Two Belgian Wins and a Belfry

Since my last blog post, us IMEC interns have definitely kept busy: working, exploring Leuven, taking day trips, and the occasional grocery store visit have made us more accustomed to living here. Being in Belgium for the summer has been especially exciting thanks to Eurocup! This past week, we saw Belgium win against Sweden and Hungary, which sent the team to quarterfinals. For the Sweden game, we staked out a spot in Oude Markt two hours early, and barely made it in time to find a place to watch one of the large TVs on display in the street. The square was full of thousands of enthusiastic Belgian fans, each dressed in red with a Stella Artois in hand. When Belgium finally scored in the second half, the crowd went wild! It’s hard to describe what happened, but it was crazy and I’m pretty sure none of us had experienced anything like that goal in Oude Markt.

This past weekend we took a day trip to Bruges, a city I’d been hyping up for a long time because I’ve seen a movie that takes place there. I wasn’t disappointed--Bruges ended up being my favorite city so far, with its canals, cobblestone streets, and quaint red buildings. We climbed a 366-step spiral staircase to get to the top of the famous Belfry, which had an amazing view of the city. The “great Belfry weather” (quote by Chris) was perfect for exploring the many historical landmarks and buildings that call Bruges home.

At IMEC I’ve been getting the hang of the lens-free imaging set-up, which once seemed to have a million pieces that each needed adjusting whenever you needed to move the set-up to another place. Luckily there’s not a million pieces, and it’s been a really useful tool to see and quantify heart cell contractions without the use of cell-toxic dyes. Last week I spent some time simulating re-entry loops in cardiac tissue by making holes in the cell monolayer, which can make the action potential of the contraction move in cool-looking patterns.

Lakyn Mayo is a rising junior in Materials Science and Engineering at Johns Hopkins University and an IMEC intern with the Johns Hopkins INBT IRES program. She likes dogs, mountains, and getting lost running in new places.

Optimizing qPCR and optimizing fun

It’s hard to believe that we’re halfway through our stay in Belgium. Work at imec has picked up and all of us are making headway on our projects.

My project is focused on optimizing cycling conditions for ultra-fast qPCR on-chip. Quantitative PCR, or real-time PCR, is similar to traditional PCR, but takes fluorescence measurements during the exponential growth phase of the amplicon. This form of PCR is preferred to qPCR in most applications because it can tell us exactly how much DNA was amplified from the original sample.

Ultra-fast qPCR, as its name would suggest, is an accelerated version of qPCR and can be performed on microfluidic chips. Traditional PCR can take several hours to complete, qPCR around an hour, and ultra-fast qPCR on the order of minutes. However, some complications arise from performing PCR so quickly. One common issue is the formation of primer dimers: primers that have annealed to one another and become amplified. Right now, I’m trying to find what the best cycling conditions and primer concentrations are to avoid the production of PDs. We’re using a new set of tailed and tag primers to circumvent PD amplification, but are running into issues with amplification of the template. I’m running a lot of experiments to see what these optimal conditions are, so hopefully I get some positive results soon!

Aside from work at imec, the other Hopkins students and I have been continuing our weekend travels. Since last time, we’ve been to Brussels and Bruges, which were super fun and beautiful to visit. Brussels is the capital of both Belgium and the EU (well, de facto capital), so it has a great city vibe and lots of buildings, museums, and parks to see. The following weekend we went to Bruges, which has been my favorite Belgian city so far. Cobblestone roads, great church spires, canals, and the famous belfry give Bruges an ancient, yet incredibly charming, feel.

This weekend, my family is here on vacation, so I’ll stay with them in Brussels and take them to some of the cities I’ve visited in Belgium. Next weekend, we’ll meet up again in Paris to spend time with family friends. I’m so glad to have my family here with me, and now that I’ve got the rest of my weekends in Europe planned out, July looks like it’s going to be a fun one!

Stephanie Cai is a rising junior BME with a focus area in Instrumentation. At Hopkins, she is a member of the Wang lab, a leader for Encore Music Group, and on the board for Society of Women Engineers.

