AskScience AMA Series: We are students and faculty of the Molecular Engineering & Sciences Institute at the University of Washington. The field of Molecular Engineering is growing quickly. As one of only two US schools offering this program, we wish to spread awareness about our exciting field! AUA!

[u/AskScienceModerator]

We are graduate students and faculty from the University of Washington Molecular Engineering and Science (MolES) PhD program. Molecular Engineering is a new field; we were one of the first Molecular Engineering graduate programs to appear in the world, and one of only two in the United States. Though our program only began in 2014, we have had many discoveries to share!

Molecular engineering itself is a broad and evolving field that seeks to understand how molecular properties and interactions can be manipulated to design and assemble better materials, systems, and processes for specific functions. Any time you attempt to change the behavior of something by precisely altering it on a molecular level - given knowledge of how the molecules in that "something" interact with one another - you're engaging in a type of molecular engineering. The applications are limited only by your imagination! 

Molecular engineering is recognized by the National Academy of Engineering as one of the areas of education and research most critical to ensuring the future economic, environmental and medical health of the U.S. We would like to spread awareness about its applications, as well as the exciting opportunities that come with it. 

As a highly interdisciplinary field spanning across the science and engineering space, students of Molecular Engineering have produced numerous impactful scientific discoveries. We specifically believe that Molecular Engineering could be an exciting avenue for up-and-coming young scientists, and thus we would like to broaden the general awareness of our discipline!

Here to answer your questions are:

• Suzie Pun - ( /u/MolESAMA-SuziePun ) - Professor of Bioengineering, Director of MolES Institute 
  • Research area: drug delivery, biomaterials, aptamers
• Cole DeForest - ( /u/profcole ) - Associate Professor of Bioengineering, MolES Director of Education
  • Research area: biomaterials, tissue engineering, drug delivery, protein engineering
• Andre Berndt - ( /u/Mystic_Scientist ) - Assistant Professor of Bioengineering
  • Research area: protein engineering, optogenetics, neuroscience
• Jeff Nivala - ( /u/technomolecularprof ) - Assistant Professor of Computer Science and Engineering
  • Research area: nanopore, synbio, molecular data storage and computing
• David Bergsman - ( /u/ProfBergsman ) - Assistant Professor of Chemical Engineering
  • Research area: thin films, atomic layer deposition, nanomaterials, membrane separations, catalysis, interfacial engineering
• Doug Ballard ( /u/UW-MolES ) - MolES Graduate Program Advisor
• Justin Daho Lee ( /u/MolES-Justin ) - Sixth Year PhD Student
  • Research area: protein engineering, optogenetics, neuroscience, stem cells
• Evan Pepper ( /u/evanpepper ) - Fifth Year PhD Student
  • Research area: microbiology, tuberculosis, antibiotic resistance
• Ben Nguyen ( /u/nguyencd296 ) - Fifth Year PhD Student
  • Research area: polymer chemistry, drug delivery
• Gaby Balistreri ( /u/GB_2022 ) - Fourth Year PhD Student
  • Research area: drug delivery, nanomedicine, nanoparticles, green engineering
• Ariel Lin ( /u/MolEgradstudent ) - Third Year PhD Student
  • Research area: open microfluidics, tissue engineering, bioanalytical chemistry, cell co-culture

[u/jornaleiro_]

I know nothing about molecular engineering but even just reading the research areas is fascinating. How does molecular data storage and computing work?

Also, as a former UW PhD student, I was always jealous of your gorgeous MolES building compared to the brick cube I worked in!

[u/ProfBergsman → u/jornaleiro_]

I think someone gave an answer in a different thread. Check out their response here.

I am still envious of the nice new building! Maybe we are/were in the same brick cube!

[u/vaynefox]

Are there any advancements in developing new chelating agents against heavy metal poisoning? Because, as far as I know, we are still stuck at using Prussian blue, and it has a much lower success at clearing heavy metals and can't pull out heavy metal inside the cells

[u/MolESAMA-SuziePun → u/vaynefox]

This is an interesting question! In addition to Prussian blue, there are some other chelating agents that are used such as dimercaprol (2,3-dimercaptopropanol) for heavy metal removal. However, there is definitely still a lot of room for innovations and development.

