AFM pulling and the folding of donor-acceptor oligorotaxanes: phenomenology and interpretation

The thermodynamic driving force in the self-assembly of the secondary structure of a class of donor-acceptor oligorotaxanes is elucidated by means of molecular dynamics simulations of equilibrium isometric single-molecule force spectroscopy AFM experiments. The oligorotaxanes consist of cyclobis(paraquat-\emph{p}-phenylene) rings threaded onto an oligomer of 1,5-dioxynaphthalenes linked by polyethers. The simulations are performed in a high dielectric medium using MM3 as the force field. The resulting force vs. extension isotherms show a mechanically unstable region in which the molecule unfolds and, for selected extensions, blinks in the force measurements between a high-force and a low-force regime. From the force vs. extension data the molecular potential of mean force is reconstructed using the weighted histogram analysis method and decomposed into energetic and entropic contributions. The simulations indicate that the folding of the oligorotaxanes is energetically favored but entropically penalized, with the energetic contributions overcoming the entropy penalty and effectively driving the self-assembly. In addition, an analogy between the single-molecule folding/unfolding events driven by the AFM tip and the thermodynamic theory of first-order phase transitions is discussed and general conditions, on the molecule and the cantilever, for the emergence of mechanical instabilities and blinks in the force measurements in equilibrium isometric pulling experiments are presented. In particular, it is shown that the mechanical stability properties observed during the extension are intimately related to the fluctuations in the force measurements.Comment: 42 pages, 17 figures, accepted to the Journal of Chemical Physic

The DNA60IFX contest

We present the full story of Genome Biology's recent DNA60IFX contest, as told by the curators and winner of what turned out to be a memorable and hotly contested bioinformatics challenge. Full solutions, including scripts, are available at http://genomebiology.com/about/update/DNA60_ANSWER

Current challenges in de novo plant genome sequencing and assembly

ABSTRACT: Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community

Fundamental Behavior of Electric Field Enhancements in the Gaps Between Closely Spaced Nanostructures

We demonstrate that the electric field enhancement that occurs in a gap between two closely spaced nanostructures, such as metallic nanoparticles, is the result of a transverse electromagnetic waveguide mode. We derive an explicit semianalytic equation for the enhancement as a function of gap size, which we show has a universal qualitative behavior in that it applies irrespective of the material or geometry of the nanostructures and even in the presence of surface plasmons. Examples of perfect electrically conducting and Ag thin-wire antennas and a dimer of Ag spheres are presented and discussed.Comment: 9 pages and 4 figure

The advantages of SMRT sequencing

Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes

On the linear response and scattering of an interacting molecule-metal system

A many-body Green's function approach to the microscopic theory of plasmon-enhanced spectroscopy is presented within the context of localized surface-plasmon resonance spectroscopy and applied to investigate the coupling between quantum-molecular and classical-plasmonic resonances in monolayer-coated silver nanoparticles. Electronic propagators or Green's functions, accounting for the repeated polarization interaction between a single molecule and its image in a nearby nanoscale metal, are explicitly computed and used to construct the linear-response properties of the combined molecule-metal system to an external electromagnetic perturbation. Shifting and finite lifetime of states appear rigorously and automatically within our approach and reveal an intricate coupling between molecule and metal not fully described by previous theories. Self-consistent incorporation of this quantum-molecular response into the continuum-electromagnetic scattering of the molecule-metal target is exploited to compute the localized surface-plasmon resonance wavelength shift with respect to the bare metal from first principles.Comment: under review at Journal of Chemical Physic