Watching the game in Oude Markt, Leuven.

The world-famous Belfry of Bruges.

View of Bruges from the top of the belfry. 

More waffles; this time on a stick.

Lab Work, Presentations, Paris, and London

My research in the last few weeks have primarily been experimental testing of acoustical systems in the Clinical Lab and 3D printing additional lenses to test. I worked with a function generator to create sinusoidal waveforms in bursts that lead to an ultrasound transducer to create far field plane waves in water. The waves pass through the lens and the amplitude of the resulting waver were measured using a hydrophone. The signal was observed and recorded along with the input signal and the trigger using an oscilloscope. I conducted further processing and analysis of the signal using Python. For the 3D printing, I am learning and working through the entire process of using the high quality ultraviolet printer including designing the CAD files, cleaning the final product, and curing the resin. We are printing two additional lensed to test.

Last week, the other JHU interns and I created presentations for a review meeting so others in the Life Science Technologies department at imec and in the Institute of Nanobiotechnology at JHU could learn about what we are working on. It was an enjoyable way to showcase my project and see what the other JHU interns were working on in the newer labs. At the end of the internship, I will also give a small presentation to my group at imec to show my work through the last two weeks.

On the weekends, I am continuing to travel to nearby areas of Europe. The last two weekends have included trips to France (Paris and Versailles) and England (London). My trip to France was generally short and rushed in order to fit in both Paris, Versailles, and the train rides there and back in only two days. I still did have the opportunity to visit the major tourist attractions like the Eiffel Tower, the Louvre, and the Palace of Versailles. However, two days was not enough to see the less-touristy areas of Paris and gain a true understanding of the culture there.

The past weekend, I traveled to London with Chris Argento. We had a four-day weekend due to holidays in Belgium last week, so we had ample time to visit amazing attractions like the British Museum, Houses of Parliament, and Tower of London along with exploring various neighborhoods, parks, and restaurants. Of all the cities I visited, London had by far the best food and public transportation. The city was very comfortable and exciting at the same time – definitely a place I would go to again.

All that remains are two weeks at work and a trip to Prague. Then, this amazing program is over, and I have to find another reason to go back and live in Europe!

Michael Signorelli is a second-year Biomedical Engineering undergraduate at Johns Hopkins University

A famous Full English Breakfast at Regency Cafe

View from the Eiffel Tower

The London Eye at night

Brussels, Bikes, and Brainwaves

Brussels, it turns out, has a Grand Place. Seriously, that’s the name of its central square, as I found out when I visited with the other interns last weekend. The skeptical side of my mind senses an ages-old translation error here, but for whatever reason it is now ingrained in the local psyche and written on maps. To be fair, the square is impressive: every building touching the Grand Place is liberally coated in gold accents and decorated with carved stone figures that probably predate the Gutenberg printing press. Besides seeing the Grand Place, Lakyn, Stephanie, Michael, Chris and I also visited three local art museums and caught the Belgium—Ireland game at a local pub. The entire country is avidly following the European Cup, so we joined an exuberant crowd in cheering Belgium on to the elimination rounds. It was awesome.

This has been an eventful week for a number of reasons. Academically, I’m gearing up to do some human subject studies with our EEG headset. Until now I’ve been analyzing old data and using it to test my classification algorithms (read: if I multiply this fancy matrix by that fancy matrix, can I tell if the subject is wiggling his right hand?). However, my real goal this summer is to add a no-movement state to the classifier, and none of our past experiments have no-movement data. This means it is my job to abduct – excuse me, recruit – fellow IMEC employees to sit still while wearing the headset so I can record no-movement data. It should make for a nice break from coding.

Unfortunately, not all breaks are the pleasant sort. Thanks to two consecutive bike crashes this week, I now have a fracture in my left wrist and right knee. Fortunately Belgian health care is merciful beyond reason: in addition to getting two days off work to recover, IMEC is covering my medical bills. All I have to do is recover and exchange my rental bike for one with handlebars. Oh yes, the handlebars came off while I was riding it. Twice.

