24 papers · ranked by Valyu relevance
Gabriel Barreiro, Vladimir Pérez-Veloz
Diffusion is a fundamental physical phenomenon with critical applications in fields such as metallurgy, cell biology, and population dynamics. While standard diffusion is well-understood, anomalous diffusion often requires complex non-local models. This paper investigates a nonlinear diffusion equation where the…
Mihatsch, Jakob, Menzel, Andreas M.
The transport of individual entities through interconnected structures is a process of practical relevance both in biology and technology. Examples are given by diffusive dynamics of molecules in porous structures. In soft environments, this transport can be strongly influenced by fluctuations of the porous structure…
Manuel Mayo, M. I. García de Soria, P. Maynar, J. Javier Brey
The self-diffusion process of a hard sphere fluid confined by two parallel plates separated by a distance on the order of the particle diameter is studied. The starting point is a closed kinetic equation for the distribution function that takes into account the effects of the confinement and that is valid in the…
Piotr Polanowski, Andrzej Sikorski, Jose Luis Riccardo, Antonio J. Ramirez-Pastor
The dynamics of dense colloidal systems are not fully understood. In the study of these types of systems, computer simulations based on the so-called hard sphere model play a significant role. In the presented work, we consider a system of hard spheres of the same size but different mobilities (molecules with high…
Bin Li, Pingcuozhuoga, Martin Kröger
We investigated diffusion of thin and thick nanorods with varying lengths and rigidities in cross-linked polymer networks using coarse-grained molecular dynamics (CGMD) simulations. Our results show that the translational diffusion of nanorods slows down with power scaling laws as their length increases, exhibiting a…
Masahiro Shirataki, Takuma Akimoto
A dynamical transition—seen as a sudden increase in the mean-squared displacement at a characteristic temperature that depends on the observation time—is widely reported in neutron-scattering experiments and molecular dynamics simulations of hydrated proteins. However, its physical origin remains elusive. We show that…
Authors not listed
Atomistic simulations provide essential mechanistic insights into chemical processes, yet many important phenomena in chemistry and materials science occur on timescales that are inaccessible to molecular dynamics. Existing computational approaches force a choice between atomic resolution on relatively short timescales…
Andrés Arango-Restrepo, J. Miguel Rubi
Energy as a Unifying Thermodynamic Framework for Active Diffusion Authors: Andrés Arango-Restrepo, J. Miguel Rubi Directed motion of particles is typically explained by phoretic mechanisms arising under externally imposed chemical, electric, or thermal gradients. In contrast, chemical reactions can enhance particle…
Bin Sun, Alec Loftus, Peter Kekenes-Huskey
We review the Brownian dynamics (BD) modeling of biomolecular binding events, with an emphasis on enzyme-substrate interactions in cellular environments. We begin with theoretical foundations of BD and its applications to association and dissociation binding processes in both homogeneous and heterogeneous media. Next…
Dmitrii E Makarov
Many of the timescales of life have speed limits set by quantum-mechanical constraints along with non-fundamental quantities, such as the temperature of the environment, which are however bounded by anthropic considerations. Here, some of such speed limits are examined, including those for the rates of elementary…
Anže Hubman, Franci Merzel
An efficient variational method is presented for estimating the diffusion coefficients and free-energy profiles along selected collective variables from projected molecular dynamics trajectories under both equilibrium and nonequilibrium conditions. The method is based on the assumption that the short-time transition…
Authors not listed
Direct air capture (DAC) using amine-functionalised adsorbents is a promising route to negative emissions. Here, we investigate how humidity influences the swelling, CO2 uptake, and mass transfer of two amine-functionalised polymeric resins, Lewatit VP OC 1065 and Purolite A110, using a combined experimental and…
B. A. Kiang, H. Schiessel
We present molecular dynamics simulations of the random walk of a dumbbell - two beads connected by a spring - in a one-dimensional periodic potential and compare our results in limiting cases to theoretical analytical equations. The relevant parameters in this system are the spring constant, the equilibrium distance…
Shariful Sakib, Cécile Fradin
Fluorescence recovery after photobleaching (FRAP) is widely used to characterize diffusion in cells, but quantitative interpretation of the data in small prokaryotes requires explicitly accounting for cell geometry. While this has been successfully achieved for spherical and rod-shaped bacteria, analytical approaches…
A. Girelli, G. Giantesio, A. Musesti, R. Penta
This work explores diffusion with scale-dependent coefficients, starting from a general advection-diffusion framework from a theoretical standpoint, and then focusing numerically on a purely diffusive regime. Advection-diffusion processes are central to modeling transport phenomena in natural and engineered systems.…
Authors not listed
Bonkowski and De Souza [Sol. Stat. Ionics 429, 116967 (2025)] provide a guide for performing molecular dynamics simulations of ion transport, including methods for estimating diffusion coefficients and their uncertainties from mean-squared displacement (MSD) data. The discussion of uncertainty in estimated diffusion…
Mankun Sang, Margaret E. Johnson
Binding reactions in effectively one-dimensional systems, such as proteins diffusing along DNA or other filaments, pose a fundamental coarse-graining challenge because stochastic trajectories are recurrent in one dimension and therefore do not admit a unique, separation-independent macroscopic association rate. As a…
Denis S. Grebenkov
Autocatalytic processes underlie diverse systems in which replication is triggered at interfaces, including heterogeneous catalysis on solid substrates, enzyme activity at membranes, viral infections, biofilm growth, and spatially structured ecosystems. In a typical scenario, particles move in a bulk medium and…
Gabriel G. da Rocha, Michely P. Rosseto, Rodrigo J. Jaronski, Derik W. Gryczak + 3 more
in Electrolytic Cells: A Generalized Poisson–Nernst–Planck Model with Memory Effects Authors: Gabriel G. da Rocha, Michely P. Rosseto, Rodrigo J. Jaronski, Derik W. Gryczak, Luiz R. Evangelista, Rafael S. Zola, Ervin K. Lenzi We present an extension of the standard Poisson-Nernst-Planck model by incorporating temporal…
Junwoo Park, Nataliya Sokolovska, Clément Cabriel, Asaki Kobayashi + 4 more
Single-molecule tracking (SMT) in live cells reveals how biomolecules explore crowded intracellular environments, yet most tracking software assumes Brownian motion, an approximation that fails when anomalous diffusion dominates. This leads to biased trajectory reconstruction and loss of biophysical information…
Authors not listed
Molten chloride fast reactors (MCFRs) are emerging as a promising class of molten salt reactor (MSR) designs due to their ability to dissolve large amounts of major actinides while keeping low melting points and sustaining a hard neutron spectrum. In this context, understanding molten salt transport properties—such as…
Authors not listed
The GENERIC framework provides a robust structure for nonequilibrium dynamics but lacks a principled method to select reversible ($L$) and irreversible ($M$) brackets. Similarly, finite-time optimizations minimizing path-averaged reciprocal temperature exist but remain isolated. Here, we introduce the \textbf{Entropy…
Authors not listed
Molecular dynamics (MD) and hybrid quantum–classical (QM/MM) methods provide powerful tools for simulating chemical and biological systems, yet their application to long-timescale, strongly coupled processes remains limited by non-integrability, chaotic sensitivity, and extreme time-scale separation. These limitations…
Authors not listed
Active colloids that convert light into motion provide insight into non-equilibrium chemical systems and routes toward microscale engines. Here we quantify the propulsion dynamics and force generation of light-activated Au-TiO2 Janus particles and their optically trappable polystyrene (PS) core-shell Au-PS@TiO2…