History and Credits

Early Work in the Mainframe Era

The origins of Kinetiscope can be traced back to research in Don L. Bunker's group at the University of California Irvine in the 1970's. Frances Houle was an undergraduate researcher in the Bunker group and developed the FORTRAN code for MSIM4 stochastic kinetics simulator [1], targeted principally for mainframe computers. MSIM4 was available to the scientific community through the Quantum Chemistry Program Exchange (QCPE) [2]. Frances still keeps a copy of the MSIM4 source code as a deck of 80-column punched cards.

Move to Microcomputers

In the 1980's Frances and Bill Hinsberg, both then at IBM's Almaden Research Center in San Jose California, collaborated to port the MSIM4 code to run under compiled BASIC on the original IBM PC and to add a user interface written in Turbo Pascal. This program, named MSIMPC, also was made available to the public through the QCPE.

Development of Chemical Kinetics Simulator

In the early 1990's Frances and Bill were assigned to a software group at IBM Almaden and headed a team tasked with developing a new version of the MSIMx stochastic simulators with the goal of a commercial-grade product. The team included Fumiko Allen on the coding effort and Eunice Yoon with responsibility for the users' manual. In 1996, the product of this effort was made available for download from IBM as the Chemical Kinetics Simulator or CKS, with a no-cost license. CKS is written in C and C++ and uses the StarView user interface class library (from Star Division GmbH, later acquired by Sun Microsystems). CKS adds extensive functionality (e.g variable volume models, user-selectable units, improved computational efficiency) to the MSIMPC code base. John Hutchinson and Greg Wallraff of IBM Research tested the CKS program extensively during its development.

The CKS code includes the first implementation of an equilibrium emulation method developed by Frances and Bill at IBM Research and patented by IBM [3] in 1997. This technique is now known as the tau-leap method following a later paper by Gillespie [4] in 2001. The temperature programming method incorporated into CKS is described in another US Patent [5].

CKS was available in versions for Microsoft Windows 3.1, Apple Macintosh 68000 and PowerPC, and IBM's OS/2. CKS has been widely used in a variety of technical areas, including organic, inorganic, physical chemistry, biochemistry, molecular biology, bacteriology, environmental science, toxicology, waste treatment, zoology, astrophysics, earth science and psychology. In 1998, Frances and Bill received an award from the American Institute of Chemical Engineers for the development of CKS.

The CKS program packages are no longer available for download from IBM. The program will not run on modern operating systems and today is essentially obsolete.

Extensions to include Transport and Three Dimensions

in the late 1990's Frances and Bill, with special project support by Juri Matisso, IBM Almaden's director, developed an experimental extension of the CKS technology, for internal use only, that added the capability for simulating transport, such as in reaction-diffusion systems and compartmental models. This program, named Visual Simulator or VSIM, was used extensively in the authors' experimental chemical research programs, for example, studying imaging chemistry and physics in semiconductor photoresists [6], polymer film dissolution [7] and photomask contamination [8].

VSIM, originally targeted for the OS/2 operating system and later ported to Windows, was programmed in C++ and uses the StarView class library. The VSIM simulation engine is implemented using a fully object-oriented design, enabling extensibility via subclassing and inheritance. The underlying architecture of the VSIM engine is described in two US Patents [9], [10].

Post-IBM

Frances and Bill both are no longer at IBM Research. In response to their request, IBM Corporation graciously has made available the source code for CKS and VSIM as an open-source distribution [11], first released in 2012.

Kinetiscope, based on that release of the CKS and VSIM source code, is an nearly complete redesign of the programs, targeting modern operating systems. Kinetiscope adds support for 64 bit computation, three-dimensional visualization of schemes and results, programmed voltage and external stimulus, and many other enhancements. Aaron Wiegel of the Lawrence Berkeley Laboratory has tested Kinetiscope extensively in his research program.

