Related papers: Ion-dependent DNA Configuration in Bacteriophage C…
Membranes consist of pores and the walls of these pores are often charged. In contact with an aqueous solution, the pores fill with water and ions migrate from solution into the pores until chemical equilibrium is reached. The distribution…
As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as…
Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which…
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors.…
We showed in our previous studies that just $3\%$ cross-links, at special points along the contour of the bacterial DNA help the DNA-polymer to get organized at micron length scales \cite{jpcm,epl}. In this work, we investigate how does the…
We investigate the localization property of an electron in the disordered two-chain system (ladder model) with long-range correlation as a simple model for electronic property in DNA sequence. The chains are constructed by repetition of the…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
Translocation of a single stranded DNA (ssDNA) through an alpha-hemolysin channel in a lipid membrane driven by applied transmembrane voltage V was extensively studied recently. While the bare charge of the ssDNA piece inside the channel is…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
We present a new dynamical model of DNA. This model has two degrees of freedom per base-pair: one radial variable related to the opening of the hydrogen bonds and an angular one related to the twisting of each base-pair responsible for the…
The osmotic coefficient of B-DNA in water may, in moderately dilute solutions, deviate as much as 100 % from predictions based on a simple 'counterion condensation' theory. We determine the results for osmotic properties via a cell model…
Biological condensates are assemblies of proteins and nucleic acids that form membraneless compartments in cells and play essential roles in cellular functions. In many cases they exhibit the physical properties of liquid droplets that…
A purely electrical sensing scheme is presented that determines the concentration of macromolecules in solution by measuring the capacitance between planar microelectrodes. Concentrations of DNA in the ng/mL range have been used in samples…
Electrostatic interactions play a central role in the assembly of single-stranded RNA viruses. Under physiological conditions of salinity and acidity, virus capsid assembly requires the presence of genomic material that is oppositely…
The volume occupied by the unconstrained genomic DNA of prokaryotes in saline solutions is thousand times larger than the cell. Moreover, it is not separated from the rest of the cell by a membrane. Nevertheless, it occupies only a small…
In this article we address the three-dimensional modeling and simulation of biological ion channels using a continuum-based approach. Our multi-physics formulation self-consistently combines, to the best of our knowledge for the first time,…
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…
A simple model is proposed aimed to investigate how the amount of dissociated ions influences the mechanical stability of viral capsids. After an osmotic and mechanical equilibrium is established with the outer solution, a non-adiabatic…