Organizing Committee
- Leyda Almodóvar Velázquez
Stonehill College - Amanda Harsy Ramsay
Lewis University - Cory Johnson
California State University, San Bernardino - Jessica Sorrells
Converse University
Abstract
The Summer@ICERM faculty advisers will present a variety of research projects on the combinatorial and graph theoretical properties of DNA self-assembly. By modeling nanostructures with discrete graphs, efficient DNA self-assembly becomes a mathematical puzzle. Faculty will also guide the development of computational tools which can be used to aid in answering fundamental questions that arise in this field.
Throughout the eight-week program, students will be introduced to the research topic with interactive lectures. Afterward, students will work on their projects in assigned groups of two to four, supervised by faculty advisors and aided by teaching assistants. Students will meet daily, give regular talks about their findings, attend mini-courses, guest talks, and professional development seminars, practice coding, and Tex typesetting, and will acquire skills in free software development. Students will learn how to collaborate mathematically, working closely in their teams to write up their research into a paper.

Program Details
- 2023 Proposed Research Topics
-
- Optimize design structures for families of graphs such as graphs with a lattice substructure and k-regular graphs.
- Create, expand, and improve current software used to nd and check optimal solutions.
- Determine relationships between optimizing bond-edge and tile types.
- Important Notes
-
- Applicants must be matriculating undergraduate students at the time of the start of Summer@ICERM 2023.
- Funding is available for 2-3 students who are not US citizens or permanent residents.
- Funding Includes*
-
- $4,000 stipend
- Providence, RI room, board, and travel funding provided for in-person programming, pandemic permitting. (Brown students who choose not to live in the dorm will waive ICERM provided housing and meal funding.)
- To Apply
-
Applications accepted via MathPrograms.org. Applications submitted by February 14, 2023, will receive full consideration.
Confirmed Speakers & Participants
Talks will be presented virtually or in-person as indicated in the schedule below.
- Speaker
- Poster Presenter
- Attendee
- Virtual Attendee
-
Leyda Almodóvar Velázquez
Stonehill College
-
Toby Anderson
Harvey Mudd College
-
Jacob Ashworth
Rose-Hulman Institute of Technology
-
Lisa Baek
Brown University
-
Grace Bielefeldt
St. Olaf College
-
Ethan Bove
Brown University
-
Katelyn Buck
The University of Texas at Austin
-
Michael Cho
Stanford University
-
Jo Ellis-Monaghan
Saint Michael's College
-
Ryann Firestine
Auburn University
-
Michaela Fitzgerald
Stonehill College
-
Olivia Greinke
Transylvania University
-
Luca Grossmann
Tufts University
-
Janelle Hammond
Stonehill College
-
Amanda Harsy Ramsay
Lewis University
-
Iris Horng
University of Pennsylvania
-
Catherine Jacobs
Wellesley College
-
Cory Johnson
California State University, San Bernardino
-
Amelia Julian
Plymouth State University
-
Andrew Lavengood-Ryan
Nevada State University
-
Holly Luebsen
University of Texas at Austin
-
Fausto Navarro
Johns Hopkins University
-
Iskandar Nazhar
University of Massachusetts Amherst
-
Eric Redmon
Marquette University
-
Steph Reyes
Claremont Graduate University
-
Luis Santori
University of Central Florida
-
Jessica Sorrells
Converse University
-
Mitchell VonEschen
Lawrence University
-
Xingyi Zhang
Carleton College
Summer Schedule
Monday, June 12, 2023
-
9:30 - 10:00 am EDTWelcome, Meet & GreetWelcome - 10th Floor Collaborative Space
-
10:00 am - 12:30 pm EDTScavenger Hunt
-
12:45 - 2:00 pm EDTLunch/Free Time
-
2:00 - 3:00 pm EDTGoals of Summer10th Floor Collaborative Space
- Leyda Almodóvar Velázquez, Stonehill College
- Amanda Harsy, Lewis University
- Cory Johnson, California State University, San Bernardino
- Jessica Sorrells, Converse University
-
3:00 - 3:30 pm EDTCoffee Break10th Floor Collaborative Space
-
3:30 - 4:30 pm EDTIntroduction to Graph Theoretical DNA Self-Assembly10th Floor Collaborative Space
- Leyda Almodóvar Velázquez, Stonehill College
- Amanda Harsy, Lewis University
- Cory Johnson, California State University, San Bernardino
- Jessica Sorrells, Converse University
Tuesday, June 13, 2023
-
9:30 - 10:30 am EDTIntroduction to Scenario 110th Floor Collaborative Space
- Cory Johnson, California State University, San Bernardino
- Jessica Sorrells, Converse University
-
11:00 am - 12:00 pm EDTScenario 1 Group WorkGroup Work - 10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTTools from Linear Algebra Minicourse10th Floor Collaborative Space
