A probability-conserving cross-section biasing mechanism for variance reduction in Monte Carlo particle transport calculations

In Monte Carlo particle transport codes, it is often important to adjust reaction cross sections to reduce the variance of calculations of relatively rare events, in a technique known as non-analogous Monte Carlo. We present the theory and sample code for a Geant4 process which allows the cross section of a G4VDiscreteProcess to be scaled, while adjusting track weights so as to mitigate the effects of altered primary beam depletion induced by the cross section change. This makes it possible to increase the cross section of nuclear reactions by factors exceeding 10^4 (in appropriate cases), without distorting the results of energy deposition calculations or coincidence rates. The procedure is also valid for bias factors less than unity, which is useful, for example, in problems that involve computation of particle penetration deep into a target, such as occurs in atmospheric showers or in shielding

Discoloration of Polyvinyl Chloride (PVC) Tape as a Proxy for Water-Table Depth in Peatlands: Validation and Assessment of Seasonal Variability

Summary 1. Discoloration of polyvinyl chloride (PVC) tape has been used in peatland ecological and hydrological studies as an inexpensive way to monitor changes in water-table depth and reducing conditions. 2. We investigated the relationship between depth of PVC tape discoloration and measured water-table depth at monthly time steps during the growing season within nine kettle peatlands of northern Wisconsin. Our specific objectives were to: (1) determine if PVC discoloration is an accurate method of inferring water-table depth in Sphagnum -dominated kettle peatlands of the region; (2) assess seasonal variability in the accuracy of the method; and (3) determine if systematic differences in accuracy occurred among microhabitats, PVC tape colour and peatlands. 3. Our results indicated that PVC tape discoloration can be used to describe gradients of water-table depth in kettle peatlands. However, accuracy differed among the peatlands studied, and was systematically biased in early spring and late summer/autumn. Regardless of the month when the tape was installed, the highest elevations of PVC tape discoloration showed the strongest correlation with midsummer (around July) water-table depth and average water-table depth during the growing season. 4. The PVC tape discoloration method should be used cautiously when precise estimates are needed of seasonal changes in the water-table

Lake-level Variability and Water Availability in the Great Lakes

Key components of water availability in a hydrologic system4 are the amount of water in storage and the variability of that amount. In the Great Lakes Basin, a vast amount of water is stored in the lakes themselves. Because of the lakes’ size, small changes in water levels cause huge changes in the amount of water in storage. Approximately 5,439 mi3 of water, measured at chart datum, is stored in the Great Lakes. A change of 1 ft in water level over the total Great Lakes surface area of 94,250 mi2 means a change of 18 mi3 of water in storage. Changes in lake level over time also play an important role in human activities and in coastal processes and nearshore ecosystems, including development and maintenance of beaches, dunes, and wetlands. The purpose of this report is to present recorded and reconstructed (pre-historical) changes in water levels in the Great Lakes, relate them to climate changes of the past, and highlight major water-availability implications for storage, coastal ecosystems, and human activities. Reconstructed water-level changes have not been completed for all Great Lakes; consequently, this report presents these changes primarily for Lakes Michigan and Huron, with some reference to Lake Superior also

Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo

Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, "replica" ensemble of walkers, whose population evolves in imaginary time independently from the first, and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality, and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, the present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation.Comment: 11 page

Multiscale modelling of drug-polymer nanoparticle assembly identifies parameters influencing drug encapsulation efficiency

Using a multiscale (dual resolution) approach combining an atomistic (GROMOS96) and coarse-grain (MARTINI) force field, we have been able to simulate the process of drug-polymer nanoparticle assembly by nanoprecipitation from mixed solvents. Here we present the development and application of this method to the interaction of three poly(glycerol adipate) polymer variants with the anti-cancer drug dexamethasone phosphate. Differences in encapsulation efficiency and drug loading between the polymers are in agreement with the experimental trend. Reference atomistic simulations at key points along the predicted aggregation pathway support the accuracy of the much more compute-efficient multiscale methodology

Distributed Acoustic Sensing of Seismic Properties in a Borehole Drilled on a Fast‐Flowing Greenlandic Outlet Glacier

