Phenotypic plasticity, and temporal and spatial variation in the relative abundance of lentic brook trout, Salvelinus fontinalis, across Ontario.

Brook trout (Salvelinus fontinalis) are a highly prized species found in lakes and streams throughout Ontario. A broadscale monitoring program (BsM) has been conducted in lakes throughout the province, in 5-year cycles, which targets Salvelinus fontinalis populations. The objective of this study was to use the data gained from the BsM and establish a contemporary baseline on the variation of relative abundance and demographics of natural lake populations of S.

Performance and Resilience Analysis of a New York Drinking Water System to Localized and System-Wide Emergencies.

Drinking water utilities are vulnerable to both human-caused and natural disasters that can impact the system infrastructure and the delivery of potable water to consumers. Analyzing system performance and resilience can help utilities identify areas of high risk or concern, understand the impacts on consumers, and evaluate response actions during disasters. In this case study, the Water Network Tool for Resilience (WNTR) was used to investigate the performance and resilience of a drinking water system in New York during increased demands due to firefighting, pipe damage, and loss of the source water emergencies.

Resilience Analysis of Potable Water Service after Power Outages in the U.S. Virgin Islands.

The two Category-5 hurricanes that impacted the United States Virgin Islands in 2017 exposed critical infrastructure vulnerabilities that must be addressed. While the drinking water utility has first-hand knowledge about how the hurricanes affected their systems, the use of modeling and simulation tools can provide additional insight to aid investment planning and preparedness. This paper provides a case study on resilience analysis for the island's potable water systems subject to long term power outages.

Near real-time event detection for watershed monitoring with CANARY.

Illicit discharges in surface waters are a major concern in urban environments and can impact ecosystem and human health by introducing pollutants (, petroleum-based chemicals, metals, nutrients) into natural water bodies. Early detection of pollutants, especially those with regulatory limits, could aid in timely management of sources or other responses. Various monitoring techniques (, sensor-based, automated sampling) could help alert decision makers about illicit discharges.

Boat-electrofishing transect location and flow levels: influence on riverine fish monitoring in non-wadeable habitats.

Fisheries monitoring can be improved by studying the influence of gear selectivity, sampling design, and habitat conditions. We used boat-electrofishing data to investigate how sample unit placement (shoreline and channel transects) and sampling conditions (low and high flow years) affect detection of fishes in a highly regulated Ontario (Canada) river system. Species detection histories associated with a spatially replicated sampling design was fit to a Bayesian hierarchical site occupancy model for 14 fishes.

Evaluating Manual Sampling Locations for Regulatory and Emergency Response.

Drinking water systems commonly use manual or grab sampling to monitor water quality, identify or confirm issues, and verify that corrective or emergency response actions have been effective. In this paper, the effectiveness of regulatory sampling locations for emergency response is explored. An optimization formulation based on the literature was used to identify manual sampling locations to maximize overall nodal coverage of the system.

Evaluating the effects of controlled flows on historical spawning site access, reproduction and recruitment of lake sturgeon Acipenser fulvescens.

Lake sturgeon Acipenser fulvescens spawn at the base of Kakabeka Falls, a 39 m waterfall on the Kaministiquia River, a tributary to Lake Superior. Access to this historical spawning site can be restricted or delayed due to hydroelectric flow fluctuations that coincide with the A. fulvescens spawning season.

Optimal sampling locations to reduce uncertainty in contamination extent in water distribution systems.

Drinking water utilities rely on samples collected from the distribution system to provide assurance of water quality. If a water contamination incident is suspected, samples can be used to determine the source and extent of contamination. By determining the extent of contamination, the percentage of the population exposed to contamination, or areas of the system unaffected can be identified.

Review of Modeling Methodologies for Managing Water Distribution Security.

Water distribution systems are vulnerable to hazards that threaten water delivery, water quality, and physical and cybernetic infrastructure. Water utilities and managers are responsible for assessing and preparing for these hazards, and researchers have developed a range of computational frameworks to explore and identify strategies for what-if scenarios. This manuscript conducts a review of the literature to report on the state of the art in modeling methodologies that have been developed to support the security of water distribution systems.

Quantifying hydraulic and water quality uncertainty to inform sampling of drinking water distribution systems.

Sampling of drinking water distribution systems is performed to ensure good water quality and protect public health. Sampling also satisfies regulatory requirements and is done to respond to customer complaints or emergency situations. Water distribution system modeling techniques can be used to plan and inform sampling strategies.

Interaction of sauger Sander canadensis and walleye Sander vitreus in a large, shallow northern river.

The objectives of this study were to: (1) determine the relative abundance of sauger Sander canadensis and walleye S. vitreus within the Rainy River using a standardized index netting technique; (2) assess the life-history characteristics of the two species in a northern river; (3) examine the spatial distribution of the two species; (4) assess year-class synchrony. At a larger scale, relative abundance of S.

Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets.

Two-dimensional (2D) atomically defined organic nanomaterials are an important material class with broad applications. However, few general synthetic methods exist to produce such materials in high yields and to precisely functionalize them. One strategy to form ordered 2D organic nanomaterials is through the supramolecular assembly of sequence-defined synthetic polymers.

Implicit-Solvent Coarse-Grained Simulation with a Fluctuating Interface Reveals a Molecular Mechanism for Peptoid Monolayer Buckling.