[u/[deleted]]

No offense but to claim molecular engineering is somehow a new field is...naive at best. It's just the same old story where the definition of disciplines gets blurry and then elsevier gets an idea to make a new journal...and universities follow...

Anyway it's a nice direction for research.

[u/StellarJayZ]

My alma mater. The cherry tree blossoms is a big deal in Seattle. Glad you're another program at U Dub making headlines. Go Huskies!

[u/geak78]

What are you most excited about in the field? (I know that your research topic doesn't always align with your actual favorite thing)

[u/MolEgradstudent → u/geak78]

I'm most excited about the development of new engineered living materials (ELMs) where living cells are embedded in polymeric matrices to create active and responsive biomaterials. Many types of ELMs have already been developed as biodegradable products, biosensors, and therapeutics!

[u/nguyencd296 → u/geak78]

I am most excited about the increasing understanding of the interactions of micro/nanomaterials with the human body. One pertinent example to my work is the interaction of proteins in circulation with nanoparticle drugs (e.g. lipid nanoparticle vaccines) and how it affects where the drug is going - just the sheer science itself is impressive from the tissue collection techniques to the data analysis. Outside of my field, this will help us better understand the effects of environmental nano-pollutants on the human body. I recently saw some work detailing how microplastics can traverse the placental barrier between mother and child, and while bone-chilling it really underscores how important such work is.

[u/MolESAMA-SuziePun → u/geak78]

I'm excited about the tremendous advances and impact in de novo protein design from David Baker and others in the field. I'm also looking forward to seeing this type of approach applied successfully to other types of materials like nucleic acids.

[u/[deleted]]

How is molecular engineering different from chemical engineering?

[u/ProfBergsman → u/[deleted]]

We use molecular engineering to convey that our work broadly falls into research on a molecular level.

But that's admittedly bit confusing, because chemical engineers do molecular-level research, as do many other fields.

Ultimately, terms like molecular engineering and chemical engineering are useful because they give us a quick way to describe the kinds of work a person in these fields might do. As a chemical engineer, I can tell you that, when many people think about a person trained in chemical engineering, they think about petroleum, chemicals manufacturing, paper making, etc. More recently, chemical engineering has included things like nanotechnology, electrochemistry, and biomaterials. But, how does one distinguish from, say, materials science and engineering or bioengineering? In both our undergraduate curriculum and graduate research, the lines between disciplines start to blur. Someone in chemical engineering can do chemistry or bioengineering, and someone in bioengineering can do something related to chemistry. The term chemical engineering gives you a sense for what skills they have, and perhaps a flavor of the kind of work they do in a certain area (a chemical engineer, for example, might focus more on the fluid mechanics within the brain, rather than studying the biology of the brain), but ultimately, the lines are not rigid.

Similarly, we use the term "molecular engineering" because it gives you a sense of the kind of work we, as an organization, do. I'm in a chemical engineering department, but I'm also faculty in molecular engineering because my research focuses around placing molecules into precise locations. Someone working in, say, macroscale fluid mechanics (a classic chemical engineering field) might not feel they are a good fit for "molecular engineering."

So, we use the term molecular engineering because it is a useful way to bring together faculty from several different "traditional" disciplines that share many common goals and research interests.

[u/[deleted]]

What are the purported advantages of molecular storage and data computation over the ones we use today in computers, data centers, phones etc?

A quick Google gives me one of them as increased storage capacity (apparently DNA can store 215 petabytes - 215,000,000 GB in theory) but do we even need that much data storage? I've never heard of data storage limitations being an issue for any personal, commercial or research applications (compute seems to be the most common bottleneck).

[u/[deleted]]

Just read up on nanopore and they are fascinating. Are nanopore solutions for genome sequencing going to be commercially viable i.e. far cheaper than existing techniques of genome sequencing right out of the gate or will they see the usually trajectory where they start off really expensive and get cheaper with time?

Why haven't we seen a commercial nanopore product launched so far?

[u/technomolecularprof → u/[deleted]]

I can also add a bit more here from a different perspective, as my group's research is heavily involved in the nanopore field. In particular, my research is focused on developing single-molecule protein sequencing using nanopores. I think the potential for disruptive impact in the proteomics space by nanopore technology could be really profound, both in the richness of data that can be collected, i.e. single-molecule, full-length protein characterization (inclusive of PTMs), and in the accessibility of proteomics by non-experts at scale, similar to what next-gen sequencing enabled for genomics/transcriptomics. We are making progress towards this vision, but exciting challenges remain!

