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The mechanical properties of polymer gels based on cytoskeleton proteins (e.g. actin) have been studied extensively due to their significant role in biological cell motility and in maintaining the cell's structural integrity. Microrheology…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
Mutations of genetic sequences are often accompanied by their recombinations, known as phylogenetic networks. These networks are typically reconstructed from coalescent processes that may arise from optimal merging or fitting together a…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
We propose using graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing, and perform molecular dynamics simulations in conjunction with electronic transport calculations to explore the potential merits of…
Short, partially complementary, single-stranded (ss)DNA strands can form nanostructures with a wide variety of shapes and mechanical properties. It is well known that semiflexible, linear dsDNA can undergo an isotropic to nematic (IN) phase…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
Feature foundation models - usually vision transformers - offer rich semantic descriptors of images, useful for downstream tasks such as (interactive) segmentation and object detection. For computational efficiency these descriptors are…
Edge states emerge in diverse areas of science, offering new opportunities for the development of novel electronic or optoelectronic devices, sound and light propagation controls in acoustics and photonics. Previous experiments on edge…
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
Chitosan (CT) is an antibacterial polysaccharide that has been investigated for drug carriers, haemostats and wound dressings. For these applications, customised CT devices can often be obtained with specific experimental conditions, which…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
As a generic model system of an asymmetric binary fluid mixture, hexadecane dissolved in carbon dioxide is considered, using a coarse-grained bead-spring model for the short polymer, and a simple spherical particle with Lennard-Jones…
Despite the widely recognized success of residual connections in modern neural networks, their design principles remain largely heuristic. This paper introduces KITINet (Kinetics Theory Inspired Network), a novel architecture that…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
Edge detection is a fundamental problem in different computer vision tasks. Recently, edge detection algorithms achieve satisfying improvement built upon deep learning. Although most of them report favorable evaluation scores, they often…
The crystallization of bundles in filament networks interacting via long-range repulsions in confinement is described by a phenomenological model. The model demonstrates the formation of the hexagonal crystalline order via the interplay of…
Bacterial biofilm segmentation poses significant challenges due to lack of apparent structure, poor imaging resolution, limited contrast between conterminous cells and high density of cells that overlap. Although there exist bacterial…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…