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Student Research Opportunities

Please click on individual student research opportunity project titles to view additional details.  Also, please check back often as the positions on this page, and their status, will change continuously.

Faculty and staff can add new or modify existing student research opportunities.

 

Biology

Determinates of Lyme disease risk in Addison County

Position Status:
active/open/recruiting

Faculty or Staff Member:
David Allen

E-mail Address:
dallen@middlebury.edu

Department(s) and/or Program(s):
Biology

Project Title:
Determinates of Lyme disease risk in Addison County

Project Description:
Lyme disease is on the rise in the state of Vermont. In the last ten years the incidence rate has jumped 10-fold, and over the last three years VT has the highest incidence rate in the country. Lyme disease is a vector-borne, zoonotic disease. Vector-borne means that it is transmitted by a vector, in this case the black-legged tick, Ixodes scapulars. Zoonotic means that the bacterium that causes Lyme (Borrelia burgdorferi) can also live in other animal hosts. These two facts mean that the incidence of Lyme disease in an area is closely tied to the populations of those vectors and hosts. So Lyme disease risk to humans is partially controlled by ecological factors. In this research project we will examine this connection between ecology and Lyme disease. There are a tremendous number of possible biotic and abiotic factors that can affect Lyme disease risk: ticks are prone to desiccation so leaf litter humidity is important; tick development rate is controlled by temperature; mice are the best hosts for ticks; ... .

Project Location(s):
MBH lab and field sites throughout Addison County

Session Dates:
summer

Eligibility and Requirements:
None

Application Process:
Please fill out this form by Feb. 22. https://goo.gl/forms/ac9562wEAjYRteq32

Dynamics of a hemlock-hardwood forest

Position Status:
active/open/recruiting

Faculty or Staff Member:
David Allen

E-mail Address:
dallen@middlebury.edu

Department(s) and/or Program(s):
Biology

Project Title:
Dynamics of a hemlock-hardwood forest

Project Description:
Understanding the dynamics of forests is important for many reasons: we can better understand how the forest will respond to disturbance or climate change, we can set sustainable harvesting levels, we can predict how much carbon the forest will sequester, ... . But forest dynamics play out over a long time scales, so directly observing or measuring them is hard. One way around that is to create models that are realistic enough to capture those dynamics. This summer my research group will continue work developing and parameterizing a spatially explicit, individual-level mechanistic model to understand dynamics in this region's hemlock-hardwood forests. The hope is that this model will be realistic enough to do the things mentioned in the paragraph above. Be warned that this summer's work will continue a multi-year process and we won't be able to fully develop this model by the end of the summer. But we will get some exciting and interesting results this summer! The work will predominately be in the field.

Project Location(s):
My BiHall lab and local field sites (Battell Research Forest and Bread Loaf lands)

Session Dates:
summer

Eligibility and Requirements:
Prefer students how have taken BIOL0323

Application Process:
Fill out this form by Feb. 22nd. https://goo.gl/forms/ac9562wEAjYRteq32

Please contact department regarding other potential opportunities.

 

Chemistry & Biochemistry

Student research opportunities in Chemistry & Biochemistry (various)

This posting is for multiple positions.

Position Status:
active/open/recruiting

Faculty or Staff Member:
various

E-mail Address:
various

Department(s) and/or Program(s):
Chemistry & Biochemistry

Project Title:
Student research opportunities in Chemistry & Biochemistry

Project Description:
We have a list of research opportunities on our website.

Project Location(s):
MBH

Session Dates:
summer

Eligibility and Requirements:
Usually mid to upper level chemistry, biochemistry or MBB majors.

Application Process:
Check each listing for details.

Additional Information:
http://www.middlebury.edu/academics/chem/resources/research & http://www.middlebury.edu/academics/chem/faculty

 

Computer Science

Student research opportunities in Computer Science (various)

This posting is for multiple positions.

Position Status:
active/open/recruiting

Faculty or Staff Member:
various

E-mail Address:
various

Department(s) and/or Program(s):
Computer Science

Project Title:
Student research opportunities in Computer Science

Project Description:
Each summer CS faculty hire students to participate in their research projects.  Potential research areas this summer include visual analytics and generative art (Andrews), theoretical and experimental algorithms (Christman), computer vision, robotics, and biometrics (Grant), operating systems, networking, security, and privacy (Johnson), quantum computing (Kimmel), software tools and methods for genome analysis (Linderman), and computer vision (Scharstein).

Project Location(s):
MBH

Session Dates:
summer

Eligibility and Requirements:
Note that many projects require CS experience (usually through at least CS 202), thought there can be exceptions depending on the project.

Application Process:
If you are interested in a position, please fill out the form at https://goo.gl/forms/gGNePZRkvOvc0svr1 . We will consider applications and fill positions on a rolling basis, so please apply as soon as possible.

