Related papers: Radial distribution of RNA genome packaged inside …
We develop equilibrium and kinetic theories that describe the assembly of viral capsid proteins on a charged central core, as seen in recent experiments in which brome mosaic virus (BMV) capsids assemble around nanoparticles functionalized…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
A theory is presented of DNA hairpins enclosed in a nanochannel. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The free energy of the hairpin computed…
Recent studies have shown that single-stranded viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison it has been suggested that wild-type…
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction $\phi \approx 0.56$, which is the same as dense, random packing of amino…
This paper develops and analyzes optimization models for rapid detection of viruses in large contact networks. In the model, a virus spreads in a stochastic manner over an undirected connected graph, under various assumptions on the spread…
We introduce a computational topology-based approach with unsupervised machine-learning algorithms to estimate the database size and content of RNA-like graph topologies. Specifically, we apply graph theory enumeration to generate all…
Electrostatic interaction is the driving force for the encapsulation by virus coat proteins of nanoparticles such as quantum dots, gold particles and magnetic beads for, e.g., imaging and therapeutic purposes. In recent experimental work,…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
We study the optimal packing of short, hard spherocylinders confined to lie tangential to a spherical surface, using simulated annealing and molecular dynamics simulations. For clusters of up to twelve particles, we map out the changes in…
The ability of virus shells to encapsulate a wide range of functional cargoes, especially multiple cargoes - siRNAs, enzymes, and chromophores - has made them an essential tool in biotechnology for advancing drug delivery applications and…
Confined thin structures are ubiquitous in nature. Spatial and length constraints have led to a number of novel packing strategies at both the micro-scale, as when DNA packages inside a capsid, and the macro-scale, seen in plant root…
The densest local packings of N identical nonoverlapping spheres within a radius Rmin(N) of a fixed central sphere of the same size are obtained using a nonlinear programming method operating in conjunction with a stochastic search of…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
Irreversible adsorption of spheres on flat collectors having dimension $d<2$ is studied. Molecules are adsorbed on Sierpinski's Triangle and Carpet like fractals ($1<d<2$), and on General Cantor Set ($d<1$). Adsorption process is modeled…
MicroRNAs (miRNAs) are small RNA molecules, about 22 nucleotide long, which post-transcriptionally regulate their target messenger RNAs (mRNAs). They accomplish key roles in gene regulatory networks, ranging from signaling pathways to…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
Inspired to understand the complex spectrum of space-filling organizations the dsDNA genome within the capsid of bacterial viruses, we study a minimal, coarse-grained model of single chains densely-packed into a finite spherical volume. We…