Peptoid polymers form extended two-dimensional nanostructures via an interface-mediated assembly process: the amphiphilic peptoids first adsorb to an air-water interface as a monolayer, then buckle and collapse into free-floating bilayer nanosheets when the interface is compressed. Here, we investigate the molecular mechanism of monolayer buckling by developing a method for incorporating interface fluctuations into an implicit-solvent coarse-grained model. Representing the interface with a triangular mesh controlled by surface tension and surfactant adsorption, we predict the direction of buckling for peptoids with a segregated arrangement of charged side chains and predict that peptoids with with an alternating charge pattern should buckle less easily than peptoids with a segregated charge pattern.

High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are accurately approximated by their average values, while retaining soft degrees of freedom (unconstrained dihedral angles) mostly responsible for conformational variability. We demonstrate that our scheme retains nearly atomistic resolution by mapping all experimental protein configurations in the Protein Data Bank onto coarse-grained configurations and then analytically backmapping those configurations back to all-atom configurations.

Modeling sequence-specific polymers using anisotropic coarse-grained sites allows quantitative comparison with experiment.

Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale dynamic processes in biology and materials science, understanding the details of this supramolecular assembly process requires a modeling approach that captures behavior on a wide range of length and time scales, from those on which individual side chains fluctuate to those on which assemblies of polymers evolve. Here, we demonstrate that a new coarse-grained modeling approach is accurate and computationally efficient enough to do so.

Peptoid nanosheets exhibit a new secondary-structure motif.

A promising route to the synthesis of protein-mimetic materials that are capable of complex functions, such as molecular recognition and catalysis, is provided by sequence-defined peptoid polymers--structural relatives of biologically occurring polypeptides. Peptoids, which are relatively non-toxic and resistant to degradation, can fold into defined structures through a combination of sequence-dependent interactions. However, the range of possible structures that are accessible to peptoids and other biological mimetics is unknown, and our ability to design protein-like architectures from these polymer classes is limited.

Crystallization and arrest mechanisms of model colloids.

We performed dynamic simulations of spheres with short-range attractive interactions for many values of interaction strength and range. Fast crystallization occurs in a localized region of this parameter space, but the character of crystallization pathways is not uniform within this region. Pathways range from one-step, in which a crystal nucleates directly from a gas, to two-step, in which substantial liquid-like clusters form and only subsequently become crystalline.

Ion-specific control of the self-assembly dynamics of a nanostructured protein lattice.

Self-assembling proteins offer a potential means of creating nanostructures with complex structure and function. However, using self-assembly to create nanostructures with long-range order whose size is tunable is challenging, because the kinetics and thermodynamics of protein interactions depend sensitively on solution conditions. Here we systematically investigate the impact of varying solution conditions on the self-assembly of SbpA, a surface-layer protein from Lysinibacillus sphaericus that forms two-dimensional nanosheets.

Structure-determining step in the hierarchical assembly of peptoid nanosheets.

Organic two-dimensional nanomaterials are of growing importance, yet few general synthetic methods exist to produce them in high yields and to precisely functionalize them. We previously developed an efficient hierarchical supramolecular assembly route to peptoid bilayer nanosheets, where the organization of biomimetic polymer sequences is catalyzed by an air-water interface. Here we determine at which stages of assembly the nanoscale and atomic-scale order appear.

Competing thermodynamic and dynamic factors select molecular assemblies on a gold surface.

Controlling the self-assembly of surface-adsorbed molecules into nanostructures requires understanding physical mechanisms that act across multiple length and time scales. By combining scanning tunneling microscopy with hierarchical ab initio and statistical mechanical modeling of 1,4-substituted benzenediamine (BDA) molecules adsorbed on a gold (111) surface, we demonstrate that apparently simple nanostructures are selected by a subtle competition of thermodynamics and dynamics. Of the collection of possible BDA nanostructures mechanically stabilized by hydrogen bonding, the interplay of intermolecular forces, surface modulation, and assembly dynamics select at low temperature a particular subset: low free energy oriented linear chains of monomers and high free energy branched chains.

Temperature-pressure scaling for air-fluidized grains near jamming.

We present experiments on a monolayer of air-fluidized beads in which a jamming transition is approached by increasing pressure, increasing packing fraction, and decreasing kinetic energy. This is accomplished, along with a noninvasive measurement of pressure, by tilting the system and examining behavior versus depth. We construct an equation of state and analyze relaxation time versus effective temperature.

Ratio of effective temperature to pressure controls the mobility of sheared hard spheres.

Using molecular dynamics simulations, we calculate fluctuations and responses for steadily sheared hard spheres over a wide range of packing fractions φ and shear strain rates γ[over ̇], using two different methods to dissipate energy. To a good approximation, shear stress and density fluctuations are related to their associated response functions by a single effective temperature T(eff) that is equal to or larger than the kinetic temperature T(kin). We find a crossover in the relationship between the relaxation time τ and the the nondimensionalized effective temperature T(eff)/pσ(3), where p is the pressure and σ is the sphere diameter.

Universal jamming phase diagram in the hard-sphere limit.

We present a new formulation of the jamming phase diagram for a class of glass-forming fluids consisting of spheres interacting via finite-ranged repulsions at temperature T, packing fraction ϕ or pressure p, and applied shear stress Σ. We argue that the natural choice of axes for the phase diagram are the dimensionless quantities T/pσ³, pσ³/ε, and Σ/p, where T is the temperature, p is the pressure, Σ is the stress, σ is the sphere diameter, ε is the interaction energy scale, and m is the sphere mass. We demonstrate that the phase diagram is universal at low pσ³/ε; at low pressure, observables such as the relaxation time are insensitive to details of the interaction potential and collapse onto the values for hard spheres, provided the observables are nondimensionalized by the pressure.