Bright Quantum Dots

Author Introduction

A wholesome tradition in academia is the notion of an “academic family tree,” which is your genealogy of mentoring relationships, and often a point of pride (or bragging rights) for scientists. If I go back a few generations in my academic family tree, I run into my academic great-grandfather, Michael Kasha. He is extremely famous in the world of chemical fluorescence and biophysics, even having a rule (aptly named “Kasha’s Rule”) describing the behavior of electronically excited molecules. Likely as a result of my academic upbringing, I find fluorescence both a beautiful and fascinating phenomenon. In my experimental toolkit, I use mostly organic fluorophores, however, I figured it's about time I looked to see what quantum dots (tiny semiconductors rather than organic materials) are all about. Hopefully, by the end of this journal club, we’ll all have a solid understanding of the chemistry of fluorescence, what is a quantum dot, and what can we do with them.

Reference Paper Citation

De Arquer PG, Dmitri VT, Victor IK, Yasuhiko A, Manfred B, Edward HS. Semiconductor quantum dots: Technological progress and future challenges. Science. 2021;373:6555. DOI: 10.1126/science.aaz8541

Summary

The Nobel Prize in chemistry in 2023 went to three scientists: Bawendi, Brus, and Yekimov, for the discovery and synthesis of quantum dots. Their initial discovery dates back to the 1980s, and since then quantum dots have not only been a useful tool for scientific research, but they can also be found in consumer electronics like televisions and computer monitors. So what are these quantum dots?

I would be amiss without taking a second to define “quantum.” It’s a word thrown around today in both the scientific community and popular media, and the true definition has become a bit blurred. When I refer to quantum here, I am talking about the smallest discrete unit of a phenomenon. For example, let's talk about photons, the elementary particles that makeup light. Photons are discrete, massless “packets” of light, that can be visualized as a little piece of a wave. A single beam of light from the sun contains millions of photons, like how a stream of water contains millions of water molecules. Photons are a “quantum” of the electromagnetic field. However, many people use quantum to mean “really small,” which in the case of our quantum dots, is also true. 

Quantum dots are nanocrystals, typically around 5 nanometers in size. They are often made from semiconductor materials, like Cadmium Selenide (CdSe) or Lead Sulfide (PbS). A semiconductor, mostly simply, is a material that is somewhere in between an insulator and a conductor. An insulator doesn’t allow for the flow of electricity through it (like a thick chunk of rubber) while a conductor does (think something metallic, like copper). Semiconductors have an electronic property known as a bandgap, which determines the level of conductance a material has. This bandgap is the minimum amount of required energy to move an electron from one energy state to another, allowing the material to act like a conductor. Essentially, a semiconductor is a conductor that needs a little kick.

When an electron is promoted to the higher energy state in the bandgap, it often won't stay there long, since the electron is much happier in the lower energy state. When the electron moves back to the ground state, it will emit a photon, which is what we perceive as light. This is how these quantum dots work. If you hit the quantum dot with a large amount of quantized energy, say using a laser, electrons will repeat this cycle of being promoted to a higher energy state and then falling to the lower energy state, all while emitting photons. The size of the crystal, and the size of the band gap, determine the color of the photon it emits, which gives a lot of control over the resultant signal.

The size of this bandgap determines the color of the photon it will emit. Take for example the first-ever quantum dot, made of CdSe. The band gap of CdSe is such that it emits photons in the visible range, so any resultant fluorescence can be seen with the naked eye. Based on the size of the particle, CdSe is typically a reddish-purple, but can be doped or altered to change the size of the band gap and produce photons that are yellow or green. 

One of the biggest issues with quantum dot technology when it comes to making biological and medical advances is the lack of biocompatibility in traditional semiconductor materials. CdSe for example, is toxic to humans if ingested, so using these quantum dots for any sort of biological imaging is extremely difficult. In a science lab, a biologist might still use quantum dots in their experiments, but most likely not in any sort of living organism. Using them for non-biological technology, however, is much simpler. QLED TVs use quantum dots to generate intense and vibrant colors, since the colors produced by the quantum dots are much brighter and clearer than anything that could be produced by LEDs alone (I highly recommend looking up images of quantum dots, the colors are stunning).

