2019 SURF Faculty and Research Areas

Alfeld Professor Scott Alfeld's research is at the intersection of machine learning and security. He studies settings where an intelligent adversary has limited access to perturb data fed into a learned or learning system. The goal of his research is two-fold: to detect attacks and to build/augment learning systems to be more robust to undetected attacks. Learn more about Professor Alfeld's research here

Bishop Professor Anthony Bishop studies the interface between organic chemistry and molecular biology. His research team uses a combination of chemical and biochemical approaches to examine two central biological processes: cellular signal transduction and protein synthesis. Learn more about Bishop's research here

Prof Palacios Professor Ivan Contreras Palacios. 
Quantum Entropy and Graph Theory. Project Description: Quantum research mechanics has revolutionized the way we understand the world and different branches of Mathematics have been developed to study quantum systems. The purpose of this project is to study the notion of entropy (or disorder) in a simpler model, called graph quantum mechanics, which gives a connection between graph theory and physics. No physics or knowledge is assumed.
Course requirement: MATH 271 or 272. 

Carter Professor Ashley Carter's
lab team studies the mechanical properties of biological molecules or cells. Her research tracks the Brownian motion of injected particles using laser optic techniques. Students in her lab examine the motion of small micron-sized polystyrene beads that are attached to a biological specimen of interest. By tracking the movement or binding of the bead researchers are able to infer the trajectory of the specimen. Learn more about Professor Carter's research here

Professor Durr Professor Chris Durr.
 Research in the Durr group is centered around developing and understanding next generation polymeric materials. This includes discovering new inorganic catalysts, as well as new techniques. One of the advantages of this research is that there is something to be found in it
for every type of chemist. Whether you are interested in inorganic, organic, physical, analytical, and biological chemistry you will be able to contribute to these projects and learn something new along the way. Leran more here
Organic Chemistry is recommended but not required. 


Professor Edwards Marc Edwards. Cell migration is an important process during the development of organisms, and it plays a role in the pathophysiology of diseases such as cancer.  We will use a range of cell biology and microscopy techniques to decipher the basic mechanisms of directed migration in the single-cell amoeba, Dictyostelium Discoideum. This project will focus on developing and testing a new obstacle course for observing migrating Dictyostelium. Intro level Chemistry would be useful.
Course Requirements BIOL 181 &191 


2016 SURF Faculty and Research Areas Professor Jonathan Friedman’s lab studies chemically synthesized magnetic materials to learn how their magnetic moments reverse direction and to explore their potential use as processing elements in quantum computers. His group also studies the properties of superconducting devices that exhibit macroscopic quantum phenomena and that can be made into “Schrödinger Cats.” Learn more about Professor Friedman's reseach here

Follette Professor Kate Follette. In my lab, we de-twinkle stars in order to hunt for baby planets. More specifically, we use sophisticated computational and image processing techniques to remove starlight from images of young stars taken with some of the world’s largest telescopes. Removing the starlight allows us to isolate light emitted directly by young planets, some of which are still in the process of growing into gas giant planets like Jupiter. Learn more about Professor Follette’s research on her website
I’d prefer that students have taken one or more of the following: ASTR 200, ASTR 228, or CS 112 or equivalent. 


2016 SURF Faculty and Research Areas Professor Caroline Goutte will lead a project on Signal Transduction. Project Description: The development of an organism is orchestrated by signaling communication between cells.  By careful analysis of genetic mutants that abrogate signaling pathways, the mechanisms of cellular regulation can be uncovered.  This project will focus on the Notch signaling pathway and use the genetic model system Caenorhabditis elegans to probe the molecular regulation of signal transduction under different conditions.  Work will involve daily microscopy work.  Course requirement: Bio191 is required. Learn more about Professor Goutte's research here


Professor David Hall. Come visit and work in the fascinating world of ultracold matter! Students will work on projects supporting the creation and manipulation of Bose-Einstein condensates at temperatures billionths of a degree above absolute zero. We will make use of and develop the experimental physicist's experimental toolbox, from electro-optical design and construction to data-taking and analysis. Learn more about Professor Hall's research here
Physics 117 or 124 recommended. 

