Related papers: Fast solver for diffusive transport times on dynam…
Consider a network embedded in the 2D plane, where a particle diffuses along the edges of the network. It is clear that over short length scales a particle moves along a single edge and thus undergoes one-dimensional diffusion. However, on…
Several organelles in eukaryotic cells, including mitochondria and the endoplasmic reticulum, form interconnected tubule networks extending throughout the cell. These tubular networks host many biochemical pathways that rely on proteins…
Quantifying how spatial disorder affects the movement of a diffusing particle or agent is fundamental to target search studies. When diffusion occurs on a network, that is on a highly disordered environment, we lack the mathematical tools…
A heterogeneous continuous time random walk is an analytical formalism for studying and modeling diffusion processes in heterogeneous structures on microscopic and macroscopic scales. In this paper we study both analytically and numerically…
In eukaryotic cells, mitochondria form networks that range from highly fused interconnected structures to fragmented populations of individual organelles that undergo transient interactions. These structures can be described as temporal…
We investigate diffusive search on planar networks, motivated by tubular organelle networks in cell biology that contain molecules searching for reaction partners and binding sites. Exact calculation of the diffusive mean first-passage time…
We developed analytical and numerical methods to study a transport of non-interacting particles in large networks consisting of M d-dimensional containers C_1,...,C_M with radii R_i linked together by tubes of length l_{ij} and radii a_{ij}…
Time plays an essential role in the diffusion of information, influence and disease over networks. In many cases we only observe when a node copies information, makes a decision or becomes infected -- but the connectivity, transmission…
Intracellular processes often rely on the timely encounter of mobile reaction partners, including intermittently motor-driven organelles. The underlying cytoskeletal network presents a complex landscape that both directs particle movement…
In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…
Many biological, social, and communication systems can be modeled by ``searchers'' moving through a complex network. For example, intracellular cargo is transported on tubular networks, news and rumors spread through online social networks,…
Transport of tracer particles through mesh-like environments such as biological hydrogels and polymer matrices is ubiquitous in nature. These tracers could be passive, such as colloids or active (self-propelled), such as synthetic…
In many biological systems, the movement of individual agents is commonly characterized as having multiple qualitatively distinct behaviors that arise from various biophysical states. This is true for vesicles in intracellular transport,…
We study the diffusion process through an ideal polymer network, using numerical methods. Polymers are modeled by random walks on the bonds of a two-dimensional square lattice. Molecules occupy the lattice cells and may jump to the…
In order to characterize the mechanisms governing the diffusion of particles in biological scenarios, it is essential to accurately determine their diffusive properties. To do so, we propose a machine learning method to characterize…
In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles,…
Mesh-like structures, such as mucus gel or cytoskeleton networks, are ubiquitous in biological systems. These intricate structures are composed of cross-linked, semi-flexible bio-filaments, crucial to numerous biological processes. In many…
We consider the diffusion-advection problem in two simple cellular flow models (often invoked as examples for subdiffusive tracer's motion) and concentrate on the intermediate time range, in which the tracer's motion indeed may show…
Network science investigates the architecture of complex systems to understand their functional and dynamical properties. Structural patterns such as communities shape diffusive processes on networks. However, these results hold under the…
Diffusion of molecules within biological cells and tissues is strongly influenced by crowding. A key quantity to characterize diffusion is the particle lifetime, which is the time taken for a diffusing particle to exit by hitting an…