In summary, quantum dots are super tiny crystals that can emit bright and vibrant colors when excited. This excitation process is a cycle, where the crystal is given some energy (from a laser, LED, etc.), which promotes an electron in the crystal across the band gap from a low energy to a high energy state. The electron, now unhappy in its high energy state, emits a photon (light packet) and goes back down to the low energy state. This cycle repeats endlessly, constantly emitting photons from the crystal, which is the fluorescence we see with our eyes. While these quantum dots have made their way from the lab bench into our everyday lives, scientists are still working to come up with ways to make these quantum dots less expensive, more tunable, and less toxic.

Antimicrobial Peptides: The Race against Antibiotic Resistance

Author Introduction

For this journal club, I decided to take a step back from some of the fundamental physical problems I’m used to discussing, and take a look at some work related to global health. Furthermore, this is work done at my alma mater, Washington State University, and primarily authored by a colleague of mine Dr. Kaitlin Witherell. Back in the day, we were working on a single molecule fluorescence project using synthetic lipid bilayers and antimicrobial peptides (AMPs) but unfortunately, like a lot of projects in academia, it never got off the ground. But today, we can take a look at some of Kaitlin’s other work during her time at Washington State, specifically about an AMP called CDP-B11. Hopefully, by the end of this journal club, we will all have a bit more knowledge about what exactly is the “antibiotic resistance crisis”, and how antimicrobial peptides might be the way of the future.

Reference Paper Citation

Witherell, K.S., Price, J., Bandaranayake, A.D. et al. In vitro activity of antimicrobial peptide CDP-B11 alone and in combination with colistin against colistin-resistant and multidrug-resistant Escherichia coli. Sci Rep 11, 2151 (2021). https://doi.org/10.1038/s41598-021-81140-8

Summary

One of the big talking points in today's conversation on global health is antibiotic-resistant infection. The root of this problem is entirely biological, with the types of new infections emerging and getting stronger and stronger with each new life cycle iteration. This makes our current line of antibiotics less and less likely to have any effect in killing the germs and bacteria that make up the infection.

The way antibiotics kill bacteria differs based on the type of medicine. Antibiotics can kill bacteria by breaking down their cell walls, or entering the bacteria and stopping critical cellular functions. The reason your doctor will remind you to take your entire course of pills even if you are feeling better is that the antibiotics need to kill every single bacterium in your system, or else you run the risk of the remaining bacteria continuing to multiply in the presence of the antibiotic. This would, in turn, make the infection more difficult to treat the next time, since the bacteria is now used to surviving it. Furthermore, these now-resistant bacteria could spread to other people, making a much larger scale problem.

One of the reasons that antibiotic resistance is such an immediate issue is the short lifespan of bacteria, and how quickly they reproduce. Most bacteria will split in half and make two new bacteria in a matter of hours. These antibiotic-resistant traits can easily morph in a matter of days. Compare that to human evolution, which can take hundreds or thousands of years, since our generational life cycles can take 20-30 years or more.

The emergence of antimicrobial peptides as a possible therapeutic target is exciting for a variety of reasons. One of those reasons is the fact that these peptides, much smaller than a lot of traditional antibiotics, have multiple modes of action, and tend to be more aggressive. Most AMPs scramble the bacterial cell membranes, ripping holes into the cell walls of these bacteria and decimating them. Unlike traditional antibiotics, which will kill just about everything in their path, AMPs are a lot more cell-selective, targeting very specific domains in infection-causing bacteria, rather than the healthy bacterial cells in your gut for example.

This publication focuses on a specific AMP called CDP-B11, which is a synthetic form of another peptide that comes from domesticated water buffalo. The way that CDP-B11 kills bacteria is by inserting itself into the bacterial membrane and opening massive pores that ultimately kill the cell, much like the mechanism of action of other AMPs.