2016 SURF Faculty and Research Areas Professor David Hanneke studies individual atoms, molecules, and sub-atomic particles to test fundamental physics principles and to develop detailed control techniques for quantum systems. His students use low-energy atomic-physics techniques for precision measurements and detailed control of quantum systems.Students have developed an atom trap, lasers, and radiofrequency electronics. Learn more about Professor Hanneke's research here
Course requirements: PHYS-116/117 or 123/124 would be a good start on coursework. 


Professor Hansen The goal of the research ongoing in the Professor David Hansen's lab is the preparation of self-assembling nanostructures of discrete size, a current challenge in the field of supramolecular chemistry.  In particular, recent results reported by the Sanders group at the University of Cambridge are being extended to prepare both nanotubes and capsules that spontaneously assemble; naphthalene diimide (NDI) derivatives, in which the aromatic core is flanked by two amino-acid residues, serve as the building blocks.  The specific approach taken by the Hansen lab is to preorganize the NDI monomers for nanotube and capsule formation through the introduction of covalent tethers.  In future, the ends of the nanotubes will be capped by selective incorporation of NDI subunits that will not permit further self-assembly.  To date the group has prepared six linked dimer derivatives, five of which have been demonstrated to form nanotubes, and has prepared a linked trimer that spontaneously forms capsules. 
The work involved in the above projects will entail organic synthesis of the derivatives under investigation and their analysis by nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. 


Prof Henderson-Stull Professor Nidanie Henderson-Stull’s laboratory studies the structure and function of a family of cellular enzymes called protein kinases. The particular protein kinases we study have been shown to cause human diseases (e.g. cancer) when mutated or expressed abnormally in cells. The long-term goal of our research efforts is to contribute a molecular understanding of the differences between normal cellular structure of these kinases and their mutant forms that can aid in drug design and improving patient well-being. 
The smaller question we aim to answer is how the do the structures of these enzymes contributes to their regulation, especially within a cellular context. Our laboratory uses a combination of molecular genetic, cellular, and biochemical, and biophysical approaches to tackle the solutions. Therefore, student researchers who work in the lab on an ongoing basis are able to learn a variety of techniques and skills from molecular biology, biochemistry, biophysics, and structural and computational biology. The students working on these projects also appreciate that our results have real-world implications in the field of medicine. 


2016 SURF Faculty and Research Areas

Professor Larry Hunter. In the first project, they hope to make high-precision measurements of long-range spin-spin interactions (LRSSI) by using the Earth as a source of electron spin. This experiment is an outgrowth of an earlier search for a violation of Local Lorentz Invariance (LLI). In the new experiment, they will compares the relative precession frequencies of Hg and Cs magnetometers as a function of the orientation of an applied magnetic field with respect to fixed directions on the Earth’s surface. Using this approach and their old LLI apparatus they established bounds on LRSSI that were as much as a million times more sensitive than previous searches. In addition, they applied this method to extract bounds on velocity-dependent LRSSI that were largely inaccessible to earlier experiments. They have now realized a new “pump-then-probe” magnetometer geometry in Cs that reduces AC light shifts and retains high magnetometer sensitivity. They propose to develop a similar magnetometer in Hg. When combined, these two magnetometers should improve their sensitivity to LRSSI by at least an order of magnitude. At this level, the experiment will provide the most stringent test of several possible suggestions for physics beyond the standard model of particle physics.
They are presently completing the last of a series of measurements in thallium fluoride (TlF) that establish the viability of a cryogenic-beam experiment to measure the electric-dipole moment (EDM) of the Tl nucleus. Their favorable results have encouraged the launching of the new CeNTREX collaboration to realize this EDM experiment. They hope to achieve improved optical cycling in TlF and to use their cryogenic-beam apparatus to demonstrate optical forces and transverse cooling in TlF. The realization of transverse cooling could substantially improve the sensitivity of a second-generation TlF EDM measurement.   
Recent publications can be found here

