Research Streams
Rather than placing individual students with individual faculty, or integrating parts of research into traditional laboratory courses, the FRI revolves around the "Research Stream,"a fully functional research laboratory in which students do cutting edge research supplemented by weekly lectures that are organized around the work being done in the lab
Each research stream is led by a faculty member who has designed a program of research using our educational model to pursue their fundamental research questions. These faculty provide guidance to their respective Research Streams, set goals and directions, and develop and teach the Research Experience course to the students within their stream. The research labs themselves are each run by a Research Educator (RE), a Ph.D. research scientist dedicated to each Research Stream
Students have the option to continue through the summer and will return in the fall to receive research credit for continued work in their lab.
Current Research Streams
Aptamer Stream
Andrew Ellington
Bradley Hall
Bradley Hall
How can we use biochemistry and nucleic acids for drug development and sensor applications. Simply put, we develop things that bind to things. More specifically, we develop nucleic acid oligonucleotides “aptamers” that can bind tightly and specifically to targets of interest.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: F 1-2 pm
Autonomous Vehicles
Peter Stone
Michael Quinlan
Michael Quinlan
The goal of this stream is to create a fully autonomous vehicle that can drive in traffic. Students will learn about, and contribute to cutting-edge research in, artificial intelligence and robotics.
Credit Options: CS 378 Lab Meeting Times: M W 11-12:30 pm CPE 2.22
Biobrick
Karen Browning
Grace Choy
Grace Choy
Our research stream involves synthesizing genes from short DNA fragments, piecing them together like Legos (BioBricks) with molecular cloning tools to build protein expression "machines" that function in bacteria. The proteins we will "build" range from factors in involved in plant protein synthesis to fluorescent proteins from coral with new properties. You will receive training in all aspects of molecular cloning as well as recombinant protein expression in bacteria.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: M 1-2 pm
Cell Fate Regulation
.jpg?1239645404)
Alan Lloyd
Antonio Gonzalez
Antonio Gonzalez
How is a cell’s fate determined?
This stream uses a comprehensive genetics approach to investigate developmental mechanisms that lead to cell fate decision events and the regulation of organ differentiation pathways. Students will design and pursue experiments using a broad range of genetic strategies such as classical, molecular, forward and reverse genetics. In the process students will learn how to clone genes, engineer DNA, generate mutant and transgenic organisms, document and analyze data, and more. While this lab focuses on a plant molecular/genetic model, all the technologies learned in this stream are common to research in all modern molecular/genetic model organisms.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: W 4-5 pm
Computational Biology: Studying Disease Dynamics
Claus Wilke and Lauren Meyers
What can math or computer science tell us about infectious diseases?
In this stream, students will use mathematical modeling, statistics, and bioinformatics to study the dynamics of infectious diseases such as influenza, HIV, or West Nile virus. Students will work on a broad range of different topics in infectious disease biology, from protein biochemistry to molecular evolution and epidemiology. This stream is a good option for students who want to study biological questions, but who also have a strong interest in math, computer science, or theoretical physics.
Credit Options: BIO 321G Lab Meeting Time:T TH 11-12:30 pm W 1-3 pm
Computational Intelligence in Game Design
Risto Miikkulainen
Vinod Valsalam
Vinod Valsalam
In this class, you will learn about different aspects of video game technology and will get hands on experience in working with a real game engine. You will also be exposed to cutting-edge AI research that may play a central role in the next generation of video games.
Credit Options: CS 378 Lab Meeting Time: TBD with student
Computational Nanoparticles
Graeme Henkelman
Zachary Pozun
Zachary Pozun
In this stream, students will be taught how to calculate properties of nanoparticles using computational methods based upon quantum chemistry. Click here for stream video.
Credit Options: CH 204/CH 108 Lab Meeting Time: M 3-4 pm
Discovery Lab in Plant Biology
Stan Roux
Greg Clark
Greg Clark
How does the environment impact what cells do?
