Showing posts sorted by relevance for query microbiology. Sort by date Show all posts
Showing posts sorted by relevance for query microbiology. Sort by date Show all posts

Monday, April 27, 2026

How a Book Pulled Me from Microbiology to Engineering

I am at the age where I find myself looking back, trying to work out why I made the certain decisions I made. Some of them I understood at the time. Most I did not. Careers, in particular, for me anyways, came out of a series of stuff I tried and realized I did not like, so my story is more a series of wrong turns than a plan. When I look honestly at how it started, with me ending up in engineering instead of medicine, one thing keeps coming back: a book.

In my senior year as a microbiology major at UMass Amherst, I signed up for a molecular genetics course. The required text was the 1978 second edition of Gunther Stent’s Molecular Genetics: An Introductory Narrative, coauthored with Richard Calendar. I expected another biology book. What I got was something closer to a systems manual.

Dr. Stent did not write like a biologist. He wrote like an engineer who happened to be studying cells. He walked through gene regulation, replication, mutation, and phage behavior the way you would walk through a circuit: inputs, outputs, feedback, control points, and mechanisms you could draw on paper. He started with the experiments that produced the model, then built the model. Chapter by chapter the book treated the cell as a system you could analyze if you respected the rules. Dr. Stent had spent his career in the phage group around Max Delbrück, and that physics-trained mindset showed. Most textbooks of that era listed facts. Dr. Stent described how the field figured the facts out, which meant you understood why the model looked the way it did instead of memorizing it.

That book is where the transition started. I have told my students for years that system is a big word. A system is the difference between a pile of facts and a working understanding of something. Dr. Stent happened to come along at the moment I had finally accumulated enough background in biology, chemistry, and math to start seeing things at the system level. Without that book at that time, I am not sure I would have made the leap. With it, the leap felt almost obvious.

The summer after graduation I reread the book on the beach. I also worked through The Double Helix, James Watson’s account of the race to figure out DNA structure. Dr. Stent gave me the mechanism, Dr Watson the connection. I was hooked, though not yet on what.

That fall I started in a hospital clinical microbiology lab, planning to save money and apply to medical school. I plated cultures, ran sensitivities, and read Gram stains. I was OK at the work. Just OK. I figured out fairly quickly that I did not like it and needed a change. The IBM PC came out in 1981 and we got one in the lab. Around the same time the lab brought in a Vitek system for automated bacterial identification and susceptibility testing. Vitek came out of a NASA-McDonnell Douglas effort to detect microbial contamination on the Voyager spacecraft. Test cards held the biochemistry, an optical scanner read the cards, and software interpreted the patterns. I spent every spare minute learning how it worked, end to end. In 2012 I wrote about that experience here. Dr. Stent’s book kept rattling around at the same time. Biological systems are the most complex engineering systems I know of, and once you have read someone describe them that way, you cannot unsee it. The cell, the card, and the computer were all the same kind of object to me by then.

After two years in the lab I decided hospital work was not for me and went back to school full time. I moved to second shift so I could take engineering courses during the day. I wrote about that decision, and my friend Doug who hired me into the lab and supported the move, here. I finished an MS in Electrical Engineering at Western New England University. From there I spent decades consulting on and designing communications systems, teaching engineering, technology, and telecommunications courses, and directing a couple of NSF Centers of Excellence. Medical school never happened.

Dr. Stent died in 2008. His textbook is long out of print and the science has moved well past 1978. A copy lives on the Internet Archive at archive.org. It still reads like an engineering text written by someone who happened to be studying cells.

My copy is in a box in my cellar somewhere. I have not opened it in years, but I guarantee that if I shake it over a sheet of paper, beach sand will fall out. I’m digging it out and plan to reread it this summer, hopefully at least part of it back on a beach. One book did not decide my career on its own, but it planted a seed, and the rest was me catching up to what I had already started reading for fun. 

