Related papers: Could Living Cells Use Phase Transitions to Proces…

Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…

Living systems continuously sense, integrate, and act on chemical information using multiscale biochemical networks whose dynamics are inherently nonlinear, adaptive, and energy-efficient. Yet, most attempts to harness such "wetware" for…

Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to…

Fluctuations in biochemical networks, e.g., in a living cell, have a complex origin that precludes a description of such systems in terms of bipartite or multipartite processes, as is usually done in the framework of stochastic and/or…

Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…

Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…

Computation, if treated as a set of physical processes that act on information represented by states of matter, encompasses biological systems, digital systems, and other constructs, and may be a fundamental measure of living systems. The…

Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…

One of the most compelling problems in science consists in understanding how living systems process information. After all, the way they process information defines their capacities to learning and adaptation. There is an increasing…

We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…

Living soft tissues appear to promote the development and maintenance of a preferred mechanical state within a defined tolerance around a so-called set-point. This phenomenon is often referred to as mechanical homeostasis. In contradiction…

The analysis and interpretation of relationships between biological molecules is done with the help of networks. Networks are used ubiquitously throughout biology to represent the relationships between genes and gene products. Network…

Organisms maintain the status quo, holding key physiological variables constant to within an acceptable tolerance, and yet adapt with precision and plasticity to dynamic changes in externalities. What organizational principles ensure such…

We argue for a convergence of crystallography, materials science and biology, that will come about through asking materials questions about biology and biological questions about materials, illuminated by considerations of information. The…

Intracellular networks process cellular-level information and control cell fate. They can be computationally modeled using Boolean networks, which are implicit-time causal models of discrete binary events. These networks can be embedded in…

In tissues, cells in direct physical contact with each other can exchange ions or molecules via protein clusters called gap junctions that form channels across the membranes of adjacent cells. Here, we use a simplified biomimetic approach,…

Confluent cell monolayers and epithelia tissues show remarkable patterns and correlations in structural arrangements and actively-driven collective flows. We simulate these properties using multiphase field models. The models are based on…

A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…

A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…

Cells sense environmental signals and transmit information intracellularly through changes in the abundance of molecular components. Such molecular abundances can be measured in single cells and exhibit significant heterogeneity in clonal…