Physics Chemistry & Materials

Editor’s Picks: Mathematical Biology

Published July 2, 2018 Partnered Collections, Special Issues

This collection showcases articles published in PLOS ONE that apply mathematics to biological questions. As the selection shows, this field is very broad, spanning topics such as angiogenesis, morphogenesis, cell dynamics and interactions, metabolism modelling, biochemical processes, and touches on all scales of biological organization. In this Editor’s Picks, PLOS ONE Associate Editor Carla Pegoraro highlights some of the latest research on mathematical and physical biology. We welcome submissions in this field and hope to grow our collection over time.

Image Credit: 10.1371/journal.pone.0149254

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Biological Systems
Growth and Morphology
Cell Dynamics
Metabolism Modelling
Biological Processes
Molecular Modelling

Biological Systems

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Fig 1. Model dynamics by Marquioni et al., CC BY 4.0

PLOS ONE Modeling neutral viral mutations in the spread of SARS-CoV-2 epidemics
July 29, 2021 Vitor M. Marquioni, Marcus A. M. de Aguiar

Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of…
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10.1371/journal.pone.0243823 CC BY 4.0

PLOS ONE Piece-wise linear models of biological systems—Application, analysis, and comparison with nonlinear models using the example of the p53 regulatory module
December 16, 2020 Magdalena Ochab, Krzysztof Puszynski

In this paper, we propose to use a linear system with switching methodology for description and analysis of complex biological systems. We…
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10.1371/journal.pone.0230430 CC BY 4.0

PLOS ONE The Community Simulator: A Python package for microbial ecology
March 24, 2020 Robert Marsland, Wenping Cui, Joshua Goldford, Pankaj Mehta

Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing…
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10.1371/journal.pone.0229738 CC BY 4.0

PLOS ONE Numerical modeling and verification of a sonobioreactor and its application on two model microorganisms
March 11, 2020 Nasim Najjarzadeh, Adolf Krige, Taraka R. K. Pamidi, Örjan Johansson, Josefine Enman, Leonidas Matsakas, Ulrika Rova, Paul Christakopoulos

Ultrasound has many uses, such as in medical imaging, monitoring of crystallization, characterization of emulsions and suspensions, and…
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10.1371/journal.pone.0149674

PLOS ONE Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters
February 24, 2016 Fei Liu, Monika Heiner, Ming Yang
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10.1371/journal.pone.0182385

PLOS ONE Modeling and simulation of biological systems using SPICE language
August 7, 2017 Morgan Madec, Christophe Lallement, Jacques Haiech

Growth and Morphology

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10.1371/journal.pone.0245205 CC BY 4.0

PLOS ONE A new analysis method for evaluating bacterial growth with microplate readers
January 12, 2021 Venkata Rao Krishnamurthi, Isabelle I. Niyonshuti, Jingyi Chen, Yong Wang

Growth curve measurements are commonly used in microbiology, while the use of microplate readers for such measurements provides better…
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10.1371/journal.pone.0210088 CC BY 4.0

PLOS ONE Threshold response to stochasticity in morphogenesis
January 30, 2019 George Courcoubetis, Sammi Ali, Sergey V. Nuzhdin, Paul Marjoram, Stephan Haas

During development of biological organisms, multiple complex structures are formed. In many instances, these structures need to exhibit a…
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10.1371/journal.pone.0206292 CC BY 4.0

PLOS ONE Modeling three-dimensional invasive solid tumor growth in heterogeneous microenvironment under chemotherapy
October 26, 2018 Hang Xie, Yang Jiao, Qihui Fan, Miaomiao Hai, Jiaen Yang, Zhijian Hu, Yue Yang, Jianwei Shuai, Guo Chen, Ruchuan Liu, Liyu Liu

A systematic understanding of the evolution and growth dynamics of invasive solid tumors in response to different chemotherapy strategies…
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10.1371/journal.pone.0083962

