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Research Lab Profile: The Mallory Group

30 March 2023
Stewart Mallory

Stewart Mallory, assistant professor of chemistry at Penn State, discusses his group's current work on soft active matter and the important roles that computer simulations and theoretical tools play in this research.


Kathryn: You joined the Penn State Chemistry faculty as an assistant professor in August of 2021. How has it been working within the department over the last year and-a-half? What were you most excited about when you first started? 

Stewart: The last year and-a-half has been, and continues to be, a real adventure. Every day offers something new and exciting. The opportunity to work with my group members, teach, and interact with other faculty makes it easy to come to the office every day. When I started, I was most excited about getting my research group off the ground and figuring out what research directions we wanted to explore. In a way, I had a blank canvas, and finding ways to fill that canvas with intellectually stimulating research questions has been fun and rewarding. I especially appreciate the support from everyone in the department. I didn’t fully appreciate this as a graduate student or postdoc, but there are many moving pieces to running a research group, and I appreciate all the help I have received while navigating these challenges. 

Kathryn: Can you give some background to the research you were doing as a postdoc and how that became the seed for research you wanted to do in your own group? 

Stewart: My Ph.D. was in a statistical mechanics group focused mainly on simulating soft active matter systems. We spent a lot of time thinking about taking what you see in a typical experiment and how to model it efficiently and accurately on a computer. We then used these computer simulation models to explore and quantify new behaviors. At the end of my Ph.D., I had a strong background in simulation techniques and became interested in some other perspectives used to approach problems in active matter. 

In looking for a postdoc position, I wanted to understand more about the analytical theory used to explain the behavior of active systems. I was looking for a way to spend more time doing pen-and-paper theory. What’s interesting about active matter is that it is highly interdisciplinary, with many researchers across different fields. So, I was lucky to spend a couple of years working in a Chemical Engineering group, which provided me with an entirely new perspective. The specific problem I worked on involved developing a new theory for phase transitions in non-equilibrium systems. This problem came with its own challenges, as many of the theoretical tools used to understand equilibrium systems cannot be used directly, and it was necessary to develop new ones.  

The most important takeaway from my postdoc work was a more holistic perspective on problem-solving. In our group, we can now blend different types of simulation and theory and approach a problem from multiple perspectives. 


mallory group
A group meeting where the members discuss some of their work on diffusion under strong confinement. (left to right) Parvin Bayati – postdoctoral scholar, David Friedenberg –  first year undergrad student, Mallory, Akin Akintude – second year grad student, and Elijah Schiltz-Rouse – second year grad student


Kathryn: Tell us about some projects your group is currently working on.  

Stewart: The common thread through all the projects in our group is that we want to develop theoretical and computational tools to understand and control the behavior of matter at the microscale. Much of our work focuses on understanding the behavior of colloidal active matter, where you have self-propelled particles, usually on the nanometer to micron size scale, immersed in some liquid. We are interested in two fundamental questions: What emergent behavior arises when you have a collection of these self-propelled colloidal particles, and what is the underlying mechanism that drives their motion? These can be an unusually challenging questions as we need to understand the details of the systems across a range of length and time scales.  

One project we have made progress on is exploring the collective behavior of self-propelled particles under extreme confinement. To give you a more concrete picture of this problem, we are considering the behavior of a suspension of self-propelled colloidal particles constricted to move in a narrow channel. Interestingly, this is an important problem as there is optimism that synthetic self-propelled particles can be used for various tasks at the microscale, from targeted drug delivery to the clean-up of environmental pollutants. All these applications require understanding how self-propelled particles move when forced to move under confinement. We have developed a theory capable of rationalizing this system's phase behavior. Additionally, this project has provided us with a platform to extend concepts that we typically take for granted when we study equilibrium systems such as temperature, kinetic energy, and free energy, and provides a pathway to extending them to have a well-defined meaning in active matter systems that are far from equilibrium. 

Kathryn: How does your group’s research relate to recent developments in the field of soft active matter?  