Despite how it sounds, I’m basically fine and ready to get back to work and exploring. I made it to the Belgium vs. Sweden game last week on foot, but it’ll be nice to be able to bike again. This week I’m hoping to get my protocol for human testing approved and maybe even tidy up my algorithms a bit before we start recording. It turns out there’s a second set of old data that I haven’t tried to classify yet, so I’m cautiously optimistic that it might yield some useful information. Outside of work, my primary goal is to catch all the upcoming Belgium soccer games. My secondary goal is to not crash off my bike again. Priorities.

Lydia Carroll is a 21-year-old biomedical engineer on her first excursion to the European mainland. In her free time she enjoys taking things apart, putting them back together, volunteering with the Maryland SPCA, and reading any paperback novel she can get her hands on. 

From left to right: me, Lakyn, and Stephanie in Brussel’s Grand Place.

Oude Maarkt in Leuven before the Belgium vs. Sweden game.

Olli and Chris geared up for the Belgium vs. Sweden game.

Computers, Cleanrooms, and Castles

Over the last few weeks, I have started working with more complex computational techniques including finite element analysis. To conduct finite element analysis, I am using COMSOL Multiphysics software and high-tech computer clusters. After I design an acoustic system, the procedure for finite element analysis involves creating a two-dimensional or three-dimensional representation of the system including geometry, physics, and boundary conditions. Finite element analysis works by approximating the solutions of the resulting differential equations numerically across a user-defined mesh. The final results involve detailed information about the system like pressure and physical stress for each element of the mesh.

Currently, my group is working on creating basic prototypes of the acoustic systems that I designed using additive manufacturing (aka 3D printing) and lab equipment. We are going to be testing these prototypes in a small lab at IMEC.

IMEC Academy also offered tours of the cleanroom and support area at IMEC 1. Fellow JHU intern Chris Argento and I decided to register for the only tour offered in English this summer. For the tour, we dressed up in white cleanroom suits and walked through a class 1000 cleanroom. While there, we learned about types of experiments they conduct such as lithography, nanofabrication, and etching. The cleanroom itself was huge and contained extremely complex equipment and sections designated as class 1. The support area tour gave an introduction to the equipment required to maintain the air quality and humidity of the room, the chemical processes used to neutralize the waste, and the safety procedures in place in a dangerous event like a fire or gas leak.

On the weekends, I have been taking both group and solo trips around Belgium to Antwerp, Brussels, and Ghent. Each city is different with its own distinct attractions and styles. Antwerp had several tourist neighborhoods lined with American brands like Subway, H&M, and McDonalds along with many residential areas. For Brussels, I have so far only visited Central Brussels where Manneken Pis, the Grand Place, and museums are the main attractions. Hopefully, I will have time to visit Brussels again on the evenings since all my weekends are booked! The highlights of Ghent were the architecture, Gravensteen Castle, St. Bavo’s Cathedral, and the Bourgoyen-Ossemeersen Nature Reserve. The city had many scenic walkways along the canals, and the view from the top of the Gravensteen Castle was an awesome sight.

The professional experience working at IMEC has introduced me to new engineering techniques, and the traveling and cleanroom tours have taken me to places that, prior to the program, I could only dream of visiting.

Michael Signorelli is a second-year Biomedical Engineering undergraduate at Johns Hopkins University

IMEC 1

Brussels Grand Place

View of Ghent from the top of the Gravensteen Castle

Belgium brews and summer views

Hallo from Belgium! We arrived in Leuven about a week and a half ago, and things have been going well so far. Our first few days were spent running around Leuven doing some administrative things and settling into our studios at Wisteria, a KU Leuven dorm building near imec. Each of us has our own bathrooms and kitchens, which I’m grateful for, and the rooms came furnished and stocked with some basic cookware and utensils. Michael, Chris, Lakyn, and I all live next to each other on the ground floor, and Lydia is living the penthouse life on the first floor.

