Related papers: Progress towards quantitative design principles of…
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…
It is largely believed that complex cognitive phenomena require the perfect orchestrated collaboration of many neurons. However, this is not what converging experimental evidence suggests. Single neurons, the so-called concept cells, may be…
Monotone systems constitute one of the most important classes of dynamical systems used in mathematical biology modeling. The objective of this paper is to extend the notion of monotonicity to systems with inputs and outputs, a necessary…
Networks are convenient mathematical models to represent the structure of complex systems, from cells to societies. In the past decade, multilayer network science -- the branch of the field dealing with units interacting in multiple…
Diffusion is a fundamental phenomenon that occurs ubiquitously in nature and remains the subject of continuous research interest. Understanding diffusion is a key to understanding leaving systems. In this Chapter, I discuss diffusion of…
In an attempt to explain the uniqueness of the coding mechanism of living cells as contrasted with multi-species structure of ecosystems we examine two models of individuals with some replicative properties. In the first model the system…
Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been…
As Physics did in previous centuries, there is currently a common dream of extracting generic laws of nature in economics, sociology, neuroscience, by focalising the description of phenomena to a minimal set of variables and parameters,…
We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
Quantization problem in digital control system have attracted more and more attention in these years. Normally, a quantized variable is regarded as a perturbed copy of the unquantized variable in the research of quantization effect, but…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics with…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
The brain is immensely complex, with diverse components and dynamic interactions building upon one another to orchestrate a wide range of functions and behaviors. Understanding patterns of these complex interactions and how they are…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
The rule technological landscape is becoming ever more complex, with an extended number of specifications and products. It is therefore becoming increasingly difficult to integrate rule-driven components and manage interoperability in…
What makes living systems flexible so that they can react quickly and adapt easily to changing environments? This question has not only engaged biologists for decades but is also of great interest to computer scientists and engineers who…
The extent to which the benefits of science can be fully realized depends critically upon the quality of the connection between researchers themselves and between researchers and members of the public. We believe that it is now possible to…
The design and engineering of molecular communication (MC) components capable of processing chemical concentration signals is the key to unleashing the potential of MC for interdisciplinary applications. By controlling the signaling pathway…