Stewart: It is an exciting time to be a theorist working on soft active matter. There are many open questions and a real opportunity for theory to guide development within the field. An emerging area where we can make a meaningful contribution is improving colloidal self-assembly. This autonomous construction process leverages environmental fluctuations to generate microstructures at practically no external cost. It is a robust approach for designing the next generation of smart, functional materials from the ground up. The biggest obstacle that has hampered the success of colloidal self-assembly is that building blocks tend to condense into an ensemble of competing metastable structures that directly compete with the formation of the target structure. Given our ability to rationalize the phase behavior of active systems, we are currently working on devising a suite of techniques that select for the exclusive formation of the desired structure. This research direction aims to leverage the unique nonequilibrium conditions generated by active systems to find alternative and more efficient self-assembly pathways for colloidal materials. 


mallory group
Mallory and second year graduate students, Schiltz-Rouse and Akintunde, use a whiteboard to discuss a theory related to their research on active matter.


Kathryn: Your group has a unique “lab” space in the sense it does not require beakers, workbenches, fume hoods, glove boxes, or any large instrumentation like many of our other chemistry labs. As a theory and computational chemist, how else does your research experience differ from other chemistry areas? 

Stewart: Well, the biggest difference is that as a theorist, we spend most of our time sitting at our desks, usually staring at a computer screen or sheet of paper. But more seriously, one of the unique things about research in a theory group is the outcomes of the work can look different than that of an experimental group. Our group doesn’t make anything tangible, at least in the material world. The currency of our work is offering a more profound understanding of physical systems using simulation and theory. Hopefully, if everything goes right, we can provide some predictive power to how systems behave under different conditions. One of the most satisfying feelings as a theorist is when the theory you are working on agrees with the results of simulations or experiments. 


mallory group
Mallory and Zak Marcus, a first-year graduate student, look at the results of a molecular dynamics simulation studying diffusion of colloidal particles.


Kathryn: Can you explain the extent to which computer simulations are used jointly with the theoretical tools your group develops? Do you find that working with computer simulations lends to creativity in your group? 

Stewart: Computer simulations are a central part of our work as they serve as a proxy for experiments and a way to gain intuition about a system's behavior. One of the most incredible things about computer simulations is the level of control you have over the details of your system. You can control the type of particles and the rules for how they move. It is one of the few places in life where you can have complete control. You can build your own world and control physics precisely. The way things go with a project in our group is that we first identify a particular problem or system we are interested in. To understand the system better, we find a way to simulate it on the computer. The next step, often the most difficult, is to devise an analytical theory capable of capturing the behavior we observe in simulation. Once we understand how a particular system behaves or responds to its environment, we think deeply about leveraging this behavior in interesting ways or where it might manifest in the natural world. It is here where we are most creative and can try to develop novel strategies for designing new materials or how to transport and direct the motion of particles at the microscale. 


mallory group
A still frame taken from a simulation of a crystal of self-propelled particles melting into a dense and dilute phase.


mallory group
A still frame taken from a simulation of self-propelled particles swimming in a narrow channel (slow particles).


Kathryn: Compared to other chemistry departments you were involved with during your academic studies and postdoctoral training, what would you say is most unique about Penn State Chemistry? 

Stewart: Unlike other departments that may focus solely on traditional areas of chemistry, what sets Penn State Chemistry apart is its unique emphasis on interdisciplinary research and its commitment to fostering a collaborative research community. This is what caught my eye and drew me to Penn State in the first place. Plus, I value how many faculty members share research interests similar to my own. This has opened the door to collaborations and a sense of community that I don’t think I would be able to find in a lot of other places. 

Kathryn: Lastly, where do you hope to see your lab in the next 5 years? Have you set yourself and your group members any specific goals? 

Stewart: In the next five years, I have set specific goals for my group to further our contribution to the theoretical understanding of active matter and its applications. One of our main objectives is to continue developing new mathematical and computational models that capture the dynamics of active particles, including improved modeling of their interactions with each other and their environment. This will allow us to gain deeper insights into the behavior and make predictions that can be tested experimentally. Another goal for my lab is to expand into new areas of active matter research, such as collective motion in biological systems and controlling the emergence of self-organized structures to design new materials. Furthermore, I am committed to providing a supportive and collaborative research environment for my group members to develop their theoretical and computational skills. By fostering an environment of open communication and teamwork, we can achieve our goals more effectively and significantly impact the field.


mallory group
Mallory works at the whiteboard on a theory for the phase behavior of active matter systems.


Media Contacts
Kathryn Harlow
Chemistry Communications Coordinator
Stewart Mallory
Assistant Professor of Chemistry