Stoichiometry (including Biodegradation and Ecotoxicology)

2024 Summer Schedule

May 30, 2024

Main Activity (Pablo/Jacob):

Pablo: Led the discussion during the subgroup meeting. The general plan for the subgroup meeting during 2024 was shown

Jacob: Introduced his soon-to-be-submitted recent model regarding cyanobacteria blooms, trophic interactions, and the effects of cyanobacteria toxins using a stoichiometric-based mathematical model. He introduced his model to the members, and a discussion was established. Furthermore, a general overview of a global sensitivity analysis was reviewed

Supplementary Activity (Tianxu):
Led the discussion on distributing future supplementary activities as follows: Pablo (Conclusion), Tianxu (Introduction), Ovi (Title), Shohel (Introduction), Jacob (Abstract), and Jitendra (General writing issues). She also presented her ongoing work on the bold-shy predator-prey model using a PDE approach. The numerical results were discussed, and primary objectives for future research were established

June 6, 2024

Main Activity (Ovi):
Ovi talked about the progress of his cholera project. He presented some theoretical and numerical results and shared a plan for data fitting to his last group presentation on the Hydra Effect.

Supplementary Activity (Jacob):
Jacob discussed abstracts by introducing their definition and general guidelines on how to write a good one. He also compared different versions of his own work, and the group members discussed the improvements and shortcomings. Additionally, he provided examples for different types of papers.

June 13, 2024

Main Activity (Shohel):
Shohel introduced his recent work on a personality-driven predator-prey model. He also led the discussion on several kinds of sensitivity analysis. The theory and numerical results were discussed, and primary objectives for future research were established. The whole group discussed some ideas and suggestions.

Supplementary Activity (Pablo):
Pablo discussed the big picture of the discussion section by using his own work as an example. He provided a detailed explanation of his thoughts and the emphasis for each part. For instance, he explained that the first paragraph extends the introduction, the second part focuses more on the mathematical model, followed by methodology and background, and then the results. He also discussed the difference between the introduction and the discussion sections.

June 20, 2024

Main Activity (Jitendra):

Jitendra presented today his current work regarding bold and shy trophic interactions when a harvesting function is introduced and affects predator populations. This introductory work establishes the main idea behind harvesting affecting bold predators with a saturating functional response. Some experiments justify harvesting affecting predators' population reasoning, but the work is still under mathematical development. Numerical simulations were provided, which showed how different population sizes of prey, the boldness of predators and the predator harvesting index affect the general system. Future work bullet points were stated, and it is expected to reach a couple of milestones in the next presentation. 

Supplementary Activity (Ovi):

Ovi showed different strategies for creating a title for academic papers. He also showed how different journals play an important role in building a title and might provide the author with specific directions that might help. The strategies presented in bullet points in Ovi's presentation were a take-home message for ILMEE members' future work. 

For the last part of the supplementary activity, the subgroup members discussed how two bifurcation diagrams can be constructed, in which different strategies, numerically, explicit, or implicit solutions for local stability, are crucial components.

June 27, 2024

Main Activity (Tianxu):

Pablo provided a detailed explanation of the background, motivation, and preliminary results of the methane emission experiments. Tianxu presented the data fitting results for hydrocarbon data, employing a two-phase function approach. The first phase is characterized by a constant function, while the second phase adopts a Holling type II function.

Supplementary Activity (Shohel):

Shohel discussed the writing skills for the introduction, highlighting key points and providing suggestions on how to write a better introduction. He then used a couple of examples to explain the application of these strategies in detail.

July 4, 2024

Main Activity (Jacob):

Jacob updated us on the progress of his paper, which is currently under review. He also introduced his recent work on a spatial stoichiometry model and shared some advancements. Group members raised several questions about the model, particularly concerning the cell quota term.

Supplementary Activity (Tianxu):

The group reviewed the grant proposal writing process, using Tianxu’s proposal as a case study. Pablo offered several suggestions for improvement.

July 11, 2024

Main Activity (Ovi):

Ovi introduced improvements in his cholera project. He conducted sensitivity analysis and used data to fit parameters. Additionally, he discussed the details of data fitting with other members, addressing issues with units, and distinguishing between the original model and the nondimensional model.

Supplementary Activity (Jitendra):

Group members discussed the grant proposal together, covering various subjects, and provided suggestions for each other.

