Related papers: Ring DNA confers enhanced bulk elasticity and rest…
Bacterial genomes are partitioned into kilobases long domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbours. This is made possible by proteins…
Polymer filaments form the foundation of biology from cell scaffolding to DNA. Their study and fabrication play an important role in a wide range of processes from tissue engineering to molecular machines. We present a simple method to…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
Tandem-duplication-random-loss (TDRL) is an important genome rearrangement operation studied in evolutionary biology. This paper investigates some of the formal properties of TDRL operations on the symmetric group (the space of permutations…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one…
The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates…
The volume occupied by the unconstrained genomic DNA of prokaryotes in saline solutions is thousand times larger than the cell. Moreover, it is not separated from the rest of the cell by a membrane. Nevertheless, it occupies only a small…
Diffusive transport of small molecules within the internal structures of biological and synthetic material systems is complex because the crowded environment presents chemical and physical barriers to mobility. We explored this mobility…
The use of coherent x-ray beams has been greatly developing for the past decades. They are now used by a wide scientific community to study biological materials, phase transitions in crystalline materials, soft matter, magnetism, strained…
DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because bacteria can express DNA chains that are very long yet perfectly monodisperse. The latter…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby…
We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise…
The effects of entanglement in solutions and melts of unknotted ring polymers have been addressed by several theoretical and numerical studies. The system properties have been typically profiled as a function of ring contour length at fixed…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
The transport of DNA polymers through nanoscale pores is central to many biological processes, from bacterial gene exchange to viral infection. In single-molecule nanopore sensing, the detection of nucleic acid and protein analytes relies…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
Elements composing complex systems usually interact in several different ways and as such the interaction architecture is well modelled by a multiplex network. However often this architecture is hidden, as one usually only has experimental…