Related papers: Radial distribution of RNA genome packaged inside …
We investigate condensation of a long confined chiral nematic polymer inside a spherical enclosure, mimicking condensation of DNA inside a viral capsid. The Landau-de Gennes nematic free energy {\sl Ansatz} appropriate for nematic polymers…
Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integrations as stochastic and…
The effectiveness of biochemical antivirals are vulnerable to mutations, motivating physical approaches. Recent experiments with ultrasound reveal viral disruption at MHz frequencies, yet the mechanism remains unclear. We model viruses as…
We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic…
We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles. The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the…
The ejection of DNA from a bacterial virus (``phage'') into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The simplest mechanism for this motion is…
We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
Crystallization of proteins, specifically proteins of medical relevance, is performed for various reasons such as to understand the protein structure and to design therapies. Obtaining kinetic constants in rate laws for nucleation and…
Efficient replication and assembly of virus particles are integral to the establishment of infection. In addition to the primary role of the capsid protein (CP) in encapsidating the RNA progeny, experimental evidence on positive sense…
In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
The behavior of colloidal particles with a hard core and a soft shell has attracted the attention for researchers in the physical-chemistry interface not only due the large number of applications, but due the unique properties of these…
In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is…
Small angle neutron scattering intensity distributions taken from cytochrome C and lysozyme protein solutions show a rising intensity at very small wave vector, Q, which can be interpreted in terms of the presence of a weak long-range…
The random sequential adsorption of various particle shapes is studied in order to determine the influence of particle anisotropy on the saturated random packing. For all tested particles there is an optimal level of anisotropy which…
A complexity-theoretic approach to studying biological networks is proposed. A simple graph representation is used where molecules (DNA, RNA, proteins and chemicals) are vertices and relations between them are directed and signed…
In this paper we consider the diffusion of nanoparticles taken up by a semi-permeable spherical cell placed in the path of a diffusive particle field generated by an external planar source. The cell interior and exterior are characterized…
The most efficient way to pack equally sized spheres isotropically in 3D is known as the random close packed state, which provides a starting point for many approximations in physics and engineering. However, the particle size distribution…