Sabbatical 2001-2002, Munich, Germany
A narrative description of work to be accomplished.
by Joseph G. Kunkel, Professor
Biology Department, University of Massachusetts Amherst

I am the director and manager of the UMass Non-invasive Ion Probe Facility which has welcomed collaborative use of our developing technology for measuring molecular fluxes about cells (URL: and has been a source of innovative analysis of the resultant information.  I have been involved in the use and development of applications using non-invasive probes since 1983.  My particular interest has been in developing mathematical approaches to collecting and using the data from such probes.  My contention is that individual measurements with this instrumentation are not particularly interesting.  I focus on collecting 3-D arrays of 3-D vectors of flux of single or multiple molecular species about living cells and tissues as well as inanimate models of the same.  I am very concerned about the calibration of the instruments we use which requires understanding the underlying physics and geometry of the problem as well as a statistical approach to estimating the net efficiency of the methods.  I have been directly involved in the computer programming of the equipment that we use in the probe lab, sometimes interacting with the programmer and at other times as the de facto programmer.  With training in mathematical statistics and statistical theory, I am the current expert in establishing the accuracy and precision of the current non-invasive probe technology.  Recently our multiple probes have been controlled by the software program ASET which was written and developed by Eric Karplus of Sciencewares.  Eric has recently signed over the ASET C++ code to me and one other lab so that we could more conveniently make the changes that our leading edge research requires.  These changes will be research in itself and may, if useful, be incorporated into the commercial version of protocols and software.

We are planning on applying our computer controlled multi-probes to measure ion flux as well as oxygen, peroxide and nitric oxide gradients about living cells.  The fluxes of some of these substances would be more easily understood if two or more different probe measurements could be made at the same time and location giving rise to knowledge of their spatial and temporal correlations.  There are many changes that need to be made in the ASET software to facilitate this use of multiple probes.

My major objective during my upcoming sabbatical will be to get into the program code for ASET and start accomplishing the changes we need for our biological research on cells.  Teaming up with Wolfram Nagel at the University of Munich will be very advantageous.  Wolfram is perhaps the one other person on this planet who is as aware as I of the programming that needs to be done to make our non-invasive ion-probes more effective.  These changes include streamlining multiple probe measurements by providing easier startup and physical registration of the multiple probe tips.   Automated calibration of the multiple probes would allow us to routinely get to measuring our perishable live tissues more quickly.  We need to develop spatial and temporal correlation procedures that we can us to visualize and publish our findings.

I will also be experimenting with establishing a real time computer operating system to control our probes which will avoid the interference which current time sharing operating systems impose on our equipment.  The smoothness of movement of our probes have direct effects on the life of the probe tip and the speed with which measurements can be made.  Time sharing operating systems like unix and Windows, slice up time and parcel the time slots to programs that are running.  The ASET program can do things at proscribed times only if it has been given an appropriate time slice that is consistent with the exact start time proscribed.  There is no very demanding issue here about sampling times since the available time slices are fine enough for any measurement resolution that is needed.  However, XYZ motion control can be variably jittery under different time sharing loads that are concurrently being experienced by the operating system.  Adjustments of smoothness-of-motion that work at one time do not necessarily work at another.  At the micron level of motion control this results in shaking of the probe.  Liquid Ion eXchanger (LIX) probes when shaken require time to settle down after a move before measurement can start.  If we could predict the exact smoothness of a move we could minimize the amount of settling time we need before we can measure.  A real time computer would allow moves to be initiated precisely in the XY and Z directions which would result in even movement.  Such an operating system has been developed by researchers in the field of astronomy, which also has needs for precisely timed motion controls of its equipment.  I will investigate adapting their approach to our biological measurement objectives.  This real time measurement system would be commercially valuable and a unique contribution to the field of biology.  The operating system would be written in C and incorporate an option to start time-sharing mode when real-time mode is not necessary.

Joe Kunkel's Publications