- Amanda Harsy, Lewis University
- Jessica Sorrells, Converse University
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:00 pm EDTIntroduction to Scenario 210th Floor Collaborative Space
- Amanda Harsy, Lewis University
- Cory Johnson, California State University, San Bernardino
-
4:00 - 4:30 pm EDTExtra time/ wrap up- 10th Floor Collaborative Space
Wednesday, June 14, 2023
-
9:30 - 10:30 am EDTScenario 2 Group Work SessionGroup Work - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTAdditional Tools from Graph Theory Minicourse10th Floor Collaborative Space
- Leyda Almodóvar Velázquez, Stonehill College
- Cory Johnson, California State University, San Bernardino
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTIntroduction to Scenario 310th Floor Collaborative Space
- Leyda Almodóvar Velázquez, Stonehill College
- Jessica Sorrells, Converse University
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:00 pm EDTScenario 3 Group Work SessionGroup Work - 10th Floor Collaborative Space
-
4:00 - 4:30 pm EDTExtra time/ Wrap up- 10th Floor Collaborative Space
Thursday, June 15, 2023
-
9:30 - 10:30 am EDTOverview of DNA Self-Assembly Research Projects10th Floor Collaborative Space
- Leyda Almodóvar Velázquez, Stonehill College
- Amanda Harsy, Lewis University
- Cory Johnson, California State University, San Bernardino
- Jessica Sorrells, Converse University
-
11:00 am - 12:00 pm EDTQ&A about Scenarios 1, 2, and 3 / Discussion of Problem SetsProblem Session - 10th Floor Collaborative Space
- Leyda Almodóvar Velázquez, Stonehill College
- Amanda Harsy, Lewis University
- Cory Johnson, California State University, San Bernardino
- Jessica Sorrells, Converse University
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTProject Otions Q&A / Work Session10th Floor Collaborative Space
- Leyda Almodóvar Velázquez, Stonehill College
- Ryann Firestine, Auburn University
- Michaela Fitzgerald, Stonehill College
- Amanda Harsy, Lewis University
- Cory Johnson, California State University, San Bernardino
- Eric Redmon, Marquette University
- Jessica Sorrells, Converse University
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:50 - 4:00 pm EDTProject Preference Surveys Due by 4:00 PM- 10th Floor Collaborative Space
-
4:00 - 4:30 pm EDTExtra time/ Wrap up- 10th Floor Collaborative Space
Friday, June 16, 2023
-
9:30 - 10:30 am EDTProject Assignments, Announcement & Introduction to Math Research10th Floor Collaborative Space
- Leyda Almodóvar Velázquez, Stonehill College
- Amanda Harsy, Lewis University
- Cory Johnson, California State University, San Bernardino
- Jessica Sorrells, Converse University
-
10:30 - 11:00 am EDTBreakCoffee Break - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 3:00 pm EDTGroup Work10th Floor Collaborative Space
-
3:00 - 3:30 pm EDTCoffee Break10th Floor Collaborative Space
-
3:30 - 4:00 pm EDTGroup Work10th Floor Collaborative Space
Tuesday, June 20, 2023
-
9:30 - 10:30 am EDTIntroduction to Python & CoCalc10th Floor Collaborative Space
- Jessica Sorrells, Converse University
-
10:30 - 11:00 am EDTBreakCoffee Break - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTIntroduction to Python & CoCalc10th Floor Collaborative Space
- Jessica Sorrells, Converse University
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTIntroduction to LaTeX & Overleaf10th Floor Collaborative Space
- Amanda Harsy, Lewis University
- Cory Johnson, California State University, San Bernardino
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Wednesday, June 21, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
10:30 - 11:00 am EDTBreakCoffee Break - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Thursday, June 22, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
10:30 - 11:00 am EDTBreakCoffee Break - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
-
6:00 - 6:45 pm EDTTBA11th Floor Lecture Hall
- Jessisa Libertini, Brown University
Friday, June 23, 2023
-
9:30 - 10:30 am EDTGroup Presentations10th Floor Collaborative Space
-
10:30 - 11:00 am EDTBreakCoffee Break - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Presentations10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:00 pm EDTOscar TutorialTutorial - 10th Floor Collaborative Space
-
2:00 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Monday, June 26, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Check-in MeetingsMeeting - 10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup WorkVirtual
Tuesday, June 27, 2023
-
9:30 - 11:30 am EDTEthics I & II10th Floor Collaborative Space
