Materials Connect

Using adsorption science to gain insight into some key characteristics of a materials scientist

Recently I’ve been mentoring a PhD candidate through their first ever manuscript to be submitted to a journal which involves determining porosity of a material with a heterogeneous pore structure. The technique we were using relied on adsorption of nitrogen at 77 K on to the surface of pores within the material. As we went on this journey, I got the impression that we had very different approaches to our work and this made me question what it takes to be a scientist: the attitudes and behaviors that come so easily to some do not seem to manifest in others. What does it mean to be a scientist and how has this influenced materials science?

We are curious

Science is about following the evidence, asking why, and finding information on the things you don’t understand. We design experiments to investigate these things and improve our understanding. We base that investigation on a question. When we design an experiment, we think about all of the factors that could affect the outcome and we decide how we can control them. We carefully consider all of the details while drawing on our experience and scientific instinct. We are careful and thoughtful.

Dewar and Ramsay appear to be the first to report on the sorption of nitrogen and other gases at low temperature. Their separate studies, reported in 1905 and 1906, focused on the composition of the atmosphere and the separation of noble gases. Their simple curiosity about the air around them kicked off a whole series of experiments that ended up being very useful for analyzing porous materials.

We strive for understanding

Science is personal. It’s about developing your own understanding and passing it on to others. Rather than glossing over the details, pretending that they’re not important to us and that someone else will take care of them, we leap on the details and turn them over in our minds; we examine them from all angles to decide their importance in our experiments. We push them together with other details and look at how they fit together. We search books and journals to help us with the details and then list everything that we still do not know. 

After the first reported gas sorption studies in the 1900’s, Langmuir went on to develop a model for ideal localized monolayer adsorption (1916) that later allowed Brunauer, Emmet and Teller to publish a theory which supported the calculation of surface area (1938). Later, the Kelvin equation was used by Barrett, Joyner and Halenda to arrive at a very popular method for finding the pore size distribution (1951). The work of one scientist or group built on the work of another, each body of work inspiring someone to ask a new question.

The International Union of Pure and Applied Chemistry initially categorized adsorption isotherms into 6 different types (King et al, 1985), which was recently refined to closely relate them to pore structures (Thommes et al, 2015).

We are transparent and honest

We make assumptions. Once we’ve pulled together this vast body of knowledge, collected by hundreds of scientists over many decades, we look at what is still unknown and as ourselves what is logical: following all of the evidence, what could be a sensible possibility? We state these assumptions clearly and loudly so that others can understand our reasoning. We invite others to test our assumptions. We communicate our logical argument with straightforward prose, carefully defining our assumptions.

Langmuir very clearly pointed out that his model relates to a flat plane where all adsorption sites are uniform. Similarly, Brunauer, Emmet and Teller specified that their theory assumes that the completed monolayer is made of close-packed spheres. For nitrogen, each sphere is usually said to cover an average area of 0.162 nm². To calculate the Brunauer-Emmet-Teller (BET) surface area, the theory should only be applied to a part of the adsorption isotherm that matches some consistency criteria, and these criteria depend on both the adsorbent and adsorptive as well as temperature. To determine pore size, we assume that the pores are rigid and all of the same simple shape with the curvature of the meniscus dependent only on the dimensions of the pores. It is generally agreed that this method is not applicable to micropores (<2 nm in width) and only applicable to macropores (>50 nm) if the conditions can be extremely well controlled.

Rearranging the BET equation allows a straight line to be plotted so that the BET parameters can be found. The section of the isotherm to which the BET fit is applied must meet the consistency criteria, indicated on the graph by the red data points.

 

We use high-tech equipment and know how it works

Much of this understanding, scientific evidence, theory and basic physics, and even some assumptions are packaged into high precision instruments – tools that we can use to delve even deeper into science and answer yet more challenging questions.

There is a plethora of equipment out there that will automatically program nitrogen sorption at different relative pressures, and will even calculate the BET surface area and pore size distribution. These results should be carefully scrutinized. Many will default to applying the BET theory to relative pressures of 0.05 – 0.35, but of course, you should check the applicability to your material before relying on the default calculation.

