Darrell Irvine - Mixing it up

Relocation brings together materials scientist, theoretical and experimental physicists as Physics of Living Systems group at MIT.
Denis Paiste | Materials Processing Center
May 7, 2014

A common set of ideas and approaches brought together a trio of MIT professors and their research teams to form the Physics of Living Systems group, which opened a new lab and offices mid-April at 400 Technology Square, sixth floor.

The group co-located at 400 Technology Square include  Jeremy L. England, assistant professor of physics; Jeff Gore, Latham Family Career Development Assistant Professor of Physics; and Alfredo Alexander-Katz, Walter Henry Gale Associate Professor of Materials Science and Engineering. A fourth member, experimental biophysicist Nikta Fakhri, is expected to join the group early next year as an assistant professor in the Department of Physics.

The 400 Technology Square space is acting as the core physical location of the Physics of Living Systems Group, whose other active members are Assistant Physics Professor Ibrahim Cisse; Francis Friedman Professor of Physics Mehran Kardar; Associate Professor of Health Sciences & Technology and Physics Leonid Mirny; Robert T. Haslam Professor of Chemical Engineering Arup K. Chakraborty, who also has appointments in physics, biological engineering and chemistry; and Alfred H. Caspary Professor of Physics and Biological Physics, Emeritus, George B. Benedek.

"The goal is that once we're all together like this that we can collaborate in various ways," Gore said. "A major limiting factor for many of us is just that we have not been physically located next to other groups that are interested in related ideas," he said.

"In my group, we study the dynamics of populations, mostly, but there is a common set of ideas and approaches that all the groups have, so I think the faculty and also the students are very much enjoying being next to each other," Gore said.

Materials scientist Alexander-Katz says, "It's going to take a little bit of time, but soon we'll have quite a bit of integration and discussion of different ideas." His group works on polymers as well as biologically inspired materials. "We try to create material that will have similar properties to natural systems, and in the way to achieve that, we seek to understand why these bio-materials behave in such a way.”

Alexander-Katz worked with Darrell Irvine at the Koch Institute at MIT and Francesco Stellacci, now at the Ecole Polytechnique de Lausanne in Switzerland, to explain the mechanism by which gold nanoparticles can penetrate cell membrane walls without damaging the cell. Reid Van Lehn, a graduate student in Alexander-Katz's Laboratory for Theoretical Soft Materials, was lead author of the paper. Irvine and Stellaci first demonstrated the technique using synthetic gold nanoparticles in 2008.

"Now we're working also in the micron range on artificially living systems, trying to understand the fundamental aspects that regulate the behavior of what we call active soft matter. You can think about it as what cells do at multiple scales. They have multiple active components that take chemical energy and put it into motion. That's crucial for life," Alexander-Katz explains. "But you can do it synthetically as well, and you can create things that self-propel and self-organize dynamically. We are particularly interested in their non-equilibrium phase behavior and their interactions." The Alexander-Katz group specializes in computer modeling of these systems but recently began its own experimental efforts as well. "If we understand the biological part, we can probably engineer systems, artificial systems, that will have similar properties," Alexander-Katz says.

Experimentalist Fakhri, who will be joining the group in January 2015, said, "I am very excited to join the Physics of Living Systems group at MIT. My interest is focused on the physics of active soft matter. I develop and use new imaging technologies to explore the role of non-equilibrium fluctuations in living systems from the cell nucleus to tissue."

Theorist Jeremy England has drawn national attention of his work on modeling bacterial reproduction and its logical outgrowth, a theory that physical laws of heat release from chemical processes drive matter, including living organisms, toward higher efficiency at shedding heat. Living beings are far more efficient at shedding heat than inanimate matter, and in particular, England showed that E. coli reproduction is close to thermodynamic limits of efficiency.

"I think it's natural that people come up with ideas to collaborate more readily when they are interacting," England says. "That sort of flexible space where creativity can take hold where you're just by accident having a conversation with someone about something, which is often when people have their best ideas. The students in all the various groups are going to have the opportunity to interact with each other a lot more, and I think having a peer group and a critical mass of a community of people with common or related research interests is really important to intellectual development for the students."

"Especially Jeff has been a real leader in this the last several years, and I'm very supportive of this idea as well and really believe in it that we really want biophysics to grow and develop and flourish and the way to do that is to try to form a critical nucleus of groups," England explains.

England uses theoretical statistical mechanics to quantify the energy behavior of biological systems — for example, Cytosol, an active material inside living cells. "We're interested in the structure of macromolecules, collections of macromolecules, and how they behave in the cell as a group phenomenon," England relates. "We're interested in the non-equilibrium thermodynamics of biological organization, so that could be construed to be about evolution and the origins of life or just about how you make or design self-replicators with desired properties."

England has also been collaborating with experimenters elsewhere on protein folding and macromolecular assembly, such as the group of Daniel Kaganovich, Assistant Professor of Cell and Developmental Biology at Hebrew University in Jerusalem. He advises five graduate students and several undergraduates. He also collaborates with Guy Bunin, a postdoctoral Pappalardo Fellow in Physics.

Increasingly there are now instruments where you can make quantitative measurements on fluorescently labeled proteins in live cells," England explains. "The cell biologists have their language and their frame of analysis that they're most comfortable with for describing the phenomenon, but if there are interesting phenomena that are only going to be identifiable if you do the right quantitative analysis on all these numbers that you can now measure in the cell, then it's useful to have people who are a bit more theoretically minded or physics minded who are there, when rubber meets road, when the data is being generated and helping to influence what kind of experiments get done."

"We're looking, for example, at diffusion of proteins in cells. Diffusion as a qualitative phenomenon is just things spreading out over space, but as a quantitative phenomenon, you can look at things like how rapidly a protein that's labeled over here in the cell will wander over to another region of the cell that's a certain distance away, and if you can make measurements of that, then you can start to say things that are more specific about characteristics of the diffusion that you are observing than simply seeing it spread out. And in those quantitative measurements, you can sometimes then see differences perhaps between different cells, or different conditions for the same type of cell, that may have biological relevance but that you wouldn't have necessarily identified without the quantitative analysis," England says.

Alexander-Katz said he is interested what might happen on the micro scale with some sort of micro-robot that does some task that the cell does and put it together with real cells, and see how real cells will respond to that. "Can you use learning algorithms to achieve certain tasks within that cellular environment or not?" he asks. "Jeff works with bacteria and yeast and those could be very interesting targets to start tinkering with."

The new lab space is designed for biology experiments and will have a temperature-controlled room kept at 30 degrees Celsius. "It's a beautiful space. We're really happy with it," Gore said.

The Physics of Living Systems group is primarily an initiative of the Physics Department. Gore's research is partially managed by the Materials Processing Center.