Related papers: Long-Time Mean Square Displacements in Proteins
The thermal mean square displacement (MSD) of hydrogen in proteins and its associated hydration water is measured by neutron scattering experiments and used an indicator of protein function. The observed MSD as currently determined depends…
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…
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.…
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…
Many physical and biological processes are modeled by "particles" undergoing L\'evy random walks. A feature of significant interest in these systems is the mean square displacement (MSD) of the particles. Long-time asymptotic approximations…
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…
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…
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…
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 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…
Chemical space which encompasses all stable compounds is unfathomably large and its dimension scales linearly with the number of atoms considered. The success of machine learning methods suggests that many physical quantities exhibit…
The mean-square displacement (MSD) is widely utilized to study the dynamical properties of stochastic processes. The time-averaged MSD (TAMSD) provides some information on the dynamics which cannot be extracted from the ensemble-averaged…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
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…
The mean squared displacement (MSD) of particles or probes is commonly estimated from microscopy videos using particle tracking approaches, which rely on tuning parameters manually, and are often unstable over the entire lag time range,…
Motion of active particles, such as catalytic micro- and nano-motors, is usually characterized via either dynamic light scattering or optical microscopy. In both cases, speed of particles is obtained from the calculus of the mean square…
Self-diffusion coefficients, $D^*$, are routinely estimated from molecular dynamics simulations by fitting a linear model to the observed mean-squared displacements (MSDs) of mobile species. MSDs derived from simulation exhibit statistical…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…