BioCAT Newsletter, December 20, 2001

In this issue:
  1. New faces at BioCAT
  2. SAXS facility operational
  3. First MIR structure of a native fiber published in Structure
  4. Bent laue analyzer for high energy edges
  5. Stopped-flow for time-resolved XAFS
  6. New on-line experimental safety review system
  7. Booth at Biophysical Society meeting
  8. Send us your proposals!

I'd like everyone to welcome two new beamline scientists, Dr. David Gore and Dr. Raul Barrea to the facility.

Dr. Gore has a B.S. from the University of Illinois at Urbana/Champaign and a Ph.D. in physics from the University of Alabama at Birmingham. His post-doctoral activities included a 1 year stint in Zygo optics. He has a strong instrumentation and optics background and will be primarily responsible for core beamline developments. He will also be doing user support, so you should see his smiling face next time you come. He joined the group on November 5.

Dr. Barrea has bachelor and doctoral degrees in physics from the University of Cordoba in Argentina. He has spent several years as an instructor and adjunct professor in physics at Cordoba and has spent the last two years as a post-doc at the LNLS in Brazil, where he has been largely instrumental in setting up their dilute fluorescence XAFS facility. He will be primarily responsible for developing our XAS user program. He will be starting in January of 2002.

Kondrashkina, Irving, Menhart group (IIT)

Over the last 6 months we have been putting a lot of effort into developing our macromolecular solution scattering facility to the point where it can be a routine instrument for Rg and Pr measurements. These efforts have been aided by significant improvements in the stability in the beam delivered by the APS and our optics as well as the excellent signal to noise characteristics of our new CCD detector. The normal setups will include a 3 m camera to access a range of q from ~0.004 to 0.13 and a 0.3 m camera for range of q from ~0.08 to 1.25. This range of q will allow reconstruction of molecular envelopes using the spherical harmonic and dummy atom modeling approaches developed by the Svergun group. The standard sample chamber is a flow cell designed by Dr. Xing-Wang Fan in Prof. T. Sosnick's lab (U. Chicago). This cell takes about 100 microliters of sample and flows it back and forth in the beam to reduce radiation damage using a Hamilton programmable dual syringe pump. This cell design also allows mixing experiments to follow relatively slow processes (seconds-minutes). Satisfactory scattering curves can be obtained in about 1 s from 5 mg/ml cytochrome C. This fall, we hosted our first outside user group (Dr. Steve Almo's group, Albert Einstein). The next run is planned for February.

Joseph P.R.O. Orgel, Andrew Miller, Thomas C. Irving, Robert F. Fischetti, Andrew P. Hammersley, and Tim J. Wess "The In Situ Supermolecular Structure of Type I Collagen", Structure 9:1061-1069, November, 2001.

This paper is a first look at the three dimensional packing structure of the fibrils in native type I collagen from rat tail tendon. It has historically been a very difficult diffraction problem. This study exploited the fine focus and excellent collimation of the BioCAT beamline to resolve the closely spaced diffraction orders on the high background characteristic of this system.

Bunker, Karanfil, Zhang

One of BioCAT's core research projects is development of a high energy bent laue analyzer for XAFS spectroscopy of those biologically relevant elements that are beyond the range of the multilayer analyzer. This novel device relies on thin silicon crystals bent to a logarithmic spiral shape to diffract the desired fluorescence radiation. The diffracted beam appears to emerge from a virtual source that is displaced from the real source of the scattered background (and fluorescence from other elements if present). Soller slits imaging the virtual source then transmit the desired fluorescence and block the scattered radiation.

Specifically we are targeting two of the most biologically relevant elements: Molybdenum (K-edge 20 KeV) and Cadmium (K-edge 26.7 KeV). Our second monochromator with Si(400) crystals can reach up to 35 KeV. We have successfully used the Cadmium analyzer on the MR-CAT beamline in late November 2001 and intend to test both analyzers on BioCAT in December. The analyzers should be available for general use by next run in early 2002. If users have a need to measure other high energy edges, please send e-mail to

Zhang, Liu

Another core project is the development of a stopped-flow apparatus for time resolved XAFS. This device has been recently upgraded in several important aspects with a user-friendly software interface now taking shape. With these enhancements, repetitive continuous flow experiments can now be done with very different flow rates and sample volumes. The slowest rate tested so far is 0.05 microL/s with the fastest rate being 1000 microL/s. Rapid mixing can now be done routinely using a vortex mixer and a small observation cell. The shortest mixing time achievable is 10 ms with two syringes delivering 40 microL solution through the mixer into the cell. An on-line optical monitoring system can be optionally installed to track changes in the absorption spectrum over the visible range. Drs. Auld (Harvard), Penner-Hahn (Michigan), and Sagi (Weizmann) have used the rapid mixing feature along with the rapid energy-scanning capabilities of the beamline to study short-lived reaction intermediates. Dr. Penner-Hahn's group has also studied the rate of reduction of Mn compounds under various conditions in the beam using the continuous flow feature.

Continuous flow appears to be an effective strategy for reducing radiation damage while avoiding the artifacts associated with freezing due to ice crystals and presence of cryoprotectants. We anticipate that continuous flow and fast scanning will find wide use for a large range of XAS experiments.


We have implemented a new web-based interface for our safety review system (developed by Dr. C. Segre, MR-CAT). It has already greatly streamlined our operations being very straightforward to use. By collecting your data into a database, experiments can be easily modified by the users for a given run, since only the changes need to be modified for each experiment. As part of the process, investigators will be asked to provide actual procedures they plan to use to protect themselves and others. Principal investigators of active and new proposals need to contact Tom Irving or Clareen Krolik to obtain a password to access the system.


Please stop by at our booth at the Biophysical Society Meeting in San Francisco in February.


We have made a great deal of progress over the last 6 months, not only implementing new experimental modalities, but also making a host of incremental improvements to hardware, software and optics that will result in a smoother and more effective operation. Potential users are invited to contact Tom Irving ( to discuss their needs for diffraction and scattering related experiments and Ke Zhang ( or Grant Bunker ( for XAFS related experiments. Our next proposal deadline is Jan 15th, but proposals will be accepted anytime.




Tom Irving
Director, BioCAT