Related papers: DNA nano-mechanics: how proteins deform the double…
The base sequences of DNA contain the genetic code and to decode it a double helical DNA has to open its base pairs. Recent studies have shown that one can use a third strand to identify the base sequences without opening the double helix…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
Solid-state nanopore and nanopipette sensors are powerful devices for the detection, quantification and structural analysis of biopolymers such as DNA and proteins, especially in carrier-enhanced resistive-pulse sensing. However, hundreds…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
A fundamental design rule that nature has developed for biological machines is the intimate correlation between motion and function. One class of biological machines is molecular motors in living cells, which directly convert chemical…
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves…
DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix,…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount…
The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…
Although DNA is often bent in vivo, it is unclear how DNA-bending forces modulate DNA-protein binding affinity. Here, we report how a range of DNA-bending forces modulates the binding of the Integration Host Factor (IHF) protein to various…
We study different configurations of permanent magnets and ferromagnetic circuit, in order to optimize the magnetic field for the so-called ``magnetic tweezers'' technique, for studing mechanical properties of DNA molecules. The magnetic…
We reinvestigate the model originally studied by Neukirch and Marko that describes the extension, torque and supercoiling in single, stretched and twisted DNA molecules, which consists of a mixture of extended and supercoiled state, using…
The folding angle distribution of stretched and negatively supercoiled DNA double-helix is investigated based on a theoretical model we proposed earlier [H. Zhou et al., Phys. Rev. Lett. 82, 4560 (1999)]. It is shown that pulling can…
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
Debates about conductivity of DNAs have been recently renewed due to contradictory results of direct measurements by use of electrical contacts to molecules. In several works it was discovered that double-stranded (ds)DNAs are conductors:…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…