 

To sum up: We are curious; we are inspired. We are scientists.

 

This article draws on a review paper by Kenneth Sing “The use of nitrogen adsorption for the characterization of porous materials”, Colloids and Surfaces A: Physicochemical and Engineering Aspects 187–188 (2001) 3–9 as well as various forum discussion on ResearchGate.

 

Beta Sheet: The Harbinger of Maladies?

The clue came from a disease endemic to the Fore people in Papua New Guinea, who happened to be occasional cannibals.

It took scientists decades to figure out that infectious misfolded protein aggregates, called prions, were the causal agent responsible for the disease, called Kuru. The specific type of encephalopathy involved in Kuru spread through consumption of human tissues containing the misfolded protein aggregates. Infectious protein aggregates are, of course, not how most communicable diseases spread (often, the nucleic acids (DNA or RNA) in viruses or bacteria are the causal factors).

The symptoms of the disease included uncontrollable shaking, due to the neurotoxic effect of the prion aggregates. Even in popular culture, sometimes cannibalism is associated with loss of motor skills (see "The Book of Eli” starring Denzel Washington). We now know a host of prion diseases — most notably Cruetzfeldt-Jacob disease.

Pathological prion aggregates tend to be rich in a form of protein structure: called beta sheet. Imagine a stack of protein strands that form tape like filaments — that’s what beta-sheet structures look like under electron microscopes. Beta sheets are stabilized by both hydrophobic effect and inter-peptide hydrogen bonds and they can be extremely stable and strong. They show up in super-strong structural proteins such as spider silk and squid suckerin.

Misfolded beta sheet aggregates have been implicated in many neurodegenerative diseases: amyloid beta for Alzheimer’s, polyglutamine for Huntington’s, and alpha-synuclein for Parkinson’s. However, targeting such amyloid aggregates has led to multiple failed clinical trials in recent years.

There is a benign side of beta sheets, which can be useful for the host organism. For example, bacteria such as E. coli use amyloid proteins to build functional fibers called curli. And, in fact, a few researchers have suggested possible positive effects of amyloid proteins against microbial infection. Traditionally, biology and materials science have been treated as two very different subjects but now they're intertwined in a most intriguing way — as research groups around the world build beta sheet based nanofibrous materials as functional biomaterials!

Thus, it’s undoubtedly true that beta sheet protein fibers can be strong functional materials, even if formation of pathological beta sheet aggregates can be disastrous for the host. What doesn't kill you, perhaps, can make you stronger indeed!

Materials that connect our body

Hi, I am Biplab Sarkar, a first-time blogger here at Materials Connect. For my first post, I decided to write about the very materials that connect our body, i.e., the materials underlying the matrix that connects the cells.

The uniqueness of the extracellular matrix (ECM) is the impressive interplay among its constituents, mainly based on supramolecular principles. We think of cells as basic building blocks of life. In the most rigid sense, ECM is ‘lifeless' — it cannot reproduce on its own.

During evolution, multicellularity emerged as a preferred way of avoiding predation and enhancing chance of overall survival. Multiple cells could perform almost any task better than a single cell. Multicellularity also enabled cells become specialized, finely tuned to perform one task. However, as cells became more ‘social', they needed an efficient medium to interact with each other. Perhaps you can call it the internet of cells.

How do you design a ‘lifeless’ medium that helps cells interact with each other, and is at the same time ‘adaptable’ to external stimuli? Cells found out a two-pronged approach- a mechanical one and a chemical one.

The physical basis of life is an oil-water interface, in other words, an aqueous medium with soluble ‘stuff’ in it and an insoluble barrier that can separate chambers of watery medium (think compartments of organelles inside a cell, or cells themselves in a tissue), or can help propagate mechanical forces efficiently. The chemical interaction between cells (and also in fact within the cells themselves) depends on the transport of soluble chemical signals. For the mechanical signal propagation, cells devised a network of insoluble fibers. Actin fibers, microtubules and intermediate filaments form the intracellular network (‘cytoskeleton'). Collagens, and to a less extent, elastins form the extracellular insoluble network. The extracellular networks can be two-dimensional sheets (basement membrane) or three dimensional materials (cartilage).

