235 citations · 321 across the 10 of their papers we have counts for
10 papers
Fitness Inference in Presence of Migrations between Coupled Evolving Populations
Yu-Han Huang, Bastien Dumont, Hong-Li Zeng +2
The phase of Quasi-Linkage Equilibrium (QLE) in evolutionary populations is analogous to the thermal equilibrium state in statistical mechanics, a concept pioneered by Kimura in 19…
Classification of SARS-CoV-2 Variants through The Epistatical Circos Plots with Convolutional Neural Networks
Bo Jing, Kai-Rui Zhang, Hong-Li Zeng +1
The COVID-19 pandemic has profoundly affected global health, driven by the remarkable transmissibility and mutational adaptability of the SARS-CoV-2 virus. Although five variants o…
Fitness inference tested by in silico population genetics
Hong-Li Zeng, Yu-Han Huang, John Barton +1
We consider populations evolving according to natural selection, mutation, and recombination, and assume that the genomes of all or a representative selection of individuals are kn…
Average entanglement entropy of a small subsystem in a constrained pure Gaussian state ensemble
Erik Aurell, Lucas Hackl, Mario Kieburg
We consider ensembles of pure Gaussian states parametrized by single-mode marginals and (optionally) specific mode-mode correlations. Such ensembles provide a model for the final s…
The curious case of operators with spectral density increasing as
Erik Aurell, Satya N. Majumdar
Motivated by a putative model of black holes as quantum objects we consider what types of operators would have a corresponding spectrum. We find that there are indeed such operator…
Two fitness inference schemes compared using allele frequencies from 1,068,391 sequences sampled in the UK during the COVID-19 pandemic
Hong-Li Zeng, Cheng-Long Yang, Bo Jing +2
Throughout the course of the SARS-CoV-2 pandemic, genetic variation has contributed to the spread and persistence of the virus. For example, various mutations have allowed SARS-CoV…
Random pure Gaussian states and Hawking radiation
Erik Aurell, Lucas Hackl, Paweł Horodecki +2
A black hole evaporates by Hawking radiation. Each mode of that radiation is thermal. If the total state is nevertheless to be pure, modes must be entangled. Estimating the minimum…
Global analysis of more than 50,000 SARS-Cov-2 genomes reveals epistasis between 8 viral genes
Hong-Li Zeng, Vito Dichio, Edwin Rodríguez Horta +2
Genome-wide epistasis analysis is a powerful tool to infer gene interactions, which can guide drug and vaccine development and lead to a deeper understanding of microbial pathogene…
Quasi-potential landscape in complex multi-stable systems
Joseph Xu Zhou, M. D. S. Aliyu, Erik Aurell +1
Developmental dynamics of multicellular organism is a process that takes place in a multi-stable system in which each attractor state represents a cell type and attractor transitio…
Optimal protocols and optimal transport in stochastic thermodynamics
Erik Aurell, Carlos Mejia-Monasterio, Paolo Muratore-Ginanneschi
Thermodynamics of small systems has become an important field of statistical physics. They are driven out of equilibrium by a control, and the question is naturally posed how such…