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Physics-Informed Machine Learning (PIML) has successfully integrated mechanistic understanding into machine learning, particularly in domains governed by well-known physical laws. This success has motivated efforts to apply PIML to biology,…

A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…

Continuum mechanics (e.g., hydrodynamics, elasticity theory) is based on the assumption that a small set of fields provides a closed description on large space and time scales. Conditions governing the choice for these fields are discussed…

Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…

Activity and autonomous motion are fundamental aspects of many living and engineering systems. Here, the scale of biological agents covers a wide range, from nanomotors, cytoskeleton, and cells, to insects, fish, birds, and people. Inspired…

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…

In this paper, I present a summary on some works that utilized static analysis techniques for understanding biological systems. Control flow analysis, context dependent analysis, and other techniques were employed to investigate the…

The hydrodynamic slippage at a solid-liquid interface is currently at the center of our understanding of fluid mechanics. For hundreds of years this science has relied upon no-slip boundary conditions at the solid-liquid interface that has…

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…

Our planet is experiencing an accelerated process of change associated to a variety of anthropogenic phenomena. The future of this transformation is uncertain, but there is general agreement about its negative unfolding that might threaten…

Complex systems are characterized by specific time-dependent interactions among their many constituents. As a consequence they often manifest rich, non-trivial and unexpected behavior. Examples arise both in the physical and non-physical…

Clinical management of cancer has continuously evolved for several decades. Biochemical, molecular and genomics approaches have brought and still bring numerous insights into cancerous diseases. It is now accepted that some phenomena,…

With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…

Fluid flow through bimodal porous media, characterized by a distinct separation in pore size distribution, is critical in various scientific and engineering applications, including groundwater management, oil and gas production, and carbon…

Biological activities are often seen entrained onto the day-night and other celestial mechanical cycles (e.g., seasonal and lunar), but studies on the origin of life have largely not accounted for such periodic external environmental…

Bioconvection, a phenomenon arising from the collective motion of motile microorganisms, plays a crucial role in shaping microbial distributions, fluid dynamics, and bloom formation in aquatic environments. While extensive research has…

Active biological flow networks pervade nature and span a wide range of scales, from arterial blood vessels and bronchial mucus transport in humans to bacterial flow through porous media or plasmodial shuttle streaming in slime molds.…

Accurate and efficient fluid flow models are essential for applications relating to many physical phenomena including geophysical, aerodynamic, and biological systems. While these flows may exhibit rich and multiscale dynamics, in many…

Water near hydrophobic surfaces is like that at a liquid-vapor interface, where fluctuations in water density are substantially enhanced compared to that in bulk water. Here we use molecular simulations with specialized sampling techniques…

Many biological processes can be thought of as the result of an underlying dynamics in which the system repeatedly undergoes distinct and abortive trajectories with the dynamical process only ending when some specific process, purpose,…