So thank you, Dr. Stent. You died in 2008 and I doubt you thought a microbiology senior in western Massachusetts would read your book on a beach and change his life because of it. But you wrote the stuff that pointed me toward the stuff I actually wanted to do. You were one of several people whose work or example bent my path in a meaningful way. I will continue to write about the others here every once in a while too. 

Saturday, August 11, 2012

Curiosity on Mars Bringing Back Memories

The Mars landing of Curiosity has brought back some memories when it comes to sensors and systems in space.....

It was 1980. I was a year out of college with an undergrad degree in microbiology and working in a hospital lab trying to figure out what I wanted to do for the rest of my life. At one time I had thought I wanted to go to medical school but the more time I spent in a hospital working in a clinical setting the more I realized I was not cut out for that kind of work. I loved the biology but I was struggling with the procedures - the work was 100% protocol - the same procedures over and over again with zero room for mistakes. So many of the people I worked with were so good at it - they thrived on it.  Me - I had always loved tinkering, taking things apart and trying to put them back together. Trying new things that did not always work was what I liked. Trying this instead of that. What if I did this? What would happen?

But.... when you are dealing with people's lives you can't do that kind of stuff. I have so much respect and envy for people who do this kind of work but I knew it ultimately was not for me. I loved the science but knew I had to change directions with respect to my career. Fortunately, something came along (as it often does in life) that helped me with my dilema.

In the lab one day we started testing a machine called the VITEK for McDonnell Douglas and NASA. VITEK was a fully automated microbial identification and susceptibility system that had been developed in the 1960's for use in space. The system is based on microbial growth in thin plastic identification cards that have small wells with sugars, enzymes, etc. After the cards have been inoculated with sample they are incubated at 37 degrees C and photometrically scanned every hour for either color change or turbidity. Different bacteria ferment different sugars, produce different byproducts, grow or don't grow based on nutrients or conditions, etc. Basically how they grow or do not grow is how they are identified.

McDonnell Douglas was looking to move the product from outer space into the hospital lab and we had engineers coming in and out of the lab weekly tweaking the system. We were running tests in parallel - we'd run a sample using traditional microbiological ID methods and run the same sample through the VITEK, comparing identification results. There was about a three week period when the engineers were in lots - the system was not working properly - something was screwed up in the incubation cycle and they were having a hard time figuring it out.

One of the engineers I had got to know came in with a large stack of green-bar  paper with thousands of lines of code one day. I had never seen actual code before - it was so logical and simple and organized. Really cool! I was able to look at it and quickly pick out where the error was - the incubation line was not properly placed in the incubation cycle loop. I showed the engineer what code lines needed to be swapped around and remember him scratching his head and shrugging his shoulders. Still, he made the mod and....... it worked! It was so trivial but it worked!! The engineers were looking too deeply into the code - this was sort of like a TV not working because it was not plugged in type of thing. That simple. I remember the guy telling me I should have been an engineer. I also remember him telling me the first time someone writes a program it never works and you always had to go back and troubleshoot it. I was intrigued - engineering - could it be for a tinkerer like me who likes to learn from my mistakes?

Well - long story short - my sister and two brothers had degrees in electrical engineering. They had been bugging me for a while to check out engineering. They talked me into going to see Dr Jim Masi (the same Jim Masi who was our first Director at www.ictcenter.org) at Western New England University and we were able to work out an agreement where I could pick up the undergrad courses I was missing and then move into an MS Electrical Engineering program. It took a while and most of the time was incredibly hard but I was able to complete the degree.

As an engineer I could now tinker and try new (sometimes off the wall) things and make mistakes and learn from those mistakes. And that microbiology background has never gone to waste - I know it has helped me think and approach problems a little differently than traditionally trained engineers. All good!

Tuesday, October 7, 2008

A Conversation with Biotechnology NSF Center Director Elaine Johnson

Bio-Link is an Advanced Technological Education (ATE) Center for Biotechnology that originated in late 1998 with a grant from the National Science Foundation. The Center is located on the campus of City College of San Francisco with office space at the University of California, San Francisco. Regional Bio-Link Centers across the country are located in Seattle, WA; San Diego, CA; San Francisco, CA; Austin, TX; Madison, WI; Graham, NC; and Portsmouth, NH.

