Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms

Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS) are a modeling framework that considers two propensity parameters for updating each node and uses one when the update has a positive impact on the variable, that is, when the update causes the variable to increase its value, and uses the other when the update has a negative impact, that is, when the update causes it to decrease its value. This framework offers additional features for simulations but also adds a complexity in parameter estimation of the propensities. This paper presents a method for estimating the propensity parameters for SDDS. The method is based on adding noise to the system using the Google PageRank approach to make the system ergodic and thus guaranteeing the existence of a stationary distribution. Then with the use of a genetic algorithm, the propensity parameters are estimated. Approximation techniques that make the search algorithms efficient are also presented and Matlab/Octave code to test the algorithms are available at http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html

Lubricating Bacteria Model for Branching growth of Bacterial Colonies

Various bacterial strains (e.g. strains belonging to the genera Bacillus, Paenibacillus, Serratia and Salmonella) exhibit colonial branching patterns during growth on poor semi-solid substrates. These patterns reflect the bacterial cooperative self-organization. Central part of the cooperation is the collective formation of lubricant on top of the agar which enables the bacteria to swim. Hence it provides the colony means to advance towards the food. One method of modeling the colonial development is via coupled reaction-diffusion equations which describe the time evolution of the bacterial density and the concentrations of the relevant chemical fields. This idea has been pursued by a number of groups. Here we present an additional model which specifically includes an evolution equation for the lubricant excreted by the bacteria. We show that when the diffusion of the fluid is governed by nonlinear diffusion coefficient branching patterns evolves. We study the effect of the rates of emission and decomposition of the lubricant fluid on the observed patterns. The results are compared with experimental observations. We also include fields of chemotactic agents and food chemotaxis and conclude that these features are needed in order to explain the observations.Comment: 1 latex file, 16 jpeg files, submitted to Phys. Rev.

Tunable itinerant spin dynamics with polar molecules

Strongly interacting spins underlie many intriguing phenomena and applications ranging from quantum magnetism and spin transport to precision quantum sensing and quantum information processing. An interacting spin system with high controllability is desired in order to understand these complex phenomena. Here, we demonstrate tunable itinerant spin dynamics enabled by dipolar interactions using a gas of potassium-rubidium molecules confined to two-dimensional planes, where the spin-1/2 is encoded in the molecular rotational levels. The dipolar interaction gives rise to a shift of the rotational transition frequency and a collision-limited Ramsey contrast decay that emerges from the coupled spin and motion. Both the Ising and spin exchange interactions are precisely tuned by varying the strength and orientation of an electric field, as well as the internal molecular state. This full tunability enables both static and dynamical control of the spin Hamiltonian, allowing reversal of the coherent spin dynamics. Our work establishes an interacting spin platform that allows for exploration of many-body spin dynamics and spin-motion physics utilizing the strong, tunable dipolar interaction.Comment: 22 pages, including 4 + 2 figure

Variant repeats within the DMPK CTG expansion protect function in myotonic dystrophy type 1

Objective: We tested the hypothesis that variant repeat interruptions (RIs) within the DMPK CTG repeat tract lead to milder symptoms compared with pure repeats (PRs) in myotonic dystrophy type 1 (DM1). Methods: We evaluated motor, neurocognitive, and behavioral outcomes in a group of 6 participants with DM1 with RI compared with a case-matched sample of 12 participants with DM1 with PR and a case-matched sample of 12 unaffected healthy comparison participants (UA). Results: In every measure, the RI participants were intermediate between UA and PR participants. For muscle strength, the RI group was significantly less impaired than the PR group. For measures of Full Scale IQ, depression, and sleepiness, all 3 groups were significantly different from each other with UA > RI > PR in order of impairment. The RI group was different from unaffected, but not significantly different from PR (UA > RI = PR) in apathy and working memory. Finally, in finger tapping and processing speed, RI did not differ from UA comparisons, but PR had significantly lower scores than the UA comparisons (UA = RI > PR). Conclusions: Our results support the notion that patients affected by DM1 with RI demonstrate a milder phenotype with the same pattern of deficits as those with PR indicating a similar disease process

Reactive nitrogen budget during the NASA SONEX Mission

The SASS Ozone and Nitrogen Oxides Experiment (SONEX) over the North Atlantic during October/November 1997 offered an excellent opportunity to examine the budget of reactive nitrogen in the upper troposphere (8–12 km altitude). The median measured total reactive nitrogen (NOy) mixing ratio was 425 parts per trillion by volume (pptv). A data set merged to the HNO3 measurement time resolution was used to calculate NOy (NOy sum) by summing the reactive nitrogen species (a combination of measured plus modeled results) and comparing it to measured NOy (NOy meas.). Comparisons were done for tropospheric air (O3 \u3c100 parts per billion by volume (ppbv)) and stratospherically influenced air (O3 \u3e 100 ppbv) with both showing good agreement between NOy sum and NOy meas. (slope \u3e0.9 and r² ≈ 0.9). The total reactive nitrogen budget in the upper troposphere over the North Atlantic appears to be dominated by a mixture of NOx (NO + NO2), HNO3, and PAN. In tropospheric air median values of NOx/NOywere ≈ 0.25, HNO3/NOy ≈ 0.35 and PAN/NOy ≈ 0.17. Particulate NO3− and alkyl nitrates together composed \u3c10% of NOy, while model estimated HNO4 averaged 12%. For the air parcels sampled during SONEX, there does not appear to be a large reservoir of unidentified NOy compounds

