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Cells self-organize into functional, ordered structures during tissue morphogenesis, a process that is evocative of colloidal self-assembly into engineered soft materials. Understanding how inter-cellular mechanical interactions may drive…
In many high-throughput experimental design settings, such as those common in biochemical engineering, batched queries are more cost effective than one-by-one sequential queries. Furthermore, it is often not possible to directly choose…
Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
Biochemical networks play a crucial role in biological systems, implementing a broad range of vital functions. They normally operate at low copy numbers and in spatial settings, but this is often ignored and well-stirred conditions are…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
Multicellular collective migration is a ubiquitous strategy of cells to translocate spatially in diverse tissue environments to accomplish a wide variety of biological phenomena, viz. embryonic development, wound healing, and tumor…
Objective : Abdominal anatomy segmentation is crucial for numerous applications from computer-assisted diagnosis to image-guided surgery. In this context, we address fully-automated multi-organ segmentation from abdominal CT and MR images…
This paper proposes a cooperative environmental learning algorithm working in a fully distributed manner. A multi-robot system is more effective for exploration tasks than a single robot, but it involves the following challenges: 1) online…
Multisite covalent modification of proteins is omnipresent in eukaryotic cells. A well-known example is the mitogen-activated protein kinase (MAPK) cascade, where in each layer of the cascade a protein is phosphorylated at two sites. It has…
One emerging approach for the fabrication of complex architectures on the nanoscale is to utilize particles customized to intrinsically self-assemble into a desired structure. Inverse methods of statistical mechanics have proven…
Fractionation is necessary for self-assembly in multicomponent mixtures. Here, reversible fractionation and crystallization are realized and studied in a two-dimensional binary colloids which is supersaturated by enhancing the attraction…
Silicate bioceramics have attracted significant attention in medical applications, particularly in hard tissue regeneration, because of their controllable chemical, physical, and biological functionalities, while ensuring biocompatibility.…
Spatiotemporal metasurfaces offer unique opportunities for wave manipulation, however, their practical realization is often constrained by the requirement for in-plane spatial modulation, which necessitates a large number of time-varying…
Substrate modification networks are ubiquitous in living, biochemical systems. A higher-level hypergraph "skeleton" captures key information about which substrates are transformed in the presence of modification-specific enzymes. Many…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
Biological sequence comparison is a key step in inferring the relatedness of various organisms and the functional similarity of their components. Thanks to the Next Generation Sequencing efforts, an abundance of sequence data is now…