Konrad Kording: A Penn Integrates Knowledge Professor Coming to Penn BE

konrad kording
Konrad Kording, PhD

The Department of Bioengineering at the University of Pennsylvania is proud to announce that Konrad Kording, PhD, currently professor of physical medicine and rehabilitation, physiology, and applied mathematics at Northwestern University, will join the BE faculty in the fall.

Dr. Kording, a neuroscientist with advanced degrees in experimental physics and computational neuroscience, is a native of Germany. After earning his PhD in 2001 at the Swiss Federal Institute of Technology in Zurich, he held fellowships at University College, London, and MIT before arriving at Northwestern in 2006.

Kording’s groundbreaking interdisciplinary research uses data science to understand brain function, improve personalized medicine, collaborate with clinicians to diagnose diseases based on mobile phone data, and even understand the careers of professors.  Across many areas of biomedical research, his group analyzes large datasets to test new models and thus get closer to an understanding of complex problems in bioengineering, neuroscience, and beyond.

Dr. Kording’s appointment will be shared between the BE Department and the Department of Neuroscience in the Perelman School of Medicine.

Phytoplankton Research Earns Award


The Scripps Institution of Oceanography at the University of California, San Diego, announced last week that one of its faculty members, Andrew Barton, PhD, received a Simons Foundation Early Career Award to study phytoplankton — a type of algae that requires sunlight to survive and that serves as the basis for much of the marine food chain.

Dr. Barton’s research will use the Scripps Plankton Camera System, which provides real-time photographic images to monitor these phytoplankton. While not exactly offering the excitement or cuteness factor of the Golden Retriever Puppy Cam, this sort of technology is incredibly important to better understanding certain aspects of marine biology.

“This is an interesting project that brings cutting edge image-processing technology to the natural habitat to study complex organismal dynamics in the real-world setting,” says Brian Chow, PhD, assistant professor of bioengineering at the University of Pennsylvania. “Establishing the critical interplay between an organism’s form and function and the forces of its local and global environments are important problems in physical biology in general. Diatoms have long been studied by bioengineers interested in self-assembly, programmed assembly, biomineralization, and biomimicry, so the work may lead to some novel insights for our field.”

Congratulations to Dr. Barton on receiving this prestigious award.

Network Visualization Program Unites Artists and Scientists

Rebecca Kellner

In high school, Rebecca Kellner (right) always had a dual love of art and science. When she entered the University of Pennsylvania as a freshman, she thought that her interest in art would always be separate from her pursuit of science. “I’ve always loved art and science and I wondered how I would integrate my passions into one area of study,” Rebecca says. “Then I heard about the Network Visualization Program run by Dr. Danielle Bassett . In this program, the intersection of art and science is celebrated, and this intersection is a place where I feel right at home.”

The Penn Network Visualization Program, begun in 2014, had long been a dream of Dr. Bassett. She wanted a forum where young artists and research scientists could interact with each other. “Science and art are often perceived to be at odds with each other, two fundamentally different ways of understanding the world. As a scientist, I’ve learned that the visual impact of the information I present is crucially important. Networks are visually intuitive,” says Bassett, “and represent an opportunity to foster a common language between scientists and artists.”

In this six-week summer program, young artists spend time with scientists at Penn who are performing cutting-edge research in network science as applied to social systems, human biology, and physical materials, with the underlying goal of advancing bioengineering. Faculty from the Warren Center for Network and Data Science who have volunteered their time and creativity to the project include Eleni Katifori, Erol Akcay, and Randy Kamien of the School of Arts and Sciences; Robert Ghrist and Victor Preciado of the School of Engineering and Applied Sciences; Sandra Gonzalez-Bailon of the Annenberg School of Communications; and Francis Diebold of the Wharton School of Business. During the course of the internship, the artists produce works of art interpreting and capturing the intricacies of these networks in novel ways. Artistic supervision and project advice are provided by local artists affiliated with the program. The goal of the internship is to provide scientists with new conceptualizations of their research and to provide the intern with new knowledge in scientific art applications.

Rebecca was thrilled when she was accepted into the program. During her internship she worked with a variety of scientists. Her final artwork focused on the research of Dr. Ann Hermundstad (Janelia), the postdoctoral researcher in the Physics of Living Matter Group, University of Pennsylvania Department of Physics and Astronomy. Dr. Hermundstad’s research focuses on what and how the brain sees. Fascinated by these networks, Rebecca created a painting and a laser-etched acrylic book.

Nicholas Hanchak

The program also invites six high school students who have exhibited creativity and academic achievement. Nicholas Hanchak (right) from Westtown School participated during the summer of 2016. “I love art, science and baseball and I am thinking about architecture as a possible career,” Nicholas says. “The Penn program challenged me to find new ways to combine these interests.” For his final project, Nicholas created a Plinko Game Board showing the difference between the networks in a healthy brain and in a brain damaged by stroke.