The authors initially wanted to look if CDP-B11 would be effective against what are known as multi-drug resistant bacteria or MDRs. They also went ahead and looked at a combination of CDP-B11 and colistin, which is a last-resort antibiotic because of its harsh side effects, to see if the needed effective dose of colistin could be reduced.

They found that indeed CDP-B11 decreased the bacterial growth of a variety of MDRs, including E. coli.  Furthermore, they found that colistin and CDP-B11 worked synergistically; the addition of CDP-B11 reduced the need for colistin to achieve the same amount of “killing power.” Most importantly, they found that CDP-B11 does not kill red blood cells, making it a viable target for further therapeutic studies.

AMPs are not our “holy grail” solution to antibiotic resistance, unfortunately. They are very expensive to produce, having to assemble the peptides amino acid by amino acid from raw materials, in most cases. Furthermore, they are relatively unstable, meaning that they easily degrade and can be hard to purify and transport. Thankfully, new methods are emerging daily to increase yields and decrease production costs of peptides, so the answer may be on the horizon yet.

Overall, CDP-B11 is a strong candidate for application in an antibiotic medication, and the effort in the scientific community continues to pursue other AMPs with pharmaceutical potential. While we aren’t out of the woods yet, there are lots of promising avenues for us to take as we race against the global antimicrobial crisis.

The “Cool” Science Behind Optical Tweezers

Author Introduction

One of the first microscopy instruments I ever built was an optical tweezing device. It was nothing fancy, but it was one of my first major scientific accomplishments that started me on the path to becoming a research chemist. Now, I’ve built all kinds of microscopes for a variety of applications, including a much more complex version of the optical tweezers I built years ago (that I will do a deep dive into later). The paper we will get into today, published in Physical Review Letters earlier this year by Cornish et al, describes the first-ever coupling of ultra-cold cesium and rubidium using optical potentials. Hopefully, by the end of this journal club, we will all have a good understanding of what optical tweezers are, how these RbCs molecules were made, and why they are so cool (literally).

Reference Paper Citation

Ruttley, D. K.; Guttridge, A.; Spence, S.; Bird, R. C.; Le Sueur, C. R.; Hutson, J. M.; Cornish, S. L. Formation of Ultracold Molecules by Merging Optical Tweezers. Phys Rev Lett 2023, 130 (22), 223401. DOI: 10.1103/PhysRevLett.130.223401.

Summary

First, let's start with what optical tweezers are on the most basic level. Optical tweezers utilize highly concentrated laser beams to trap molecules and hold them tight at a focus point. The physics concept behind why this works is Newton’s third law, which states: “For every action, there is an equal and opposite reaction.” The highly focused laser beam refracts (or is bent) through objects caught in its path. The energy of the laser light is imparted on the object caught in the trap. Because of Newton's third law, the object then experiences a “restoring force” that holds it in place. This restoring force is greatest in the center of the trap, where the highest energy of the laser beam is concentrated, resulting in objects near the center of the laser beam to be “pulled in” and kept there. 

For this to happen, the laser power must be extremely high relative to the object size. This is why we don’t have to worry about walking into a stray reflection of sunlight and being stuck there forever. For example, to trap a red blood cell, you would need a laser beam in the milliwatt power regime, which is strong enough to cause damage to biological tissues if proper experimental design precautions aren’t taken. However, in this study, Cornish and coworkers were looking at single atoms of cesium and rubidium. A red blood cell is approximately 7000 nanometers in diameter, while the atomic radius of rubidium is 0.248 nanometers. 

Cesium and rubidium are both alkali earth metals. Among other things, this means they are both very reactive and likely to complex with each other. Furthermore, at extremely low temperatures, they both have interesting quantum mechanical properties. At temperatures near absolute 0, they form what are called Bose-Einstein condensates, which means that all the atoms come together and act like one entity, from a quantum mechanical point of view. This behavior has a wide variety of possible technical applications, from ultra-precise atomic clocks to extremely sensitive and high-resolution detectors and sensors. 

