Related papers: Double Helical Conformation and Extreme Rigidity i…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
We study how the three-dimensional shape of rigid filaments determines the microscopic dynamics and macroscopic rheology of entangled semi-dilute Brownian suspensions. To control the filament shape we use bacterial flagella, which are…
Motivated by experimental and numerical studies revealing that discoidal high-density lipoprotein (HDL) particles may adopt flat elliptical and nonplanar saddle-like configurations, it is hypothesized that these might represent stabilized…
Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal…
We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
Micelles and vesicles are promising candidates in targeted drug/gene delivery, bioreactors, and templates for nanoparticle synthesis. We investigated the morphology and dynamics of PEG-PDMS-PEG triblock copolymer nano-scale assemblies…
Although carbon nanotubes are potential candidates for DNA encapsulation and subsequent delivery of biological payloads to living cells, the thermodynamical spontaneity of DNA encapsulation under physiological conditions is still a matter…
The discovery of archetypal two-dimensional (2D) materials provides enormous opportunities in both fundamental breakthroughs and device applications, as evident by the research booming in graphene, atomically thin transition-metal…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…
The in vivo free energy of looping double-stranded DNA by the lac repressor has a remarkable behavior whose origins are not fully understood. In addition to the intrinsic periodicity of the DNA double helix, the in vivo free energy has an…
Atomic Force Microscopy analysis is employed to study the geometrical and topological properties of $3000$kbp DNA molecules fixed in mica substrates with $MgCl_{2}$. We found that the aggregates on the substrate surface for certain salt…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT)…
We derive formulae for the electrostatic interaction between two long, rigid macromolecules that may have arbitrary surface charge patterns and cross at an arbitrary interaxial angle. We calculate the dependence of the interaction energy on…
Relying on symmetry considerations appropriate for helical biopolymers such as DNA and filamentous actin, we argue that crystalline packings of mutually repulsive helical macromolecules fall principally into two categories: unfrustrated…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
The DNA double helix is a polyanionic macromolecule that in water solutions is neutralized by metal ions (counterions). The property of the counterions to stabilize the water network (positive hydration) or to make it friable (negative…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…