Robust Parameter Selection for Parallel Tempering

This paper describes an algorithm for selecting parameter values (e.g. temperature values) at which to measure equilibrium properties with Parallel Tempering Monte Carlo simulation. Simple approaches to choosing parameter values can lead to poor equilibration of the simulation, especially for Ising spin systems that undergo $1^st$-order phase transitions. However, starting from an initial set of parameter values, the careful, iterative respacing of these values based on results with the previous set of values greatly improves equilibration. Example spin systems presented here appear in the context of Quantum Monte Carlo.Comment: Accepted in International Journal of Modern Physics C 2010, http://www.worldscinet.com/ijmp

Algorithmic approach to adiabatic quantum optimization

It is believed that the presence of anticrossings with exponentially small gaps between the lowest two energy levels of the system Hamiltonian, can render adiabatic quantum optimization inefficient. Here, we present a simple adiabatic quantum algorithm designed to eliminate exponentially small gaps caused by anticrossings between eigenstates that correspond with the local and global minima of the problem Hamiltonian. In each iteration of the algorithm, information is gathered about the local minima that are reached after passing the anticrossing non-adiabatically. This information is then used to penalize pathways to the corresponding local minima, by adjusting the initial Hamiltonian. This is repeated for multiple clusters of local minima as needed. We generate 64-qubit random instances of the maximum independent set problem, skewed to be extremely hard, with between 10^5 and 10^6 highly-degenerate local minima. Using quantum Monte Carlo simulations, it is found that the algorithm can trivially solve all the instances in ~10 iterations.Comment: 7 pages, 3 figure

Functional rescue of dystrophin deficiency in mice caused by frameshift mutations using Campylobacter jejuni Cas9

Duchenne muscular dystrophy (DMD) is a fatal, X-linked muscle wasting disease caused by mutations in the DMD gene. In 51% of DMD cases, a reading frame is disrupted because of deletion of several exons. Here, we show that CjCas9 derived from Campylobacter jejuni can be used as a gene editing tool to correct an out-of-frame Dmd exon in Dmd knockout mice. Herein, we used Cas9 derived from S. pyogenes to generate Dmd knockout (KO) mice with a frameshift mutation in Dmd gene. Then, we expressed CjCas9, its single-guide RNA, and the eGFP gene in the tibialis anterior muscle of the Dmd KO mice using an all-in-one adeno-associated virus (AAV) vector. CjCas9 cleaved the target site in the Dmd gene efficiently in vivo and induced small insertions or deletions at the target site. This treatment resulted in conversion of the disrupted Dmd reading frame from out-of-frame to in-frame, leading to the expression of dystrophin in the sarcolemma. Importantly, muscle strength was enhanced in the CjCas9-treated muscles, without off-target mutations, indicating high efficiency and specificity of CjCas9. This work suggests that in vivo DMD frame correction, mediated by CjCas9 has great potential for the treatment of DMD and other neuromuscular diseases

Self-consistent symmetries in the proton-neutron Hartree-Fock-Bogoliubov approach

Symmetry properties of densities and mean fields appearing in the nuclear Density Functional Theory with pairing are studied. We consider energy functionals that depend only on local densities and their derivatives. The most important self-consistent symmetries are discussed: spherical, axial, space-inversion, and mirror symmetries. In each case, the consequences of breaking or conserving the time-reversal and/or proton-neutron symmetries are discussed and summarized in a tabulated form, useful in practical applications.Comment: 26 RevTex pages, 1 eps figure, 9 tables, submitted to Physical Review

Purification and Characterization of meta-Cresol Purple for Spectrophotometric Seawater pH Measurements

Spectrophotometric procedures allow rapid and precise measurements of the pH of natural waters. However, impurities in the acid–base indicators used in these analyses can significantly affect measurement accuracy. This work describes HPLC procedures for purifying one such indicator, meta-cresol purple (mCP), and reports mCP physical–chemical characteristics (thermodynamic equilibrium constants and visible-light absorbances) over a range of temperature (T) and salinity (S). Using pure mCP, seawater pH on the total hydrogen ion concentration scale (pHT) can be expressed in terms of measured mCP absorbance ratios (R = λ2A/λ1A) as follows:where −log(K2Te2) = a + (b/T) + c ln T – dT; a = −246.64209 + 0.315971S + 2.8855 × 10–4S2; b = 7229.23864 – 7.098137S – 0.057034S2; c = 44.493382 – 0.052711S; d = 0.0781344; and mCP molar absorbance ratios (ei) are expressed as e1 = −0.007762 + 4.5174 × 10–5T and e3/e2 = −0.020813 + 2.60262 × 10–4T + 1.0436 × 10–4 (S – 35). The mCP absorbances, λ1A and λ2A, used to calculate R are measured at wavelengths (λ) of 434 and 578 nm. This characterization is appropriate for 278.15 ≤ T ≤ 308.15 and 20 ≤ S ≤ 40

Early Effects on the Morphology of Mouse Small Intestine of Single or Combined Modality Treatment with Hyperthermia and X-Irradiation

This study describes the effects of hyperthermia and X-irradiation on the morphological appearance of normal, at risk tissues in the ileum of the mouse. The early morphological effects day after a combined modality treatment are compared with those due to either hyperthermia or X-irradiation given alone. The response was assessed qualitatively and semiquantitatively using scanning electron microscopy and a villous scoring technique. Early post-irradiation effects on topography did not differ significantly from those observed after small intestine exteriorisation without treatment. The villous scores for the combined modality treatments reflected greater damage than would be expected from the sum of villous scores for each modality treatment on its own. This suggests that the combined modality treatment had a synergistic or enhancing effect. A 4 hour time interval between the two treatments did not seem to reduce the enhancing effect. Further studies are required to investigate the effects of fractionated combined treatment

Algebro-Geometric Solutions of the Boussinesq Hierarchy

We continue a recently developed systematic approach to the Bousinesq (Bsq) hierarchy and its algebro-geometric solutions. Our formalism includes a recursive construction of Lax pairs and establishes associated Burchnall-Chaundy curves, Baker-Akhiezer functions and Dubrovin-type equations for analogs of Dirichlet and Neumann divisors. The principal aim of this paper is a detailed theta function representation of all algebro-geometric quasi-periodic solutions and related quantities of the Bsq hierarchy.Comment: LaTeX, 48 page