Modelling the role of chance in mating dynamics

This undergraduate honors thesis examines the role of chance in mating dynamics, focusing on the popular measures of Is and OSR and whether or not they are accurate measures of sexual selection. The first chapter is an overview of sexual selection and how biologists typically measure it, and the second chapter describes the modelling scenarios we created to assess the interaction of Is and OSR with both chance and parental investment. Our results show that Is and OSR have indeed been used incorrectly, and that we should shift our focus to trait-based methods when measuring sexual selection

Entanglement Patterns in Mutually Unbiased Basis Sets for N Prime-state Particles

A few simply-stated rules govern the entanglement patterns that can occur in mutually unbiased basis sets (MUBs), and constrain the combinations of such patterns that can coexist (ie, the stoichiometry) in full complements of p^N+1 MUBs. We consider Hilbert spaces of prime power dimension (as realized by systems of N prime-state particles, or qupits), where full complements are known to exist, and we assume only that MUBs are eigenbases of generalized Pauli operators, without using a particular construction. The general rules include the following: 1) In any MUB, a particular qupit appears either in a pure state, or totally entangled, and 2) in any full MUB complement, each qupit is pure in p+1 bases (not necessarily the same ones), and totally entangled in the remaining p^N-p. It follows that the maximum number of product bases is p+1, and when this number is realized, all remaining p^N-p bases in the complement are characterized by the total entanglement of every qupit. This "standard distribution" is inescapable for two qupits (of any p), where only product and generalized Bell bases are admissible MUB types. This and the following results generalize previous results for qubits and qutrits. With three qupits there are three MUB types, and a number of combinations (p+2) are possible in full complements. With N=4, there are 6 MUB types for p=2, but new MUB types become possible with larger p, and these are essential to the realization of full complements. With this example, we argue that new MUB types, showing new entanglement characteristics, should enter with every step in N, and when N is a prime plus 1, also at critical p values, p=N-1. Such MUBs should play critical roles in filling complements.Comment: 27 pages, one figure, to be submitted to Physical Revie

On fault-tolerance with noisy and slow measurements

It is not so well-known that measurement-free quantum error correction protocols can be designed to achieve fault-tolerant quantum computing. Despite the potential advantages of using such protocols in terms of the relaxation of accuracy, speed and addressing requirements on the measurement process, they have usually been overlooked because they are expected to yield a very bad threshold as compared to error correction protocols which use measurements. Here we show that this is not the case. We design fault-tolerant circuits for the 9 qubit Bacon-Shor code and find a threshold for gates and preparation of $p_{(p,g) thresh}=3.76 \times 10^{-5}$ (30% of the best known result for the same code using measurement based error correction) while admitting up to 1/3 error rates for measurements and allocating no constraints on measurement speed. We further show that demanding gate error rates sufficiently below the threshold one can improve the preparation threshold to $p_{(p)thresh} = 1/3$. We also show how these techniques can be adapted to other Calderbank-Shor-Steane codes.Comment: 11 pages, 7 figures. v3 has an extended exposition and several simplifications that provide for an improved threshold value and resource overhea

Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection

Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O. sativa accessions from the Rice Mini-Core (RMC) collection. Significant differences between RMC accessions made the five indices suitable for genome-wide association study (GWAS) based quantitative trait loci (QTL) mapping. For young seedling stage indices, japonica and indica subspecies clustered into chilling tolerant and chilling sensitive accessions, respectively, while both subspecies had similar low temperature germinability distributions. Indica subspecies were shown to have chilling acclimation potential. GWAS mapping uncovered 48 QTL at 39 chromosome regions distributed across all 12 rice chromosomes. Interestingly, there was no overlap between the germination and seedling stage QTL. Also, 18 QTL and 32 QTL were in regions discovered in previously reported bi-parental and GWAS based QTL mapping studies, respectively. Two novel low temperature seedling survivability (LTSS)–QTL, qLTSS3-4 and qLTSS4-1, were not in a previously reported QTL region. QTL with strong effect alleles identified in this study will be useful for marker assisted breeding efforts to improve chilling tolerance in rice cultivars and enhance gene discovery for chilling tolerance

Tight-binding study of interface states in semiconductor heterojunctions

Localized interface states in abrupt semiconductor heterojunctions are studied within a tight-binding model. The intention is to provide a microscopic foundation for the results of similar studies which were based upon the two-band model within the envelope function approximation. In a two-dimensional description, the tight-binding Hamiltonian is constructed such that the Dirac-like bulk spectrum of the two-band model is recovered in the continuum limit. Localized states in heterojunctions are shown to occur under conditions equivalent to those of the two-band model. In particular, shallow interface states are identified in non-inverted junctions with intersecting bulk dispersion curves. As a specific example, the GaSb-AlSb heterojunction is considered. The matching conditions of the envelope function approximation are analyzed within the tight-binding description.Comment: RevTeX, 11 pages, 3 figures, to appear in Phys. Rev.

