Related papers: Radial distribution of RNA genome packaged inside …
Viruses are known to tolerate wide ranges of pH and salt conditions and to withstand internal pressures as high as 100 atmospheres. In this paper we investigate the mechanical properties of viral capsids, calling explicit attention to the…
The present study focuses on the receptor driven endocytosis typical of viral entry into a cell. A locally increased density of receptors at the time of contact between the cell and the virus is necessary in this case. The virus is…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
During the alphavirus lifecycle, a nucleocapsid core buds through the cell membrane to acquire an outer envelope of lipid membrane and viral glycoproteins. However, the presence of a nucleocapsid core is not required for assembly of…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
The energetic and transport properties of a double-stranded DNA dodecamer encapsulated in hydrophobic carbon nanotubes are probed employing two limiting nanotube diameters, D=4 nm and D=3 nm, corresponding to (51,0) and (40,0) zig-zag…
We present results relevant to the equilibrium organization of DNA strands of arbitrary length interacting with a spherical organizing center, suggestive of DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in which a…
By a combination of analytical and numerical methods, the density profile of a momentarily at rest spherical star is varied, and the corresponding response in the area of the spherical shells is monitored. It is shown that the inner…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
We show that the icosahedral packings of protein capsomeres proposed by Caspar and Klug for spherical viruses become unstable to faceting for sufficiently large virus size, in analogy with the buckling instability of disclinations in…
The RNA Inverse Folding problem comes from computational biology. The goal is to find a molecule that has a given folding. It is important for scientific fields such as bioengineering, pharmaceutical research, biochemistry, synthetic…
We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…
Formation of base pairs between the nucleotides of an RNA sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching --…
The protective capsid encasing the genetic material of Human Immunodeficiency Virus (HIV) has been shown to traverse the nuclear pore complex (NPC) intact, despite exceeding the passive diffusion threshold by over three orders of magnitude.…
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with…
Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells.…