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At least 811 records · Page 45

Gate-based quantum computing for protein design

Protein design is a technique to engineer proteins by permuting amino acids in the sequence to obtain novel functionalities. However, exploring all possible combinations of amino acids is generally impossible due to the exponential growth of possibilities with the number of designable sites. The present work introduces circuits implementing a pure quantum approach, Grover’s algorithm, to solve protein design problems. Our algorithms can adjust to implement any custom pair-wise energy tables and protein structure models. Moreover, the algorithm’s oracle is designed to consist of only adder functions. Quantum computer simulators validate the practicality of our circuits, containing up to 234 qubits. However, a smaller circuit is implemented on real quantum devices. Our results show that using iterations, the circuits find the correct results among all N possibilities, providing the expected quadratic speed up of Grover’s algorithm over classical methods (i.e.,).

59 BASIC BIOLOGICAL SCIENCES↗

Stability study of aqueous foams under high-temperature and high-pressure conditions relevant to Enhanced Geothermal Systems (EGS)

In Enhanced Geothermal System (EGS) hydraulic fracturing is carried out by injecting cold water into deep Hot Dry Rocks (HDR) under carefully controlled conditions to create new or reopen existing fractures. Water-based fracturing fluids demonstrate some challenges including immense quantity of water usage, water sensitivity of the formations, water blocking, and lack of proppant carrying capacity and transportation. Thus, an alternative is to use foam-based fracturing fluid which offers potential advantage over conventional water-based fracturing fluid such as minimum water usage, reduced wellbore damage, high proppant carrying capacity, and less environmental damage. However, foams are complex mixture of gaseous phase and liquid phase which are thermodynamically unstable at downhole conditions, and their stability can decrease over time due to liquid drainage, bubble coarsening, and coalescence. This paper shows laboratory experiments executed to study foam stability at high temperature (200°C) and high pressure (6.9MPa) conditions which simulates the geothermal environment. Foam stability was characterized by half-life of foam, which is defined as the time taken by the foam to decreases by 50% of its original height due to drainage. In this paper, two types of gaseous phases, nitrogen (N 2 ) and carbon dioxide (CO 2 ) were investigated. Also, based on successful practice of foam-based fracturing fluid in oil and gas industries, four surfactants, including Alpha olefin sulfonate (AOS), Sodium dodecyl sulfonate (SDS), Tergitol™ (NP – 40), and Cetyltrimethylammonium chloride (CTAC) at optimum concentration of 1wt.% were tested for best stability performance. In addition, different stabilizing agents including guar gum, bentonite clay, crosslinker, silicon dioxide nanoparticles (SiO 2 ), graphene oxide (GO) were also studied. Experimental results showed that N 2 foams were more stable than CO 2 foams. It was observed that foam half-life decreased with the increase in temperature. Among all the surfactants, AOS foams showed the most promising thermal stability at high temperatures. Moreover, with the addition of stabilizing agents, foam's half-life was enhanced. Stabilizing agents such as crosslinker and GO dispersion showed the most stable foams with half-life recorded at 20min and 17min, respectively, at 200°C and 6.9MPa. Finally, pressure also showed a positive effect on foam stability; with increased pressure, foam half-life was increased. Based on the experimental data, analytical models for the effect of temperature and pressure were developed, considering foam degradation is a first-order kinetic reaction that linearly depends on the foam drainage mechanism. The effect of temperature on foam half-life was studied as an exponential decay model. In this model, foam half-life is a function of drainage rate constant (D A ) and activation energy (E a ) of the foam system. The effect of pressure on foam half-life was found to obey a power-law model where an increase in pressure showed an increase in foam half-life. Furthermore, a linear relation was studied for the effect of pressure on foam activation energy and drainage rate. Then the combined effects of temperature and pressure were studied, which yielded an analytical model to predict the foam stabilities in terms of half-life for different foam compositions. In conclusion, this research indicates that with an appropriate selection of surfactants and stabilizing agents, it is possible to obtain stable foams, which could replace conventional water fracturing fluid under EGS conditions.

