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The shapes of epithelial tissues result from a complex interplay of contractile forces in the cytoskeleta of the cells in the tissue, and adhesion forces between them. A host of discrete, cell-based models describe these forces by assigning…
Transport across heterogeneous, patchy environments is a ubiquitous phenomenon spanning fields of study including ecological movement, intracellular transport and regions of specialised function in a cell. These regions or patches may be…
Dynamic positron emission tomography (PET) images can reveal the distribution of tracers in the organism and the dynamic processes involved in biochemical reactions, and it is widely used in clinical practice. Despite the high effectiveness…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Dielectric elastomers are an emerging class of highly deformable electro-active materials employed for electromechanical transduction technology. For practical applications, the design of such transducers requires a model accounting for…
Many real world networks are characterized by adaptive changes in their topology depending on the dynamic state of their nodes. Here we study epidemic dynamics in an adaptive network, where susceptibles are able to avoid contact with…
The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level…
A living cell's interior is one of the most complex and intrinsically dynamic systems, providing an elaborate interplay between cytosolic crowding and ATP-driven motion, which controls cellular functionality. Here, we investigated two…
This chapter shows how toroidal diffusions are convenient methodological tools for modelling protein evolution in a probabilistic framework. The chapter addresses the construction of ergodic diffusions with stationary distributions equal to…
Whether it be physical, biological or social processes, complex systems exhibit dynamics that are exceedingly difficult to understand or predict from underlying principles. Here we report a striking correspondence between the collective…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
It is well established that a wide variety of phenomena in cellular and molecular biology involve anomalous transport e.g. the statistics for the motility of cells and molecules are fractional and do not conform to the archetypes of simple…
We study the robustness and stability of the yeast cell regulatory network by using a general inhomogeneous discrete model. We find that inhomogeneity, on average, enhances the stability of the biggest attractor of the dynamics and that the…
Recently, we reported the electrorheoimaging (ERI) technique (Bahraminasr et al, 2026), and found that frequency-dependent electric field of an oil-in-oil emulsion yields two distinct regimes: a high-frequency dipolar, electrorheological…
This thesis is a compendium of research which brings together ideas from the fields of Complex Networks and Computational Neuroscience to address two questions regarding neural systems: 1) How the activity of neurons, via synaptic changes,…
Low-density lipoproteins (LDLs) serve as nutrient reservoirs in egg yolk for embryonic development and as promising drug carriers. Both roles critically depend on their mobility in densely crowded biological environments. Under these…
Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery.…
Diffusion, a fundamental internal mechanism emerging in many physical processes, describes the interaction among different objects. In many learning tasks with limited training samples, the diffusion connects the labeled and unlabeled data…
Cellularized tissue and polymer networks can both transition from floppy to rigid as a function of their control parameters, and, yet, the two systems often mechanically interact, which may affect their respective rigidities. To study this…
Active semiflexible filaments are crucial in various biophysical processes, yet insights into their single-filament behavior have predominantly relied on theory and simulations, owing to the scarcity of controllable synthetic systems. Here,…