SasCalc Periodic Boundary Conditions Ian Hunt-Isaak, Joseph E. - - PowerPoint PPT Presentation

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SasCalc Periodic Boundary Conditions Ian Hunt-Isaak, Joseph E. - - PowerPoint PPT Presentation

Nov 28, 2023 10 likes •340 views

SasCalc Periodic Boundary Conditions Ian Hunt-Isaak, Joseph E. Curtis, Steven C. Howell Road Map 1. Question to answer 2. Issue with current approach 3. Alternative approaches 4. Results 5. Next Steps Why are concentrated proteins so

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SasCalc Periodic Boundary Conditions

Ian Hunt-Isaak, Joseph E. Curtis, Steven C. Howell

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Road Map

1. Question to answer 2. Issue with current approach 3. Alternative approaches 4. Results 5. Next Steps

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Why are concentrated proteins so viscous?

https://openclipart.org/image/2400px/svg_to_png/2058 86/remigho-syringe.png
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Small-Angle Scattering (SAS)

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Small-Angle Scattering (SAS)

Form Factor, P(Q) I(Q) ∝ P(Q) S(Q) Structure Factor, S(Q)

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SAS of dilute proteins used to determine shape

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Concentration Affects the Scattering

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Concentration Affects the Scattering

Form Factor Form Factor

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Co-solutes modulate protein interactions

Change in scattering is not dominated by P(q) or S(q) alone.

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Molecular Simulation

Adapted from http://nmschneider.com/blog/2014/5/9/nearest-image-for-particle-simulations-in-matlab
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Molecular Simulation

Adapted from http://nmschneider.com/blog/2014/5/9/nearest-image-for-particle-simulations-in-matlab
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Fourier Transform: g(r) → S(Q)

  • Most general
  • Slow
  • Limited to spherical systems
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Finite size effects

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Finite size effects

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Desired Features of Calculator

  • Simultaneously calculate both P(Q) and S(Q)
  • Avoid finite size effects
  • Fast
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Debye Formula

Not universally applicable: vs

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Explicit Fourier Transform

  • Most general

○ Contains P(Q) and S(Q)

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Removing finite size effects

  • Fancy Stat Mech - g(r)

○ Limited to spherical systems

  • Bigger Box

○ Num Atoms ~ (Box Length)3

  • Calculate Box scattering and remove
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First Test System - Lennard Jones Particles

Radial Distribution Function for Liquid Argon at 85 K - Yarnell, et al.

Verify Radial Distribution of Simulation

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Removing Box Effects

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Removing Box Effects

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Removing Box Effects

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Integrating g(r) vs Box Subtraction

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Next Steps

  • Apply this to a periodic box of proteins (lysozyme, mAb)
  • Automate algorithm to subtract box effects
  • Parallelize using GPUs
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Thank you!

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Backup Slides

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Existing Calculators

Experiment Simulation Watch out S(Q) ≠ I(Q).

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S(Q) via Fourier Transform

  • g(r) simple to

calculate

  • Can extend h(r)

via use of Ornstein-Zernike Equation

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SasCalc (Golden Vector)

  • Multiple Molecules?
  • Separation of S and P?

Two questions:

  • Can Extract S?
  • Periodic Boundary Conditions effects?
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Scattering of test system

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Current Limitations

10 mg/ml 100 mg/ml Of Medical interest? YES YES Can we calculate Scattering? YES NO (somewhat)

Simulation Boxes:

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Integrating g(r) vs Box Subtraction

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Integrating g(r) vs Box Subtraction