15 GEOTHERMAL ENERGY↗

Dynamics at the crystal-melt interface in a supercooled chalcogenide liquid near the glass transition

Direct quantitative measurements of nanoscale dynamical processes associated with structural relaxation and crystallization near the glass transition are a major experimental challenge. These type of processes have been primarily treated as macroscopic phenomena within the framework of phenomenological models and bulk experiments. Here, we report x-ray photon correlation spectroscopy measurements of dynamics at the crystal-melt interface during the radiation induced formation of Se nano-crystallites in pure Se and in binary AsSe 4 glass-forming liquids near their glass transition temperature. We observe a heterogeneous dynamical behaviour where the intensity correlation functions g 2 (q, t) exhibits either a compressed or a stretched exponential decay, depending on the size of the Se nano-crystallites. The corresponding relaxation timescale for the AsSe 4 liquid increases as the temperature is raised, which can be attributed to changes in the chemical composition of the melt at the crystal-melt interface with the growth of the Se nano-crystallites.

36 MATERIALS SCIENCE↗

Universal scaling of potential energy functions describing intermolecular interactions. II. The halide-water and alkali metal-water interactions

The scaled versions of the newly introduced [S. S. Xantheas and J. C. Werhahn, J. Chem. Phys.141, 064117 (2014)] generalized forms of some popular potential energy functions (PEFs) describing intermolecular interactions – Mie, Lennard-Jones, Morse, and Buckingham exponential-6 – have been used to fit the ab initio relaxed approach paths and fixed approach paths for the halide-water, X - (H 2 O), X = F, Cl, Br, I, and alkali metal-water, M + (H 2 O), M = Li, Na, K, Rb, Cs, interactions. The generalized forms of those PEFs have an additional parameter with respect to the original forms and produce fits to the ab initio data that are between one and two orders of magnitude better in the χ 2 than the original PEFs. They were found to describe both the long-range, minimum and repulsive wall of the respective potential energy surfaces quite accurately. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gBe-6) potentials were found to best fit the ab initio data for these two classes of ion-water interactions. Finally, the fitted values of the parameter of the (eM) and (gBe-6) PEFs that control the repulsive wall of the potential correlate remarkably well with the ionic radii of the halide and alkali metal ions.

Werhahn, Jasper C.↗

Using a pruned, nondirect product basis in conjunction with the multi-configuration time-dependent Hartree (MCTDH) method

In this paper, we propose a pruned, nondirect product multi-configuration time dependent Hartree (MCTDH) method for solving the Schrödinger equation. MCTDH uses optimized 1D basis functions, called single particle functions, but the size of the standard direct product MCTDH basis scales exponentially with D, the number of coordinates. We compare the pruned approach to standard MCTDH calculations for basis sizes small enough that the latter are possible and demonstrate that pruning the basis reduces the CPU cost of computing vibrational energy levels of acetonitrile (D = 12) by more than two orders of magnitude. Using the pruned method, it is possible to do calculations with larger bases, for which the cost of standard MCTDH calculations is prohibitive. Pruning the basis complicates the evaluation of matrix-vector products. In this paper, they are done term by term for a sum-of-products Hamiltonian. When no attempt is made to exploit the fact that matrices representing some of the factors of a term are identity matrices, one needs only to carefully constrain indices. In this paper, we develop new ideas that make it possible to further reduce the CPU time by exploiting identity matrices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optical waveguiding by atomic entanglement in multilevel atom arrays

The optical properties of subwavelength arrays of atoms or other quantum emitters have attracted significant interest recently. For example, the strong constructive or destructive interference of emitted light enables arrays to function as nearly perfect mirrors, support topological edge states, and allow for exponentially better quantum memories. In these proposals, the assumed atomic structure was simple, consisting of a unique electronic ground state. Within linear optics, the system is then equivalent to a periodic array of classical dielectric particles, whose periodicity supports the emergence of guided modes. However, it has not been known whether such phenomena persist in the presence of hyperfine structure, as exhibited by most quantum emitters. Here, we show that waveguiding can arise from rich atomic entanglement as a quantum many-body effect and elucidate the necessary conditions. Our work represents a significant step forward in understanding collective effects in arrays of atoms with realistic electronic structure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

