🍩 Database of Original & Non-Theoretical Uses of Topology

(found 3 matches in 0.001153s)

  1. Structural Insight Into RNA Hairpin Folding Intermediates (2008)

    Gregory R. Bowman, Xuhui Huang, Yuan Yao, Jian Sun, Gunnar Carlsson, Leonidas J. Guibas, Vijay S. Pande
    Abstract , Hairpins are a ubiquitous secondary structure motif in RNA molecules. Despite their simple structure, there is some debate over whether they fold in a two-state or multi-state manner. We have studied the folding of a small tetraloop hairpin using a serial version of replica exchange molecular dynamics on a distributed computing environment. On the basis of these simulations, we have identified a number of intermediates that are consistent with experimental results. We also find that folding is not simply the reverse of high-temperature unfolding and suggest that this may be a general feature of biomolecular folding.

  2. Persistent Voids: A New Structural Metric for Membrane Fusion (2007)

    Peter M. Kasson, Afra Zomorodian, Sanghyun Park, Nina Singhal, Leonidas J. Guibas, Vijay S. Pande
    Abstract Motivation: Membrane fusion constitutes a key stage in cellular processes such as synaptic neurotransmission and infection by enveloped viruses. Current experimental assays for fusion have thus far been unable to resolve early fusion events in fine structural detail. We have previously used molecular dynamics simulations to develop mechanistic models of fusion by small lipid vesicles. Here, we introduce a novel structural measurement of vesicle topology and fusion geometry: persistent voids.Results: Persistent voids calculations enable systematic measurement of structural changes in vesicle fusion by assessing fusion stalk widths. They also constitute a generally applicable technique for assessing lipid topological change. We use persistent voids to compute dynamic relationships between hemifusion neck widening and formation of a full fusion pore in our simulation data. We predict that a tightly coordinated process of hemifusion neck expansion and pore formation is responsible for the rapid vesicle fusion mechanism, while isolated enlargement of the hemifusion diaphragm leads to the formation of a metastable hemifused intermediate. These findings suggest that rapid fusion between small vesicles proceeds via a small hemifusion diaphragm rather than a fully expanded one.Availability: Software available upon request pending public release.Contact:kasson@cmgm.stanford-edu or pande@stanford.eduSupplementary information: Supplementary data are available on Bioinformatics online.

  3. A Barcode Shape Descriptor for Curve Point Cloud Data (2004)

    Anne Collins, Afra Zomorodian, Gunnar Carlsson, Leonidas J. Guibas
    Abstract In this paper, we present a complete computational pipeline for extracting a compact shape descriptor for curve point cloud data (PCD). Our shape descriptor, called a barcode, is based on a blend of techniques from differential geometry and algebraic topology. We also provide a metric over the space of barcodes, enabling fast comparison of PCDs for shape recognition and clustering. To demonstrate the feasibility of our approach, we implement our pipeline and provide experimental evidence in shape classification and parametrization.