thesisbiblio.bib

@article{foxTutorialVariationalBayesian2012a,
  title = {A Tutorial on Variational {{Bayesian}} Inference},
  author = {Fox, Charles W. and Roberts, Stephen J.},
  year = {2012},
  month = aug,
  journal = {Artificial Intelligence Review},
  volume = {38},
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  issn = {1573-7462},
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}



@article{maBayesianEstimationBeta2011,
  title = {Bayesian {{Estimation}} of {{Beta Mixture Models}} with {{Variational Inference}}},
  author = {Ma, Zhanyu and Leijon, Arne},
  year = {2011},
  month = nov,
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {33},
  number = {11},
  pages = {2160--2173},
  issn = {1939-3539},
  doi = {10.1109/TPAMI.2011.63},
  keywords = {Approximation methods,Bayesian estimation,Bayesian methods,beta distribution,Data models,factorized approximation.,maximum likelihood estimation,Maximum likelihood estimation,mixture modeling,Numerical models,Probability density function,variational inference}
}



@article{lipscombStructureMechanismsEscherichia2012,
  title = {Structure and {{Mechanisms}} of {{Escherichia}} Coli {{Aspartate Transcarbamoylase}}},
  author = {Lipscomb, William N. and Kantrowitz, Evan R.},
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}



@article{cockrellNewParadigmAllosteric2013,
  title = {New {{Paradigm}} for {{Allosteric Regulation}} of {{Escherichia}} Coli {{Aspartate Transcarbamoylase}}},
  author = {Cockrell, Gregory M. and Zheng, Yunan and Guo, Wenyue and Peterson, Alexis W. and Truong, Jennifer K. and Kantrowitz, Evan R.},
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}



@article{liuAllosteryOverviewIts2016,
  title = {Allostery: {{An Overview}} of {{Its History}}, {{Concepts}}, {{Methods}}, and {{Applications}}},
  shorttitle = {Allostery},
  author = {Liu, Jin and Nussinov, Ruth},
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@article{changeuxAllostericModulationUnifying2016,
  title = {Allosteric {{Modulation}} as a {{Unifying Mechanism}} for {{Receptor Function}} and {{Regulation}}},
  author = {Changeux, Jean-Pierre and Christopoulos, Arthur},
  year = {2016},
  month = aug,
  volume = {166},
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  issn = {0092-8674},
  doi = {10.1016/j.cell.2016.08.015},
  journal = {Cell},
  language = {en},
  number = {5}
}



@phdthesis{duvenaudAutomaticModelConstruction2014,
  title = {Automatic Model Construction with {{Gaussian}} Processes},
  author = {Duvenaud, David},
  year = {2014},
  month = nov,
  doi = {10.17863/CAM.14087},
  annotation = {Accepted: 2015-04-08T08:37:46Z},
  copyright = {Attribution-ShareAlike 2.0 UK: England \& Wales},
  language = {en},
  school = {University of Cambridge},
  type = {Thesis}
}



@article{sechiEstimationKoopmanGenerator2021,
  title = {Estimation of the {{Koopman Generator}} by {{Newton}}'s {{Extrapolation}}},
  author = {Sechi, Renata and Sikorski, Alexander and Weber, Marcus},
  year = {2021},
  month = jan,
  volume = {19},
  pages = {758--774},
  publisher = {{Society for Industrial and Applied Mathematics}},
  issn = {1540-3459},
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  journal = {Multiscale Modeling \& Simulation},
  keywords = {37M10,47N60,60J28,Koopman generator,Markov process,Newton's polynomial extrapolation},
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}



@article{nuskeSpectralPropertiesEffective2021,
  title = {Spectral {{Properties}} of {{Effective Dynamics}} from {{Conditional Expectations}}},
  author = {N{\"u}ske, Feliks and Koltai, P{\'e}ter and Boninsegna, Lorenzo and Clementi, Cecilia},
  year = {2021},
  month = feb,
  volume = {23},
  pages = {134},
  publisher = {{Multidisciplinary Digital Publishing Institute}},
  doi = {10.3390/e23020134},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  journal = {Entropy},
  keywords = {coarse graining,extended dynamic mode decomposition,infinitesimal generator,Kramers–Moyal formulae,Langevin dynamics,spectral analysis,stochastic differential equations},
  language = {en},
  number = {2}
}



@article{varolgunesInterpretableEmbeddingsMolecular2020,
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  year = {2020},
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  pages = {015012},
  publisher = {{IOP Publishing}},
  issn = {2632-2153},
  doi = {10.1088/2632-2153/ab80b7},
  journal = {Machine Learning: Science and Technology},
  language = {en},
  number = {1}
}



@article{liNeuralCanonicalTransformation2020,
  title = {Neural {{Canonical Transformation}} with {{Symplectic Flows}}},
  author = {Li, Shuo-Hui and Dong, Chen-Xiao and Zhang, Linfeng and Wang, Lei},
  year = {2020},
  month = apr,
  volume = {10},
  pages = {021020},
  publisher = {{American Physical Society}},
  doi = {10.1103/PhysRevX.10.021020},
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  number = {2}
}



@article{wangMachineLearningCoarseGrained2019,
  title = {Machine {{Learning}} of {{Coarse}}-{{Grained Molecular Dynamics Force Fields}}},
  author = {Wang, Jiang and Olsson, Simon and Wehmeyer, Christoph and P{\'e}rez, Adri{\`a} and Charron, Nicholas E. and {de Fabritiis}, Gianni and No{\'e}, Frank and Clementi, Cecilia},
  year = {2019},
  month = may,
  volume = {5},
  pages = {755--767},
  publisher = {{American Chemical Society}},
  issn = {2374-7943},
  doi = {10.1021/acscentsci.8b00913},
  journal = {ACS Central Science},
  number = {5}
}



@article{nuskeCoarsegrainingMolecularSystems2019,
  title = {Coarse-Graining Molecular Systems by Spectral Matching},
  author = {N{\"u}ske, Feliks and Boninsegna, Lorenzo and Clementi, Cecilia},
  year = {2019},
  month = jul,
  volume = {151},
  pages = {044116},
  publisher = {{American Institute of Physics}},
  issn = {0021-9606},
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  number = {4}
}



@misc{MarkovmodelMdshare2021,
  title = {Markovmodel/Mdshare},
  year = {2021},
  month = mar,
  copyright = {LGPL-3.0},
  howpublished = {Markov model},
  keywords = {trajectories}, 
  url={https://github.com/markovmodel/mdshare}
}



@book{claeskens_hjort_2008,
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  year = {2008},
  publisher = {{Cambridge University Press}},
  address = {{Cambridge}},
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}



@article{kellsMeanFirstPassage2019,
  title = {Mean First Passage Times in Variational Coarse Graining Using {{Markov}} State Models},
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}



@article{jasHelixCoilTransition2018,
  title = {Helix\textendash{{Coil Transition Courses Through Multiple Pathways}} and {{Intermediates}}: {{Fast Kinetic Measurements}} and {{Dimensionality Reduction}}},
  shorttitle = {Helix\textendash{{Coil Transition Courses Through Multiple Pathways}} and {{Intermediates}}},
  author = {Jas, Gouri S. and Kuczera, Krzysztof},
  year = {2018},
  month = dec,
  volume = {122},
  pages = {10806--10816},
  publisher = {{American Chemical Society}},
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}



@article{wilsonRenormalizationGroupCritical1983,
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  author = {Wilson, Kenneth G.},
  year = {1983},
  month = jul,
  volume = {55},
  pages = {583--600},
  publisher = {{American Physical Society}},
  doi = {10.1103/RevModPhys.55.583},
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  number = {3}
}



@article{jainHierarchicalFoldingFree2014,
  title = {Hierarchical {{Folding Free Energy Landscape}} of {{HP35 Revealed}} by {{Most Probable Path Clustering}}},
  author = {Jain, Abhinav and Stock, Gerhard},
  year = {2014},
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@article{mukherjeeMarkovModelsApo2016,
  title = {Markov Models of the Apo -{{MDM2}} Lid Region Reveal Diffuse yet Two-State Binding Dynamics and Receptor Poses for Computational Docking},
  author = {Mukherjee, Sudipto and Pantelopulos, George A. and Voelz, Vincent A.},
  year = {2016},
  month = aug,
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  copyright = {2016 The Author(s)},
  journal = {Scientific Reports},
  language = {en},
  number = {1}
}



@article{pohleSelectingNumberStates2017,
  title = {Selecting the {{Number}} of {{States}} in {{Hidden Markov Models}}: {{Pragmatic Solutions Illustrated Using Animal Movement}}},
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}



@article{shuklaConformationalHeterogeneityCalmodulin2016,
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  year = {2016},
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  copyright = {2016 The Author(s)},
  journal = {Nature Communications},
  language = {en},
  number = {1}
}



@article{islamExploringDynamicsPropeller2017,
  title = {Exploring the {{Dynamics}} of {{Propeller Loops}} in {{Human Telomeric DNA Quadruplexes Using Atomistic Simulations}}},
  author = {Islam, Barira and Stadlbauer, Petr and {Gil-Ley}, Alejandro and {P{\'e}rez-Hern{\'a}ndez}, Guillermo and Haider, Shozeb and Neidle, Stephen and Bussi, Giovanni and Banas, Pavel and Otyepka, Michal and Sponer, Jiri},
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}



@article{wieczorekMHCClassII2016,
  title = {{{MHC}} Class {{II}} Complexes Sample Intermediate States along the Peptide Exchange Pathway},
  author = {Wieczorek, Marek and Sticht, Jana and Stolzenberg, Sebastian and G{\"u}nther, Sebastian and Wehmeyer, Christoph and El Habre, Zeina and {\'A}lvaro-Benito, Miguel and No{\'e}, Frank and Freund, Christian},
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  copyright = {2016 The Author(s)},
  journal = {Nature Communications},
  language = {en},
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}



@article{plattnerProteinConformationalPlasticity2015,
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}



@article{henzler-wildmanDynamicPersonalitiesProteins2007,
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@article{kellsCorrelationFunctionsMean2020,
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@article{mcconnellSeasonalVariationsPhysical2008,
  title = {Seasonal Variations of the Physical and Optical Characteristics of {{Saharan}} Dust: {{Results}} from the {{Dust Outflow}} and {{Deposition}} to the {{Ocean}} ({{DODO}}) Experiment},
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  journal = {Journal of Geophysical Research: Atmospheres},
  keywords = {aerosol,climate,dust},
  language = {en},
  number = {D14}
}



@article{farmerAtmosphericProcessesTheir2015,
  title = {Atmospheric {{Processes}} and {{Their Controlling Influence}} on {{Cloud Condensation Nuclei Activity}}},
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@article{irvineHalvingWarmingIdealized2019,
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  copyright = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
  journal = {Nature Climate Change},
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  number = {4}
}