In their experimental setup, Cornish and coworkers used laser cooling to chill the cesium and rubidium atoms before merging. Laser cooling works much like optical trapping, where the atoms caught in the laser focus get trapped, causing their motion to slow, thus dropping them to a lower energy state. This drop to a lower energy state is what causes the cooling to happen (think about how much warmer you get doing jumping jacks versus standing in place). Once each atom was cooled, the beams were brought into close proximity, and their interaction potential energy was measured. This energy has been theoretically calculated, and compared well to the results found by Cornish and coworkers.

This publication highlights the first-ever RbCs molecules made using optical tweezers. Typically, these ultra-cold complexes are made using magnetic fields, also known as magneto-association. However, one of the conditions for magneto-association to work is the two atoms must have a Feshbach resonance, which means they “vibrate” in a way that allows them to interact and form a molecule. This optical tweezing technique sidesteps this requirement, opening the door to study a wider variety of atomic interactions, and in turn more complex physics. Specifically, the authors are looking towards investigating high-fidelity entangling gates between molecules, which is currently a very hot area of research for quantum information processing. 

Exploiting Newton’s third law, we can trap objects as big as cells and as small as atoms using highly focused light beams. Photons (the energy packets that light is made of) impart energy onto a molecule, and the molecule refracts some of it back, keeping it nicely in place. We can then move these beams around with the molecules trapped inside to measure how they interact with other particles in their surroundings. Making RbCs is an exciting step forward when it comes to understanding the fundamental quantum-mechanical interactions between the atoms that make up our world. 

DNA Origami: Art on the Molecular Scale

Author Introduction

As someone who has worked as a professional chemist for the majority of my academic career, I would argue that making a reaction run is just as much an art as a science. Following a well-outlined protocol is relatively trivial, but having the finesse and feeling to get a meaningful and high yield is a craft, that requires both time and patience to master. Today's journal club takes this idea of melding art and science to talk about DNA origami, an exciting area of research that has started taking off in the past few years in order to make biologically compatible single-molecule machines and drug delivery systems. The paper we will dive into today, published in Nature Nanotechnology earlier this year by Ray et al, describes a nano-scale molecular machine made from DNA, that can drive itself forward using two propeller “arms”, and bring a “follower” molecule along with it. By the end of his journal club, I hope that we all walk away with an insight into the rapidly developing field of DNA origami, and a new appreciation of the art of science.

Reference Paper Citation

Centola, M., Poppleton, E., Ray, S. et al. A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower. Nat. Nanotechnol. (2023). https://doi.org/10.1038/s41565-023-01516-x

*For a note on the history of origami

https://www.britannica.com/art/origami/History-of-origami

Reis, J. (2016). Origami: History, folds, bases and napkins in the art of folding. In Guimarães, N., Paio, A., Osório, F. C., Oliveira, M. J., e Oliveira, S. (Ed.), Architecture In-Play International Conferences Proceedings 2016. (pp. 211-218). Lisboa: Instituto Universitário de Lisboa (ISCTE-IUL).

Summary

The argument over who invented the art of paper folding we know as origami is still hotly debated. Most scholars would agree, however, that it likely began in or near modern-day China, thousands of years ago, coinciding closely with the invention of paper by Cai Lun, a Chinese court official in 105 AD. The influence of these origami folding techniques can be seen in the history of peoples across the world, with different cultures having a signature style or fold pattern in a variety of mediums, including traditional paper, hemp, cloth, and other textiles. I highly recommend doing a deeper dive into the cultural history of origami for anyone who might be interested.

When it comes to DNA origami, scientists quite literally fold custom fragments of DNA like paper to make specific shapes and designs with particular functions. DNA, or deoxyribonucleic acid, is a polymer made up of four base pairs (adenine, thymine, cytosine, and guanine) attached to a double-stranded helix phosphate backbone. Scientists can build custom strands of DNA by attaching these four base pairs together one by one. In order to make these origami folds, “staples” are made by exploiting the fact that base pairs bind specifically; in this case, adenine and thymine only bind to each other, and so do cytosine and guanine. By carefully calculating and placing these base pairs, the DNA will fold into a variety of shapes with different functionalities.

