Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction.
Sign Up to like & getrecommendations! Published in 2018 at "International journal for numerical methods in biomedical engineering"
DOI: 10.1002/cnm.2914
Abstract: Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, and gene expression. Accurate prediction of protein-ligand binding affinities is… read more here.
Keywords: persistent homology; topology; protein ligand; ligand binding ... See more keywords
Relative-perfectness of discrete gradient vector fields and multi-parameter persistent homology
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Combinatorial Optimization"
DOI: 10.1007/s10878-021-00729-x
Abstract: The combination of persistent homology and discrete Morse theory has proven very effective in visualizing and analyzing big and heterogeneous data. Indeed, topology provides computable and coarse summaries of data independently from specific coordinate systems… read more here.
Keywords: gradient vector; perfectness; discrete gradient; homology ... See more keywords
Fractal dimension and the persistent homology of random geometric complexes
Sign Up to like & getrecommendations! Published in 2020 at "Advances in Mathematics"
DOI: 10.1016/j.aim.2020.107291
Abstract: We prove that the fractal dimension of a metric space equipped with an Ahlfors regular measure can be recovered from the persistent homology of random samples. Our main result is that if $x_1,\ldots, x_n$ are… read more here.
Keywords: ldots right; persistent homology; fractal dimension; left ldots ... See more keywords
Quantification of LSS using the persistent homology in the SDSS fields
Sign Up to like & getrecommendations! Published in 2017 at "Advances in Space Research"
DOI: 10.1016/j.asr.2017.04.020
Abstract: Abstract Using galaxy samples from the Sloan Digital Sky Survey (SDSS) Data Release 12 (DR12), we first estimate the topology of cosmic large-scale structure (LSS) by means of a new method of persistent homology which… read more here.
Keywords: quantification lss; persistent homology; topology; lss using ... See more keywords
Adsorbate Organization Characterized by Sublevelset Persistent Homology.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.3c00090
Abstract: Interfacial adsorbate organization influences a variety physicochemical properties and reactivity. Surfaces that are rough, defect laden, or have large fluctuations (as in soft matter interfaces) can lead to complex adsorbate structures. This is amplified if… read more here.
Keywords: sublevelset persistent; adsorbate; liquid; persistent homology ... See more keywords
Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-66710-6
Abstract: It has long been observed that trimethylamine N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work on these two osmolytes, various aspects… read more here.
Keywords: aggregation hydrogen; network; molecular aggregation; persistent homology ... See more keywords
Higher-order structure of polymer melt described by persistent homology
Sign Up to like & getrecommendations! Published in 2021 at "Scientific Reports"
DOI: 10.1038/s41598-021-80975-5
Abstract: The optimal method of the polymer Materials Informatics (MI) has not been developed because the amorphous nature of the higher-order structure affects these properties. We have now tried to develop the polymer MI’s descriptor of… read more here.
Keywords: order; polymer; higher order; persistent homology ... See more keywords
Flow estimation solely from image data through persistent homology analysis
Sign Up to like & getrecommendations! Published in 2021 at "Scientific Reports"
DOI: 10.1038/s41598-021-97222-6
Abstract: Topological data analysis is an emerging concept of data analysis for characterizing shapes. A state-of-the-art tool in topological data analysis is persistent homology, which is expected to summarize quantified topological and geometric features. Although persistent… read more here.
Keywords: persistent homology; image data; homology; homology analysis ... See more keywords
Selecting embedding delays: An overview of embedding techniques and a new method using persistent homology.
Sign Up to like & getrecommendations! Published in 2023 at "Chaos"
DOI: 10.1063/5.0137223
Abstract: Delay embedding methods are a staple tool in the field of time series analysis and prediction. However, the selection of embedding parameters can have a big impact on the resulting analysis. This has led to… read more here.
Keywords: time; selecting embedding; embedding methods; method ... See more keywords
Persistent Homology of Complex Networks for Dynamic State Detection
Sign Up to like & getrecommendations! Published in 2019 at "Physical review. E"
DOI: 10.1103/physreve.100.022314
Abstract: In this paper we develop an alternative topological data analysis (TDA) approach for studying graph representations of time series of dynamical systems. Specifically, we show how persistent homology, a tool from TDA, can be used… read more here.
Keywords: homology complex; time series; complex networks; homology ... See more keywords
Persistent homology analysis of craze formation.
Sign Up to like & getrecommendations! Published in 2017 at "Physical Review E"
DOI: 10.1103/physreve.95.012504
Abstract: We apply a persistent homology analysis to investigate the behavior of nanovoids during the crazing process of glassy polymers. We carry out a coarse-grained molecular dynamics simulation of the uniaxial deformation of an amorphous polymer… read more here.
Keywords: persistent homology; craze formation; homology; homology analysis ... See more keywords