Jaswal Professor Sheila Jaswal's SURF projects: Project 1: Experimental Hydrogen exchange mass spectrometry (HXMS). This combined experimental and computational project will extend ongoing work investigating the HXMS behavior of protein L, trypsin, and/or mitoNEET to probe the relationship between protein function and dynamics. Methods will include growing bacterial cultures, inducing protein production, biochemical purification, biophysical characterization using UV-Vis absorbance spectroscopy, SDS-PAGE gel electrophoresis, fluorescence, mass spectrometry and hydrogen exchange mass spectrometry. Software programs such as Kaleidagraph, Prism, R, Mathematica and Java may be used to analyze data. Students will be required to document all work in a specific format daily, to write instructions, protocols and overviews of process workflow, to analyze results and generate figures, and to actively engage with the relevant scientific literature, independently seek background information, and to ask questions and constantly take notes. Course requirements: CHEM 151, 161,  BIOL 191. Experience with some of the techniques described above would be helpful.

Project 2: Numerical simulations to fit HXMS experimental results. This computational project will build on ongoing work modeling protein folding dynamics and hydrogen exchange behavior for intact proteins, and for protein fragments. Work will include annotating and updating existing code, as well as writing new code in R, Java, Mathematica and Matlab. In addition, students will be required to document all work in a specific format daily, to write instructions, protocols and overviews of process workflow, to analyze results and generate figures, and to actively engage with the relevant scientific literature, independently seek background information, and to ask questions and constantly take notes. Course requirement: CHEM 151, 161. Experience with computer science and/or programming in some of the formats described above would be helpful. Learn more about Jaswal's research here

Jeong Professor Jeeyon Jeong. Iron is essential for nearly all organisms, but potentially cytotoxic. Therefore, iron homeostasis is tightly controlled. A key task in iron homeostasis is to safely allocate iron to specific organelles for usage or storage. Mitochondria are of particular interest for iron nutrition. Essential metabolic processes such as respiration that require iron occur in mitochondria, but mitochondria are susceptible to iron-induced oxidative damage. Despite the significance of iron in mitochondria, mitochondrial iron transport is not well-understood in plants. My lab aims to understand iron homeostasis by investigating the role of a mitochondrial ferroportin and advance our knowledge on iron transport in mitochondria. In the long term, elucidating the molecular mechanisms of plant iron homeostasis will offer insights to enhance plant growth and yield, and to develop strategies to enhance iron content of crops. Learn more about Professor Jeong's research here

Professor Kristensen Thea Kristensen. Population Ecology and Genetics of Black Bears (Ursus americanus) in Massachusetts. The goal of this project is to gather information that will allow us to estimate population size and evaluate patterns of relatedness across the landscape for black bears in Massachusetts. Students involved in the project will have the opportunity to complete both field and lab components. In the field, students will collect hair samples and re-set hair snares. We will then extract DNA from the hair follicles, run PCRs, and genotype samples. Individual student projects may consider genetic structure, relatedness, patterns of trap success in relation to habitat characteristics, and preliminary population estimates. Depending on the individual project, students may gain additional skills with specific software including ArcGIS Mapper and program R. 
Course requirement: Biology 181. Preferred (not required): Valid driver’s license 

Professor Lee Professor Joohyun Lee. The goal of the Lee laboratory is to understand the epigenetic regulation of chromatin switches in response to environmental cues, using a well-established, cold-induced epigenetic switch in plants. Plants are an excellent model for epigenetic research because epigenetic mutants are typically viable and heritable, whereas mammalian epigenetic mutations are often lethal and difficult to study in the whole organism. In addition, the well-studied vernalization system, a temperature-sensing process by which exposure to prolonged cold during winter leads to an epigenetic switch that permits flowering in the spring, provides a controllable experimental model for epigenetic studies. Cold memory is a mitotically-maintained epigenetic switch that promotes flowering in spring. Our efforts expect to understanding epigenetic mechanisms that occur the upstream of Polycomb Repressive Complex 2 (PRC2) -mediated gene silencing, which is highly conserved among eukaryotes. 

