Related papers: DNA Looping Kinetics Analyzed Using Diffusive Hidd…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
DNA helicases are molecular motors that use the energy from ATP hydrolysis to move along DNA, promoting the unwinding or rewinding of the double helix. Here, we use magnetic and optical tweezers to track the motion of three helicases, gp41,…
We observed reptation of single DNA molecules in fused silica nanoslits of sub-30 nm height. The reptation behavior and the effect of confinement are quantitatively characterized using orientation correlation and transverse fluctuation…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
We demonstrate the use of multiscale polymer modelling to quantitatively predict DNA linear dichroism (LD) in shear flow. LD is the difference in absorption of light polarised along two perpendicular axes, and has long been applied to study…
There have been increasing reports that the diffusion coefficient of macromolecules depends on time and fluctuates randomly. Here, a novel method to elucidate the fluctuating diffusivity from trajectory data is developed. The time-averaged…
We study the impact of DNA coiling on the search rate of proteins moving along the DNA contour interspersed by three-dimensional (3D) bulk excursions. When the DNA is coiled proteins performing short 3D hops along a DNA segment can be…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
We develop a (nearly) unbiased particle filtering algorithm for a specific class of continuous-time state-space models, such that (a) the latent process $X_t$ is a linear Gaussian diffusion; and (b) the observations arise from a Poisson…
Biomarker measurements obtained by blood sampling are often used as a non-invasive means of monitoring tumour progression in cancer patients. Diseases evolve dynamically over time, and studying longitudinal observations of specific…
DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater…
Evolution of the reduced density matrix for a subsystem is studied to determine deviations from its Markov character for a system consisting of a closed chain of $N$ oscillators with one of them serving as a subsystem. The dependence on $N$…
Mode-locked lasers, which produce ultrashort pulses in the picosecond and femtosecond range, have enabled some of the most precise measurements. However, despite significant recent progress, resolving the temporal behavior of their short…
Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics. Major protein contributors to chromosome structure and dynamics are condensin and…
We consider the problem of learning two families of time-evolving random measures from indirect observations. In the first model, the signal is a Fleming--Viot diffusion, which is reversible with respect to the law of a Dirichlet process,…
In this paper, we study DNA-based molecular communication with microarray-style reception under reversible hybridization, where the bound-state observation exhibits both inter-symbol interference and colored counting noise. To capture these…
One of the proposed damping mechanisms of coronal (transverse) loop oscillations in the kink-mode is resonant absorption as a result of the Alfven speed variation at the outer boundary of coronal loops. Analytical expressions for the period…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
In charged current weak interaction processes, neutrinos are produced in an entangled state with the charged lepton. This correlated state is disentangled by the measurement of the charged lepton in a detector at the production site. We…