Update paper

cadet · Nov 20, 2024 · 522ffda · 522ffda
1 parent c2de0dc
commit 522ffda
Show file tree

Hide file tree

Showing 3 changed files with 66 additions and 74 deletions.
diff --git a/paper/CADET_Figure.jpg b/paper/CADET_Figure.jpg
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -1,5 +1,5 @@
 @article{Breuer:2023,
-author = {Breuer, J. and Leweke, S. and Schmölder, J. and Gassner, G. and von Lieres, E.},
+author = {Breuer, J. and Leweke, S. and Schmölder, J. and Gassner, G. and {von Lieres}, E.},
 title = {Spatial discontinuous Galerkin spectral element method for a family of chromatography models in CADET},
 journal = {Computers and Chemical Engineering},
 volume = {177},
@@ -21,7 +21,7 @@ @article{Schmoelder:2020
 }
 
 @article{Leweke:2018,
-author = {Leweke, S. and von Lieres, E.},
+author = {Leweke, S. and {von Lieres}, E.},
 title = {Chromatography Analysis and Design Toolkit (CADET)},
 journal = {Computers and Chemical Engineering},
 volume = {113},
@@ -31,8 +31,8 @@ @article{Leweke:2018
 url = {https://doi.org/10.1016/j.compchemeng.2018.02.025}
 }
 
-@article{Püttmann:2016,
-author = {Püttmann, A. and Schnittert, S. and Leweke, S. and von Lieres, E.},
+@article{Puttmann:2016,
+author = {Püttmann, A. and Schnittert, S. and Leweke, S. and {von Lieres}, E.},
 title = {Utilizing algorithmic differentiation to efficiently compute chromatograms and parameter sensitivities},
 journal = {Chemical Engineering Science},
 volume = {139},
@@ -43,7 +43,7 @@ @article{Püttmann:2016
 }
 
 @article{vonLieres:2010,
-author = {von Lieres, E. and Andersson, J.},
+author = {{von Lieres}, E. and Andersson, J.},
 title = {A fast and accurate solver for the general rate model of column liquid chromatography},
 journal = {Computers and Chemical Engineering},
 volume = {34},
@@ -54,72 +54,55 @@ @article{vonLieres:2010
 url = {https://doi.org/10.1016/j.compchemeng.2010.03.008}
 }
 
-
 @article{Zhang1:2024,
+author = {Zhang, Wendi and Przybycien, Todd and Schmölder, Johannes and Leweke, Samuel and {von Lieres}, Eric},
 title = {Solving crystallization/precipitation population balance models in {CADET}, part {I}: {Nucleation} growth and growth rate dispersion in batch and continuous modes on nonuniform grids},
+journal = {Computers and Chemical Engineering},
 volume = {183},
-issn = {0098-1354},
-shorttitle = {Solving crystallization/precipitation population balance models in {CADET}, part {I}},
-url = {https://www.sciencedirect.com/science/article/pii/S0098135424000309},
-doi = {10.1016/j.compchemeng.2024.108612},
-urldate = {2024-04-10},
-journal = {Computers \& Chemical Engineering},
-author = {Zhang, Wendi and Przybycien, Todd and Schmölder, Johannes and Leweke, Samuel and von Lieres, Eric},
-month = apr,
 year = {2024},
 pages = {108612},
+doi = {10.1016/j.compchemeng.2024.108612},
+url = {https://doi.org/10.1016/j.compchemeng.2024.108612}
 }
 
-
-@article{BUHLER2014131,
-title = {A class of compartmental models for long-distance tracer transport in plants},
-journal = {Journal of Theoretical Biology},
-volume = {341},
-pages = {131-142},
-year = {2014},
-issn = {0022-5193},
-doi = {https://doi.org/10.1016/j.jtbi.2013.09.023},
-url = {https://www.sciencedirect.com/science/article/pii/S0022519313004530},
-author = {Jonas Bühler and Eric {von Lieres} and Gregor Huber},
-keywords = {Mechanistic modeling, Model filter, Model selection, Phloem transport, PET data analysis}}
+@article{Lanzrath:2024,
+author = {Lanzrath, Hannah and {von Lieres}, Eric and Metzner, Ralf and Huber, Gregor Johannes},
+title = {Analyzing Time Activity Curves from Spatio-Temporal Tracer Data to Determine Tracer Transport Velocity in Plants},
+journal = {Mathematical Biosciences},
+year = {2024},
+doi = {10.2139/ssrn.4957804},
+url = {http://dx.doi.org/10.2139/ssrn.4957804}
 }
 
