Robert G. Scharein
Research Subjects
Research Interests
Robert G. Scharein has a total of 6 co-authors. Here are the top co-authors by number of shared publications:
- Eric J. Rawdon
University of St Thomas
4 shared publications - Javier Arsuaga
Department of Molecular and Cellular Biology and Department of Mathematics, University of California Davis, Davis, CA, USA
1 shared publication - Mariel Vazquez
Department of Mathematics Department of Microbiology & Molecular Genetics University of California, Davis One Shields Avenue Davis CA 95616 USA
1 shared publication - Mark Robert Segal
Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
1 shared publication - Reyka G. Jayasinghe
Washington University in St. Louis 4 Saint Louis, MO
1 shared publication - Robert H. Stolz
Department of Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
1 shared publication
Latest Publications
- 20 June 2024
- Published by Springer Nature
- p. 319-342
Using the HOMFLYPT Polynomial to Compute Knot Types
- 20 June 2024
- Published by Springer Nature
- p. 319-342
Using the HOMFLYPT Polynomial to Compute Knot Types
- Open Access
Using the HOMFLY-PT polynomial to compute knot types
The HOMFLY-PT polynomial is a link invariant which is effective in determining chiral knot and link types with small crossing numbers. In this chapter, we concentrate on knots. We provide a guide for computing the knot types of configurations from 3D coordinates via the HOMFLY-PT polynomial using publicly-available Linux freeware. We include data on the efficacy of HOMFLY-PT for knot types through crossing number 16.
Open AccessUsing the HOMFLY-PT polynomial to compute knot types
The HOMFLY-PT polynomial is a link invariant which is effective in determining chiral knot and link types with small crossing numbers. In this chapter, we concentrate on knots. We provide a guide for computing the knot types of configurations from 3D coordinates via the HOMFLY-PT polynomial using publicly-available Linux freeware. We include data on the efficacy of HOMFLY-PT for knot types through crossing number 16.
- Open Access
An introduction to KnotPlot
We give a brief introduction to the software KnotPlot. The goals of this chapter are twofold: 1) to help a new user get started with using KnotPlot and 2) to provide veteran users with additional background and functionality available in the software.
Open AccessAn introduction to KnotPlot
We give a brief introduction to the software KnotPlot. The goals of this chapter are twofold: 1) to help a new user get started with using KnotPlot and 2) to provide veteran users with additional background and functionality available in the software.
- Open Access
- 21 August 2015
- Published by Frontiers Media SA in Frontiers in Molecular Biosciences
- Vol. 2, 48
Current theoretical models fail to predict the topological complexity of the human genome
Understanding the folding of the human genome is a key challenge of modern structural biology. The emergence of chromatin conformation capture assays ({\it 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 \textcolor{red}{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. \textcolor{red}{{\it In vivo} and {\it 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.
- 21 August 2015
- Published by Frontiers Media SA in Frontiers in Molecular Biosciences
- Vol. 2, 48
Open AccessCurrent theoretical models fail to predict the topological complexity of the human genome
Understanding the folding of the human genome is a key challenge of modern structural biology. The emergence of chromatin conformation capture assays ({\it 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 \textcolor{red}{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. \textcolor{red}{{\it In vivo} and {\it 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.