Welcome to the q-bio Summer School and Conference!

Core Lectures at the New Mexico campus

From Q-bio

Class Locations

All main lectures and student talks will be held in the main auditorium (Rm 1041) of Centennial Engineering Center (Building number 112. link here).

Parking: See map here. Parking permit is required for parking on campus including parking at [Casas del Rio Student Housing]. Please check in with our onsite administrator if you need a parking permit.

Unless stated otherwise in the schedule below, the five courses will hold their breakout sessions in the following locations:

  • Stochastic Gene Regulation -- 1006
  • Cell Signaling -- 1026
  • Biomolecular Simulation -- 1028
  • Cancer Dynamics -- 1032
  • Membrane Dynamics -- 1030

Week 1

Sunday, July 27

  • 13:00 - 17:30: Check-In
  • 17:30 - 18:30: Welcome Reception
  • 18:30 - 20:30: ImprovScience Workshop

Monday, July 28

  • 08:15 - 09:00: Welcoming remarks and orientation (Bridget Wilson, Steve Graves, Katharine Chartrand, Gnana, Bill Hlavacek and Brian Munsky), Room 1041
  • 09:00 - 10:15: Lecture 1, Brian Munsky, "Introduction to stochastic effects in gene regulation.", Room 1041, slides available here
  • 10:45 - 12:00: Lecture 2, Bill Hlavacek, Introduction to Rule-Based Modeling (Part 1), slides; and Jim Faeder, Methods for Simulating Rule-Based Models (Part 2) slides, Room 1041
  • 12:00 - 14:00: Lunch
  • 13:00 - 14.00: CD only, Introductions and Project presentation Room 1032
  • 14:00 - 17:00: Breakout Labs 1
  • 17:15 - 18:30: Student Talks 1-3, Room 1041
    • 1. Mohit Kumar Jolly - Cancer Cell Migration: Yes, No, Maybe
    • 2. Mohammad Soltani - Stochastic Hybrid Systems & Moment Closure
    • 3. First Last - title
  • 18:30 - 20:00: Dinner

Tuesday, July 29

  • 08:30 - 10:00: Lecture 3, Marek Kimmel, "Modeling Evolution of the Myelodysplastic Syndrome," Room 1041
  • 10:30 - 12:00: Lecture 4, Bridget Wilson, "Introduction to Membrane Biology" Room 1041, | slides here
  • 12:00 - 14:00: Lunch
  • 13:00 - 14.00: CD only, Introductions and Project presentation Room 1032
  • 14:00 - 17:00: Breakout Labs 2
    • CD/SGR -- Crash Course in Stochastic Processes 2 (Nicolas Flores), Room 1032, See Nicolas' website here for more background information.
    • CS/MB -- Introduction to group projects; Introduction to MCell with Jim Faeder, Room 1026
    • BMS -- Introduction to Gromacs: From PDB to GMX - Christoph Junghans, Room 1028
  • 17:15 - 18:30: Student Talks 4-6, Room 1041
    • 4. Deborah Shutt - HIV Dynamics
    • 5. Johannes Keegrstra - Influence of network topology on cell-to-cell variability in bacterial chemotaxis
    • 6. Thanh Vo - Rejection based stochastic simulation
  • 18:30 - 20:00: Dinner
  • 17:00 - 19:00: MB -- laboratory session, 5-7 PM (single particle tracking or localization microscopy) [students participating in this session will miss student talks and dinner]
  • 19:00 - 21:00: SGR/BMS/CS/CD -- Stochastic Simulation Algorithms and other Kinetic Monete Carlo approaches, Room 1032, slides available here, Code1-Direct SSA, Code2-Get SSA Distributions.