Additional Information:
http://www.middlebury.edu/academics/cs/work & http://www.middlebury.edu/academics/cs/faculty

Additional Notes:
If you want to learn more about the nature of our research, feel free to get in touch with us!

MySeq.js: A single page application for distributed genome analysis and education

Position Status:
active/open/recruiting

Faculty or Staff Member:
Michael Linderman

E-mail Address:
mlinderman@middlebury.edu

Department(s) and/or Program(s):
Computer Science

Project Title:
MySeq.js: A single page application for distributed genome analysis and education

Project Description:
Using React and other modern web technologies we will develop MySeq.js (https://github.com/mlinderm/myseq.js), a single page application for privacy protecting, hands-on analysis of genomic data that supports both self-guided exploration and structured laboratory exercises (such as predicting bitter tasting response from an individual’s genome). Modern browser APIs enable efficient querying of genome-scale variant files stored locally on the user’s computer or available remotely via URL (without downloading the entire multi-GB file). With the former, we can easily distribute sophisticated genome analysis tools that do not depend on local computational resources (other than the user’s web browser) nor require uploading sensitive data to external servers.

Project Location(s):
MBH

Session Dates:
summer

Eligibility and Requirements:
Experience with object oriented programming is a prerequisite. Previous javascript/html/css experience, such as completion of CS321 or CS465, is highly desired.

Application Process:
Send your resume/CV including a list of relevant of coursework or other experience, the dates you will be available in Summer 2017, and a brief statement of interest to mlinderman@middlebury.edu.

Additional Information:
http://go.middlebury.edu/linderman

Non-parametric genotyping of structural variants in whole genome sequencing data

Position Status:
active/open/recruiting

Faculty or Staff Member:
Michael Linderman

E-mail Address:
mlinderman@middlebury.edu

Department(s) and/or Program(s):
Computer Science

Project Title:
Non-parametric genotyping of structural variants in whole genome sequencing data

Project Description:
Modern short-read DNA sequencers can’t directly detect variants, e.g. insertions or deletions of nucleotides, larger than the read length. These larger “structural” variants (SV), which can cause numerous genetic diseases, must be inferred from secondary, probabilistic, signals in the sequencing data. The existing parametric models for these signals do not take into account sample, region and pipeline-specific biases, reducing the accuracy of SV genotyping. Instead we will pursue a non-parametric approach using detailed simulations of the sequencing process. Specifically we will be bringing up a prototype simulation pipeline on Middlebury computing resources, and refining that pipeline into a practical tool for genotyping putative SVs in a cohort of children with congenital heart defects. As part of that pipeline we will implement annotators for the different types of evidence for SVs from raw sequencing data.

Project Location(s):
MBH

Session Dates:
summer

Eligibility and Requirements:
Enrollment in (or completion of) CS321 Bioinformatics Algorithms or other advanced algorithms course and strong programming skills.

Application Process:
Send your resume/CV including a list of relevant of coursework or other experience, the dates you will be available in Summer 2017, and a brief statement of interest to mlinderman@middlebury.edu.

Additional Information:
http://go.middlebury.edu/linderman

 

Environmental Studies

Please contact program directly.

 

Geography

Please contact department directly.

 

Geology

Please contact department directly.

 

Mathematics

Intersection of Computational Fluid Dynamics with Machine Learning

Position Status:
active/open/recruiting

Faculty or Staff Member:
Michaela Kubacki

E-mail Address:
mkubacki@middlebury.edu

Department(s) and/or Program(s):
Mathematics

Project Title:
Intersection of Computational Fluid Dynamics with Machine Learning

Project Description:
The field of computational fluid dynamics (CFD) plays a crucial role in many real-life applications, from the design of medical apparatus to the accurate forecasting of weather, and has strong ties with big data. Machine learning (ML) constitutes a new approach in CFD, one in which a machine extracts knowledge from data without knowledge of the underlying physical principles governing the fluid flow. Previously, CFD practitioners used data to validate predictions made from mathematical models, whereas ML could (potentially) use data to inform and discover new hypotheses and models. This new direction of research is inherently interdisciplinary, requiring researchers to obtain some level of working background knowledge in mathematics/statistics, computer science, physics, and engineering. The undergraduate portion of this research project will be a multi-year endeavor to (1) build/maintain a literature knowledge base on the intersection of CFD+ML, (2) recreate existing experiments in CFD+ML using MATLAB and/or

Project Location(s):
Middlebury (in-person vs remote TBD)

Session Dates:
summer

Eligibility and Requirements:
Pre-reqs for math majors MATH 0225, plus experience with MATLAB or a similar coding platform like Python. Other helpful (but not required) mathematics courses include MATH 0218, MATH 0315, MATH 0328, MATH 410, and MATH 0728. Pre-reqs for other majors MATH 0122 plus experience with MATLAB or a similar coding platform like Python. Additional experience in a subject area related to the research is encouraged, such as coursework in Physics (e.g.PHYS 0212, PHYS 0330) and/or Computer Sciences (e.g. CSCI 0311, 0451).