“Artists and scientists are kindred spirits because they both are interested in observing what is in front of them,” says Dr. Bassett. “The Network Visualization program offers an opportunity for scientists and artists to inform each other in very tangible ways.”

The program runs every other summer. During the fall, several of the artists’ pieces are showcased in Philadelphia-area middle and high schools, particularly in disadvantaged areas. These efforts are enabled by ongoing collaborations with the Netter Center for Community Partnerships and Penn’s Center for Curiosity, and they are partially funded by the National Science Foundation. Bassett hopes this outreach effort will encourage children to explore intersections between the arts and sciences, while instilling a growing appreciation of their networked world.

A Career of Accomplishments: Daniel Bogen

Daniel K. Bogen,, MD, PhD
Department chair David Meaney toasts Daniel Bogen

Daniel K. Bogen, MD, PhD, a professor in Penn’s Department of Bioengineering, is retiring. A Harvard alumnus (AB, 1972;  PhD, 1977; MD, 1979). Dr. Bogen was the the first MD/PhD hired by the department in its history.  Starting at Penn in 1982, Dr. Bogen spent his entire career on the faculty.

Early in his career, Dr. Bogen focused on cardiac tissue mechanics and understanding the functional changes that occur to heart tissue after ischemic insult.  These publications were among the first to use finite element techniques to address the critical problem of how heart wall contraction changes after injury.  Some of these papers are continually cited even today. Motivated to work on practical and applied clinical bioengineering-based problems, Dr. Bogen transformed his research to build items that patients would use.  Rather than a timescale from discovery to application that can last decades for most academic researchers, Dr. Bogen’s new direction allowed him to put items in the hands of patients within months.  In addition, Dr. Bogen’s led the PENNToys program, a nationally known program designing toys for children with disabilities.

The passion for impact also extended into the classroom. Reimagining the laboratory education in bioengineering, he used NSF-sponsored funding to create a discovery-based educational experience for undergraduates. This laboratory educational experience became an international model program, copied by many highly ranked bioengineering/biomedical engineering programs. This educational program was the cornerstone of the proposal funded by the Whitaker Foundation, leading to the construction of Skirkanich Hall, the current home of the Department of Bioengineering, in 2006. As a testament to his gifts as an education, Dr. Bogen’s teaching excellence was rewarded in 2005 with the Christian R. and Mary F. Lindback Award, which is the highest university teaching award bestowed by Penn.

Dr. Bogen will remain active in his retirement, and always enjoys hearing from alumni and students. Feel free to send him a congratulatory note — dan@seas.upenn.edu.

A Solution for Liver Testing for 10 Dollars

Brianna Wronko (left) and Guyrandy Jean-Gilles (right)

One of the Penn Bioengineering Department’s senior projects was the work of a two-person team: Brianna Wronko and Guyrandy Jean-Gilles. The result of their work was the MultiDiagnostic, a microfluidics platform that the two students describe as “A Fast, Inexpensive, and Accessible Diagnostic Solution.”

Brianna says that the project was originally conceived as a way for HIV clinics and treatment centers to test biological parameters such as viral load. However, the inability of Brianna and Guy to handle HIV-infected blood in the lab, as well as the desire to generate a product that could both serve patients directly and have a commercial focus. They decided their first offering would consist of liver function tests.

Manufactured by an automated process, the MultiDiagnostic is a paper microfluidics platform with a software component that can be run on a computer or cell phone. When a bodily fluid is placed into the platform, it diffuses into separate chambers of the platform, where colorimetric analysis is then conducted and data communicated via the software’s graphical user interface to the user.

The students currently have the platform in preclinical trials for the testing of aspartase aminotransferase and alkaline phosphatase; the ability to test alanine aminotransferase, bilirubin, and total protein are in the prototyping stage. Their current model is priced at a $10 customer price, which is considerably less expensive than competing technologies already on the market.

Among the most interesting aspects of this senior project team, other than the product itself, was that it had only two members. Asked how this fact affected their work, Brianna admitted that it posed a bit of an obstacle at first. However, she said, “we decided to break up the concept into parts, with me doing the wet lab parts, in which I have a background and Guy, whose background is in software, doing those parts.” In the end, they’re very happy with their final product.

Students Receive Awards for the Year

students receiving awards
Students in the BE Department have received several awards

Every year the Penn Bioengineering Department presents several awards to students. In addition to the Senior Design Awards, which will be featured over the course of the month, students were awarded for their service, originality, leadership, and scholarship.

The Hugo Otto Wolf Memorial Prize, endowed more than a century ago by the Philadelphia architect Otto Wolf, in memory of his son, was given to Margaret Nolan and Ingrid Lan. The Herman P. Schwan Award, named for a former faculty member in Bioengineering, was given to Elizabeth Kobe and Lucy Chai.