@article{StopDenyingRisks2019,
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  copyright = {2021 Nature},
  journal = {Nature},
  language = {en},
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}



@article{antoniouProteinDynamicsEnzymatic2011,
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@article{adamczykCatalysisDihydrofolateReductase2011,
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  year = {2011},
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  year = {1989},
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  publisher = {{American Association for the Advancement of Science}},
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  journal = {Science},
  language = {en},
  number = {4896},
  pmid = {2646716}
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@article{kamerlinMultiscaleModelingBiological2011,
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  publisher = {{The Royal Society of Chemistry}},
  issn = {1463-9084},
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@article{pisliakovEnzymeMillisecondConformational2009,
  title = {Enzyme Millisecond Conformational Dynamics Do Not Catalyze the Chemical Step.},
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@article{akkeOutHotWater2004,
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  copyright = {2004 Nature Publishing Group},
  journal = {Nature Structural \& Molecular Biology},
  language = {en},
  number = {10}
}

@article{eisenmesserIntrinsicDynamicsEnzyme2005,
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  journal = {Nature},
  language = {en},
  number = {7064}
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@article{olssonSoluteSolventDynamics2004,
  title = {Solute {{Solvent Dynamics}} and {{Energetics}} in {{Enzyme Catalysis}}: {{The SN2 Reaction}} of {{Dehalogenase}} as a {{General Benchmark}}},
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  volume = {126},
  pages = {15167--15179},
  publisher = {{American Chemical Society}},
  issn = {0002-7863},
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  number = {46}
}

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  shorttitle = {Coupling between {{Protein}} and {{Reaction Dynamics}} in {{Enzymatic Processes}}},
  author = {Roca, Maite and Moliner, Vicente and Tu{\~n}{\'o}n, I{\~n}aki and Hynes, James T.},
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@incollection{dellagoTransitionPathSampling2002a,
  title = {Transition {{Path Sampling}}},
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  language = {en}
}





%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%





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%   publisher = {{Omnipress}},
%   address = {{Haifa, Israel}}, 
%   url={https://icml.cc/Conferences/2010/papers/422.pdf}
% }

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@misc{hansenCMAEvolutionStrategy2016,
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      primaryClass={cs.LG}
}
% @article{hansenCMAEvolutionStrategy2016,
%   title = {The {{CMA Evolution Strategy}}: {{A Tutorial}}},
%   shorttitle = {The {{CMA Evolution Strategy}}},
%   author = {Hansen, Nikolaus},
%   year = {2016},
%   month = apr,
%   archivePrefix = {arXiv},
%   eprint = {1604.00772},
%   eprinttype = {arxiv},
%   journal = {arXiv:1604.00772 [cs, stat]},
%   keywords = {Computer Science - Machine Learning,Statistics - Machine Learning},
%   language = {en},
%   primaryClass = {cs, stat}
% }



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% @inproceedings{eberhart1998comparison,
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% }




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@Inbook{feurer2019hyperparameter,
author={Feurer, Matthias
and Hutter, Frank},
editor={Hutter, Frank
and Kotthoff, Lars
and Vanschoren, Joaquin},
title={Hyperparameter Optimization},
bookTitle={Automated Machine Learning: Methods, Systems, Challenges},
year={2019},
publisher={Springer International Publishing},
address={Cham},
pages={3--33},
isbn={978-3-030-05318-5},
doi={10.1007/978-3-030-05318-5_1}
}
% @incollection{feurer2019hyperparameter,
%   title = {Hyperparameter Optimization},
%   booktitle = {Automated Machine Learning},
%   author = {Feurer, Matthias and Hutter, Frank},
%   year = {2019},
%   pages = {3--33},
%   publisher = {{Springer, Cham}}
% }



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% @misc{LoopMotionTriosephosphate,
%   title = {Loop {{Motion}} in {{Triosephosphate Isomerase Is Not}} a {{Simple Open}} and {{Shut Case}} | {{Journal}} of the {{American Chemical Society}}},
%   howpublished = {https://pubs.acs.org/doi/10.1021/jacs.8b09378}
% }



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}


@Misc{gpyopt2016,
  author =   {{The GPyOpt authors}},
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%   howpublished = {\url{http://github.com/SheffieldML/GPyOpt}},
  url={http://github.com/SheffieldML/GPyOpt},
  year = {2016}
}
% @article{gpyopt2016,
%   title = {{{GPyOpt}}: {{A}} Bayesian Optimization Framework in Python},
%   author = {{authors}, The GPyOpt},
%   year = {2016}
% }



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author={Hutter, Frank
and Hoos, Holger H.
and Leyton-Brown, Kevin},
editor={Coello, Carlos A. Coello},
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}
% @article{hutterSequentialModelbasedOptimization2011,
%   title = {Sequential Model-Based Optimization for General Algorithm Configuration},
%   author = {Hutter, Frank and Hoos, Holger H. and {Leyton-Brown}, Kevin},
%   year = {2011},
%   volume = {6683 LNCS},
%   pages = {507--523},
%   issn = {03029743},
%   doi = {10.1007/978-3-642-25566-3_40},
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%   pmid = {20675462}
% }




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@InProceedings{ bergstraHyperoptPythonLibrary2013,
  author    = { {J}ames {B}ergstra and {D}an {Y}amins and {D}avid {D}. {C}ox },
  title     = { {H}yperopt: {A} {P}ython {L}ibrary for {O}ptimizing the {H}yperparameters of {M}achine {L}earning {A}lgorithms },
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  doi       = { 10.25080/Majora-8b375195-003 }
}
% @inproceedings{bergstraHyperoptPythonLibrary2013,
%   title = {Hyperopt: {{A Python Library}} for {{Optimizing}} the {{Hyperparameters}} of {{Machine Learning Algorithms}}},
%   shorttitle = {Hyperopt},
%   booktitle = {Python in {{Science Conference}}},
%   author = {Bergstra, James and Yamins, Dan and Cox, David},
%   year = {2013},
%   pages = {13--19},
%   address = {{Austin, Texas}},
%   doi = {10.25080/Majora-8b375195-003},
%   language = {en}
% }



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%   eprinttype = {arxiv},
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% @article{mcgibbonUnderstandingProteinDynamics,
%   title = {Understanding {{Protein Dynamics}} with {{L1}}-{{Regularized Reversible Hidden Markov Models}}},
%   author = {McGibbon, Robert T and Ramsundar, Bharath and Sultan, Mohammad M and Kiss, Gert and Pande, Vijay S},
%   pages = {9},
%   language = {en}
% }

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  journal = {Biophysical Journal},
  language = {en},
  number = {7}
}

@article{furiniIontriggeredSelectivityBacterial2018,
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  author = {Furini, Simone and Domene, Carmen},
  year = {2018},
  month = may,
  volume = {115},
  pages = {5450--5455},
  publisher = {{National Academy of Sciences}},
  issn = {0027-8424, 1091-6490},
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  chapter = {Biological Sciences},
  copyright = { 2018 . http://www.pnas.org/site/aboutpnas/licenses.xhtmlPublished under the PNAS license.},
  journal = {Proceedings of the National Academy of Sciences},
  keywords = {conduction,ion channels,Markov state models,membrane proteins,molecular dynamics},
  language = {en},
  number = {21},
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}

@article{hansonWhatMakesKinase2019,
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  keywords = {ABL,crystallography,DDR1,DFG,drug promiscuity,Folding@home,kinase inhibition,Markov state model,molecular dynamics,selectivity},
  language = {en},
  number = {3}
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@article{juarez-jimenezDynamicDesignManipulation2020,
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  publisher = {{Royal Society of Chemistry}},
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  journal = {Chemical Science},
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}

@article{mondalAtomicResolutionMechanism2018a,
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  keywords = {Benzene,Binding analysis,Biochemical simulations,Biophysical simulations,Crystal structure,Free energy,Protein structure,Thermodynamics},
  language = {en},
  number = {5}
}

@article{olaposiMembraneBoundTranscriptionFactor2019,
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  month = nov,
%   edition = {14.08.2019},
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@article{plattnerCompleteProteinProtein2017,
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  author = {Remington, Jacob Michael},
  year = {2019},
  pages = {1--214},
  publisher = {{Montana State University - Bozeman, College of Letters \& Science}},
  copyright = {Copyright 2019 by Jacob Michael Remington},
  language = {en},
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@article{wangDynamicalBehaviorVLactamases2019,
  title = {Dynamical {{Behavior}} of {$\beta$}-{{Lactamases}} and {{Penicillin}}- {{Binding Proteins}} in {{Different Functional States}} and {{Its Potential Role}} in {{Evolution}}},
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  journal = {Entropy},
  keywords = {catalytic mechanism,conformational changes,DD-transpeptidase,evolution,PBP-A,TEM-1,TOHO-1},
  language = {en},
  number = {11}
}

@article{xiaoNaBindingModes2019,
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  publisher = {{Royal Society of Chemistry}},
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@article{yangMappingPathwayDynamics2018,
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  publisher = {{John Wiley \& Sons, Ltd}},
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}
% @article{jaegerDiscretetimeDiscretevaluedObservable,
%   title = {Discrete-Time, Discrete-Valued Observable Operator Models: A Tutorial},
%   author = {Jaeger, Herbert},
%   pages = {72},
%   language = {en}
% }

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volume = {8},
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% @article{kuoLumpingAnalysisMonomolecular,
%   title = {Lumping {{Analysis}} in {{Monomolecular Reaction Systems}}. {{Analysis}} of {{Approximately Lumpable System}}},
%   author = {Kuo, J C W and Wei, James},
%   pages = {10},
%   language = {en}
% }

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@article{eastmanOpenMMRapidDevelopment2017,
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@incollection{klinmanbeyond2009,
  title = {Chapter 6 beyond Tunnelling Corrections: {{Full}} Tunnelling Models for Enzymatic {{C}} -- {{H}} Activation Reactions},
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  publisher = {{The Royal Society of Chemistry}},
  doi = {10.1039/9781847559975-00132},
  isbn = {978-0-85404-122-0}
}





% @book{allemannQuantumTunnellingEnzymecatalysed2009,
%   title = {Quantum Tunnelling in Enzyme-Catalysed Reactions},
%   editor = {Allemann, Rudolf K and Scrutton, Nigel S},
%   year = {2009},
%   pages = {P001-P385},
%   publisher = {{The Royal Society of Chemistry}},
%   doi = {10.1039/9781847559975},
%   isbn = {978-0-85404-122-0},
%   series = {{{RSC}} Biomolecular Sciences}
% }

@article{antoniouInternalEnzymeMotions2001,
  title = {Internal {{Enzyme Motions}} as a {{Source}} of {{Catalytic Activity}}: {{Rate}}-{{Promoting Vibrations}} and {{Hydrogen Tunneling}}},
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  author = {Antoniou, Dimitri and Schwartz, Steven D.},
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}

@article{antoniouLargeKineticIsotope1997,
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@article{kohenEnzymeCatalysisClassical1998,
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}

