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1. Using a Lattice Model to Study the Nuclear Pore Complex
Samantha Norris Mentors: Meredith Betterton, Loren Hough, Mike
Stefferson August 6, 2015
2. What is the Nuclear Pore Complex (NPC)? "NuclearPore crop"
by The original uploader was R. S. Shaw at English Wikipedia -
Transferred from en.wikipediato Commons.. Licensed under CC BY-SA
2.5 via Wikimedia Commons -
https://commons.wikimedia.org/wiki/File:NuclearPore_crop.png#/media/File:NuclearPore_crop.png
protein Transport factor Strands of nucleoporins with FG sequence
repeats (FG nups) Nucleus Cytoplasm
3. What I Did To better understand the diffusion of proteins
through the NPC To find the parameters which most significantly
affect diffusion Purpose Built Monte-Carlo lattice model from
scratch Included particle and polymer lattice moves Tested various
sets of parameters
4. Experimental Progress Modelling the NPC with a hydrogel
mimic Hydrogel consists of FG-nups in strands Figure: Loren
Hough
5. A Lattice Model Monte Carlo method each particle (whether TF
or FG) takes random walk around the grid When a TF and FG collide,
probability of binding When separating, probability of
unbinding
6. A Lattice Model Probability: Probability:
7. A Lattice Model inlet outlet
8. Strand Statistics Movement rules adapted from Haire et. al.
Anchored at one point If movement breaks strand in 1 place, rest of
strand compensates If movement breaks strand in 2 places, move
rejected
9. Strand Statistics Deviation from center # 1 strand, length
200, T = 100,000
10. Strand Statistics Leftmost figure reprinted from "A Monte
Carlo Lattice model for Chain Diffusion in Dense Polymer Systems
and its Interlocking with Molecular Dynamics Simulation," by K.R.
Haire et. al., 2001, Computational and Theoretical Polymer
Science
12. Calculating Mean Square Displacement Old Method: Find
distance from starting position for each particle at each time
steps, average over particles New Method: Same as above, but
average over different time origins, doesnt choose starting
position preferentially
13. Parameters kon, koff (binding and unbinding probability)
Concentration of FG-nups and TFs Gel width TF size
16. FG conc. =10% = 0.5 TF # = 1 Length = 100 Gel width = 100
Conclusion: Significant only when
17. FG radius Conclusion: No effect, requires more study FG
conc. = 5% of gel =0.5 = /10 TF # = 1 Length = 100
18. Future Plans Reproduce figures from other papers on
diffusion on lattice grid Study the long-time behavior of diffusion
Possibly add more complex situations (TFs moving and pushing FGs,
etc.)
19. Thank you! REU organizers Meredith Betterton, Loren Hough
(mentors) Mike Stefferson (graduate student) Jeff Moore, Adam
Lamson, Andrea Egan