Most molecular machines in the body are passive, moving via what is known as Brownian motion, which is the random, intrinsic motion of molecules in a fluid (a very well described, but often forgotten, contribution to physics by Albert Einstein). Small molecule motion can also be driven by chemical gradients, temperature fluctuations, or a host of other downstream effects. In this article, Ray and coworkers exploit the reaction of RNA polymerase to control their nanoscale origami motor. The motor itself looks much like a triangle without the base. Mostly simply, the motor is two DNA arms connected in the middle by an RNA polymerase, which lengthens and contracts in order to make the motor “swim”.

These motors are incredibly small, only around 70 nanometers in length on the long end, which is almost 10 times smaller than an average bacterium. This is advantageous for a variety of reasons, but one of the most immediate is the ability of these molecular motors to incorporate very easily into the body.

RNA is a lot like DNA; however, it is single-stranded, and the base thymine is replaced by uracil. A polymerase is an enzyme found in the body whose primary function is to take one chemical in and make it something else. Putting these two concepts together, the RNA polymerase’s main job is to synthesize RNA, which is a polymer, from nucleoside triphosphates (NTPs). The way that this motor swims is by the RNA polymerase enzyme consuming NTP, lengthening the strand of RNA attached to each arm of the motor, allowing it to spring open. Further chemical modifications were used to alter the rate of RNA transcription, allowing the machines to swim at different rates, and open and close based on how long the newly strung RNA stayed bound to the other arm of the machine.

In order to make a passive “follower”, Ray and coworkers made another similar triangle motor, without the RNA polymerase in the center, that simply bound to the original motor at the tips, effectively making a diamond shape. Once linked, the original motor moved with its passive follower, opening and closing to propel the entire diamond forward. 

DNA motors like these have a variety of possible future applications. For example, this motor can change the rate it swims based on the amount of NTP present, meaning it is responsive to a chemical gradient. One can imagine a DNA origami construct being designed to respond to a very specific chemical, maybe one leached by a certain disease or infection. A DNA origami construct could be engineered to carry a drug payload specifically made to treat a specific disease, which would then directly “swim” and deposit the drug at the infection site. Because these motors are so small and are made up of DNA base pairs that already exist in the body, incorporation into your cells would be relatively easy. Furthermore, drugs that often give rise to nasty side effects when consumed by traditional methods (orally, intravenously, et cetera) could have their adverse effects mitigated by the fact that they would be absorbed only where needed, and not throughout the entire body. 

While drug delivery is one of the most common themes in the development of different DNA origami motors, scientists are also looking at how these machines can be designed for applications like biological computing, and highly specific biological-based sensors. The field of DNA origami is rapidly evolving, however, the design and construction of these motors is limited by the computational power needed to design these long strands of DNA, as well as their one-by-one assembly method.

When it comes to looking for the next generation of scientific breakthroughs, scientists are turning to inspiration from the natural world to engineer solutions made from bio-compatible materials. By exploiting the chemistry of DNA, scientists have been able to make mechanically active motors that can move with and deliver passive payloads. The world today looks like a very different place than when our ancestors were developing the technology to make paper and fold it into a variety of shapes for aesthetic and industrial purposes. However, the same artistic curiosity permeates through generations, and still inspires the work being done by scientists today.

Ocular Aquaporins

Author Introduction

Most of my dissertation work for my Ph.D. was on aquaporins, which are tiny water-transport proteins that live in your cell membranes. I spent five years studying the single-molecule interactions between aquaporin proteins, and they will always hold a special place in my academic heart. The review article for this journal club, published in the Journal of Physiology on October 14th, 2023, by Schey et al., dives into the complex relationship between aquaporins and the biology of the eye. I hope by the end of this journal club, we will all have a better understanding of what aquaporins are, and what role they play specifically when it comes to our vision.