@article{masgrau2004hydrogen,
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@article{glowackiProteinDynamicsEnzyme2012,
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@article{glowackiTakingOckhamRazor2012b,
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@article{ranaghanComputerSimulationsQuantum2010,
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@article{mcgeaghProteinDynamicsEnzyme2011,
  title = {Protein Dynamics and Enzyme Catalysis: {{Insights}} from Simulations},
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  author = {McGeagh, John D. and Ranaghan, Kara E. and Mulholland, Adrian J.},
  year = {2011},
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  keywords = {Computational enzymology,Conformational change,Enzyme catalysis,Functional dynamics,Molecular dynamics,Molecular mechanics,Protein dynamics,Quantum mechanics,Quantum tunnelling},
  language = {en},
  number = {8}
%   series = {Protein {{Dynamics}}: {{Experimental}} and {{Computational Approaches}}}
}



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@article{johannissenEnzymeAromaticAmine2008,
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  shorttitle = {Proton {{Tunneling}} in {{Aromatic Amine Dehydrogenase}} Is {{Driven}} by a {{Short}}-{{Range Sub}}-{{Picosecond Promoting Vibration}}},
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}

@article{masgrauTunnelingClassicalPaths2007,
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@incollection{duvenaud2011additive,
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author = {Duvenaud, David K and Nickisch, Hannes and Carl E. Rasmussen},
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% @inproceedings{duvenaud2011additive,
%   title = {Additive Gaussian Processes},
%   booktitle = {Advances in Neural Information Processing Systems},
%   author = {Duvenaud, David K and Nickisch, Hannes and Rasmussen, Carl E},
%   year = {2011},
%   pages = {226--234}
% }



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title = {Predictive Entropy Search for Efficient Global Optimization of Black-box Functions},
author = {Hern\'{a}ndez-Lobato, Jos\'{e} Miguel and Hoffman, Matthew W and Ghahramani, Zoubin},
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% @inproceedings{hernandez2014predictive,
%   title = {Predictive Entropy Search for Efficient Global Optimization of Black-Box Functions},
%   booktitle = {Advances in Neural Information Processing Systems},
%   author = {{Hern{\'a}ndez-Lobato}, Jos{\'e} Miguel and Hoffman, Matthew W and Ghahramani, Zoubin},
%   year = {2014},
%   pages = {918--926}
% }
@misc{shahriariEntropySearchPortfolio2015,
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      year={2015},
      eprint={1406.4625},
      archivePrefix={arXiv},
      primaryClass={stat.ML}
}
% @article{shahriariEntropySearchPortfolio2015,
%   title = {An {{Entropy Search Portfolio}} for {{Bayesian Optimization}}},
%   author = {Shahriari, Bobak and Wang, Ziyu and Hoffman, Matthew W. and {Bouchard-C{\^o}t{\'e}}, Alexandre and {de Freitas}, Nando},
%   year = {2015},
%   month = mar,
%   archivePrefix = {arXiv},
%   eprint = {1406.4625},
%   eprinttype = {arxiv},
%   journal = {arXiv:1406.4625 [cs, stat]},
%   keywords = {Computer Science - Machine Learning,Statistics - Machine Learning},
%   primaryClass = {cs, stat}
% }

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% url={https://doi.org/10.1007/978-3-662-38527-2_55}
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% @article{mockus1978application,
%   title = {The Application of {{Bayesian}} Methods for Seeking the Extremum},
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% }


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@misc{brochuTutorialBayesianOptimization2010,
      title={A Tutorial on Bayesian Optimization of Expensive Cost Functions, with Application to Active User Modeling and Hierarchical Reinforcement Learning}, 
      author={Eric Brochu and Vlad M. Cora and Nando de Freitas},
      year={2010},
      eprint={1012.2599},
      archivePrefix={arXiv},
      primaryClass={cs.LG}
}



@article{breiman2001,
  title = {Statistical {{Modeling}}: {{The Two Cultures}} (with Comments and a Rejoinder by the Author)},
  author = {Breiman, Leo},
  year = {2001},
  month = aug,
  volume = {16},
  pages = {199--231},
  publisher = {{The Institute of Mathematical Statistics}},
  doi = {10.1214/ss/1009213726},
  fjournal = {Statistical Science},
  journal = {Statistical Science. A Review Journal of the Institute of Mathematical Statistics},
  number = {3}
}





@book{friedman2001elements,
  title = {The Elements of Statistical Learning},
  author = {Friedman, Jerome and Hastie, Trevor and Tibshirani, Robert},
  year = {2009},
  edition = {Second edition},
  doi = {10.1007/978-0-387-84858-7},
  publisher = {{Springer-Verlag New York}}
}

@article{prinzMarkovModelsMolecular2011,
  title = {Markov Models of Molecular Kinetics: {{Generation}} and Validation},
  author = {Prinz, Jan Hendrik and Wu, Hao and Sarich, Marco and Keller, Bettina and Senne, Martin and Held, Martin and Chodera, John D. and Schtte, Christof and No{\'e}, Frank},
  year = {2011},
  volume = {134},
  issn = {00219606},
  doi = {10.1063/1.3565032},
  journal = {Journal of Chemical Physics},
  number = {17},
  pmid = {21548671}
}



@book{harrelRegressionModelingStrategies2015,
  title = {Regression {{Modeling Strategies}}},
  author = {Harrel, Frank},
  year = {2015},
  edition = {Second edition},
  publisher = {{Springer International Publishing}},
  isbn = {978-3-319-19425-7}
}



@misc{gpy2014,
  title = {{{GPy}}: {{A Gaussian}} Process Framework in Python},
  author = {{GPy Authors}},
  year = {2012}, 
  url={https://github.com/SheffieldML/GPy}
}


@article{salvatierProbabilisticProgrammingPython2016a,
  title = {Probabilistic Programming in {{Python}} Using {{PyMC3}}},
  author = {Salvatier, John and Wiecki, Thomas V. and Fonnesbeck, Christopher},
  year = {2016},
  month = apr,
  volume = {2},
  pages = {e55},
  publisher = {{PeerJ Inc.}},
  issn = {2376-5992},
  doi = {10.7717/peerj-cs.55},
  journal = {PeerJ Computer Science},
  language = {en}
}


@article{dalyDummyCodingVs2016,
  title = {Dummy Coding vs Effects Coding for Categorical Variables: {{Clarifications}} and Extensions},
  shorttitle = {Dummy Coding vs Effects Coding for Categorical Variables},
  author = {Daly, Andrew and Dekker, Thijs and Hess, Stephane},
  year = {2016},
  month = dec,
  volume = {21},
  pages = {36--41},
  issn = {1755-5345},
  doi = {10.1016/j.jocm.2016.09.005},
  journal = {Journal of Choice Modelling},
  keywords = {Categorical variables,Discrete choice,Dummy coding,Effects coding},
  language = {en},
  series = {Standalone Technical Contributions in Choice Modelling}
}



@book{gelmanBayesianDataAnalysis2014,
  title = {Bayesian {{Data Analysis}}},
  author = {Gelman, Andrew and Carlin, John B. and Stern, Hal S. and Dunson, David B. and Vehtari, Aki and Rubin, Donald B.},
  year = {2014},
  edition = {Third edition},
  publisher = {{CRC Press}},
  isbn = {978-1-4398-9820-8}
}


@book{rasmussenGaussianProcessesMachine2006,
  title = {Gaussian {{Processes}} for {{Machine Learning}}},
  author = {Rasmussen, Carl Edward and Williams, K. I., Christopher},
  year = {2006},
  edition = {First edition},
  publisher = {{The MIT press}},
  isbn = {0-262-18253-X}
}


@article{polsonHalfCauchyPriorGlobal2012,
  title = {On the {{Half}}-{{Cauchy Prior}} for a {{Global Scale Parameter}}},
  author = {Polson, Nicholas G. and Scott, James G.},
  year = {2012},
  month = dec,
  volume = {7},
  pages = {887--902},
  publisher = {{International Society for Bayesian Analysis}},
  issn = {1936-0975, 1931-6690},
  doi = {10.1214/12-BA730},
  journal = {Bayesian Analysis},
  keywords = {hierarchical models,normal scale mixtures,shrinkage},
  language = {EN},
  mrnumber = {MR3000018},
  number = {4},
  zmnumber = {1330.62148}
}



@article{quinonero-candelaUnifyingViewSparse2005,
  title = {A {{Unifying View}} of {{Sparse Approximate Gaussian Process Regression}}},
  author = {{Qui{\~n}onero-Candela}, Joaquin and Rasmussen, Carl Edward},
  year = {2005},
  volume = {6},
  pages = {1939--1959},
  issn = {ISSN 1533-7928},
  journal = {Journal of Machine Learning Research},
  number = {Dec}, 
  url={https://jmlr.csail.mit.edu/papers/volume6/quinonero-candela05a/quinonero-candela05a.pdf}
}

@incollection{bergstraAlgorithmsHyperParameterOptimizationa,
title = {Algorithms for Hyper-Parameter Optimization},
author = {James S. Bergstra and Bardenet, R\'{e}mi and Bengio, Yoshua and Bal\'{a}zs K\'{e}gl},
booktitle = {Advances in Neural Information Processing Systems 24},
editor = {J. Shawe-Taylor and R. S. Zemel and P. L. Bartlett and F. Pereira and K. Q. Weinberger},
pages = {2546--2554},
year = {2011},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/4443-algorithms-for-hyper-parameter-optimization.pdf}
}



@inproceedings{bergstraMakingScienceModel2013,
  title = {Making a {{Science}} of {{Model Search}}: {{Hyperparameter Optimization}} in {{Hundreds}} of {{Dimensions}} for {{Vision Architectures}}},
  booktitle = {Proceedings of the 30th {{International Conference}} on {{Machine Learning}}},
  author = {Bergstra, James and Yamins, Daniel and Cox, David},
  editor = {Dasgupta, Sanjoy and McAllester, David},
  year = {2013},
  month = jun,
  volume = {28},
  pages = {115--123},
  publisher = {{PMLR}},
  address = {{Atlanta, Georgia, USA}},
  series = {Proceedings of {{Machine Learning Research}}}, 
  url = {http://proceedings.mlr.press/v28/bergstra13.pdf}
}

@article{bowmanQuantitativeComparisonAlternative2013,
  title = {Quantitative Comparison of Alternative Methods for Coarse-Graining Biological Networks},
  author = {Bowman, Gregory R. and Meng, Luming and Huang, Xuhui},
  year = {2013},
  month = jul,
  volume = {139},
  pages = {121905},
  publisher = {{American Institute of Physics}},
  issn = {0021-9606},
  doi = {10.1063/1.4812768},
  journal = {The Journal of Chemical Physics},
  language = {en},
  number = {12}
}

