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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.…
A practical correction formula relating the self-diffusion coefficient of dense liquids from molecular dynamics simulations with periodic boundary conditions to the self-diffusion coefficient in the thermodynamic limit is discussed. This…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
Diffusion models have shown remarkable empirical success in sampling from rich multi-modal distributions. Their inference relies on numerically solving a certain differential equation. This differential equation cannot be solved in closed…
In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using the Einstein relation, the particle positions need to be…
To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the…
Real data are constrained to finite sampling rates, which calls for a suitable mathematical description of the corrections to the finite-time estimations of the dynamic equations. Often in the literature, lower order discrete time…
Diffusion coefficients are essential microphysics input for modeling white dwarf evolution, as they impact phase separation at crystallization and sedimentary heat sources. Present schemes for computing diffusion coefficients are accurate…
A system of diffusion-reaction equations coupled with a dissolution-precipitation model is discussed. We start by introducing a microscale model together with its homogenized version. In the present paper, we first derive the corrector…
A procedure is presented to estimate the diffusion coefficient of a uniform patch of argon gas in a uniform background of helium gas. Molecular Dynamics (MD) simulations of the two gases interacting through the Lennard-Jones potential are…
[ This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in The Journal of Chemical Physics, 157, 024504 (2022) and may be found at:…
When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is…
The simulation of the metabolism in mammalian cells becomes a severe problem if spatial distributions must be taken into account. Especially the cytoplasm has a very complex geometric structure which cannot be handled by standard…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
The experimental literature on the motion of mesoscopic probe particles through polymer solutions is systematically reviewed. The primary focus is the study of diffusive motion of small probe particles. Comparison is made with measurements…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
When applied to binary solutions, thermal gradients lead to the generation of concentration-gradients and thus to inhomogeneous systems. While being known for more than 150 years, the molecular origins for this phenomenon are still debated,…
Ordinary differential equations (ODEs) are widely used to describe dynamical systems in science, but identifying parameters that explain experimental measurements is challenging. In particular, although ODEs are differentiable and would…
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…
Recently, an analytical expression for the system size dependence and direction-dependence of self-diffusion coefficients for neat liquids due to hydrodynamic interactions has been derived for molecular dynamics (MD) simulations using…