Related papers: Tiling solutions for optimal biological sensing

The physical interpretation of the functioning of the adaptive immune system, which has been thoroughly characterized on genetic and molecular levels, provides a unique opportunity to define an adaptive self-organizing biological system in…

Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…

Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…

The control of gene expression involves complex mechanisms that show large variation in design. For example, genes can be turned on either by the binding of an activator (positive control) or the unbinding of a repressor (negative control).…

The dynamic range of stimulus processing in living organisms is much larger than a single neural network can explain. For a generic, tunable spiking network we derive that while the dynamic range is maximal at criticality, the interval of…

Numerous biological functions-such as enzymatic catalysis, the immune response system, and the DNA-protein regulatory network-rely on the ability of molecules to specifically recognize target molecules within a large pool of similar…

Biological neural networks operate in the presence of task disruptions as they guide organisms toward goals. A familiar stream of stimulus-response causations can be disrupted by subtask streams imposed by the environment. For example,…

Nature has engineered complex designs to achieve advanced properties and functionalities through evolution, over millions of years. Many organisms have adapted to their living environment producing extremely efficient materials and…

A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to…

Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…

Combining a spatiotemporal, multi-agent based model of a foraging ecosystem with linear, genetically programmed rules for the agents' behaviors results in implicit, endogenous, objective functions and selection algorithms based on "natural…

In order to transmit biochemical signals, biological regulatory systems dissipate energy with concomitant entropy production. Additionally, signaling often takes place in challenging environmental conditions. In a simple model regulatory…

A coupled map is suggested to investigate various spatial or temporal designs in biology: Several cells (or tissues) in an organ are considered as connected to each other in terms of some molecular diffusions or electrical potential…

Organisms that grow and survive in uncertain environments may need to change their physiological state as the environment changes. When the environment is uncertain, one strategy known as bet-hedging is to make these changes randomly and…

Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…

Biological and artificial information processing systems form representations of the world that they can use to categorize, reason, plan, navigate, and make decisions. How can we measure the similarity between the representations formed by…

How cells reliably infer information about their environment is a fundamentally important question. While sensing and signaling generally start with cell-surface receptors, the degree of accuracy with which a cell can measure external…

In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…

In many biological networks the responses of individual elements are ambiguous. We consider a scenario in which many sensors respond to a shared signal, each with limited information capacity, and ask that the outputs together convey as…

Living systems adapt to various environmental conditions by changing their internal states. Inspired by gene expression and epigenetic modification dynamics, we herein propose a generic mechanism for adaptation by combining fast oscillatory…