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Compositional generalization is a key ability of humans that enables us to learn new concepts from only a handful examples. Neural machine learning models, including the now ubiquitous Transformers, struggle to generalize in this way, and…
Legged locomotion is a challenging task in the field of robotics but a rather simple one in nature. This motivates the use of biological methodologies as solutions to this problem. Central pattern generators are neural networks that are…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
The bifurcation and chaotic behaviour of unidirectionally coupled deterministic ratchets is studied as a function of the driving force amplitude ($a$) and frequency ($\omega$). A classification of the various types of bifurcations likely to…
Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In…
We analyse the dynamics of networks in which a central pattern generator (CPG) transmits signals along one or more feedforward chains in a synchronous or phase-synchronous manner. Such propagating signals are common in biology, especially…
Genetically encoded regulatory circuits control biological function. A major focus of systems biology is to understand these circuits by establishing the relationship between specific structures and functions. Of special interest are…
Modeling biological rhythms helps understand the complex principles behind the physical and psychological abnormalities of human bodies, to plan life schedules, and avoid persisting fatigue and mood and sleep alterations due to the…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Inhibitory circuits of relaxation oscillators are often-used models for the dynamics of biological networks. We present a qualitative and quantitative stability analysis of such a circuit constituted by three reciprocally coupled…
Understanding gene perturbation effects across diverse cellular contexts is a central challenge in functional genomics, with important implications for therapeutic discovery and precision medicine. Single-cell technologies enable…
Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network model of integrate and…
Elucidating the neurophysiological mechanisms underlying neural pattern formation remains an outstanding challenge in Computational Neuroscience. In this paper, we address the issue of understanding the emergence of neural patterns by…
The activity generated by an ensemble of neurons is affected by various noise sources. It is a well-recognised challenge to understand the effects of noise on the stability of such networks. We demonstrate that the patterns of activity…
Macroscopic oscillations of different brain regions show multiple phase relationships that are persistent across time and have been implicated routing information. Various cellular level mechanisms influence the network dynamics and…
Arrhythmias are potentially fatal disruptions to the normal heart rhythm, but their underlying dynamics is still poorly understood. Theoretical modeling is an important tool to fill this gap. Typical studies often employ detailed…
In this work, a wide family of LFSR-based sequence generators, the so-called Clock-Controlled Shrinking Generators (CCSGs), has been analyzed and identified with a subset of linear Cellular Automata (CA). In fact, a pair of linear models…
We consider homogeneous coupled cell networks with asymmetric inputs. We obtain general results concerning codimension-one steady-state bifurcations for networks with any number of cells and any number of asymmetric inputs. These results…
Multipotent stem or progenitor cells undergo a sequential series of binary fate decisions, which ultimately generate the diversity of differentiated cells. Efforts to understand cell fate control have focused on simple gene regulatory…
Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmental biology. In particular, an understanding of these…