(found 2 matches in 0.000772s)
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Current Theoretical Models Fail to Predict the Topological Complexity of the Human Genome
(2015)
Javier Arsuaga, Reyka G. Jayasinghe, Robert G. Scharein, Mark R. Segal, Robert H. Stolz, Mariel Vazquez
Abstract
Understanding the folding of the human genome is a key challenge of modern structural biology. The emergence of chromatin conformation capture assays (e.g., Hi-C) has revolutionized chromosome biology and provided new insights into the three dimensional structure of the genome. The experimental data are highly complex and need to be analyzed with quantitative tools. It has been argued that the data obtained from Hi-C assays are consistent with a fractal organization of the genome. A key characteristic of the fractal globule is the lack of topological complexity (knotting or inter-linking). However, the absence of topological complexity contradicts results from polymer physics showing that the entanglement of long linear polymers in a confined volume increases rapidly with the length and with decreasing volume. In vivo and in vitro assays support this claim in some biological systems. We simulate knotted lattice polygons confined inside a sphere and demonstrate that their contact frequencies agree with the human Hi-C data. We conclude that the topological complexity of the human genome cannot be inferred from current Hi-C data.
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Grasping Objects With Holes: A Topological Approach
(2013)
F. T. Pokorny, J. A. Stork, D. Kragic
Abstract
This work proposes a topologically inspired approach for generating robot grasps on objects with `holes'. Starting from a noisy point-cloud, we generate a simplicial representation of an object of interest and use a recently developed method for approximating shortest homology generators to identify graspable loops. To control the movement of the robot hand, a topologically motivated coordinate system is used in order to wrap the hand around such loops. Finally, another concept from topology - namely the Gauss linking integral - is adapted to serve as evidence for secure caging grasps after a grasp has been executed. We evaluate our approach in simulation on a Barrett hand using several target objects of different sizes and shapes and present an initial experiment with real sensor data.