Disciplinary Evolution and the Rise of the Transdiscipline

This paper challenges readers to reflect on academic disciplines in a new way, through the lens of the theory of evolution. Indeed, how disciplines came into being has been largely left unexplored. This paper shows how the concepts of evolution can be productively applied to describe the development, creation, and diminishment of disciplines. These concepts include natural selection, speciation, parallel evolution, extinction, and heterosis, among others. The paper concludes that these forces lead to a prediction that a new form of organization, the transdiscipline, is evolving to become perhaps predominant

Engineering Disulfide Cross‐Links in RNA Using Thiol‐Disulfide Interchange Chemistry

Protocols for postsynthetic modification of 2‐amino‐containing oligoribonucleotides with either an alkyl‐phenyl disulfide or an alkyl thiol group are described. These groups react under mild conditions to form disulfide cross‐links by thiol‐disulfide interchange. These reactants do not form a disulfide bond when incorporated on opposite faces of a short continuous RNA helix, but do form disulfide bonds rapidly when they are placed in proximity. In addition, by incorporating these groups at various positions on large RNAs by semisynthesis, the dynamics of thermal motions can be detected. Such motions are believed to be linked to biological function, and the protocols presented in this unit are among the few simple ways to assess such dynamics.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143724/1/cpnc0501.pd

Atemporal diagrams for quantum circuits

A system of diagrams is introduced that allows the representation of various elements of a quantum circuit, including measurements, in a form which makes no reference to time (hence ``atemporal''). It can be used to relate quantum dynamical properties to those of entangled states (map-state duality), and suggests useful analogies, such as the inverse of an entangled ket. Diagrams clarify the role of channel kets, transition operators, dynamical operators (matrices), and Kraus rank for noisy quantum channels. Positive (semidefinite) operators are represented by diagrams with a symmetry that aids in understanding their connection with completely positive maps. The diagrams are used to analyze standard teleportation and dense coding, and for a careful study of unambiguous (conclusive) teleportation. A simple diagrammatic argument shows that a Kraus rank of 3 is impossible for a one-qubit channel modeled using a one-qubit environment in a mixed state.Comment: Minor changes in references. Latex 32 pages, 13 figures in text using PSTrick

Properties of Pb(Zr,Ti)O3_3 ultrathin films under stress-free and open-circuit electrical boundary conditions

A first-principles-based scheme is developed to simulate properties of (001) PbO-terminated Pb(Zr$_{1-x}$Ti$_{x}$)O$_3$ thin films that are under stress-free and open-circuit boundary conditions. Their low-temperature spontaneous polarization never vanishes down to the minimal thickness, and continuously rotates between the in-plane and directions when varying the Ti composition around x=0.50. Such rotation dramatically enhances piezoelectricity and dielectricity. Furthermore, the order of some phase transitions changes when going from bulk to thin films.Comment: 11 pages, 3 figure

Effects of Landscape Composition and Configuration on Migrating Songbirds: Inference from an Individual-Based Model

The behavior of long-distance migrants during stopover is constrained by the need to quickly and safely replenish energetic reserves. Replenishing fuel stores at stopover sites requires adjusting to unfamiliar landscapes with little to no information about the distribution of resources. Despite their critical importance to the success of songbird migration, the effects of landscape composition and configuration on fuel deposition rates (FDR [g/d]), the currency of migration, has not been tested empirically. Our objectives were to understand the effects of heterogeneous landscapes on FDR of forest-dwelling songbirds during spring migration. The results of field experiments were used to parameterize a spatially explicit, individual-based model of forest songbird movement and resulting FDR. Further field experiments were used to validate the results from the individual-based model. In simulation experiments, we altered a Gulf South landscape in a factorial design to predict the effects of future patterns under different scenarios of land use change in which the abundance of high-quality hardwood habitat and the spatial aggregation of habitat varied. Simulated FDR decreased as the amount of hardwood in the landscape decreased from 41% to 22% to 12%. Further, migrants that arrived in higher-quality habitat types gained more mass. Counter to our expectations, FDR was higher with lower spatial aggregation of habitat. Differences in refueling rates may be most influenced by whether or not an individual experiences an initial searching cost after landing in poor-quality habitat. Therefore, quickly locating habitat with sufficient food resources at each stopover may be the most important factor determining a successful migration. Our findings provide empirical evidence for the argument that hardwood forest cover is a primary determinant of the quality of a stopover site in this region. This study represents the first effort to empirically quantify FDRs based on the configuration of landscapes

