Karl Jan Clinckspoor
My personal site
Links
https://orcid.org/0000-0002-0916-2773Overview
In this page, I will place the few articles I have written and give some general, and personal, comments about what went into each article.
Articles in journals
(2022) Mechanical Degradation of Biopolymers for Enhanced Oil Recovery Applications
This article was a journey and I learned a lot. I’ve been so focused on bulk rheology that I didn’t even know how polymers behaved inside porous media, where they’re very limited regarding where and how they can stretch. This, allied with one really excellent reviewer, taught me much. And, note to self, don’t be lazy when answering the questions. I didn’t do one thing one reviewer wanted and later regretted it. Did it in a later stage, and it showed exactly what the reviewer wanted.
(2021) Optimization of an in-situ polymerized and crosslinked hydrogel formulation for lost circulation control
This article is I was the most involved in, from its conception, to the publication. It has quite a story attached to it.
We were working on this project, and we had to develop a gel to stop flow through fractures in a well (lost circulation). It was a rough start, since I had to learn quite a lot in a very short time. When we were progressing well, then pandemic struck, and we could not do any work whatsoever. We had an initial formulation we thought would work, but we had no experimental evidence. We had to plan something that would give an answer, and relatively quickly. The PI insisted we look for experimental design (DOE), and so we did.
In my studies of chemometrics, I was focused on techniques such as PCA, HCA, etc, and not in experimental design. However, I was a bit fascinated by the area, and thought it would greatly improve my technical repertoire. My wife studied the subject a few months earlier, during her Master’s, so I bounced off a few ideas and questions to her. Unfortunately, I didn’t learn too much from her, I just got very very confused with the bunch of plusses and minuses and how to interpret that. I figured I had to learn it by myself, so I got the book she used (loaned by her sister) and proceeded to study. I had a lot of “free” time, so why not. I did every exercise, took copious notes, and even book bound my notes for posterity. I think it took me 1 month, but I left feeling like I was an expert in the area. That’s never a healthy mindset, especially in statistics, with its wildly variable nomenclature and expectations, but this hasn’t caused us much trouble, yet.
Then, we (me and Fuat) sat down (remotely) and established the variables we were going to study. It’s funny, he was adamant we should include pH, and I was against, but mostly due to laziness - adjusting and measuring pH is something I truly loathe. In the end, he was very right in including it. When the pandemic slowed down, we came back to the lab briefly, and he started his experiments. We faced so many problems you wouldn’t believe. We had to alter the starting formulation several times, and we discovered many aspects about our system. But in the end, we got to an acceptable starting composition, and we had the experiments and outputs very well established. And so Fuat did all the experiments in a record time (two formulations per day, starting at 8 and going well past 6).
One of the techniques consisted on monitoring the gelation using NMR. It was something entirely new in our group, and not very much used for this application in the literature. Because of that, the equipment wasn’t entirely built to support it. For example, we had to monitor the gel for several hours, analysing it from time to time. That had to be done manually, since the equipment software didn’t support automation. Then, we had to analyse that in the software, and it also didn’t support automated analysis. The total was ~107 measurements, and each had to be inverted, so ~214 data files, for each composition. That is about ~4000 individual files in total, only for NMR. We would have gone absolutely crazy if we had to analyse them one by one. Thankfully, the wonderful Python package PyAutoGUI came to our rescue. We just had to insert the sample and push start on my script, and it would analyse the data at specific intervals. After that, we ran another script that passed the data through the CONTIN inverter. Much simpler.
We now had to analyse the results. I taught Fuat how to do some of the fits in Origin, and wrote some scripts to extract data from NMR, be it the peak value or the monoexponential fits of the curves. Fuat merged everything in a homeric effort into a single Excel spreadsheet. We sat down (in person) and I taught him how to perform the matrix operations required to obtain the model parameters. Then, how to analyse the results, and how to reduce the model to have more “free” degrees of freedom. Fuat then defended and had to write the article.
Some time later, he hadn’t advanced much, a lot due to lack of motivation and time. Having to find a job during the pandemic consumes everyone, and I had other responsibilities. The time came to write it finally, and so I started. For precaution, I re-analysed everything. I found some discrepancies. The fit parameters were all 100% matching, but not the variable names. After some looking around, it was just some confusion in the variable names. Since I wrote the analysis in a Jupyter notebook, I thought we could publish the data too, so I worked to make it more readable.
Then I started to write the article itself. That came quite easily, since I was so involved in the project, and had spent so much time reading about the theme itself, focusing on more fundamental aspects, rather than practical. In the end, I was able to explain everything we observed, and gave some general directions for future work. It was done in less than a month I think, from re-analysis to final article version.