-
11:30 am - 1:00 pm EDTLunch/Free Time
-
1:00 - 2:00 pm EDTResearch in Quantative Justice PanelPanel Discussion - 10th Floor Collaborative Space
-
2:00 - 2:30 pm EDTCoffee Break10th Floor Collaborative Space
-
2:30 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Wednesday, June 28, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Thursday, June 29, 2023
-
9:30 - 10:30 am EDTGroup Check-in MeetingsMeeting - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Friday, June 30, 2023
-
9:30 - 10:30 am EDTGroup Presentations10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Presentations10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Presentations10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Wednesday, July 5, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Thursday, July 6, 2023
-
9:30 - 10:30 am EDTGroup Check-in MeetingsMeeting - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work -Suggested: Prepare Weekly PresentationGroup Work - 10th Floor Collaborative Space
Friday, July 7, 2023
-
9:30 - 10:30 am EDTGroup Presentations10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Presentations10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:00 pm EDTBrief Presentation Feedback10th Floor Collaborative Space
-
2:00 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work - Suggested: Strategize for nex weekGroup Work - 10th Floor Collaborative Space
Monday, July 10, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Tuesday, July 11, 2023
-
9:30 - 10:30 am EDTGroup Check-in MeetingsMeeting - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Wednesday, July 12, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 3:30 pm EDTGroup Work10th Floor Collaborative Space
-
3:30 - 4:30 pm EDTThe geometric nature of polynomial equations10th Floor Collaborative Space
Thursday, July 13, 2023
-
9:30 - 10:30 am EDTGroup Check-in MeetingsMeeting - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTSuggested: Prepare Weekly PresentationGroup Work - 10th Floor Collaborative Space
-
6:30 - 8:00 pm EDTMovie NightMovie Night - 11th Floor Lecture Hall
Friday, July 14, 2023
-
9:30 - 10:30 am EDTGroup Presentations10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Presentations10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:00 pm EDTBrief Presentation Feedback10th Floor Collaborative Space
-
2:00 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTSuggested: Strategize for next weekGroup Work - 10th Floor Collaborative Space
Monday, July 17, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTYellow Pig DayCoffee Break - 10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Tuesday, July 18, 2023
-
9:30 - 10:30 am EDTGroup Check-In MeetingsMeeting - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 3:30 pm EDTGroup Work10th Floor Collaborative Space
-
3:30 - 4:30 pm EDTOutput of a pot with exactly one bond-edge type10th Floor Collaborative Space
- Andrew Lavengood-Ryan, Nevada State University
Wednesday, July 19, 2023
-
10:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
-
5:00 - 6:00 pm EDTGroup Work10th Floor Collaborative Space
-
6:00 - 7:00 pm EDTPanel Discussion10th Floor Collaborative Space
- Panelists
- Andrew Lavengood-Ryan, Nevada State University
- José Pabón, New Jersey Institute of Technology
- Rachel Roca, Michigan State University
Thursday, July 20, 2023
-
9:30 - 10:30 am EDTGroup Check-In MeetingsMeeting - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Friday, July 21, 2023
-
9:30 - 10:30 am EDTGroup Presentations10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Presentations10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:00 pm EDTBrief Presentation Feeback10th Floor Collaborative Space
-
2:00 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Monday, July 24, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 3:30 pm EDTGroup Work10th Floor Collaborative Space
-
3:30 - 4:30 pm EDTMetamodeling and uncertainty quantification of a simulation chain for urban air quality10th Floor Collaborative Space
- Janelle Hammond, Stonehill College
Tuesday, July 25, 2023
-
9:30 - 10:30 am EDTGroup Check-in MeetingsMeeting - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Wednesday, July 26, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
-
5:00 - 6:00 pm EDTPowerPoint Party- 10th Floor Collaborative Space
Thursday, July 27, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTPractice Run for Final PresentationsGroup Presentations - 10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTPractice Run for Final PresentationsGroup Presentations - 10th Floor Collaborative Space