At the SAME-TEC conference this past July, I had the opportunity to interview Bio-Link Director Dr Elaine Johnson. In the interview Elaine discusses the work the Bio-Link Center and Regional Centers are doing to bring students the knowledge and skills essential to the field as well as the ability to continue with more advanced education in math, science and engineering.

My undergraduate background is in Microbiology so I've always had an interest in biotechnology and related fields. If you are faculty and considering starting a biotechnology program or maybe a student thinking about a biotechnology career, you will find her interview very interesting.


Elaine and her Center's work are outstanding! You can get more information on Elaine and Bio-Link here.

We have several interviews from SAME-TEC posted and you can get them different ways:

YouTube: Watch our YouTube Channel at: http://www.youtube.com/user/NatCtrTelecomTech

Streaming
and Downloading: View streaming videos and download content using your web browser at: http://nctt.org/podcast


iTunes
: If you have iTunes installed you can watch and listen to this one, watch and listen to others, and subscribe to our video and audio podcasts by following this link.

We're planning and looking forward to next years conference. Watch here, our center websites and SAME-TEC.ORG for 2009 Conference information and updates.

Thursday, September 25, 2025

My Friend Doug

Me, Cedric, Doug - around 1982
Two weeks ago, we talked. Really talked - about work, about old times, about nothing important that felt like everything. His voice was weaker than before, but it was still him. Still Doug, the guy I'd known for forty-five years, whose expertise in yeast and fungi identification had earned him recognition nationally as a mycologist.

Each visit since showed me less of my friend. First, the conversations grew shorter, his words more labored. Then came the days he mostly slept, stirring only when I gave his hand a shake. Last week, even that response faded.

His breathing changed completely. What was once steady became urgent, desperate. Each breath sounded like a struggle I couldn't help him win. He thrashed against sheets, against pain, against something I couldn't see or understand.

Was he dreaming? Was some part of him still in there, wrestling with memories from four and a half decades of friendship? Maybe he felt the strength that once earned him multiple degree black belts in judo, or remembering those early Pan-Mass Challenge rides we tackled together every summer - pushing each other through the hills, sharing water and encouragement, pedaling together for cancer research, raising money to beat the very disease that finally took him. Or maybe he was laughing at one of countless crazy memories - so many things that still make me smile.

I sat beside this man who changed my life in 1980. I'd just finished a one-year internship in clinical laboratory science, trying to figure out my next steps, when I interviewed for a position in the clinical microbiology lab. Competition was fierce, he was on the interview team and hired me. He saw something in me I hadn't yet seen in myself. Three of us became inseparable - Doug, Cedric, and me. But by 1982, my mind started to drift. Hospital work wasn't for me; I wasn't a good fit. When I decided to leave and a new direction, and Cedric headed off to Hawaii, Doug stayed behind. As he put it then, "Someone has to stick around and save lives."

It was difficult when I left the lab. In some ways, I was giving up, admitting I did not like the work. Back in 2012 I wrote about my decision to leave here.  Some were upset with my decision. But Doug - Doug encouraged me always. He understood that sometimes the best thing you can do is recognize when a path isn't right for you, even when others see it as failure.

And he did stay, saving lives for decades through his work, his dedication to understanding the microscopic world that could heal or harm. Doug was amazing at fungi identification - a skill that required incredible technique. Growing the fungi, using sticky tape to collect the flowering head, staining it, then identifying it under the microscope. I sucked at that. Doug was incredible at it. Over the years, he rose to become laboratory director, leading with the same precision and expertise he brought to every slide he examined. Through all these years, no matter where life took us, we remained in touch. If I needed anything - anything at all - he was always there. That steady presence, that unwavering friendship, became a bedrock I could always count on.

