Watt's Up

College of Optical Sciences News for February 21, 2008

Today's Colloquium

Michael Cusanovich will present PAS Domain Containing Light-Activated Switches.  Stanley Pau is the host.  Abstract:  Photoactive yellow protein (PYP), a small (~15,000 mol. wt.) water soluble blue light sensor, is a member of a superfamily of PAS domain containing sensor proteins, and is the structural prototype for over 5,000 known PAS domain containing sensor proteins found throughout the evolutionary tree. PYP is a blue light sensor, however, the PAS superfamily is not restricted to light sensing, and depending on species functions can range from oxygen, electric field and redox sensing to small molecule sensing (for example, a wide range of small organic molecules and metabolites). The functional diversity of PAS domains is an outstanding example of the use of a common structural motif, which adapted through evolution to address the specific metabolic needs of a specific organism. PYP undergoes a photoisomerization (trans  p-hydroxy cinnamic acid to cis) in ~3 ps, that initiates a series of structural changes (photocycle) leading to the lit or signaling state, which then activates a response regulator leading to function. The lit state spontaneously reverts to the dark state to complete the photocyclye. The formation of the lit state is coupled with a major conformational change. Many of the PAS domain containing sensor proteins are complex consisting of two or more interacting domains.

A major focus of our work is on a blue-red light sensing protein, called Ppr, which contains PYP, bacteriophytochrome and histidine kinase domain, that phosphorylates a transcriptional regulator when activated, which turns on the expression of a polyketide synthase. Our goal is to characterize the transient structural changes leading to the lit state, and the mechanism by which the PYP, Bph and histidine kinase interact leading to the light activation of the kinase.

Photoactive Yellow Protein: A Prototypic PAS Domain Sensory Protein and Development of a Common Mechanism for the Two-Component Regulatory Family. M. A. Cusanovich and T. E. Meyer, Biochem. 42, 4759-70 (2003).

The Photoactivated PYP Domain of Rhodospirillum centenum  Ppr Accelerates Recovery of  the Bacteriophytochrome Domain After White Light Illumination.‘  John A. Kyndt, John C. Fitch, Terry E. Meyer, and Michael A. Cusanovich,  Biochem 46, 8256-62 (2007).

Tomorrow's OSC Community Speakers

Jose Sasian will present Optical Alignment at the South Pole.  Noon in Meinel 410.  Everyone is welcome.

Next Week's Colloquium

David Brady will present Snapshot Spectral Imaging, Focal Plane Interferometry and Compressive Imaging.  Hong Hua is the host.  Abstract:  This talk describes coded aperture snapshot spectral imaging (CASSI) systems. CASSI systems rely on static aperture masks and decompressive data cube inference algorithms. We consider extensions of CASSI to alternative physical codes using interferometers or filters and we discuss application of snapshot spectral imaging to coherence imaging for 3D imaging and imaging through turbulence.   Bio:  David Brady is Professor of Electrical and Computer Engineering at Duke University, where he leads the Duke Imaging and Spectroscopy Program (www.disp.duke.edu). Professor Brady graduated from Caltech in 1990 and was on the faculty at the University of Illinois at Urbana-Champaign from 1990-2001, when he moved to Duke to become the founding director of the Fitzpatrick Institute for Photonics. He specializes in computational optical imaging and spectroscopy, with a recent focus on snapshot spectral imaging systems using compressive sampling and nonlinear signal inference, multiaperture imaging systems and on spatial coherence sensing.

We Welcome a New Industrial Affiliate

SRI International, an independent, nonprofit research institute, has joined our Industrial Affiliate family at the Associate level.  Founded in 1946 as the Stanford Research Institute, SRI International conducts client-sponsored research and development for government agencies, commercial businesses, foundations, and other organizations.  SRI also brings its innovations to the marketplace by licensing its intellectual property and creating new ventures.  For more information about SRI International, please visit www.sri.com

On Campus

February 22

ACMS Seminar.  Wolfgang Stolz, Material Sciences Center and Faculty of Physics at Philipps-University, will present Novel Dilute Nitride III/V-Semiconductor Laser System for the Integration for Si-Microelectronics.  10:00 a.m.  Meinel 821.

February 22

Physics Colloquium.  At 2:30 p.m. Jeff Weiss will present Superconductivity-Induced Macroscopic Resonant Tunneling.  At 3:00 p.m. Frederick Lamb, University of Illinois, Urbana-Champaign, will present Would Proposed Defenses Against Nuclear-Armed Long-Range Missiles Work?.  PAS 220.

February 25

Biomedical Engineering Seminar.  Nolan L. Boyd, University of Georgia Regenerative Bioscience Center, will present Human Embryonic stem Cells as a Vasculogenesis Model and Potential Cell Source for Regenerative medicine/Tissue Engineering.  Jennifer Barton is the host.  2:00 p.m.  Keating 103.

February 25

Special Physics Colloquium.  Dieter Meschede, University of Bonn, will present Taming individual Neutral Atoms with Light.  3:00 p.m.  PAS 218.