PLOS ONE Computational Modeling of 3D Tumor Growth and Angiogenesis for Chemotherapy Evaluation
January 3, 2014 Lei Tang, Anne L. van de Ven, Dongmin Guo, Vivi Andasari, Vittorio Cristini, King C. Li, Xiaobo Zhou
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10.1371/journal.pone.0159478

PLOS ONE Computational Screening of Tip and Stalk Cell Behavior Proposes a Role for Apelin Signaling in Sprout Progression
November 9, 2016 Margriet M. Palm, Marchien G. Dallinga, Erik van Dijk, Ingeborg Klaassen, Reinier O. Schlingemann, Roeland M. H. Merks
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10.1371/journal.pone.0166655

PLOS ONE Normal Wound Healing and Tumor Angiogenesis as a Game of Competitive Inhibition
December 9, 2016 Irina Kareva, Abdo Abou-Slaybi, Oliver Dodd, Olga Dashevsky, Giannoula Lakka Klement
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10.1371/journal.pone.0099116

PLOS ONE CellFIT: A Cellular Force-Inference Toolkit Using Curvilinear Cell Boundaries
June 12, 2014 G. Wayne Brodland, Jim H. Veldhuis, Steven Kim, Matthew Perrone, David Mashburn, M. Shane Hutson
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10.1371/journal.pone.0093207

PLOS ONE How Does a Single Cell Know When the Liver Has Reached Its Correct Size?
April 1, 2014 Nadine Hohmann, Wei Weiwei, Uta Dahmen, Olaf Dirsch, Andreas Deutsch, Anja Voss-Böhme
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10.1371/journal.pone.0054802

PLOS ONE The Flux-Based PIN Allocation Mechanism Can Generate Either Canalyzed or Diffuse Distribution Patterns Depending on Geometry and Boundary Conditions
January 28, 2013 Michael Luke Walker, Etienne Farcot, Jan Traas, Christophe Godin
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10.1371/journal.pone.0127972

PLOS ONE Emergent Stratification in Solid Tumors Selects for Reduced Cohesion of Tumor Cells: A Multi-Cell, Virtual-Tissue Model of Tumor Evolution Using CompuCell3D
June 17, 2015 Maciej H. Swat, Gilberto L. Thomas, Abbas Shirinifard, Sherry G. Clendenon, James A. Glazier
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10.1371/journal.pone.0085585

PLOS ONE The Fiber Walk: A Model of Tip-Driven Growth with Lateral Expansion
January 22, 2014 Alexander Bucksch, Greg Turk, Joshua S. Weitz
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10.1371/journal.pone.0149254

PLOS ONE Spiral and Rotor Patterns Produced by Fairy Ring Fungi
March 2, 2016 Nathaniel Karst, David Dralle, Sally Thompson
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10.1371/journal.pone.0174946

PLOS ONE Turing mechanism underlying a branching model for lung morphogenesis
April 4, 2017 Hui Xu, Mingzhu Sun, Xin Zhao
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10.1371/journal.pone.0191089

PLOS ONE Cell death as a trigger for morphogenesis
March 22, 2018 Boris Aguilar, Ahmadreza Ghaffarizadeh, Christopher D. Johnson, Gregory J. Podgorski, Ilya Shmulevich, Nicholas S. Flann

Cell Dynamics

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10.1371/journal.pone.0238955 CC BY 4.0

PLOS ONE Improved 3D cellular morphometry of Caenorhabditis elegans embryos using a refractive index matching medium
September 30, 2020 Rain Xiong, Kenji Sugioka

Cell shape change is one of the driving forces of animal morphogenesis, and the model organism Caenorhabditis elegans has played a…
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10.1371/journal.pone.0231137 CC BY 4.0

PLOS ONE A hybrid model of tumor growth and angiogenesis: In silico experiments
April 10, 2020 Caleb M. Phillips, Ernesto A. B. F. Lima, Ryan T. Woodall, Amy Brock, Thomas E. Yankeelov