IMFIT: A FAST, FLEXIBLE NEW PROGRAM FOR ASTRONOMICAL IMAGE FITTING

I describe a new, open-source astronomical image-fitting program called IMFIT, specialized for galaxies but potentially useful for other sources, which is fast, flexible, and highly extensible. A key characteristic of the program is an object-oriented design that allows new types of image components (two-dimensional surface-brightness functions) to be easily written and added to the program. Image functions provided with IMFIT include the usual suspects for galaxy decompositions (Sérsic, exponential, Gaussian), along with Core-Sérsic and broken-exponential profiles, elliptical rings, and three components that perform line-of-sight integration through three-dimensional luminosity-density models of disks and rings seen at arbitrary inclinations. Available minimization algorithms include Levenberg-Marquardt, Nelder-Mead simplex, and Differential Evolution, allowing trade-offs between speed and decreased sensitivity to local minima in the fit landscape. Minimization can be done using the standard χ{sup 2} statistic (using either data or model values to estimate per-pixel Gaussian errors, or else user-supplied error images) or Poisson-based maximum-likelihood statistics; the latter approach is particularly appropriate for cases of Poisson data in the low-count regime. I show that fitting low-signal-to-noise ratio galaxy images using χ{sup 2} minimization and individual-pixel Gaussian uncertainties can lead to significant biases in fitted parameter values, which are avoided if a Poisson-based statistic is used; this is true even when Gaussian read noise is present.

79 ASTRONOMY AND ASTROPHYSICS↗

Effect of repulsion on superconductivity at low density

Here we examine the effect of repulsion on superconductivity in a three-dimensional system with a Bardeen-Pines-like interaction in the low-density limit, where the chemical potential μ is much smaller than the phonon frequency ω L . We parametrize the strength of the repulsion by a dimensionless parameter f, and find that the superconducting transition temperature T c approaches a nonzero value in the μ = 0 limit as long as f is below a certain threshold f * . In this limit, we find that T c goes to zero as a power of f * - f, in contrast to the high density limit, where T c goes to zero exponentially quickly as f approaches f * . For all nonzero f, the gap function Δ(ω m ) changes sign along the Matsubara axis, which allows the system to partially overcome the repulsion at high frequencies. We trace the position of the gap node with f and show that it approaches zero frequency as f approaches f * . To investigate the robustness of our conclusions, we then go beyond the Bardeen-Pines model and include full dynamical screening of the interaction, finding that T c still saturates to a nonzero value at μ = 0 when f < f * .

36 MATERIALS SCIENCE↗

Exploiting fast detectors to enter a new dimension in room-temperature crystallography

A departure from a linear or an exponential decay in the diffracting power of macromolecular crystals is observed and accounted for through consideration of a multi-state sequential model. A departure from a linear or an exponential intensity decay in the diffracting power of protein crystals as a function of absorbed dose is reported. The observation of a lag phase raises the possibility of collecting significantly more data from crystals held at room temperature before an intolerable intensity decay is reached. A simple model accounting for the form of the intensity decay is reintroduced and is applied for the first time to high frame-rate room-temperature data collection.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Broadband Spectral Investigations of Magnetar Bursts

We present our broadband (2–250 keV) time-averaged spectral analysis of 388 bursts from SGR J1550−5418, SGR 1900+14, and SGR 1806−20 detected with the Rossi X-ray Timing Explorer ( RXTE ) here and as a database in a companion web-catalog. We find that two blackbody functions (BB+BB), the sum of two modified blackbody functions (LB+LB), the sum of a blackbody function and a power-law function (BB+PO), and a power law with a high-energy exponential cutoff (COMPT) all provide acceptable fits at similar levels. We performed numerical simulations to constrain the best fitting model for each burst spectrum and found that 67.6% of burst spectra with well-constrained parameters are better described by the Comptonized model. We also found that 64.7% of these burst spectra are better described with the LB+LB model, which is employed in the spectral analysis of a soft gamma repeater (SGR) for the first time here, than with the BB+BB and BB+PO models. We found a significant positive lower bound trend on photon index, suggesting a decreasing upper bound on hardness, with respect to total flux and fluence. We compare this result with bursts observed from SGR and AXP (anomalous X-ray pulsar) sources and suggest that the relationship is a distinctive characteristic between the two. We confirm a significant anticorrelation between burst emission area and blackbody temperature, and find that it varies between the hot and cool blackbody temperatures differently than previously discussed. We expand on the interpretation of our results in the framework of a strongly magnetized neutron star.