Tropospheric Bromine Chemistry: Implications for Present and Pre-Industrial Ozone and Mercury

We present a new model for the global tropospheric chemistry of inorganic bromine (Bry) coupled to oxidant-aerosol chemistry in the GEOS-Chem chemical transport model (CTM). Sources of tropospheric Bry include debromination of sea-salt aerosol, photolysis and oxidation of short-lived bromocarbons, and transport from the stratosphere. Comparison to a GOME-2 satellite climatology of tropospheric BrO columns shows that the model can reproduce the observed increase of BrO with latitude, the northern mid-latitudes maximum in winter, and the Arctic maximum in spring. This successful simulation is contingent on the HOBr + HBr reaction taking place in aqueous aerosols and ice clouds. Bromine chemistry in the model decreases tropospheric ozone mixing ratios by <1–8 nmol mol−1 (6.5% globally), with the largest effects in the northern extratropics in spring. The global mean tropospheric OH concentration decreases by 4%. Inclusion of bromine chemistry improves the ability of global models (GEOS-Chem and p-TOMCAT) to simulate observed 19th-century ozone and its seasonality. Bromine effects on tropospheric ozone are comparable in the present-day and pre-industrial atmospheres so that estimates of anthropogenic radiative forcing are minimally affected. Br atom concentrations are 40% higher in the pre-industrial atmosphere due to lower ozone, which would decrease by a factor of 2 the atmospheric lifetime of elemental mercury against oxidation by Br. This suggests that historical anthropogenic mercury emissions may have mostly deposited to northern mid-latitudes, enriching the corresponding surface reservoirs. The persistent rise in background surface ozone at northern mid-latitudes during the past decades could possibly contribute to the observations of elevated mercury in subsurface waters of the North Atlantic.Engineering and Applied Science

Two-dimensional optomechanical crystal resonator in gallium arsenide

In the field of quantum computation and communication there is a compelling need for quantum-coherent frequency conversion between microwave electronics and infra-red optics. A promising platform for this is an optomechanical crystal resonator that uses simultaneous photonic and phononic crystals to create a co-localized cavity coupling an electromagnetic mode to an acoustic mode, which then via electromechanical interactions can undergo direct transduction to electronics. The majority of work in this area has been on one-dimensional nanobeam resonators which provide strong optomechanical couplings but, due to their geometry, suffer from an inability to dissipate heat produced by the laser pumping required for operation. Recently, a quasi-two-dimensional optomechanical crystal cavity was developed in silicon exhibiting similarly strong coupling with better thermalization, but at a mechanical frequency above optimal qubit operating frequencies. Here we adapt this design to gallium arsenide, a natural thin-film single-crystal piezoelectric that can incorporate electromechanical interactions, obtaining a mechanical resonant mode at f_m ~ 4.5 GHz ideal for superconducting qubits, and demonstrating optomechanical coupling g_om/(2pi) ~ 650 kHz

Bidirectional multi-photon communication between remote superconducting nodes

Quantum communication testbeds provide a useful resource for experimentally investigating a variety of communication protocols. Here we demonstrate a superconducting circuit testbed with bidirectional multi-photon state transfer capability using time-domain shaped wavepackets. The system we use to achieve this comprises two remote nodes, each including a tunable superconducting transmon qubit and a tunable microwave-frequency resonator, linked by a 2 m-long superconducting coplanar waveguide, which serves as a transmission line. We transfer both individual and superposition Fock states between the two remote nodes, and additionally show that this bidirectional state transfer can be done simultaneously, as well as used to entangle elements in the two nodes.Comment: Main Paper has 6 pages, 4 figures. Supplementary has 14 pages, 16 figures, 2 table

Paediatrician\u27s guide to post-operative care for functionally univentricular CHD: A review

IMPORTANCE: Single ventricle CHD affects about 5 out of 100,000 newborns, resulting in complex anatomy often requiring multiple, staged palliative surgeries. Paediatricians are an essential part of the team that cares for children with single ventricle CHD. These patients often encounter their paediatrician first when a complication arises, so it is critical to ensure the paediatrician is knowledgeable of these issues to provide optimal care. OBSERVATIONS: We reviewed the subtypes of single ventricle heart disease and the various palliative surgeries these patients undergo. We then searched the literature to detail the general paediatrician\u27s approach to single ventricle patients at different stages of surgical palliation. CONCLUSIONS AND RELEVANCE: Single ventricle patients undergo staged palliation that drastically changes physiology after each intervention. Coordinated care between their paediatrician and cardiologist is requisite to provide excellent care. This review highlights what to expect when these patients are seen by their paediatrician for either well child visits or additional visits for parental or patient concern

Developing a platform for linear mechanical quantum computing

Linear optical quantum computing provides a desirable approach to quantum computing, with a short list of required elements. The similarity between photons and phonons points to the interesting potential for linear mechanical quantum computing (LMQC), using phonons in place of photons. While single-phonon sources and detectors have been demonstrated, a phononic beamsplitter element remains an outstanding requirement. Here we demonstrate such an element, using two superconducting qubits to fully characterize a beamsplitter with single phonons. We further use the beamsplitter to demonstrate two-phonon interference, a requirement for two-qubit gates, completing the toolbox needed for LMQC. This advance brings linear quantum computing to a fully solid-state system, along with straightforward conversion between itinerant phonons and superconducting qubits