February 28

Biomedical Engineering Seminar.  Michael L. Smith of the Swiss Federal Institute of Technology will present The Changing Face of the Extracellular Matrix Under Force: Role of Fibronectin in Mechanotransduction.  Jennifer Barton is the host.  1:00 p.m.  MRB 102.

Optics Employment Opportunities

Please visit our optics employment Web site at

http://www.optics.arizona.edu/employment/default.htm

Fellowships and PostDocs.  Universitat Paderborn.  Die Universität der Informationsgesellschaft.  The Graduate Program “Micro- and Nanostructures in Optoelectronics and Photonics” at the University of Paderborn, Germany, invites international applications for Ph.D. fellowships and postdoc positions.  Due to generous support from the German Research Foundation (DFG Research Training Group 1464), the university can offer in 2008 up to 11 Ph.D. fellowships and 2 postdoctoral positions.  Ph.D. candidates seeking an excellent research environment will find ideal conditions and maximum support.  The Ph.D. fellowships include a monthly scholarship about € 1.444 (depending on age and family status) and are offered for one year with the possibility of two extensions, each of a year. No tuition fees need to be paid.  The postdoctoral position (TV-L 13) is limited to two years.  All fellowships start on April 1^st, 2008.  Acceptance of a fellowship requires participation in the study and research program ^(*).  The University of Paderborn encourages applicants who have graduated with excellent marks from their home universities in one of the program’s research subjects ^(*) or in physics, chemistry or electrical engineering.  Candidates for the post-doctoral fellowship should have an excellent Ph.D. in one of these fields.  Candidates must have fluency in English or German.  The research areas include the production of micro-and nanostructures and devices by epitaxy, self organization and other processes, their characterization and spectroscopy, and the theoretical analysis and simulation of their properties.  To apply, please complete and submit our online application form and send the required materials ^(*) by mail to: Prof. Dr. H. Kitzerow, Speaker GRK 1464, University of Paderborn, Warburger Str. 100, 33098 Paderborn, Germany.  Applications must be received by march 10^th, 2008.  ^(*)  For details, see http://www.ceopp.de/grk/ 

Senior Vision Engineer.  Intuitive Surgical.  Department:  Vision Engineering.  Reports to:  Director, Vision Engineering.  Intuitive Surgical, Inc. develops computer-enhanced minimally invasive surgery systems that use proprietary electronics, advanced mechanics, and enhanced visualization to greatly improve surgical technique and take surgical precision far beyond what is possible today.  Primary Function of Position:  The da Vinci® Surgical system includes six manipulator arms with a total of 41 degrees of freedom, along with a stereo endoscope and 3D video display, with over 700 installations worldwide.  Surgeons use it to perform tens of thousands of minimally invasive surgeries per year.  da Vinci represents an outstanding platform for the development and application of new technologies to surgery. This position offers an opportunity for a candidate with exceptional design and project management skills to be responsible for Intuitive’s next generation of vision systems, including cameras and endoscopes.  A successful candidate will be equally comfortable leading architecture development, designing optical subsystems, managing third-party designers and OEM vendors, and managing transfer to production.  He or she must excel in a high-energy team, must have excellent communication skills and must be able to balance independent production of results with the need to collaborate during planning, system integration, and testing of larger projects. This engineer will work closely with other members of the Vision Group and several other product development groups, as well as Clinical Engineering, Regulatory, Quality, and Production teams.  Roles and Responsibilities:  This position has responsibility and authority for developing vision systems for the da Vinci platform, including: Working with clinical and engineering teams within Intuitive to set design requirements for vision system designs.  Validating third party endoscope, camera, and display designs and making design modifications to those designs using optical CAD software such as Zemax and mechanical CAD software such as Solidworks or Pro-E.  Project management of vision system projects from conception through manufacturing transfer, using proven project management skills.  Shepherding vision system projects through the design control process (design reviews, risk analysis, etc.), and support New Product Introduction personnel in initial builds (procurement, assembly, and troubleshooting).  An exceptional candidate will also have the ability to:  Become the acknowledged in-house expert for cameras and endoscopes, able to develop next-generation designs and assist with production difficulties involving cameras, endoscopes, and other vision system components.  Conduct detailed prototype design, test, and iteration - potentially including electronics hardware, firmware and/or software processing.  Champion novel new system-level and software features through the product development process.  Act as a consulting engineer for other groups with optical system design needs.  Seek out, evaluate, and select industrial partners possessing specific visual systems expertise.  Skill/Job Requirements: Competency Requirements: (Competency is based on: education, training, skills and experience.).  In order to adequately perform the responsibilities of this position the individual must have:  Ø A Bachelors’ Degree in mechanical engineering, physics, optics, electrical engineering, similar discipline or commensurate experience; Masters’ preferred.  Demonstrated exceptional proficiency at robust, professional optics and vision system designs.  Five to eight (5-8) years or more of industrial experience strongly preferred, though a truly exceptional candidate with less experience could be considered.  Comfortable making complex, multidisciplinary tradeoff recommendations in the face of technical uncertainty.  Demonstrated ability to inspire and lead other engineers by technical example.  A passion for creating robust and reliable products.  Proficiency in all phases of the development lifecycle including design, implementation, verification, validations, and transfer.  Demonstrated history of products reaching the marketplace.  Experience selecting and managing OEM partners.  Sufficient visual acuity to see surgical images.  Ability to occasionally roll medical equipment distances of approximately 100 feet from lab to lab.  Frequent connection and disconnection of video cables and other connectors is required.  Some travel required.  Resumes may be submitted to www.intuitivesurgical.com

