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At least 1,243 records · Page 69

Controlled synthesis of highly-branched plasmonic gold nanoparticles through peptoid engineering

Inspired by peptide- and protein-controlled formation of hierarchical inorganic nanostructures in nature, herein we report the design of sequence-defined peptoids for biomimetic synthesis of flower-like gold nanosuperstruc-tures. We demonstrate that the peptoid-induced morphosyn-thesis of gold nanoflowers is sequence-dependent. By varying the hydrophobicity, number of carboxylate and amino groups, and side-chain positions of peptoids, we develop a rule of thumb for designing peptoids that yield gold nanoflowers. Through a combination of hyperspectral UV-Vis absorption micro-spectroscopy (H-UVVIS-AMS) and three-photon photoemission electron microscopy (TP-PEEM), we measured the plasmonic properties of individual nanoflowers. Whereas H-UVVIS-AMS experiments revealed well-defined plasmon resonances centered at ~528 nm, TP-PEEM measurements showed an unprecedented plasmonic enhancement as high as 105 for a single nanoflower. A com-bination of the unique plasmonic property and the high sta-bility endows the peptoid-engineered nanoflowers with po-tential applications in chemical and biological imaging. FY, YC, HJ and C-LC acknowledge support by the Materials Synthesis and Simulation Across Scales (MS3) Initiative, through the Laboratory Directed Research & Development (LDRD) fund at Pacific Northwest National Laboratory (PNNL). FY was also partially supported by fellowships from Shandong Provincial Education Association for International Exchanges. YG was supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PZE acknowledges support from the Laboratory Directed Research and Development Program through a Linus Pauling Fellowship at PNNL. PNNL is multi-program national laboratory operated for the Department of Energy by Battelle under Contracts No. DE-AC05-76RL01830. The authors are most grateful to Alan Joly and Wayne Hess (PNNL) for their support with the PEEM measurements and several useful discussions.

Yan, Feng↗

Advanced Seismic Probabilistic Risk Assessment Methodology: Development of Beta 1.0 MASTODON Toolset

Design of nuclear power plant (NPP) facilities to resist natural hazards has been a part of the regulatory process from the beginning of the NPP industry in the United States, but has evolved substantially over time. The original set of approaches and methods was entirely deterministic in nature and focused on a traditional engineering margins-based approach. However, over time probabilistic and risk-informed approaches were also developed and implemented in US Nuclear Regulatory Commission guidance and regulation. A defense-in-depth framework has also been incorporated into US regulatory guidance over time. As a result, today, the US regulatory framework incorporates deterministic and probabilistic approaches for a range of different applications and for a range of natural hazard considerations. Although the US regulatory framework has continued to evolve over time, the tools, methods and data available to the US nuclear industry to meet the changing requirements have not kept pace. Notably, there is room for improvement in the tools and methods available for external event probabilistic risk assessment (PRA), which is the principal assessment approach used in risk-informed regulations and risk-informed decision-making applied to natural hazard assessment and design. Development of a new set of tools and methods that incorporate current knowledge, modern best practice, and state-of-the-art computational resources would lead to more reliable assessment of facility risk and risk insights (e.g., the plant elements and accident sequences that are most risk-significant), with less uncertainty and reduced conservatisms. Development of the next generation tools and methods for external events PRA is ongoing under the Risk Informed Safety Margins Characterization (RISMC) technical pathway. The RISMC toolkit development centers on integration of the tools and methods under a common framework, MOOSE. These tools and methods make use of existing and newly developed tools and methods, coupled with the experience and data gained in the past decades, to define and analyze more realistic risk assessment models. Specific focus in this report is on the capability to model seismic risk using advanced SPRA methods. Over the last year, significant capability has been added to Mastodon to simulate 3-D wave passage effects through nonlinear soil. Verification has demonstrated the capability of Mastodon to model wave passage effects in 1-D, 2-D, and 3-D. Methods have been developed to incorporate probabilistic floor response capabilities. Additional capability will be added to Mastodon over the next year to implement a robust gapping and sliding element for cyclic shaking, web-based verification and user manuals, stochastic finite elements, and frequency independent damping. Verification of added capabilities has occured in parallel with code writing activities.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