Deterministic and Unambiguous Dense Coding

Optimal dense coding using a partially-entangled pure state of Schmidt rank $\bar D$ and a noiseless quantum channel of dimension $D$ is studied both in the deterministic case where at most $L_d$ messages can be transmitted with perfect fidelity, and in the unambiguous case where when the protocol succeeds (probability $\tau_x$) Bob knows for sure that Alice sent message $x$, and when it fails (probability $1-\tau_x$) he knows it has failed. Alice is allowed any single-shot (one use) encoding procedure, and Bob any single-shot measurement. For $\bar D\leq D$ a bound is obtained for $L_d$ in terms of the largest Schmidt coefficient of the entangled state, and is compared with published results by Mozes et al. For $\bar D > D$ it is shown that $L_d$ is strictly less than $D^2$ unless $\bar D$ is an integer multiple of $D$, in which case uniform (maximal) entanglement is not needed to achieve the optimal protocol. The unambiguous case is studied for $\bar D \leq D$, assuming $\tau_x>0$ for a set of $\bar D D$ messages, and a bound is obtained for the average \lgl1/\tau\rgl. A bound on the average \lgl\tau\rgl requires an additional assumption of encoding by isometries (unitaries when $\bar D=D$) that are orthogonal for different messages. Both bounds are saturated when $\tau_x$ is a constant independent of $x$, by a protocol based on one-shot entanglement concentration. For $\bar D > D$ it is shown that (at least) $D^2$ messages can be sent unambiguously. Whether unitary (isometric) encoding suffices for optimal protocols remains a major unanswered question, both for our work and for previous studies of dense coding using partially-entangled states, including noisy (mixed) states.Comment: Short new section VII added. Latex 23 pages, 1 PSTricks figure in tex

Categorification of persistent homology

We redevelop persistent homology (topological persistence) from a categorical point of view. The main objects of study are diagrams, indexed by the poset of real numbers, in some target category. The set of such diagrams has an interleaving distance, which we show generalizes the previously-studied bottleneck distance. To illustrate the utility of this approach, we greatly generalize previous stability results for persistence, extended persistence, and kernel, image and cokernel persistence. We give a natural construction of a category of interleavings of these diagrams, and show that if the target category is abelian, so is this category of interleavings.Comment: 27 pages, v3: minor changes, to appear in Discrete & Computational Geometr

Measuring the Primordial Deuterium Abundance During the Cosmic Dark Ages

We discuss how measurements of fluctuations in the absorption of cosmic microwave background (CMB) photons by neutral gas during the cosmic dark ages, at redshifts z ~ 7--200, could reveal the primordial deuterium abundance of the Universe. The strength of the cross-correlation of brightness-temperature fluctuations due to resonant absorption of CMB photons in the 21-cm line of neutral hydrogen with those due to resonant absorption of CMB photons in the 92-cm line of neutral deuterium is proportional to the fossil deuterium to hydrogen ratio [D/H] fixed during big bang nucleosynthesis (BBN). Although technically challenging, this measurement could provide the cleanest possible determination of [D/H], free from contamination by structure formation processes at lower redshifts, and has the potential to improve BBN constraints to the baryon density of the Universe \Omega_{b} h^2. We also present our results for the thermal spin-change cross-section for deuterium-hydrogen scattering, which may be useful in a more general context than we describe here.Comment: 4 pages, 3 figures, submitted to Phys. Rev. Let

The Daisho Peptides Mediate Drosophila Defense Against a Subset of Filamentous Fungi.

Fungal infections, widespread throughout the world, affect a broad range of life forms, including agriculturally relevant plants, humans, and insects. In defending against fungal infections, the fruit fly Drosophila melanogaster employs the Toll pathway to induce a large number of immune peptides. Some have been investigated, such as the antimicrobial peptides (AMPs) and Bomanins (Boms); many, however, remain uncharacterized. Here, we examine the role in innate immunity of two related peptides, Daisho1 and Daisho2 (formerly IM4 and IM14, respectively), found in hemolymph following Toll pathway activation. By generating a CRISPR/Cas9 knockout of both genes, Δdaisho, we find that the Daisho peptides are required for defense against a subset of filamentous fungi, including Fusarium oxysporum, but not other Toll-inducible pathogens, such as Enterococcus faecalis and Candida glabrata. Analysis of null alleles and transgenes revealed that the two daisho genes are each required for defense, although their functions partially overlap. Generating and assaying a genomic epitope-tagged Daisho2 construct, we detected interaction in vitro of Daisho2 peptide in hemolymph with the hyphae of F. oxysporum. Together, these results identify the Daisho peptides as a new class of innate immune effectors with humoral activity against a select set of filamentous fungi