Wednesday, July 30

  • 08:30 - 10:00: Lecture 5, Alexandra Jilkine, "Stochastic models of stem cell renewal and dedifferentiation in cancer," Room 1041
  • 10:30 - 12:00: Lecture 6, Greg Voth, The Multiscale Challenge for Biomolecular Systems: A Systematic Approach Room 1041
  • 12:00 - 14:00: Lunch
  • 13:00 - 14:00: Follow up on coding the SSA, Room 1030.
  • 14:00 - 17:00: Breakout Labs 3
  • 17:15 - 18:30: Student Talks 7-9, Room 1041
    • 7. Emine Guven - VEGF Clustering
    • 8. Martin Lopez-Garcia - The Matrix-analytic approach in Biology
    • 9. Eshan Mitra - Investigating IgE receptor signaling with super-resolution microscopy
  • 18:30 - 20:00: Dinner
  • 19:30 - 20:30: All -- Nicolas Flores, Continuous time Markov processes, Room 1030
  • 20:00 - 21:00: BMS -- Project Work - Cesar Lopez, Room 1028

Thursday, July 31

  • 08:30 - 10:00: Lecture 7, (Part 1) Jim Faeder Methods for Simulating Rule-Based Models and New Directions (slides), and (Part2) William S. Hlavacek, Combining MS-based proteomics and computational modeling to characterize immunoreceptor signaling, Room 1041
  • 10:30 - 12:00: Lecture 8, Diane Lidke, Room 1041
  • 12:00 - 14:00: Lunch
  • 14:00 - 15:30: Lecture 9, Jessica Swanson, Multiscale Reactive Molecular Dynamics for quantifying pH and deprotonation effects,University of Chicago, Room 1041
  • 15:30 - 17:00: Breakout Labs 4
    • MB/SGR -- Simulating anomalous diffusion, Adam Halasz; project work, Room 1030
    • BMS -- Generalized-ensemble MC and MD at work: self-assembly of coarse-grained lipids into membranes, Thomas Vogel, Room 1028
    • CS -- Computer Lab, the RuleBender/BioNetGen/NFsim software stack, Room 1026
    • CD -- Dominik Wodarz (15:30-17:00) Feedbacks, delays, and bifurcation structures of cancer related regulatory systems and their biological interpretations Room 1032
  • 17:15 - 18:30: Student Talks 10-12, Room 1041
    • 10. Nicola Gritti - Rolling dice during development
    • 11. Prashant Dogra - A PBPK mode to predict biodistribution of NPs
    • 12. Josh Scrull - From missiles to Cancer
  • 18:30 - 20:00: Dinner
  • 17:00 - 19:00: MB -- laboratory session, 5-7 PM (single particle tracking or localization microscopy) [students participating in this session will miss student talks and dinner]
  • 19:30: CD -- Review of progress in project assignments (brief), Room 1032
  • 20:00 - 21:00: BMS -- Project Work - Cesar Lopez, Room 1028

Friday, August 1

  • 08:30 - 10:00: Lecture 10, Mike Crowley, Sampling and forcefield limitations in large-scale MD simulations Room 1041
  • 10:30 - 12:00: Lecture 11, Natalia Komarova, "Cooperation, space, and evolution in cancer", Room 1041
  • 12:00 - 14:00: Lunch
  • 14:00 - 17:00: Breakout Labs 5
    • SGR -- Time for project work.
    • CS -- Time for project work.
    • BMS/MB -- Molecular Simulations of Biomolecular systems using MARTINI - Cesar Lopez (14:00-16:00) / Project Work (16:00-17:00) Room 1041
    • CD -- Natalia Komarova, course unit 3 (14:00-15.30), Alexandra Jilkine, course unit 2 (15:45 - 17.15) Room 1032
  • 17:15 - 18:30: Student Talks 13-15, Room 1041
    • 13. first last - title
    • 14. Cesar Alvadado - Uncertainty Quantification for cell proliferation
    • 15. first last - title
  • 18:30 - 20:00: Dinner

