28 papers · ranked by Valyu relevance
Marcelo Kaminski Lenzi, E. K. Lenzi, L.M.S. Guilherme, L. R. Evangelista + 1 more
'L. R. Evangelista' 'Haroldo V. Ribeiro'] We investigate a diffusion process in heterogeneous media where particles stochastically reset to their initial positions at a constant rate. The heterogeneous media is modeled using a spatialdependent diffusion coefficient with a power-law dependence on particles' positions.…
Benjamin Partridge, Sara Gonzalez Anton, Reema Khorshed, George Adams + 3 more
Multi-potent progenitor (MPP) cells act as a key intermediary step between haematopoietic stem cells and the entirety of the mature blood cell system. Their eventual fate determination is thought to be achieved through migration in and out of spatially distinct niches. Here we first analyze statistically MPP cell…
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…
Ignasi Alemany, Jan N Rose, Jérôme Garnier-Brun, Andrew D. Scott + 1 more
'Denis Doorly'] In this paper we present analytical and random walk based solutions to diffusion in semi-permeable layered media with varying diffusivity. We propose a new random walk transit model (hybrid model) based on treating the membrane permeability and the change in diffusion as two infinitesimal separate…
Samuele Giannini, Wei-Tao Peng, Lorenzo Cupellini, Daniele Padula + 2 more
'Antoine Carof' 'Jochen Blumberger'] Designing molecular materials with very large exciton diffusion lengths would remove some of the intrinsic limitations of present-day organic optoelectronic devices. Yet, the nature of excitons in these materials is still not sufficiently well understood. Here we present Frenkel…
Lim Heo, Katukurunde Gamage, Gilberto Valdes-Garcia, Lisa J. Lapidus + 1 more
Transient protein-protein interactions occur frequently under the crowded conditions encountered in biological environments, yet they remain poorly understood. Here, tryptophan-cysteine quenching is introduced as an experimental approach that is ideally suited to characterize such interactions between proteins with…
Ben A. Johnson, Ashleigh T. Castner, Hemlata Agarwala, Sascha Ott
Electrical conductivity through redox conducting MOFs (RCMOFs) proceeds by electron hopping between linkers of differing oxidation states. While this process is treated as a purely diffusional process in the literature, we show herein that this prevalent description is an oversimplification, and that emerging electric…
Eric Fagerberg, Samuel Lenton, Tommy Nylander, Tilo Seydel + 1 more
Protein Histatin 5 and the Impact of Crowding Thereon: A Combined Neutron Spectroscopy and Molecular Dynamics Simulation Study Authors: ['Eric Fagerberg' 'Samuel Lenton' 'Tommy Nylander' 'Tilo Seydel' 'Marie Skepö'] Intrinsically disordered proteins (IDPs) are proteins that, in comparison with globular/structured…
Arthur Chakwizira, Filip Szczepankiewicz, Markus Nilsson
Double diffusion encoding (DDE) makes diffusion MRI sensitive to a wide range of microstructural features, and the acquired data can be analysed using different approaches. Correlation tensor imaging (CTI) uses DDE to resolve three components of the diffusional kurtosis: isotropic, anisotropic, and microscopic…
Francesco Reina, Christian Eggeling, Christoffer Lagerholm
Lateral diffusion measurements have been -used to infer information about the nano-organization of membranes. We employed interferometric scattering (ISCAT) microscopy at an acquisition rate of 2 kHz to revisit the diffusion dynamics of a phospholipid analog on the plasma membrane of Ptk2 cells. The ISCAT trajectory…
Jixin Chen
This report uses Monte Carlo simulations to connect stochastic single-molecule and ensemble surface adsorption of molecules from dilute solutions. Monte Carlo simulations often use a fundamental time resolution to simulate each discrete step for each molecule. The adsorption rate obtained from such a simulation…
Authors not listed
Conventional directed colloidal assembly enables fabricating complex hierarchical structures using external stimuli like electric fields, but lacks control over the assembly state in time. Chemical reaction networks have been discovered that transiently assemble colloids; however, they have slow dynamics (hrs – days)…
M. Ross Kunz, Debtanu Maiti, Gregory S. Yablonsky, Rebecca Fushimi
This paper introduces the use of statistical distributions based on transport differential equations for clear distinction of transport modes within transient kinetic experiments. More specifically, novel techniques are developed for the transient data obtained through the Temporal Analysis of Products (TAP) reactor…
Konstantin Speckner, Florian Rehfeldt, Matthias Weiss
The interior of cellular nuclei, the nucleoplasm, is a crowded fluid that is pervaded by protein-decorated DNA polymers, the chromatin. Due to the complex architecture of chromatin and a multitude of associated non-equilbrium processes, e.g. DNA repair, the nucleoplasm can be expected to feature non-trivial material…
