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The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
Cell injection is an approach used for the delivery of small sample substances into a biological cell and is widely used in drug development, gene injection, intracytoplasmic sperm injection (ICSI) and in-virto fertilization (IVF). Robotic…
Large language models (LLMs) are transforming cellular biology by enabling the development of "virtual cells"--computational systems that represent, predict, and reason about cellular states and behaviors. This work provides a comprehensive…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
In silico, cell based approaches for modeling biological morphogenesis are used to test and validate our understanding of the biological and mechanical process that are at work during the growth and the organization of multi-cell tissues.…
System-level design, once the province of board designers, has now become a central concern for chip designers. Because chip design is a less forgiving design medium -- design cycles are longer and mistakes are harder to correct --…
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…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
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…
Since the turn of the millennium, computational modelling of biological systems has evolved remarkably and sees matured use spanning basic and clinical research. While the topic of the peri-millennial debate about the virtues and…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
Complex system simulation has been playing an irreplaceable role in understanding, predicting, and controlling diverse complex systems. In the past few decades, the multi-scale simulation technique has drawn increasing attention for its…
The traditional methods of the biology, based on illustrative descriptions and linear logic explanations, are discussed. This work aims to improve this approach by introducing alternative tools to describe and represent complex biological…
This study explores the emergence of life through a simulation model approach. The model "Multi-set chemical lattice model" is a model that allows virtual molecules of multiple types to be placed in each lattice cell on a two-dimensional…
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…
We describe software and a language for quasibiological computations. Its theoretical basis is a unified theory of complex (adaptive) systems where all laws are regularities of relations between things or agents, and dynamics is made from…
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
Computational models are quantitative representations of systems. By analyzing and comparing the outputs of such models, it is possible to gain a better understanding of the system itself. Though as the complexity of model outputs…
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…