Application Process:
Apply via math department google form: https://forms.gle/LgEugrvLH2tKBPYSA

Additional Notes:
2 positions available, pending funding from Middlebury

Modeling synaptic plasticity

Position Status:
active/open/recruiting

Faculty or Staff Member:
Jennifer Crodelle

E-mail Address:
jcrodelle@middlebury.edu

Department(s) and/or Program(s):
Mathematics

Project Title:
Modeling synaptic plasticity

Project Description:
Synaptic plasticity underlies the formation of important circuits in the brain, including those necessary for vision and other sensory functions. Recently, experiments have shown that a different type of connection between neurons, called a gap junction, can influence the formation of synaptic circuits in the visual cortex during development. Interestingly, the gap junction itself undergoes some plasticity as well, though experimental studies of this plasticity are scarce. This summer project involves incorporating gap junctions into existing mathematical frameworks for development and plasticity and using this model to understand the interaction between the gap junction and the plasticity. Feel free to look at my website (https://sites.middlebury.edu/jcrodelle/) for more information.

Project Location(s):
Unknown, but hopefully on campus

Session Dates:
summer

Eligibility and Requirements:
MATH 0225 or familiarity with differential equations

Application Process:
Fill out the following google form https://forms.gle/xqF8rSdpBsuBPL3L8 by March 31.

Additional Information:
https://docs.google.com/document/d/1TqjJiyZROKfa-lBK68SYCCuP7Z9hvO9Y1bXH...

Please contact department regarding other potential opportunities.

 

Molecular Biology & Biochemistry

Student research opportunities in Molecular Biology & Biochemistry (various)

This posting is for multiple positions.

Position Status:
active/open/recruiting

Faculty or Staff Member:
various

E-mail Address:
various

Department(s) and/or Program(s):
Molecular Biology & Biochemistry

Project Title:
Student research opportunities in Molecular Biology & Biochemistry

Project Description:
We have a list of research opportunities on our website.

Project Location(s):
MBH

Session Dates:
summer

Eligibility and Requirements:
Usually mid to upper level chemistry, biochemistry or MBB majors.

Application Process:
Check each listing for details.

Additional Information:
http://www.middlebury.edu/academics/mbb/resources/summer_research & http://www.middlebury.edu/academics/mbb/faculty

 

Neuroscience

Please contact program directly.

 

Physics

Biomedical Optics

Position Status:
active/open/recruiting

Faculty or Staff Member:
Prof. Michael Durst

E-mail Address:
mdurst@middlebury.edu

Department(s) and/or Program(s):
Physics

Project Title:
Biomedical Optics

Project Description:
I study two-photon microscopy, which uses lasers to image deep within scattering tissue. Students gain hands-on experience with laser beam alignment, fiber coupling, and the development of breadboard optical systems. In addition, students will have the opportunity to become fluent in Matlab, Mathematica, and LabVIEW programming languages in order to create beam propagation simulations and operate equipment.

Project Location(s):
MBH -- Biomedical Optics Lab

Session Dates:
summer

Eligibility and Requirements:
Students majoring in physics are preferred, but I welcome students from other departments and majors, including neuroscience, MBB, chemistry, and biology, to apply if they have taken PHYS 0241: Biomedical Imaging.

Application Process:
Contact Prof. Durst, introduce yourself, and get an application form. Applications are due by the end of February.

Additional Information:
http://sites.middlebury.edu/durst/

Computational Quantum Physics

Position Status:
active/open/recruiting

Faculty or Staff Member:
Chris Herdman

E-mail Address:
cherdman@middlebury.edu

Department(s) and/or Program(s):
Physics

Project Title:
Computational Quantum Physics

Project Description:
In our group, we use computational methods to study quantum mechanical systems. In particular, we focus on numerical simulations of physical systems containing a large number of strongly interacting quantum particles. Potential projects may include: simulations of quantum fluids (e.g. a Bose-Einstein condensate or superfluid helium), numerical studies of quantum computer architectures, and applying machine learning methods to identify exotic quantum phases of matter. These projects may involve interfacing with Linux systems and computer clusters, coding in Python, Mathematica, Julia or C++ and applying numerical techniques to solve linear algebra problems.

Project Location(s):
Herdman Lab in MBH

Session Dates:
summer

Eligibility and Requirements:
No particular background in physics or coding is required. Prior experience with coding, linear algebra, and quantum mechanics (e.g. PHYS 202 or PHY 401) is helpful.