@article{brooksCHARMMBiomolecularSimulation2009,
  title = {{{CHARMM}}: {{The}} Biomolecular Simulation Program},
  shorttitle = {{{CHARMM}}},
  author = {Brooks, B. R. and Brooks, C. L. and Mackerell, A. D. and Nilsson, L. and Petrella, R. J. and Roux, B. and Won, Y. and Archontis, G. and Bartels, C. and Boresch, S. and Caflisch, A. and Caves, L. and Cui, Q. and Dinner, A. R. and Feig, M. and Fischer, S. and Gao, J. and Hodoscek, M. and Im, W. and Kuczera, K. and Lazaridis, T. and Ma, J. and Ovchinnikov, V. and Paci, E. and Pastor, R. W. and Post, C. B. and Pu, J. Z. and Schaefer, M. and Tidor, B. and Venable, R. M. and Woodcock, H. L. and Wu, X. and Yang, W. and York, D. M. and Karplus, M.},
  year = {2009},
  volume = {30},
  pages = {1545--1614},
  issn = {1096-987X},
  doi = {10.1002/jcc.21287},
  copyright = {Copyright  2009 Wiley Periodicals, Inc.},
  journal = {Journal of Computational Chemistry},
  keywords = {biomolecular simulation,biophysical computation,CHARMM program,energy function,molecular dynamics,molecular mechanics,molecular modeling},
  language = {en},
  number = {10}
}

@article{harveyACEMDAcceleratingBiomolecular2009,
  title = {{{ACEMD}}: {{Accelerating Biomolecular Dynamics}} in the {{Microsecond Time Scale}}},
  shorttitle = {{{ACEMD}}},
  author = {Harvey, M. J. and Giupponi, G. and Fabritiis, G. De},
  year = {2009},
  month = jun,
  volume = {5},
  pages = {1632--1639},
  publisher = {{American Chemical Society}},
  issn = {1549-9618},
  doi = {10.1021/ct9000685},
  journal = {Journal of Chemical Theory and Computation},
  number = {6}
}

@article{huangCHARMM36AllatomAdditive2013,
  title = {{{CHARMM36}} All-Atom Additive Protein Force Field: {{Validation}} Based on Comparison to {{NMR}} Data},
  author = {Huang, Jing and Mackerell, Alexander D.},
  year = {2013},
  volume = {34},
  pages = {2135--2145},
  issn = {01928651},
  doi = {10.1002/jcc.23354},
  journal = {Journal of Computational Chemistry},
  keywords = {calmodulin,cold-shock protein A,empirical force field,fatty acid binding protein,G protein B1,J-coupling,lysozyme,molecular mechanics,residual dipolar coupling,ubiquitin},
  number = {25},
  pmid = {23832629}
}

@article{hunterMatplotlib2DGraphics2007,
  title = {Matplotlib: {{A 2D}} Graphics Environment},
  author = {Hunter, J. D.},
  year = {2007},
  volume = {9},
  pages = {90--95},
  publisher = {{IEEE COMPUTER SOC}},
  doi = {10.1109/MCSE.2007.55},
  journal = {Computing in Science \& Engineering},
  number = {3}
}

@article{husicMarkovStateModels2018,
  title = {Markov {{State Models}}: {{From}} an {{Art}} to a {{Science}}},
  shorttitle = {Markov {{State Models}}},
  author = {Husic, Brooke E. and Pande, Vijay S.},
  year = {2018},
  month = feb,
  volume = {140},
  pages = {2386--2396},
  issn = {0002-7863},
  doi = {10.1021/jacs.7b12191},
  journal = {Journal of the American Chemical Society},
  number = {7}
}

@article{husicOptimizedParameterSelection2016,
  title = {Optimized Parameter Selection Reveals Trends in {{Markov}} State Models for Protein Folding},
  author = {Husic, Brooke E. and McGibbon, Robert T. and Sultan, Mohammad M. and Pande, Vijay S.},
  year = {2016},
  month = nov,
  volume = {145},
  pages = {194103},
  issn = {0021-9606},
  doi = {10.1063/1.4967809},
  journal = {The Journal of Chemical Physics},
  number = {19}
}


@article{jonesEfficientGlobalOptimization1998,
  title = {Efficient {{Global Optimization}} of {{Expensive Black}}-{{Box Functions}}},
  author = {Jones, Donald R. and Schonlau, Matthias and Welch, William J.},
  year = {1998},
  month = dec,
  volume = {13},
  pages = {455--492},
  issn = {1573-2916},
  doi = {10.1023/A:1008306431147},
  journal = {Journal of Global Optimization},
  language = {en},
  number = {4}
}


@inproceedings{kluyverJupyterNotebooksPublishing2016,
  title = {Jupyter {{Notebooks}} ? A Publishing Format for Reproducible Computational Workflows},
  booktitle = {Positioning and {{Power}} in {{Academic Publishing}}: {{Players}}, {{Agents}} and {{Agendas}}},
  author = {Kluyver, Thomas and {Ragan-Kelley}, Benjamin and P{\'e}rez, Fernando and Granger, Brian and Bussonnier, Matthias and Frederic, Jonathan and Kelley, Kyle and Hamrick, Jessica and Grout, Jason and Corlay, Sylvain and Ivanov, Paul and Avila, Dami{\'a}n and Abdalla, Safia and Willing, Carol and development {team}, Jupyter},
  editor = {Loizides, Fernando and Scmidt, Birgit},
  year = {2016},
  pages = {87--90},
  publisher = {{IOS Press}}
}

@article{martinez-cantinBayesOptBayesianOptimization2014,
  title = {{{BayesOpt}} : {{A Bayesian Optimization Library}} for {{Nonlinear Optimization}}, {{Experimental Design}} and {{Bandits}}},
  author = {{Martinez-cantin}, Ruben},
  journal = {Journal of Machine Learning Research},
  year = {2014},
  volume = {15},
  pages = {3915--3919},
  keywords = {bayesian optimization,efficient global optimization,gaussian processes,optimization,sequential experimental design,sequential model-based}, 
  url={https://jmlr.csail.mit.edu/papers/volume15/loh14a/loh14a.pdf}
}


@article{mcgibbonMDTrajModernOpen2015,
  title = {{{MDTraj}}: {{A Modern Open Library}} for the {{Analysis}} of {{Molecular Dynamics Trajectories}}},
  author = {McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hern{\'a}ndez, Carlos X. and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
  year = {2015},
  volume = {109},
  pages = {1528--1532},
  doi = {10.1016/j.bpj.2015.08.015},
  journal = {Biophysical Journal},
  number = {8}
}

% @book{mcgibbonOspreyHyperparameterOptimization2016,
%   title = {Osprey: {{Hyperparameter Optimization}} for {{Machine Learning}}},
%   author = {McGibbon, Robert T. and Hern{\'a}ndez, Carlos X. and Harrigan, Matthew P. and Kearnes, Steven and Sultan, Mohammad M. and Jastrzebski, Stanislaw and Husic, Brooke E. and Pande, Vijay S.},
%   year = {2016},
%   month = sep,
%   doi = {10.21105/joss.000341}
% }

@article{mcgibbonVariationalCrossvalidationSlow2015,
  title = {Variational Cross-Validation of Slow Dynamical Modes in Molecular Kinetics},
  author = {McGibbon, Robert T. and Pande, Vijay S.},
  year = {2015},
  volume = {142},
  issn = {00219606},
  doi = {10.1063/1.4916292},
  journal = {Journal of Chemical Physics},
  number = {12},
  pmid = {25833563}
}

@article{mckinneyPandasFoundationalPython2011,
  title = {Pandas: A Foundational {{Python}} Library for Data Analysis and Statistics},
  author = {McKinney, Wes},
  year = {2011},
  volume = {14},
  journal = {Python for High Performance and Scientific Computing}
}

@misc{michaelwaskomMwaskomSeabornV02020,
  title = {Mwaskom/Seaborn:  V0.10.1 ({{April}} 2020)},
  shorttitle = {Mwaskom/Seaborn},
  author = {Michael Waskom and Olga Botvinnik and Joel Ostblom and Maoz Gelbart and Saulius Lukauskas and Paul Hobson and David C Gemperline and Tom Augspurger and Yaroslav Halchenko and John B. Cole and Jordi Warmenhoven and {Julian de Ruiter} and Cameron Pye and Stephan Hoyer and Jake Vanderplas and Santi Villalba and Gero Kunter and Eric Quintero and Pete Bachant and Marcel Martin and Kyle Meyer and Corban Swain and Alistair Miles and Thomas Brunner and Drew O'Kane and Tal Yarkoni and Mike Lee Williams and Constantine Evans and Clark Fitzgerald and Brian},
  year = {2020},
  month = apr,
  doi = {10.5281/zenodo.3767070},
  howpublished = {Zenodo}
}

@article{nuskeMarkovStateModels2017b,
  title = {Markov State Models from Short Non-Equilibrium Simulations\textemdash{{Analysis}} and Correction of Estimation Bias},
  author = {N{\"u}ske, Feliks and Wu, Hao and Prinz, Jan-Hendrik and Wehmeyer, Christoph and Clementi, Cecilia and No{\'e}, Frank},
  year = {2017},
  month = mar,
  volume = {146},
  pages = {094104},
  publisher = {{American Institute of Physics}},
  issn = {0021-9606},
  doi = {10.1063/1.4976518},
  journal = {The Journal of Chemical Physics},
  number = {9}
}

% @article{nuskeVariationalApproachConformational2017,
%   title = {The {{Variational Approach}} to {{Conformational Dynamics}}},
%   author = {N{\"u}ske, Feliks},
%   year = {2017}
% }

@article{nuskeVariationalApproachMolecular2014,
  title = {Variational {{Approach}} to {{Molecular Kinetics}}},
  author = {N{\"u}ske, Feliks and Keller, Bettina G. and {P{\'e}rez-Hern{\'a}ndez}, Guillermo and Mey, Antonia S. J. S. and No{\'e}, Frank},
  year = {2014},
  month = apr,
  volume = {10},
  pages = {1739--1752},
  issn = {1549-9618},
  doi = {10.1021/ct4009156},
  journal = {Journal of Chemical Theory and Computation},
  number = {4}
}

@article{pedregosaScikitlearnMachineLearning2011,
  title = {Scikit-Learn: {{Machine Learning}} in {{Python}}},
  author = {Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P. and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
  year = {2011},
  volume = {12},
  pages = {2825--2830},
  journal = {Journal of Machine Learning Research}
}



@article{salvatierProbabilisticProgrammingPython2016,
  title = {Probabilistic Programming in {{Python}} Using {{PyMC3}}},
  author = {Salvatier, John and Wiecki, Thomas V. and Fonnesbeck, Christopher},
  year = {2016},
  month = apr,
  volume = {2},
  pages = {e55},
  publisher = {{PeerJ}},
  doi = {10.7717/peerj-cs.55},
  journal = {PeerJ Computer Science}
}