For chemical signaling between cells, you need signal transduction pathways. These pathways become activated as soluble signals bind to cell-surface receptors, and operate through a series of phosphorylation/dephosphorylation reactions. Local concentration gradients of these soluble signals is thus instrumental for ‘talk’ among cells. Individual cells can sense chemicals in their vicinity, and the concentration gradient of those chemicals.

For propagation of mechanical stimuli, the intercellular cytoskeleton must be linked to extracellular fibrillar framework across the cell membrane, or to the cytoskeleton of another neighboring cell. Integrins, and cadherins, respectively, are transmembrane receptors that perform these roles. The organization of the extracellular matrix thus has two preconditions: it has to be an insoluble network, and it should be mechanically coupled to the intercellular cytoskeleton.

And the most amazing aspect is that perhaps the very cells that interact with these rope-like fibrous materials are responsible for producing the materials in the first place. Extracellular materials of the tissue, produced by the cells, for the cells!

…

You can reach me via Twitter (@biplab_chem).

Invest in your future: Go to seminars

When I was working on my PhD (over six years ago now), I was so focused on my own research that I never really saw any value in attending seminars or guest talks from invited speakers. Unless their research was directly relevant to my own work I just didn’t see how it would benefit me. With hindsight, this was a pretty daft viewpoint.

At the time I was so wrapped up in my research that I’d totally failed to see all the other benefits that the PhD experience provides, benefits that would be much more useful to my future career development.

While part of the PhD experience is certainly about carrying out novel research, a much bigger part of this experience is all the skills that you learn along the way. I’m not necessarily talking about the skills required to collect high quality microscope images or to use data processing software, what I found far more valuable were the transferrable skills. These skills are things like the ability to apply critical thinking to some results, the best way to talk about my work so that other people could understand it, and how to tackle a problem from different angles to find a good solution. Yes, I developed some of these skills by immersing myself in my own research but I think I’d have picked them up far more quickly if I’d made the effort to actively listen to other people talk about their work, and really tried to understand it. I think this would also have helped with the inevitable job-hunt that ensues once you’ve finished a PhD.

It’s fair to say that I now make much more effort to engage with these research seminars and, rather than just letting the words wash over me like they would have all those years ago, I now find it easier to stay attentive and can usually think of a question or two to ask at the end. This hasn’t exactly come easy but I’ve discovered a few tricks that have helped.

The easiest trick is simply to write down what the person is saying. Much like I did when I was an undergraduate who sat in a lot of lectures, I find that picking out the key points, or those that seem important really help me to stay focused. To continue the undergraduate lecture analogy, it also helps to imagine that someone might ask you to summarize the talk afterwards, a bit like the exam you’d sit at the end of the semester.

Another good idea is to make use of social media, although of course I don’t mean during the talk itself. I find LinkedIn and Twitter really useful for finding out about wider research and, since social media usually encompasses a broad audience, its often pitched in a way that you don’t need to work in that exact field to understand it. Just twenty minutes of daily browsing has really improved my general science knowledge which in turn has helped me understand the more specific information provided in someone’s talk. I guess you could say that it makes the talk more meaningful to me.

My final piece of advice is; if you’re really struggling to pay attention then you could assess the style and delivery of the talk, rather than the actual scientific content. Ask yourself whether the talk is logically structured, are the slides too cluttered, can you easily match up what the person is saying with the content of visual aid. It’s also worth asking yourself if there are any aspects of the presentation that you like and could apply to your own talks, or conversely, if there something about the talk is really off-putting then know to avoid doing something similar for your own work. When I do this I often find that I’ve actually taken in quite a lot, and could probably explain to someone what I found interesting about that person’s work.

The skills that I’ve now developed from critically listening to someone else’s work have certainly helped me with my own research. More broadly, these critical thinking skills would be just as useful should I choose in the future to change my career path and move away from research. It seems to me that, although you’ll develop as an independent researcher during your PhD, the transferable skills you acquire will be even more valuable.