25 papers · ranked by Valyu relevance
Pawel Romanczuk, Markus Bär, W. Ebeling, Benjamin Lindner + 1 more
'Lutz Schimansky-Geier'] > Abstract. We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework…
Yann Lanoiselée, Nicolas Moutal, Denis S. Grebenkov
Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid rearrangements of the medium constantly change the effective diffusivity felt locally by a diffusing particle and thus impact the distribution of the first-passage…
Mayumi Hamada, Pietro de Anna
Molecular diffusion in liquids is a key process in numerous systems: it is often the reaction rate limiting factor in biological or chemical reaction. Molecular diffusion has been recognized as the ultimate mechanism by which substances concentration get homogenized and, thus, their mixing and dilution occur. Here, we…
Svyatoslav Kondrat
| 1 | | Introduction | | | | | | | | | | | | | | | | | | | | 2 | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | 2 | | Macromolecular self-diffusion | | | | | | | | | | | | | | | | | | | | 2 | | | 2.1 | How to characterize…
Aleksandar Donev, Thomas G. Fai, Eric Vanden‐Eijnden
We study diffusive mixing in the presence of thermal fluctuations under the assumption of large Schmidt number. In this regime we obtain a limiting equation that contains a diffusive stochastic drift term with diffusion coefficient obeying a Stokes-Einstein relation, in addition to the expected advection by a random…
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…
Aleksandar Donev, Thomas G. Fai, Eric Vanden‐Eijnden
A model for diffusion in liquids that couples the dynamics of tracer particles to a fluctuating Stokes equation for the fluid is investigated in the limit of large Schmidt number. In this limit, the concentration of tracers is shown to satisfy a closed-form stochastic advection-diffusion equation that is used to…
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…
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…
Jakub Spiechowicz, Ivan G. Marchenko, Peter Hänggi, Jerzy Łuczka + 1 more
'Antonio M. Scarfone'] The diffusion of small particles is omnipresent in many processes occurring in nature. As such, it is widely studied and exerted in almost all branches of sciences. It constitutes such a broad and often rather complex subject of exploration that we opt here to narrow our survey to the case of the…
Surajith N. Wanasundara, Raymond J. Spiteri, Richard K. Bowles
Monte Carlo simulation is used to study the dynamical crossover from single file diffusion to normal diffusion in fluids confined to narrow channels. We show that the long time diffusion coefficients for a series of systems involving hard and soft interaction potentials can be described in terms of a hopping time that…
Enrico Lorenzetti, Celia Municio-Diaz, Nicolas Minc, Arezki Boudaoud + 1 more
Fluorescence recovery after photobleaching (FRAP) is broadly used to investigate the dynamics of molecules in cells and tissues, notably to quantify diffusion coefficients. FRAP is based on the spatiotemporal imaging of fluorescent molecules following an initial bleaching of fluorescence in a region of the sample.…
Limin Xiang, Kun Chen, Rui Yan, Wan Li + 1 more
Intracellular diffusion underlies vital processes of the cell. However, it remains difficult to elucidate how an average-sized protein diffuses in the cell with good spatial resolution and sensitivity. Here we report single-molecule displacement/diffusivity mapping (SMdM), a super-resolution strategy that enables the…
Tadeusz Kosztołowicz, Aldona Dutkiewicz, Katarzyna D. Lewandowska
Normal and anomalous diffusion processes are characterized by the time evolution of the mean square displacement of a diffusing molecule $σ2(t)$. When $σ2(t)$ is a power function of time, the process is described by a fractional subdiffusion, fractional superdiffusion or normal diffusion equation. However, for other…
Debabrata Dey, Shir Marciano, Gideon Schreiber
A cell is a densely packed conglomerate of macromolecules, where diffusion is essential for their function. The crowded conditions may affect diffusion both through hard (occluded space) and soft (weak, non-specific) interactions. Multiple-methods have been developed to measure diffusion rates at physiological protein…
Stephen Smith, Claudia Cianci, Ramon Grima
It is now well established that cell interiors are significantly crowded by macromolecules, which impede diffusion and enhance binding rates. However, it is not fully appreciated that levels of crowding are heterogeneous, and can vary substantially between subcellular regions. In this article, starting from a…
Mohammad Azimi, Yousef Jamali, Mohammad R. K. Mofrad, Nic D. Leipzig
Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and subcellular compartments where molecular crowding limits the interaction between particles. We investigate the application of a computational method for modeling the…
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…
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…
Srijana Pandey, Dinesh Gautam, Jixin Chen
Many interactions between small molecules and particles occur in solutions. They are surrounded by other molecules that do not react, for example, biological processes in water, chemical reactions in gas or liquid solutions, and environmental reactions in air and water. Predicting the rate of such interactions involves…
Johanna Busch, Dietmar Paschek
In a recent paper [J. Phys. Chem.B 127, 7983-7987 (2023)] , we have shown that for molecular dynamics (MD) simulations using orthorhombic periodic boundary conditions with "magic" box length ratios of $L_z/L_x=L_z/L_y=2.7933596497$, the self-diffusion coefficients $D_x$ and $D_y$ in $x$- and $y$-direction are…
Jack D. Evans, Simon Krause, Ben L. Feringa
Molecules in gas and liquid states, as well as in solution, exhibit significant and random Brownian motion. Molecules in the solid-state, although strongly immobilized, can still exhibit significant intramolecular dynamics. However, in most framework materials, these intramolecular dynamics are driven by temperature…
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…
Ruth E. Baker, Matthew J Simpson
Transport of cells and biochemical molecules often takes place in crowded, heterogeneous environments. As such, it is important we understand how to quantify crowded transport phenomena, and the possibilities of extracting transport coefficients from limited observations. We employ a volume-excluding random walk model…