We submitted the article to the Journal of Petroleum Science and Engineering. A lot of time passed, and we got an answer - minor corrections! I never, ever got an article so well accepted at first. You can read the other tales I have here, and how I suffered to publish some articles. Correction was very easy, just a few adjustments here and there. A lot of time later, we were accepted! Such a good feeling. Our hard work paid off. This is one of the articles I’m most proud of.
(2021) Urea induces (unexpected) formation of lamellar gel-phase in low concentration of cationic surfactants
I received news of this one and the next article literally 1 week apart! Academia is truly an unexpected place. Anyway, on to the story of this one.
This is the last remaining part of the work I conducted during my PhD. I was certain I didn’t have enough data, or enough answers, to warrant publication as a full article. Some suggested I publish this as a letter to a journal. Letters are typically very short, only include the most relevant information. So that’s what we did.
First, we tried with ACS Omega, in the format of a letter. It fell on the lap of some dude called who has beef with my advisor. He was part of a friend’s thesis committee and snubbed my supervisor, in front of everyone. My supervisor was, and is, a very fine and controlled person, but he looked definitely down after that. Since then, I’ve had this guy in my personal “black book” of names, a position reserved for very few. Why do so many academics need to be so distasteful?
When we got the answers to our paper, I could feel this dude was happy at our failure, despite not having any evidence of the fact. Reviewer 1 made good observations, but his comments were focused as if we were trying to basically create a phase diagram of this system, which was not the case. We were simply showing that the formation of this lamellar gel-phase is unusual, and we reported it. And he said the packing parameter is useful in water only, which is false. I had to remove some data and text from the original draft because otherwise it wouldn’t fit in the letter format, which is much more limited than a normal paper, so his additional information would probably not even fit in the format.
Reviewer 2 receives the medal, though. Here’s how their review starts:
These kind of papers are annoying for both the reviewer(s) and the editor. The submitted
manuscript is a lab report rather than a decent scientific paper and certainly deserves not
publishing. Although it should not be my task to read and comment these kind of
contributions I will briefly outline my main points of criticism:
And they go on to state that the results are obvious - which the last reviewers noted wasn’t the case. If it was obvious, why is it so hard to find anything on the subject in the literature? Then, they give a long list of papers we should have cited - the majority of which are, being generous, tangentially related to the subject, and not helpful to the case the paper was trying to make, at all. For example, none of them mentioned urea, which was the main point we were trying to make! The cherry on top was that the first paper they ask us to cite has as corresponding author one of the reviewers I recommended, and this name repeated itself twice more in the reference list. Now, there’s no proof that this isn’t a coincidence, but if it isn’t, that really unprofessional of you, C. S.
Then, we tried in this new journal called “Experimental Results”. The whole stick of this journal is that they are focused on publishing results, not necessarily answers. They advertised the paper focusing on this aspect. I thought this was a fine opportunity, so we submitted to this journal. Man, I got one of the worst reviews I ever had the displeasure of reading. Here it is, in full:
Conductivity could be monitored during the transitions to check for urea degradation!.
That’s it. Nothing else. The worst part is that the suggestion is basically nonsense. The other reviewer was better, asked for some adjustments here and there, the normal stuff. I was quite furious with something so unprofessional, so I contacted our liaison with the journal, Dr. A. B. I expressed my disgust (not the words I used) with the review I got, and told them I understood if they kept their decision, but I wanted another reviewer to judge my paper. Literally 1 month later, to the day, I got an answer, saying they understand my disappointment but there was nothing they could do, and that I should take the reviewers comments into consideration and resubmit it. And you know what? I didn’t. I will never try publishing in this journal, and will speak ill of it to everyone I meet - not that this will affect them in any way, it’s for the principle.
A long time passes, but my supervisor hasn’t given up on this paper yet. He enlists the help of a new master’s student, the second author of the paper, Fernando Okasaki. He was once a student of mine during experimental physical-chemistry lab - I just hope I wasn’t an ass with him or anyone else in general (I overthink my social interactions sometimes). He made some additional measurements and found a few good references to the paper and, together with my supervisor, they shape the paper up to something much more presentable. We submit to a journal, much better than the two previous ones, and we get some very good reviewer comments, and finally get it accepted. Hooray! What a journey. I can’t thank him enough for his part in helping this paper get published, and also I can’t thank my supervisor enough for not giving up on me.