79 ASTRONOMY AND ASTROPHYSICS↗

Observations of the ionization states of energetic particles accelerated in solar flares

Results of a survey of ten solar flare particle events, in which the ionization states and spectra of 0.3 to 2.4 MeV/nuc He, C, O and Fe were measured, are reported. He+ was present in all events (He+/He++ approximately 0.1 to 0.25), and the mean ionization states of C, O and Fe are high. The distribution functions of He+, He++ and heavier elements are well represented by simple exponentials of the particle speed times its rigidity to a power n, where n is between O and 1, and equal e-folding values. Results are consistent with a model whereby ions are accelerated in the corona by multi-dimensional shocks out of a population taken from both hot and cold coronal regions.

Gloeckler, G.↗

Distribution function representation of energy spectra of H, He, C, O and Fe in corotating particle streams

From an analysis of nine corotating events observed near 1 AU during the 1974-1976 solar minimum, the spectral parameters for H, He, C, O and Fe and relative abundances of these elements and of Ne, Mg, Si, and S-Ca were determined. The distribution functions of H, He, O and Fe are well represented by an exponential in particle speed over the energy range of the measurements from 0.3 to 5 MeV/nucleon. The composition resembles that of the solar corona, particularly in the O/C ratio which is 0.95 + or - 0.19, and the He/H and He/Ne ratios are similar to the respective ratios in the solar wind. The results are consistent with interplanetary statistical acceleration of these particles out of the high-energy tail of the high-speed solar wind.

Gloeckler, G.↗

On the acceleration of thermal coronal ions by flare induced shock waves

The energy spectra of solar flare ions are calculated by assuming that the process which accelerates solar wind ions to MeV/ nucleon energies in the interplanetary corotating interaction region (CIR) also occurs in flare induced magnetosonic fast-mode (MFM) shocks in the corona. Solar wind ions are considered to be accelerated to MeV/nucleon energies by wave-particle interactions in the shock front and the downstream flow, being compressed between upstream and downstream magnetic field irregularities, and then accelerated by the shock drift acceleration mechanism. The energy spectra of the accelerated ions is calculated from the number of shock encounters as a function of the post- and preacceleration energies. A best fit by an exponential in momentum is determined for ions in the 50 MeV to a few GeV range, and from 20-80 MeV by a suitable power law in kinetic energy with a mean spectral index. Comparisons with observed solar protons show good agreement.

Decker, R. B.↗

A model of the radiative properties of the El Chichon stratospheric aerosol layer

An accurate multiple-scattering model has been employed to examine the effect of an aerosol layer at 25 mb, corresponding to the El Chichon observations, on the reflection, transmission and absorption of radiation by the stratosphere as a function of latitude, optical thickness and aerosol size distribution. Results are presented and parameterized for each of two wavelength intervals in the shortwave region and 17 wavelength intervals in the longwave region for three models of the aerosol size distribution. They include one model representing the unperturbed stratospheric aerosol plus two models based on measurements of the El Chichon aerosol size distribution. In addition to models of the radiative properties of the aerosol layer, a simple model of the latitudinal distribution of aerosol optical thickness as a function of time is developed, based on diffusive transport in latitude and exponential decay in time. These parameterizations for solar and infrared radiation, together with the dispersion model, permit climate models to account for the evolution of an aerosol size distribution from post-volcanic conditions to background conditions.

King, M. D.↗

Analytic solution for vertical launch into orbit

An approximate analytic solution is presented for the motion and heating of nonlifting spacecraft launched vertically for ascending flight through the atmosphere into earth orbit. The solution is based on Chapman's Z-function transformation of the equations of motion with the assumption of an exponential atmosphere. The transformed equations have been modified to include the effects of thrusting with mass loss. It is assumed that the vehicle negotiates a gravity turn during ascent so that the thrust vector is aligned in the flight-path direction. Numerical results are presented to document the analytic solution and provide evidence of the useful information generated by it.