Five years ago, he had his bladder removed - the first major battle against cancer. Every three months after that, the trip to Dana-Farber in Boston for stent exchanges. He hung in there with that same determination he brought to everything - the judo mat, the Pan-Mass Challenge, his meticulous lab work, his life. He fought the good fight until the very end. 

The last word I heard him say was "pizza" a few days ago, when a dietician came in and asked what he wanted for dinner. She asked if he wanted fish - he hated fish. Even then, even barely able to speak, he managed to tell her he wanted pizza. That was so Doug, holding onto his preferences, his personality, his fight, right until the end.

Yesterday morning, things slipped away. His wife, his son, his dog, family - all left behind, trying to navigate a world that suddenly feels a lot smaller without him. The cruelest part is losing a rock-solid constant, a person who dedicated his life to saving others, who gave people a start and then a push, and who spent forty-five years being a true friend.

Rest up buddy. 

Monday, October 18, 2010

Paper City Goes Green High Performance Computing - Holyoke, MA

I've been swamped with proposal work - the end of this week is a a major National Science Foundation Advanced Technological Education submission deadline - and have not had a chance to write about the Massachusetts Green High Performance Computing Center groundbreaking in Holyoke, MA held on October 5.

I've written about this project in the past - the idea was launched over a year ago by the Massachusetts Institute of Technology, the University of Massachusetts, Harvard University, Boston University, and Northeastern University. Each school kicked in $10 million and Massachusetts kicked in $25 million from a state fund that provides money to improve roads and other public works to support economic development. At the groundbreaking both Cisco and EMC announced $2.5 million contributions to the project for a total of $80 million committed.

I've been fortunate to have been involved with the planning process (on a technician / workforce / education / economic development level) and it's been interesting to watch the process and progress of the center. Some said it would never happen but - the ground was broken a couple of weeks ago so...... it's happening!

The center has the potential to turn around the first industrially designed city in the U.S. Holyoke was built around a series of man-made canals extending from the Connecticut River that were designed to provide water power to run paper mills. Holyoke once had so many paper mills it's nickname was (and still is) "Paper City". Most of those mills shut down years ago but now - new life for an old New England mill town.

Governor Deval Patrick
missed the ground breaking because he was out on Cape Cod, attending the funeral of PFC Clinton E. Springer II who had died in Kabul, Afghanistan on September 24.

The Governor did come to Holyoke after the funeral though and got the chance to attend a Town Meeting following the groundbreaking. We had John Reynolds there with his camera and he got some great video of the Holyoke Mayor Elaine A. Pluta and Governor Patrick.



I don't think I've ever been this excited about a technical project - computers, networks, high-performance research including microbiology, genetics, chemistry, physics..... all performed in a green environmentally friendly way. The economic development potential and the kinds of companies and people the center will attract are potentially huge. It will be very interesting to watch. Pretty cool stuff!

To see more pictures, here's a link to my October 5 event Flickr photo set.

Thursday, January 10, 2013

Tektronix Oscilloscope Tutorials

I came into Electrical Engineering a different way than most - starting as a graduate student with an undergraduate degree in Microbiology. These two disciplines are slightly different - Microbiologists use microscopes and EE's use oscilloscopes :) I knew I had some catching up to do and remember one of my major goals for the summer before I started grad school was to learn how to use an oscilloscope. Fortunately I came across a free tutorial booklet from Tektronix on understanding and using an oscilloscope which made it pretty easy.


Well, even though that was over 30 years ago now, the Tektronix free tutorial materials still exist and they are even better than before. If you are starting from scratch or just want to brush up these are highly recommended. Here's a link to the tutorial page. Good stuff!

Tuesday, September 29, 2026

950 Claude Agents Found Something in Phage DNA

PCR (Polymerase Chain Reaction) was still something being figured out when I was an undergrad studying microbiology at UMass Amherst. ELISA (Enzyme-Linked Immunosorbent Assay) had been out for a few years but very few labs were running it. . Most of our work still ran on overnight cultures: streak a plate, incubate it overnight, read the colonies in the morning. A literature search meant pulling bound journals off library shelves.