ELF oscillations associated with electron beam injections from the Space Shuttle

ELF oscillations (f less than 500 Hz) were observed during the electron beam emissions of the space experiments with particle accelerators (SEPAC) flown on the Spacelab 1 Shuttle mission. The beams had energies up to 5 keV and currents up to 300 mA, and the oscillations were present in the data from a Langmuir probe, a floating probe, an electron energy analyzer, and a photometer. The power density and frequency of the fundamental increased with the Shuttle charge-up potential. The emission level observed during the beam sequences increased with the charge-up potential of the Orbiter, which largely depended on the wake structure. It is most likely that the ELF oscillations are expressions of fluctuations in the return current and the Shuttle potential and that these fluctuations are caused by processes involving charge imbalances in the near environment of the Shuttle, possibly in a comoving plasma cloud.

Cai, D.↗

Demonstration of solar echoes using the Air Force OTH-B radar

From the late 50s to early 70s, attempts were made by at least two different groups to obtain information on physical conditions in the corona by means of active radar soundings. While echoes from the Sun were unquestionably detected. difficulties in their interpretation led to inconclusive results. A major hindrance to these efforts was the limited understanding of the day-to-day structure of the corona then available (e.g., pioneering work in solar wind studies were just underway. and coronal holes had not yet been discovered). With the end of the Cold War, the very large over-the-horizon (OTH) radars operated by the Air Force have been opened up to basic science research through the end of the fiscal year. In light of advances made in coronal physics and in signal processing technology since these early experiments were undertaken. access to the state-of-the art OTH-B radar offers a rare opportunity to gauge anew the scientific potential for radar sounding of the Sun. In principle, it should be possible to obtain useful data on plasma densities and motions over a range of heights in the corona near 0.5R(solar mass) above the solar surface We report here the preliminary findings from a sequence of observations taken over the course of a solar rotation.

Pizzo, V. J.↗

Software Architecture of Sensor Data Distribution In Planetary Exploration

Data from mobile and stationary sensors will be vital in planetary surface exploration. The distribution and collection of sensor data in an ad-hoc wireless network presents a challenge. Irregular terrain, mobile nodes, new associations with access points and repeaters with stronger signals as the network reconfigures to adapt to new conditions, signal fade and hardware failures can cause: a) Data errors; b) Out of sequence packets; c) Duplicate packets; and d) Drop out periods (when node is not connected). To mitigate the effects of these impairments, a robust and reliable software architecture must be implemented. This architecture must also be tolerant of communications outages. This paper describes such a robust and reliable software infrastructure that meets the challenges of a distributed ad hoc network in a difficult environment and presents the results of actual field experiments testing the principles and actual code developed.

Lee, Charles↗

Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress

Microalgae that are of interest for biofuel production must be able to tolerate environmental changes that occur in outdoor cultivation systems. While algal cultures may experience daily temperature fluctuations and seasonal environmental changes, the underlying mechanisms that control and regulate physiological responses and adaptation to environmental pressures are largely unknown. Systems-level characterization enabled by functional genomics can help identify biochemical pathways that promote stability and productivity of algae in various environmental conditions. Monoraphidium minutum 26B-AM, a freshwater green microalga, was identified as a top performer in biomass production in winter season screens. We sequenced the genome of M. minutum 26B-AM and applied our multi-omics pipeline to profile this high potential strain under high salt and cold temperature perturbations. Through comparative analysis, including other green algae in the class Chlorophyceae, we identified gene families unique to the genus Monoraphidium, including a desaturase that has been linked to cold tolerance in plants. We observed that osmolytes, such as trehalose, proline and betaine, accumulate under salt stress, coinciding with upregulation of genes involved in biosynthesis of these metabolites. From the genome annotation, we reconstructed a metabolic model to provide a detailed map of the metabolic pathways and can be used to simulate growth and reaction fluxes. This multi-omics analysis provides a foundation to explore algal strain potential for biofuel applications, guides strain engineering, and expands our understanding of metabolic and regulatory mechanisms of algae in applied systems.

