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· 4 min read

Recently I started a position as a lab technician with Australian National Fabrication Facility (ANFF). One of the requirements of this position is to maintain the ICP (Fig 1). Therefore, I decided to write a short post here about ICP, which I will update with the various things that I have learned along the way.

Fig 1. The ICP in my lab at the University of Wollongong, with the labelled components

What is ICP?

Inductively coupled plasma (ICP) mass spectrometry (MS) or optical emission spectroscopy (OES) is a method of elemental analysis which utilises a plasma source. In ICP-MS, the ions are directly measured. In contract, ICP-OES uses an optical spectrometer to measure the photons emitted as they pass through the plasma. While both methods are extremely fast to use, cheap and straightforward, the ICP-OES has a higher sensitivity to detection.

How does ICP work?

Schematic of ICP
Figure 2. Schematic of ICP: (a) engineered setup and (b) behaviour of the sample inside the sample channel. Images taken from (Hou and Jones) and (McCurdy and Potter)

A schematic of an ICP is displayed in Fig 2. The liquid sample is injected into a spray chamber which is converted to an aerosol via a nebuliser. During this process, only the very fine particles are injected into the inductor. In the inductor, the sample aerosol is further dried and vapourised due to the high temperatures (10000 K) in the sample carrier. In this process, all chemical bonds are broken, allowing for the vapourisation of each individual atom (Fig 2b). The free atoms collide with plasma, allowing them to transition to an excited state. Upon relaxation to ground state, the ions/atoms will emit a photon of characteristic energies, which can be used to determine the elemental origin of the ions. The total number of photons emitted is proportional to the concentration.

The ionisation plasma is typically argon gas as it is chemically inert and contains a high proportion of cations and electrons with a high electron density. In the set up shown in Fig 2a, radiofrequency (RF) is applied to a coil which produces “seed” electrons which are accelerated and collide with argon gas to form argon plasma and electrons:

Ar(g) → Ar+ + e-

About sample preparation

Solubilised solutions (aqueous or organic) are required to perform ICP analysis. Therefore, samples (<0.2 %>) are typically treated with nitric acid (HNO3) or HCl, in a process referred to as "acid digestion". Sample concentrations of <0.2% are crucial to avoid any matrix effects.

Matrix effects

Matrix effects are interferences in the analysis due ton signal dift caused by the deposition of solids on the sample apertures or signal suppression caused by salt ions. The typical salt interference is caused by oxide formation, which seems to reduce the ion flow and promotes clogging at the sample cone (the interface that analyses ion extraction). With years of research, matrix effects have typically solved through the use of OES compared to MS. ICP-OES relies on photon emission rather than ion acceleration, which makes it less susceptible to interferences.

Advantages of ICP compared to other elemental analyses

As ICP heats to very high temperatures, samples undergo more efficient vaporisation, atomisation and excitation. This allows for a wider range of elements to be analysed by ICP. In addition, the high temperature means that there is less water vapour present, in turn reducing the concentration of oxygen species and thus a lower level of matrix interferences caused by oxide formation.

References

  1. Ammann, A.A., Inductively coupled plasma mass spectrometry (ICP MS): a versatile tool. Journal of Mass Spectrometry, 2007. 42(4): p. 419-427.
  2. Hou, X. and B.T. Jones, Inductively Coupled Plasma Optical Emission Spectrometry, in Encyclopedia of Analytical Chemistry. 2000, John Wiley & Sons Ltd: Chichester. p. 9468-6485.
  3. McCurdy, E. and D. Potter, Optimising ICP-MS for the determination of trace metals in high matrix samples. Spectroscopy Europe, 2001. 13: p. 14+16-20.
  4. Kopru, S. and M. Soylak, Inductively coupled plasma-mass spectrometry (ICP-MS) detection of trace metal contents of children cosmetics. Optical and Quantum Electronics, 2024. 56(3): p. 399.

· 9 min read

9.5.2024
Over the past few weeks, I have had the desire to improve my baking skills, so I have invested time into making a perfect loaf of bread. With every small tweak in a recipe, I realised that there are dramatic changes, which motivated me to write about the changes in bread quality in relation to the chemistry.

Flour contains proteins glutenin and gliadin, which combine in the presence of water to form gluten (Fig 1). Prior to the addition of water, glutenin exists as a colloid. Upon addition of water to the flour, the chains are allowed to stretch, seperate, and form new disulfide linkages. These disulfide linkages create a network of glutenin polymer that produces the strength and elasticity of bread dough. At the same time, the smaller gliadin proteins will disperse through the glutenin polymer network, which allows the bread to "rise". It is the constituent that facilitates formation of the gluten network. Due to it's self-assembling properties (as it is highly hydrophobic), it will associate into spherical particles and absorb other nutrients such as vitamin E. Thus, the quality of the gluten network that forms is dependent on the type of flour that is used.