We stayed in Leuven for our first weekend since we wanted to get a better feel of the city. A member of Lydia’s lab, Eric, was nice enough to give us a bike tour of Leuven and we got to see Stadhuis (Town Hall), Groot Begijnhof (a monastery built in the 1200s), Botanical Garden Kruidtuin, and Oude Markt (Old Market, also known as the longest bar in the world!). I loved seeing all the old Gothic architecture and seeing how easy-going Belgians are. There are always people sitting outside cafes, sipping on cold beers and talking with friends.

By Monday, we had fallen into our summer work routine. At 8:30 am, we bike from Wisteria to imec and work for a few hours until lunch at 11:30 am with some of our other lab mates. Occasionally, we join a few of them for coffee at Java – the Brody Café of imec – and return to our desks a little before 1 pm. Our workdays usually comes to an end at 4 or 4:30 pm. However, I suspect our afternoons at imec will become longer as our projects progress and more experiments need to be performed.

Leuven is a fairly small city – it has the vibes of a nice college town – and the cheapest and most convenient way to get around is by bike. Oude Markt is a great place to hang out and have a cold beer (surprisingly, the legal drinking age is 16 here) with friends after work. In fact, Lakyn’s lab organizes weekly dinners at Oude Markt, which we all joined in on this past Tuesday.

During our second weekend, we took a day trip to Antwerp. Antwerp is an old city with a lot of history, and it was super cool to see the different style of architecture, art, and beer this city had in comparison to Leuven. Unfortunately, some of the museums and churches we wanted to see were closed for that day, so we spent most of our time outside admiring the beautiful building facades. I think our bad luck was made up for by the food: fries and Belgian waffles. So yum! We got back to Wisteria around 8 pm and after walking over 10 miles, we were beat.

Even though it feels like we just got here, the time seems to be flying by fast. Many more weekend trips are to come, and I’m excited to see where our travels take us. Until next time!

Stephanie Cai is a rising junior BME with a focus area in Instrumentation. At Hopkins, she is a member of the Wang lab, a leader for Encore Music Group, and on the board for Society of Women Engineers. 

Weekend Trips to Bruges and Amsterdam

The recent personal highlights of my summer are trips to Bruges and Amsterdam. Two weekends ago, Chris, Lakyn, Stephanie, and I visited Bruges. Chris and I decided to stay overnight in a hostel. Since the weather that weekend was warm and sunny, the train to Bruges was packed with families and school groups heading to the beach city Ostend.

Bruges is the capital of West Flanders and the location where the movie “In Bruges” was filmed. The first and probably the most interesting attraction we visited was the Belfort. We climbed up hundreds of narrow stairs to view different exhibits pertaining to the history and function of the Belfort and culminating with a 360 degree view of the city at the top. While there, we purchased a museum pass that gave us access to several attractions in the city, notably the Groeningmuseum (art) and the Sint-Janshospitaal (a historic hospital that has since been converted into a museum). We also did a canal boat ride, and stayed out until dark to see the canals, the Historic Centre, and the Burg Square lit up at night.

The trip to Amsterdam this past weekend was the most exciting trip yet. I met up with Chris and a BME undergraduate from JHU. We decided to rent bikes, which turned out to be a great idea since there were thousands of bikers and lots to see in the relatively large city. After biking through several famous neighborhoods like The Jordaan, we got free entry to the number one museum in Amsterdam: Rijksmuseum. The Rijksmuseum was huge with artwork ranging from paintings to doll houses to furniture to porcelain. We visited all the exhibits except the “Gallery of Honor” which had about a three-hour wait. We rounded out the day with biking around Vondelpark and taking a canal boat ride. Chris couch-surfed for the night, while I stayed in a hostel.

On the second and final day in Amsterdam, we met up and visited the Anne Frank house (we snatched tickets online a few days before to avoid the long wait). The historical aspects of the place made it an especially intriguing place. We also found cheap student tickets to the Dutch National Opera and visited the Dutch Royal Palace. For dinner, Chris and I tried bitterballen, which are a Dutch snack consisting of a meat paste covered with breadcrumbs that're fried with a side of mustard. That, along with the Dutch version of chicken tikka masala, were interesting meals.

