Optimal control of transitions between nonequilibrium steady states

Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have an interest in optimizing such transitions. Using the Hatano-Sasa Y-value, we extend a recently developed geometrical framework for determining optimal protocols so that it can be applied to systems driven from nonequilibrium steady states. We calculate and numerically verify optimal protocols for a colloidal particle dragged through solution by a translating optical trap with two controllable parameters. We offer experimental predictions, specifically that optimal protocols are significantly less costly than naive ones. Optimal protocols similar to these may ultimately point to design principles for biological energy transduction systems and guide the design of artificial molecular machines.Comment: Accepted for publication at PLoS ON

Evaluation of the capture efficiency and size selectivity of four pot types in the prospective fishery for North Pacific giant octopus (Enteroctopus dofleini)

Over 230 metric tons of octopus is harvested as bycatch annually in Alaskan trawl, long-line, and pot fisheries. An expanding market has fostered interest in the development of a directed fishery for North Pacific giant octopus (Enteroctopus dofleini). To investigate the potential for fishery development we examined the efficacy of four different pot types for capture of this species. During two surveys in Kachemak Bay, Alaska, strings of 16 –20 sablefish, Korean hair crab, shrimp, and Kodiak wooden lair pots were set at depths ranging between 62 and 390 meters. Catch per-unit-of-ef for t estimates were highest for sablefish and lair pots. Sablefish pots caught significantly heavier North Pacific giant octopuses but also produced the highest bycatch of commercially important species, such as halibut (Hippoglossus stenolepis), Pacific cod (Gadus macrocephalus), and Tanner crab (Chionoecetes bairdi)

WETLAND OCCUPANCY OF POND-BREEDING AMPHIBIANS IN YOSEMITE NATIONAL PARK, USA

We estimated wetland occupancy and population trends for three species of pond-breeding anurans in Yosemite National Park from 2007 – 2011. We used a double survey technique in which two observers independently surveyed each site on the same day. Double surveys allowed us to calculate detectability for the three most common anurans within the park: Rana sierrae, Anaxyrus canorus, and Pseudacris regilla. Annual estimates of detectability were generally high; mean detectability ranged from 73.7% + 0.6 (SE) for any life history stage of A. canorus to 86.7% + 0.7 for sites with P. regilla reproduction (eggs or larvae present). Detectability was most variable for Anaxyrus canorus, which ranged from 45.9% to 99.7%. The probability of occupancy for R. sierrae was highest in larger, low-elevation wetlands that lacked fish. Anaxyrus canorus were more common in shallow high-elevation ponds; their occurrence was minimally impacted by the presence of fish. Finally, occurrence of P. regilla was largely unrelated to wetland size and elevation, but like R. sierrae, they were less likely to occupy sites with fish. Occupancy showed no trend over the five years of our study for R. sierrae or A. canorus when considering either sites with any life stage or only sites with reproduction. However, P. regilla showed a modest downward trend for sites with any life stage and sites with reproduction. Our results for R. sierrae run counter to expectations given recent concern about the decline of this species, while our findings for P. regilla raise concerns for this widespread and generally common species

The Effects of Forest Practices on a Maine Amphibian Community

Changes in forest habitat have been linked to global declines in amphibian populations, but little research has been conducted into the mechanisms causing these declines. This study evaluated the effects of changes in forest habitat on the spatial distribution of a Maine amphibian community, focusing on juvenile wood frogs, Rana sylvatica. Juvenile wood frogs emerging from artificial ponds did not orient towards preferred habitat and a significant number of animals maintained the same directionality documented at the site from which larval individuals were collected. Abundance and habitat use differed among adults of 9 species of amphibians in a replicated landscape (n = 4, each 10 ha in size) of 4 forestry treatments (clearcut with coarse woody debris [CWD] removed, clearcut with CWD retained, partial-cut of 50% of canopy cover, and an uncut control) centered on a breeding pool. Lower captures of juveniles of all species (statistically significant for 7 of 9 species) were seen in clearcuts compared to forested treatments. Juvenile wood frogs marked as they emerged from the breeding pools preferred forested treatments to the clearcuts, but patterns of captures within each treatment at different distances from the pond’s edge did not differ. The response of juvenile wood frogs to habitat heterogeneity (in the 10 ha landscapes, a 12x16 m area of hexagonal patches, 1x4 m pens, and a 10x10 m pen) changed from coarse scale habitat selection during emigration, to fine scale selection when settling. Spatial simulations designed to predict the effects of habitat change on the spatial distribution of juvenile wood frogs best predicted field data when specific movement behavior, and a heterogeneous landscape were included. Model results demonstrated the importance of comparing densities of frogs in different habitat types following emigration, as well as the distribution of frogs over distance when considering effects of habitat change on local populations. The study demonstrated the complex responses of amphibians to habitat change and the importance of conducting research at multiple spatial and temporal scales. Simulations highlighted the need for species-specific information when predicting the effects of habitat change on the spatial distribution of amphibians, and managing habitat accordingly