Related papers: Intrinsic Mean Square Displacements in Proteins
We propose a method for obtaining the intrinsic, long time mean square displacement (MSD) of atoms and molecules in proteins from finite time molecular dynamics (MD) simulations. Typical data from simulations are limited to times of 1 to 10…
The mean-square displacement (MSD) was measured by neutron scattering at various temperatures and pressures for a number of molecular glass-forming liquids. The MSD is invariant along the glass-transition line at the pressure studied, thus…
We compute the mean square displacement (MSD) of intruders immersed in a freely cooling granular gas made up of smooth inelastic hard spheres. In general, intruders and particles of the granular gas are assumed to have different mechanical…
When probe molecules of interest are embedded in a container or aggregate under stochastic motion, one needs to rely on the so-called two-point mean square displacement (MSD) measurement to extract the intrinsic mobility of the probes. We…
The mean square displacement (MSD) of intruders (tracer particles) immersed in a multicomponent granular mixture made up of smooth inelastic hard spheres in a homogeneous cooling state is explicitly computed. The multicomponent granular…
For one-dimension Brownian motion in the confined system with the size $L$, the mean-squared displacement(MSD) defined by $\left \langle (x-x_0)^2 \right\rangle$ should be proportional to $t^{\alpha(t)}$. The power $\alpha(t)$ should range…
The mean-squared displacement (MSD) of a hard sphere and of a dumbbell molecule consisting of two fused hard spheres immersed in a dense hard-sphere system is calculated within the mode-coupling theory for ideal liquid-glass transitions. It…
Recent advances in light microscopy have spawned new research frontiers in microbiology by working around the diffraction barrier and allowing for the observation of nanometric biological structures. Microrheology is the study of the…
We study the mean-square displacement (MSD) of a tracer particle diffusing in a granular gas of inelastic hard spheres under homogeneous cooling state (HCS). Tracer and granular gas particles are in general mechanically different. Our…
There have been increasing reports that the diffusion coefficient of macromolecules depends on time and fluctuates randomly. Here, a novel method to elucidate the fluctuating diffusivity from trajectory data is developed. The time-averaged…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…
In conventional glassformers at sufficiently short times and low enough temperatures, molecules are mutually caged by the intermolecular potential. The fluctuation and dissipation from motion of caged molecules when observed by elastic…
Experimental studies of the variation of the mean square displacement (MSD) of a particle in a confined colloid suspension that exhibits density variations on the scale length of the particle diameter are not in agreement with the…
The mean square displacement (MSD) of an argon molecule as a function of time is studied. Its deviations from the standard asymptotic law for intermediate times are analyzed in details. It is shown that these deviations are mainly connected…
We present neutron scattering measurements on the dynamics of hemoglobin (Hb) in human red blood cells in vivo. Global and internal Hb dynamics were measured in the ps to ns time- and {\AA} length-scale using quasielastic neutron…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
We describe a new technique to estimate the mean square velocity of a Brownian particle from time series of the position of the particle sampled at frequencies several orders of magnitude smaller than the momentum relaxation frequency. We…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
The mean-squared displacement (MSD) is an averaged quantity widely used to assess anomalous diffusion. In many cases, such as molecular motors with finite processivity, dynamics of the system of interest produce trajectories of varying…
We have used an NMR technique to measure the short-time, three-dimensional displacement of grains in a system of mustard seeds vibrated vertically at 15g. The technique averages over a time interval in which the grains move ballistically,…