59 BASIC BIOLOGICAL SCIENCES↗

Femtosecond-resolved observation of the fragmentation of buckminsterfullerene following X-ray multiphoton ionization

X-ray free-electron lasers have, over the past decade, opened up the possibility of understanding the ultrafast response of matter to intense X-ray pulses. In earlier research on atoms and small molecules, new aspects of this response were uncovered, such as rapid sequences of inner-shell photoionization and Auger ionization. Here, we studied a larger molecule, buckminsterfullerene (C 60 ), exposed to 640 eV X-rays, and examined the role of chemical effects, such as chemical bonds and charge transfer, on the fragmentation following multiple ionization of the molecule. To provide time resolution, we performed femtosecond-resolved X-ray pump/X-ray probe measurements, which were accompanied by advanced simulations. The simulations and experiment reveal that despite substantial ionization induced by the ultrashort (20 fs) X-ray pump pulse, the fragmentation of C 60 is considerably delayed. This work uncovers the persistence of the molecular structure of C 60 , which hinders fragmentation over a timescale of hundreds of femtoseconds. Furthermore, we demonstrate that a substantial fraction of the ejected fragments are neutral carbon atoms. In conclusion, these findings provide insights into X-ray free-electron laser-induced radiation damage in large molecules, including biomolecules.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Direct observation of the exotic β – γ – α decay mode in the T z = – 1 nucleus Na 20

The exotic β – γ – α decay mode of 20 Na has been directly observed for the first time in the Day-one experiment at the Beijing Radioactive Ion-beam Facility. The 20 Na source was produced by using a 100-MeV proton beam bombarding a stack of microporous MgO thick target and delivered as an intense mass separated beam after online ionization. A high-efficiency simultaneous measurement of β, γ, and α transitions enables the β-delayed γ – γ and α – γ coincidence spectroscopy. Here three β – γ – α exotic decay sequences in 20 Na are discovered, which expands the rare decay modes observed in β decay. Moreover, a β – α –decay sequence to the 6130-keV 3 – state of 16 O is observed, which is likely through the 12367-keV 1 + state in 20 Ne. The experimentally deduced B(F) and B(GT) are compared to the shell-model calculation, the allowed β transition strengths can be well accounted for by using sd shell-model space interactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Gap Resolution

Gap Resolution is a software package that was developed to improve Newbler genome assemblies by automating the closure of sequence gaps caused by repetitive regions in the DNA. This is done by performing the follow steps:1) Identify and distribute the data for each gap in sub-projects. 2) Assemble the data associated with each sub-project using a secondary assembler, such as Newbler or PGA. 3) Determine if any gaps are closed after reassembly, and either design fakes (consensus of closed gap) for those that closed or lab experiments for those that require additional data. The software requires as input a genome assembly produce by the Newbler assembler provided by Roche and 454 data containing paired-end reads.

Labutti, Kurt↗

Clarification process: Resolution of decision-problem conditions

A model of a general process which occurs in both decisionmaking and problem-solving tasks is presented. It is called the clarification model and is highly dependent on information flow. The model addresses the possible constraints of individual indifferences and experience in achieving success in resolving decision-problem conditions. As indicated, the application of the clarification process model is only necessary for certain classes of the basic decision-problem condition. With less complex decision problem conditions, certain phases of the model may be omitted. The model may be applied across a wide range of decision problem conditions. The model consists of two major components: (1) the five-phase prescriptive sequence (based on previous approaches to both concepts) and (2) the information manipulation function (which draws upon current ideas in the areas of information processing, computer programming, memory, and thinking). The two components are linked together to provide a structure that assists in understanding the process of resolving problems and making decisions.

Dieterly, D. L.↗

An application for multi-person task synchronization

Computer applications are studied that will enable a group of people to synchronize their actions when following a predefined task sequence. It is assumed that the people involved only have computer workstations available to them for communication. Hence, the approach is to study how the computer can be used to help a group remain synchronized. A series of applications were designed and developed that can be used as vehicles for experimentation. An example of how this technique can be used for a remote coaching capability is explained in a report describing an experiment that simulated a Life Sciences experiment on-board Space Station Freedom, with a ground based principal investigator providing the expertise by coaching the on-orbit mission specialist.