Week 2

Monday, August 4

  • 08:30 - 10:00: Lecture 12, Gerry Ostheimer, Room 1041
  • 10:30 - 12:00: Lecture 13, Douglas Shepherd Introduction to mechanisms of membrane curvature and a lesson in staying (false) positive, Room 1041
  • 12:00 - 14:00: Lunch
    • 12:30 - 14:00 CD -- Natalia Komarova, course unit 4 Room 1032
  • 14:00 - 17:00: Breakout Labs 6
    • CS/SGR -- Partial least squares regression lab with Gerry Ostheimer, Room 1026
    • MB/SGR -- Special spectroscopy techniques (FCS, FRET/FRAP) -- James Werner; project work, Room 1041
    • BMS -- Review/Evaluate progress of student projects,Cesar Lopez, Giovanni Bellesia, Justin Lemkul Room 1028
    • CD -- Marek Kimmel, course unit 1, Project progress review Room 1032
  • 17:15 - 18:30: Student Talks 16-18, Room 1041
    • 16. Soheil Fatehi - Mapping the constitutive law of bio-filaments from thier atomistic structure
    • 17. Natasha Wilson - Developing tools toward B-amyloid neuron interaction discovery
    • 18. Dongya Jia - Modeling the effect of OVOL in EMT
  • 18:30 - 20:00: Dinner

Tuesday, August 5

  • 08:30 - 10:00: Lecture 14, Seth Corey, Room 1041
  • 10:30 - 12:00: Lecture 15, Monte Carlo Methods, Giovanni Bellesia, UCSB, Room 1041
  • 12:00 - 14:00: Lunch
  • 13:00 - 14:00: BMS -- Project Work - Justin Lemkul, Giovanni Bellesia, Room 1028
  • 14:00 - 17:00: Breakout Labs 7
    • MB 14:00 - 15:30 -- Hands-on single-molecule localization and data analysis workshop -- Doug Shepherd Room 1026
    • MB 15:30 - 17:00 -- project work or Stochastic Simulation Software lecture
    • SGR/BMS/CS 14:00 - 15:30 -- Hands-on Monte Carlo Tutorial - Giovanni Bellesia, Room 1041
    • SGR/BMS/CS 15:30 - 17:00 -- Hands on Stochastic Simulation Software -Giovanni Bellesia, Room 1041
    • CD -- Rosemary Braun, course unit 1, Project progress review Room 1032 Media:Rosemary Brown.pdf
  • 17:15 - 18:30: Student Talks 19-21, Room 1041
    • 19. Pedro Baldera Aguayo - Quantum Mechanics calculations of Mycobacterium tuberculosis Pyrazinamidase
    • 20. Tye Martin - A Computational Study of Amyloid Proteins and their Interactions with Oligomeric Conjugated Polyelectrolytes
    • 21. Hoong Chuin Lim - bacterial chromosome segregation
  • 18:30 - 20:00: Dinner
  • 19:00-21:00 CS -- PySB tutorial, Leonard Harris, Room 1026

Wednesday, August 6

  • 08:30 - 10:00: Lecture 16, Eric Klavins, Computation with Multicellular Systems, Room 1041
  • 10:30 - 12:00: Lecture 17, John Pearson, Aggregated Markov chains for single-molecule kinetics, Room 1041
  • 12:00 - 14:00: Lunch
  • 13:00 - 14:00: BMS -- Project Work - Justin Lemkul, Giovanni Bellesia, Room 1028
  • 14:00 - 17:00: Breakout Labs 8
    • MB -- Data analysis for single-particle tracking -- Samantha Schwartz; project work, Room 1026
    • SGR/CS -- Eric Klavins, Programming Multicellular Systems with gro, Room 1041
    • BMS 14:00 - 15:30 -- Biomolecular Force Fields: Fundamentals and Improvements for the Next Generation - Justin Lemkul Room 1028
    • BMS 15:30 - 17:00 -- Hands on tutorials of Free energy calculations - Justin Lemkul Room 1028
    • CD -- Marek Kimmel, course unit 2, Project progress review Room 1032
  • 17:00 - 18:00: q-bio Organizers Meeting, Room 1006
  • 17:15 - 18:30: Student Talks 22-24, Room 1041
    • 22. Samantha Erwin - Mathematical Model of Germinal Center Formation
    • 23. Kasra Manavi - Simulation and Analysis of Antibody Aggregation
    • 24. Florian Uhlitz - Transcript Dynamics in Response to MAP Kinase Signaling
  • 18:30 - 20:00: Dinner