The Albert Giandomenico Award, presented to four students who “reflect several traits that include teamwork, leadership, creativity, and knowledge applied to discovery-based learning in the laboratory,” was given to Justin Averback, Jake Budlow, Justin Morena, and Young Shin.

In addition, Sushmitha Yarrabothula received the Bioengineering Student Leadership Award and four students — Hayley Williamson, Amey Vrudhula, Jane Shmushkis, and Ikshita Singh, won the Penn Engineering Exceptional Service Award.

Finally, the Biomedical Applied Science Senior Project Award, presented annually to the students who have “best demonstrated originality and creativity in the integration of knowledge,” was awarded to Derek Yee and Andrea Simi.

“These awards recognize many aspects of our students: their high academic achievement,  exceptional collaborative spirit, and leadership abilities,” said BE department chair David Meaney. “However, these traits are not limited to the only these students. Every single one of our undergraduates at Penn pushes themselves well beyond the classroom and into the community to make a unique difference.”

Creativity, Curiosity, and Engineering

by Dave Meaney and Dani Bassett

James Dyson
James Dyson

One can easily see that many of the world’s greatest challenges — producing enough food for the world population, providing each person with a set of fundamental human rights, or creating a sustainable environmental footprint as our societies move forward — must tap into two uniquely human traits: creativity and curiosity. In the fields of science and engineering, one can look at history and easily find creative and curious pioneers who ranged from Leonardo de Vinci (pioneered the field of human physiology), Grace Hopper (invented computer compilers), and Sir James Dyson (brought elegance to common household tools – the vacuum cleaner, the fan, the hand dryer, and the hair dryer).

Grace Hopper
Grace Hopper

Although we can look around and identify creative people, a natural question would be: What events in these individuals’ lives led to this creativity? We may see people around us who are creative and curious, but we often simply shrug and say ,“Wow, pretty ingenious person there.” Maybe we even think of this with a bit of yearning: “Boy, I wish I could think of things like that.”  We often make the observation and get back to our daily lives, accepting that creative people are born or “just happen.” In other words, we are either struck by lightning, or we are not. Nothing could be further from the truth.

Leonardo da Vinci
Leonardo da Vinci

Creative and curious people are not genetically wired differently than others. Curiosity and creativity are not rare skills conferred by serendipity. Instead, creative and curious people have benefited from mentors who pushed them to ask “Why?” at the right time in their lives: perhaps being in the right science class with the right teacher in middle school or reading a novel that made them imagine a world they could not see.

What does all of this have to do with engineering?  Well, some research suggests that many U.S. engineering undergraduates are weaker than their international counterparts in divergent and convergent thinking, which are two critical ingredients for creativity. These two thinking modalities may be propelled by different sorts of curiosity. Assessment tests for creative thinking traits often measure the ability to synthesize ideas, observations, and other information to make something new. From many possibilities, only one emerges as the ideal solution. This process is generally referred to as convergent thinking.  A second creativity trait is the raw ability to generate ideas, given a particular problem.  For example, one could be asked to generate as many possible uses of a brick that one can think of, and the resulting ideas are scored — both in terms of the number of ideas generated and the distinctiveness of each idea separately. This assessment, known as the alternative use test, measures divergent thinking. Ideally, engineers would have high ability in both divergent and convergent thinking, which would mean that they could both think of many possible solutions and pick the best among them.  However, one study performed almost a decade ago showed that half of the engineering undergraduates in the U.S. showed deficiencies in both convergent and divergent thinking — troubling, to say the least.

Adapted from an image in: Hany EA, Heller KA, “Entwicklung kreativen Denkens im kulturellen Kontext,” in Entwicklung und Denken im kulturellen Kontext, Mandl H, Dreher M, Kornadt H-J, eds (Toronto: Hogrefe Verlag für Psychologie, 1993), pp. 99-118. Reprinted with generous permission of Hogrefe Verlag.

However, all is not lost. Many changes have occurred over the last decade for engineering education in the U.S. We embraced the laboratory as a platform for problem-based learning, which cultivates the ideation phase of creativity and the convergence to a solution. We have also ‘tipped’ and ‘flipped’ the classroom to introduce more methods of open-ended problems as teaching tools, again using this change to reinforce that there are many ways and, rarely, one best way to solve a particular problem.

Yet with all of these very positive changes, we still don’t have a good road map for how ideas form in the mind, how we trade off one idea versus another, and how we decide which is the best idea. Our tools for creativity are based on countless efforts to try different methods, measure whether they have an effect, and take the most successful empirical methods and transform them into practice. Until recently, we had no idea what was going on in the mind during the creative process.