Boltz, Frederick W.↗

Skeletal Recovery Following Long-Duration Spaceflight Missions as Determined by Preflight and Postflight DXA Scans of 45 Crew Members

Introduction: The loss of bone mineral in astronauts during spaceflight has been investigated throughout the more than 40 years of bone research in space. Consequently, it is a medical requirement at NASA that changes in bone mass be monitored in crew members by measurements of bone mineral density (BMD) with dual-energy x-ray absorptiometry (DXA). This report is the first to evaluate medical data to address the recovery of bone mineral that is lost during spaceflight. Methods: DXA scans are performed before and after flight in astronauts who serve on long-duration missions (4-6 months) to ensure that medical standards for flight certification are met, to evaluate the effects of spaceflight and to monitor the restoration to preflight BMD status after return to Earth. Through cooperative agreements with the Russian Space Agency, the Bone and Mineral Lab at NASA Johnson Space Center (Houston, TX), also had access to BMD data from cosmonauts who had flown on long-duration missions yielding data from a total of 45 individual crew members. Changes in BMD (between 56 different sets of pre- and postflight measurements) were plotted as a function of time (days after landing); plotted data were fitted to an exponential mathematical model that determined i) BMD change at day 0 after landing and ii) the number of days after which 50% of the lost bone was recovered ("Recovery Half-Life"). These fits were performed for BMD of the lumbar spine, trochanter, pelvis, femoral neck and calcaneus. Results: In sum, averaged losses of bone mineral after spaceflight ranged between 2-9% for sites in the axial and appendicular skeleton. The fitted postflight BMD values predicted a 50% recovery of bone loss for all sites within 9 months.

Sibonga, J. D.↗

Shuttle Risk Progression: Use of the Shuttle Probabilistic Risk Assessment (PRA) to Show Reliability Growth

It is important to the Space Shuttle Program (SSP), as well as future manned spaceflight programs, to understand the early mission risk and progression of risk as the program gains insights into the integrated vehicle through flight. The risk progression is important to the SSP as part of the documentation of lessons learned. The risk progression is important to future programs to understand reliability growth and the first flight risk. This analysis uses the knowledge gained from 30 years of operational flights and the current Shuttle PRA to calculate the risk of Loss of Crew and Vehicle (LOCV) at significant milestones beginning with the first flight. Key flights were evaluated based upon historical events and significant re-designs. The results indicated that the Shuttle risk tends to follow a step function as opposed to following a traditional reliability growth pattern where risk exponentially improves with each flight. In addition, it shows that risk can increase due to trading safety margin for increased performance or due to external events. Due to the risk drivers not being addressed, the risk did not improve appreciably during the first 25 flights. It was only after significant events occurred such as Challenger and Columbia, where the risk drivers were apparent, that risk was significantly improved. In addition, this paper will show that the SSP has reduced the risk of LOCV by almost an order of magnitude. It is easy to look back afte r 30 years and point to risks that are now obvious, however; the key is to use this knowledge to benefit other programs which are in their infancy stages. One lesson learned from the SSP is understanding risk drivers are essential in order to considerably reduce risk. This will enable the new program to focus time and resources on identifying and reducing the significant risks. A comprehensive PRA, similar to that of the Shuttle PRA, is an effective tool quantifying risk drivers if support from all of the stakeholders is given.

Hamlin, Teri L.↗

Computing partition functions in the one-clean-qubit model

We present a method to approximate partition functions of quantum systems using mixed-state quantum computation. For positive-semidefinite Hamiltonians, our method has an expected running-time that is almost linear in [M/( ε rel Z )] 2 , where M is the dimension of the quantum system, Z is the partition function, and ε rel is the relative precision. It is based on approximations of the exponential operator as linear combinations of certain operators related to block-encoding of Hamiltonians or Hamiltonian evolutions. The trace of each operator is estimated using a standard algorithm in the one-clean-qubit model. For large values of Z , our method may run faster than exact classical methods, whose complexities are polynomial in M . We also prove that a version of the partition function estimation problem within additive error is complete for the so-called DQC1 complexity class, suggesting that our method provides a superpolynomial speedup for certain parameter values. Overall, to attain a desired relative precision, we develop a classical procedure based on a sequence of approximations within predetermined additive errors that may be of independent interest.

97 MATHEMATICS AND COMPUTING↗