Lexicon for classifying ear-canal shapes [PDF]
Scientific Reports, 2023 The ear canal is usually described as an S-shaped funnel. In attempting to classify ear-canal shapes obtained from point clouds digitized from molds of 300 ears, the problem of designing criteria for distinguishing and organizing the canal shapes arose ...
J. C. Martinez +9 more
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Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families. [PDF]
PLoS Computational BiologyIdentifying the key order parameters that connect a protein's native structure to its dynamical and evolutionary behavior remains a central challenge. We introduce topological and geometrical metrics-specifically, writhe and Local Topological Energy (LTE)
Nikhil Ramesh +2 more
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The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement. [PDF]
PLoS Computational Biology, 2023 We present fast and simple-to-implement measures of the entanglement of protein tertiary structures which are appropriate for highly flexible structure comparison.
Arron Bale +2 more
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Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy [PDF]
Nature CommunicationsDNA topology is essential for regulating cellular processes and maintaining genome stability, yet it is challenging to quantify due to the size and complexity of topologically constrained DNA molecules.
Elizabeth P. Holmes +14 more
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Innovative Tools for DNA Topology Probing in Human Cells Reveal a Build-Up of Positive Supercoils Following Replication Stress at Telomeres and at the FRA3B Fragile Site [PDF]
CellsLinear unconstrained DNA cannot harbor supercoils since these supercoils can diffuse and be eliminated by free rotation of the DNA strands at the end of the molecule.
Claire Ghilain +5 more
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DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. [PDF]
PLoS Computational BiologyIn eukaryotes, DNA achieves a highly compact structure primarily due to its winding around the histone cores. The nature wrapping of DNA around histone core form a 1.7 left-handed superhelical turns, contributing to negative supercoiling in chromatin ...
Chunhong Long, Hongqiong Liang, Biao Wan
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Aggregation and structural phase transitions of semiflexible polymer bundles: A braided circuit topology approach [PDF]
iScienceSummary: We present a braided circuit topology framework for investigating topology and structural phase transitions in aggregates of semiflexible polymers.
Jonas Berx, Alireza Mashaghi
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Mathematical topology and geometry-based classification of tauopathies [PDF]
Scientific ReportsNeurodegenerative diseases, like Alzheimer’s, are associated with the presence of neurofibrillary lesions formed by tau protein filaments in the cerebral cortex.
Masumi Sugiyama +2 more
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GISA: using Gauss Integrals to identify rare conformations in protein structures [PDF]
PeerJ, 2020 The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research.
Christian Grønbæk +2 more
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Scientific Reports, 2021 We introduce the Writhe Application Software Package (WASP) which can be used to characterisze the topology of ribbon structures, the underlying mathematical model of DNA, Biopolymers, superfluid vorticies, elastic ropes and magnetic flux ropes.
Zachary Sierzega +2 more
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