On September 23, Anthropic announced that Claude agents found a previously uncharacterized enzyme system in bacteriophages, the viruses that infect bacteria. Anthropic scientists gave Claude one prompt: search a massive DNA sequence database for interesting reverse transcriptases, enzymes that copy RNA into DNA. About 950 agents ran for 21 hours and used 210 million tokens. The output:

•       200,000+ reverse transcriptases gathered

•       3,500 new candidate systems flagged

•       20 candidates written up as human-readable reports

One agent reading raw DNA beside an unusual enzyme spotted a tandem repeat array by eye. It counted the repeats, measured their spacing, compared the layout with known systems, and checked the literature before filing a report. Anthropic named the system Array-associated Reverse Transcriptases, or ART: the enzyme, a partner gene, and a repeat array. Lab work confirmed the array is transcribed into short RNAs.

Earlier studies had identified the enzyme; Claude was first to connect the array and partner protein. Nobody knows what ART does. The preprint has no peer review yet, and reruns struggled to reproduce the find. CRISPR pioneer Feng Zhang reviewed the preprint and said the result merits further investigation.

Anthropic says this kind of genome mining takes an expert weeks to months. Humans still run every experiment in its lab. The constraint now sits at the bench.

PCR took years to move from a new method into every teaching lab, and it needed Taq polymerase from a Yellowstone hot spring bacterium to get there. ART has 21 hours of agent time and one lab result behind it. Robots can pipette these days but so far anyways, they cannot dream up what to test next…. At least not very well.

950 agents turned a search that would take an expert months into a Tuesday afternoon, and handed a lab twenty leads worth checking.

Friday, August 3, 2007

Innovative Faculty and the Dyson AirBlade

A couple of weeks ago I was in Providence, RI visiting my daughter. We ended up going over to the Providence Place Mall for lunch and then we spent some time walking around the mall. We spent considerable time in both the Apple store and the Sony Style store, as we always do, playing around with as much as we could get our hands on. The piece of technology that impressed me the most on this day (I had already spent a couple of hours with the iPhone on a previous visit) was actually in the Men's Room.

You may or may not be familiar with Dyson - a UK company started by James Dyson to make bag-less vacuum cleaners. In the 1970's James did a lot of vacuuming and found himself constantly emptying the bag on his Hoover Junior to maintain a high level of suction. Frustrated with the performance of bag vacuum cleaners, he became obsessed with developing a new vacuum cleaner that would not clog up and brainstormed the use of cyclonic separation. After 5 years and 5,127 prototypes his pink (yes pink!) G-Force vacuum cleaner was born - the world's first bagless vacuum cleaner. Incredible design and wonderful product but without a manufacturer or distributor in the UK. Not one to give up, James started his own manufacturing company and started selling the product via catalog sales in Japan. Well it took off there winning the Japanese 1991 International Design Fair prize. Fast forward to today - James and his research team have developed products that have achieved sales of over $10 billion worldwide.

Let's get back to that Men's Room in Providence - attached to the wall were a couple of shiny new Dyson AirBlades. The AirBlade is a hand dryer that is unlike any air hand dryer you have ever seen. Hand dryers in rest rooms have always given me the creeps. Perhaps it's my Microbiology undergrad background - I've always seen them as a great way to spread germs around. Think about it - and the next time you are in a rest room read the instructions on the traditional blower models. They tell you to first shake the excess water off your hands (!) and then blow the rest of the water off your hands with warm air. Makes sense right - let's shake and then blow germ aerosols (bacteria, mold and viruses) at a nice warm temperature around the rest room............ How long can you hold your breath?

Well Dyson has come up with something a little different - here's a video to give you an idea if you have not seen one.


400 mph room temperature air scraping the water off your hands with the water passing through a HEPA filter that remove 99.9% of bacteria and mold from the washroom air it sucks in - in 10 seconds. Sounds a little far fetched right? I can give a testimonial - it works extremely well - fast, cost efficient and hygienic just as the Dyson website claims. You need to try one of these things out!

