Search results for "molecular dynamics"
showing 10 items of 1075 documents
Molecular Dynamics Computer Simulation of Cooling Rate Effects in a Lennard-Jones Glass
1995
We present the results of a molecular dynamics computer simulation of a binary Lennard-Jones mixture. We simulate a quench of the system from a liquid state at high temperatures to a glass state at zero temperature by coupling the system to a heat bath that has a temperature that decreases linearly (with slope -γ) with time. We investigate how the residual density of the system varies as a function of the cooling rate γ and rationalize our results by means of the dependence of the coordination number of the particles on the cooling rate.
Single-Molecule Optical Switching: A Mechanistic Study of Nonphotochemical Hole-Burning
2001
Persistent spectral hole-burning of dopant chromophores embedded in solid matrices has proven to be a sensitive high-resolution spectroscopic tool to investigate structural and dynamic properties of amorphous and crystalline hosts at low temperature [1]. A commonly encountered mechanism of holeformation is the nonphotochemical process, for which it is assumed that the frequency selective laser excitation and the subsequent relaxation of guest and host eventually leads to a change of configurational degrees of freedom in the nearby environment of the photo-excited centers or in the impurities themselves (or both) [2]. However, detailed knowledge about the microscopic mechanism of the nonphot…
Specific Heat of Amorphous Silica within the Harmonic Approximation
1999
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…
Dynamics of a Supercooled Lennard-Jones System: Qualitative and Quantitative Tests of Mode-Coupling Theory
1996
We present the results of a molecular dynamics computer simulation of a supercooled binary Lennard-Jones mixture. By investigating the temperature dependence of the diffusion constant and of the intermediate scattering function, we show that the ideal version of the mode-coupling theory of the glass transition is able to give a good qualitative description of the dynamics of this system. Using the partial structure factors, as determined from the simulation, as input, we solve the mode-coupling equations in the long time limit. From the comparison of the prediction of the theory for the critical temperature, the exponent parameter, the wave-vector dependence of the nonergodicity parameters …
Theory and Simulations of Friction between Flat Surfaces Lubricated by Submonolayers
2001
Recent simulations suggest that wearless friction between two solid surfaces can only be obtained if the two surfaces are commensurate or if they are lubricated by a film. Some simple theoretical arguments are given why the presence of a submonolayer film between two solids leads to friction. Possible implications of the symmetry of the confining walls on the tribological properties of the system are then investigated in the presence of a thin film by means of molecular dynamics simulation. Erratic stick-slip motion of the incommensurate system and oscillating friction forces for the commensurate system in the sliding regime are observed.
Modelling of Orientational Ordering in Lipid Monolayers
1993
Lipid monolayers at high densities are modelled as rigid rods grafted to an interface at the sites of a regular lattice. The transition between the state where the rods are uniformly tilted to a disordered state with no (average) tilt is studied by computer simulation methods. For the one-dimensional model, the molecular dynamics approach is found much less suitable to equilibrate the system rather than Monte Carlo methods. Both in d=2 discretized versions of Monte Carlo codes are much more efficient than continuum Monte Carlo methods, in spite of huge storage requirements. While in d=l the transition occurs at temperature T=0 via the spontaneous creation of solitons, at d=2 a finite temper…
Diffusion processes and growth on aluminum cluster surfaces
1997
Diffusion processes of adatoms on icosahedral and Wulff polyhedral aluminum cluster surfaces have been studied by molecular dynamics simulations using the effective medium theory. Activation energies of diffusion mechanisms along {111} and {100} facets and from one facet to another, including different hopping and exchange processes as well as more exotic events, have been calculated. Exchange diffusion of an adatom by a chain mechanism through a {100} facet between two {111} facets and hopping diffusion across the edge between two {111} facets via a pull of another adatom on the neighbour facet are shown to play an important role. Adatoms on {111} facets are mobile already at very low temp…
Tension causes structural unfolding of intracellular intermediate filaments
2020
AbstractIntermediate filament (IF) proteins are a class of proteins that constitute different filamentous structures in mammalian cells. As such, IF proteins are part of the load-bearing cytoskeleton and support the nuclear envelope. Molecular dynamics simulations have shown that IF proteins undergo secondary structural changes to compensate mechanical loads, which has been confirmed by experimental in vitro studies on IF hydrogels. However, the structural response of intracellular IF to mechanical load has yet to be elucidated in cellulo. Here, we use in situ nonlinear Raman imaging combined with multivariate data analysis to quantify the intracellular secondary structure of the IF cytoske…
Glass transition in 1,4-polybutadiene: Mode-coupling theory analysis of molecular dynamics simulations using a chemically realistic model.
2006
We present molecular dynamics simulations of the glass transition in a chemically realistic model of 1,4-polybutadiene (PBD). Around 40 K above the calorimetric glass transition of this polymer the simulations reveal a well-developed two-stage relaxation of all correlation functions. We have analyzed the time-scale separation between vibrational degrees of freedom (subpicosecond dynamics) and the alpha relaxation behavior (nanosecond to microsecond dynamics) using the predictions of mode-coupling theory (MCT). Our value for the mode-coupling critical temperature Tc agrees perfectly with prior experimental estimates for PBD. The predictions of MCT for the scaling behavior of the so-called be…
Fluorescence Lifetime of a Single Molecule as an Observable of Meta-Basin Dynamics in Fluids Near the Glass Transition
2006
Using single molecule spectroscopy, we show that the fluorescence lifetime trajectories of single probe molecules embedded in a glass-forming polymer melt exhibit strong fluctuations of a hopping character. Using molecular dynamics simulations targeted to explain these experimental observations, we show that the lifetime fluctuations correlate strongly with the average square displacement function of the matrix particles. The latter observable is a direct probe of the meta-basin transitions in the potential energy landscape of glass-forming liquids. We thus show here that single molecule experiments can provide detailed microscopic information on system properties that hitherto have been ac…