-@article{LEBARRE2024464772,
+@article{LeBarre:2024,
+author = {LeBarre, Jacob P. and Chu, Wenning and Altern, Scott H. and Kocot, Andrew J. and Bhandari, Dipendra and Barbieri, Eduardo and Sly, Jae and Crapanzano, Michael and Cramer, Steven M. and Phillips, Michael and Roush, David and Carbonell, Ruben and Boi, Cristiana and Menegatti, Stefano},
 title = {Mixed-mode size-exclusion silica resin for polishing human antibodies in flow-through mode},
 journal = {Journal of Chromatography A},
 volume = {1720},
-pages = {464772},
 year = {2024},
-issn = {0021-9673},
-doi = {https://doi.org/10.1016/j.chroma.2024.464772},
-url = {https://www.sciencedirect.com/science/article/pii/S0021967324001456},
-author = {Jacob P. LeBarre and Wenning Chu and Scott H. Altern and Andrew J. Kocot and Dipendra Bhandari and Eduardo Barbieri and Jae Sly and Michael Crapanzano and Steven M. Cramer and Michael Phillips and David Roush and Ruben Carbonell and Cristiana Boi and Stefano Menegatti}
+pages = {464772},
+doi = {10.1016/j.chroma.2024.464772},
+url = {https://doi.org/10.1016/j.chroma.2024.464772}
 }
 
-@article{LORENZCRISTEA2024465512,
-title = {A Systematic Approach for Estimating Colloidal Particle Adsorption Model Parameters},
+@article{LorenzCristea:2024,
+author = {Lorenz-Cristea, Oliver and Wiebe, Angela and Thoma, Judith and Veelders, Maik and Briskot, Till and Kluters, Simon and Wang, Gang and Saleh, David and Rischawy, Federico},
+title = {A systematic approach for estimating colloidal particle adsorption model parameters},
 journal = {Journal of Chromatography A},
-pages = {465512},
+volume = {1720},
 year = {2024},
-issn = {0021-9673},
-doi = {https://doi.org/10.1016/j.chroma.2024.465512},
-url = {https://www.sciencedirect.com/science/article/pii/S0021967324008860},
-author = {Oliver Lorenz-Cristea and Angela Wiebe and Judith Thoma and Maik Veelders and Till Briskot and Simon Kluters and Gang Wang and David Saleh and Federico Rischawy},
+pages = {465512},
+doi = {10.1016/j.chroma.2024.465512},
+url = {https://doi.org/10.1016/j.chroma.2024.465512}
 }
 
-@article{altern_high-throughput,
+@article{Altern:2024,
+author = {Altern, Scott H. and Lyall, Jessica Y. and Welsh, John P. and Burgess, Sean and Kumar, Vijesh and Williams, Chris and Lenhoff, Abraham M. and Cramer, Steven M.},
 title = {High-throughput in silico workflow for optimization and characterization of multimodal chromatographic processes},
-volume = {n/a},
-copyright = {© 2024 American Institute of Chemical Engineers.},
-issn = {1520-6033},
-url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/btpr.3483},
-doi = {10.1002/btpr.3483},
-language = {en},
-number = {n/a},
-year = {2024},
 journal = {Biotechnology Progress},
-author = {Altern, Scott H. and Lyall, Jessica Y. and Welsh, John P. and Burgess, Sean and Kumar, Vijesh and Williams, Chris and Lenhoff, Abraham M. and Cramer, Steven M.},
-note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/btpr.3483},
-keywords = {high-throughput experimentation, mechanistic modeling, monoclonal antibody, multimodal chromatography, process characterization, process development, process optimization},
+year = {2024},
 pages = {e3483},
+doi = {10.1002/btpr.3483},
+url = {https://doi.org/10.1002/btpr.3483}
 }
+
diff --git a/paper/paper.md b/paper/paper.md
@@ -9,42 +9,51 @@ tags:
   - CADET
 
