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Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
In this work, we focus on the family of shell formulations referred to as "solid shells", where the simulation of shell-type structures is performed by means of a mesh of 3D solid elements, with typically only one element through the…
We investigate methods for modelling metabolism within populations of cells. Typically one represents the interaction of a cloned population of cells with their environment as though it were one large cell. The question is as to whether any…
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
Previous divide-and-conquer segmentation analyses of DNA sequences do not provide a satisfactory stopping criterion for the recursion. This paper proposes that segmentation be considered as a model selection process. Using the tools in…
This paper presents the first in a series of results that allow us to develop a theory providing finer control over the complexity of normalisation, and in particular of cut elimination. By considering atoms as self-dual non-commutative…
Drying of biologically-relevant sessile droplets, including passive systems (like DNA and proteins), as well as active microbial systems comprising bacteria and algae, have garnered considerable attention over the last decades. Distinct…
We study the collective behaviour of an ensemble of coupled motile elements whose interactions depend on time and are alternatively attractive or repulsive. The evolution of interactions is driven by individual internal variables with…
Semiconstrained systems were recently suggested as a generalization of constrained systems, commonly used in communication and data-storage applications that require certain offending subsequences be avoided. In an attempt to apply…
Homoclinic snaking is a widespread phenomenon observed in many pattern-forming systems. Demonstrating its occurrence in non-perturbative regimes has proven difficult, although a forcing theory has been developed based on the identification…
Splice detection models are the need of the hour since splice manipulations can be used to mislead, spread rumors and create disharmony in society. However, there is a severe lack of image splicing datasets, which restricts the capabilities…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
Cell crawling requires the generation of intracellular forces by the cytoskeleton and their transmission to an extracellular substrate through specific adhesion molecules. Crawling cells show many features of excitable systems, such as…
Branched actin networks at the leading edge of a crawling cell evolve via protein-regulated processes such as polymerization, depolymerization, capping, branching, and severing. A formulation of these processes is presented and analyzed to…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
We propose a mechanism to explain what occurs when a mixture of grains of different sizes and different shapes (i.e. different repose angles) is poured into a quasi-two-dimensional cell. Specifically, we develop a model that displays…
Confined thin structures are ubiquitous in nature. Spatial and length constraints have led to a number of novel packing strategies at both the micro-scale, as when DNA packages inside a capsid, and the macro-scale, seen in plant root…
A (closed) dynamical system is a notion of how things can be, together with a notion of how they may change given how they are. The idea and mathematics of closed dynamical systems has proven incredibly useful in those sciences that can…
Complexity has been a recurrent research topic in cellular automata because they represent systems where complex behaviors emerge from simple local interactions. A significant amount of previous research has been conducted proposing…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…