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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…

A primary goal of physics is to create mathematical models that allow both predictions and explanations of physical phenomena. We weave maths extensively into our physics instruction beginning in high school, and the level and complexity of…

The purpose of this review is to analyze the physics at play in particle resuspension in order to bring insights into the rich complexity of this common but challenging concern. Following the more-is-different vision, this is performed by…

Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vision and natural language processing, its development in…

A complex system comprises multiple interacting entities whose interdependencies form a unified whole, exhibiting emergent behaviours not present in individual components. Examples include the human brain, living cells, soft matter, Earth's…

This paper introduces and defends an account of model-based science that I dub model pluralism. I argue that despite a growing awareness in the philosophy of science literature of the multiplicity, diversity, and richness of models and…

Classical approaches to analyzing dynamical systems, including bifurcation analysis, can provide invaluable insights into underlying structure of a mathematical model, and the spectrum of all possible dynamical behaviors. However, these…

Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…

Quantitative modeling has become an essential tool in modern biophysics, driven by advances in both experimental techniques and theoretical frameworks. Powerful high-resolution techniques now provide detailed datasets spanning molecular to…

We recently presented the so-called allagmatic method, which includes a system metamodel providing a framework for describing, modelling, simulating, and interpreting complex systems. Its development and programming was guided by…

Key questions that scientists and engineers typically want to address can be formulated in terms of predictive science. Questions such as: "How well does my computational model represent reality?", "What are the most important parameters in…

Various research initiatives try to utilize the operational principles of organisms and brains to develop alternative, biologically inspired computing paradigms and artificial cognitive systems. This paper reviews key features of the…

Quantum physics is a linear theory, so it is somewhat puzzling that it can underlie very complex systems such as digital computers and life. This paper investigates how this is possible. Physically, such complex systems are necessarily…

Reliable predictions of the behaviour of chemical systems are essential across many industries, from nanoscale engineering over validation of advanced materials to nanotoxicity assessment in health and medicine. For the future we therefore…

Modellers of complex biological or social systems are often faced with an invidious choice: to use simple models with few mechanisms that can be fully analysed, or to construct complicated models that include all the features which are…

Modeling complex physical dynamics is a fundamental task in science and engineering. Traditional physics-based models are sample efficient, and interpretable but often rely on rigid assumptions. Furthermore, direct numerical approximation…

Mathematical software systems are becoming more and more important in pure and applied mathematics in order to deal with the complexity and scalability issues inherent in mathematics. In the last decades we have seen a cambric explosion of…

Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…

We argue that traditional Western science cannot adequately describe sports and other types of human behavior. Then we make an argument why a complex adaptive systems approach has the potential to provide the foundation for such a theory.…

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…