Small Angle Neutron Scattering SANS A DANSE Subproject

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Small Angle Neutron Scattering (SANS) A DANSE Subproject DANSE meeting Jan 22 -24 Oak Small Angle Neutron Scattering (SANS) A DANSE Subproject DANSE meeting Jan 22 -24 Oak Ridge TN

SANS measures time averaged structure of 1 – 300 nm or more • Mesoporous SANS measures time averaged structure of 1 – 300 nm or more • Mesoporous structures • Biological structures (membranes, vesicles, proteins in solution) • Polymers • Colloids and surfactants • Magnetic films and nanoparticles • Voids and Precipitates

Challenges and opportunities Different communities = very different sociologies and expectations Three main communities Challenges and opportunities Different communities = very different sociologies and expectations Three main communities 80 -90% materials science (including bio physics) 5 -10% “physics” (colloidal, scattering, etc) 5 -10% structural biology (proteins, protein complexes, membranes, viruses etc) The Challenge: Demands of the small biological community could easily outstrip, on their own, the resources in DANSE for SANS. The opportunity: Much of the foundations needed would also provide interesting new tools for the materials community

Challenges and opportunities • The NIST IGOR macro packages have a large installed material Challenges and opportunities • The NIST IGOR macro packages have a large installed material science user base, particularly in the US (for flux line work, ILL’s GRASP is the preferred package). • The ATSAS package (now in release 2. 1) is the package of choice for the Biology SANS community if they don’t write their own. NIST IGOR macros have had ~8 years of formal releases, complete with certification and documentation. Current release in August 2006 Vers 5. 0 SANS Reduction Vers 3. 0 Analysis Vers 2. 0 USANS Reduction * Nearly 350 unique IP downloads/year for Analysis (most popular – followed by nearly 300 for SANS reduction)

Challenges and opportunities Furthermore: • Argonne has a variety of IGOR macro pacakges for Challenges and opportunities Furthermore: • Argonne has a variety of IGOR macro pacakges for SANS, SAXS, and USAXS, most popular being Jan Ilavsky’s packages • ORNL is currently planning on IGOR as its initial framework • ANSTO is planning on using the NIST reduction and analysis packages directly. The problem: Dealing with this large installed base using a long term stable package based on a solid commercial “framework” presents a HUGE barrier for migration away from IGOR towards the DANSE platform. The opportunity: IGOR is a proprietary framework, carries a cost for each license, and has limitations for next generation SANS software. All of these can be addressed through DANSE

Challenges and opportunities What are the obstacles to optimal/novel use of beam time: • Challenges and opportunities What are the obstacles to optimal/novel use of beam time: • Need time to think weak source … or FAST tools. Eventually feed back directly to experiment • Use neutrons to do the thinking (poorly planned experiment): will it work? how long to count? what configurations to use? Etc? • What to do with the data? Lack of ability to extract information in timely fashion for publication Applications: 1. Model-Independent Analysis 2. Model Fitting Analysis 3. Experimental Planning Tools

1. Model-Independent Analysis Guinier and other linear fits P(r) Inversion Peak fitting (1 D 1. Model-Independent Analysis Guinier and other linear fits P(r) Inversion Peak fitting (1 D and 2 D) Anisotropy Zimm Analysis DBA, and other “correlation” analysis Kratky and Bending rod plots etc Ab-initio Parametric analysis (peak intensity, peak position, Rg, anisotropy etc. as function of temperature, shear, magnetic field, angle, time etc) -Required for eventual feedback to experiment.

2. Model Fitting Analysis • Analytical form factors – ever increasing list (as long 2. Model Fitting Analysis • Analytical form factors – ever increasing list (as long as the one can write the integral) Advantage = speed! (polydispersity and resolution smearing take longer). Analysis of 2 D patterns! • Calculating P(r) from structures then FFT to get I(q) • PDB file • painted with a canvas • Ab-initio • Analytical structure factors • Non analytical Interactions (g(r) or potential) ? ? Parametric analysis (Shape, size, etc. as function of temperature, shear, magnetic field, time etc)