Application Process:
Please fill out this form: https://forms.gle/jrXWcF9wrQFvvAMt6

Ion Trapping Lab

Position Status:
active/open/recruiting

Faculty or Staff Member:
Paul Hess

E-mail Address:
phess@middlebury.edu

Department(s) and/or Program(s):
Physics

Project Title:
Ion Trapping Lab

Project Description:
Our lab is building the capability to trap, image, and manipulate ions of interest for quantum information experiments. Most student projects will be focused on building, testing, and configuring laboratory apparatus (i.e. lasers, optics, electronics, vacuum equipment) for eventual trapped ion experiments. Some projects will also involve computer simulations of the classical and/or quantum mechanical behavior of trapped ions.

Project Location(s):
McCardell Bicentennial Hall

Session Dates:
summer

Eligibility and Requirements:
Projects are open to students at all levels who have completed some coursework in physics at Middlebury. Preference given to physics majors.

Application Process:
First, be in touch with Prof. Hess to schedule a meeting and discuss your interest. I will then send you a short application form, which includes a brief written statement of interest and goals.

Additional Information:
http://go.middlebury.edu/hesslab

Additional Notes:
Upper level courses that prepare you particularly well for work in my lab include PHYS 321, 220/230, 221, 241, and 401.

Launching Laser-Cooled Atoms

Position Status:
active/open/recruiting

Faculty or Staff Member:
Anne Goodsell

E-mail Address:
agoodsell@middlebury.edu

Department(s) and/or Program(s):
Physics

Project Title:
Launching Laser-Cooled Atoms

Project Description:
This is fundamental research in atomic and optical physics; most of the work is primarily experimental, with some elements of theory and calculation.  The interaction of laser light and atoms in a gas results in slow-moving atoms that we characterize and control.

Project Location(s):
MBH -- Goodsell Lab

Session Dates:
summer

Eligibility and Requirements:
Appropriate for students majoring or planning to major in Physics.  For some projects, students need to complete Phys 0202 before the summer; some aspects require additional coursework.

Application Process:
Submit a list of your relevant coursework, relevant experience, weeks when you're available for the summer, and a brief statement of interest to agoodsell@middlebury.edu by February 15; more materials may be requested.

Additional Info:
http://sites.middlebury.edu/goodsellresearch

Additional Notes:
I encourage interested students to come introduce yourself to me before applying.

Scattering Approach to Quantum Fluctuations

Position Status:
active/open/recruiting

Faculty or Staff Member:
Noah Graham

E-mail Address:
ngraham@middlebury.edu

Department(s) and/or Program(s):
Physics

Project Title:
Scattering Approach to Quantum Fluctuations

Project Description:
Applications of computational wave scattering to problems drawn from nanotechnology, particle physics, and general relativity

Project Location(s):
MBH, Physics Department

Session Dates:
summer

Eligibility and Requirements:
PHYS 0212 is essential; other courses including PHYS 0111, PHYS 0202, PHYS 0301/302, PHYS 0330, PHYS 0350, PHYS 0380, and PHYS 0401 are all helpful

Application Process:
please contact Prof. Graham for more information

Please contact department regarding other potential opportunities.

 

Psychology

Please contact department directly.

Interdisciplinary

Modeling synaptic plasticity

Position Status:
active/open/recruiting

Faculty or Staff Member:
Jennifer Crodelle

E-mail Address:
jcrodelle@middlebury.edu

Department(s) and/or Program(s):
Mathematics

Project Title:
Modeling synaptic plasticity

Project Description:
Synaptic plasticity underlies the formation of important circuits in the brain, including those necessary for vision and other sensory functions. Recently, experiments have shown that a different type of connection between neurons, called a gap junction, can influence the formation of synaptic circuits in the visual cortex during development. Interestingly, the gap junction itself undergoes some plasticity as well, though experimental studies of this plasticity are scarce. This summer project involves incorporating gap junctions into existing mathematical frameworks for development and plasticity and using this model to understand the interaction between the gap junction and the plasticity. Feel free to look at my website (https://sites.middlebury.edu/jcrodelle/) for more information.

Project Location(s):
Unknown, but hopefully on campus

Session Dates:
summer

Eligibility and Requirements:
MATH 0225 or familiarity with differential equations

Application Process:
Fill out the following google form https://forms.gle/xqF8rSdpBsuBPL3L8 by March 31.

Additional Information:
https://docs.google.com/document/d/1TqjJiyZROKfa-lBK68SYCCuP7Z9hvO9Y1bXH...

 

Director of Sciences
Rick Bunt
McCardell Bicentennial Hall 550
802.443.2559
rbunt@middlebury.edu

Science & Mathematics
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802.443.5000
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