(2021) Bulk rheology characterization of biopolymer solutions and discussions of their potential for enhanced oil recovery applications
This is my first journal article published while working in LABORE. This one was a doozy. It was started by my predecessor, was revised several times, then overhauled to include more data, then politics dictated some of this data had to be removed, and then this was reviewed several mores times, rejected at least twice before we decided to submit to CT&F, a journal of the Colombian firm Ecopetrol. The review process was unusual - we submitted a docx document and received 4 docx documents, each with comments. Funnily, some were not anonymized. In any case, the article turned out very satisfactory, and the aesthetics of this journal made it look even better.
(2020) Safety, Tolerability and Effects of Sodium Bicarbonate Inhalation in Cystic Fibrosis
This was an interesting article. I was contacted by one of the coauthors, Prof. Pessine, to do some rheological analyses of mucus. A bit grossed out, I accepted. After a ton of work and more than 500 experiments (each with 3 separate data sets), we finished a part of the work necessary. And it’s funny how sometimes stuff just aligns. Had I not decided to learn Python a few months prior, I would not have been able to analyze the absolutely huge amounts of data in any reasonable time. I made some time ago a short demo video of one of the scripts I developed at work. Dr. Carla, the leader, conducted the rest of the enormous work necessary, and contacted a statistician to provide the rest of the calculations necessary.
I was very satisfied with the work, a very noble endeavor. In short, we noticed that inhaling sodium bicarbonate led to patients with the genetic disease cystic fibrosis experienced an improvement in their quality of life. A far cry from my more fundamental studies so far, and very inspiring.
(2019) A new interpretation of the mechanism of wormlike micelle formation involving a cationic surfactant and salicylate
I had minimal contributions to this work itself. My main contribution was obtaining the initial data and performing preliminary experiments. As I was focused on something else, my group colleagues noticed how interesting some of the results I had were and developed this work.
This article is very niche, basically deals with something only our group studied at that time, which is the formation of wormlike micelles based on isothermal titration calorimetry. We had a previous interpretation of the results after much thinking, and this article updates that interpretation using some additional spectroscopic techniques.
(2018) Rheological and calorimetric study of alkyltrimethylammonium bromide-sodium salicylate wormlike micelles in aqueous binary systems
This article explains the core part of my thesis. Normally, studies focus on the effects a small amount of additives that place themselves on the micellar palisade and change their properties, e. g., sodium salicylate (NaSal) leads to growth of cetyltrimethylammonium bromide (CTAB). Few studies consider what the solvent is doing. In this work, I kept the wormlike micelle system (CTAB+NaSal) and changed the solvent by adding relatively large amounts of water-soluble compounds.
The inspiration came from the work of Prof. Hoffmann, who we befriended in a congress in Cyprus in 2014. He explained how adding glycerol led to a change in the properties due to changes in the attractive forces between the micelles, which can be indirectly viewed by the diffractive index difference between solvent and micelle. We tested this hypothesis and added more parameters that would explain our results, such as the Gordon parameter.
Of all the additives, two were most surprising. First, sucrose had almost no effect on the system, despite it having several similar properties to Glycerol. The other aspect is that urea led to crystallization at higher concentrations (>35%). We still don’t fully understand this fact and have tried to publish our findings, but so far our work wasn’t accepted anywhere.
The idea of the camel and dromedary was mine and I’m still proud of it. I think having light-hearted parts to science is very beneficial.
(2016) The thermal signature of wormlike micelles
This article came after several students of my supervisor used isothermal titration calorimetry to study wormlike micelles, and we had sufficient data to propose some better hypotheses to what was happening.
(2015) A Rehage-Hoffmann rheological approach to worm-like micelles of C16TAB and ortho-hydroxycinnamate
This is the main article of my master’s dissertation. I studied this weird additive, ortho-hydroxycinnamate, and how pH affected the properties of the micelles. The most pleasant part was working with the additive, since it smelled good. Adjusting the pH still gives me nightmares. Don’t trust any person reporting pH measurements to within 0.01 (or even 0.1) of any complex system, especially one that has a cationic surfactant.
(2012) Triboelectricity: Macroscopic Charge Patterns Formed by Self-Arraying Ions on Polymer Surfaces
This article came out when I was still an undergrad. I did a lot of the work and plots contained in it, but the interpretation and writing was left to the other people. I’m still a bit upset that another student that helped me a lot wasn’t added to the author list because, in the words of my supervisor, “she didn’t truly understand what was happening because she’s an engineer”.
Book chapters
New Insights into the Formation of Wormlike Micelles: Kinetics and Thermodynamics
My advisor wrote most of the writing, I was tasked with literature review, text revision, making the figures prettier and formatting stuff. It was a great honor to participate in this, and I have Dr. Dreiss to thank for that. I hope I get to meet her in the future, even though I’m not in the area anymore.