Agnese Barbensi

Agnese Barbensi
University of Melbourne | MSD · School of Mathematics and Statistics

About

19
Publications
2,444
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
93
Citations

Publications

Publications (19)
Preprint
Full-text available
Interactions and relations between objects may be pairwise or higher-order in nature, and so network-valued data are ubiquitous in the real world. The "space of networks", however, has a complex structure that cannot be adequately described using conventional statistical tools. We introduce a measure-theoretic formalism for modeling generalized net...
Article
The last years have witnessed remarkable advances in our understanding of the emergence and consequences of topological constraints in biological and soft matter. Examples are abundant in relation to (bio)polymeric systems and range from the characterization of knots in single polymers and proteins to that of whole chromosomes and polymer melts. At...
Preprint
Full-text available
Deep learning methods have revolutionized our ability to predict protein structures, allowing us a glimpse into the entire protein universe. As a result, our understanding of how protein structure drives function is now lagging behind our ability to determine and predict protein structure. Here, we describe how topology, the branch of mathematics c...
Article
Full-text available
Quantification and classification of protein structures, such as knotted proteins, often requires noise-free and complete data. Here, we develop a mathematical pipeline that systematically analyses protein structures. We showcase this geometric framework on proteins forming open-ended trefoil knots, and we demonstrate that the mathematical tool, pe...
Preprint
Full-text available
The problem of finding robust and effective methods for locating entanglement in embedded curves is relevant to both applications and theoretical investigations. Rather than focusing on an exact determination, we introduce the knot intensity distribution, a local quantifier for the contribution of a curve's region to global entanglement. The integr...
Preprint
Full-text available
Scientific data has been growing in both size and complexity across the modern physical, engineering, life and social sciences. Spatial structure, for example, is a hallmark of many of the most important real-world complex systems, but its analysis is fraught with statistical challenges. Topological data analysis can provide a powerful computationa...
Preprint
Full-text available
Grid diagrams are a combinatorial version of classical link diagrams, widely used in theoretical, computational and applied knot theory. Motivated by questions from (bio)-physical knot theory, we introduce GridPyM, a Sage compatible Python module that handles grid diagrams. GridPyM focuses on generating and simplifying grids, and on modelling local...
Preprint
Full-text available
Quantification and classification of protein structures, such as knotted proteins, often requires noise-free and complete data. Here we develop a mathematical pipeline that systematically analyzes protein structures. We showcase this geometric framework on proteins forming open-ended trefoil knots, and we demonstrate that the mathematical tool, per...
Article
Full-text available
Understanding how knotted proteins fold is a challenging problem in biology. Researchers have proposed several models for their folding pathways, based on theory, simulations and experiments. The geometry of proteins with the same knot type can vary substantially and recent simulations reveal different folding behaviour for deeply and shallow knott...
Preprint
Full-text available
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a protein's planar projections using topological objects called knotoids. We approach the analysis of proteins wit...
Article
Full-text available
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here, we investigate the relation between knotoids differing only by small perturbations of the direction of projection. Since suc...
Article
Full-text available
Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process such as the topoisomerase-mediated preferential unknotting of DNA molecules. We model here topoisomerase-media...
Preprint
Full-text available
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here we investigate the relation between knotoids differing only by small perturbations of the direction of projection. Since such...
Preprint
Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process such as the topoisomerase-mediated preferential unknotting of DNA molecules. We model here topoisomerase-media...
Preprint
By using double branched covers, we prove that there is a 1-1 correspondence between the set of knotoids in the 2-sphere, up to orientation reversion and rotation, and knots with a strong inversion, up to conjugacy. This correspondence allows us to study knotoids through tools and invariants coming from knot theory. In particular, concepts from geo...
Article
We describe two locally finite graphs naturally associated to each knot type K, called Reidemeister graphs. We determine several local and global properties of these graphs and prove that in one case the graph-isomorphism type is a complete knot invariant up to mirroring. Lastly, we introduce another object, relating the Reidemeister and Gordian gr...
Preprint
We describe two locally finite graphs naturally associated to each knot type K, called Reidemeister graphs. We determine several local and global properties of these graphs and prove that in one case the graph-isomorphism type is a complete knot invariant up to mirroring. Lastly, we introduce another object, relating the Reidemeister and Gordian gr...

Network

Cited By