Fortunately, we now have ways to both interrogate and model how the mind works when we think and create.  Inspired by the principle that blood flow will increase to areas of the brain with high neural activity (side note: the brain is a remarkable energy hog for the body, representing less than 3% of body mass but consuming nearly 20% of its energy resources), researchers are measuring how flow to different areas of the brain change when people are asked to perform specific tasks. Early work showed these beautiful, color-coded images of how one task would increase blood flow to one area, while another task would increase blood flow to a different area.

Patterns of connectivity in the brain can be represented as
dynamic networks, which change in their configuration as
humans change mental states or cognitive processes while
performing a task.

However, scientists began to realize, that instead of looking at one pattern of brain activation at one time, we needed to study how the pattern changed over time. Analyzing these changes over time allowed us to estimate the brain areas that activated simultaneously with another during a mental task. If they activated together frequently, we assumed that they would have a functional connectivity between them. Simply put, areas that fire together are wired together, metaphorically speaking.  Very quickly, we saw maps of the brain’s own functional network emerge when volunteers would work on math problems, navigate a maze, and even when they were asked to just daydream.

Where does this lead us? Well, we stand on the cusp of learning and predicting the coordinated steps that our mind takes when we imagine different ideas and pick one as ‘the best.’  Not only can we map this process in real time, but we can also develop new theories about how to ‘steer’ from one brain network state to another. We can also apply this new knowledge to individuals on a case-by-case basis, rather than relying on the one-size-fits-all approach that is the current and common practice in cultivating divergent and convergent thinking.  In practice, this means that we would move away from prescribing the same creativity training exercise for everyone — with a large variation in the results — to a far more customized, efficient cognitive exercise. In fact, we could directly test the possibility that some of these exercises work for some people and not others because of an individual’s brain wiring map.  Science fiction? Nope, just modern day bioengineering at work.

David F. Meaney, Professor of Bioengineering and Neurosurgery

Danielle S. Bassett, Associate Professor of Bioengineering and Electrical and Systems Engineering

Hey, it’s Hey Day! Penn Juniors Become Seniors

Since 1916, University of Pennsylvania undergraduates have celebrated their last class day as juniors to mark Hey Day. While initially conceived as something solemn and rather formal, today it is an opportunity for students to get decked out in red T-shirts and novelty straw hats and bamboo canes (fashions from 1916) and celebrate.

This year, Hey Day was on April 27, and it was no exception to previous years. Several of our rising seniors were celebrating with everyone on College Green.

Hey Day for Penn Juniors
Penn BE students celebrating Hey Day

In addition to the gathering of students to be “officially” be made seniors by University President Amy Gutmann (see video here) and a passing of the gavel to next year’s junior class president, some students dropped in on their favorite teachers and staff members to say hello.

Sevile on Hey Day
BE Lab director Sevile Mannickarottu with Penn juniors

Dan Huh Receives Ryan Medal

Ryan Medical recipient Dan Huh
Professor Dan Huh

A professor in the Penn Department of Bioengineering, Dongeun (Dan) Huh, PhD, has been awarded the John J. Ryan Medal, which is given annually by the Royal College of Surgeons in Ireland (RCSI).

Every year this honor recognizes a scientist who has made major contributions to developing innovative biomedical technologies with the potential to have a broad impact on the life sciences. Dr. Huh, who is Wilf Family Term Endowed Chair in the BE Department, received the medal at an RCSI Research Retreat on March 9 on the RCSI campus in Dublin, and he delivered the John J. Ryan Distinguished Lecture.

“As an engineer, I am honored to have been selected by a group of biologists and clinicians for this prestigious award that recognizes significant contributions to biomedical research,” Professor Huh said. “It is truly rewarding and encouraging to experience strong support and enthusiasm for our pursuit of innovative biomedical technologies.”

Penn BE Lab Associate Wins Goldwater Scholarship

Michael Duong
Michael Duong

One of two Penn students recently awarded Barry Goldwater Scholarships is sophomore Michael Tran Duong, who works in the lab of Bioengineering Department faculty member Jennifer Phillips-Cremins.

“It is a wonderful honor for Michael to receive this extremely competitive award,” Professor Phillips-Cremins said. We are fortunate that Michael landed in a lab within Bioengineering at Penn, as this award indicates he has a very bright future well beyond Penn.”

Barry Goldwater
Senator Barry Goldwater (R-AZ)

Michael said, “I feel honored to receive this award and really appreciate the mentorship of Dr. Phillips-Cremins and her 3D Genome Folding and Neurobiology lab. Conducting research with Dr. Cremins as a high school student and undergraduate and receiving this award have strengthened my resolve to help patients with brain disease as a physician-scientist.”

The Goldwater Scholarship, named for the late U.S. Senator and Republican presidential candidate Barry Goldwater is awarded annually to 240 students who intend to pursue careers in math or science research. The amount of the award is as much as $7,500.