Abstract Distributed Acoustic Sensing (DAS) is a new technology in which seismic energy is detected, at high spatial and temporal resolution, using the propagation of laser pulses in a fiber‐optic cable. We show analyses from the first glaciological borehole DAS deployment to measure the englacial and subglacial seismic properties of Store Glacier, a fast‐flowing outlet of the Greenland Ice Sheet. We record compressional and shear waves in 1,043 m‐deep vertical seismic profiles, sampled at 10 m vertical resolution, and detect a transition from isotropic to anisotropic ice at 84% of ice thickness, consistent with the Holocene‐Wisconsin transition. We identify subglacial reflections originating from the base of a 20 m‐thick layer of consolidated sediment and, from attenuation measurements, interpret temperate ice in the lowermost 100 m of the glacier. Our findings highlight the promising potential of DAS technology to constrain the seismic properties of glaciers and ice sheets. Plain Language Summary Distributed Acoustic Sensing (DAS) is a new technology for seismic surveying in which the transmission of light through fiber‐optic cables is used to record seismic energy, with unprecedented spatial resolution compared to traditional techniques. Our paper presents data from the first borehole‐glaciological deployment of DAS, in which fiber‐optic cable was installed in a 1,043 m‐deep vertical borehole on Store Glacier, a fast‐flowing outlet of the Greenland Ice Sheet. The detailed seismic anatomy of the glacier that our survey provides—an independent measurement of the seismic response every 10 m—gives new insights about its internal flow regime and temperature and even allows us to detect layers of sediment underlying it. We predict that DAS surveying will play an increasingly large role in future glaciological investigations as the recognition of its promising potential grows

Late Holocene Lake-level Variation in Southeastern Lake Superior: Tahquamenon Bay, Michigan

Internal architecture and ages of 71 beach ridges in the Tahquamenon Bay embayment along the southeastern shore of Lake Superior on the Upper Peninsula of Michigan were studied to generate a late Holocene relative lake-level curve. Establishing a long-term framework is important to examine the context of historic events and help predict potential future changes critical for effective water resource management. Ridges in the embayment formed between about 4,200 and 2,100 calendar years before 1950 (cal. yrs. B.P.) and were created and preserved every 28 ± 4.8 years on average. Groups of three to six beach ridges coupled with inflections in the lake-level curve indicate a history of lake levels fluctuations and outlet changes. A rapid lake-level drop (approximately 4 m) from about 4,100 to 3,800 cal. yrs. B.P. was associated with a fall from the Nipissing II high-water-level phase. A change from a gradual fall to a slight rise was associated with an outlet change from Port Huron, Michigan/Sarnia, Ontario to Sault Ste. Marie, Michigan/Ontario. A complete outlet change occurred after the Algoma high-water-level phase (ca. 2,400 cal. yrs. B.P.). Preliminary rates of vertical ground movement calculated from the strandplain are much greater than rates calculated from historical and geologic data. High rates of vertical ground movement could have caused tectonism in the Whitefish Bay area, modifying the strandplain during the past 2,400 years. A tectonic event at or near the Sault outlet also may have been a factor in the outlet change from Port Huron/Sarnia to Sault Ste. Marie

Structural and functional analyses of glycoside hydrolase 138 enzymes targeting chain A galacturonic acid in the complex pectin rhamnogalacturonan II

The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiome. The selection pressures in this environment have spurred the evolution of a complex reservoir of microbial genes encoding carbohydrate-active enzymes (CAZymes). Previously, we have shown that the human gut bacterium Bacteroides thetaiotaomicron (Bt) can depolymerize the most structurally complex glycan, the plant pectin rhamnogalacturonan II (RGII), commonly found in the human diet. Previous investigation of the RGII-degrading apparatus in Bt identified BT0997 as a new CAZyme family, classified as glycoside hydrolase 138 (GH138). The mechanism of substrate recognition by GH138, however, remains unclear. Here, using synthetic substrates and biochemical assays, we show that BT0997 targets the D-galacturonic acid-α-1,2-L-rhamnose linkage in chain A of RGII and that it absolutely requires the presence of a second D-galacturonic acid side chain (linked β-1,3 to L-rhamnose) for activity. NMR analysis revealed that BT0997 operates through a double displacement retaining mechanism. We also report the crystal structure of a BT0997 homolog, BPA0997 from Bacteroides paurosaccharolyticus, in complex with ligands at 1.6 Å resolution. The structure disclosed that the enzyme comprises four domains, including a catalytic TIM (α/β)8 barrel. Characterization of several BT0997 variants identified Glu-294 and Glu-361 as the catalytic acid/base and nucleophile, respectively, and we observed a chloride ion close to the active site. The three-dimensional structure and bioinformatic analysis revealed that two arginines, Arg-332 and Arg-521, are key specificity determinants of BT0997 in targeting D-galacturonic acid residues. In summary, our study reports the first structural and mechanistic analyses of GH138 enzymes

Breakdown of continuum models for spherical probe adhesion tests on micropatterned surfaces

Funding Information: SB, DY, EA, and RH acknowledge funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP/2007–2013)/ERC Advanced Grant No. 340929 . RMM acknowledges the Alexander von Humboldt Foundation for awarding the “Virtual Humboldt Cluster on the Mechanics and Physics of Adhesion and Grip”.Peer reviewedPublisher PD