 authors:
-  - name: Samuel Leweke
+  - name: "Samuel Leweke"
     orcid: 0000-0001-9471-4511
     affiliation: 1 
-  - name: Jan Breuer
+  - name: "Jan Breuer"
     orcid: 0000-0002-1999-2439
     affiliation: 1
-  - name: Johannes Schmölder
+  - name: "Johannes Schmölder"
     orcid: 0000-0003-0446-7209
     affiliation: 1
-  - name: Ronald Jäpel
+  - name: "Ronald Jäpel"
     orcid: 0000-0002-4912-5176
     affiliation: 1
-  - name: Hannah Lanzrath
+  - name: "Hannah Lanzrath"
     orcid: 0000-0002-2675-9002
     affiliation: "1, 2"
-  - name: Wendi Zhang
+  - name: "Jayghosh Rao"
+    orcid: 0000-0002-1216-9394
+    affiliation: 1
+  - name: "Jazib Hassan"
+    orcid: 0000-0003-2741-5460
+    affiliation: 1
+  - name: "Wendi Zhang"
     orcid: 0000-0002-6127-1408
     affiliation: 3
-  - name: Antonia Berger
+  - name: "Antonia Berger"
     orcid: 0009-0002-0207-9042
     affiliation: "1, 2"
+  - name: "William Heymann"
+    orcid: 0000-0002-5093-0797
+    affiliation: 1
   - name:
-      given-names: Eric
-      surname: von Lieres
+      given-names: "Eric"
+      surname: "von Lieres"
     corresponding: true # (This is how to denote the corresponding author)
     orcid: 0000-0002-0309-8408
-    affiliation: "1, 2" # (Multiple affiliations must be quoted) 
+    affiliation: "1, 2" 
 
 affiliations:
-  - name: Forschungszentrum Jülich, IBG-1':' Biotechnology, Jülich, Germany
+  - name: "Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, 52428, Germany"
     index: 1
     ror: 02nv7yv05
-  - name: RWTH Aachen University, Computational Systems Biotechnology, 52074 Aachen, Germany
+  - name: "RWTH Aachen University, Computational Systems Biotechnology, Aachen, 52074, Germany"
     index: 2
     ror: 04xfq0f34
-  - name: Rensselaer Polytechnic Institute, Department of Chemical and Biological Engineering, USA
+  - name: "Rensselaer Polytechnic Institute, Department of Chemical and Biological Engineering, Troy, 12180, NY, USA"
     index: 3
     ror: 01rtyzb94
 
@@ -56,7 +65,7 @@ bibliography: paper.bib
 
 # Summary
 
-Biotechnology process modeling integrates detailed scientific insight into mass transfer phenomena and phase transitions with the practical demands of industrial process design and optimization. [CADET-Core](https://github.com/cadet/CADET-Core) is an open-source software platform offering powerful tools for comprehensive modeling and simulation of biotechnology processes, powered by state-of-the-art numerical algorithms. Originally developed in 2004 at Forschungszentrum Jülich for chromatography simulation [vonLieres:2010], CADET-Core has since evolved into a versatile tool serving a wide range of biotechnology applications.
+Biotechnology process modeling integrates detailed scientific insight into mass transfer phenomena and phase transitions with the practical demands of industrial process design and optimization. [CADET-Core](https://github.com/cadet/CADET-Core) is an open-source software platform offering powerful tools for comprehensive modeling and simulation of biotechnology processes, powered by state-of-the-art numerical algorithms. Originally developed in 2004 at Forschungszentrum Jülich for chromatography simulation [@vonLieres:2010], CADET-Core has since evolved into a versatile tool serving a wide range of biotechnology applications.
 
 CADET-Core supports unit operations such as chromatography, filtration, and crystallization, along with auxiliary components such as hold tanks, tubes, valves, and detectors. These elements can be interconnected to form complex networks, supporting closed-loop feedback and flexible structures. The modular design and computational efficiency of CADET-Core enable simulation and advanced optimization of such processes.
 
@@ -67,9 +76,9 @@ The development and optimization of modern biotechnology processes are increasin
 CADET-Core addresses these challenges with a high-performance C++ solver for domain-specific partial differential-algebraic equations that supports an extensive range of established [biotechnology process models](https://cadet.github.io/master/modelling/).
 This includes a hierarchical family of transport models, which can be combined with various adsorption and reaction models to describe physicochemical processes in biotechnological unit operations. CADET-Core supports strongly coupled networks of these unit operations, including cyclic systems. Its modular design provides flexibility in customizing and connecting models to meet specific user requirements while automatically assembling the spatially discretized governing and constitutive equations in a numerically efficient manner.
 
-The latest major release, version 5.0, introduces several key advancements. Numerical improvements substantially enhance computational performance, particularly through the development and implementation of a spatial discontinuous Galerkin discretization method [Breuer:2023].
-Further, a modular family of crystallization models is implemented that are solved with specifically designed size-based finite volume (FV) methods [Zhang1:2024], ensuring compatibility across all unit operations.
-Moreover, the existing axial transport models are extended to support radial transport in cylindrical confinements and parallel transport in multiple channels [BUHLER2014131].
+The latest major release, version 5.0, introduces several key advancements. Numerical improvements substantially enhance computational performance, particularly through the development and implementation of a spatial discontinuous Galerkin discretization method [@Breuer:2023].
+Further, a modular family of crystallization models is implemented that are solved with specifically designed size-based finite volume (FV) methods [@Zhang1:2024], ensuring compatibility across all unit operations.
+Moreover, the existing axial transport models are extended to support radial transport in cylindrical confinements and parallel transport in multiple channels [@Lanzrath:2024].
 
