Related papers: Viral RNA as a branched polymer
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
Highly connected and yet sparse graphs (such as expanders or graphs of high treewidth) are fundamental, widely applicable and extensively studied combinatorial objects. We initiate the study of such highly connected graphs that are, in…
Disordered networks of semiflexible filaments are common support structures in biology. Familiar examples include fibrous matrices in blood clots, bacterial biofilms, and essential components of cells and tissues of plants, animals, and…
We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…
In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…
The advent of high-throughput sequencing technologies has lead to vast comparative genome sequences. The construction of gene-gene interaction networks or dependence graphs on the genome scale is vital for understanding the regulation of…
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…
Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional…
The rapid worldwide spread of severe viral infections, often involving novel modifications of viruses, poses major challenges to our health care systems. This means that tools that can efficiently and specifically diagnose viruses are much…
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins:…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
This work examines field theories for RNA-like polymers with single strand and double strand polymers and a periodic base sequence. These field theories originate from lattice models, describe polymers in a good solvent, and in principle…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
Protein chains of the (FG)$_n$ ($n \simeq$ 300) type cap the cytoplasmatic side of the nucleopore complex, which connects the nucleus to the remainder of an eukaryotic cell. We study the properties of three fundamental polymer models that…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native…
The locations of different mRNA molecules can be revealed by multiplexed in situ RNA detection. By assigning detected mRNA molecules to individual cells, it is possible to identify many different cell types in parallel. This in turn enables…
Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is widely used for gene delivery. It is considered here in terms of discrete charges of DNA. We concentrate on the worst scenario case when in the…
Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in…
In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and…