David Winogradoff, Han-Yi Chou, Christopher Maffeo, Aleksei Aksimentiev
Nuclear pore complexes (NPCs) control biomolecular transport in and out of the nucleus. Disordered nucleoporins in the complex”s central pore form a permeation barrier, preventing unassisted transport of large biomolecules. Here, we combine coarse-grained simulations of an experimentally-derived NPC structure with a…
Ignasi Alemany, Jan N. Rose, Jérôme Garnier-Brun, Andrew D. Scott + 1 more
'Denis J. Doorly'] In this paper we present random walk based solutions to diffusion in semi-permeable layered media with varying diffusivity. We propose a novel transit model for solving the interaction of random walkers with a membrane. This hybrid model is based on treating the membrane permeability and the step…
Olivier Destrian, Nicolas Moisan, René-Marc Mege, Benoit Ladoux + 2 more
Intracellular transport of macromolecules is crucial for the proper functioning of most cellular processes. Although intracellular crowding is known to strongly alter macromolecule mobility, how cytoplasmic structures physically modulate diffusion remains largely unexplored. Here we investigated the mechanisms by which…
A. Barletta, Pedro Vayssière Brandão, Florinda Capone, Roberta De Luca
Rayleigh number Authors: ['A. Barletta' 'Pedro Vayssière Brandão' 'Florinda Capone' 'Roberta De Luca'] This work investigates the influence of a generic anomalous diffusion model on mass convection in a fluid-saturated porous medium, focusing on superdiffusive regimes. A mathematical model is developed, and stability…
Ashwin V. S. Nelanuthala, Bitan Saha, Jagadish Sankaran, Tom J. Carney + 2 more
Morphogenesis is controlled by signalling morphogens that form gradients across the embryo. The gradient formation requires that the low molecular weight morphogens slow down their diffusion by at least one order of magnitude. However, the precise slow-down of diffusion across the relevant micrometre scales has not…
Achuthan Raja Venkatesh, Kathy H. Le, David M. Weld, Onn Brandman
While inhomogeneous viscosity has been identified as a ubiquitous feature of the cellular interior, its implications for particle mobility and concentration at different length scales have remained unexplored. In this work, we use agent-based simulations of diffusion to investigate how diverse manifestations of…
Authors not listed
Antimicrobial peptides (AMPs) are highly effective broad-spectrum antibiotics, found as components of the immune system in almost all forms of life. It is well established that their primary target is the cell membrane where they are hypothesized to permeabilize the bilayer. However, it is a long-standing question…
Jixin Chen
Predicting the reaction kinetics, that is, how fast a reaction can happen in a solution, is essential information for many processes, such as industrial chemical manufacturing, refining, synthesis and separation of petroleum products, environmental processes in air and water, biological reactions in cells, biosensing…
Spencer Wozniak, Michael Feig
The viscosity and diffusion properties of crowded protein systems were investigated with molecular dynamics simulations of SH3 mixtures with different crowders, and results were compared with experimental data. The simulations accurately reproduced experimental trends across a wide range of protein concentrations…
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…
Alexander Schlaich, Jean‐Louis Barrat, Benoît Coasne
Microscopic to Coarse-Grained Descriptions Authors: ['Alexander Schlaich' 'Jean‐Louis Barrat' 'Benoît Coasne'] This review presents the state of the art on the theory, molecular simulation, and coarse-grained strategies applied to the transport of gases and liquids in nanoporous materials (pore size in the range 1 –…
Jixin Chen
Predicting the reaction kinetics, that is, how fast a reaction can happen in a solution, is essential information for many processes, such as industrial chemical manufacturing, refining, synthesis and separation of petroleum products, environmental processes in air and water, biological reactions in cells, biosensing…
Authors not listed
CO hydrogenation is a promising approach for the storage of renewable energy in the form of hydrocarbons via the Fischer-Tropsch synthesis (FTS). Since transient operation of FTS reactors might be necessary and even be beneficial, transient kinetics for a rational catalyst and reactor design are essential. In order to…
Authors not listed
Obtaining quantitative information about residence time behavior (i.e., the residence time distribution function) in realistic experimental systems is oftentimes experimentally challenging and numerically complex. The conventional way is to conduct very simple pulse or step tracer experiments or construct elaborate…