Biofuel Boom, Aquifer Doom?

Resource /Energy Economics and Policy,

Nearly-frustration-free ground state preparation

Solving for quantum ground states is important for understanding the properties of quantum many-body systems, and quantum computers are potentially well-suited for solving for quantum ground states. Recent work has presented a nearly optimal scheme that prepares ground states on a quantum computer for completely generic Hamiltonians, whose query complexity scales as $\delta^{-1}$, i.e. inversely with their normalized gap. Here we consider instead the ground state preparation problem restricted to a special subset of Hamiltonians, which includes those which we term "nearly-frustration-free": the class of Hamiltonians for which the ground state energy of their block-encoded and hence normalized Hamiltonian $\alpha^{-1}H$ is within $\delta^y$ of -1, where $\delta$ is the spectral gap of $\alpha^{-1}H$ and $0 \leq y \leq 1$. For this subclass, we describe an algorithm whose dependence on the gap is asymptotically better, scaling as $\delta^{y/2-1}$, and show that this new dependence is optimal up to factors of $\log \delta$. In addition, we give examples of physically motivated Hamiltonians which live in this subclass. Finally, we describe an extension of this method which allows the preparation of excited states both for generic Hamiltonians as well as, at a similar speedup as the ground state case, for those which are nearly frustration-free.Comment: 13 pages, 1 figur

Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1.

UnlabelledDespite evidence for the prevalence of horizontal gene transfer of respiratory genes, little is known about how pathways functionally integrate within new hosts. One example of a mobile respiratory metabolism is bacterial chlorate reduction, which is frequently encoded on composite transposons. This implies that the essential components of the metabolism are encoded on these mobile elements. To test this, we heterologously expressed genes for chlorate reduction from Shewanella algae ACDC in the non-chlorate-reducing Shewanella oneidensis MR-1. The construct that ultimately endowed robust growth on chlorate included cld, a cytochrome c gene, clrABDC, and two genes of unknown function. Although strain MR-1 was unable to grow on chlorate after initial insertion of these genes into the chromosome, 11 derived strains capable of chlorate respiration were obtained through adaptive evolution. Genome resequencing indicated that all of the evolved chlorate-reducing strains replicated a large genomic region containing chlorate reduction genes. Contraction in copy number and loss of the ability to reduce chlorate were also observed, indicating that this phenomenon was extremely dynamic. Although most strains contained more than six copies of the replicated region, a single strain with less duplication also grew rapidly. This strain contained three additional mutations that we hypothesized compensated for the low copy number. We remade the mutations combinatorially in the unevolved strain and determined that a single nucleotide polymorphism (SNP) upstream of cld enabled growth on chlorate and was epistatic to a second base pair change in the NarP binding sequence between narQP and nrfA that enhanced growth.ImportanceThe ability of chlorate reduction composite transposons to form functional metabolisms after transfer to a new host is an important part of their propagation. To study this phenomenon, we engineered Shewanella oneidensis MR-1 into a chlorate reducer. We defined a set of genes sufficient to endow growth on chlorate from a plasmid, but found that chromosomal insertion of these genes was nonfunctional. Evolution of this inoperative strain into a chlorate reducer showed that tandem duplication was a dominant mechanism of activation. While copy number changes are a relatively rapid way of increasing gene dosage, replicating almost 1 megabase of extra DNA is costly. Mutations that alleviate the need for high copy number are expected to arise and eventually predominate, and we identified a single nucleotide polymorphism (SNP) that relieved the copy number requirement. This study uses both rational and evolutionary approaches to gain insight into the evolution of a fascinating respiratory metabolism

Fluorescent Nanoparticles for the Measurement of Ion Concentration in Biological Systems

Tightly regulated ion homeostasis throughout the body is necessary for the prevention of such debilitating states as dehydration.1 In contrast, rapid ion fluxes at the cellular level are required for initiating action potentials in excitable cells.2 Sodium regulation plays an important role in both of these cases; however, no method currently exists for continuously monitoring sodium levels in vivo3 and intracellular sodium probes 4 do not provide similar detailed results as calcium probes. In an effort to fill both of these voids, fluorescent nanosensors have been developed that can monitor sodium concentrations in vitro and in vivo.5,6 These sensors are based on ion-selective optode technology and consist of plasticized polymeric particles in which sodium specific recognition elements, pH-sensitive fluorophores, and additives are embedded.7-9 Mechanistically, the sodium recognition element extracts sodium into the sensor. 10 This extraction causes the pH-sensitive fluorophore to release a hydrogen ion to maintain charge neutrality within the sensor which causes a change in fluorescence. The sodium sensors are reversible and selective for sodium over potassium even at high intracellular concentrations.6 They are approximately 120 nm in diameter and are coated with polyethylene glycol to impart biocompatibility. Using microinjection techniques, the sensors can be delivered into the cytoplasm of cells where they have been shown to monitor the temporal and spatial sodium dynamics of beating cardiac myocytes.11 Additionally, they have also tracked real-time changes in sodium concentrations in vivo when injected subcutaneously into mice.3 Herein, we explain in detail and demonstrate the methodology for fabricating fluorescent sodium nanosensors and briefly demonstrate the biological applications our lab uses the nanosensors for: the microinjection of the sensors into cells; and the subcutaneous injection of the sensors into mice

Nearly-frustration-free ground state preparation

Solving for quantum ground states is important for understanding the properties of quantum many-body systems, and quantum computers are potentially well-suited for solving for quantum ground states. Recent work [1] has presented a nearly optimal scheme that prepares ground states on a quantum computer for completely generic Hamiltonians, whose query complexity scales as $\delta^{-1}$, i.e. inversely with their normalized gap. Here we consider instead the ground state preparation problem restricted to a special subset of Hamiltonians, which includes those which we term "nearly-frustration-free": the class of Hamiltonians for which the ground state energy of their block-encoded and hence normalized Hamiltonian $\alpha^{-1}H$ is within $\delta^y$ of -1, where $\delta$ is the spectral gap of $\alpha^{-1}H$ and $0 \leq y \leq 1$. For this subclass, we describe an algorithm whose dependence on the gap is asymptotically better, scaling as $\delta^{y/2-1}$, and show that this new dependence is optimal up to factors of $\log \delta$. In addition, we give examples of physically motivated Hamiltonians which live in this subclass. Finally, we describe an extension of this method which allows the preparation of excited states both for generic Hamiltonians as well as, at a similar speedup as the ground state case, for those which are nearly frustration-free

Mixing of Supersonic Streams

The Strutjet approach to Rocket Based Combined Cycle (RBCC) propulsion depends upon fuel-rich flows from the rocket nozzles and turbine exhaust products mixing with the ingested air for successful operation in the ramjet and scramjet modes. A model of the Strutjet device has been built and is undergoing test to investigate the mixing of the streams as a function of distance from the Strutjet exit plane. Initial cold flow testing of the model is underway to determine both, the behavior of the ingested air in the duct and to validate the mixing diagnostics. During the tests, each of the two rocket nozzles ejected up to two pounds mass per second into the 13.6 square inch duct. The tests showed that the mass flow of the rockets was great enough to cause the entrained air to go sonic at the strut, which is the location of the rocket nozzles. More tests are necessary to determine whether the entrained air chokes due to the reduction in the area of the duct at the strut (a physical choke), or because of the addition of mass inside the duct at the nozzle exit (a Fabri choke). The initial tests of the mixing diagnostics are showing promise