Thursday, August 7

Friday, August 8

  • 08:30 - 10:00: Lecture 20, Tomasz Lipniacki Feedbacks, delays, and bifurcation structures of cancer related regulatory systems and their biological interpretations, Room 1041
  • 10:30 - 12:00: Lecture 21, Angel Garcia Molecular Simulations of the Folding Unfolding Equilibrium of Biomolecules, Room 1041
  • 12:00 - 14:00: Lunch
  • 14:00 - 17:00: Breakout Labs 10
    • MB -- Geometric and physics-based simulation of macromolecular complex assembly with Lydia Tapia; project work, Room 1030
    • CS -- Discussion with Dr. Lipniacki, Room 1026
    • BMS/SGR 13:00 - 14:00 -- The power of simple models: polymer physics for biologists - Anton Zilman, Room 1028
    • BMS/SGR 14:00 - 15:00 -- Counter-intuitive probablility - Anton Zilman, Room 1028
    • BMS 15:00 - 17:00 -- Wrap-up of student projects - Gnana Gnanakaran, Justin Lemkul, Cesar Lopez,Giovanni Bellesia, Anurag Sethi Room 1028
    • SGR 16:00 - 17:00 -- Wrap-up of student projects, Room 1006
    • CD -- Marek Kimmel, course unit 3, Project progress review Room 1032
  • 17:15 - 18:30: Student Talks 29-31, Room 1041
    • 29. Bruna Jacobson - Unraveling the mechanochemistry of molecular motors via simulated annealing
    • 30. First Last - title
    • 31. First Last - title
  • 18:30 - 20:00: Dinner

Week 3

The 3rd Annual q-bio Student Symposium, Room 1041

Monday, August 11

  • 09:00 - 09:15: Group Project 1, SGR
  • 09:15 - 09:30: Group Project 2, SGR
  • 09:30 - 09:45: Group Project 3, CS
  • 10:00 - 10:15: Group Project 4, CS
  • 10:15 - 10:30: Group Project 5, BMS
  • 10:30 - 10:45: Group Project 6, BMS
  • 11:00 - 11:15: Group Project 7, CD
  • 11:15 - 11:30: Group Project 8, CD
  • 11:30 - 11:45: Group Project 9, Computational Synthetic Biology, 1
  • 12:00 - 14:00: Lunch
  • 14:00 - 14:15: Group Project 10, MD
  • 14:15 - 14:30: Group Project 11, MD
  • 14:30 - 14:45: Group Project 12, Computational Synthetic Biology, 2
  • 15:00 - 15:30: Group Project 13, Experimental Synthetic Biology, 1
  • 16:00 - 18:30: Poster Presentations
  • 18:30 - 20:00: Dinner

Tuesday, August 12

  • 09:00 - 09:40, Invited Talk 1, Steve Andrews, Fred Hutchinson Cancer Research Center
  • 09:40 - 10:20, Invited Talk 2, Cynthia Reichhardt, Los Alamos National Laboratory
  • 10:20 - 10:30, Break
  • 10:30 - 11:10, Invited Talk 3, Ilya Nemenman, Emory University
  • 11:10 - 11:50, Invited Talk 4, Roy Wollman, University of California, San Diego
  • 12:00 - 13:30, Lunch
  • 13:30 - 14:10, Invited Talk 5, Ruy Ribeiro, Los Alamos National Laboratory
  • 14:10 - 14:50, Invited Talk 6, Gerry Ostheimer, UN Sustainable Energy For All
  • 14:50 - 15:00, Break
  • 15:00 - 15:40, Invited Talk 7, Karissa Sanbonmatsu, Los Alamos National Laboratory
  • 15:40 - 16:20, Invited Talk 8, Rosemary Braun, Northwestern University
  • 16:20 - 18:30: Poster Presentations
  • 18:30 - 20:00: Dinner
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