July 18, 2024

Main Activity (Shohel):

Shohel discussed data-driven modeling and analysis of a personality-dependent predator-prey system. He elaborated on some interpretations of the stochastic model, including potential wells, eigenvalues, and the depth and width of the basin of attraction for multistable equilibrium states. He also covered the transition of bi-stability. His results included insights into phase-induced tipping and noise-induced tipping. Other subgroup members provided suggestions and feedback on his work.

Supplementary Activity (Jacob):

Jacob discussed the basic strategy for abstract writing. He provided his recent abstract, and other group members gave him suggestions and feedback. We also discussed another abstract for a published paper.

July 25, 2024

Main Activity (Jitendra):

Jitendra presented his work on data-driven, personality-based predator-prey dynamics, including modeling, stability analysis, and bifurcation diagrams that demonstrate bistability. Other group members provided constructive feedback and suggestions for improvement. Specifically, Shohel recommended enhancing the biological implications depicted in each figure and ensuring the results are explained meaningfully.

Supplementary Activity (Jitendra):

Jitendra presented strategies for effective paper writing, focusing on enhancing cohesion through the repetition of keywords and phrases and effectively providing data commentary by highlighting trends and regularities while excluding unnecessary details. He emphasized the importance of hedging to moderate and qualify claims, carefully varying the degree of assertiveness, and avoiding strong verbs to maintain a balanced academic tone. He illustrated these strategies by showcasing examples from his own writing, which prompted a productive discussion among the other group members.

Subgroup  Meeting Materials

https://drive.google.com/drive/folders/1ar8rVVfRKbsEOsUnHaXaJ6q5lzU00yKS?usp=drive_link

Stoichiometry (including Biodegradation and Ecotoxicology)

• Date: Aug 1, 2023

• Participants: Pablo Venegas Garcia, Shohel Ahmed, Shan Gao, Jacob Serpico, Murshed Ahmed Ovi, Yawen Yan, Tianxu Wang, Zhenyao Sun, Peta Prokopiou

• Activities: Peta led the reading part, Jacob the writing skills and Yawen the Presentation.

• Reading Skills:  Peta read important passages from the paper “A New Approach to Sustainability: A Moore's Law for Chemistry.” She explained “sustainable chemistry” and “green chemistry”  with its wide range of applications. Afterward, the group members discussed how these kinds of research would impact the goals of our group.

Writing Skills:   Jacob discussed Effectively Writing about our research work and how to represent our data in writing. He talked about different strategies like “Locating,” "Highlighting," "Combining," and "Hedging" to represent outcomes of data in an effective way for readers. He also represented Casual vs. academic language style and showed different expressing connections.

Presentation: Yawen introduced her current mathematical model on ecotoxicology about the impact of multi-nutrient on the dynamics of Phytoplankton. Initially, She introduced the biological paper that motivated her to this research direction, and group members discussed these ideas. Later, Yawen presented her model incorporating toxic and nontoxic phytoplankton with allopathic interaction competing with two different resources. To find the effect of multi-nutrient on the dynamics, She pointed out some questions the team members discussed to improve the current model.

• Date: July 25, 2023

• Participants: Pablo Venegas Garcia, Shohel Ahmed, Shan Gao, Jacob Serpico, Murshed Ahmed Ovi, Tianxu Wang, Zhenyao Sun, Peta Prokopiou,Yawen Yan (Online).

• Activities: Shohel led the reading part, Murshed the writing skills and Zhenyao the Presentation.

• Reading Skills: Shohel chose the paper “Eco-Evolutionary Dynamics of Ecological Stoichiometry in Plankton Communities” for the reading, and all group members participated in reading the introduction. Afterward, all the members were involved in a group discussion regarding the structure and highlights of the papers, which was then compared with the abstract through the reading by Shohel.

Writing Skills:  Murshed discussed different Strategies for Structuring Academic Writing. He elaborately described the "General-to-Specific" vs "Problem-Solution" strategy, which helps to organize the ideas in texts in a way that makes sense and effectively communicates our research to the reader.

Presentation: Zhenyao introduced his research direction towards proposing a hybrid PDE and ODE model to describe the dynamics of algae affected by pollutants on a shoreline. He introduced different approaches found in the literature as a beginning point, and group members discussed the main ideas. Then, Zhenyao presented his model and results, in which team members helped with new ideas to improve his current results. 