@article{schererPyEMMASoftwarePackage2015a,
  title = {{{PyEMMA}} 2: {{A Software Package}} for {{Estimation}}, {{Validation}}, and {{Analysis}} of {{Markov Models}}},
  shorttitle = {{{PyEMMA}} 2},
  author = {Scherer, Martin K. and {Trendelkamp-Schroer}, Benjamin and Paul, Fabian and {P{\'e}rez-Hern{\'a}ndez}, Guillermo and Hoffmann, Moritz and Plattner, Nuria and Wehmeyer, Christoph and Prinz, Jan-Hendrik and No{\'e}, Frank},
  year = {2015},
  month = oct,
  volume = {11},
  pages = {5525--5542},
  issn = {1549-9618},
  doi = {10.1021/acs.jctc.5b00743},
  journal = {Journal of Chemical Theory and Computation}
}


@article{shahriariTakingHumanOut2016,
  title = {Taking the {{Human Out}} of the {{Loop}}: {{A Review}} of {{Bayesian Optimization}}},
  shorttitle = {Taking the {{Human Out}} of the {{Loop}}},
  author = {Shahriari, Bobak and Swersky, Kevin and Wang, Ziyu and Adams, Ryan P. and {de Freitas}, Nando},
  year = {2016},
  month = jan,
  volume = {104},
  pages = {148--175},
  issn = {1558-2256},
  doi = {10.1109/JPROC.2015.2494218},
  journal = {Proceedings of the IEEE},
  keywords = {Bayes methods,Bayesian optimization,Big data,Big Data,Big data application,decision making,Decision making,design of experiments,Design of experiments,Genomes,genomic medicine,human productivity,large-scale heterogeneous computing,Linear programming,massive complex software system,optimisation,optimization,Optimization,product quality,response surface methodology,Statistical analysis,statistical learning,storage allocation,storage architecture},
  number = {1}
}


@misc{snoekInputWarpingBayesian2014a,
      title={Input Warping for Bayesian Optimization of Non-stationary Functions}, 
      author={Jasper Snoek and Kevin Swersky and Richard S. Zemel and Ryan P. Adams},
      year={2014},
      eprint={1402.0929},
      archivePrefix={arXiv},
      primaryClass={stat.ML}
}
% @article{snoekInputWarpingBayesian2014a,
%   title = {Input {{Warping}} for {{Bayesian Optimization}} of {{Non}}-Stationary {{Functions}}},
%   author = {Snoek, Jasper and Swersky, Kevin and Zemel, Richard S. and Adams, Ryan P.},
%   year = {2014},
%   month = jun,
%   archivePrefix = {arXiv},
%   eprint = {1402.0929},
%   eprinttype = {arxiv},
%   journal = {arXiv:1402.0929 [cs, stat]},
%   keywords = {Computer Science - Machine Learning,Statistics - Machine Learning},
%   primaryClass = {cs, stat}
% }


@incollection{NIPS2012_4522,
  title = {Practical Bayesian Optimization of Machine Learning Algorithms},
  booktitle = {Advances in Neural Information Processing Systems 25},
  author = {Snoek, Jasper and Larochelle, Hugo and Adams, Ryan P},
  editor = {Pereira, F. and Burges, C. J. C. and Bottou, L. and Weinberger, K. Q.},
  year = {2012},
  pages = {2951--2959},
  publisher = {{Curran Associates, Inc.}}, 
  url = {https://papers.nips.cc/paper/4522-practical-bayesian-optimization-of-machine-learning-algorithms.pdf}
}


@article{thorntonAutoWEKACombinedSelection2013,
  title = {Auto-{{WEKA}} : {{Combined Selection}} and {{Hyperparameter Optimization}} of {{Classification Algorithms}}},
  author = {Thornton, Chris and {Leyton-brown}, Kevin},
  year = {2013},
  pages = {847--855},
  keywords = {hyperparameter optimization,model selection,weka}
}

@article{virtanenSciPyFundamentalAlgorithms2020,
  title = {{{SciPy}} 1.0: {{Fundamental Algorithms}} for {{Scientific Computing}} in {{Python}}},
  author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and {van der Walt}, St{\'e}fan J. and Brett, Matthew and Wilson, Joshua and Jarrod Millman, K. and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, CJ and Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and {Vand erPlas}, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R and Archibald, Anne M. and Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and {van Mulbregt}, Paul and Contributors, SciPy 1. 0},
  year = {2020},
  volume = {17},
  pages = {261--272},
  doi = {10.1038/s41592-019-0686-2},
  journal = {Nature Methods}
}

@article{waltNumPyArrayStructure2011,
  title = {The {{NumPy Array}}: {{A Structure}} for {{Efficient Numerical Computation}}},
  author = {van der Walt, S. and Colbert, S. C. and Varoquaux, G.},
  year = {2011},
  volume = {13},
  pages = {22--30},
  journal = {Computing in Science Engineering},
  number = {2}
}

@article{wehmeyerTimelaggedAutoencodersDeep2018a,
  title = {Time-Lagged Autoencoders: {{Deep}} Learning of Slow Collective Variables for Molecular Kinetics},
  shorttitle = {Time-Lagged Autoencoders},
  author = {Wehmeyer, Christoph and No{\'e}, Frank},
  year = {2018},
  month = jun,
  volume = {148},
  pages = {241703},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/1.5011399},
  journal = {The Journal of Chemical Physics},
  language = {en},
  number = {24}
}


%%% WATER PAPER

% 1
@article{Nascimento2010,
  title = {Does Viscosity Describe the Kinetic Barrier for Crystal Growth from the Liquidus to the Glass Transition?},
  author = {Nascimento, Marcio Luis Ferreira and Dutra Zanotto, Edgar},
  year = {2010},
  volume = {133},
  issn = {00219606},
  doi = {10.1063/1.3490793},
  isbn = {00219606},
  journal = {Journal of Chemical Physics},
  number = {17},
  pmid = {21054059}
}

% 2 & 49
@article{Mikhailov2009a,
  title = {Amorphous and Crystalline Aerosol Particles Interacting with Water Vapor: Conceptual Framework and Experimental Evidence for Restructuring, Phase Transitions and Kinetic Limitations},
  author = {Mikhailov, E. and Vlasenko, S. and Martin, S. T. and Koop, T. and P{\"o}schl, U.},
  year = {2009},
  month = dec,
  volume = {9},
  pages = {9491--9522},
  issn = {1680-7324},
  doi = {10.5194/acp-9-9491-2009},
  journal = {Atmospheric Chemistry and Physics},
  number = {24}
}

% 3
@article{Koop2011,
  title = {Glass Transition and Phase State of Organic Compounds: Dependency on Molecular Properties and Implications for Secondary Organic Aerosols in the Atmosphere.},
  author = {Koop, Thomas and Bookhold, Johannes and Shiraiwa, Manabu and P{\"o}schl, Ulrich},
  year = {2011},
  month = nov,
  volume = {13},
  pages = {19238--55},
  issn = {1463-9084},
  doi = {10.1039/c1cp22617g},
  journal = {Physical Chemistry Chemical Physics},
  keywords = {Aerosols,Aerosols: chemistry,Atmosphere,Atmosphere: chemistry,Glass,Glass: chemistry,Organic Chemicals,Organic Chemicals: chemistry,Oxidation-Reduction,Particle Size,Phase Transition,Temperature,Viscosity,Water,Water: chemistry},
  number = {43},
  pmid = {21993380}
}

% 4
@book{hidy1984aerosols,
  title = {Aerosols, an Industrial and Environmental Science},
  author = {Hidy, G.M.},
  year = {1984},
  publisher = {{Academic Press}},
  isbn = {978-0-12-347260-1},
  lccn = {84002743}
}

% 5
@article{Hancock1997,
  title = {Characteristics and Significance of the Amorphous State in Pharmaceutical Systems},
  author = {Hancock, Bruno C. and Zografi, George},
  year = {1997},
  volume = {86},
  pages = {1--12},
  issn = {00223549},
  doi = {10.1021/js9601896},
  isbn = {1520-6017},
  journal = {Journal of Pharmaceutical Sciences},
  number = {1},
  pmid = {9002452}
}

% 6
@article{Lorenz2011,
  title = {Nanosized Aerosols from Consumer Sprays: {{Experimental}} Analysis and Exposure Modeling for Four Commercial Products},
  author = {Lorenz, Christiane and Hagendorfer, Harald and Von Goetz, Natalie and Kaegi, Ralf and Gehrig, Robert and Ulrich, Andrea and Scheringer, Martin and Hungerb{\"u}hler, Konrad},
  year = {2011},
  volume = {13},
  pages = {3377--3391},
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  doi = {10.1007/s11051-011-0256-8},
  isbn = {1388-0764},
  journal = {Journal of Nanoparticle Research},
  number = {8}
}

% 7
@article{Haddrell2014,
  title = {Dynamics of Aerosol Size during Inhalation: {{Hygroscopic}} Growth of Commercial Nebulizer Formulations},
  author = {Haddrell, Allen E. and Davies, James F. and Miles, Rachael E.H. and Reid, Jonathan P. and Dailey, Lea Ann and Murnane, Darragh},
  year = {2014},
  volume = {463},
  pages = {50--61},
  publisher = {{Elsevier B.V.}},
  issn = {03785173},
  doi = {10.1016/j.ijpharm.2013.12.048},
  isbn = {0378-5173},
  journal = {International Journal of Pharmaceutics},
  number = {1},
  pmid = {24406674}
}

% 8
@article{Shiraiwa2012a,
  title = {Equilibration Timescale of Atmospheric Secondary Organic Aerosol Partitioning},
  author = {Shiraiwa, Manabu and Seinfeld, John H.},
  year = {2012},
  month = dec,
  volume = {39},
  issn = {0094-8276},
  doi = {10.1029/2012GL054008},
  journal = {Geophysical Research Letters},
  number = {24}
}

% 9
@article{mai2015under,
  title = {Under What Conditions Can Equilibrium Gas\textendash Particle Partitioning Be Expected to Hold in the Atmosphere?},
  author = {Mai, Huajun and Shiraiwa, Manabu and Flagan, Richard C and Seinfeld, John H},
  year = {2015},
  volume = {49},
  pages = {11485--11491},
  publisher = {{ACS Publications}},
  journal = {Environmental science \& technology},
  number = {19}
}

% 10
@article{Maclean2017,
  title = {Mixing Times of Organic Molecules within Secondary Organic Aerosol Particles: A Global Planetary Boundary Layer Perspective},
  author = {Maclean, Adrian M. and Butenhoff, Christopher L. and Grayson, James W. and Barsanti, Kelley and Jimenez, Jose L. and Bertram, Allan K.},
  year = {2017},
  month = nov,
  volume = {17},
  pages = {13037--13048},
  issn = {1680-7324},
  doi = {10.5194/acp-17-13037-2017},
  journal = {Atmospheric Chemistry and Physics},
  number = {21}
}

