The Clustering of Massive Halos

The clustering properties of dark matter halos are a firm prediction of modern theories of structure formation. We use two large volume, high-resolution N-body simulations to study how the correlation function of massive dark matter halos depends upon their mass and formation history. We find that halos with the lowest concentrations are presently more clustered than those of higher concentration, the size of the effect increasing with halo mass; this agrees with trends found in studies of lower mass halos. The clustering dependence on other characterizations of the full mass accretion history appears weaker than the effect with concentration. Using the integrated correlation function, marked correlation functions, and a power-law fit to the correlation function, we find evidence that halos which have recently undergone a major merger or a large mass gain have slightly enhanced clustering relative to a randomly chosen population with the same mass distribution.Comment: 10 pages, 8 figures; text improved, references and one figure added; accepted for publication in Ap

Heterocyst placement strategies to maximize growth of cyanobacterial filaments

Under conditions of limited fixed-nitrogen, some filamentous cyanobacteria develop a regular pattern of heterocyst cells that fix nitrogen for the remaining vegetative cells. We examine three different heterocyst placement strategies by quantitatively modelling filament growth while varying both external fixed-nitrogen and leakage from the filament. We find that there is an optimum heterocyst frequency which maximizes the growth rate of the filament; the optimum frequency decreases as the external fixed-nitrogen concentration increases but increases as the leakage increases. In the presence of leakage, filaments implementing a local heterocyst placement strategy grow significantly faster than filaments implementing random heterocyst placement strategies. With no extracellular fixed-nitrogen, consistent with recent experimental studies of Anabaena sp. PCC 7120, the modelled heterocyst spacing distribution using our local heterocyst placement strategy is qualitatively similar to experimentally observed patterns. As external fixed-nitrogen is increased, the spacing distribution for our local placement strategy retains the same shape while the average spacing between heterocysts continuously increases.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher-authenticated version will be available onlin

The connection between the host halo and the satellite galaxies of the Milky Way

Many properties of the Milky Way's dark matter halo, including its mass assembly history, concentration, and subhalo population, remain poorly constrained. We explore the connection between these properties of the Milky Way and its satellite galaxy population, especially the implication of the presence of the Magellanic Clouds for the properties of the Milky Way halo. Using a suite of high-resolution $N$-body simulations of Milky Way-mass halos with a fixed final Mvir ~ 10^{12.1}Msun, we find that the presence of Magellanic Cloud-like satellites strongly correlates with the assembly history, concentration, and subhalo population of the host halo, such that Milky Way-mass systems with Magellanic Clouds have lower concentration, more rapid recent accretion, and more massive subhalos than typical halos of the same mass. Using a flexible semi-analytic galaxy formation model that is tuned to reproduce the stellar mass function of the classical dwarf galaxies of the Milky Way with Markov-Chain Monte-Carlo, we show that adopting host halos with different mass-assembly histories and concentrations can lead to different best-fit models for galaxy-formation physics, especially for the strength of feedback. These biases arise because the presence of the Magellanic Clouds boosts the overall population of high-mass subhalos, thus requiring a different stellar-mass-to-halo-mass ratio to match the data. These biases also lead to significant differences in the mass--metallicity relation, the kinematics of low-mass satellites, the number counts of small satellites associated with the Magellanic Clouds, and the stellar mass of Milky Way itself. Observations of these galaxy properties can thus provide useful constraints on the properties of the Milky Way halo.Comment: 20 pages, 12 figures, accepted for publication in ApJ. A new section on the effect of host halo mass-assembly history on the central galaxy stellar mass is adde

Close Pairs as Proxies for Galaxy Cluster Mergers

Galaxy cluster merger statistics are an important component in understanding the formation of large-scale structure. Unfortunately, it is difficult to study merger properties and evolution directly because the identification of cluster mergers in observations is problematic. We use large N-body simulations to study the statistical properties of massive halo mergers, specifically investigating the utility of close halo pairs as proxies for mergers. We examine the relationship between pairs and mergers for a wide range of merger timescales, halo masses, and redshifts (0<z<1). We also quantify the utility of pairs in measuring merger bias. While pairs at very small separations will reliably merge, these constitute a small fraction of the total merger population. Thus, pairs do not provide a reliable direct proxy to the total merger population. We do find an intriguing universality in the relation between close pairs and mergers, which in principle could allow for an estimate of the statistical merger rate from the pair fraction within a scaled separation, but including the effects of redshift space distortions strongly degrades this relation. We find similar behavior for galaxy-mass halos, making our results applicable to field galaxy mergers at high redshift. We investigate how the halo merger rate can be statistically described by the halo mass function via the merger kernel (coagulation), finding an interesting environmental dependence of merging: halos within the mass resolution of our simulations merge less efficiently in overdense environments. Specifically, halo pairs with separations less than a few Mpc/h are more likely to merge in underdense environments; at larger separations, pairs are more likely to merge in overdense environments.Comment: 12 pages, 9 figures; Accepted for publication in ApJ. Significant additions to text and two figures changed. Added new findings on the universality of pair mergers and added analysis of the effect of FoF linking length on halo merger

