Related papers: Foundations of a Compositional Systems Biology
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…
Biologists and physicists have a rich tradition of modeling living systems with simple models composed of a few interacting components. Despite the remarkable success of this approach, it remains unclear how to use such finely tuned models…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
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…
At its core, the physics paradigm adopts a reductionist approach, aiming to understand fundamental phenomena by decomposing them into simpler, elementary processes. While this strategy has been tremendously successful in physics, it has…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…
Monotone systems constitute one of the most important classes of dynamical systems used in mathematical biology modeling. The objective of this paper is to extend the notion of monotonicity to systems with inputs and outputs, a necessary…
It has been increasingly recognized that effective human-AI co-creation requires more than prompts and results, but an environment with empowering structures that facilitate exploration, planning, iteration, as well as control and…
Compositional learning, mastering the ability to combine basic concepts and construct more intricate ones, is crucial for human cognition, especially in human language comprehension and visual perception. This notion is tightly connected to…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
Compositional generalization, the ability to recognize familiar parts in novel contexts, is a defining property of intelligent systems. Although modern models are trained on massive datasets, they still cover only a tiny fraction of the…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Classical approaches like process algebras or labelled transition systems deal with static composition to model non-trivial concurrent or distributed systems; this is not sufficient for systems with dynamic architecture and with variable…
In this paper I elaborated on the idea of David Harel and Amir Pnueli to think systems and their interaction from the point of view of their compositional behaviour. The obvious idea to base the composition of systems on the concept of…
The infrastructure upon which the functioning of society depends is composed of complex ecosystems of systems. Consequently, we must reason about the properties of such ecosystems, which requires that we construct models of them. There are…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…