Professor Leung Professor Helen Leung studies intermolecular interactions due to van der Waals forces between nonchemically bonded molecules. Her research team employs a high resolution, pulsed molecular beam, Fourier transform microwave spectrometer to obtain the rotational spectrum of a complex that can then be analyzed to yield molecular information. Leung's researchers may collaborate with researchers in Mark Marshall's lab. Learn more about Professor Leung's research here

Prof Loinaz Professor Will Loinaz’s research is in theoretical elementary particle physics and related topics.  He compares theoretical models of new physics beyond the Standard Model to data obtained from many types of experiments to see what sorts of new physics are favored or ruled out by experiments.  In addition, he performs Monte Carlo simulations of simple quantum field theories and equilibrium and non-equilibrium statistical mechanical systems, and he looks at subtle and interesting mathematical features of very simple quantum mechanical systems. Learn more on Professor Loinaz's webpage

Professor Marshall Professor Mark Marshall studies the nature of intermolecular forces, and students conducting research in his lab seek to apply the detailed molecular information obtained from high resolution spectroscopy to address questions concerning these forces. Recently he has been working towards the development of a new method of chiral analysis, called chiral tagging, that utilizes microwave spectroscopy to determine the structures of non-covalently bound complexes formed between an analyte and a molecular tag of known absolute stereochemistry. Marshall's researchers may collaborate with researchers in Helen Leung's lab. Learn more about Professor Marshall's research here

Professor Miller Professor Jill Miller. Previous investigations have discovered within-species variation in Lycium australe in chromosome number (individuals are either diploid, 2n or tetraploid, 4n) and documented correlated genetic differences in plastid haplotypes.  In this project, students will determine plastid haplotypes using herbarium collections to expand our sampling of individuals across Australia and infer the geographic distribution of chromosomal variation in this species.  Several laboratory skills will be used to genotype individuals, including DNA extraction, PCR amplification, electrophoresis, and DNA sequencing.
Course requirements: No prior laboratory experience is necessary, but suggested coursework includes BIOL-181 and BIOL-191. 


 Professor Pat O’Hara’s research, using fluorescence has studied the binding of pesticides and environmental toxins to the estrogen receptor, structural changes in the oligomerization of the protein alpha crystallin in the lens of the eye, signal transduction in the calcium binding protein, calmodulin, and affinity maturation in antibodies. In addition her lab has built and is using a single molecule spectrometer to gain even more information in these systems since individual molecules can be imaged instead of ensembles of molecules. 
On a slight tangent to this research, her interest has recently been drawn to the chemistry of olive oil and in particular to understanding some of its many health benefits such as its antioxidant properties and the links to cancer, cardiovascular disease and dementia.   Her lab also hopes to develop consumer ready assays to detect the quality and age of olive oil, some 80% of which is mislabeled as extra virgin oil in the US. Towards that end we are exploring chlorophyll clocks and antioxidant assays. Learn more about Professor O'Hara's research here

Professor Palmquist Professor Carrie Palmquist. My lab explores questions of how children learn from other people. We are particularly interested in how preschoolers determine who is a good source of information, and who should be avoided. Research assistants in my lab are involved in all aspects of data collection and processing: contacting families, running children through studies, and coding and analyzing data. This summer, we will be focused on three different projects (details can be found here). In coordination with me, SURF students will determine which project is best suited to their goals and interests.
Course requirements: Students need to have taken Introduction to Psychology (or AP Psychology in high school); those who have taken Developmental Psychology are preferred. 