3. Experimental Planning Tools: going beyond the “rule of thumb” (or “myth? ”) Questions: 3. Experimental Planning Tools: going beyond the “rule of thumb” (or “myth? ”) Questions: • What Q range to I need? • Will I have enough overlap (maximize intensity and Q range but minimize number of configurations)? • How long should I count? How long should I count the backgrounds? • Will I be able to see the features of interest (background from optics and sample, resolution effects, strength of signal etc. )? In other words: Can I see what I want and if so how do I set up the instrument to optimize the experiment to do so? • Analytical tools based on beam intensity and optics • Full MC simulation of instrument with sample

Current Status: development • Planning phase on 1 D models • core shell disc/cylinder Current Status: development • Planning phase on 1 D models • core shell disc/cylinder -- Divia Singh (+Barbell) • Application 2 concept design • First review and prototyping of concepts for 3 D shapes • Progress on components

Application Overview Example: Protein Apoferritin (Hollow Sphere) Application Overview Example: Protein Apoferritin (Hollow Sphere)

GUI design: initial draft Geometric objects for space filling models (sphere, cylinder…) Analytical models GUI design: initial draft Geometric objects for space filling models (sphere, cylinder…) Analytical models PDB files Molecular Viewer User: rotate&shift Calculate I(Q) Q vs I(Q) Input Qmax & # of I(Q) Jan, 2006

Class Diagram Jan, 2006 (modified during code development) Class Diagram Jan, 2006 (modified during code development)

Python Components Jan, 2006 Python Components Jan, 2006

First Demo Oct, 2006 First Demo Oct, 2006

Current Progress Current Progress

API example Import IQ Import geoshapes Import pointsmodel lm = pointsmodel. new_loresmodel(0. 1) s API example Import IQ Import geoshapes Import pointsmodel lm = pointsmodel. new_loresmodel(0. 1) s 1 = geoshapespy. new_sphere(10) geoshapespy. set_center(s 1, 2, 5, 3) pointsmodel. lores_add(lm, a, 1. 0) c 1 = geoshapespy. new_cylinder(10, 40) geoshapespy. set_center(c 1, 3, 3, 3) Geoshapespy. set_orientation(c 1, 45, 90, 45) Pointsmodel. lores_add(lm, c 1, 2. 0) vp = pointsmodel. new_point 3 dvec() pointsodel. get_lorespoints(lm, vp) pointsmodel. distribution(lm, vp) Iq = IQ. new_iq(100, 0. 001, 0. 4) pointsmodel. calculate. IQ(lm, iq)

Current Status: Challenges • Mid Feb: Second hire (shared for 6 months) will be Current Status: Challenges • Mid Feb: Second hire (shared for 6 months) will be a senior programmer, PM, and facility liaison • March: Facility software co-ordination complete • Nov 2006 -Jan 2007 discussion with ORNL • Jan 2007 discussion with ANSTO • Jan 30, 2007 tentative video conference NIST/ORNL Future may include ANSTO • Feb 2007 NIST to have all 3 IGOR packages in SVN with TRAC • April target for first meeting of facility and SANS DANSE developers DANSE to help guide future IGOR releases and facilities to help guide priorities of SANS DANSE

Deployment plan and Looking forward for the next year • Demo (pre-alpha) Release by Deployment plan and Looking forward for the next year • Demo (pre-alpha) Release by late spring 2007 • Alpha release of application 2 by end of year (issue of core services standards def. need to be worked out) • New components distributed through IGOR and available to community Pending agreement by facility and SANS DANSE developers • P(R) calculation from 1 D data • Analysis of full 2 D anisotropic patterns • New 1 D form factors

Risks and Mitigation RISKS: Acceptance of new platform by community Can both the bio Risks and Mitigation RISKS: Acceptance of new platform by community Can both the bio and materials community be satisfied MITIGATING RISKS REQUIRES: Managing expectations Getting facility buy-in to ease transition Providing new and useful tools in a timely fashion to significant numbers MITIGATING ACTIVITIES • Co-ordinate early with SANS facilities to allow and plan for an orderly migration • Leverage (and co-ordinate with) current efforts in SANS, particularly structural biology, software (NIST, ORNL, UMBC, others – Svergun? ? ) • Release components early for use in existing frameworks

Summary • Staffing is nearly complete • Outlook for dealing with challenges/opportunities looks very Summary • Staffing is nearly complete • Outlook for dealing with challenges/opportunities looks very good • Progress on core application concept and components • Look forward to releases of new functionality and tools




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