A recent exciting discovery in plants is that ATP is released into the cell wall during plant growth where it plays a major role in controlling how fast cells grow. Students in this stream carry out never-done-before experiments on this topic and discover significant new findings on how extracellular ATP controls growth. They learn methods of experimental design, data gathering, data interpretation, and data presentation, and they learn principles of stimulus-response coupling that apply equally well to animals and plants. Specifically, students will do their experiments on extracellular ATP signaling in root hairs, an agriculturally important model system for studying plant growth.
Credit Options: BIO 205L/BIO 170C Lab Meeting Time: TH 2:30-3:30 pm
Electronic and Magnetic Materials Research
John Markert
Isaac Manzanera and Rosa Cardenas
Isaac Manzanera and Rosa Cardenas
How do you create materials with new electronic and magnetic properties and structures?
This Research Stream focuses on materials physics and the design and development of materials for use in data storage, optics, sensors, and optical and infrared astronomy. Students will learn new materials synthesis via solid state reaction, followed by structural, microscopic, magnetic, thermal, and superconducting characterization of the materials. Students may also perform cantilever micromagnetometry, interferometry, and magnetic resonance microscopy.
Credit Options:Concurrent enrollment/credit in PHY 301 or 316; enroll in either PHY 101L-FRI or PHY 116L-FRI & PHY 108-FRI Lab Meeting Time: M 4-5 pm
Exploring the Universe with White Dwarf Stars
Don Winget
Mike Montgomery
Mike Montgomery
What can white dwarfs tell us about axions and dark matter?
Students in this stream will make astronomical observations of pulsating white dwarf stars. They will analyze the data and participate in building theoretical models through which we will explore the properties of neutrinos and the hypothetical axions, as well as the physics of convection and crystallization in stellar plasmas. Axions are a leading candidate for dark matter, the unseen component comprising the vast majority of matter in the universe. They will perform numerical experiments studying how pulsations allow us to “see beneath the surface” of stars. Go here for stream video.
Credit Options: PHY 116L/PHY 210 or PHY 110/PHY 210 Lab Meeting Time: M 4-5 pm
Frontiers of Linear Algebra Library Development
Robert van de Geijn
Linear algebra is not just a subject in mathematics, it is a fundamental tool of scientific computing since many applications at their core require compute intensive matrix operations to be performed. In this course we examine new techniques for developing high-performance libraries for these operations, targeting modern architectures including processors with multiple cores. Importantly, these techniques allow novices with little background in linear algebra and computer science to develop algorithms and implementations that outperform traditional libraries.
Credit Options: To be determined depending on the student
Lab Meeting Time: To be determined with each student
Functional Genomics Research
Vishy Iyer
Patrick Killion
Patrick Killion
How can we use genome sequences to better understand the biology of organisms in molecular detail? Emerging large-scale sequencing technologies explore the molecular biology of organisms on a genome-wide scale. Click here for stream videos.
Credit Options: CH 204/CH 108 or BIO 205L/BIO170C Lab Meeting Time: T 2:30-3:30 pm
Functional Materials Based on Metal Complexes
Richard Jones and Brad Holliday
Xiaoping Yang
Xiaoping Yang
How do we make and characterize new metal-containing compounds that have useful properties?
Some chemical compounds that contain metal atoms have useful properties such luminescence, or the ability to “glow in the dark”. The efficiency or brightness of these compounds is related to the specific arrangementnof the atoms within the chemical structure. In this research stream, students will learn to make new luminescent compounds and using state-of-the-art techniques explore both the exact chemical structure (X-ray diffraction) and luminescence properties (fluorescence, phosphorescence, and luminescence). The relationship between chemical structure and physical properties will be studied to develop new functional materials.