Back at IMEC, we fabricated my prototype using a special type of 3D printer that builds upside down using an ultraviolet laser to cure resin on a plate. It is extremely detailed (albeit expensive) with a precision of 25 microns. I recently received certification to work in the former Clinical Lab at IMEC to conduct the acoustical experiments on my prototype. I will be working with ultrasound transducers, acoustical waveguides, and oscilloscopes.

Michael Signorelli is a second-year Biomedical Engineering undergraduate at Johns Hopkins University

View from the top of the Belfry in Bruges

The Belfry in Bruges at night

Canal in Amsterdam

Figure Captions

· View from the top of the Belfry in Bruges

· Canal in Amsterdam

Groovin’ in Leuven

It’s been a crazy two weeks over here, getting accustomed to living in a new country with a different language, unexplored streets, and countless people to meet. Though it was a little rough at first, I think we’ve finally settled in here in Leuven and we’re starting to fall into a routine.

The first few days of work at IMEC involved a lot of training, reading, and getting to know the people in my lab group. I didn’t have the greatest background knowledge in my project before I came, but now I’m getting the hang of things and starting experiments next week. Our group is developing heart cell on-a-chip technology for the evaluation of pharmaceuticals in development—with lens-free imaging, contractile measurements with electrode arrays, and calcium imaging, one can analyze a drug’s effect on the typical behaviors of cardiac cells before putting it on the market. I’m excited to start working with electronics, as I’ve learned about them in various classes, but haven’t had a chance to get practical, working knowledge until now.

Besides the 9-5 weekdays at IMEC, we’ve been able to explore some new places. Leuven has fields and rolling countryside in addition to its bustling city center—when we first arrived to our dorm, we saw a couple of goats next door as well as a field of horses down the street. The city has amazing architecture, cobblestone streets, and countless shops and cafes. One of my favorite places that we visited in Leuven was Kruidtuin, Belgium’s oldest botanical garden. It had hundreds of different kinds of flowers, plants, and trees, and the weather was perfect to just walk around and take in the sights. We walked around the Groot Begijnhof, a neighborhood built in the 13th century that once served as a community for pious women and nuns. Within the heart of Leuven is Oude Markt, a street lined with bars, restaurants, and cafes that is always full of people, whether weekday or weekend, night or day.

This past weekend a few of us went on a day trip to Antwerp, a city with more cool architecture and statues. Though some of the museums we wanted to visit were closed, there was plenty of other sites to see, including the train station, which was gigantic and beautiful. We toured a brewery and spent the day walking around sightseeing, which wasn’t complete without a Belgian waffle ;)

Excited to see what else is in store for us here in Leuven! Thanks for reading! 

Lakyn Mayo is a rising junior in Materials Science and Engineering at Johns Hopkins University and an IMEC intern with the Johns Hopkins Institute for NanoBioTechnology International Research Experience for Students program. 

Train station in Antwerp 

Belgian waffle topped with chocolate

Oude Markt

Just a Drop

I have certainly hit the cobblestones running in my first taste of Belgium. Within the course of a week I have moved into my apartment in the converted monastery of Wisteria, biked the storybook streets of Leuven, and sampled one of the local badminton clubs. Badminton is a very popular sport here, which is ideal for an avid player like me. This weekend four of us Johns Hopkins students visited Antwerp, arrived in the world famous rail station and toured the brewery of the local beer, “De Koninck.” We also enjoyed traditional waffles with dark Belgian chocolate drizzled on top, completing the cultural trifecta of beer, waffles, chocolate. Antwerp was a gorgeous, fashionable city, far larger and more tourist-oriented than our new home of Leuven. Already there are machinations for more trips on the days between our diligent weeks of work at IMEC.

