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With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
The problem of the transformation of microscopic information to the macroscopic level is an intriguing challenge in computational neuroscience, but also of general mathematical importance. Here, a phenomenological mathematical model is…
Molecular communication is a biologically-inspired method of communication with attractive properties for microscale and nanoscale devices. In molecular communication, messages are transmitted by releasing a pattern of molecules at a…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
Here we analyze synaptic transmission from an information-theoretic perspective. We derive closed-form expressions for the lower-bounds on the capacity of a simple model of a cortical synapse under two explicit coding paradigms. Under the…
Metastasis is a process of cell migration that can be collective and guided by chemical cues. Viewing metastasis in this way, as a physical phenomenon, allows one to draw upon insights from other studies of collective sensing and migration…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
Nowadays the question `what is complexity?' is a challenge to be answered. This question is triggering a great quantity of works in the frontier of physics, biology, mathematics and computer science. Even more when this century has been…
Speech is a multiplexed signal displaying levels of complexity, organizational principles and perceptual units of analysis at distinct timescales. This critical acoustic signal for human communication is thus characterized at distinct…
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…
Information theory provides powerful tools for understanding communication systems. This analysis can be applied to intercellular signal transduction, which is a means of chemical communication among cells and microbes. We discuss how to…
Flow cytometry is a powerful quantitative assay supporting high-throughput collection of single-cell data with a high dynamic range. For flow cytometry to yield reproducible data with a quantitative relationship to the underlying biology,…
Time-fluctuating signals are ubiquitous and diverse in many physical, chemical, and biological systems, among which random telegraph signals (RTSs) refer to a series of instantaneous switching events between two discrete levels from…
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of…
In Diffusive Molecular Communication (DMC), information is transmitted by diffusing molecules. Synaptic signaling, as a natural implementation of this paradigm, encompasses functional components that, once understood, can facilitate the…
Optical imaging relies on the ability to illuminate an object, collect and analyze the light it scatters or transmits. Propagation through complex media such as biological tissues was so far believed to degrade the attainable depth as well…
This chapter sheds light on the synaptic organization of the brain from the perspective of computational neuroscience. It provides an introductory overview on how to account for empirical data in mathematical models, implement such models…
Receptor-induced apoptosis is a complex signal transduction pathway involving numerous protein/protein interactions and post-transcriptional modifications. The response to death receptor stimulation varies significantly from one cell line…
A computational model incorporating insights from quantum theory is proposed to describe and explain synaptic message transmission. We propose that together, neurotransmitters and their corresponding receptors, function as a physical…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…