Estimating the relative order of speciation or coalescence events on a given phylogeny

The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices of the tree? In this paper we investigate this problem, assuming a uniform distribution on the order of the inner vertices of the tree (which includes, but is more general than, the popular Yule distribution on trees). We derive fast algorithms for computing the probability that (i) any given vertex in the tree was the j--th speciation event (for each j), and (ii) any one given vertex is earlier in the tree than a second given vertex. We show how the first algorithm can be used to calculate the expected length of any given interior edge in any given tree that has been generated under either a constant-rate speciation model, or the coalescent model

Proposal for an Integrated Raman-free Correlated Photon Source

We propose a dual-pump third-order nonlinear scheme for producing pairs of correlated photons that is less susceptible to Raman noise than typical spontaneous four wave mixing methods (SFWM). Beginning with the full multimode Hamiltonian we derive a general expression for the joint spectral amplitude, from which the probability of producing a pair of photons can be calculated. As an example, we demonstrate that a probability of 0.028 pairs per pulse can be achieved in an appropriately designed fused silica microfiber. As compared with single pump SFWM in standard fiber, we calculate that our process shows significant suppression of the spontaneous Raman scattering and an improvement in the signal to noise ratio.Comment: 7 pages, 3 figures (two containing 2 subfigures

Generation of frequency sidebands on single photons with indistinguishability from quantum dots

Generation and manipulation of the quantum state of a single photon is at the heart of many quantum information protocols. There has been growing interest in using phase modulators as quantum optics devices that preserve coherence. In this Letter, we have used an electro-optic phase modulator to shape the state vector of single photons emitted by a quantum dot to generate new frequency components (modes) and explicitly demonstrate that the phase modulation process agrees with the theoretical prediction at a single photon level. Through two-photon interference measurements we show that for an output consisting of three modes (the original mode and two sidebands), the indistinguishability of the mode engineered photon, measured through the secondorder intensity correlation (g2(0)) is preserved. This work demonstrates a robust means to generate a photonic qubit or more complex state (e.g., a qutrit) for quantum communication applications by encoding information in the sidebands without the loss of coherence

Non-local nuclear spin quieting in quantum dot molecules: Optically-induced extended two-electron spin coherence time

We demonstrate the extension of coherence between all four two-electron spin ground states of an InAs quantum dot molecule (QDM) via non-local suppression of nuclear spin fluctuations in both constituent quantum dots (QDs), while optically addressing only the upper QD transitions. Long coherence times are revealed through dark-state spectroscopy as resulting from nuclear spin locking mediated by the exchange interaction between the QDs. Lineshape analysis provides the first measurement of the quieting of the Overhauser field distribution correlating with reduced nuclear spin fluctuations.Comment: Supplementary materials can be found on the publication page of our website. http://research.physics.lsa.umich.edu/dst/Publications.htm

Adjusting Inferential Thresholds to Reflect Nonepistemic Values

Many philosophers have challenged the ideal of value-free science on the grounds that social or moral values are relevant to inferential thresholds. But given this view, how precisely and to what extent should scientists adjust their inferential thresholds in light of nonepistemic values? We suggest that signal detection theory provides a useful framework for addressing this question. Moreover, this approach opens up further avenues for philosophical inquiry and has important implications for philosophical debates concerning inductive risk. For example, the signal detection theory framework entails that considerations of inductive risk and inferential-threshold placement cannot be conducted in isolation from base-rate information