相关论文: Intrinsic Mean Square Displacements in Proteins
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…
We demonstrate the densification of a granular model system of polystyrene spheres over time by shaking with varying excitation amplitudes or effective temperatures. This densification is quantified by the mean square displacement (MSD),…
Molecular dynamics (MD) simulations provide atomistic insights into the structure, dynamics, and function of biomolecules by generating time-resolved, high-dimensional trajectories. Analyzing such data benefits from estimating the minimal…
We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially-varying diffusivity $D(r)$, mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this…
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…
To solve the obscureness in measurement brought about from the weak ergodicity breaking appeared in anomalous diffusions we have suggested the time-averaged mean squared displacement (MSD) $\bar{\delta^2 (\tau)}_\tau$ with a integral…
The diffusional dynamics and vibrational spectroscopy of molecular hydrogen (H$_2$) in myoglobin (Mb) is characterized. Hydrogen has been implicated in a number of physiologically relevant processes, including cellular aging or…
Photothermal microscopy is an emerging tool for measuring light-matter interactions with single-molecule sensitivity. It is generally believed that the spectral acquisition speed in photothermal microscopy is limited by the slow thermal…
It is commonly believed that melting occurs when mean square displacement (MSD) of a particle of crystalline solid exceeds a threshold value. This is known as the Lindemann criterion, first introduced in the year of 1910 by Lindemann.…
Smoothed Dissipative Particle Dynamics (SDPD) is a mesoscopic method which allows to select the level of resolution at which a fluid is simulated. In this work, we study the consistency of the resulting thermodynamic properties as a…
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…
The standardized mean difference (SMD) is a widely used measure of effect size, particularly common in psychology, clinical trials, and meta-analysis involving continuous outcomes. Traditionally, under the equal variance assumption, the SMD…
We report applications of analytical formalisms and Molecular Dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of…
In two previous papers (Price & Monaghan 2004a,b) (papers I,II) we have described an algorithm for solving the equations of Magnetohydrodynamics (MHD) using the Smoothed Particle Hydrodynamics (SPH) method. The algorithm uses dissipative…
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…
The observable results for desorption kinetics by powder of metal hydride on the example of mangesium hydride are reproduced with the model formulated in terms of specific surface of powder. A volumetric measurement of hydrogen desorption…
In diverse biological applications, particle tracking of passive microscopic species has become the experimental measurement of choice -- when either the materials are of limited volume, or so soft as to deform uncontrollably when…
It is proposed that the rate of relaxation in a liquid is better described by the geometric mean of the van Hove distribution function, rather than the standard arithmetic mean used to obtain the mean squared displacement. The difference…
We investigate the effective friction encountered by an intruder moving through a sedimented medium which consists of transparent granular hydrogels immersed in water, and the resulting motion of the medium. We show that the effective…
Small-angle neutron scattering (SANS) from cationic globular micellar solutions composed of sodium dodecyl sulfate (SDS) and in water was studied with contrast variation approach. Extensive computational studies have demonstrated that the…