Credit Options: CH 204/CH 108 Lab Meeting Time: F 2-3 pm
Mitochondrial Gene Expression
Dean Appling
Anne Tibbetts
Anne Tibbetts
Genetic Dissection of the Mitochondrial Gene Expression Machinery: Mitochondria possess the machinery to replicate and express their own DNA, which is essential for the proper function of this critical cellular organelle. This Research Stream will utilize the power of yeast genetics to identify and dissect the mitochondrial gene expression machinery.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: M 2-3 pm
Nanomaterials for Chemical Catalysis
Keith Stevenson, Co-PIs David Vanden Bout and Richard Crook
Katherine Marvin
Katherine Marvin
In our lab, we make nanoparticles that are in the nanometer scale (10-9m!), and use them as catalysts to efficiently convert reactants into useful products that have potential applications for fuels production, environmental remediation, and specialty chemicals production. To limit the particles to nano scale, we use "dendrimers", a class of large organic molecules resembling a tree-branch structure, as "containers" or "molecular templates" in synthesis to make nanomaterials with uniform size, shape and composition.
Credit Options: CH 204/CH 108 Lab Meeting Time: M 3-4 pm
Supramolecular Sensors
Eric Anslyn
Alona Umali
Alona Umali
In the Supramolecular Sensors Stream, students take on the challenge of constructing differential array sensors that can be used to further homeland security, food industry, environmental science, and metabolomics, in general. The current project of the whole stream is the construction of a peptidic array sensor that can be used to differentiate wines. The individual sensors in the array work via the indicator displacement assay, a supramolecular chemistry technique pioneered by Dr. Eric Anslyn and his research group at the Department of Chemistry and Biochemistry.
Credit Options: CH 204/CH 108 Lab Meeting Time: M 3-4 pm
Synthesis and Biological Recognition
Steve Martin
Kristen Procko
Kristen Procko
How do medicinal chemists design potent drugs?
Designing small organic molecules that bind tightly to proteins is a fundamental problem in discovering new therapeutic agents. In this multidisciplinary Stream, students will learn how to model interactions between proteins and drug-like molecules using the computer program, PyMOL. They will then design and synthesize novel molecules that target the protein MUP-I, and then determine their binding affinities using the technique of isothermal titration calorimetry (ITC). Students in this Stream will thus learn some of the basic skills used by chemists and biologists to study protein–ligand interactions, a key step in drug discovery.
Credit Options: CH 204/CH 108 Lab Meeting Time: W 1-2 pm
Vertebrate Interactome Mapping
Scott Stevens
Albert MacKrell
Albert MacKrell
Essential functions in gene expression and other cell functions are performed by complexes containing large numbers of proteins, and an important step in understanding these processes is cataloging the proteins present and characterizing the interactions between them. We are using genetic recombination in bacteria and in animal cells to attach tags to vertebrate genes and to replace the normal gene in cultured cell with the tagged version, allowing us to purify the protein as it is normally expressed using the tag, and identify the other proteins that interact with it.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: M 3-4 pm
Viral Evolution
James J. Bull
Richard Heineman
Richard Heineman
How do viruses evolve?
Studies of experimental evolution help us uncover general evolutionary processes using model organisms that are easily manipulated and evolve quickly. In this stream, you will evolve viruses that infect bacteria to new environmental or genetic conditions and determine the genetic bases of adaptation. This will help us answer questions about how organisms evolve, as well as the predictability of evolution in an organism with a well studied genetic interaction map.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: W 3-4 pm
Virtual Drug Screening
Jon Robertus
Josh Beckham
Josh Beckham
Can new drugs be identified from virtual libraries of drug-like molecules?
Identifying new drug leads using traditional methods is an expensive and time consuming process. This research stream uses computers to sift through libraries of chemical structures and predict which ones may bind most effectively to a protein that is a potential drug target. Through this work students will be introduced to fundamental features of protein structures and of protein-ligand interactions. They will learn how to run Virtual Drug Screening software and will use molecular graphics programs to interpret the results. Then students will test several of the best candidate molecules in the wet lab to determine their efficacy in comparison to the computational screening predictions.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: T 3:30-4:30 pm
