Significant improvements in long trace profiler measurement performance

A Modifications made to the Long Trace Profiler (LTP II) system at the Advanced Photon Source at Argonne National Laboratory have significantly improved the accuracy and repeatability of the instrument The use of a Dove prism in the reference beam path corrects for phasing problems between mechanical efforts and thermally-induced system errors. A single reference correction now completely removes both error signals from the measured surface profile. The addition of a precision air conditioner keeps the temperature in the metrology enclosure constant to within {+-}0.1{degrees}C over a 24 hour period and has significantly improved the stability and repeatability of the system. We illustrate the performance improvements with several sets of measurements. The improved environmental control has reduced thermal drift error to about 0.75 microradian RMS over a 7.5 hour time period. Measurements made in the forward scan direction and the reverse scan direction differ by only about 0.5 microradian RMS over a 500mm, trace length. We are now able to put 1-sigma error bar of 0.3 microradian on an average of 10 slope profile measurements over a 500mm long trace length, and we are now able to put a 0.2 microradian error bar on an average of 10 measurements over a 200mm trace length. The corresponding 1-sigma height error bar for this measurement is 1.1 run

Effects of intersegmental transfers on target location by proteins

We study a model for a protein searching for a target, using facilitated diffusion, on a DNA molecule confined in a finite volume. The model includes three distinct pathways for facilitated diffusion: (a) sliding - in which the protein diffuses along the contour of the DNA (b) jumping - where the protein travels between two sites along the DNA by three-dimensional diffusion, and finally (c) intersegmental transfer - which allows the protein to move from one site to another by transiently binding both at the same time. The typical search time is calculated using scaling arguments which are verified numerically. Our results suggest that the inclusion of intersegmental transfer (i) decreases the search time considerably (ii) makes the search time much more robust to variations in the parameters of the model and (iii) that the optimal search time occurs in a regime very different than that found for models which ignore intersegmental transfers. The behavior we find is rich and shows surprising dependencies, for example, on the DNA length.Comment: 40 pages, 14 figure

Convergence of dynamic vegetation net productivity responses to precipitation variability from 10 years of MODIS EVI

According to Global Climate Models (GCMs) the occurrence of extreme events of precipitation will be more frequent in the future. Therefore, important challenges arise regarding climate variability, which are mainly related to the understanding of ecosystem responses to changes in precipitation patterns. Previous studies have found that Above-ground Net Primary Productivity (ANPP) was positively related to increases in annual precipitation and this relation may converge across biomes during dry years. One challenge in studying this ecosystem response at the continental scale is the lack of ANPP field measurements over extended areas. In this study, the MODIS EVI was utilized as a surrogate for ANPP and combined with precipitation datasets from twelve different experimental sites across the United States over a 10-year period. Results from this analysis confirmed that integrated-EVI for different biomes converged toward common precipitation use efficiency during water-limited periods and may be a viable surrogate for ANPP measurements for further ecological research

Classes of fast and specific search mechanisms for proteins on DNA

Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for a fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.Comment: 65 pages, 23 figure

General Stability Analysis of Synchronized Dynamics in Coupled Systems

We consider the stability of synchronized states (including equilibrium point, periodic orbit or chaotic attractor) in arbitrarily coupled dynamical systems (maps or ordinary differential equations). We develop a general approach, based on the master stability function and Gershgorin disc theory, to yield constraints on the coupling strengths to ensure the stability of synchronized dynamics. Systems with specific coupling schemes are used as examples to illustrate our general method.Comment: 8 pages, 1 figur

Ecosystem resilience despite large-scale altered hydroclimatic conditions

Climate change is predicted to increase both drought frequency and duration, and when coupled with substantial warming, will establish a new hydroclimatological model for many regions. Large-scale, warm droughts have recently occurred in North America, Africa, Europe, Amazonia and Australia, resulting in major effects on terrestrial ecosystems, carbon balance and food security. Here we compare the functional response of above-ground net primary production to contrasting hydroclimatic periods in the late twentieth century (1975-1998), and drier, warmer conditions in the early twenty-first century (2000-2009) in the Northern and Southern Hemispheres. We find a common ecosystem water-use efficiency (WUE e: Above-ground net primary production/ evapotranspiration) across biomes ranging from grassland to forest that indicates an intrinsic system sensitivity to water availability across rainfall regimes, regardless of hydroclimatic conditions. We found higher WUE e in drier years that increased significantly with drought to a maximum WUE e across all biomes; and a minimum native state in wetter years that was common across hydroclimatic periods. This indicates biome-scale resilience to the interannual variability associated with the early twenty-first century drought - that is, the capacity to tolerate low, annual precipitation and to respond to subsequent periods of favourable water balance. These findings provide a conceptual model of ecosystem properties at the decadal scale applicable to the widespread altered hydroclimatic conditions that are predicted for later this century. Understanding the hydroclimatic threshold that will break down ecosystem resilience and alter maximum WUE e may allow us to predict land-surface consequences as large regions become more arid, starting with water-limited, low-productivity grasslands. © 2013 Macmillan Publishers Limited. All rights reserved

Electric Grid Vulnerability Analysis to Identify Communities Prone to Wildfires

Natural hazards, like wildfires, present various challenges to the electric grid that can leave many communities without power. To identify vulnerabilities in the grid and the corresponding at-risk communities, this work considers the implementation of two Graph Theory assessment approaches, namely betweenness centrality and minimum cut, and combines the results from each with spatial fire probability data to produce a novel assessment of communities at-risk of losing service because of a wildfire. The results from a betweenness centrality analysis identified at-risk communities whose critical lines, necessary for routing power to the community from the numerous generators, were found to be at-risk if they were located within high probability burn zones. Communities at-risk of separation from the grid with one cut (or electrical shorting) of a transmission line due its proximity to a high burn probability (BP) area were also identified using the minimum cut Graph Theory algorithm. When the methodologies were applied to a demonstration transmission grid, the results found that about one third of the 585 substations had centrally located lines in high BP areas. About 46% of the substations require just one cut to be removed from the grid, and the average length of these one-cut segments was 37 km and the longest was 188 km

Geospatial Assessment Methodology to Estimate Power Line Restoration Access Vulnerabilities After a Hurricane in Puerto Rico

Limited access to transmission lines after a major contingency event can inhibit restoration efforts. After Hurricane Maria, for example, flooding and landslides damaged roads and thus limited travel. Transmission lines are also often situated far from maintained roadways, further limiting the ability to access and repair them. Therefore, this paper proposes a methodology for assessing Puerto Rico’s infrastructure (i.e., roads and transmission lines) to identify potentially hard to reach areas due to natural risks or distance to roads. The approach uses geographic information system (GIS) data to define vulnerable areas, that may experience excessive restoration times. The methodology also uses graph theory analysis to find transmission lines with high centrality (or importance). Comparison of these important transmission lines with the vulnerability results found that many reside near roads that are at risk for landslides or floods