Agency Listing.  Optical Engineer/Software Testing.  Southern California.  Description:  We have an opening for a full time position as an Optical Engineer/Software Testing. The work involves using a wide variety of optical system models, planning and conducting manual testing of new and existing features. My client develops, markets and supports state-of-the-art optical CAD/CAE programs for the layout, design and analysis of optical systems.  The applicant should have skills in the use of advanced optical design tools, have an interest in optical design and optical system modeling, have an interest in software development, be able to understand optical engineering issues associated with new and advancing technology applications, and solve problems accurately, quickly, and effectively. The applicant should be able to interface equally well with a staff of Software Development Engineers, Optical Design Engineers, as well as development managers in a team-oriented environment. The successful candidate will contribute to the quality of my client’s products.  Primary responsibilities of the position include, but are not limited to: Creation and/or use of optical models for the purpose of optical domain testing new and existing features against user requirements.  Manually testing of Client’s software products  and identifying problems in any feature, whether it is related to optical computation or not.  Developing test plans.  Detecting, submitting and updating defect reports in an on-line database.  The applicant must become familiar with the software development process and the software development life cycle. He/she will be supporting all software development at the firm.  The applicant should possess the following qualifications:  A Bachelors, Masters, or Ph.D. degree in a technical discipline (Optics, Optical Sciences, Engineering, Physics, Mathematics, Astronomy)  Aptitude and interest in applied development of optical systems.  Experience in advanced optical design tools with the ability to understand and use their products.  Ability to understand customer requirements and expectations of a commercial scientific software package.  Strong problem solving, troubleshooting and organizational skills.  Demonstrated strong verbal and written communication skills.  Willingness to learn established and accepted software testing techniques.  Experience using optical design tools and/or CAD software are pluses.  Interact with some of the most talented engineers in the optics field both inside the company and in the customer community. Impact the development of Client’s software. My client is a world class, high tech optical software and optical engineering services company with an international client base and three branch offices. My client is in southern CA and was founded in 1963 by the current Chairman. The company  is privately held and employee owned and is an equal opportunity employer with over 85 employees (including over 50 engineers). The firm provides excellent employee benefits including medical insurance, an Employee Stock Ownership Plan (ESOP), and a 401k plan.  Contact: Ron Powers @ 951-676-8715 or r.mpowers@verizon.net  in California for questions and resume submission.

Agency Listing.  Software Test Engineer.  Description:  My client  has an opening for a Software Test Engineer.  This is a full-time position.  The work involves manual testing, maintaining suites of automated test cases, and product release testing across multiple hardware platforms. We develop, market and support state-of-the-art optical CAD/CAE programs for the layout, design and analysis of lens systems.  This applicant must have experience with Windows and Unix environments and must be comfortable maintaining operating systems used for testing. The applicant should be able to interface equally well with a staff of Software Development Engineers, Computer Systems Engineers as well as development managers in a team-oriented environment.  The successful candidate will contribute to the quality of our products. Primary responsibilities of the position include, but are not limited to:  • Manually testing of corporate software products   • Writing test plans and matrices  • Assessing a GUI for the purpose of creating and documenting manual test scenarios  • Maintenance of the automated test case suites, including adding new tests, executing tests, and verifying test results  • Submitting and maintaining defect reports in an on-line database  The applicant must be familiar with the software development process, the software development life cycle and software testing methodologies. He/she will be supporting all software development of the corporation.  Requirements of the position:  • Bachelors degree in a technical discipline (Physics, Math, Engineering)  • 2 + years experience in software testing  • Strong knowledge of software testing concepts and methodologies  • Proven record in writing and executing software test plans  • Ability to plan and implement testing from the requirements stage to shipment
• Ability to work in a testing team environment to accomplish group goals  • Strong problem solving, troubleshooting and organizational skills  • Strong verbal and written communication skills  • Ability to interface with a team of software developers with diverse technical backgrounds  • Experience using Windows and Unix operating systems  • Knowledge of software programming concepts • A proven record of accomplishment with excellent references  • Ability to use additional tools and utilities, such as file comparison, Ghost, Install Analyzer, and source control (ClearCase) is a plus  • Experience using CAD software and/or SolidWorks is a plus  My client is a world class, high tech optical software and optical engineering services company with an international client base and three branch offices. The firm is headquartered in southern CA and was founded in 1963 by the current Chairman. We are an equal opportunity employer with over 85 employees (including over 50 engineers).  We provide excellent company benefits including medical insurance, an Employee Stock Ownership Plan (ESOP), and a 401(k) plan.  Contact: Ron Powers @ 951-676-8715 or r.mpowers@verizon.net  in California for questions and resume submission.

cathy.alexander@optics.arizona.edu