• Date: July 18, 2023

• Participants: Pablo Venegas Garcia, Shohel Ahmed, Shan Gao, Jacob Serpico, Murshed Ahmed Ovi, Yawen Yan, Tianxu Wang, Zhenyao Sun, Peta Prokopio

• Activities: Yawen led the reading part, Tianxu the writing skills and Shohel the Presentation.

Reading Skills: Yawen read the introduction of the paper “Spatial modelling and dynamics of organic matter biodegradation in the absence or presence of bacterivorous grazing.” Afterward, the group members extracted the key ideas from the introduction and discussed the conventional way of writing an introduction in general.

Writing Skills:  Tianxu led the workshop and discussed implementing cohesion and coherence in scientific writing.  She prepared an exercise passage where each member tried to improve it using these writing tools. 

Presentation: Shohel presented interesting results regarding part of his research on the ongoing optimal foraging theory project considering two prey and one predator interactions. During his presentation, he provided enough background for the team members and led a discussion about how feeding efforts' cost helps predators choose strategies for acquiring food. To explore how food quality or quantity may affect predator foraging behaviour, Shohel proposed different numerical experiments and quantified the results using a previously defined index.  He pointed out questions related to bistability. Group members provided feedback and evaluation to Shohel.

• Date: July 11, 2023

• Participants: Pablo Venegas Garcia, Shohel Ahmed, Shan Gao, Jacob Serpico, Murshed Ahmed Ovi, Yawen Yan, Tianxu Wang, Zhenyao Sun

• Activities: Tianxu led the reading part, Zhenyao the writing skills and Murshed the Presentation.

Reading Skills: Tianxu read the abstract of the paper “The impact of environmental toxins on predator–prey dynamics.” and "Somatic Growth Dilution of a toxicant in a predator–prey model under stoichiometric constraints." Tianxu took the lead in discussing with group members what was the difference between these two papers. The group members had 10 minutes to extract the key ideas from the abstract and discuss from which approaches each model was constructed as goals.

Writing Skills:  Zhenyao led the writing workshop and discussed common grammar mistakes during writing. Zhenyao focused on common mistakes when using commas and verb tenses while writing. He also prepared an exercise based on what he reviewed, which consisted of editing different sentences and correcting them using the proper use of commas for different cases. 

Presentation: Murshed presented the continuation of his research journey on the "Hydra effect." He discussed different experiments and literature reviews stating the difference between “Stage-specific Overcompensation" vs "Hydra effect." Also, he pointed out some questions related to modelling that team members discussed. Finally, group members provided feedback and evaluation to Murshed.

• Date: July 4, 2023

• Participants: Pablo Venegas Garcia, Shohel Ahmed, Shan Gao, Jacob Serpico, Murshed Ahmed Ovi, Yawen Yan, Tianxu Wang, Zhenyao Sun, Peta Prokopiou (Online)

• Activities:

Pablo led the first group meeting by providing information about how important the subgroup meetings are for group members and how positively they can participate to improve members' academic skills. During his presentation, he collected information and pictures requested from each group member so that everybody could introduce themselves. Further, Pablo proposed a new structure for the subgroup meetings, which includes reading out loud, 10 minutes abstract, writing skills, presentation of a subgroup member, and general questions. This new structure will cover the two hours scheduled for each subgroup meeting. 

Reading Skills: Pablo read the introduction of the paper “Bacterivorous grazers facilitate organic matter decomposition: a stoichiometric modelling approach.” Consequently, group members created a 10 minutes abstract, which first was compared against the author's abstract and then the ideas from each 10 minutes abstract were discussed, as group members suggested.

Writing Skills: Pablo presented a general panorama of how good research can be done, focusing on organization skills, which can define the purpose and help flow our research ideas. He continued to explain how these ideas are extended in academic writing. Using the book “Academic Writing for Graduate Students” and slides provided by Tim Cho from the C4W workshop that Pablo attended, he further discussed unit one of the book: “An Approach to Academic Writing.” Other team members will continuously use these slides.