Tumor associated angiogenesis is the development of new blood vessels in response to proteins secreted by tumor cells. These new blood…
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10.1371/journal.pone.0204393 CC BY 4.0

PLOS ONE A stochastic model of myeloid cell lineages in hematopoiesis and pathway mutations in acute myeloid leukemia
October 1, 2018 Frank Jäkel, Oliver Worm, Sascha Lange, Roland Mertelsmann

A model for hematopoiesis is presented that explicitly includes the erythrocyte, granulocyte, and thrombocyte lineages and their common…
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10.1371/journal.pone.0224787 CC BY 4.0

PLOS ONE Mathematical modeling reveals the factors involved in the phenomena of cancer stem cells stabilization
November 11, 2019 Nikolay Bessonov, Guillaume Pinna, Andrey Minarsky, Annick Harel-Bellan, Nadya Morozova

Cancer Stem Cells (CSC), a subset of cancer cells resembling normal stem cells with self-renewal and asymmetric division capabilities, are…
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10.1371/journal.pone.0205031 CC BY 4.0

PLOS ONE Tracking intracellular dynamics through extracellular measurements
October 17, 2018 Franz Hamilton, Tyrus Berry, Timothy Sauer

Extracellular recordings of neuronal cells are frequently a part of in vitro and in vivo experimental studies as a means of monitoring…
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10.1371/journal.pone.0204171 CC BY 4.0

PLOS ONE Bone remodeling: A tissue-level process emerging from cell-level molecular algorithms
September 19, 2018 Clemente F. Arias, Miguel A. Herrero, Luis F. Echeverri, Gerardo E. Oleaga, José M. López

The human skeleton undergoes constant remodeling throughout the lifetime. Processes occurring on microscopic and molecular scales degrade…
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10.1371/journal.pone.0165570

PLOS ONE Modelling Chemotactic Motion of Cells in Biological Tissues
October 31, 2016 Bakhtier Vasiev
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10.1371/journal.pone.0065864

PLOS ONE A Mechanochemical Model of Cell Reorientation on Substrates under Cyclic Stretch
June 6, 2013 Jin Qian, Haipei Liu, Yuan Lin, Weiqiu Chen, Huajian Gao
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10.1371/journal.pone.0104969

PLOS ONE Directional Collective Cell Migration Emerges as a Property of Cell Interactions
September 2, 2014 Mae L. Woods, Carlos Carmona-Fontaine, Chris P. Barnes, Iain D. Couzin, Roberto Mayor, Karen M. Page
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10.1371/journal.pone.0111896

PLOS ONE A Three-Dimensional Computational Model of Collagen Network Mechanics
November 11, 2014 Byoungkoo Lee, Xin Zhou, Kristin Riching, Kevin W. Eliceiri, Patricia J. Keely, Scott A. Guelcher, Alissa M. Weaver, Yi Jiang
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10.1371/journal.pone.0193975

PLOS ONE Distinguishing cell shoving mechanisms
March 12, 2018 Pingyu Nan, Darragh M. Walsh, Kerry A. Landman, Barry D. Hughes
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10.1371/journal.pone.0198420

PLOS ONE Mathematical modelling of reversible transition between quiescence and proliferation
June 1, 2018 Nishtha Pandey, P. K. Vinod
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10.1371/journal.pone.0150578

PLOS ONE The Combined Effect of Hydrophobic Mismatch and Bilayer Local Bending on the Regulation of Mechanosensitive Ion Channels
March 9, 2016 Omid Bavi, Manouchehr Vossoughi, Reza Naghdabadi, Yousef Jamali
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10.1371/journal.pone.0161915

PLOS ONE Spheroid Formation of Hepatocarcinoma Cells in Microwells: Experiments and Monte Carlo Simulations
August 29, 2016 Yan Wang, Myung Hee Kim, Seyed R. Tabaei, Jae Hyeok Park, Kyuhwan Na, Seok Chung, Vladimir P. Zhdanov, Nam-Joon Cho

