Placing Arrows in Directed Graph Drawings

We consider the problem of placing arrow heads in directed graph drawings without them overlapping other drawn objects. This gives drawings where edge directions can be deduced unambiguously. We show hardness of the problem, present exact and heuristic algorithms, and report on a practical study.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Topological Methods for Exploring Low-density States in Biomolecular Folding Pathways

Characterization of transient intermediate or transition states is crucial for the description of biomolecular folding pathways, which is however difficult in both experiments and computer simulations. Such transient states are typically of low population in simulation samples. Even for simple systems such as RNA hairpins, recently there are mounting debates over the existence of multiple intermediate states. In this paper, we develop a computational approach to explore the relatively low populated transition or intermediate states in biomolecular folding pathways, based on a topological data analysis tool, Mapper, with simulation data from large-scale distributed computing. The method is inspired by the classical Morse theory in mathematics which characterizes the topology of high dimensional shapes via some functional level sets. In this paper we exploit a conditional density filter which enables us to focus on the structures on pathways, followed by clustering analysis on its level sets, which helps separate low populated intermediates from high populated uninteresting structures. A successful application of this method is given on a motivating example, a RNA hairpin with GCAA tetraloop, where we are able to provide structural evidence from computer simulations on the multiple intermediate states and exhibit different pictures about unfolding and refolding pathways. The method is effective in dealing with high degree of heterogeneity in distribution, capturing structural features in multiple pathways, and being less sensitive to the distance metric than nonlinear dimensionality reduction or geometric embedding methods. It provides us a systematic tool to explore the low density intermediate states in complex biomolecular folding systems.Comment: 23 pages, 6 figure

Towards Characterizing Graphs with a Sliceable Rectangular Dual

\u3cp\u3eLet G be a plane triangulated graph. A rectangular dual of G is a partition of a rectangle R into a set R of interior-disjoint rectangles, one for each vertex, such that two regions are adjacent if and only if the corresponding vertices are connected by an edge. A rectangular dual is sliceable if it can be recursively subdivided along horizontal or vertical lines. A graph is rectangular if it has a rectangular dual and sliceable if it has a sliceable rectangular dual. There is a clear characterization of rectangular graphs. However, a full characterization of sliceable graphs is still lacking. The currently best result (Yeap and Sarrafzadeh, 1995) proves that all rectangular graphs without a separating 4-cycle are slice- able. In this paper we introduce a recursively defined class of graphs and prove that these graphs are precisely the nonsliceable graphs with exactly one separating 4-cycle.\u3c/p\u3

Improving the Sampling Strategy for Point-to-Point Line-Of-Sight Modelling in Urban Environments

Visibility modelling calculates what an observer could theoretically see in the surrounding region based on a digital model of the landscape. In some cases it is not necessary, nor desirable, to compute the visibility of an entire region (i.e. a viewshed), but instead it is sufficient and more efficient to calculate the visibility from point-to-point, or from a point to a small set of points, such as computing the intervisibility of predators and prey in an agent based simulation. This paper explores how different line-of-sight (LoS) sample ordering strategies increases the number of early target rejections, where the target is considered to be obscured from view, thereby improving the computational efficiency of the LoS algorithm. This is of particular importance in dynamic environments where the locations of the observers, targets and other surface objects are being frequently updated. Trials were conducted in three UK cities, demonstrating a robust five-fold increase in performance for two strategies (hop, divide and conquer). The paper concludes that sample ordering methods do impact overall efficiency, and that approaches which disperse samples along the LoS perform better in urban regions than incremental scan methods. The divide and conquer method minimises elevation interception queries, making it suitable when elevation models are held on disk rather than in memory, while the hopping strategy was equally fast, algorithmically simpler, with minimal overhead for visible target cases

Recent Surveys in the Forests of Ulu Segama Malua, Sabah, Malaysia, Show That Orang-utans (P. p. morio) Can Be Maintained in Slightly Logged Forests

BACKGROUND: Today the majority of wild great ape populations are found outside of the network of protected areas in both Africa and Asia, therefore determining if these populations are able to survive in forests that are exploited for timber or other extractive uses and how this is managed, is paramount for their conservation. METHODOLOGY/PRINCIPAL FINDINGS: In 2007, the "Kinabatangan Orang-utan Conservation Project" (KOCP) conducted aerial and ground surveys of orang-utan (Pongo pygmaeus morio) nests in the commercial forest reserves of Ulu Segama Malua (USM) in eastern Sabah, Malaysian Borneo. Compared with previous estimates obtained in 2002, our recent data clearly shows that orang-utan populations can be maintained in forests that have been lightly and sustainably logged. However, forests that are heavily logged or subjected to fast, successive coupes that follow conventional extraction methods, exhibit a decline in orang-utan numbers which will eventually result in localized extinction (the rapid extraction of more than 100 m(3) ha(-1) of timber led to the crash of one of the surveyed sub-populations). Nest distribution in the forests of USM indicates that orang-utans leave areas undergoing active disturbance and take momentarily refuge in surrounding forests that are free of human activity, even if these forests are located above 500 m asl. Displaced individuals will then recolonize the old-logged areas after a period of time, depending on availability of food sources in the regenerating areas. CONCLUSION/SIGNIFICANCE: These results indicate that diligent planning prior to timber extraction and the implementation of reduced-impact logging practices can potentially be compatible with great ape conservation

Potential links between surging ice sheets, circulation changes and the Dansgaard Oeschger cycles in the Irminger Sea, 60-18 kyr.

Surface and deepwater paleoclimate records in Irminger Sea core SO82-5 (59°N, 31°W) and Icelandic Sea core PS2644 (68°N, 22°W) exhibit large fluctuations in thermohaline circulation (THC) from 60 to 18 calendar kyr B.P., with a dominant periodicity of 1460 years from 46 to 22 calendar kyr B.P., matching the Dansgaard-Oeschger (D-O) cycles in the Greenland Ice Sheet Project 2 (GISP2) temperature record [Grootes and Stuiver, 1997]. During interstadials, summer sea surface temperatures (SST<inf>su</inf>) in the Irminger Sea averaged to 8°C, and sea surface salinities (SSS) averaged to ∼36.5, recording a strong Irminger Current and Atlantic THC. During stadials, SST<inf>su</inf> dropped to 2°-4°C, in phase with SSS drops by ∼1-2. They reveal major meltwater injections along with the East Greenland Current, which turned off the North Atlantic deepwater convection and hence the heat advection to the north, in harmony with various ocean circulation and ice models. On the basis of the IRD composition, icebergs came from Iceland, east Greenland, and perhaps Svalbard and other northern ice sheets. However, the southward drifting icebergs were initially jammed in the Denmark Strait, reaching the Irminger Sea only with a lag of 155-195 years. We also conclude that the abrupt stadial terminations, the D-O warming events, were tied to iceberg melt via abundant seasonal sea ice and brine water formation in the meltwater-covered northwestern North Atlantic. In the 1/1460-year frequency band, benthic δ18O brine water spikes led the temperature maxima above Greenland and in the Irminger Sea by as little as 95 years. Thus abundant brine formation, which was induced by seasonal freezing of large parts of the northwestern Atlantic, may have finally entrained a current of warm surface water from the subtropics and thereby triggered the sudden reactivation of the THC. In summary, the internal dynamics of the east Greenland ice sheet may have formed the ultimate pacemaker of D-O cycles