Correction: The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

The authors would like to amend this article based on the discovery that the originally published Acacia ligulata sequence contains assembly errors, which came to light after the publication of the article

A method of enciphering quantum states

In this paper, we propose a method of enciphering quantum states of two-state systems (qubits) for sending them in secrecy without entangled qubits shared by two legitimate users (Alice and Bob). This method has the following two properties. First, even if an eavesdropper (Eve) steals qubits, she can extract information from them with certain probability at most. Second, Alice and Bob can confirm that the qubits are transmitted between them correctly by measuring a signature. If Eve measures m qubits one by one from n enciphered qubits and sends alternative ones (the Intercept/Resend attack), a probability that Alice and Bob do not notice Eve's action is equal to (3/4)^m or less. Passwords for decryption and the signature are given by classical binary strings and they are disclosed through a public channel. Enciphering classical information by this method is equivalent to the one-time pad method with distributing a classical key (random binary string) by the BB84 protocol. If Eve takes away qubits, Alice and Bob lose the original quantum information. If we apply our method to a state in iteration, Eve's success probability decreases exponentially. We cannot examine security against the case that Eve makes an attack with using entanglement. This remains to be solved in the future.Comment: 21 pages, Latex2e, 10 epsf figures. v2: 22 pages, added two references, several clarifying sentences are added in Sec. 5, typos corrected, a new proof is provided in Appendix A and it is shorter than the old one. v3: 23 pages, one section is adde

CdZnTe strip detectors as sub-millimeter resolution imaging gamma radiation spectrometers

We report γ-ray detection performance measurements and computer simulations of a sub-millimeter pitch CdZnTe strip detector. The detector is a prototype for γ-ray measurements in the range of 20-600 keV. The prototype is a 1.5 mm thick, 64×64 orthogonal stripe CdZnTe detector of 0.375 mm pitch in both dimensions, with approximately one square inch of sensitive area. Using discrete laboratory electronics to process signals from an 8×8 stripe region of the prototype we measured good spectroscopic uniformity and sub-pitch (~0.2 mm) spatial resolution in both x and y dimensions. We present below measurements of the spatial uniformity, relative timing and pulse height of the anode and cathode signals. We simulated the photon interactions and signal generation in the strip detector and the test electronics and we compare these results with the data. The data indicate that cathode signal-as well as the anode signal-arises more strongly from the conduction electrons rather than the holes

Pharmacology of DB844, an orally active aza analogue of pafuramidine, in a monkey model of second stage human African trypanosomiasis

Novel drugs to treat human African trypanosomiasis (HAT) are still urgently needed despite the recent addition of nifurtimox-eflornithine combination therapy (NECT) to WHO Model Lists of Essential Medicines against second stage HAT, where parasites have invaded the central nervous system (CNS). The pharmacology of a potential orally available lead compound, N-methoxy-6-{5-[4-(N-methoxyamidino) phenyl]-furan-2-yl}-nicotinamidine (DB844), was evaluated in a vervet monkey model of second stage HAT, following promising results in mice. DB844 was administered orally to vervet monkeys, beginning 28 days post infection (DPI) with Trypanosoma brucei rhodesiense KETRI 2537. DB844 was absorbed and converted to the active metabolite 6-[5-(4-phenylamidinophenyl)-furanyl-2-yl]-nicotinamide (DB820), exhibiting plasma C(max) values of 430 and 190 nM for DB844 and DB820, respectively, after the 14th dose at 6 mg/kg qd. A 100-fold reduction in blood trypanosome counts was observed within 24 h of the third dose and, at the end of treatment evaluation performed four days post the last drug dose, trypanosomes were not detected in the blood or cerebrospinal fluid of any monkey. However, some animals relapsed during the 300 days of post treatment monitoring, resulting in a cure rate of 3/8 (37.5%) and 3/7 (42.9%) for the 5 mg/kg×10 days and the 6 mg/kg×14 days dose regimens respectively. These DB844 efficacy data were an improvement compared with pentamidine and pafuramidine both of which were previously shown to be non-curative in this model of CNS stage HAT. These data show that synthesis of novel diamidines with improved activity against CNS-stage HAT was possible