Design and characterization of programmable DNA nanotubes

DNA self-assembly provides a programmable bottom-up approach for the synthesis of complex structures from nanoscale components. Although nanotubes are a fundamental form encountered in tile-based DNA self-assembly, the factors governing tube structure remain poorly understood. Here we report and characterize a new type of nanotube made from DNA double-crossover molecules (DAE-E tiles). Unmodified tubes range from 7 to 20 nm in diameter (4 to 10 tiles in circumference), grow as long as 50 μm with a persistence length of ~4 μm, and can be programmed to display a variety of patterns. A survey of modifications (1) confirms the importance of sticky-end stacking, (2) confirms the identity of the inside and outside faces of the tubes, and (3) identifies features of the tiles that profoundly affect the size and morphology of the tubes. Supported by these results, nanotube structure is explained by a simple model based on the geometry and energetics of B-form DNA

Protein folding disorders: Toward a basic biological paradigm

Mechanistic 'physics' models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a more appropriately biological paradigm will be needed for understanding the etiology, prevention, and treatment of these diseases

On the link pattern distribution of quarter-turn symmetric FPL configurations

We present new conjectures on the distribution of link patterns for fully-packed loop (FPL) configurations that are invariant, or almost invariant, under a quarter turn rotation, extending previous conjectures of Razumov and Stroganov and of de Gier. We prove a special case, showing that the link pattern that is conjectured to be the rarest does have the prescribed probability. As a byproduct, we get a formula for the enumeration of a new class of quasi-symmetry of plane partitions.Comment: 12 pages, 6 figures. Submitted to FPSAC 200

Limits of economy and fidelity for programmable assembly of size-controlled triply-periodic polyhedra

We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply-periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid cubic minimal surfaces. Inspired by a recent class of programmable DNA origami colloids, we demonstrate that the economy of design in these crystalline assemblies -- in terms of the growth of the number of distinct particle species required with the increased size-scale (e.g. periodicity) -- is comparable to viral shells. We further test the role of geometric specificity in these assemblies via dynamical assembly simulations, which show that conditions for simultaneously efficient and high-fidelity assembly require an intermediate degree of flexibility of local angles and lengths in programmed assembly. Off-target misassembly occurs via incorporation of a variant of disclination defects, generalized to the case of hyperbolic crystals. The possibility of these topological defects is a direct consequence of the very same symmetry principles that underlie the economical design, exposing a basic tradeoff between design economy and fidelity of programmable, size controlled assembly.Comment: 15 pages, 5 figures, 6 supporting movies (linked), Supporting Appendi

Symmetry and Asymmetry in Quasicrystals or Amorphous Materials

About forty years after its discovery, it is still common to read in the literature that quasicrystals (QCs) occupy an intermediate position between amorphous materials and periodic crystals. However, QCs exhibit high-quality diffraction patterns containing a collection of discrete Bragg reflections at variance with amorphous phases. Accordingly, these materials must be properly regarded as long-range ordered materials with a symmetry incompatible with translation invariance. This misleading conceptual status can probably arise from the use of notions borrowed from the amorphous solids framework (such us tunneling states, weak interference effects, variable range hopping, or spin glass) in order to explain certain physical properties observed in QCs. On the other hand, the absence of a general, full-fledged theory of quasiperiodic systems certainly makes it difficult to clearly distinguish the features related to short-range order atomic arrangements from those stemming from long-range order correlations. The contributions collected in this book aim at gaining a deeper understanding on the relationship between the underlying structural order and the resulting physical properties in several illustrative aperiodic systems, including the border line between QCs and related complex metallic alloys, hierarchical superlattices, electrical transmission lines, nucleic acid sequences, photonic quasicrystals, and optical devices based on aperiodic order designs

The Panchromatic Hubble Andromeda Treasury

The Panchromatic Hubble Andromeda Treasury (PHAT) is an on-going HST Multicycle Treasury program to image ~1/3 of M31's star forming disk in 6 filters, from the UV to the NIR. The full survey will resolve the galaxy into more than 100 million stars with projected radii from 0-20 kpc over a contiguous 0.5 square degree area in 828 orbits, producing imaging in the F275W and F336W filters with WFC3/UVIS, F475W and F814W with ACS/WFC, and F110W and F160W with WFC3/IR. The resulting wavelength coverage gives excellent constraints on stellar temperature, bolometric luminosity, and extinction for most spectral types. The photometry reaches SNR=4 at F275W=25.1, F336W=24.9, F475W=27.9, F814W=27.1, F110W=25.5, and F160W=24.6 for single pointings in the uncrowded outer disk; however, the optical and NIR data are crowding limited, and the deepest reliable magnitudes are up to 5 magnitudes brighter in the inner bulge. All pointings are dithered and produce Nyquist-sampled images in F475W, F814W, and F160W. We describe the observing strategy, photometry, astrometry, and data products, along with extensive tests of photometric stability, crowding errors, spatially-dependent photometric biases, and telescope pointing control. We report on initial fits to the structure of M31's disk, derived from the density of RGB stars, in a way that is independent of the assumed M/L and is robust to variations in dust extinction. These fits also show that the 10 kpc ring is not just a region of enhanced recent star formation, but is instead a dynamical structure containing a significant overdensity of stars with ages >1 Gyr. (Abridged)Comment: 48 pages including 22 pages of figures. Accepted to the Astrophysical Journal Supplements. Some figures slightly degraded to reduce submission siz