% 11 & 16
@article{powerTransitionLiquidSolidlike2013,
  title = {The Transition from Liquid to Solid-like Behaviour in Ultrahigh Viscosity Aerosol Particles},
  author = {Power, R. M. and Simpson, S. H. and Reid, J. P. and Hudson, A. J.},
  year = {2013},
  month = may,
  volume = {4},
  pages = {2597--2604},
  publisher = {{The Royal Society of Chemistry}},
  issn = {2041-6539},
  doi = {10.1039/C3SC50682G},
  journal = {Chemical Science},
  language = {en},
  number = {6}
}

% 12
@article{chenStokesEinsteinRelationSupercooled2006,
  title = {Stokes-{{Einstein Relation}} in {{Supercooled Aqueous Solutions}} of {{Glycerol}}},
  author = {Chen, Bo and Sigmund, E. E. and Halperin, W. P.},
  year = {2006},
  month = apr,
  volume = {96},
  pages = {145502},
  publisher = {{American Physical Society}},
  doi = {10.1103/PhysRevLett.96.145502},
  journal = {Physical Review Letters},
  number = {14}
}

% 13
@article{Price2014,
  title = {Quantifying Water Diffusion in High-Viscosity and Glassy Aqueous Solutions Using a {{Raman}} Isotope Tracer Method},
  author = {Price, H. C. and Murray, B. J. and Mattsson, J. and O'Sullivan, D. and Wilson, T. W. and Baustian, K. J. and Benning, L. G.},
  year = {2014},
  month = apr,
  volume = {14},
  pages = {3817--3830},
  issn = {1680-7324},
  doi = {10.5194/acp-14-3817-2014},
  journal = {Atmospheric Chemistry and Physics},
  number = {8}
}

%14
@article{Molinero2005,
  title = {Microscopic Mechanism of Water Diffusion in Glucose Glasses},
  author = {Molinero, Valeria and Goddard, William},
  year = {2005},
  month = jul,
  volume = {95},
  pages = {045701},
  issn = {0031-9007},
  doi = {10.1103/PhysRevLett.95.045701},
  journal = {Physical Review Letters},
  number = {4}
}

%15
@article{Bones2012,
  title = {Comparing the Mechanism of Water Condensation and Evaporation in Glassy Aerosol.},
  author = {Bones, David L and Reid, Jonathan P and Lienhard, Daniel M and Krieger, Ulrich K},
  year = {2012},
  month = jul,
  volume = {109},
  pages = {11613--8},
  issn = {1091-6490},
  doi = {10.1073/pnas.1200691109},
  journal = {Proc. Nat. Acad. Sci.},
  keywords = {Aerosols,Aerosols: chemistry,Atmosphere,Chemical,Kinetics,Models,Particle Size,Phase Transition,Raman,Sodium Chloride,Sodium Chloride: chemistry,Spectrum Analysis,Sucrose,Sucrose: chemistry,Viscosity,Water,Water: chemistry},
  number = {29},
  pmid = {22753520}
}

%17
@article{Price2015,
  title = {Water Diffusion in Atmospherically Relevant Alpha-Pinene Secondary Organic Material},
  author = {Price, Hannah C. and Mattsson, Johan and Zhang, Yue and Bertram, Allan K. and Davies, James F. and Grayson, James W. and Martin, Scot T. and O'Sullivan, Daniel and Reid, Jonathan P. and Rickards, Andrew M. J. and Murray, Benjamin J.},
  year = {2015},
  volume = {6},
  pages = {4876--4883},
  issn = {2041-6520},
  doi = {10.1039/C5SC00685F},
  journal = {Chemical Science},
  number = {8}
}

% 18
@article{Chenyakin2017,
  title = {Diffusion Coefficients of Organic Molecules in Sucrose-Water Solutions and Comparison with {{Stokes}}-{{Einstein}} Predictions},
  author = {Chenyakin, Yuri and Ullmann, Dagny A. and Evoy, Erin and {Renbaum-Wolff}, Lindsay and Kamal, Saeid and Bertram, Allan K.},
  year = {2017},
  volume = {17},
  pages = {2423--2435},
  issn = {1680-7375},
  doi = {10.5194/acp-2016-740},
  journal = {Atmospheric Chemistry and Physics}
}

% 19
@article{Harris2009,
  title = {The Fractional {{Stokes}}-{{Einstein}} Equation: {{Application}} to {{Lennard}}-{{Jones}}, Molecular, and Ionic Liquids},
  author = {Harris, Kenneth R.},
  year = {2009},
  volume = {131},
  pages = {054503},
  issn = {00219606},
  doi = {10.1063/1.3183951},
  isbn = {0021-9606},
  journal = {Journal of Chemical Physics},
  number = {5},
  pmid = {19673570}
}

% 20
@article{price2016sucrose,
  title = {Sucrose Diffusion in Aqueous Solution},
  author = {Price, Hannah C and Mattsson, Johan and Murray, Benjamin J},
  year = {2016},
  volume = {18},
  pages = {19207--19216},
  publisher = {{Royal Society of Chemistry}},
  journal = {Physical Chemistry Chemical Physics},
  number = {28}, 
  doi={10.1039/C6CP03238A}
}

% 21
@article{Fernandez-Alonso2007,
  title = {Observation of Fractional {{Stokes}}-{{Einstein}} Behavior in the Simplest Hydrogen-Bonded Liquid},
  author = {{Fernandez-Alonso}, F. and Bermejo, F. J. and McLain, S. E. and Turner, J. F.C. and Molaison, J. J. and Herwig, K. W.},
  year = {2007},
  volume = {98},
  pages = {077801},
  issn = {00319007},
  doi = {10.1103/PhysRevLett.98.077801},
  journal = {Physical Review Letters},
  number = {7},
  pmid = {244250300065}
}

% 22
@article{Shrestha2015,
  title = {On Surface Order and Disorder of {{alpha}}-{{Pinene}}-{{Derived}} Secondary Organic Material},
  author = {Shrestha, Mona and Zhang, Yue and Upshur, Mary Alice and Liu, Pengfei and Blair, Sandra L. and Wang, Hong-fei and Nizkorodov, Sergey A. and Thomson, Regan J. and Martin, Scot T. and Geiger, Franz M.},
  year = {2015},
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  pages = {4609--4617},
  issn = {1089-5639},
  doi = {10.1021/jp510780e},
  journal = {The Journal of Physical Chemistry A},
  number = {19}
}

% 23
@article{Chen2006a,
  title = {Breakdown of the {{Stokes}}-{{Einstein}} Relation in Supercooled Water},
  author = {Kumar, P.},
  year = {2006},
  volume = {103},
  pages = {12955--12956},
  issn = {0027-8424},
  doi = {10.1073/pnas.0605880103},
  isbn = {0027-8424},
  journal = {Proceedings of the National Academy of Sciences},
  number = {35},
  pmid = {16920792}
}

% 24
@article{Gonzalez2015,
  title = {Diffusion-Viscosity Decoupling in Supercooled Glycerol Aqueous Solutions},
  author = {Gonz{\'a}lez, Jos{\'e} A. Trejo and Longinotti, M. Paula and Corti, Horacio R.},
  year = {2015},
  volume = {119},
  pages = {257--262},
  doi = {10.1021/jp509055v},
  journal = {Journal of Physical Chemistry B},
  number = {1}
}

% 25
@article{Bastelberger2017a,
  title = {Diffusivity Measurements of Volatile Organics in Levitated Viscous Aerosol Particles},
  author = {Bastelberger, Sandra and Krieger, Ulrich K. and Luo, Beiping and Peter, Thomas},
  year = {2017},
  month = jul,
  volume = {17},
  pages = {8453--8471},
  issn = {1680-7324},
  doi = {10.5194/acp-17-8453-2017},
  journal = {Atmospheric Chemistry and Physics},
  number = {13}
}

% 26
@article{rothfuss2017influence,
  title = {Influence of Functional Groups on the Viscosity of Organic Aerosol},
  author = {Rothfuss, Nicholas E and Petters, Markus D},
  year = {2017},
  volume = {51},
  pages = {271--279},
  publisher = {{ACS Publications}},
  journal = {Environmental science \& technology},
  number = {1}, 
  doi={10.1021/acs.est.6b04478}
}

% 27
@article{Zhao2009,
  title = {Mesoporous Silica Nanoparticle-Based Double Drug Delivery System for Glucose-Responsive Controlled Release of Insulin and Cyclic {{AMP}}},
  author = {Zhao, Yannan and Trewyn, Brian G. and Slowing, Igor I. and Lin, Victor S.Y.},
  year = {2009},
  volume = {131},
  pages = {8398--8400},
  issn = {00027863},
  doi = {10.1021/ja901831u},
  isbn = {0002-7863},
  journal = {Journal of the American Chemical Society},
  number = {24},
  pmid = {19476380}
}

% 28
@article{Sinha2001,
  title = {Polysaccharides in Colon-Specific Drug Delivery},
  author = {Sinha, V. R. and Kumria, Rachna},
  year = {2001},
  volume = {224},
  pages = {19--38},
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  isbn = {0378-5173},
  journal = {International Journal of Pharmaceutics},
  number = {1-2},
  pmid = {11472812}
}

% 29
@article{Sastry2000,
  title = {Recent Technological Advances in Oral Drug Delivery - a Review.},
  author = {Sastry, Sv and Nyshadham, Jr and Fix, Ja},
  year = {2000},
  volume = {3},
  pages = {138--145},
  issn = {1461-5347},
  doi = {10.1016/S1461-5347(00)00247-9},
  isbn = {1461-5347},
  journal = {Pharmaceutical science \& technology today},
  number = {4},
  pmid = {10754543}
}

% 30
@article{Andya1999,
  title = {The Effect of Formulation Excipients on Protein Stability and Aerosol Performance of Spray-Dried Powders of a Recombinant Humanized Anti-{{IgE}} Monoclonal Antibody},
  author = {Andya, James D. and Maa, Yuh Fun and Costantino, Henry R. and Nguyen, Phuong Anh and Dasovich, Nancy and Sweeney, Theresa D. and Hsu, Chung C. and Shire, Steven J.},
  year = {1999},
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  doi = {10.1023/A:1018805232453},
  isbn = {0724-8741 (Print)\textbackslash r0724-8741 (Linking)},
  journal = {Pharmaceutical Research},
  number = {3},
  pmid = {10213364}
}

% 31
@article{Vehring2008,
  title = {Pharmaceutical Particle Engineering via Spray Drying},
  author = {Vehring, Reinhard},
  year = {2008},
  volume = {25},
  pages = {999--1022},
  issn = {07248741},
  doi = {10.1007/s11095-007-9475-1},
  isbn = {0724-8741 (Print)\textbackslash r0724-8741 (Linking)},
  journal = {Pharmaceutical Research},
  number = {5},
  pmid = {18040761}
}