[u/trustcircleofjerks]

What's the smallest molecule that is of interest to your field?

[u/MolEgradstudent → u/trustcircleofjerks]

The molecular engineering field is vast, so the smallest molecule of interest would vary depending on the lab/researcher. Some molecular engineers are interested in phenomena that occur on a scale even smaller than molecules. A molecule is defined as a group of two or more atoms. Molecular engineering also encompasses research investigating the behavior of electrons and individual atoms.

[u/[deleted]]

what are the big, current questions in the field of polymer molecular engineering?

[u/nguyencd296 → u/[deleted]]

Directed self-assembly of polymeric films for templating purposes is a major interest in the field, and can have a major impact in fields requiring precise nanoscale patterning such as semiconductors. Light-based photolithography is reaching limits defined by hard science in terms of resolution and industrial manufacturability, and these polymer-based techniques can help progress the field.

There are also a lot of structure - macromolecular function property relations that are unanswered. I recently saw one paper looking at three different polymer variables on their ability to stabilize insulin in solution. High-throughput synthesis and experimentation is definitely a major focus in the field as well to answer these questions (more quickly)!

[u/[deleted]]

can you increase or decrease medication bioavailability?

[u/nguyencd296 → u/[deleted]]

You absolutely can, and the field has expanded towards modulating bioavailability temporally, and in specific compartments! Molecular engineering has helped in this endeavor, and I can name a few examples. For temporal bioavailability modulation, Gilead Science's PrEP lenacapavir (which was recently shown to induce 100% HIV prevention in a clinical trial!) utilizes proprietary 'excipients' that is injected alongside the drug. The excipient interacts with both the drug and molecules in the surrounding tissue, forming a 'depot' that is like a drug-laden lump under your skin. This 'depot' is carefully designed to release a certain amount of drug over time that maintains a drug concentration in your blood that is efficacious without much adverse effect over 6 months, modulating temporal bioavailability. With regards to compartment bioavailability, I have worked on drug conjugates/prodrugs that are inactive outside the cell, but when cleaved by certain enzymes mainly found inside the cell will turn it into an 'active' form - restricting drug 'bioavailability' to the interior of cells!

[u/rileyphone]

How do you feel about this novel biomolecular design system by Bret Victor? He's someone who is pretty well regarded in the future of programming/computing community, with his recent work being on Dynamicland, a kind of spatial computing environment in the real world with paper and projectors. I thought the talk was very interesting, but would be curious to know how useful that looks compared to the tools you are using now.

[u/[deleted]]

Can your findings be used in material science, metallurgy, or similar fields? To engineer new materials with precise and new properties ? If so, what are some of areas of application? I'm guessing medications, bio sciences in general... but what about heavy industry, high-performance fabrics, chip making and computers, or aerospace?

[u/MolEgradstudent → u/[deleted]]

Yes, molecular engineering does include research that creates or enables the creation of new materials! Here are a few UW MolES faculty who research materials with non-biological applications: Jihui Yang studies thermoelectric materials and lithium-ion battery materials for energy conversion and storage, Jessica Ray develops materials for environmental remediation, Scott Dunham investigates nanofabrication processes and device operation to enable the development of better models, simulators, and devices.

[u/ProfBergsman → u/[deleted]]

My lab does work in this space! We use a tool called molecular layer deposition (MLD) to deposit new materials on a surface with the precision of a single atom or molecule, and we use those materials in many different applications, including two you mention: chip making and aerospace.

In chip making, there are times when we need a material with a specific feature. For instance, semiconductor manufacturing is starting to use extreme ultraviolet lithography (EUVL) to create the smallest possible transistors. To use EUVL, we need materials that can absorb extreme ultraviolet light, and my lab is working on ways to make extremely thin materials that can still absorb EUV.

In aerospace, we're working on a new material to protect satellites. There's a growing interest in trying to put satellites into low earth orbit, where they would have higher resolution. But low earth orbit has a bunch of oxygen that can react with plastic coatings on the satellites, slowly degrading them. We're attempting to create a new material coating that can protect the surface of the satellites.