P5_2 Spaghettification: Surviving a Black Hole Event Horizon

We found that it is possible to stay conscious falling through the event horizon of aBlack Hole if the mass exceeds 19,000M_sol. This assumes the average person is ofgood health and can stay conscious with a relative force less than 5 g acting upon them

P5_3 Pigs on the Wing

This article explores the possibility of a pig flying over Battersea Power Station, as shown on the Pink Floyd album ’Animals,’ and the time it would take for the pig’s height to exceed the height of the chimneys. Using the lift force equation, we graphically show the minimum wind velocity required to lift a 70 kg pig 101 m, the height of the Battersea Power Station. We find that for a pig of this mass, a wind velocity of 20.4 ms-1 was required. Furthermore, in order to measure the time for the pig to reach the height of Battersea Power Station, an acceleration of 3.8 ms-2 was calculated; this assumes a severe gale wind velocity of 24 ms-1 as defined by The Met Office. We find that it would take 7.3 s to travel the required height, assuming only vertical movement.

P5_1 ”Everybody knows the Moon is made of cheese...”: Return of the Cheddar

This Letter explores the repercussions of the Moon turning into cheddar, and finds that with the same volume and lighter mass of m = 2.49 × 1022kg, it would escape the Earth’s sphere of influence. We looked at two possible escape trajectories, prograde and retrograde, and found the new orbital distances to be between 0.73AU and 1.00AU, and between 1.00AU and 1.51AU, respectively. Thus potentially carrying the Moon very near to the orbits of Venus or Mars.

Conformations of closed DNA

We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic expressions leading to the spatial configuration of a family of solutions representing distortions that interpolate between the circular form of DNA and a figure-eight form that represents the onset of interwinding. We are also able to generate knotted loops. We suggest ways to use our approach to produce other configurations relevant to studies of DNA structure. The stability of the distorted configurations is assessed, along with the effects of fluctuations on the free energy of the various configurations.Comment: 39 pages in REVTEX with 14 eps figures. Submitted to Phys. Rev. E. This manuscript updates, expands and revises, to a considerable extent, a previously posted manuscript, entitled "Conformations of Circular DNA," which appeared as cond-mat/970104

A stitch in time: Efficient computation of genomic DNA melting bubbles

Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic. Results: An efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a maximal bubble length. No approximations, such as windowing, have been introduced to reduce the time complexity. More than just finding the bubbles, the algorithm produces a stitch profile, which is a probabilistic graphical model of bubbles and helical regions. The algorithm applies a probability peak finding method based on a hierarchical analysis of the energy barriers in the Poland-Scheraga model. Conclusions: Exact and fast computation of genomic stitch profiles is thus feasible. Sequences of several megabases have been computed, only limited by computer memory. Possible applications are the genome-wide comparisons of bubbles with promotors, TSS, viral integration sites, and other melting-related regions.Comment: 16 pages, 10 figure

Superhelical Duplex Destabilization and the Recombination Position Effect

The susceptibility to recombination of a plasmid inserted into a chromosome varies with its genomic position. This recombination position effect is known to correlate with the average G+C content of the flanking sequences. Here we propose that this effect could be mediated by changes in the susceptibility to superhelical duplex destabilization that would occur. We use standard nonparametric statistical tests, regression analysis and principal component analysis to identify statistically significant differences in the destabilization profiles calculated for the plasmid in different contexts, and correlate the results with their measured recombination rates. We show that the flanking sequences significantly affect the free energy of denaturation at specific sites interior to the plasmid. These changes correlate well with experimentally measured variations of the recombination rates within the plasmid. This correlation of recombination rate with superhelical destabilization properties of the inserted plasmid DNA is stronger than that with average G+C content of the flanking sequences. This model suggests a possible mechanism by which flanking sequence base composition, which is not itself a context-dependent attribute, can affect recombination rates at positions within the plasmid

Greenland subglacial lakes detected by radar

This is the final version of the article. Available from AGU via the DOI in this record.Subglacial lakes are an established and important component of the basal hydrological system of the Antarctic ice sheets, but none have been reported from Greenland. Here we present airborne radio echo sounder (RES) measurements that provide the first clear evidence for the existence of subglacial lakes in Greenland. Two lakes, with areas ~8 and ~10 km2, are found in the northwest sector of the ice sheet, ~40 km from the ice margin, and below 757 and 809 m of ice, respectively. The setting of the Greenland lakes differs from those of Antarctic subglacial lakes, being beneath relatively thin and cold ice, pointing to a fundamental difference in their nature and genesis. Possibilities that the lakes consist of either ancient saline water in a closed system or are part of a fresh, modern open hydrological system are discussed, with the latter interpretation considered more likely.Funding was provided by NERC grant NE/ H020667. Additional support was provided by NASA grant NNX11AD33G and the G. Unger Vetlesen foundation

GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes

We present an interactive web application for visualizing genomic data of prokaryotic chromosomes. The tool (GeneWiz browser) allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. The tool is available online from http://www.cbs.dtu.dk/services/gwBrowser. Supplemental material including interactive atlases is available online at http://www.cbs.dtu.dk/services/gwBrowser/suppl/

Conformations of Linear DNA

We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link number. We derive a fundamental relation between the Euler angles that describe the curve and the topological linking number. Analytical expressions for the spatial configurations of the molecule in the infinite- length limit were obtained. A unique configuraion minimizes the energy for a given set of physical conditions. An elastic model incorporating thermal fluctuations provides excellent agreement with experimental results on the plectonemic transition.Comment: 5 pages, RevTeX; 6 postscript figure

Hydrology and water quality of a field and riparian buffer adjacent to a mangrove wetland in Jobos Bay watershed, Puerto Rico

Agriculture in coastal areas of Puerto Rico is often adjacent to or near mangrove wetlands. Riparian buffers, while they may also be wetlands, can be used to protect mangrove wetlands from agricultural inputs of sediment, nutrients, and pesticides. We used simulation models and field data to estimate the water, nitrogen, and phosphorus inputs from an agricultural field and riparian buffer to a mangrove wetland in Jobos Bay watershed, Puerto Rico. We used the Agricultural Policy/Environmental eXtender (APEX) and the Riparian Ecosystem Management Model (REMM) models sequentially to simulate the hydrology and water quality of the agricultural fields and an adjacent riparian buffer, respectively. Depth to the water table surface was measured monthly at numerous sites in both field and riparian areas and were used with recording well data from outside the field to estimate daily water table depths in the field and riparian buffer and to calibrate field-scale hydrologic processes. Calibration and validation of the models were successful for the riparian buffer and in three of four field quadrants. In these areas the average simulated depth to water table for the field and the riparian buffer were within ±7% of field estimated water table depths. Over the 3-year study period, the riparian buffer represented by REMM reduced agricultural loadings to the mangrove wetland by 24% for sediment yield, and about 30% for total nitrogen and phosphorus. Simulations indicated that tropical storms and hurricanes played an important role in water and nutrient transport on this site contributing at least 63% of total sediment and nutrient loads