Friday, July 28, 2023
-
9:30 - 10:30 am EDTSuggested: Make Revisions to Final PresentationGroup Work - 10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee Break10th Floor Collaborative Space
-
3:00 - 4:30 pm EDTSuggested: Strategize for next weekGroup Work - 10th Floor Collaborative Space
Monday, July 31, 2023
-
9:00 - 10:00 am EDTAlgorithmic Generation of DNA Self-Assembly Graph11th Floor Lecture Hall
- Grace Bielefeldt, St. Olaf College
- Iris Horng, University of Pennsylvania
- Holly Luebsen, University of Texas at Austin
- Mitchell VonEschen, Lawrence University
Abstract
With recent advancements in the field of nanotechnology, there has been increasing interest in self-assembling nanostructures. These are constructed through the process of branched junction DNA molecules bonding with each other without external guidance. Using a flexible tile-based model, we represent molecules as vertices of a graph and cohesive ends of DNA strands as complementary half-edges allowing the molecules to bond with each other. Due to the unpredictability of DNA self-assembly in a laboratory setting and the risk of undesirable products being incidentally constructed, predicting what structures can be produced from a given list of components, referred to as a “pot of tiles,” is useful but has been proven NP-hard. Our project introduces an algorithm to computationally generate and visualize at least one valid graph given a pot of tiles. By adjusting a number of construction parameters, we can produce graphs of various orders and proportions of tiles.
-
10:00 - 11:00 am EDTOptimal Constructions for DNA Self-Assembly of k-Regular Graphs11th Floor Lecture Hall
- Lisa Baek, Brown University
- Ethan Bove, Brown University
- Michael Cho, Stanford University
- Xingyi Zhang, Carleton College
Abstract
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented abstractly in the language of graph theory, where edges are understood to be strands of DNA joined at junctions, represented by vertices. Because guided construction of such structures is inefficient, design strategies for DNA self-assembly are desirable. Branched DNA molecules are referred to as tiles, each consisting of flexible unpaired cohesive ends with the ability to form bond-edges. We thus consider the minimum number of tiles and bond-edge types to construct a graph G (corresponding to a DNA target structure) without allowing the formation of smaller graphs, or non-isomorphic graphs of the same size. In this paper, we specifically investigate the case where G is k-regular. We introduce the concept of (un)swappable graphs, using the property to establish lower bounds on bond-edge and tile types in the unswappable case. We also introduce a method of generating upper bounds using a vertex-cover model. We apply both of these methods to prove new bounds on a number of regular families, including crown graphs, prism graphs, Kneser graphs, Johnson graphs, Antiprism Graphs and Archimedean solid graphs.
-
11:00 am - 12:00 pm EDTExploring Relationships Between Optimal Flexible Tile and Bond-Edge Types of Self-Assembling DNA11th Floor Lecture Hall
- Toby Anderson, Harvey Mudd College
- Olivia Greinke, Transylvania University
- Iskandar Nazhar, University of Massachusetts Amherst
- Luis Santori, University of Central Florida
Abstract
DNA self-assembly is an emerging area of study within the field of biology and nanotechnology with applications in targeted drug delivery, biomolecular computing, and biosensing. Branched molecules of DNA bond to each other with complementary strands of base pairs to form a target nanostructure. Using a flexible tile model, these structures can be modeled mathematically as graphs that are constructed from vertices with extending half-edges. These vertices are referred to as tiles, and their extending half-edges are labeled with bond-edge types that represent different extending sequences of DNA base pairs. Most mathematical research using the flexible tile model seeks to find optimal constructions for various graphs and graph families in an effort to maximize laboratory efficiency within three scenarios of increasing restriction. Our research focuses on searching for underlying relationships between the minimum number of bond-edge types and tile types needed to construct a graph across these scenarios. Building on previous work, we explore a variety of low-order graphs and present optimal constructions for all graphs of order five and below in all scenarios. In addition, we present results for various lattice graphs, particularly hexagonal lattices, and web graphs.
