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We revisit the classical concept of near-decomposability in complex systems, introduced by Herbert Simon in his foundational article The Architecture of Complexity, by developing an explicit quantitative analysis based on singular…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
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…
Complex systems and their underlying convoluted networks are ubiquitous, all we need is an eye for them. They pose problems of organized complexity which cannot be approached with a reductionist method. Complexity science and its emergent…
We analyse the complexity of environments according to the policies that need to be used to achieve high performance. The performance results for a population of policies leads to a distribution that is examined in terms of policy…
Large complexes of classical particles play central roles in biology, in polymer physics, and in other disciplines. However, physics currently lacks mathematical methods for describing such complexes in terms of component particles,…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…
Advances in biology have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. Theoretical biology used to primarily provide a basis to rationally examine the frameworks…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
A central problem in systems biology is to identify parameter values such that a biological model satisfies some behavioral constraints (\eg, time series). In this paper we focus on parameter synthesis for hybrid (continuous/discrete)…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
The advent of molecular biology has led to the identification of definitive causative factors for a number of diseases, most of which are monogenic. Causes for most common diseases across the population, however, seem elusive and cannot be…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…
Mathematical models come in many forms across biological applications. In the case of complex, spatial dynamics and pattern formation, stochastic models also face two main challenges: pattern data is largely qualitative, and model…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…
Coupled natural systems are generally modeled at multiple abstraction levels. Both structural scale and behavioral complexity of these models are determinants in the kinds of questions that can be posed and answered. As scale and complexity…
This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the…
Recent cellular-level volumetric brain reconstructions have revealed high levels of anatomic complexity. Determining which structural aspects of the brain to focus on, especially when comparing with computational models and other organisms,…