 As a feature-complete tool, CADET-Core offers a comprehensive platform for modeling and simulating biotechnology processes, while ongoing active development targets emerging needs in a rapidly evolving field. Continuous integration, automated testing, and delivery pipelines ensure the reliability and robustness of CADET-Core. Computation results are documented with comprehensive metadata, including model configurations and commit hashes, to maintain full reproducibility and compliance with FAIR standards.
 
@@ -81,27 +90,27 @@ CADET-Core is readily accessible through the [Conda-Forge package manager](https
 
 To date, CADET has been mentioned in more than 250 articles as highlighted in the [Helmholtz Software Directory](https://helmholtz.software/software/cadet). These studies demonstrate the relevance of CADET-Core as a versatile tool for biotechnology process modeling and optimization across a wide range of applications. Most recent examples include:
 
-LeBarre et al. (2024) used CADET-Core to optimize a mixed-mode size-exclusion chromatography method for polishing human antibodies in flow-through mode. By improving mass transfer and interaction effects within the chromatography column, antibody purification could be enhanced [@LEBARRE2024464772].
+@LeBarre:2024 used CADET-Core to optimize a mixed-mode size-exclusion chromatography method for polishing human antibodies in flow-through mode. By improving mass transfer and interaction effects within the chromatography column, antibody purification could be enhanced.
 
-Lorenz-Cristea et al. (2024) utilized CADET-Core to estimate adsorption parameters for colloidal particle interactions in chromatography. This application involved the development and validation of adsorption models to improve parameter estimation techniques for colloidal behavior [@LORENZCRISTEA2024464772].
+@LorenzCristea:2024 utilized CADET-Core to estimate adsorption parameters for colloidal particle interactions in chromatography. This application involved the development and validation of adsorption models to improve parameter estimation techniques for colloidal behavior.
 
-Altern et al. (2024) incorporated CADET-Core into a high-throughput in silico workflow to optimize multimodal chromatography in monoclonal antibody purification. This enabled rapid simulation of chromatographic conditions to support process optimization and accelerate development cycles for large-scale bioprocessing [@altern_high-throughput].
+@Altern:2024 incorporated CADET-Core into a high-throughput in silico workflow to optimize multimodal chromatography in monoclonal antibody purification. This enabled rapid simulation of chromatographic conditions to support process optimization and accelerate development cycles for large-scale bioprocessing.
 
 # Community and Contributions
 
 CADET-Core is an open-source project that welcomes community contributions. Participation is encouraged through issue submission or pull requests via the [GitHub repository](https://github.com/cadet/CADET-Core). A [developer guide](https://cadet.github.io/master/developer_guide/index.html) provides direction for contributors, and the [CADET forum](https://forum.cadet-web.de/) offers active support for both users and developers. To foster a welcoming and supportive environment, the project follows the [contributor covenant](https://www.contributor-covenant.org/) code of conduct. 
 
 # License and Citation
 
-CADET-Core is distributed under the [GPL 3.0 License](https://www.gnu.org/licenses/gpl-3.0.en.html). 
+CADET-Core is distributed under the [GPL 3.0 license](https://www.gnu.org/licenses/gpl-3.0.en.html). 
 For publications, CADET-Core should be cited following the [citation recommendations](https://github.com/cadet/CADET-Core/blob/master/README.rst).
 
 # Figures
 
-![CADET-Core is the central module within the broader CADET framework (adapted from Figure 1 in [Leweke:2018]).](CADET_Figure.jpg)
+![CADET-Core is the central module within the broader CADET framework (adapted from Figure 1 in @Leweke:2018).](CADET_Figure.jpg)
 
 # Acknowledgements
 
-We sincerely acknowledge Joel Andersson, Andreas Püttmann, Sebastian Schnittert, William Heymann, Jazib Hassan and Jayghosh Subodh Rao for substantial contributions to earlier versions of CADET-Core.
+We gratefully acknowledge Joel Andersson, Andreas Püttmann and Sebastian Schnittert for substantial contributions to earlier versions of CADET-Core.
 
 # References