Metabolism Modelling

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10.1371/journal.pone.0210558 CC BY 4.0

PLOS ONE Machine learning framework for assessment of microbial factory performance
January 15, 2019 Tolutola Oyetunde, Di Liu, Hector Garcia Martin, Yinjie J. Tang

Metabolic models can estimate intrinsic product yields for microbial factories, but such frameworks struggle to predict cell performance…
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10.1371/journal.pone.0229408 CC BY 4.0

PLOS ONE An adjustable algal chloroplast plug-and-play model for genome-scale metabolic models
February 24, 2020 Gunvor Bjerkelund Røkke, Martin Frank Hohmann-Marriott, Eivind Almaas

The chloroplast is a central part of plant cells, as this is the organelle where the photosynthesis, fixation of inorganic carbon, and…
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10.1371/journal.pone.0226243 CC BY 4.0

PLOS ONE Hydrogenotrophic methanogens of the mammalian gut: Functionally similar, thermodynamically different—A modelling approach
December 11, 2019 Rafael Muñoz-Tamayo, Milka Popova, Maxence Tillier, Diego P. Morgavi, Jean-Pierre Morel, Gérard Fonty, Nicole Morel-Desrosiers

Methanogenic archaea occupy a functionally important niche in the gut microbial ecosystem of mammals. Our purpose was to quantitatively…
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10.1371/journal.pone.0208282 CC BY 4.0

PLOS ONE A quantitative model of nitrogen fixation in the presence of ammonium
November 29, 2021
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10.1371/journal.pone.0207983 CC BY 4.0

PLOS ONE Delving deeper: Relating the behaviour of a metabolic system to the properties of its components using symbolic metabolic control analysis
November 28, 2018 Carl D. Christensen, Jan-Hendrik S. Hofmeyr, Johann M. Rohwer

High-level behaviour of metabolic systems results from the properties of, and interactions between, numerous molecular components.…
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10.1371/journal.pone.0198060 CC BY 4.0

PLOS ONE Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models
September 13, 2018 Xiao Fu, James P. Sluka, Sherry G. Clendenon, Kenneth W. Dunn, Zemin Wang, James E. Klaunig, James A. Glazier

Computational models of normal liver function and xenobiotic induced liver damage are increasingly being used to interpret in vitro and in…
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10.1371/journal.pone.0064567

PLOS ONE Community Flux Balance Analysis for Microbial Consortia at Balanced Growth
May 31, 2013 Ruchir A. Khandelwal, Brett G. Olivier, Wilfred F. M. Röling, Bas Teusink, Frank J. Bruggeman
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10.1371/journal.pone.0162428

PLOS ONE A Liver-Centric Multiscale Modeling Framework for Xenobiotics
September 16, 2016 James P. Sluka, Xiao Fu, Maciej Swat, Julio M. Belmonte, Alin Cosmanescu, Sherry G. Clendenon, John F. Wambaugh, James A. Glazier
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10.1371/journal.pone.0103582

PLOS ONE Simulating Metabolism with Statistical Thermodynamics
August 4, 2014 William R. Cannon
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10.1371/journal.pone.0147651

PLOS ONE Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis
January 28, 2016 Andrew S. Krueger, Christian Munck, Gautam Dantas, George M. Church, James Galagan, Joseph Lehár, Morten O. A. Sommer
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10.1371/journal.pone.0182570

PLOS ONE Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects
August 18, 2017 Joseph R. Peterson, John A. Cole, Zaida Luthey-Schulten

Biological Processes

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10.1371/journal.pone.0225988 CC BY 4.0

PLOS ONE Time optimal entrainment control for circadian rhythm
December 18, 2019 A. Agung Julius, Jiawei Yin, John T. Wen