Schematic of gluten formation
Fig 1. Schematic of gluten formation

Mixing and kneading of the flour/water mixture encourages the gluten network to further develop. During this process, carbon dioxide is incorporated, producing a more porous dough once it is baked. Yet, we dont want the gluten networks to be so strong that they become chewy and tough. This is the reason that people turn to a "no-knead" method. Sometimes, a high water content is enough to facilitate formation of strong gluten networks.

Yet, there is one more ingredient that is required to create the gluten network... and that is salt. As mentioned in the "salting-out" post, salt helps to decrease the water content. In this instance, salt will remove water from the protein/polymer network to increase the strength and elasicity.


The initial recipe that I started with came from Nagi: RecipeTinEats. The ingredients required were:

450 g flour
2 tsp yeast
2 tsp salt
375 mL of warm watern (~40 °C)

First, I started off with a "no kneading" approach to bread making. I was unsure of the measurements for the yeast. I had the large container of active yeast as well as the packets. I initially used the packets, and with a quick google search I saw that 7 g was an equivalent of 2 tsp of yeast. Therefore, in my first attempt to make this bread, I activated one packet of the yeast in warm water. The bread was left for a few hours in a warm-ish environment to rise, and then it was moulded into a round ball and baked using the dutch oven.

After baking, the bread was very tough to cut and very dense, but it was still quite tasty and full of flavour. These bread flavours arise from fermentation. The high density is possibly attributed to a low water content. Thus, for the subsequent loaves, I went for weighing out the ingredients using a scale instead of the "cups" measurement as a scale is more accurate.

A few days later, I used the recommended amount of yeast (2 tsp), weighed out the flour (450 g to be exact) and the water. I saw that the dough was still a bit "doughy", so I added an extra 20 mL of water to the batch (395 mL in total). It was too sticky to be able to knead (Fig 2, img1), yet it felt very soft and after allowing it to rise for several hours, I baked it using the dutch oven. NOTE: I was sure that it had risen well, when the dough (before baking) was very bubbly on the surface and small movements of the bowl containing the dough resulted in a "jiggling" of the dough surface. This time, it rose more than the previous batch (likely due to the extra yeast) and was less dense than the last batch (owing to the excess water added).

second batch
Fig 2. Batch 2: (img 1) sticky dough, (img 2) moulded dough for baking, (img 3) final product.

Without a job at this point, I wanted to bake more and change the conditions to geet the best loaf. I wondered what is the impact of leaving the dough to sit for longer? What is the impact of kneading? Surely I can google this, but I wanted to experience the feeling and taste differences. Therefore, the next batch that I made, was using the same contents as above only, I allowed the dough to sit for 3 hours at room temperature, then 2 days in the fridge (covered). The day before cooking, I pulled out the dough, moulded it into a ball and allowed it to sit covered in plastic wrap in the fridge overnight. When I baked this loaf, it rose slightly more than the last batch, and was also more porous (Fig 3). From what I understand, it seems that when you put the dough in the fridge, fermentation is slowed down to allow the development of more complex flavours.

third batch
Fig 3. Batch 3: (img 1) moulded dough for baking, (img 2) final product and (img 3) a photo of the sliced bread, observing the porosity of the loaf.

15.5.2024

The next parameter that I wanted to test is the impact of kneading on the dough. Therefore, a dough was prepared as previous, however, it was kneaded for 5 minutes of before allowing the dough to rise. Due to the better properties of the previous batch of bread, the dough was immediately placed in the fridge, in a covered bowel. The dough was left for close to 22 hours in the fridge. The dough appeared to have similar textures as the previous batch, however, was less soft upon touching it.

The dough was moulded and scored (using tips that I got from vegpatchkitchen) and baked from it's cold state. The idea behind scoring is that it allows the gases to uniformly escape, making bread the rise more uniform, instead of having that weird bubble in the middle of the loaf (as seen in img 2 of Fig 3).

While the final bread loaf in Fig 4 (img 3) appears to be more uniform, without the ugly bubble in the middle, it was less porous than batch 3 (Fig 3). This was attributed to the small additions of flour that I added in order to knead the bread. As small amounts of excess flour decreases the water content, the bread ultimately became more dense. I thought this bread was the tastiest and best looking so far.

fourth batch
Fig 4. Batch 4: (img 1) dough after kneading and ready to be placed in the frige, (img 2) moulded dough for baking, (img 3) final product and (img 4) a photo of the sliced bread, observing the porosity of the loaf.