% 32
@article{Mosen2004,
  title = {Particle Formation and Capture during Spray Drying of Inhalable Particles},
  author = {Mos{\'e}n, Kristina and B{\"a}ckstr{\"o}m, Kjell and Thalberg, Kyrre and Schaefer, Torben and Kristensen, Henning G. and Axelsson, Anders},
  year = {2004},
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  doi = {10.1081/PDT-200035795},
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  journal = {Pharmaceutical Development and Technology},
  number = {4},
  pmid = {15581077}
}

% 33
@article{Liu2006,
  title = {Glass Transition and Enthalpy Relaxation of Amorphous Food Saccharides: {{A}} Review},
  author = {Liu, Yeting and Bhandari, Bhesh and Zhou, Weibiao},
  year = {2006},
  volume = {54},
  pages = {5701--5717},
  issn = {00218561},
  doi = {10.1021/jf060188r},
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  keywords = {Amorphous solid,DSC,Enthalpy relaxation,Food saccharides,Glass transition},
  number = {16},
  pmid = {16881667}
}

% 34
@article{Zobrist2008,
  title = {Do Atmospheric Aerosols Form Glasses?},
  author = {Zobrist, B. and Marcolli, C. and a. Pedernera, D. and Koop, T.},
  year = {2008},
  volume = {8},
  pages = {5221--5244},
  issn = {1680-7324},
  doi = {10.5194/acp-8-5221-2008},
  isbn = {1680-7316},
  journal = {Atmospheric Chemistry and Physics},
  number = {17}
}

% 35
@article{Reid2018,
  title = {The Viscosity of Atmospherically Relevant Organic Particles},
  author = {Reid, Jonathan P. and Bertram, Allan K. and Topping, David O. and Laskin, Alexander and Martin, Scot T. and Petters, Markus D. and Pope, Francis D. and Rovelli, Grazia},
  year = {2018},
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  pages = {956},
  issn = {2041-1723},
  doi = {10.1038/s41467-018-03027-z},
  journal = {Nature Communications},
  number = {1}
}

% 36
@article{Song2016a,
  title = {Measurements and Predictions of Binary Component Aerosol Particle Viscosity},
  author = {Song, Young Chul and Haddrell, Allen E. and Bzdek, Bryan R. and Reid, Jonathan P. and Bannan, Thomas and Topping, David O. and Percival, Carl and Cai, Chen},
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  month = oct,
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  issn = {1089-5639},
  doi = {10.1021/acs.jpca.6b07835},
  journal = {The Journal of Physical Chemistry A},
  number = {41}
}

% 37
@article{Decesari2006,
  title = {Characterization of the Organic Composition of Aerosols from {{Rond\^onia}}, {{Brazil}}, during the {{LBA}}-{{SMOCC}} 2002 Experiment and Its Representation through Model Compounds},
  author = {Decesari, S. and Fuzzi, S. and Facchini, M. C. and Mircea, M. and Emblico, L. and Cavalli, F. and Maenhaut, W. and Chi, X. and Schkolnik, G. and Falkovich, A. and Rudich, Y. and Claeys, M. and Pashynska, V. and Vas, G. and Kourtchev, I. and Vermeylen, R. and Hoffer, A. and Andreae, M. O. and Tagliavini, E. and Moretti, F. and Artaxo, P.},
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  doi = {10.5194/acp-6-375-2006},
  isbn = {1680-7324},
  journal = {Atmospheric Chemistry and Physics},
  number = {2}
}

% 38
@article{Ingram2017,
  title = {Characterising the Evaporation Kinetics of Water and Semi-Volatile Organic Compounds from Viscous Multicomponent Organic Aerosol Particles},
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  volume = {19},
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  issn = {1463-9076},
  doi = {10.1039/C7CP05172G},
  journal = {Physical Chemistry Chemical Physics},
  number = {47}
}

% 39
@article{Rickards2015,
  title = {Variabilities and Uncertainties in Characterising Water Transport Kinetics in Glassy and Ultraviscous Aerosol},
  author = {Rickards, Andrew M. J. and Song, Young-Chul and Miles, Rachael E. H. and Preston, Thomas C. and Reid, Jonathan P.},
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  doi = {10.1039/C4CP05383D},
  journal = {Physical Chemistry Chemical Physics},
  number = {15}
}

% 40
@article{Tong2011,
  title = {Measurements of the Timescales for the Mass Transfer of Water in Glassy Aerosol at Low Relative Humidity and Ambient Temperature},
  author = {Tong, H. J. and Reid, J. P. and Bones, D. L. and Luo, B. P. and Krieger, U. K.},
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  doi = {10.5194/acp-11-4739-2011},
  isbn = {1680-7316},
  journal = {Atmospheric Chemistry and Physics},
  number = {10}
}

% 41
@article{lienhard2015viscous,
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  publisher = {{Copernicus}},
  journal = {Atmospheric Chemistry and Physics},
  number = {23}, 
  doi={10.5194/acp-15-13599-2015}
}

% 42
@article{Liu2015,
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}

% 43
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}

%44
@article{Shiraiwa2011,
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%45
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  journal = {Macromolecules},
  number = {11}
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%46
@article{Marshall2016,
  title = {Diffusion and Reactivity in Ultraviscous Aerosol and the Correlation with Particle Viscosity},
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%47
@article{Chen2013,
  title = {Modeling Organic Aerosol from the Oxidation of {{$\alpha$}}-Pinene in a {{Potential Aerosol Mass}} ({{PAM}}) Chamber},
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  number = {9}
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%48
@article{zhang2015formation,
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%50
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%51
@article{Jia2018,
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% 52
@article{huang2018alpha,
  title={{$\alpha$}-Pinene secondary organic aerosol at low temperature: chemical composition and implications for particle viscosity},
  author={Huang, Wei and Saathoff, Harald and Pajunoja, Aki and Shen, Xiaoli and Naumann, Karl-Heinz and Wagner, Robert and Virtanen, Annele and Leisner, Thomas and Mohr, Claudia},
  journal={Atmospheric Chemistry and Physics},
  volume={18},
  number={4},
  pages={2883--2898},
  year={2018},
  publisher={Copernicus GmbH}, 
  doi={10.5194/acp-18-2883-2018}
}

%53
@article{Kourtchev2016,
  title = {Enhanced {{Volatile Organic Compounds}} Emissions and Organic Aerosol Mass Increase the Oligomer Content of Atmospheric Aerosols},
  author = {Kourtchev, Ivan and Giorio, Chiara and Manninen, Antti and Wilson, Eoin and Mahon, Brendan and Aalto, Juho and Kajos, Maija and Venables, Dean and Ruuskanen, Taina and Levula, Janne and Loponen, Matti and Connors, Sarah and Harris, Neil and Zhao, Defeng and {Kiendler-Scharr}, Astrid and Mentel, Thomas and Rudich, Yinon and Hallquist, Mattias and Doussin, Jean-Francois and Maenhaut, Willy and B{\"a}ck, Jaana and Pet{\"a}j{\"a}, Tuukka and Wenger, John and Kulmala, Markku and Kalberer, Markus},
  year = {2016},
  month = dec,
  volume = {6},
  pages = {35038},
  issn = {2045-2322},
  doi = {10.1038/srep35038},
  journal = {Scientific Reports},
  number = {1}
}

% WAT SI

% 1
@article{powerProbingMicrorheologicalProperties2014,
  title = {Probing the Micro-Rheological Properties of Aerosol Particles Using Optical Tweezers},
  author = {Power, Rory M. and Reid, Jonathan P.},
  year = {2014},
  month = jul,
  volume = {77},
  pages = {074601},
  publisher = {{IOP Publishing}},
  issn = {0034-4885},
  doi = {10.1088/0034-4885/77/7/074601},
  journal = {Reports on Progress in Physics},
  language = {en},
  number = {7}
}

% 2
% Song2016a

% 3
@article{prestonAccurateEfficientDetermination2013,
  title = {Accurate and Efficient Determination of the Radius, Refractive Index, and Dispersion of Weakly Absorbing Spherical Particle Using Whispering Gallery Modes},
  author = {Preston, Thomas C. and Reid, Jonathan P.},
  year = {2013},
  month = aug,
  volume = {30},
  pages = {2113--2122},
  publisher = {{Optical Society of America}},
  issn = {1520-8540},
  doi = {10.1364/JOSAB.30.002113},
  copyright = {\&\#169; 2013 Optical Society of America},
  journal = {Journal of the Optical Society of America B},
  keywords = {Fundamental processes,Raman scattering,Raman spectroscopy,Refractive index,Total internal reflection,Whispering gallery modes},
  language = {EN},
  number = {8}
}

% 4
@article{reidSpectroscopicStudiesSize2007,
  title = {Spectroscopic Studies of the Size and Composition of Single Aerosol Droplets},
  author = {Reid, Jonathan P. and Meresman, Helena and Mitchem, Laura and Symes{\textdagger}, Rachel},
  year = {2007},
  month = jan,
  volume = {26},
  pages = {139--192},
  publisher = {{Taylor \& Francis}},
  issn = {0144-235X},
  doi = {10.1080/01442350601081899},
  annotation = {\_eprint: https://doi.org/10.1080/01442350601081899},
  journal = {International Reviews in Physical Chemistry},
  number = {1}
}

% 5
@article{reidLaserProbingSingleaerosol2006,
  title = {Laser Probing of Single-Aerosol Droplet Dynamics},
  author = {Reid, Jonathan P. and Mitchem, Laura},
  year = {2006},
  month = apr,
  volume = {57},
  pages = {245--271},
  publisher = {{Annual Reviews}},
  issn = {0066-426X},
  doi = {10.1146/annurev.physchem.57.032905.104621},
  journal = {Annual Review of Physical Chemistry},
  number = {1}
}

% 6
% Rickards2015

% 7
% Tong2011

% 8
@article{chenLiteratureReviewSupplemented2000,
  title = {Literature {{Review}}: {{Supplemented Phase Diagram}} of the {{Trehalose}}\textendash{{Water Binary Mixture}}},
  shorttitle = {Literature {{Review}}},
  author = {Chen, Tani and Fowler, Alex and Toner, Mehmet},
  year = {2000},
  month = may,
  volume = {40},
  pages = {277--282},
  issn = {0011-2240},
  doi = {10.1006/cryo.2000.2244},
  journal = {Cryobiology},
  keywords = {anhydrobiosis,binary mixture,cryoprotectant,freeze-drying,glass transition,maximal freeze concentration,melting point,supplemented phase diagram,trehalose,water},
  language = {en},
  number = {3}
}

% 9
@article{fosterGlassTransitionRelated2006,
  title = {Glass Transition Related Cohesion of Amorphous Sugar Powders},
  author = {Foster, Kylie D. and Bronlund, John E. and Paterson, A. H. J. (Tony)},
  year = {2006},
  month = dec,
  volume = {77},
  pages = {997--1006},
  issn = {0260-8774},
  doi = {10.1016/j.jfoodeng.2005.08.028},
  journal = {Journal of Food Engineering},
  keywords = {Amorphous sugar,Caking,Food powders,Glass transition temperature,Stickiness},
  language = {en},
  number = {4}
}

