Fly Models of Human Diseases: \u3ci\u3eDrosophila\u3c/i\u3e as a Model for Understanding Human Mitochondrial Mutations and Disease

Mitochondrial diseases are a prevalent, heterogeneous class of diseases caused by defects in oxidative phosphorylation, whose severity depends upon particular genetic mutations. These diseases can be difficult to diagnose, and current therapeutics have limited efficacy, primarily treating only symptoms. Because mitochondria play a pivotal role in numerous cellular functions, especially ATP production, their diminished activity has dramatic physiological consequences. While this in and of itself makes treating mitochondrial disease complex, these organelles contain their own DNA, mtDNA, whose products are required for ATP production, in addition to the hundreds of nucleus-encoded proteins. Drosophila offers a tractable whole-animal model to understand the mechanisms underlying loss of mitochondrial function, the subsequent cellular and tissue damage that results, and how these organelles are inherited. Human and Drosophila mtDNAs encode the same set of products, and the homologous nucleusencoded genes required for mitochondrial function are conserved. In addition, Drosophila contain sufficiently complex organ systems to effectively recapitulate many basic symptoms of mitochondrial diseases, yet are relatively easy and fast to genetically manipulate. There are several Drosophila models for specific mitochondrial diseases, which have been recently reviewed (Foriel, Willems, Smeitink, Schenck, & Beyrath, 2015). In this review, we highlight the conservation between human and Drosophila mtDNA, the present and future techniques for creating mtDNA mutations for further study, and how Drosophila has contributed to our current understanding of mitochondrial inheritance

Information-Based Physics: An Observer-Centric Foundation

It is generally believed that physical laws, reflecting an inherent order in the universe, are ordained by nature. However, in modern physics the observer plays a central role raising questions about how an observer-centric physics can result in laws apparently worthy of a universal nature-centric physics. Over the last decade, we have found that the consistent apt quantification of algebraic and order-theoretic structures results in calculi that possess constraint equations taking the form of what are often considered to be physical laws. I review recent derivations of the formal relations among relevant variables central to special relativity, probability theory and quantum mechanics in this context by considering a problem where two observers form consistent descriptions of and make optimal inferences about a free particle that simply influences them. I show that this approach to describing such a particle based only on available information leads to the mathematics of relativistic quantum mechanics as well as a description of a free particle that reproduces many of the basic properties of a fermion. The result is an approach to foundational physics where laws derive from both consistent descriptions and optimal information-based inferences made by embedded observers.Comment: To be published in Contemporary Physics. The manuscript consists of 43 pages and 9 Figure

The Hubbard Model at Infinite Dimensions: Thermodynamic and Transport Properties

We present results on thermodynamic quantities, resistivity and optical conductivity for the Hubbard model on a simple hypercubic lattice in infinite dimensions. Our results for the paramagnetic phase display the features expected from an intuitive analysis of the one-particle spectra and substantiate the similarity of the physics of the Hubbard model to those of heavy fermion systems. The calculations were performed using an approximate solution to the single-impurity Anderson model, which is the key quantity entering the solution of the Hubbard model in this limit. To establish the quality of this approximation we compare its results, together with those obtained from two other widely used methods, to essentially exact quantum Monte Carlo results.Comment: 29 pages, 16 figure

Phase diagram of the one-dimensional extended attractive Hubbard model for large nearest-neighbor repulsion

We consider the extended Hubbard model with attractive on-site interaction U and nearest-neighbor repulsions V. We construct an effective Hamiltonian H_{eff} for hopping t<<V and arbitrary U<0. Retaining the most important terms, H_{eff} can be mapped onto two XXZ models, solved by the Bethe ansatz. The quantum phase diagram shows two Luttinger liquid phases and a region of phase separation between them. For density n<0.422 and U<-4, singlet superconducting correlations dominate at large distances. For some parameters, the results are in qualitative agreement with experiments in BaKBiO.Comment: 6 pages, 3 figures, submitted to Phys. Rev.