Presentation: The presentation was divided into two parts. Pablo presented an example of bad scientific writing, and then Tianxu presented her new research directions. During Pablo’s presentation, he encouraged team members to participate as a reviewer for an abstract that was not academically well written. During his discussion, he guided team members into the decomposition of the text and showed how he improved it. Then, Tianxu presented her new research directions about a model which includes adverse toxic conditions that may affect a dynamic system of two species. She pointed out important questions that team members discussed to find possible solutions or suggestions. Finally, group members provided feedback and evaluation to Pablo and Tianxu.

• Date: Mar 3, 2023

• Participants: Everyone

• Activirties: Tianxu talked about her research on fear effect of predator-prey model. Shohel shared his questions of his research and we had a discussion on them.  

• Date: Feb 17, 2023

• Participants: Everyone

• Activirties: Pablo presented some results on the improved methane biogenesis predictions against in-field data using three other models. . Shohel gives the talk of writing skills.

• Date: Feb 10, 2023

• Participants: Everyone

• Activities: Juping introduced chaos and chaotic solutions with examples. Tianxu gives the talk of writing skills.

• Date: Feb 3, 2023

• Participants: Everyone

• Activities: Pablo shared examples of examples of punctuation choice. Shohel presented  stoichiometric producer–grazer models he was working on. We discussed the problems we encountered during the programming process.

• Date: Jan 27, 2023

• Participants: Everyone

• Activities: Shan introduced basic ideas of machine learning and presented some ecological applications. Ovi shared writing skills.

• Date: Jan 20, 2023

• Participants: Everyone

• Activities: Tianxu gave the presentation. Shohel shared the difficulties he encountered in his research during the winter break and some new ideas. 

• Date: Nov 10, 2022

• Participants: Everyone

• Activities: Shan presented a document titled, “How to write clearly” as the beginning of lecture series towards the development of our scientific writing.  Within the discussion Pablo gave an example using different versions of an abstract of his recent work (from old to the most improved version). Professor Hao also participated in the discussion, answered our questions and gave suggestions. 

In the second part, Juping presented her new “MRL” model and answered the questions we posed about that model.

• Date: Nov 3, 2022

• Participants: Juping Ji, Murshed Ahmed Ovi, Shohel Ahmed, Shan Gao, Tianxu Wang

• Activities: Juping gave a presentation on “ Loladze, I., Kuang, Y., & Elser, J. J. (2000). Stoichiometry in producer-grazer systems: linking energy flow with element cycling. Bulletin of mathematical biology, 62(6), 1137-1162.” She will give two presentations on it. Today she discussed the model derivation and used other two articles and a book to explain term by term in the first part.

In the second part, we set up a plan regarding the improvement of our scientific writing practices. Also, Juping and Shohel shared the ways of using computer simulations to deal with complex bifurcation analysis. In the next week, Juping will continue her series presentation and Shan will lead the discussion on improving scientific writing.

• Date: Oct 27, 2022

• Participants: Juping Ji, Murshed Ahmed Ovi, Pablo Venegas Garcia, Shohel Ahmed, Shan Gao

• Activities: Shan shared some of problems he encountered regarding to his research, including mathematical analysis technics, parameterization. The group had a discussion on how to find parameter estimation for a certain model and proposed some doable ideas.

• Date: Oct 20, 2022

• Participants: Juping Ji, Murshed Ahmed Ovi, Tianxu Wang, Pablo Venegas Garcia, Shohel Ahmed

• Activities: Tianxu Wang presented a paper "Yuan, S., Wu, D., Lan, G., & Wang, H. (2020). Noise-induced transitions in a nonsmooth Producer–Grazer model with stoichiometric constraints. Bulletin of Mathematical Biology, 82(5), 1-22.". She also presented her progress in her recent work and threw some questions about her doubts for discussion. Some valuable suggestions regarding her progression were given by the members as well as Prof. Wang Hao himself.

• Date: Oct 13, 2022

• Participants: Juping Ji, Murshed Ahmed Ovi, Tianxu Wang, Pablo Venegas Garcia, Shohel Ahmed, Shan Gao

• Activities: Pablo Venegas Garcia presented a paper '' Heggerud, C. M., Wang, H., & Lewis, M. A. (2020). Transient dynamics of a stoichiometric cyanobacteria model via multiple-scale analysis. SIAM Journal on Applied Mathematics, 80(3), 1223-1246.  ". The presentation and discussion were mainly focused on Multiple Scale Analysis to identify its implementation in Pablo's recent work. Some ways regarding its usage in Pablo's work were suggested by the sub-group members.