The circadian rhythm functions as a master clock that regulates many physiological processes in humans including sleep, metabolism,…
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10.1371/journal.pone.0222401 CC BY 4.0

PLOS ONE The rotating magnetocaloric effect as a potential mechanism for natural magnetic senses
October 1, 2019 A. Martin Bell, Jacob T. Robinson

Many animals are able to sense the earth’s magnetic field, including varieties of arthropods and members of all major vertebrate groups.…
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10.1371/journal.pone.0235750 CC BY 4.0

PLOS ONE Machine learning for modeling animal movement
July 27, 2020 Dhanushi A. Wijeyakulasuriya, Elizabeth W. Eisenhauer, Benjamin A. Shaby, Ephraim M. Hanks

Animal movement drives important ecological processes such as migration and the spread of infectious disease. Current approaches to…
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10.1371/journal.pone.0222906 CC BY 4.0

PLOS ONE Multiscale Modelling Tool: Mathematical modelling of collective behaviour without the maths
September 30, 2019 James A. R. Marshall, Andreagiovanni Reina, Thomas Bose

Collective behaviour is of fundamental importance in the life sciences, where it appears at levels of biological complexity from single…
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10.1371/journal.pone.0212044 CC BY 4.0

PLOS ONE Modelling collective motion based on the principle of agency: General framework and the case of marching locusts
February 20, 2019 Katja Ried, Thomas Müller, Hans J. Briegel

Collective phenomena are studied in a range of contexts—from controlling locust plagues to efficiently evacuating stadiums—but the central…
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10.1371/journal.pone.0128111

PLOS ONE Obstructions in Vascular Networks: Relation Between Network Morphology and Blood Supply
June 18, 2015 Aimee M. Torres Rojas, Alejandro Meza Romero, Ignacio Pagonabarraga, Rui D. M. Travasso, Eugenia Corvera Poiré
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10.1371/journal.pone.0153297

PLOS ONE A Simple, Realistic Stochastic Model of Gastric Emptying
April 8, 2016 Jiraphat Yokrattanasak, Andrea De Gaetano, Simona Panunzi, Pairote Satiracoo, Wayne M. Lawton, Yongwimon Lenbury
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10.1371/journal.pone.0145309

PLOS ONE A Spatially Continuous Model of Carbohydrate Digestion and Transport Processes in the Colon
December 17, 2015 Arun S. Moorthy, Stephen P. J. Brooks, Martin Kalmokoff, Hermann J. Eberl

Molecular Modelling

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10.1371/journal.pone.0255693 CC BY 4.0

PLOS ONE Prediction of HIV drug resistance based on the 3D protein structure: Proposal of molecular field mapping
August 4, 2021 Ryosaku Ota, Kanako So, Masahiro Tsuda, Yuriko Higuchi, Fumiyoshi Yamashita

A method for predicting HIV drug resistance by using genotypes would greatly assist in selecting appropriate combinations of antiviral…
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10.1371/journal.pone.0226825 CC BY 4.0

PLOS ONE An agent-based model of molecular aggregation at the cell membrane
February 7, 2020 Juliette Griffié, Ruby Peters, Dylan M. Owen

Molecular clustering at the plasma membrane has long been identified as a key process and is associated with regulating signalling…
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10.1371/journal.pone.0214126 CC BY 4.0

PLOS ONE A new benchmark illustrates that integration of geometric constraints inferred from enzyme reaction chemistry can increase enzyme active site modeling accuracy
April 4, 2019 Steve J. Bertolani, Justin B. Siegel

Enzymes play a critical role in a wide array of industrial, medical, and research applications and with the recent explosion of genomic…
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10.1371/journal.pone.0172072

PLOS ONE Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential
February 16, 2017 Katja Ostermeir, Martin Zacharias
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10.1371/journal.pone.0176229

PLOS ONE Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state
April 24, 2017 Becka M. Warfield, Peter C. Anderson