About Kinetiscope's Authors

William Hinsberg
Bill is founder and Principal of Columbia Hill Technical Consulting in Fremont California. He received his BS in Chemistry from the University of Michigan and his PhD in Chemistry from the California Institute of Technology. Following postdoctoral work at Stanford University, and a research position at Chevron Research, Bill joined IBM's General Products Division, working in thin-film process chemistry for magnetic recording devices. Soon after he moved to IBM's Research Division, serving twice as manager of the Lithography Materials group at the IBM's Almaden Research Center. Four photoresists developed by Bill and co-workers have been used for the commercial manufacture of microelectronic devices. He has received a number of awards for his technical work, including the Leo J. Friend Award sponsored by the Industrial and Engineering Chemistry Section of the American Chemical Society, the 1999 American Institute of Chemical Engineers Northern California Section Research Project of the Year, and the 1998 IBM Environmental Affairs Excellence Award. He currently serves as Associate Editor for the Journal of Vacuum Science and Technology. Bill has authored or co-authored over 150 scientific articles and is an inventor on more than 30 US Patents.
Frances Houle
Frances is Department Head for Science of Large Scale Systems at the Joint Center for Artificial Photosynthesis and a Senior Scientist in the Chemical Sciences Division at Lawrence Berkeley National Laboratory. She received the BA from the University of California at Irvine and the PhD from the California Institute of Technology, both in chemistry. Following her postdoctoral work at LBNL and the UC Berkeley Chemistry Department she held professional appointments as Research Staff Member in the IBM Research Division in San Jose, California, Manager of Materials Development at InVisage Technologies, a startup company making nanoparticle-based image sensors, and Director of Strategic Initiatives in the Chemical Sciences Division at LBNL. She has received numerous awards including the 2009 American Vacuum Society John A Thornton Memorial Award and Lecture, the 1999 American Institute of Chemical Engineers Northern California Section Research Project of the Year, and the 1998 IBM Environmental Affairs Excellence Award. She is a Fellow of the American Physical Society and Fellow of the AVS, and member of the American Chemical Society and Materials Research Society. She has been active in professional service, including the Council and Executive Board of the APS, Editorial Committee of the Annual Reviews of Physical Chemistry, Board of Trustees of the AVS, and Selection and Scheduling Committee of the Gordon Research Conferences. She currently serves on the New Meetings Subcommittee of the Materials Research Society, and on several LBNL committees. She has over 125 publications and 26 US patents and patent applications.

References

  1. F.A. Houle and D.L. Bunker, J. Chem. Educ., 58 405-407 (1981).
  2. "Quantum Chemistry Program Exchange, Facilitator of Theoretical and Computational Chemistry in Pre-Internet History," Donald B. Boyd, Pioneers of Quantum Chemistry, ACS Symposium Series, Vol. 1122, Ch. 8, pp 222-273 (2013).
  3. W. Hinsberg and F.A. Houle, "Stochastic Simulation Method for Processes containing Equilibrium Steps," United States Patent 5,625,579 (April 29, 1997).
  4. D.T. Gillespie, J. Chem. Phys. 115, 1716 (2001).
  5. W. Hinsberg and F.A. Houle, "Method for Stochastic and Deterministic Timebase control in Stochastic Simulations," United States Patent 5,745,385 (April 28, 1998).
  6. F.A. Houle, W. Hinsberg, M. Sanchez and J. Hoffnagle, J. Vac. Sci. Technol. B, 20, 924 (2002); F.A. Houle, W. Hinsberg, and M. Sanchez, J. Vac. Sci. Technol. B 22, 747 (2004).
  7. F. Houle, W. Hinsberg and M. Sanchez, Macromolecules, 35, 3591 (2002); W. Hinsberg, F.A. Houle, S-W Lee H. Ito and K. Kanazawa, Macromolecules, 38, 1882 (2005).
  8. John Bruley et al., Proc. of Soc. Photo-opt. Instr. Eng., 7272, 727215-1 (2009).
  9. W. Hinsberg and F.A. Houle, "Spatially Resolved Stochastic Simulation Systems," United States Patent 5,446,870 (August 29, 1995).
  10. W. Hinsberg and F.A. Houle, "Software Architecture for Stochastic Simulation of Non-homogeneous Systems," United States Patent 5,826,065 (October 20, 1998).
  11. http://code.google.com/p/chemical-kinetics-simulator/