Related papers: Systematizing Cellular Complexity: A Hilbertian Ap…
The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and…
Understanding realistic complex systems requires confronting significant conceptual, theoretical and experimental limitations rooted in the persistence of views that originated in the mechanics of simple moving bodies. We define the…
Ordered polarity alignment of a cell population plays a vital role in biology, such as in hair follicle alignment and asymmetric cell division. Here, we propose a theoretical framework for the understanding of generic dynamical properties…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Cell systems consist of a huge number of various molecules that display specific patterns of interactions, which have a determining influence on the cell's functioning. In general, such complexity is seen to increase with the complexity of…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Quantum physics is a linear theory, so it is somewhat puzzling that it can underlie very complex systems such as digital computers and life. This paper investigates how this is possible. Physically, such complex systems are necessarily…
I describe my path to unconventionality in my exploration of theoretical and applied aspects of computation towards revealing the algorithmic and reprogrammable properties and capabilities of the world, in particular related to applications…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
From bird flocking to neural dynamics, complex systems generate fascinating structures and correlations. Often, seemingly simple dynamics lead to intricate emergent properties. Despite their visceral appeal, defining complex systems lacks…
Noisy fluctuations are ubiquitous in complex systems. They play a crucial or delicate role in the dynamical evolution of gene regulation, signal transduction, biochemical reactions, among other systems. Therefore, it is essential to…
Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
In nature, biological organisms jointly evolve both their morphology and their neurological capabilities to improve their chances for survival. Consequently, task information is encoded in both their brains and their bodies. In robotics,…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
Complex systems thinking is applied to a wide variety of domains, from neuroscience to computer science and economics. The wide variety of implementations has resulted in two key challenges: the progenation of many domain-specific…
Stochasticity (or noise) at cellular and molecular levels has been observed extensively as a universal feature for living systems. However, how living systems deal with noise while performing desirable biological functions remains a major…
Compositional Explanations is a method for identifying logical formulas of concepts that approximate the neurons' behavior. However, these explanations are linked to the small spectrum of neuron activations (i.e., the highest ones) used to…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…