相关论文: Viscosity and Diffusion: Crowding and Salt Effects…
Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie…
We report on a comprehensive theory-simulation-experimental study of collective and self-diffusion in suspensions of charge-stabilized colloidal spheres. In simulation and theory, the spheres interact by a hard-core plus screened Coulomb…
The Enskog kinetic theory is applied to compute the mean square displacement of intruders immersed in a granular gas of smooth inelastic hard spheres (grains). Both species (intruders and grains) are surrounded by an interstitial molecular…
In recent years, diffusion models trained on equilibrium molecular distributions have proven effective for sampling biomolecules. Beyond direct sampling, the score of such a model can also be used to derive the forces that act on molecular…
The vibrational anomalies of glasses, in particular the boson peak, are addressed from the standpoint of heterogeneous elasticity, namely the spatial fluctuations of elastic constants caused by the structural disorder of the amorphous…
In this letter, following an extensive experimental validation, we perform constant-volume shearing simulations of non-Brownian granular suspensions using the discrete element method coupled with the lattice Boltzmann method. We choose a…
Enormous enhancement in the viscosity of a liquid near its glass transition is generally connected to the growing many-body static correlations near the transition, often coined as `amorphous ordering'. Estimating the length scales of such…
We use X-ray imaging to study viscous resuspension. In a Taylor-Couette geometry, we shear an initially settled layer of spherical glass particles immersed in a Newtonian fluid and measure the local volume fraction profiles. In this…
Glycerol acts as a natural cryoprotectant by depressing the temperature of ice nucleation and slowing down the dynamics of water mixtures. In this work we characterize dynamics -- diffusion, viscosity, and hydrogen-bond dynamics -- as well…
The interest in the extracellular vesicles (EVs) is rapidly growing as they became reliable biomarkers for many diseases. For this reason, fast and accurate techniques of EVs size characterization are the matter of utmost importance. One…
Supercooled liquids exhibit complicated dynamical behaviors: At the microscopic level, the dynamics is heterogeneous spatially, known as dynamic heterogeneity. At the macroscopic level, the shear viscosity $\eta$ decreases as shear rate…
In this paper, we propose a Generalized Langevin Equation (GLE)-based model to describe the lateral diffusion of a protein in a lipid bilayer. The memory kernel is represented in terms of a viscous (instantaneous) and an elastic (non…
Self Consistent Normal Mode Analysis (SCNMA) is applied to heme c type cytochrome f to study temperature dependent protein motion. Classical Normal Mode Analysis (NMA) assumes harmonic behavior and the protein Mean Square Displacement (MSD)…
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…
Monoclonal antibodies are among the most promising therapeutic agents in modern medicine, yet their formulation into high-concentration solutions for subcutaneous self-administration poses a major challenge. A key obstacle is the marked…
We investigated the viscoelastic response of model interphase chromosomes by tracking the three-dimensional motion of hundreds of dispersed Brownian particles of sizes ranging from the thickness of the chromatin fiber up to slightly above…
Phase change materials are exploited in non-volatile electronic memories and photonic devices that rely on a fast and reversible transformation between the amorphous and crystalline phase upon heating. The recrystallization of the amorphous…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of…
Diffusion models have emerged as a powerful class of generative models by learning to iteratively reverse the noising process. Their ability to generate high-quality samples has extended beyond high-dimensional image data to other complex…
A discretization scheme is introduced for a set of convection-diffusion equations with a non-linear reaction term, where the convection velocity is constant for each reactant. This constancy allows a transformation to new spatial variables,…