Brown, Robert L.↗

Timing Noise in SGR 1806-20

We have phase connected a sequence of Rossi X-ray Timing Explorer Proportional Counter Array observations of SGR 1806-20 covering 178 days. We find a simple secular spin-down model does not adequately fit the data. The period derivative varies gradually during the observations between 8.1 and 11.7 x 10(exp -11) s/s (approx. 40% larger than the long term trend), while the average burst rate as seen with the Burst and Transient Source Experiment drops throughout the time interval. The phase residuals show no evidence for periodicity, but more closely resemble timing noise as seen ill radio pulsars. The magnitude of the timing noise., however, is large relative to the noise level typically found in radio pulsars (Delta(sub 8) = 4.8; frequency derivative average power approx. = 8 X 10(exp -20) Hz/sq s). Combined with the noise levels measured for some AXPs. we find all magnetar candidates have A8 values larger than those expected from a simple extrapolation of the correlation found in radio pulsars. We find the timing noise ill SGR 1806-20 is greater than or equal to the levels found in some accreting systems (e.g., Vela X-1, 4U 1538-52 and 4U 1626-67). Alternatively, an orbital model with a period P(sub orb) = 733 days provides a statistically acceptable fit to the data. If the phase residuals are created by Doppler shifts from a gravitationally bound companion. then the allowed parameter space for the mass function (small) and orbital separation (large) rule out the possibility of accretion from the companion sufficient to power the persistent emission from the SGR.

Woods, Peter M.↗

Comparison of a space shuttle flight (STS-78) and bed rest on human muscle function

The purpose of this investigation was to assess muscle fiber size, composition, and in vivo contractile characteristics of the calf muscle of four male crew members during a 17-day spaceflight (SF; Life and Microgravity Sciences Spacelab Shuttle Transport System-78 mission) and eight men during a 17-day bed rest (BR). The protocols and timelines of these two investigations were identical, therefore allowing for direct comparisons between SF and the BR. The subjects' age, height, and weight were 43 +/- 2 yr, 183 +/- 4 cm, and 86 +/- 3 kg for SF and 43 +/- 2 yr, 182 +/- 3 cm, and 82 +/- 4 kg for BR, respectively. Calf muscle strength was examined before SF and BR; on days 2, 8, and 12 during SF and BR; and on days 2 and 8 of recovery. Muscle biopsies were obtained before and within 3 h after SF (gastrocnemius and soleus) and BR (soleus) before reloading. Maximal isometric calf strength and the force-velocity characteristics were unchanged with SF or BR. Additionally, neither SF nor BR had any effect on fiber composition or fiber size of the calf muscles studied. In summary, no changes in calf muscle strength and morphology were observed after the 17-day SF and BR. Because muscle strength is lost during unloading, both during spaceflight and on the ground, these data suggest that the testing sequence employed during the SF and BR may have served as a resistance training countermeasure to attenuate whole muscle strength loss.

Non-NASA Center↗

Experiments in control of flexible structures with noncolocated sensors and actuators

While the stable control of such flexible structures as limber spacecraft is easily achieved through the colocation of control actuators with sensors, noncolocation renders this extremely difficult. The most difficult case in point is that in which structural damping is low and spacecraft stiffness and inertia values are uncertain and changing. Attention is presently given to an apparatus in which each basic sensor/actuator noncolocation configuration is available, and inertias can be abruptly halved or doubled during control maneuvers. This feature can impose a sudden reversal in the plant's pole-zero sequence, which is a very difficult condition for the controller. Test results obtained to date demonstrate the inherent difficulty of achieving robustness in the case of noncolocation. It is noted that there may be very simple configurations in which there is no alternative to adaptive control.

