Related papers: Measuring the force ejecting DNA from phage
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…
We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by…
We study unzipping of a complementary RNA-DNA helix applied to an external force, focusing on the force-force correlations. While at the microscopic level these are given by the sequence, the experiment measures effective, macroscopic…
Cells and other soft particles are often forced to flow in confined geometries in both laboratory and natural environments, where the elastic deformation induces an additional drag and pressure drop across the particle. In contrast with…
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA…
Bacteriophages, viruses that infect bacteria, store their micron long DNA inside an icosahedral capsid with a typical diameter of 40 nm to 100 nm. Consistent with experimental observations, such confinement conditions induce an arrangement…
The terminase motors of bacteriophages have been shown to be among the strongest active machines in the biomolecular world, being able to package several tens of kilobase pairs of viral genome into a capsid within minutes. Yet these motors…
The complex interplay between the various attractive and repulsive forces that mediate between biological membranes governs an astounding array of biological functions: cell adhesion, membrane fusion, self-assembly, binding-unbinding…
Using molecular dynamics (MD) simulations we study the interactions between elongated colloidal particles (length to breath ratio > 1) in a nematic host. The simulation results are compared to the results of a Landau-de Gennes elastic free…
The rapid worldwide spread of severe viral infections, often involving novel modifications of viruses, poses major challenges to our health care systems. This means that tools that can efficiently and specifically diagnose viruses are much…
Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes…
The stopping force is the force exerted on a charged projectile by the excess charge of the wake generated by the projectile in the surrounding plasma. Since the wake does not instantly adjust to the projectile velocity, the stopping force…
DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical…
We study by using Monte Carlo simulations the hysteresis in unzipping and rezipping of a double stranded DNA (dsDNA) by pulling its strands in opposite directions in the fixed force ensemble. The force is increased, at a constant rate from…
A large conformational change in the reaction co-ordinate and the role of the solvent in the formation of base-pairing are combined to settle a long standing issue {\it i.e.} prediction of re-entrance in the force induced transition of DNA.…
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase…
With a loose reference to problems of penetration in biomechanics (for instance, a nanoparticle penetrating through a cell's membrane or a cell sucked with a pipette), the role of configurational forces is investigated during the process in…
The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum…
Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the…
Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be…