Variational Trajectory Optimization Tool Set: Technical description and user's manual

The algorithms that comprise the Variational Trajectory Optimization Tool Set (VTOTS) package are briefly described. The VTOTS is a software package for solving nonlinear constrained optimal control problems from a wide range of engineering and scientific disciplines. The VTOTS package was specifically designed to minimize the amount of user programming; in fact, for problems that may be expressed in terms of analytical functions, the user needs only to define the problem in terms of symbolic variables. This version of the VTOTS does not support tabular data; thus, problems must be expressed in terms of analytical functions. The VTOTS package consists of two methods for solving nonlinear optimal control problems: a time-domain finite-element algorithm and a multiple shooting algorithm. These two algorithms, under the VTOTS package, may be run independently or jointly. The finite-element algorithm generates approximate solutions, whereas the shooting algorithm provides a more accurate solution to the optimization problem. A user's manual, some examples with results, and a brief description of the individual subroutines are included

Plant trait covariance and nonlinear averaging: A reply to Koussoroplis et al.

SADIE (Spatial Analysis by Distance Indices) is designed specifically to quantify patterns in spatially-referenced count-based data. It was developed for dealing with data that can be considered ‘patchy’. Such distributions are commonly found, for example, in insect populations where discrete patches of individuals are often evident. The distributions of such populations have ‘hard edges’, with patches and gaps occurring spatially. In these cases variance of abundance does not vary smoothly, but discontinuously. In this paper we outline the use of SADIE and provide free access to the SADIE software suite, establishing Rethinking Ecology as its permanent home. Finally, we review the use of SADIE and demonstrate its use in a wide variety of sub-disciplines within the general field of ecology

Chapter 9: Aquatic Macroinvertebrates, Section A: Aquatic Macroinvertebrates (Exclusive of Mosquitoes)

Final Report. Excerpt (Chapter 9, Section A) from The Des Plaines River Wetlands Demonstration Project, Volume II, Baseline Survey, edited by Donald L. Hey and Nancy S. PhilippiReport issued on: October 1985INHS Technical Report prepared for Wetlands Research, Inc

Evolution of giant molecular clouds across cosmic time

Giant molecular clouds (GMCs) are well studied in the local Universe, however, exactly how their properties vary during galaxy evolution is poorly understood due to challenging resolution requirements, both observational and computational. We present the first time-dependent analysis of GMCs in a Milky Way-like galaxy and an Large Magellanic Cloud (LMC)-like dwarf galaxy of the FIRE-2 (Feedback In Realistic Environments) simulation suite, which have sufficient resolution to predict the bulk properties of GMCs in cosmological galaxy formation self-consistently. We show explicitly that the majority of star formation outside the galactic centre occurs within self-gravitating gas structures that have properties consistent with observed bound GMCs. We find that the typical cloud bulk properties such as mass and surface density do not vary more than a factor of 2 in any systematic way after the first Gyr of cosmic evolution within a given galaxy from its progenitor. While the median properties are constant, the tails of the distributions can briefly undergo drastic changes, which can produce very massive and dense self-gravitating gas clouds. Once the galaxy forms, we identify only two systematic trends in bulk properties over cosmic time: a steady increase in metallicity produced by previous stellar populations and a weak decrease in bulk cloud temperatures. With the exception of metallicity, we find no significant differences in cloud properties between the Milky Way-like and dwarf galaxies. These results have important implications for cosmological star and star cluster formation and put especially strong constraints on theories relating the stellar initial mass function to cloud properties

The aggregation-enhancing huntingtin N-terminus is helical in amyloid fibrils

The 17-residue N-terminus (httNT) directly flanking the polyQ sequence in huntingtin (htt) N-terminal fragments plays a crucial role in initiating and accelerating the aggregation process that is associated with Huntington's disease pathogenesis. Here we report on magic-angle-spinning solid-state NMR studies of the amyloid-like aggregates of an htt N-terminal fragment. We find that the polyQ portion of this peptide exists in a rigid, dehydrated amyloid core that is structurally similar to simpler polyQ fibrils and may contain antiparallel β-sheets. In contrast, the httNT sequence in the aggregates is composed in part of a well-defined helix, which likely also exists in early oligomeric aggregates. Further NMR experiments demonstrate that the N-terminal helical segment displays increased dynamics and water exposure. Given its specific contribution to the initiation, rate, and mechanism of fibril formation, the helical nature of httNT and its apparent lack of effect on the polyQ fibril core structure seem surprising. The results provide new details about these disease-associated aggregates and also provide a clear example of an amino acid sequence that greatly enhances the rate of amyloid formation while itself not taking part in the amyloid structure. There is an interesting mechanistic analogy to recent reports pointing out the early-stage contributions of transient intermolecular helix-helix interactions in the aggregation behavior of various other amyloid fibrils. © 2011 American Chemical Society

Live Fast, Die Young: GMC lifetimes in the FIRE cosmological simulations of Milky Way-mass galaxies

We present the first measurement of the lifetimes of giant molecular clouds (GMCs) in cosmological simulations at z = 0, using the Latte suite of FIRE-2 simulations of Milky Way (MW) mass galaxies. We track GMCs with total gas mass ≳10⁵ M⊙ at high spatial (∼1 pc), mass (7100 M⊙), and temporal (1 Myr) resolution. Our simulated GMCs are consistent with the distribution of masses for massive GMCs in the MW and nearby galaxies. We find GMC lifetimes of 5–7 Myr, or 1–2 freefall times, on average, with less than 2 per cent of clouds living longer than 20 Myr. We find decreasing GMC lifetimes with increasing virial parameter, and weakly increasing GMC lifetimes with galactocentric radius, implying that environment affects the evolutionary cycle of GMCs. However, our GMC lifetimes show no systematic dependence on GMC mass or amount of star formation. These results are broadly consistent with inferences from the literature and provide an initial investigation into ultimately understanding the physical processes that govern GMC lifetimes in a cosmological setting