Related papers: Dynamic sampling and information encoding in bioch…
Understanding how the complex connectivity structure of the brain shapes its information-processing capabilities is a long-standing question. By focusing on a paradigmatic architecture, we study how the neural activity of excitatory and…
We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g. protein interaction networks involving complex formation and dissociation reactions. We propose the use of model…
In vivo calcium imaging through microscopes has enabled deep brain imaging of previously inaccessible neuronal populations within the brains of freely moving subjects. However, microendoscopic data suffer from high levels of background…
Eukaryotic cells transmit information by signaling through complex networks of interacting proteins. Here we develop a theoretical and computational framework that relates the biophysics of protein-protein interactions (PPIs) within a…
In a mathematical model of interacting biological organisms, where external interventions may alter behavior over time, traditional models that assume fixed parameters usually do not capture the evolving dynamics. In oncology, this is…
Exchange of molecules allows cells to exchange information. How robust is the information to changes in cell parameters? We use a mapping between the stochastic dynamics of two cells sharing a stimulatory molecule, and parameters akin to an…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
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…
The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level…
Information theory and the framework of information dynamics have been used to provide tools to characterise complex systems. In particular, we are interested in quantifying information storage, information modification and information…
Living cell signaling systems include multistep biochemical signaling reaction cascades (BSCs) comprising modifications of molecular signaling proteins. Substantial data on BSCs have been accumulated in the field of molecular biology and…
Living microorganisms have evolved dedicated sensory machinery to detect environmental perturbations, processing these signals through biochemical networks to guide behavior. Replicating such capabilities in synthetic active matter remains…
Understanding the dynamical processes that govern the performance of functional materials is essential for the design of next generation materials to tackle global energy and environmental challenges. Many of these processes involve the…
Cell decision-making refers to the process by which cells gather information from their local microenvironment and regulate their internal states to create appropriate responses. Microenvironmental cell sensing plays a key role in this…
Living cells are continually exposed to environmental signals that vary in time. These signals are detected and processed by biochemical networks, which are often highly stochastic. To understand how cells cope with a fluctuating…
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized…
Assessing where and how information is stored in biological networks (such as neuronal and genetic networks) is a central task both in neuroscience and in molecular genetics, but most available tools focus on the network's structure as…
What does the informational complexity of dynamical networked systems tell us about intrinsic mechanisms and functions of these complex systems? Recent complexity measures such as integrated information have sought to operationalize this…
Neural signals are characterized by rich temporal and spatiotemporal dynamics that reflect the organization of cortical networks. Theoretical research has shown how neural networks can operate at different dynamic ranges that correspond to…