Reference Paper Citation

Donaldson, P.J., Petrova, R.S., Nair, N., Chen, Y. and Schey, K.L. (2023), Regulation of water flow in the ocular lens: new roles for aquaporins. J Physiol. https://doi.org/10.1113/JP284102

Summary

Proteins are small molecules that reside in every cell in your body. They are biological workhorses, making sure chemicals get metabolized, and your cells get all the nutrients they need.  Aquaporins are a specific group of proteins, known as a family, whose specific function is to ensure that your cells have a healthy flow of water in and out of them by forming small pores in your cell membranes to facilitate what’s called an osmotic gradient. This osmotic gradient is a force that balances salts and other dehydrating ions in your system to ensure that water will only flow in the direction it is needed. This is a lot like when you grab a warm coffee cup with cold hands. Your hands will get warmer, and the cup will get colder…it is quite literally against the laws of physics for the reverse to happen (unless some work is involved, but that’s a different discussion about the second law of thermodynamics).

These aquaporins are found in all different tissues in your body, including the eye. The eye is a complicated organ, but in the context of this aquaporin discussion, we can think of our eye as a lens (like the ones found in your glasses), made up of a bunch of different types of cells, that is connected to the wall of your eye by a complex bundle of muscles, nerves, and other tissues. These tissues flex and relax to adjust the lens to keep whatever you are looking at in focus. Changing the shape of the lens changes the image that is projected on the retina at the back of your eye, which is read by the optic nerve and transmitted through your nervous system to be perceived by the brain as sight.

There are 12 different types of aquaporins in humans, all with slightly different functions. This review article specifically focuses on aquaporin 5 (AQP5), because recent experiments have found the AQP5 variant in all the different cell types in the lens. Other variants like AQP1 and AQP0 are also found in the eye, but not as prevalently, and serve more specific functions. AQP5 regulates the flow of water in and out of cells, and the eye tissues respond much like a sponge, expanding when they're full of water, and shrinking when dry. AQP5 regulates the function of the eye in a similar way. By controlling the amount of water in the eye, the tissues expand and contract, putting more or less tension on the lens to focus the image projected onto your retina.

Some common afflictions of the eye include cataracts, which is a clouding of the lens, and presbyopia, which is the inability of the eye to focus due to the breakdown of the tissues that put tension on the lens. This is why a lot of people will require reading glasses at some point in their lives, especially as they age. With AQP5 being found in basically every tissue type in the eye, it is a great candidate for looking at possible cures or preventative treatments for these types of diseases. Proteins don’t usually work alone, however. They are part of a vast protein and small molecule network called signaling pathways, with one protein transporting a molecule or chemical to another, like a complicated game of telephone. One of the reasons for this cascade is to have multiple points of control in the body when it comes to regulating cellular function.

Physiologists have recently found that transient receptor potential vanilloids 1 and 4 (TRPV1 and TRPV 4), which are proteins that transport calcium in your cells, (amongst other things) are involved in a signaling cascade that regulates the influx and behavior of AQP5 in the eye. The passing of calcium, potassium, and other small molecules between these proteins in the signaling cascade are part of a two-armed feedback system, that both up and down regulates the amount of pressure inside the lens tissues. Discovering these protein relationships is key to understanding exactly how the body regulates the water pressure and flow in the eye. Once these complex protein networks are uncovered, work can begin to try and modulate this biological telephone game to prevent the wrong code word from being transmitted. Although these scientific studies can seem highly specific, they are an integral part of putting together a much bigger picture.

Water flow in our bodies is key for maintaining the optimal health of all our organ systems, both on the macro and micro scale. When it comes to our eyes maintaining precise water pressure is imperative for keeping clear vision, and preventing ocular degeneration as we age. One of the key players in this is aquaporin proteins. Recent work has started to unfurl the complex relationships between proteins, water, and eye function, with the ultimate goal of preventing or curing these often-age-related degenerative diseases.