Dyson is one of those innovators with different ideas - you can bet people laughed at him with his vacuum cleaners - some are probably getting a chuckle right now over these hand dryers. I also bet the ones who are chuckling have never tried one.

Why am I writing about this stuff ? This summer I've been around the country giving presentations on new technology and its use in the classroom. Combined audience over 1000 people. In my travels I've met some faculty with amazing drive, ideas and ambition that lack one critical piece for success in the classroom - administrative support. So many incredible people who are not being encouraged or supported by their fellow faculty, Dept Chairs, Deans, VP's, etc.

On the flip side I've met just as many faculty who are supported and encouraged by their administration and yes - actually implementing some incredible work. You can pick the lucky ones right out - new laptops and smiling faces:)

If you are in an administrative position perhaps you've been on the fence about things like blogs, wikis, podcasts, video, etc. Maybe you have not taken the time to learn about these things. Maybe you've even flat out told your faculty no. Times are rapidly changing and this stuff is not going away. It's time to start encouraging and rewarding your motivated and innovative faculty.

If you are faculty in a position where you are not being supported stay motivated, keep plugging away and keep your options open like Dyson.

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Note: If you are viewing at www.nctt.org/blog go to ictcenter.blogspot.com to see the video version of this blog.

Thursday, May 1, 2025

The Birth of Modern Computer Communications: The Hayes Smartmodem

Another looking back post - it was 1982, and I was still trying to figure out what I wanted to do in life. At one time I thought I wanted to go to medical school but after working in a hospital microbiology lab, I realized that was not the path for me. Maybe I could do something in the communications field….


In the early 1980s, connecting computers over phone lines was a complex and frustrating process requiring specialized knowledge and equipment. That all changed in 1981 when Dennis Hayes and Dale Heatherington introduced the Hayes Smartmodem, a revolutionary device that would fundamentally transform how computers communicate. The Hayes Smartmodem 300 was the first modem to combine communication hardware with an intelligent microprocessor control system. Unlike previous modems that required manual configuration, the Smartmodem could be controlled through a standard command set—the now-famous "AT commands" (where AT stood for "Attention"). This innovation allowed software to directly control the modem, automating the complex process of establishing connections.

The AT Command Revolution

The AT command set, sometimes called the Hayes command set, revolutionized communications because it created a standardized way for computers to control modems through simple text commands.

 

Basic Structure and Function

AT commands follow a simple structure: they begin with "AT" followed by specific command
letters and parameters. For example:

·      ATD (Dial) - Instructs the modem to dial a number

·      ATH (Hang up) - Terminates the current connection

·      ATA (Answer) - Instructs the modem to answer an incoming call

·      ATZ (Reset) - Resets the modem to its default configuration

The genius of this system was its simplicity. Before Hayes, controlling modems required specialized hardware interfaces or complicated software. The AT command set turned modem control into simple text strings that any program could generate.

Historical Impact

When Dennis Hayes introduced this command set with the Smartmodem in 1981, he effectively created the first "smart" modem that could be programmed and controlled by software. This innovation:

  • Allowed software to handle complex connection procedures automatically
  • Enabled features like auto-dialing and auto-answering
  • Created a standard that was widely adopted across the industry
  • Made modems accessible to non-technical users

Legacy and Modern Applications

Remarkably, variants of the AT command set are still used today in many communication devices. Modern cellular modems, some smartphones, and IoT devices continue to use AT commands for configuration and control. For example, sending an SMS from some embedded systems still involves AT commands like AT+CMGS.

The AT command set represents one of those rare technological innovations that was so fundamentally sound that its basic principles have outlived the hardware for which it was originally designed. From controlling 300 bps modems in the early 1980s to configuring LTE and 5G modules today, the basic concept of "Attention + Command" has proven remarkably durable.