20.5.2024

This time, I doubled the batch size using the following ingredients:

900 g bread flour
656 g warm water (~ 40°C)
4 tsp salt
4 tsp of yeast

In this batch, the process was as follows. First, 4 tsp of dried yeast was added to 2 cups of warm water (equivalent to 427 g of water). The yeast was allowed to grow for 5 minutes and then added to the flour/salt mixture. The mixture was combined with a wooden spoon. As it appeared to be very flaky and floury, an extra 229 g of water was added. It appeared to be very slicky and slimy. It was too sticky to be kneaded, or even handled. This large batch was left in the mixing bowl, covered and put straight into the fridge for 22 hours.

The oven was preheated to 220°C and the dutch oven was preheated for 30 minutes. During this time, half of the mixture was taken from the large mixing bowl, moulded and scored and put back in the fridge (covered) until it was ready to bake it. The dough (on the baking paper) was gently placed into the dutch oven and baked for 30 mins with the lid on, and a further 10 mins with the lid off.

The bread was probably the best that I have made so far (I know I say this everytime... but is true). The defining features were the high porosity caused by the high water content, the uniform growth in the dough due to scoring of the loaf and the softness of the inside!

fifth batch
Fig 5. Batch 5. (img 1) risen dough, (img 2) scored dough, (img 3) baked bread out of the oven and (img 4) image of the face of the bread, showing a higher level of porosity.

The second half of the mixture was left in the fridge for 2 more days. When I removed it from the fridge (22.5.24), the dough revealed bubbles which is indicative of gas being released. It was very sticky and very difficuit to pick up. I managed to mould it into a ball, with the aid of a small amount of flour. The dough was then wrapped in plastic wrap and placed in the freezer, where it sits until I am ready to bake again. Unfortunately due to my new working commitments, I get less time to bake! I will probably bake this loaf next week. Stay tuned!

References

  1. Cho, I.H. and D.G. Peterson, Chemistry of bread aroma: A review. Food Science and Biotechnology, 2010. 19(3): p. 575-582.
  2. Sha, X., et al., The prolamins, from structure, property, to the function in encapsulation and delivery of bioactive compounds. Food Hydrocolloids, 2024. 149: p. 109508.

· One min read

It's been just over a month since I've wrote something in my blog.

For the last month and a half, I have been working through the comments that I received back. It's been a real tough time, because there were a lot of comments. I honestly felt like everything I knew about my topic was wrong. I have been reading so much and redoing all my figures/analyses. Each day, I started work at 7 am and continued until 10 pm. I even spent all my weekends working on it. Until finally, I felt proud of my thesis! Now, it is being reviewed by one of my supervisors.

The plan now is to write a couple of research papers. However, my current dilemma is that I dont want to write a paper if my supervisors do not agree with what I wrote in my thesis.

· One min read

Over the weekend, Nick and I headed to the Hunter Valley for a wedding. It was great to get away, and now I am feeling fresh to resume writing.

· One min read
  • As it stands, I have completed writing my PhD thesis. Below is a table summary of the chapters, with type of chapter, number of words (in total, incl. references, and figures) and number of pages
  • I still have a few more experiments to conduct for Research Chapter 5 and 7.
  • I still need to write up the supporting information (which will be a lot)
  • I still need to write papers.
  • I plan to complete my thesis and send by Friday 27 Oct.
Table Summary of my PhD thesis:
ChapterContentWordsPages
1Intro1193736
2Methods915027
3Research628929
4Research1125739
5Research635127
6Research688724
7Research990834
8Conclusions370011
Total65479227

· 3 min read

Last Thursday, my supervisor cancelled my weekly PhD meeting and instead requested that we sit down and go through my thesis and decide what we need to do moving forward. Both Pawel and David agreed that I should not be doing anymore lab work and just focus on writing my thesis! There it is "only focus on writing".

Productivity: From Friday onwards, I started writing all my results down. I wrote a lot in the span of 4 days and I felt that if I kept writing then I could be finished by the end of the month.

Unproductive: On Wednesday 23 August, I had a really bad day of writing. By 3 pm, I was on the lounge watching a TV show. I did not attempt to recommence writing for the rest of the evening. It really messed me around on Thursday. At this rate, I won't finish my PhD in time!

A tip to improve productivity: I was lucky this week in my Thursday meeting. I got a few tips from my supervisors about writing. David commented that the best thing to do when you are not feeling like thinking is to write out the methods chapter. He was right. Writing out my methods chapter is a simple way to get myself in the mood of writing and to continue my writing routine.