Nitrogen and phosphorus loads to temperate seepage lakes associated with allochthonous dissolved organic carbon loads

Terrestrial loads of dissolved organic matter (DOM) have increased in recent years in many north temperate lakes. While much of the focus on the “browning” phenomena has been on its consequences for carbon cycling, much less is known about how it influences nutrient loading to lakes. We characterize potential loads of nitrogen and phosphorus to seepage lakes in northern Wisconsin, USA, based on a laboratory soil leaching experiment and a model that includes landscape cover and watershed area. In these seepage lakes, nutrient concentrations are positively correlated with dissolved organic carbon concentrations (nitrogen: r = 0.68, phosphorus: r = 0.54). Using long‐term records of browning, we found that dissolved organic matter‐associated nutrient loadings may have resulted in substantial increases in nitrogen and phosphorus in seepage lakes and could account for currently observed nutrient concentrations in the lake. “Silent” nutrient loadings to brown‐water lakes may lead to future water‐quality concerns. PLAIN LANGUAGE SUMMARY: The color of many temperate lakes is changing; some lakes are becoming more darkly stained brown. The tea‐colored stain is due to dissolved organic matter from the surrounding landscape. Much of the research related to the causes and consequences of increased staining, or “brownification,” relate to its connection to the carbon cycle. However, by examining long‐term lake chemical records, analyzing the properties of the organic compounds, and modeling potential flows of the compounds, we find that carbon is not the only element that is influenced by browning. Nitrogen and phosphorus, two nutrients important to growth of organisms at the base of the food web, may also be increasing in lakes due to brownification."Funding for this research was supported by the Northern Research Station and the Chequamegon-Nicolet National Forest (CNNF) of the United States Department of Agriculture (USDA) Forest Service and a National Science Foundation (NSF) grant to the University of Wisconsin-Madison to support the North Temperate Lakes Long-Term Ecological Research (NTLLTER) Site (DEB-#1440297)."https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018GL07721

The Excursion Set Theory of Halo Mass Functions, Halo Clustering, and Halo Growth

I review the excursion set theory (EST) of dark matter halo formation and clustering. I recount the Press-Schechter argument for the mass function of bound objects and review the derivation of the Press-Schechter mass function in EST. The EST formalism is powerful and can be applied to numerous problems. I review the EST of halo bias and the properties of void regions. I spend considerable time reviewing halo growth in the EST. This section culminates with descriptions of two Monte Carlo methods for generating halo mass accretion histories. In the final section, I emphasize that the standard EST approach is the result of several simplifying assumptions. Dropping these assumptions can lead to more faithful predictions and a more versatile formalism. One such assumption is the constant height of the barrier for nonlinear collapse. I review implementations of the excursion set approach with arbitrary barrier shapes. An application of this is the now well-known improvement to standard EST that follows from the ellipsoidal-collapse barrier. Additionally, I emphasize that the statement that halo accretion histories are independent of halo environments is a simplifying assumption, rather than a prediction of the theory. I review the method for constructing correlated random walks of the density field in more general cases. I construct a simple toy model with correlated walks and I show that excursion set theory makes a qualitatively simple and general prediction for the relation between halo accretion histories and halo environments: regions of high density preferentially contain late-forming halos and conversely for regions of low density. I conclude with a brief discussion of this prediction in the context of recent numerical studies of the environmental dependence of halo properties. (Abridged)Comment: 62 pages, 19 figures. Review article based on lectures given at the Sixth Summer School of the Helmholtz Institute for Supercomputational Physics. Accepted for Publication in IJMPD. Comments Welcom