2016 SURF Faculty and Research Areas

Professor Alexandra Purdy. Microbiology, genetics, and host-microbe interactions. Project description:  In our lab, we are interested in understanding the molecular mechanisms through which bacteria regulate and influence the health and physiology of the host organisms they colonize. We look at these questions in the beneficial bacterial symbiont Vibrio fischeri, which bioluminesces as it grows in the Hawaiian bobtail squid, and in the related bacterial pathogen Vibrio cholerae, which causes disease. In this context, we study how bacteria regulate expression of genes involved in metabolism, and we ask questions that span multiple biological scales including biochemistry, genetics, signal transduction, metabolism, and evolution of gene regulatory networks. No previous biology laboratory experience is necessary. 
Biol-181 and/or Biol-191 preferred, with Biol-191 strongly preferred.   

Professor Ragkousi Professor Katerina Ragkousi. Project: role of tumor suppressor and cell polarity proteins in sea anemone epithelial tissue development. We use genetics, imaging and cell biology approaches to investigate how sea anemone embryos develop a polarized cell layer.
Required courses: Bio 191. Also suitable for students that have taken Bio 241. 

Professor Riondato Professor Riondato’s research focuses on algorithms for knowledge discovery, data mining, and machine learning. He develop theory and methods to extract the most information from large datasets, as fast as possible and in a statistically sound way. The problems studied include pattern extraction, graph mining, and time series analysis. The algorithms often use concepts from statistical learning theory and sampling. More details available at http://matteo.rionda.to/

Required course: COSC 211 Data Structures 
Suggested (but not required) courses: Any of COSC 311 Algorithms, COSC 247 Machine Learning, COSC 254 Data Mining, COSC 223 Probability & Computing.


Professor Schulkind Professor Matthew Schulkind. My research program explores issues related to autobiographical memory.  Currently, I am working on projects investigating the organization of autobiographical memory (how memories of the past are related to each other) and the way that autobiographical narratives vary as a function of sex, gender, and personality (further description can be found here).  SURF students would be involved in coding data from current projects and helping develop materials and protocols for future experiments. 


2016 SURF Faculty and Research Areas Professor Josef Trapani's research explores sensory transduction and neuronal encoding of sensory information. Using the lateral-line system of the zebrafish, his lab studies these processes using molecular biology, fluorescence microscopy, and electrophysiology. Learn more about Professor Trapani's research here

  Professor Wagaman Professor Amy Wagaman. Can we predict protein unfolding rate using protein structural features? What can we learn about protein stability by viewing proteins as graphs? There is data waiting for you to investigate these questions. Alternative projects may be explored depending on student background and could include developing an R package for use with a nonparametric test of interaction in an ANOVA setting, analyzing data to assess pedagogy related to writing in statistics, assessing algorithmic stability for a Gibbs sampler, or analyzing some other data set for an applied project of interest. 
Course requirements: Intro Stat (111/135, required), Stat 230 (required); A few others would be great pluses, but not necessary: COSC 111/112, Stat 231. 


Ward-Duong  Kimberly Ward-Duong. The SURF student will work on an observational astronomy project involving very high-resolution infrared images of nearby stars. The datasets the student will work with involve images taken from some of the world's largest telescopes using a technique called adaptive optics. This approach produces very sharp, deep images that allow us to search for new binary star systems and to discover fainter brown dwarfs (objects intermediate between the sizes of planets and stars) orbiting our nearest neighbor stars. Through this project, the student will learn to process and analyze adaptive optics images and search for new candidate systems. Once identified, the student will measure the stars' properties to confirm or reject new binaries, and measure their orbits. There are no specific course requirements. However, any familiarity with programming (e.g., via ASTR 200 or introductory CS) and ease working with spreadsheets would be valuable.