This standardization was perhaps the Hayes Smartmodem's most enduring contribution to computing history - creating a common language that allowed computers and communication devices to work together seamlessly, helping to build the connected world we know today.

Saturday, May 23, 2026

From Petri Dishes to Quantum Proteins

Gemini Generated Image
I’ve written here a bit about my undergrad degree in microbiology, The path to that degree came with a strong dose of biochemistry along the way. UMass Amherst, mid-1970s. I worked through enzyme kinetics, the Michaelis-Menten equation, and the standard biochem textbook of the day, Lehninger's Biochemistry. Then I spent a few years in a hospital clinical lab, plating cultures and squinting at gram stains, before I shifted into electrical engineering. The proteins we now talk about in quantum computing papers were, back then, things you drew mechanisms for on an exam and tried not to confuse.

When I saw the May 19 Phys.org piece on a 12,635-atom protein simulation, the old biochem brain lit up. Cleveland Clinic, RIKEN, and IBM used a quantum-centric supercomputing workflow to model two real proteins, T4-Lysozyme and Trypsin, sitting in water with the small molecules they bind to. Trypsin is a serine protease from your pancreas. It cuts other proteins at specific spots, after the amino acids lysine and arginine. T4-Lysozyme is an enzyme that breaks down peptidoglycan, the mesh that holds bacterial cell walls together. Both are fundamental biochem topics.

So.... what does "simulate a protein" mean? A protein is a folded chain of atoms. It does its job because of its shape and because of how the electrons inside it are arranged. Simulating it means using physics to figure out where every electron is and how it is moving. That information is what tells you whether a drug molecule will fit into the protein and stick, or just bounce off. The bigger the protein, the harder that calculation gets, and the difficulty grows fast.

Six months earlier, the same team did a 303-atom Trp-cage, a tiny model protein biochemists use as a folding test case. This run jumped to 12,635 atoms. That is a 40-fold increase in size and a 210-fold gain in accuracy on a key step. The hardware was IBM's 156-qubit Heron r2 quantum processors at Cleveland Clinic and RIKEN, working alongside Fugaku and Miyabi-G, two of the largest classical supercomputers in Japan. The team ran the quantum machines for more than 100 hours and collected 1.3 billion measurements.

So why is quantum better here? Think about it this way. Electrons in a molecule don't sit still like marbles. They behave like little waves that overlap and influence each other. To keep track of just one electron on a regular computer, you need to store some numbers describing its wave. Add a second electron that interacts with the first, and you don't double the work, you square it. Add a third, you cube it. The work doubles with every electron you add. Ten electrons is easy. Fifty electrons fills up a big supercomputer. A hundred electrons would need more memory than there are atoms in the Earth. A protein has thousands.

A quantum computer is built out of the same kind of stuff the electrons are made of. Each qubit is itself a tiny quantum object that can hold the wave behavior directly. So instead of storing a giant list of numbers to fake the physics, the qubits just do the physics. Fifty electrons need about fifty qubits, not a supercomputer. One hundred electrons need about one hundred qubits. The problem stops blowing up. Richard Feynman pointed this out in 1981: if you want to simulate nature, use a computer made of the same stuff as nature.

Back to classical computers for a moment. There is a method that gets the right answer exactly, called full configuration interaction. It is the gold standard. The problem is that every electron you add explodes the work, which is exactly the blowup I just described. It works fine for a water molecule. It is impossible for a protein.

So computational chemists fake it. They use an approximation called density functional theory, or DFT, which gives a fast, decent answer for most of a molecule. DFT is the workhorse of computational biochemistry today. It has a known weak spot, though. It struggles in the active site of an enzyme, the small pocket where the actual chemistry happens and where a drug would bind. That is the one place you need the answer to be right, and it is the one place DFT gets shaky.

That is where the hybrid setup comes in. Use the quantum computer on the small, tricky pocket where DFT fails. Use the classical supercomputer on the rest of the protein and the surrounding water, where DFT works fine. Each machine does the part it is good at. Neither could do this protein alone. Together they can.

