Related papers: Radial distribution of RNA genome packaged inside …
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication…
In bacteria such as $\textit{Escherichia coli}$, DNA is compacted into a nucleoid near the cell center, while ribosomes$-$molecular complexes that translate messenger RNAs (mRNAs) into proteins$-$are mainly localized at the poles. We study…
An extension of the Random Sequential Adsorption (RSA) model has been proposed recently, motivated by the coverage of oil droplets by DNA-functionalized colloidal particles. Particles arrive to a flat substrate with a uniform flux F but…
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…
Obtaining general relations between macroscopic properties of random assemblies, such as density, and the microscopic properties of their constituent particles, such as shape, is a foundational challenge in the study of amorphous materials.…
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…
It is conceivable that an RNA virus could use a polysome, that is, a string of ribosomes covering the RNA strand, to protect the genetic material from degradation inside a host cell. This paper discusses how such a virus might operate, and…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides…
Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of…
Viruses can amplify their genomes following different replication modes (RMs) ranging from the stamping machine replication (SMR) model to the geometric replication (GR) model. Different RMs are expected to produce different evolutionary…
We have studied the packing of congruent disks on a spherical cap, for caps of different size and number of disks, $N$. This problem has been considered before only in the limit cases of circle packing inside a circle and on a sphere…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
Nanoparticles, such as viruses, can enter cells via endocytosis. During endocytosis, the cell surface wraps around the nanoparticle to effectively eat it. Prior focus has been on how nanoparticle size and shape impacts endocytosis. However,…
We investigate the thermodynamics of complexation of functionalized charged nano-spheres with viral proteins. The physics of this problem is governed by electrostatic interaction between the proteins and the nano-sphere cores (screened by…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
The volume occupied by unconstrained bacterial DNA in physiological solutions exceeds 1000 times the volume of the cell. Still, it is confined to a well defined region of the cell called the nucleoid, which occupies only a fraction of the…
While small single stranded viral shells encapsidate their genome spontaneously, many large viruses, such as the Herpes virus or Infectious Bursal Disease Virus (IBDV), typically require a template, consisting of either scaffolding proteins…
RNA viruses exist in large intra-host populations which display great genotypic and phenotypic diversity. We analyze a model of viral competition between two different viral strains infecting a constantly replenished cell pool, in which we…
Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ~500 mg/ml. This high density requires substantial compression of the normal B form…