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTGroup Work10th Floor Collaborative Space
-
2:30 - 3:00 pm EDTCoffee BreakVirtual
-
3:00 - 4:00 pm EDTGroup Work10th Floor Collaborative Space
-
4:00 - 4:30 pm EDTReception with Spring 2021 Reunion GroupReception - 11th Floor Collaborative Space
Tuesday, August 1, 2023
-
9:15 - 9:30 am EDTGroup Photo (Immediately After Talk)11th Floor Collaborative Space
-
9:30 - 10:30 am EDTMulti-dimensional Graphs Modeling Self-Assembling DNA Nanostructures11th Floor Lecture Hall
- Katelyn Buck, The University of Texas at Austin
- Catherine Jacobs, Wellesley College
- Amelia Julian, Plymouth State University
Abstract
Employing tools from graph theory and linear algebra, we model the biological process of the creation of nanostructures from self-assembling DNA complexes. We represent $k$-armed branch junction molecules with tiles which are vertices in a graph with half-edges. The half-edges depict the cohesive-end types of a DNA strand. We aim to determine the minimum number of tiles and cohesive-end types necessary to form the complete complex of a given multi-dimensional graph structure. The problem of modeling DNA self-assembly is particularly challenging when considering graph families which change in multiple dimensions. In this research, we present the minimum number of tiles and cohesive-end types necessary to create the stacked book graphs, the square lattice graphs, and the Mongolian tent graphs, under different laboratory constraints.
-
10:30 - 11:30 am EDTAlgorithmic Pot Generation for DNA Self-Assembly11th Floor Lecture Hall
- Jacob Ashworth, Rose-Hulman Institute of Technology
- Luca Grossmann, Tufts University
- Fausto Navarro, Johns Hopkins University
Abstract
Recent advancements in microbiology have motivated the study of the production of nano-structures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to allow small DNA molecules to join together with complementary DNA branches. A practical question is: given a target nanostructure, what is the optimal set of DNA molecules that can assemble such a structure? We use a flexible-tile graph theoretic model to develop algorithmic approaches, which, given an undirected graph representing a target structure, finds the optimal collection of smaller structures which can construct that graph under certain constraints. Our exploration into these algorithmic approaches has also lead to several mathematical results.
-
11:30 am - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTWhat's Next?10th Floor Collaborative Space
- Leyda Almodóvar Velázquez, Stonehill College
- Amanda Harsy, Lewis University
- Cory Johnson, California State University, San Bernardino
- Jessica Sorrells, Converse University
-
2:30 - 3:00 pm EDTCoffee BreakVirtual
-
3:30 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Wednesday, August 2, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work10th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
1:30 - 2:30 pm EDTSelf-Assembly with DNA Origami10th Floor Collaborative Space
- Jo Ellis-Monaghan, Saint Michael's College
-
2:30 - 3:00 pm EDTCoffee BreakVirtual
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Thursday, August 3, 2023
-
9:30 - 10:30 am EDTGroup Work10th Floor Collaborative Space
-
11:00 am - 12:00 pm EDTGroup Work11th Floor Collaborative Space
-
12:00 - 1:30 pm EDTLunch/Free Time
-
2:30 - 3:00 pm EDTCoffee BreakVirtual
-
3:00 - 4:30 pm EDTGroup Work10th Floor Collaborative Space
Friday, August 4, 2023
-
9:30 - 10:30 am EDTSummer Research Symposium Set Up- Sayles Hall
-
10:30 am - 1:00 pm EDTSummer Research Symposium- Sayles Hall
-
1:00 - 1:30 pm EDTLunch/Free Time
All event times are listed in ICERM local time in Providence, RI (Eastern Standard Time / UTC-5).
All event times are listed in .
ICERM local time in Providence, RI is Eastern Standard Time (UTC-5). Would you like to switch back to ICERM time or choose a different custom timezone?