Non‐native species have multiple abundance–impact curves

The abundance–impact curve is helpful for understanding and managing the impacts of non‐native species. Abundance–impact curves can have a wide range of shapes (e.g., linear, threshold, sigmoid), each with its own implications for scientific understanding and management. Sometimes, the abundance–impact curve has been viewed as a property of the species, with a single curve for a species. I argue that the abundance–impact curve is determined jointly by a non‐native species and the ecosystem it invades, so that a species may have multiple abundance–impact curves. Models of the impacts of the invasive mussel Dreissena show how a single species can have multiple, noninterchangeable abundance–impact curves. To the extent that ecosystem characteristics determine the abundance–impact curve, abundance–impact curves based on horizontal designs (space‐for‐time substitution) may be misleading and should be used with great caution, it at all. It is important for scientists and managers to correctly specify the abundance–impact curve when considering the impacts of non‐native species. Diverting attention from the invading species to the invaded ecosystem, and especially to the interaction between species and ecosystem, could improve our understanding of how non‐native species affect ecosystems and reduce uncertainty around the effects of management of populations of non‐native species.The abundance–impact curve is a useful tool for understanding and managing the impacts of invasive species. Using models based on the impacts of the zebra mussel, I show that a single invasive species can have radically different abundance–impact curves in different habitats. This means that managers must be careful to use the correct abundance–impact curve and that scientists should avoid using space‐for‐time substitution to understand the impacts of invaders.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156222/2/ece36364.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156222/1/ece36364_am.pd

Molecular basis for passive immunotherapy of Alzheimer's disease

Amyloid aggregates of the amyloid-{beta} (A{beta}) peptide are implicated in the pathology of Alzheimer's disease. Anti-A{beta} monoclonal antibodies (mAbs) have been shown to reduce amyloid plaques in vitro and in animal studies. Consequently, passive immunization is being considered for treating Alzheimer's, and anti-A{beta} mAbs are now in phase II trials. We report the isolation of two mAbs (PFA1 and PFA2) that recognize A{beta} monomers, protofibrils, and fibrils and the structures of their antigen binding fragments (Fabs) in complex with the A{beta}(1–8) peptide DAEFRHDS. The immunodominant EFRHD sequence forms salt bridges, hydrogen bonds, and hydrophobic contacts, including interactions with a striking WWDDD motif of the antigen binding fragments. We also show that a similar sequence (AKFRHD) derived from the human protein GRIP1 is able to cross-react with both PFA1 and PFA2 and, when cocrystallized with PFA1, binds in an identical conformation to A{beta}(1–8). Because such cross-reactivity has implications for potential side effects of immunotherapy, our structures provide a template for designing derivative mAbs that target A{beta} with improved specificity and higher affinity

Interactions between sunlight and microorganisms influence dissolved organic matter degradation along the aquatic continuum

CO2 emissions from inland surface waters to the atmosphere are almost as large as the net carbon transfer from the atmosphere to Earth’s land surface. This large flux is supported by dissolved organic matter (DOM) from land and its complete oxidation to CO2 in freshwaters. A critical nexus in the global carbon cycle is the fate of DOM, either complete or partial oxidation. Interactions between sunlight and microbes control DOM degradation, but the relative importance of photodegradation vs. degradation by microbes is poorly known. The knowledge gaps required to advance understanding of key interactions between photochemistry and biology influencing DOM degradation include: (1) the efficiencies and products of DOM photodegradation, (2) how do photo‐products control microbial metabolism of photo‐altered DOM and on what time scales, and (3) how do water and DOM residence times and light exposure interact to determine the fate of DOM moving across the landscape to oceans?Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/144226/1/lol210060_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144226/2/lol210060.pd

High‐Frequency Sensor Data Reveal Across‐Scale Nitrate Dynamics in Response to Hydrology and Biogeochemistry in Intensively Managed Agricultural Basins

An edited version of this paper was published by AGU. Copyright 2018 American Geophysical Union.Excess nitrate in rivers draining intensively managed agricultural watersheds has caused coastal hypoxic zones, harmful algal blooms, and degraded drinking water. Hydrology and biogeochemical transformations influence nitrate concentrations by changing nitrate supply, removal, and transport. For the Midwest Unites States, where much of the land is used for corn and soybean production, a better understanding of the response of nitrate to hydrology and biogeochemistry is vital in the face of high nitrate concentrations coupled with projected increases of precipitation frequency and magnitude. In this study, we capitalized on the availability of spatially and temporally extensive sensor data in the region to evaluate how nitrate concentration (NO3−) interacts with discharge (Q) and water temperature (T) within eight watersheds in Iowa, United States, by evaluating land use characteristics and multiscale temporal behavior from 5‐year, high‐frequency, time series records. We show that power spectral density of Q, NO3−, and T, all exhibit power law behavior with slopes greater than 2, implying temporal self‐similarity for a range of scales. NO3− was strongly cross correlated with Q for all sites and correlation increased significantly with drainage area across sites. Peak NO3− increased significantly with crop coverage across watersheds. Temporal offsets in peak NO3− and peak Q, seen at all study sites, reduced the impact of extreme events. This study illustrates a relatively new approach to evaluating environmental sensor data and revealed characteristics of watersheds in which extreme discharge events have the greatest consequences