% 10
@article{luTimescalesWaterTransport2014,
  title = {Timescales of Water Transport in Viscous Aerosol: Measurements on Sub-Micron Particles and Dependence on Conditioning History},
  shorttitle = {Timescales of Water Transport in Viscous Aerosol},
  author = {Lu, Jessica W. and Rickards, Andrew M. J. and Walker, Jim S. and Knox, Kerry J. and Miles, Rachael E. H. and Reid, Jonathan P. and Signorell, Ruth},
  year = {2014},
  month = may,
  volume = {16},
  pages = {9819--9830},
  publisher = {{The Royal Society of Chemistry}},
  issn = {1463-9084},
  doi = {10.1039/C3CP54233E},
  journal = {Physical Chemistry Chemical Physics},
  language = {en},
  number = {21}
}

% 11
@article{omearaRateEquilibrationViscous2016,
  title = {The Rate of Equilibration of Viscous Aerosol Particles},
  author = {O'Meara, Simon and Topping, David O. and McFiggans, Gordon},
  year = {2016},
  month = apr,
  volume = {16},
  pages = {5299--5313},
  publisher = {{Copernicus GmbH}},
  issn = {1680-7316},
  doi = {10.5194/acp-16-5299-2016},
  journal = {Atmospheric Chemistry and Physics},
  language = {English},
  number = {8}
}

%12
% Ingram2017

% 13
% powerTransitionLiquidSolidlike2013

% 14
@article{abascalGeneralPurposeModel2005,
  title = {A General Purpose Model for the Condensed Phases of Water: {{TIP4P}}/2005},
  shorttitle = {A General Purpose Model for the Condensed Phases of Water},
  author = {Abascal, J. L. F. and Vega, C.},
  year = {2005},
  month = dec,
  volume = {123},
  pages = {234505},
  publisher = {{American Institute of Physics}},
  issn = {0021-9606},
  doi = {10.1063/1.2121687},
  journal = {The Journal of Chemical Physics},
  number = {23}
}

%15
@article{oostenbrinkBiomolecularForceField2004,
  title = {A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: {{The GROMOS}} Force-Field Parameter Sets {{53A5}} and {{53A6}}},
  shorttitle = {A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation},
  author = {Oostenbrink, Chris and Villa, Alessandra and Mark, Alan E. and Gunsteren, Wilfred F. Van},
  year = {2004},
  volume = {25},
  pages = {1656--1676},
  issn = {1096-987X},
  doi = {10.1002/jcc.20090},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20090},
  copyright = {Copyright  2004 Wiley Periodicals, Inc.},
  journal = {Journal of Computational Chemistry},
  keywords = {force-field parameterization,free-energy calculation,GROMOS force field,hydration,solvation},
  language = {en},
  number = {13}
}

%16
@article{koziaraTestingValidationAutomated2014,
  title = {Testing and Validation of the {{Automated Topology Builder}} ({{ATB}}) Version 2.0: Prediction of Hydration Free Enthalpies},
  shorttitle = {Testing and Validation of the {{Automated Topology Builder}} ({{ATB}}) Version 2.0},
  author = {Koziara, Katarzyna B. and Stroet, Martin and Malde, Alpeshkumar K. and Mark, Alan E.},
  year = {2014},
  month = mar,
  volume = {28},
  pages = {221--233},
  issn = {1573-4951},
  doi = {10.1007/s10822-014-9713-7},
  journal = {Journal of Computer-Aided Molecular Design},
  language = {en},
  number = {3}
}

%17
@article{maldeAutomatedForceField2011,
  title = {An {{Automated Force Field Topology Builder}} ({{ATB}}) and {{Repository}}: {{Version}} 1.0},
  shorttitle = {An {{Automated Force Field Topology Builder}} ({{ATB}}) and {{Repository}}},
  author = {Malde, Alpeshkumar K. and Zuo, Le and Breeze, Matthew and Stroet, Martin and Poger, David and Nair, Pramod C. and Oostenbrink, Chris and Mark, Alan E.},
  year = {2011},
  month = dec,
  volume = {7},
  pages = {4026--4037},
  publisher = {{American Chemical Society}},
  issn = {1549-9618},
  doi = {10.1021/ct200196m},
  journal = {Journal of Chemical Theory and Computation},
  number = {12}
}

%18
@article{schmidDefinitionTestingGROMOS2011,
  title = {Definition and Testing of the {{GROMOS}} Force-Field Versions {{54A7}} and {{54B7}}},
  author = {Schmid, Nathan and Eichenberger, Andreas P. and Choutko, Alexandra and Riniker, Sereina and Winger, Moritz and Mark, Alan E. and {van Gunsteren}, Wilfred F.},
  year = {2011},
  month = apr,
  volume = {40},
  pages = {843},
  issn = {1432-1017},
  doi = {10.1007/s00249-011-0700-9},
  journal = {European Biophysics Journal},
  language = {en},
  number = {7}
}

%%%
@article{martinez2009packmol,
  title={PACKMOL: a package for building initial configurations for molecular dynamics simulations},
  author={Mart{\'i}nez, Leandro and Andrade, Ricardo and Birgin, Ernesto G and Mart{\'i}nez, Jos{\'e} Mario},
  journal={Journal of computational chemistry},
  volume={30},
  number={13},
  pages={2157--2164},
  year={2009},
  publisher={Wiley Online Library}, 
  doi={10.1002/jcc.21224}
}

% 19
@article{hess1997lincs,
  title = {{{LINCS}}: A Linear Constraint Solver for Molecular Simulations},
  author = {Hess, Berk and Bekker, Henk and Berendsen, Herman JC and Fraaije, Johannes GEM},
  year = {1997},
  volume = {18},
  pages = {1463--1472},
  publisher = {{Wiley Online Library}},
  journal = {Journal of computational chemistry},
  number = {12}, 
  doi={10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H}
}

%20
@article{essmannSmoothParticleMesh1995,
  title = {A Smooth Particle Mesh {{Ewald}} Method},
  author = {Essmann, Ulrich and Perera, Lalith and Berkowitz, Max L. and Darden, Tom and Lee, Hsing and Pedersen, Lee G.},
  year = {1995},
  month = nov,
  volume = {103},
  pages = {8577--8593},
  publisher = {{American Institute of Physics}},
  issn = {0021-9606},
  doi = {10.1063/1.470117},
  journal = {The Journal of Chemical Physics},
  number = {19}
}

%21
@article{pallFlexibleAlgorithmCalculating2013,
  title = {A Flexible Algorithm for Calculating Pair Interactions on {{SIMD}} Architectures},
  author = {P{\'a}ll, Szil{\'a}rd and Hess, Berk},
  year = {2013},
  month = dec,
  volume = {184},
  pages = {2641--2650},
  issn = {0010-4655},
  doi = {10.1016/j.cpc.2013.06.003},
  journal = {Computer Physics Communications},
  keywords = {GPU,Molecular dynamics,Pair interactions,SIMD,Verlet list},
  language = {en},
  number = {12}
}

%22 
%bussiCanonicalSamplingVelocity2007

%23
@article{parrinelloPolymorphicTransitionsSingle1981,
  title = {Polymorphic Transitions in Single Crystals: {{A}} New Molecular Dynamics Method},
  shorttitle = {Polymorphic Transitions in Single Crystals},
  author = {Parrinello, M. and Rahman, A.},
  year = {1981},
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  pages = {7182--7190},
  publisher = {{American Institute of Physics}},
  issn = {0021-8979},
  doi = {10.1063/1.328693},
  journal = {Journal of Applied Physics},
  number = {12}
}

%24
@article{abrahamGROMACSHighPerformance2015,
  title = {{{GROMACS}}: {{High}} Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers},
  shorttitle = {{{GROMACS}}},
  author = {Abraham, Mark James and Murtola, Teemu and Schulz, Roland and P{\'a}ll, Szil{\'a}rd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik},
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  volume = {1-2},
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  issn = {2352-7110},
  doi = {10.1016/j.softx.2015.06.001},
  journal = {SoftwareX},
  keywords = {Free energy,GPU,Molecular dynamics,SIMD},
  language = {en}
}

%25
@article{michaletMeanSquareDisplacement2010,
  title = {Mean Square Displacement Analysis of Single-Particle Trajectories with Localization Error: {{Brownian}} Motion in an Isotropic Medium},
  shorttitle = {Mean Square Displacement Analysis of Single-Particle Trajectories with Localization Error},
  author = {Michalet, Xavier},
  year = {2010},
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  pages = {041914},
  publisher = {{American Physical Society}},
  doi = {10.1103/PhysRevE.82.041914},
  journal = {Physical Review E},
  number = {4}
}

%26
@article{alcazar-canoGeneralPhenomenologicalRelation2018,
  title = {A General Phenomenological Relation for the Subdiffusive Exponent of Anomalous Diffusion in Disordered Media},
  author = {{Alc{\'a}zar-Cano}, Nerea and {Delgado-Buscalioni}, Rafael},
  year = {2018},
  month = dec,
  volume = {14},
  pages = {9937--9949},
  publisher = {{The Royal Society of Chemistry}},
  issn = {1744-6848},
  doi = {10.1039/C8SM01961D},
  journal = {Soft Matter},
  language = {en},
  number = {48}
}

%27
@article{zwanzigDiffusionRoughPotential1988,
  title = {Diffusion in a Rough Potential},
  author = {Zwanzig, R.},
  year = {1988},
  month = apr,
  volume = {85},
  pages = {2029--2030},
  publisher = {{National Academy of Sciences}},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.85.7.2029},
  chapter = {Research Article},
  journal = {Proceedings of the National Academy of Sciences},
  language = {en},
  number = {7},
  pmid = {3353365}
}

%28
@article{mesteGlassTransitionFood2002,
  title = {Glass {{Transition}} and {{Food Technology}}: {{A Critical Appraisal}}},
  shorttitle = {Glass {{Transition}} and {{Food Technology}}},
  author = {Meste, M. Le and Champion, D. and Roudaut, G. and Blond, G. and Simatos, D.},
  year = {2002},
  volume = {67},
  pages = {2444--2458},
  issn = {1750-3841},
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  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2621.2002.tb08758.x},
  journal = {Journal of Food Science},
  keywords = {amorphous regions,glass transition,glassy state,relaxation,water activity,WLF},
  language = {en},
  number = {7}
}

%29
% Liu2006

%30-32: MSM refs

%33
%Price2014

%34
@article{C0CP01273D,
  title = {Ultra-Slow Water Diffusion in Aqueous Sucrose Glasses},
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  year = {2011},
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  publisher = {{The Royal Society of Chemistry}},
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}