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A ubiquitous observation in cell biology is that diffusion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Biologically inspired pressure actuated cellular structures can alter their shape through pressure variations. Previous work introduced a computational framework for pressure actuated cellular structures which was limited to two cell rows…
The classical problem of optimal transportation can be formulated as a linear optimization problem on a convex domain: among all joint measures with fixed marginals find the optimal one, where optimality is measured against a cost function.…
Although coarse-grained models have been widely used to explain exotic phenomena in complex fluids, such as droplet formation in living cells, these conventional approaches often fail to capture the intricate microscopic degrees of freedom…
A stochastic birth-death competition model for particles with excluded volume is proposed. The particles move, reproduce, and die on a regular lattice. While the death rate is constant, the birth rate is spatially nonlocal and implements…
We introduce a simple physical picture to explain the process of molecular sorting, whereby specific proteins are concentrated and distilled into submicrometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based…
One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…
We introduce a novel approach to reduce the computational effort of solving mixed-integer convex chance constrained programs through the scenario approach. Instead of reducing the number of required scenarios, we directly minimize the…
Encapsulation of chemicals using polymer membranes enables to control their transport and delivery for applications such as agrochemistry or detergency. To rationalize the design of polymer capsules, it is necessary to understand how the…
Computational models have become an essential part of exploratory protocols in cell biology, as a complement to in vivo or in vitro experiments. These virtual models have the twofold advantage of enabling access to new types of data and…
A two-dimensional mathematical model for cells migrating without adhesion capabilities is presented and analyzed. Cells are represented by their cortex, which is modelled as an elastic curve, subject to an internal pressure force. Net…
Polymer networks formed by cross linking flexible polymer chains are ubiquitous in many natural and synthetic soft-matter systems. Current micromechanics models generally do not account for excluded volume interactions except, for instance,…
The collision avoidance constraints are prominent as non-convex, non-differentiable, and challenging when defined in optimization-based motion planning problems. To overcome these issues, this paper presents a novel non-conservative…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
The statistical-mechanical study of the equilibrium properties of fluids, starting from the knowledge of the interparticle interaction potential, is essential to understand the role that microscopic interaction between individual particles…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Self-regulation of living tissue as an example of self-organization phenomena in active fractal systems of biological, ecological, and social nature is under consideration. The characteristic feature of these systems is the absence of any…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, where a whole macromolecule is represented by a small number of particles, can be of…