Quantitative Biology

Authors and titles for November 2020

[301] arXiv:2011.12846 (cross-list from physics.soc-ph) [pdf, other]

Title: Multiwave pandemic dynamics explained: How to tame the next wave of infectious diseases

Giacomo Cacciapaglia, Corentin Cot, Francesco Sannino

Comments: 12 pages, 5 figures

Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

[302] arXiv:2011.12859 (cross-list from cs.AI) [pdf, other]

Title: Anytime Prediction as a Model of Human Reaction Time

Omkar Kumbhar, Elena Sizikova, Najib Majaj, Denis G. Pelli

Comments: 7 pages, 7 figures

Subjects: Artificial Intelligence (cs.AI); Computer Vision and Pattern Recognition (cs.CV); Neurons and Cognition (q-bio.NC)

[303] arXiv:2011.12865 (cross-list from eess.IV) [pdf, other]

Title: Contrastive Representation Learning for Whole Brain Cytoarchitectonic Mapping in Histological Human Brain Sections

Christian Schiffer, Katrin Amunts, Stefan Harmeling, Timo Dickscheid

Comments: Accepted to ISBI 2021

Subjects: Image and Video Processing (eess.IV); Computer Vision and Pattern Recognition (cs.CV); Neurons and Cognition (q-bio.NC)

[304] arXiv:2011.13027 (cross-list from stat.ME) [pdf, other]

Title: Protein Structure Parameterization via Mobius Distributions on the Torus

Mohammad Arashi, Najmeh Nakhaei Rad, Andriette Bekker, Wolf Dieter Schubert

Comments: Plagiarism

Subjects: Methodology (stat.ME); Biomolecules (q-bio.BM); Quantitative Methods (q-bio.QM)

[305] arXiv:2011.13479 (cross-list from math.CO) [pdf, other]

Title: Combinatorial perspectives on Dollo-$k$ characters in phylogenetics

Remco Bouckaert, Mareike Fischer, Kristina Wicke

Subjects: Combinatorics (math.CO); Populations and Evolution (q-bio.PE)

[306] arXiv:2011.13778 (cross-list from cond-mat.dis-nn) [pdf, other]

Title: Heterogeneous excitable systems exhibit Griffiths phases below hybrid phase transitions

Géza Ódor, Beatriz de Simoni

Comments: 10 pages 11 figures, accepted version to appear in Phys. Rev. Research

Journal-ref: Phys. Rev. Research 3, 013106 (2021)

Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Neurons and Cognition (q-bio.NC)

[307] arXiv:2011.13826 (cross-list from physics.soc-ph) [pdf, other]

Title: Path-dependent course of epidemic: are two phases of quarantine better than one?

Varun Nimmagadda, Oleg Kogan, Evgeniy Khain

Comments: 6 pages, 4 figures, accepted to EPL (Europhysics Letters)

Subjects: Physics and Society (physics.soc-ph); Statistical Mechanics (cond-mat.stat-mech); Populations and Evolution (q-bio.PE)

[308] arXiv:2011.13867 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Fluctuating diffusivity of RNA-protein particles: Analogy with thermodynamics

Yuichi Itto

Comments: 19 pages, no figures. The discussion developed further and some references added. Published version

Journal-ref: Entropy 2021, 23, 333

Subjects: Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM)

[309] arXiv:2011.13960 (cross-list from stat.AP) [pdf, other]

Title: Finding Optimal Cancer Treatment using Markov Decision Process to Improve Overall Health and Quality of Life

Navonil Deb, Abhinandan Dalal, Gopal Krishna Basak

Subjects: Applications (stat.AP); General Economics (econ.GN); Quantitative Methods (q-bio.QM); Computation (stat.CO)

[310] arXiv:2011.14532 (cross-list from cs.DS) [pdf, other]

Title: Batch Optimization for DNA Synthesis

Konstantin Makarychev, Miklos Z. Racz, Cyrus Rashtchian, Sergey Yekhanin

Comments: Improved Theorem 1.2 and its proof

Subjects: Data Structures and Algorithms (cs.DS); Information Theory (cs.IT); Combinatorics (math.CO); Probability (math.PR); Quantitative Methods (q-bio.QM)

[311] arXiv:2011.14592 (cross-list from physics.bio-ph) [pdf, other]

Title: Examining the assembly pathways and active microtubule mechanics underlying spindle self-organization

Lucan Yan, Tatsuya Fukuyama, Megumi Yamaoka, Yusuke T. Maeda, Yuta Shimamoto

Comments: 22 pages, 5 + 2 figures

Journal-ref: Proc. Natl. Acad. Sci. USA 119, e2209053119 (2022)

Subjects: Biological Physics (physics.bio-ph); Subcellular Processes (q-bio.SC)

[312] arXiv:2011.14722 (cross-list from cs.DS) [pdf, other]

Title: Distributed Algorithms from Arboreal Ants for the Shortest Path Problem

Shivam Garg, Kirankumar Shiragur, Deborah M. Gordon, Moses Charikar

Comments: Changes in presentation. Published in PNAS 2023

Subjects: Data Structures and Algorithms (cs.DS); Adaptation and Self-Organizing Systems (nlin.AO); Quantitative Methods (q-bio.QM)

[313] arXiv:2011.14827 (cross-list from math.NA) [pdf, other]

Title: The role of spectral complexity in connectivity estimation

Elisabetta Vallarino, Michele Piana, Alberto Sorrentino, Sara Sommariva

Comments: 14 pages, 5 figures, 1 table

Subjects: Numerical Analysis (math.NA); Quantitative Methods (q-bio.QM)

[314] arXiv:2011.14839 (cross-list from physics.chem-ph) [pdf, other]

Title: Natural radioactive environments as sources of local disequilibrium for the emergence of life

Thiago Altair, Larissa M. Sartori, Fabio Rodrigues, Marcio G. B. de Avellar, Douglas Galante

Comments: 51 pages, 9 figures, supplementary material included. Astrobiology

Subjects: Chemical Physics (physics.chem-ph); Earth and Planetary Astrophysics (astro-ph.EP); Geophysics (physics.geo-ph); Populations and Evolution (q-bio.PE)

[315] arXiv:2011.14994 (cross-list from cond-mat.stat-mech) [pdf, other]

Title: Reformulating non-equilibrium steady-states and generalised Hopfield discrimination

Ugur Cetiner, Jeremy Gunawardena

Comments: Central results unchanged from previous version. The entropy production index, a new graph-theoretic measure of non-equilibrium complexity, has been introduced. Added numerical simulations demonstrating that optimal discrimination is still possible on a complex graph with only a single energetic edge

Subjects: Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Molecular Networks (q-bio.MN)

[316] arXiv:2011.15031 (cross-list from cs.NE) [pdf, other]

Title: A biologically plausible neural network for local supervision in cortical microcircuits

Siavash Golkar, David Lipshutz, Yanis Bahroun, Anirvan M. Sengupta, Dmitri B. Chklovskii

Comments: Abstract presented at the NeurIPS 2020 workshop "Beyond Backpropagation". arXiv admin note: text overlap with arXiv:2010.12660

Subjects: Neural and Evolutionary Computing (cs.NE); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)

[317] arXiv:2011.15105 (cross-list from physics.soc-ph) [pdf, other]

Title: Moderate immigration may promote a peak of cooperation among natives

Alessandra Friedrich Lütz, Marco Antonio Amaral, Lucas Wardil

Journal-ref: Phys. Rev. E 104, 014304 (2021)

Subjects: Physics and Society (physics.soc-ph); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Populations and Evolution (q-bio.PE)