Related papers: Macroscopic loop formation in circular DNA denatur…
Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate…
Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Understanding the motion of particles with ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or…
The decay of metastable states is dominated by quantum tunneling at low temperatures and by thermal activation at high temperatures. The escape rate of a particle out of a square well is calculated within a semi-classical approximation and…
We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects…
Deformation twinning, which occurs in fcc metals only under particular conditions of intrinsic material properties, microstructure, and loading conditions, occupies an indispensable place in their deformation mechanism maps. Nonetheless,…
Within the t-J model of copper-oxides, the condensation energy can be related to the change in the dynamical spin structure factor between the superconducting and the normal states. By analyzing previous experimental data, we show that the…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
Advances in scanning tunneling spectroscopy reveal the presence of superconducting nanoregions well past the bulk thermal transition in strongly disordered superconductors. We use a Monte Carlo tool to capture the spatially differentiated…
We show that minuscule entropic forces, on the order of 100 fN, can prevent the formation of DNA loops--a ubiquitous means of regulating the expression of genes. We observe a tenfold decrease in the rate of LacI-mediated DNA loop formation…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
In this paper I intend to show that macroscopic entanglement is possible at high temperatures. I analyze multipartite entanglement produced by the $\eta$ pairing mechanism which features strongly in the fermionic lattice models of high…
Understanding why and how crystalline solids melt remains a central problem in condensed-matter physics. Dislocation loops are fundamental topological excitations that control the thermodynamic stability of crystals, yet their role in…