Cannon, R. H., Jr.↗

Soil Microbes Trade-Off Biogeochemical Cycling for Stress Tolerance Traits in Response to Year-Round Climate Change

Winter air temperatures are rising faster than summer air temperatures in high-latitude forests, increasing the frequency of soil freeze/thaw events in winter. To determine how climate warming and soil freeze/thaw cycles affect soil microbial communities and the ecosystem processes they drive, we leveraged the Climate Change across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest in the northeastern United States, where replicate field plots receive one of three climate treatments: warming (+5°C above ambient in the growing season), warming in the growing season + winter freeze/thaw cycles (+5°C above ambient +4 freeze/thaw cycles during winter), and no treatment. Soil samples were taken from plots at six time points throughout the growing season and subjected to amplicon (rDNA) and metagenome sequencing. We found that soil fungal and bacterial community composition were affected by changes in soil temperature, where the taxonomic composition of microbial communities shifted more with the combination of growing-season warming and increased frequency of soil freeze/thaw cycles in winter than with warming alone. Warming increased the relative abundance of brown rot fungi and plant pathogens but decreased that of arbuscular mycorrhizal fungi, all of which recovered under combined growing-season warming and soil freeze/thaw cycles in winter. The abundance of animal parasites increased significantly under combined warming and freeze/thaw cycles. We also found that warming and soil freeze/thaw cycles suppressed bacterial taxa with the genetic potential for carbon (i.e., cellulose) decomposition and soil nitrogen cycling, such as N fixation and the final steps of denitrification. These new soil communities had higher genetic capacity for stress tolerance and lower genetic capacity to grow or reproduce, relative to the communities exposed to warming in the growing season alone. Our observations suggest that initial suppression of biogeochemical cycling with year-round climate change may be linked to the emergence of taxa that trade-off growth for stress tolerance traits.

54 ENVIRONMENTAL SCIENCES↗

Incremental planning to control a blackboard-based problem solver

To control problem solving activity, a planner must resolve uncertainty about which specific long-term goals (solutions) to pursue and about which sequences of actions will best achieve those goals. A planner is described that abstracts the problem solving state to recognize possible competing and compatible solutions and to roughly predict the importance and expense of developing these solutions. With this information, the planner plans sequences of problem solving activities that most efficiently resolve its uncertainty about which of the possible solutions to work toward. The planner only details actions for the near future because the results of these actions will influence how (and whether) a plan should be pursued. As problem solving proceeds, the planner adds new details to the plan incrementally, and monitors and repairs the plan to insure it achieves its goals whenever possible. Through experiments, researchers illustrate how these new mechanisms significantly improve problem solving decisions and reduce overall computation. They briefly discuss current research directions, including how these mechanisms can improve a problem solver's real-time response and can enhance cooperation in a distributed problem solving network.

Durfee, E. H.↗

Integrating planning and reactive control

Artificial intelligence research on planning is concerned with designing control systems that choose actions by manipulating explicit descriptions of the world state, the goal to be achieved, and the effects of elementary operations available to the system. Because planning shifts much of the burden of reasoning to the machine, it holds great appeal as a high-level programming method. Experience shows, however, that it cannot be used indiscriminately because even moderately rich languages for describing goals, states, and the elementary operators lead to computational inefficiencies that render the approach unsuitable for realistic applications. This inadequacy has spawned a recent wave of research on reactive control or situated activity in which control systems are modeled as reacting directly to the current situation rather than as reasoning about the future effects of alternative action sequences. While this research has confronted the issue of run-time tractability head on, in many cases it has done so by sacrificing the advantages of declarative planning techniques. Ways in which the two approaches can be unified are discussed. The authors begin by modeling reactive control systems as state machines that map a stream of sensory inputs to a stream of control outputs. These machines can be decomposed into two continuously active subsystems: the planner and the execution module. The planner computes a plan, which can be seen as a set of bits that control the behavior of the execution module. An important element of this work is the formulation of a precise semantic interpretation for the inputs and outputs of the planning system. They show that the distinction between planned and reactive behavior is largely in the eye of the beholder: systems that seem to compute explicit plans can be redescribed in situation-action terms and vice versa. They also discuss practical programming techniques that allow the advantages of declarative programming and guaranteed reactive response to be achieved simultaneously.

Rosenschein, Stanley J.↗