Related papers: Viral RNA as a branched polymer

This methods paper presents computational protocols for the identification of non-coding RNA genes or RNA motifs within genomic sequences. An application to bacterial small RNA is proposed.

{\it Transcription} is the process whereby RNA molecules are polymerized by molecular machines, called RNA polymerase (RNAP), using the corresponding DNA as the template. Recent {\it in-vivo} experiments with single cells have established…

RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…

Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…

RNA molecules in living cells form what look like liquid droplets formed by liquid/liquid phase separation. But unlike the molecules in conventional phase separating mixtures, RNA molecules are transported by molecular motors that consume…

RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…

The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…

We study theoretically the structure of sliding grafted polymer layers or SGP layers. These interfacial structures are built by attaching each polymer to the substrate with a ring-like molecule such as cyclodextrins. Such a topological…

Emerging evidence suggests that the introns and intergenic sequences of the genomes of higher eukaryotes (the ``junk'' DNA) codes for a vast, RNA-based, genetic regulatory network. It is believed that this network is responsible for the…

We consider an inextensible, semiflexible polymer or worm-like chain which is confined in the transverse direction by a parabolic potential and subject to a longitudinal force at the ends, so that the polymer is stretched out and…

This is the last part of a series of five articles published in Journal of Rheology (Maier et al. (1998), Thimm et al. (1999a), Thimm et al. (2000a), Thimm et al. (2000c)) in which progress on the determination of binary molecular weight…

DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…

We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by…

We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…

Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…

RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…

Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…

We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…

Ribonucleic Acid (RNA) can fold into shapes that perform functions in the cell. These foldings are governed by Watson-Crick base pairing, namely Adenine to Uracil and Cytosine to Guanine (A-U and G-C). The properties of the H-P…

In the present work, we further study the computational power of virus machines (VMs in short).VMs provide a computing paradigm inspired by the transmission and replication networks of viruses.VMs consist of process units (called hosts)…