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Life is a nonequilibrium phenomenon: metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e. their energetic…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
Control of gas exchange between a leafs interior and the surrounding air is accomplished by variations in the turgor pressures in the small epidermal and guard cells that cover the leafs surface. These pressures respond to changes in light…
In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…
Biological molecular machines are bifunctional enzymes that catalyze two processes: one donating free energy and the other accepting it. Recent studies show that most protein enzymes have rich stochastic dynamics of transitions between 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 rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
Biological information processing is generally assumed to be classical. Measured cellular energy budgets of both prokaryotes and eukaryotes, however, fall orders of magnitude short of the power required to maintain classical states of…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
Tissue homeostasis, the biological process of maintaining a steady state in tissue via control of cell proliferation, death, and metabolic function, is essential for the development, growth, maintenance, and proper function of living…
The motion of molecules across channels is critically important for understanding mechanisms of cellular processes. Here we investigate the mechanism of interactions in the molecular transport by analyzing exactly solvable discrete…
Number-conserving cellular automata are discrete dynamical systems that simulate interacting particles like e.g. grains of sand. In an earlier paper, I had already derived a uniform construction for all transition rules of one-dimensional…
Bioelectrical interfaces represent a significant evolution in the intersection of nanotechnology and biophysics, offering new strategies for probing and influencing cellular processes. These systems capitalize on the subtle but powerful…
Information delivery via molecular signals is abundant in nature and potentially useful for industry sensing. Many propagation channels (e.g., tissue membranes and catalyst beds) contain porous medium materials and the impact this has on…
The organization of live cells into tissues and their subsequent biological function involves inter-cell mechanical interactions, which are mediated by their elastic environment. To model this interaction, we consider cells as spherical…
Many intracellular processes continue to oscillate during the cell cycle. Although it is not well-understood how they are affected by discontinuities in the cellular environment, the general assumption is that oscillations remain robust…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…