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We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
Several orders of magnitude typically separate the contour length of eukaryotic chromosomes and the size of the nucleus where they are confined. The ensuing topological constraints can slow down the relaxation dynamics of genomic filaments…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
Cellular functions crucially depend on the precise execution of complex biochemical reactions taking place on the chromatin fiber in the tightly packed environment of the cell nucleus. Despite the availability of large data sets probing…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
The rapid progress in the field of molecular electronics has led to an increasing interest on DNA oligomers as possible components of electronic circuits at the nanoscale. For this, however, an understanding of charge transfer and transport…
Epigenetic modifications to histones may promote either activation or repression of the transcription of nearby genes. Recent experimental studies show that the promoters of many lineage-control genes in stem cells have "bivalent domains"…
The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally-occurring polymers can navigate a vast phase space and rapidly find their lowest free energy (folded) state. Thus,…
Animal morphogenesis often involves significant shape changes of epithelial tissue sheets. Great progress has been made in understanding the underlying cellular driving forces and their coordination through biomechanical feedback loops.…
Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such…
Polymers, macromolecules formed from covalently bonded monomers, underpin countless technologies and are indispensable to modern life. While deep learning is advancing polymer science, existing methods typically represent the whole polymer…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
Morphogenetic dynamics of tissue sheets require coordinated cell shape changes regulated by global patterning of mechanical forces. Inspired by such biological phenomena, we propose a minimal mechanochemical model based on the notion that…
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the…