefficients such as the collective and tracer diffusion coefficients ${D}_{C}$ and ${D}_{T},$ respectively. The successive terms in this expansion for ${D}_{C}$ describe rapidly decaying memory effects of the center-of-mass motion, leading to fast convergence when evaluated numerically. For ${D}_{T},$ one obtains an expansion of similar form that contains terms describing memory effects in single-particle motion. As an example we evaluate ${D}_{C}$ and ${D}_{T}$ for three strongly interacting surface systems through Monte Carlo simulations, and for a simple model diffusion system via molecular dynamics calculations. We show that the n…
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge
2014
Ewald summation, which has become the de facto standard for computing electrostatic interactions in biomolecular simulations, formally requires that the simulation box is neutral. For non-neutral systems the Ewald algorithm implicitly introduces a uniform background charge distribution that e ectively neutralizes the simulation box. Because a uniform distribution of counter charges typically deviates from the spatial distribution of counterions in real systems, artifacts may arise, in particular in systems with an inhomogeneous dielectric constant. Here we derive an analytical expression for the e ect of using an implicit background charge instead of explicit counterions, on the chemical po…
Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase
2018
The origin of the catalytic power of enzymes has been a question of debate for a long time. In this regard, the possible contribution of protein dynamics in enzymatic catalysis has become one of the most controversial topics. In the present work, the hydride transfer step in the formate dehydrogenase (FDH EC 1.2.1.2) enzyme is studied by means of molecular dynamic (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials in order to explore any correlation between dynamics, tunnelling effects and the rate constant. The temperature dependence of the kinetic isotope effects (KIEs), which is one of the few tests that can be studied by experiments and simulations to shed li…
Linear-scaling self-consistent field theory based molecular dynamics: application to C60buckyballs colliding with graphite
2018
In this work, we investigate the collision of a C fullerene with graphite using large-scale molecular dynamics simulations, where the interatomic forces are computed ‘on-the-fly’ by means of self-c...
LATTICE–BOLTZMANN SIMULATION OF DENSE NANOFLOWS: A COMPARISON WITH MOLECULAR DYNAMICS AND NAVIER–STOKES SOLUTIONS
2007
In a recent work, a dense fluid flow across a nanoscopic thin plate was simulated by means of Molecular Dynamics (MD) and Lattice Boltzmann (LB) methods. It was found that in order to recover quantitative agreement with MD results, the LB simulation must be pushed down to sub–nanoscopic scales, i.e. fractions of the range of molecular interactions. In this work, we point out that in this sub–nanoscopic regime, the LB method works outside the hydrodynamic limit at the level of a single cell spacing. A quantitative comparison with the Navier–Stokes (NS) solution shows however that LB and NS results are quite similar, thereby indicating that, apart for a small region past the plate, this nano…
Rotational echoes as a tool for investigating ultrafast collisional dynamics of molecules
2019
We show that recently discovered rotational echoes of molecules provide an efficient tool for studying collisional molecular dynamics in high-pressure gases. Our study demonstrates that rotational echoes enable the observation of extremely fast collisional dissipation, at timescales of the order of a few picoseconds, and possibly shorter. The decay of the rotational alignment echoes in ${\mathrm{CO}}_{2}$ gas and ${\mathrm{CO}}_{2}\text{\ensuremath{-}}\mathrm{He}$ mixture up to 50 bar was studied experimentally, delivering collision rates that are in good agreement with the theoretical expectations. The suggested measurement protocol may be used in other high-density media, and potentially …