Related papers: Emergent Spatiotemporal Organization in Stochastic…
The ability of cells to reorganize in response to external stimuli is important in areas ranging from morphogenesis to tissue engineering. Elongated cells can co-align due to steric effects, forming states with local order. We show that…
In development and homeostasis, multi-cellular systems exhibit spatial and temporal heterogeneity in their biochemical and mechanical properties. Nevertheless, it remains unclear how spatiotemporally heterogeneous forces affect the…
Despite substantial research into the biological basis of memory, the precise mechanisms by which experiences are encoded, stored, and retrieved in the brain remain incompletely understood. A growing body of evidence supports the engram…
We describe a system of stochastic differential equations (SDEs) which model the interaction between processive molecular motors, such as kinesin and dynein, and the biomolecular cargo they tow as part of microtubule-based intracellular…
Understanding how biological constraints shape neural computation is a central goal of computational neuroscience. Spatially embedded recurrent neural networks provide a promising avenue to study how modelled constraints shape the combined…
Elastic confinements are an important component of many biological systems and dictate the transport properties of suspended particles under flow. In this chapter, we review the Brownian motion of a particle moving in the vicinity of a…
Migratory and tissue resident cells exhibit highly branched morphologies to perform their function and to adapt to the microenvironment. Immune cells, for example, display transient branched shapes while exploring the surrounding tissues.…
Complexity in the temporal organization of neural systems may be a reflection of the diversity of its neural constituents. These constituents, excitatory and inhibitory neurons, comprise an invariant ratio in vivo and form the substrate for…
Many biological, physical, and social interactions have a particular dependence on where they take place. In living cells, protein movement between the nucleus and cytoplasm affects cellular response (i.e., proteins must be present in the…
Due to inherent noise in intracellular networks cellular decisions can be random, so genetically identical cells can display different phenotypic behavior even in identical environments. Most previous work in understanding the…
The counterintuitive emergence of order from noise is a central phenomenon in science, ranging from pattern formation and synchronization to order-by-disorder in frustrated systems. While large-scale spatial self-organization induced by…
We introduce and theoretically investigate a minimal particle-based model for a new class of active matter where particles exhibit directional, volume-conserving division in confinement while interacting sterically, mimicking cells in early…
The cargo motion in living cells transported by two species of motor protein with different intrinsic directionality is discussed in this study. Similar to single motor movement, cargo steps forward and backward along microtubule…
The study of many-body quantum systems out of equilibrium remains a significant challenge with complexity barriers arising in both state and operator-based representations. In this work, we review recent approaches based on finding better…
The cytoskeleton -- a composite network of biopolymers, molecular motors, and associated binding proteins -- is a paradigmatic example of active matter. Particle transport through the cytoskeleton can range from anomalous and heterogeneous…
Intracellular cargo transport can arise from passive diffusion, active motor-driven transport along cytoskeletal filament networks, and passive advection by fluid flows entrained by such motor/cargo motion. Active and advective transport…
Intracellular transport of cargoes in the cell is essential for the organization and functioning cells, especially those that are large and elongated. The cytoskeletal networks inside large cells can be highly complex, and this cytoskeletal…
Cells sense their surrounding by employing intracellular signaling pathways that transmit hormonal signals from the cell membrane to the nucleus. TGF-$\beta$/SMAD signaling encodes various cell fates, controls tissue homeostasis and is…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
Fluid in interstitial spaces accounts for ~20% of an adult body weight. Does it circulate around the body like vascular circulations besides a diffusive and short-ranged transport? This bold conjecture has been debated for decades. As a…