UNC-CH Comp/Phys/Mtsc 715 Custom Applications for nanoScale Science - PDF document

4/19/2012 UNC-CH Comp/Phys/Mtsc 715 Custom Applications for nanoScale Science 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 1 Administrative • Final Project Turn-in – Due 7PM, Thursday May 3 rd – Written report • Described in link from schedule page • Example sent out earlier – Videos and Paraview State Files – Upload to FTP server • Or DropBox and tell me where to find • Demo to me and scientist – At or before the final turn-in 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 2 Overview • Three Custom microscope control & molecular manipulation applications • Advanced Model Fitting and Analysis • Coupling visualization and control (beyond toolkits) • Scientist & computer scientist collaboration Chem CS Phys Phys Phys CS CS CS CS Industry Phys MatSci CS CS->Phys CS BioEng BioEng MatSci • A Crazy Idea 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 3 1

4/19/2012 Docker • Ming Ouh-Young’s dissertation project – Showed NTE factor-of-2 speedup with haptics – 6-DOF positioning task – “Lock and Key” problem – Hard surface + electrostatic 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 4 Rendering SPM Data has always been a problem 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor What this rendering seems like to me 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 6 2

4/19/2012 What they’ve done with it • Simply Incredible! • Imagine what they could do with ink! 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 7 nanoManipulator A virtual environment interface to SPM The Goal: • Remove boundaries between user and sample • Can we make experiments on the molecular scale as easy as rolling a pencil or pushing a golf ball? 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 8 Conception • R. Stanley Williams – Then professor of Chemistry at UCLA – Now head of nanocomputing research at HP • Warren Robinett – Then director of HMD research at UNC – Now doing nanocomputing research at HP • My dissertation topic in Computer Science – Under direction of Frederick P. Brooks, Jr. 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 9 3

4/19/2012 Interoperability 3D graphics Analysis PC Optical microscope Force GUI Commercial interface Test & measurement 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 10 nanoManipulator Collaborators Information & Library Science Education CS Dist. Sys. WPAFB Gene Therapy Psychology Belgium Physics CS Graphics Chemistry Toronto ASU Biology CS Image 3rdTech NIEHS NIST RTP 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 11 Now a Commercial System! • nanoManipulator DP-100 • 2001 R&D 100 Award Winner • www.nanomanipulator.com 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 12 4

4/19/2012 Adenovirus: Imaging icosahedral shape with advanced rendering AFM Images Adenovirus 85 nm Icosahedral Color by slope: Flat=dark Steep=bright ps sphere virus Specular highlights through Directional illumination TEM 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor Measurements on Individual Fibers B fiber Tip 800 nm Tip hits Partial surface Deformation Rupture Translocation fiber Detachment F r 3 6000 Lateral force F s 2.5 5000 Lateral force (nN) 2 4000 F t 1.5 3000 1 2000 Tip position 0.5 1000 0 0 0 1000 2000 3000 4000 5000 6000 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor s(nm) Stacking Carbon Nanotubes A B 1 2 2 3 1 3 b C D a 1 2 1 3 2 3 b a 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 5

4/19/2012 Bending and Buckling 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor Question: Which Interface is Best ? 5 1 3 2 4 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 17 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 18 6

4/19/2012 NIMS: SEM + AFM Combine the best of: SEM: • Imaging • elemental analysis • ebeam lithography Topometrix Hitachi S4700 AFM: Observer • topography • local (mech., elect,..) properties • manipulation nM: • Manipulation (XYZ control) • Multiple Data Set Rendering • Registration 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor SEM/AFM in action • Hand-controlled AFM • Zooms in on nanotube • “Twangs” nanotube • Play movie 4/24/2012 nanoScience Comp/Phys/Mtsc 715 Taylor Applications SEM/AFM in action 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 21 7

4/19/2012 SEM/AFM in action • Two paddles – Suspended on tube • Tip comes down • Paddle sticks • Tries to pry off • Game over 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 22 Measuring Torsion Force curves all at single point (+/-50nm)on single paddle Force gets 20x larger after repeats! 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor SEM/AFM Challenges: •Real-Time overlay/registration •E Beam Lith Integration •Optimized Integration of Data Sets •3D manipulation-where is the tip? 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 8

4/19/2012 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 25 3DFM: The Next Step in Biological Force Microscopy • How to do force microscopy inside a cell? * Puncture the cell membrane to image inside the cell? 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor One Solution: Put the Probe Inside the Cell • Problems: – How to measure the probe’s position? – How to apply forces? 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 27 9

4/19/2012 Our Solution 3-D Force Microscope Magnetic Solenoid Particle pole tips Cell optical tracking substrate • Magnetic fields apply forces to magnetic particle • Particle position is monitored using optical tracking 1. Very specific forces 2. Little localized optical heating 3. Relatively high forces 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 3DFM: Concept Video • Link to video 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 29 VTK UI Prototype 2D Video More controls Slivered surf Wireframe bd 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 30 10

4/19/2012 CCD camera Optical Layout: Laser tracking filter tube lens, f=100mm Pigtail fiber connector 50/50 beam splitter optical Collimating fiber Lens Upper 100x Diode Laser objective lens sample chamber Lower 100x objective lens polarizing beam fiber light splitter cube BFP Imaging lens, f=50mm quadrant q1 q2 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor photo mirror q3 q4 diode Optical Tracking • Incident beam (maximum in center) • Bead Scattering • Resulting pattern (maximum in center) • Terrible Visualization – Rainbow scale – No shading on surfaces – Down/blue is more 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 32 Z Tracking, QPD Image Theoretical Image Measured Image 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 33 11

4/19/2012 3D Tracking: Bead Capture • Bead 2.8 microns in diameter attached to cilium – Two beats uncaptured – Several captured – Note background (XY) – Note focus (Z) – Video link 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 34 3dFM: Magnetic Drive 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 35 3DFM: From CS Point of View RTS3 RTS2 RTS1 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 36 12

4/19/2012 Initial Experiment Target: CF • CF gene controls Cl - and Na + transport through cells • Affects airway secretions (mucin) • Mucociliary clearance is the first line of defense against inhaled particulates, aerosols, etc. • Particulate-laden mucus transported by cilia – beating in a mucus-free periciliary liquid (PCL) – to the glottis where it is expelled and swallowed 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 37 Tracked cilium beating at 15 Hz 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 38 Next Target: Optical Microscopy • Enable Natural Exploration in X,Y, and Z • Use all of the Data (video, motion) • Construct 3D (+ time) scene • Enable Flexible Review/Summary 4/24/2012 nanoScience Comp/Phys/Mtsc 715 Taylor Applications 13

4/19/2012 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 40 Tools to help Scientists Build Better Models System Sensors and Visualize Under Study Actuators Transform • Extract Model Combine • Display Model Merged Model Simulator Macromolecule Idea of system Under study with Experiment AFM • Simulate scan of Real Optical Structure, model with Macromolecule or Cell 3DFM microscope Natural Control And Manipulation • Enable direct visual comparisons 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 41 Carbon Nanotubes What the scientist infers The Data Computed Centerline 4/24/2012 nanoScience Applications Comp/Phys/Mtsc 715 Taylor 14