Quantum Monte Carlo with Directed Loops

We introduce the concept of directed loops in stochastic series expansion and path integral quantum Monte Carlo methods. Using the detailed balance rules for directed loops, we show that it is possible to smoothly connect generally applicable simulation schemes (in which it is necessary to include back-tracking processes in the loop construction) to more restricted loop algorithms that can be constructed only for a limited range of Hamiltonians (where back-tracking can be avoided). The "algorithmic discontinuities" between general and special points (or regions) in parameter space can hence be eliminated. As a specific example, we consider the anisotropic S=1/2 Heisenberg antiferromagnet in an external magnetic field. We show that directed loop simulations are very efficient for the full range of magnetic fields (zero to the saturation point) and anisotropies. In particular for weak fields and anisotropies, the autocorrelations are significantly reduced relative to those of previous approaches. The back-tracking probability vanishes continuously as the isotropic Heisenberg point is approached. For the XY-model, we show that back-tracking can be avoided for all fields extending up to the saturation field. The method is hence particularly efficient in this case. We use directed loop simulations to study the magnetization process in the 2D Heisenberg model at very low temperatures. For LxL lattices with L up to 64, we utilize the step-structure in the magnetization curve to extract gaps between different spin sectors. Finite-size scaling of the gaps gives an accurate estimate of the transverse susceptibility in the thermodynamic limit: chi_perp = 0.0659 +- 0.0002.Comment: v2: Revised and expanded discussion of detailed balance, error in algorithmic phase diagram corrected, to appear in Phys. Rev.

Binding Energy of Charged Excitons in ZnSe-based Quantum Wells

Excitons and charged excitons (trions) are investigated in ZnSe-based quantum well structures with (Zn,Be,Mg)Se and (Zn,Mg)(S,Se) barriers by means of magneto-optical spectroscopy. Binding energies of negatively () and positively (X+) charged excitons are measured as functions of quantum well width, free carrier density and in external magnetic fields up to 47 T. The binding energy of shows a strong increase from 1.4 to 8.9 meV with decreasing quantum well width from 190 to 29 A. The binding energies of X+ are about 25% smaller than the binding energy in the same structures. The magnetic field behavior of and X+ binding energies differ qualitatively. With growing magnetic field strength, increases its binding energy by 35-150%, while for X+ it decreases by 25%. Zeeman spin splittings and oscillator strengths of excitons and trions are measured and discussed

Horizontal Branch Stars: The Interplay between Observations and Theory, and Insights into the Formation of the Galaxy

We review HB stars in a broad astrophysical context, including both variable and non-variable stars. A reassessment of the Oosterhoff dichotomy is presented, which provides unprecedented detail regarding its origin and systematics. We show that the Oosterhoff dichotomy and the distribution of globular clusters (GCs) in the HB morphology-metallicity plane both exclude, with high statistical significance, the possibility that the Galactic halo may have formed from the accretion of dwarf galaxies resembling present-day Milky Way satellites such as Fornax, Sagittarius, and the LMC. A rediscussion of the second-parameter problem is presented. A technique is proposed to estimate the HB types of extragalactic GCs on the basis of integrated far-UV photometry. The relationship between the absolute V magnitude of the HB at the RR Lyrae level and metallicity, as obtained on the basis of trigonometric parallax measurements for the star RR Lyrae, is also revisited, giving a distance modulus to the LMC of (m-M)_0 = 18.44+/-0.11. RR Lyrae period change rates are studied. Finally, the conductive opacities used in evolutionary calculations of low-mass stars are investigated. [ABRIDGED]Comment: 56 pages, 22 figures. Invited review, to appear in Astrophysics and Space Scienc

A leap forward in geographic scale for forest ectomycorrhizal fungi

Published versio

Measurement-based quantum foundations

I show that quantum theory is the only probabilistic framework that permits arbitrary processes to be emulated by sequences of local measurements. This supports the view that, contrary to conventional wisdom, measurement should not be regarded as a complex phenomenon in need of a dynamical explanation but rather as a primitive -- and perhaps the only primitive -- operation of the theory.Comment: 8 pages, version to appear in Found. Phy

Search for a W' boson decaying to a bottom quark and a top quark in pp collisions at sqrt(s) = 7 TeV

Results are presented from a search for a W' boson using a dataset corresponding to 5.0 inverse femtobarns of integrated luminosity collected during 2011 by the CMS experiment at the LHC in pp collisions at sqrt(s)=7 TeV. The W' boson is modeled as a heavy W boson, but different scenarios for the couplings to fermions are considered, involving both left-handed and right-handed chiral projections of the fermions, as well as an arbitrary mixture of the two. The search is performed in the decay channel W' to t b, leading to a final state signature with a single lepton (e, mu), missing transverse energy, and jets, at least one of which is tagged as a b-jet. A W' boson that couples to fermions with the same coupling constant as the W, but to the right-handed rather than left-handed chiral projections, is excluded for masses below 1.85 TeV at the 95% confidence level. For the first time using LHC data, constraints on the W' gauge coupling for a set of left- and right-handed coupling combinations have been placed. These results represent a significant improvement over previously published limits.Comment: Submitted to Physics Letters B. Replaced with version publishe