Hybrid classical-quantum is how real chemistry gets done in the near term, not pure quantum and not pure classical. Biochemistry is one of the applications pulling the field forward, especially structure-based drug design. And atom count is becoming the benchmark people compare against, the way transistor count once was for chips.

Tuesday, April 5, 2011

Non-Destructively Checking Airplanes for Cracks

By now, everyone has seen the story about the Southwest airliner that took off from Phoenix and had a hole open up in the fuselage skin. I thought it would be interesting to take a look at one of the ways Southwest is testing their planes.

My academic background is microbiology and electrical engineering but I do have a little bit of experience (it's been a while) in material science and non-destructive testing. I spent one summer in graduate school checking ferrite plastic materials, made from a mix of plastic and iron for microscopic cracks using something called an Eddy-Current Tester.

Most of the testing we did that summer was done on little donut shaped toroids we cast ourselves using a mixture of bakelight and iron powder. After casting, these magnetic/plastic toroids were wrapped with wire and used in sensor circuits - things like ground fault interuptors that sense a rapid change in household electrical current and open the circuit before someone gets electrocuted.

This work was done in Dr Jim Masi's materials lab at Western New England College (WNEC). When Jim retired from WNEC he came over to Springfield Technical Community College for three years and was the first ICT Center Director (our Center was called the Northeast Center for Telecommunications Technologies back then) which is the position that I now hold. When Jim retired I inherited his old desk and guess what he left for me inside - some of those old toroids! These are the first things I see when I open my desk and they always make me think of Jim. Here's a picture of a couple.


So, what do little donut shaped pieces of plastic with iron mixed in have to do with testing 737 jetliners? It turns out - quite a bit. The trick with those toroids was to find a way to test them for cracks without actually breaking them - something called non-destructive testing. There are  different ways this kind of testing is typically done, one uses holography and lasers and works really well for small objects but does not work so great with large things like 737's.The other method is something called eddy-current testing and this is what Southwest is using to test their planes.

Here's how Eddy-current testing works:
  • It uses electromagnetic induction to check for microscopic cracks in conductive materials. Conductive is a key work here - the material has to be able to conduct electricity. Eddy-current testing does not work on things like wood or plain-old plastic. 
  • The testing process on something as large as an airplane involves using a circular coil (a toroid!) passed across the surface being tested. The toroid is made of magnetic material and wrapped with wire.
  • Alternating current is then passed through the coil wire, generating an alternating magnetic field around the coil.
  • The coil's alternating magnet field inductively interacts with the conductive airplane metal and generates eddy currents.
  • A second search or detector coil is then used to detect eddy currents coming from the material.
If there are no cracks or other flaws in the material, eddy current patterns are smooth and continuous. Any variations/disruptions (amplitude and phase) in wave patterns are easily picked up by the search coil and can indicate flaws in the material being tested. I like to think of a smoothy flowing stream with a large rock in the middle and how the flow pattern changes as the water goes around the rock. Think of a crack as that rock, disrupting the flow pattern of the surrounding magnetic field.

There are some limitations with Eddy Current testing - the one that concerns me the most when it comes to airplane testing is limited depth of penetration but I'm thinking airplane skins are fairly thin so maybe that really does not worry me. There are also problems detecting cracks that are parallel to the detecting coil which can be usually be worked around by rotating the detector so that one does not worry me much either.

When done correctly, eddy-current testing is a simple and highly effective method to find small microscopic cracks that can't be seen - perhaps hidden behind paint on objects like airplane skins. Eddy-current testers are inexpensive, portable, provide immediate feedback, and do not need to contact the item being tested. It works.

On Sunday, Southwest COO Mike Van de Ven issued a statement saying:
Prior to the event regarding Flight 812, we were in compliance with the FAA-mandated and Boeing-recommended structural inspection requirements for that aircraft.
I would hope the FAA, manufacturers and airlines are using eddy-current testing as part of routine airplane maintenance.