In the laboratory at IMEC, I am working on microfluidic droplet technology under Yannick Vervoort, a PhD student who is collaborating through KU Leuven. In this technique, liquid droplets are captured in an emulsion within the micrometer-scale channels of a glass-silicon chip, where they can be manipulated and analyzed in various ways. In one application, numerous different genetically-engineered yeast strains can be grown in separate droplets and evaluated at rapid speeds. The process is orders of magnitude faster than traditional culturing of yeast in flasks. The ultimate goals of this application are characteristically Belgian: to identify superior yeast strains for the production of biofuels, chocolate, and beer.

I have completed most of the procedural and training tasks and have already begun my earliest experiments. My first challenge is to determine a method to extract droplets from the silicon chip, store them in a larger vessel, and then later reintroduce them for examination. This way we can process even more droplets! For now, I’m simply trying to avoid the rain droplets that fall frequently but delicately on the ancient city of Leuven.

Chris Argento graduated from Johns Hopkins with a bachelor’s degree in Chemical and Biomolecular Engineering and has continued on in the same department to pursue a master’s degree in the laboratory of Joelle Frechette.

Leuven badminton club.

Droplets travel through a microfluidic chip

Living in Leuven and Other Alliterative Accidents

Good morning America! Or, in a more accurate summary of my readership, hi Mom! My name is Lydia and I am one of the five Johns Hopkins students interning with the Inter-university MicroElectronics Center (IMEC) this summer through the Institute for NanoBioTechnology (INBT). I just finished my undergraduate degree in biomedical engineering (BME) and will be starting my Master’s in robotics this fall.

As someone who always wanted to study abroad, applying for the INBT internship program with IMEC wasn’t a hard decision. I’ve worked with robotic prosthetic limbs in the past and am hugely fascinated by the idea of interfacing the human nervous system with machines; I probably read a bit too much science fiction as a child. I was therefore thrilled to find out that I would be working with a new electroencephalography (EEG) headset for the summer. EEG is a non-invasive way to record brain signals. While it can be used to record all kinds of signals, I am most interested in how it could be applied to interpret motor intentions (i.e., this change of voltage indicates my desire to wiggle my robot hand). The headset I’m working with for the summer uses only four dry electrodes and can be easily put on and taken off quickly, so it could potentially be used in real-world settings outside the lab.

However, using dry electrodes instead of the more common gel-based ones comes with drawbacks. So far the headset can only distinguish between two motor classes, left and right. My goal for the summer is to introduce at least one more state, no movement, so the headset can also tell when no command is being sent.

I officially started with the rest of the interns on June 2, but in actuality, that first half week was dedicated to finding internet passwords, hunting down grocery stores and passing safety training. This week the work began for real. Reading someone else’s code is always a tricky business, so it wasn’t until this last Thursday that I really started changing things and trying new approaches. I had brief delusions of grandeur on Friday and thought I had solved the whole problem in my first week; not surprisingly, that did not happen. On the bright side, I still have something to work on for the next nine weeks.

Outside of work, Leuven looks so different from any American town I’ve ever seen. From an infrastructure perspective, the streets are narrower and the bike lanes are wider; from a historical perspective, more than half the buildings are older than the country I was born in. Fortunately I’ve met some really great people who have shown me and the other students around on our recently rented bikes. I share an office with Eric, a PhD student from Beijing, who took us on a bike tour of the city last weekend. We also went out to dinner twice this week, first with Lakyn Mayo’s lab (Lakyn being another INBT-IMEC intern), then with some other interns we met. It’s a really beautiful place to work, and I’m looking forward to exploring more.

Lydia Carroll is a 21-year-old biomedical engineer on her first excursion to the European mainland. In her free time she enjoys taking things apart, putting them back together, volunteering with the Maryland SPCA, and reading any paperback novel she can get her hands on. 

Lakyn and me after a night exploring Oude Maarkt.

Eric, our volunteer tour guide, showing us the KU Leuven library.

The convent in the center of Leuven. Built in the 1200s, for centuries it was one of the only places women could come and be educated. It now serves as dorms for one of the many local universities.