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Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…

Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…

Effective control requires knowledge of the process dynamics to guide the system toward desired states. In many control applications this knowledge is expressed mathematically or through data-driven models, however, as complexity grows…

Many dynamical phenomena display a cyclic behavior, in the sense that time can be partitioned into units within which distributional aspects of a process are homogeneous. In this paper, we introduce a class of models - called conjugate…

Many complex systems can be modeled as multiagent systems in which the constituent entities (agents) interact with each other. The global dynamics of such a system is determined by the nature of the local interactions among the agents.…

Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in…

The social organization of microorganisms has long been a fascinating and challenging subject in both biology and sociology. In these organisms, the role of the individual is far less dominant than that of the community, which functions as…

The donation game is a well-established framework for studying the emergence and evolution of cooperation in multi-agent systems. The cooperative behavior can be influenced by the environmental noise in partially observable settings and by…

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…

Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…

By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…

The relationship between division of labor and individuals' spatial behavior in social insect colonies provides a useful context to study how social interactions influence the spreading of agent (which could be information or virus) across…

Simulation of population dynamics is a central research theme in computational biology, which contributes to understanding the interactions between predators and preys. Conventional mathematical tools of this theme, however, are incapable…

Segregation of populations is a key question in evolution theory. One important aspect is the relation between spatial organization and the population's composition. Here we study a specific example -- sectors in expanding bacterial…

The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…

We study the effect of discreteness on various models for patterning in bacterial colonies. In a bacterial colony with branching pattern, there are discrete entities - bacteria - which are only two orders of magnitude smaller than the…

This paper introduces two ongoing research projects which seek to apply computer modelling techniques in order to simulate human behaviour within organisations. Previous research in other disciplines has suggested that complex social…

Many collective systems exist in nature far from equilibrium, ranging from cellular sheets up to flocks of birds. These systems reflect a form of active matter, whereby individual material components have internal energy. Under specific…

Bacterial quorum sensing is the communication that takes place between bacteria as they secrete certain molecules into the intercellular medium that later get absorbed by the secreting cells themselves and by others. Depending on cell…

The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…