More unproductivity: This morning, I went driving around Wollongong to try and get a quote to fix my passenger-side mirror of my car. Grant from Fernhill Smash Repairs told me that he would be in touch later in the afternoon. NOTE: the passenger side-mirror is no longer afixed to the car as I nipped it off on the way home from the beach yesterday. Without a passenger side-mirror, I cannot drive my car. This means that I can't drive to North Wollongong beach! I need to paddle in the morning for me to feel fresh for a day of writing! This screwed up my whole day. At 10 am, I gave up on writing and decided to head to Innovation Campus to get some data off the computers. I ran there and remained until 4 pm..... and that is all I did today.

In the evening, Nick and I walked to The Barrel Shephard for dinner and drinks. I felt aweful, like I didn't deserve to be going out after a day of very little work and progress. Note to future self: stop going into the lab, save it for the weekend or afternoons.

· 4 min read

When I woke up at 5.55 am, it seemed like it was going to be another cracker of a day. I prepared for teaching, went for a run, did some stretching and showered all before 8.30 am. I was more than ready to make huge progress today!

I arrived at work at 9 am and from the minute I began to do things in the lab, everything went wrong. I couldn't get any good data. Around 10 am, I went to get help to fix a cable for my potentiostat (as the wires lost connection to reduce the signal). However, I was unsuccessful in getting help. A colleague/researcher said to meet her at 3 pm to repair the cable; but I couldnt wait this long as I was due to teach at 1.30 til 4.30 pm (Week 3 of Semester 2)..

By this point it was 11 am - I was feeling really tired and unmotivated.

My first thought was to go home. I lost motivation when I realised that I would only be home for 1 hour before having to leave again. Instead, I pulled out my soft back warmer from my draw and used it as a pillow. I put my head down on the desk and had an hour nap.

I woke up less tired than before, but really groggy. I packed my safety glasses and water bottle into my handbag and walked towards my car, then drove to the main campus. Travel between the innovation campus and the main campus is really tedious and it is often difficult to find parking in the middle of the day.

I was parked and ready to get out of the car at 1 pm. I walked towards Panzinis, a cafe located in front of the UOW library. I go here for coffee because they offer staff discounts and I love discouts! I ordered my coffee and it was made within 5 minutes. It was a rather pleasant experience - too bad that I was not in a good mood.

The undergraduate chemistry labs are located in building 21 on level 3. I headed here after I was handed my coffee - but I was at least 20 minutes early. When I walked into the lab, it was empty abar one demonstrator - Sue. I chatted for less than a minute before rereading over my emails that said I was only rostered for Week 9. In sheer disbelief, I spent a few minutes researching my emails and was convinced that I showed up for no reason! In embarrassment, I left and drove to North Wollongong beach. "Wow" I thought. "How stupid". "Why didn't I read my emails?"

I was pretty relieved though, because I didn't really want to teach. I don't need the extra funds that bad and it's not worth taking time away from my writing. Excited that I could fix the potentiostat, I also sent an email to a colleague, indicating my error and that I would be there at 3 pm.

Just as I was about to get out of my car and go for a dip in the ocean to calm down my anxiety and embarrassment, I received an email from Giel (the subject coordinator) who asked me to come back because I was rostered to work. Can you believe how embarrassed I was after this? It took me 15 minutes to return, park and walk to the labs. I quickly walked into the service room, dodging the lines of students waiting to collect a pH probe for their experiment. I threw on a red lab coat, my safety glasses and grabbed a pen.

I apologised several times to Giel and I literally felt like slapping my forehead because it was such a stupid thing that happened. The worst thing though, was sending a third email to my colleague telling her that I was wrong and I was meant to teach!

The labs were very slow and very basic. The students were working on acid-base titrations. In that moment, I thought that it wasn't too bad. I actually enjoyed it. I'm just glad that I don't have to teach all the time. The labs ended at 4.30 pm. I drove straight home and relaxed until dinner time.

I honestly feel like I wasted the whole day.

· One min read

Lately, I have been freaking out with the amount of work still left in my PhD. Today, I had planned to have a writing day but I realised as I opened various thesis chapters, that I have actually written a lot! At 11 am, I decided to head into the lab to try to resynthesise a monomer for my second research chapter. While searching the freezer for my materials, I came across a molecule that I had synthesised previously, but never used. It was a dibromo-compound that was initially synthesised for a grignard reaction.

For fun, I set up a 1 mL (200 mg) scale direct arylation polymerisation. For the rest of the day, I felt so happy and accomplished. I feel so excited to work this polymer up and characterise it.

To hear more about this, and see the fun I have with these reactions, visit side projects.