Related papers: Geometry controls diffusive target encounters and …
Intercellular signaling has an important role in organism development, but not all communication occurs using the same mechanism. Here, we analyze the energy efficiency of intercellular signaling by two canonical mechanisms: diffusion of…
We focus on an important yet challenging problem: using a 2D deep network to deal with 3D segmentation for medical image analysis. Existing approaches either applied multi-view planar (2D) networks or directly used volumetric (3D) networks…
Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by…
We theoretically address minimal search strategies of active, self-propelled particles towards hidden targets in three-dimensional space. The particles can sense if a target is close, e.g., by detecting signaling molecules released by a…
How do the topology and geometry of a tubular network affect the spread of particles within fluid flows? We investigate patterns of effective dispersion in the hierarchical, biological transport network formed by Physarum polycephalum. We…
Internet, social media, neuronal or blood vessel are organized in complex networks. These networks are characterized by several quantities such as the underlying graph connectivity (topology), how they grow in time, scaling laws or by the…
Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
Entangled networks of stiff biopolymers exhibit complex dynamic response, emerging from the topological constraints that neighboring filaments impose upon each other. We propose a class of reference models for entanglement dynamics of stiff…
Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure, but rather…
We are concerned with the estimation of the exterior surface and interior summaries of tube-shaped anatomical structures. This interest is motivated by two distinct scientific goals, one dealing with the distribution of HIV microbicide in…
Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…
The role of incoherent tunneling in the diffusion of light atoms on surfaces is investigated. With this purpose, a Chudley-Elliot master equation constrained to nearest neighbors is considered within the Grabert-Weiss approach to quantum…
When considering flows in biological membranes, they are usually treated as flat, though more often than not, they are curved surfaces, even extremely curved, as in the case of the endoplasmic reticulum. Here, we study the topological…
Entity resolution (ER) is a key data integration problem. Despite the efforts in 70+ years in all aspects of ER, there is still a high demand for democratizing ER - humans are heavily involved in labeling data, performing feature…
Transferrable neural architecture search can be viewed as a binary optimization problem where a single optimal path should be selected among candidate paths in each edge within the repeated cell block of the directed a cyclic graph form.…
In 1977 Berg & Purcell published a landmark paper entitled "Physics of Chemoreception" which examined how a bacterium can sense a chemical attractant in the fluid surrounding it. At small scales the attractant molecules move by Brownian…
Understanding how pore structure influences flow and transport behaviour in granular materials is essential for addressing a wide range of geotechnical, hydraulic, and environmental challenges. These processes are largely shaped by the…
Transport of viscous fluid through porous media is a direct consequence of the pore structure. Here we investigate transport through a specific class of two-dimensional porous geometries, namely those formed by fluid-mechanical erosion. We…
We investigate the behavior of {\it Lumbriculus variegatus} in circular and polygonal chambers and show that the worms align with the boundaries as they move forward and then become dynamically trapped at the concave corners over prolonged…