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The development of complex multicellular organisms from a single parent cell is a highly orchestrated process that cells conduct collectively without central guidance, creating intricate dynamic patterns essential for development and…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
The bi-continuum model composed of two interpenetrating and dynamically coupled material continua is analysed as a simplified but relatively accurate way to describe some physical phenomena in crystalline solids. The essential novelty of…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
Diffusion is a fundamental phenomenon that occurs ubiquitously in nature and remains the subject of continuous research interest. Understanding diffusion is a key to understanding leaving systems. In this Chapter, I discuss diffusion of…
Living cells are soft bodies of a characteristic form, but endowed with a capacity for a steady turnover of their structures. Both of these material properties, i.e. recovery of the shape after an external stress has been imposed and…
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…
In this review we summarize theoretical progress in the field of active matter, placing it in the context of recent experiments. Our approach offers a unified framework for the mechanical and statistical properties of living matter:…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non uniform density profile. Results match quite well as long as the lengthscale of density…
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…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…
Nonlocality is important in realistic mathematical models of physical and biological systems when local models fail to capture the essential dynamics and interactions that occur over a range of distances. This review illustrates different…
This paper is an invitation to the process systems engineering community to change the paradigm for process plants. The goal is to achieve much easier convergence while retaining accuracy on par with the rigorous models. Accurate plant…