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We describe our experiences in using SPIN to verify parts of the Multi Purpose Daemon (MPD) parallel process management system. MPD is a distributed collection of processes connected by Unix network sockets. MPD is dynamic: processes and…
The response of cells during spreading and motility is dictated by several multi-physics events, which are triggered by extracellular cues and occur at different time-scales. For this sake, it is not completely appropriate to provide a cell…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Active emulsions and liquid crystalline shells are intriguing and experimentally realisable types of topological matter. Here we numerically study the morphology and spatiotemporal dynamics of a double emulsion, where one or two passive…
Membrane systems represent a computational model that operates in a distributed and parallel manner, inspired by the behavior of biological cells. These systems feature objects that transform within a nested membrane structure. This…
Sporulation in Bacillus subtilis serves as a paradigm for the development of two different cell types (mother cell and prespore) from a single cell. The mechanism by which the two different developmental programs are initiated has been much…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
Clustering is a fundamental data mining tool that aims to divide data into groups of similar items. Generally, intuition about clustering reflects the ideal case -- exact data sets endowed with flawless dissimilarity between individual…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
The dynamical behavior of two types of non-equilibrium systems is discussed: $(a)$ two-dimensional cellular structures, and $(b)$ living polymers. Simple models governing their evolution are introduced and steady state distributions (cell…
Entangled states are ubiquitous amongst fibrous materials, whether naturally occurring (keratin, collagen, DNA) or synthetic (nanotube assemblies, elastane). A key mechanical characteristic of these systems is their ability to reorganise in…
Using numerical simulations, we examine a simple model of two or more coupled one-dimensional channels of driven particles with repulsive interactions in the presence of quenched disorder. We find that this model exhibits a remarkably rich…
A Boolean network is a discrete dynamical system operating on vectors of Boolean variables. The action of a Boolean network can be conveniently expressed as a system of Boolean update functions, computing the new values for each component…
Spin coating is an out-of-equilibrium technique for producing polymer films and colloidal crystals quickly and reproducibly. In this review, we present an overview of theoretical and experimental studies of the spin coating of colloidal…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…
We propose a new model based on the Ising model with the aim to study synaptic plasticity phenomena in neural networks. It is today well established in biology that the synapses or connections between certain types of neurons are…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
The cytoskeleton is an important subsystem of cells that is involved for example in cell division and locomotion. It consists of filaments that are cross-linked by molecular motors that can induce relative sliding between filaments and…