Membrane Pharmacy Structure Dynamics 

Research group : Priv.Doz. Dr. Thomas Nawroth


Programs and hardware for data evaluation, molecular modelling, simulation and experiment control

    The computing list is organized in seven object classes :

      Evaluation   Data evaluation programs
      Modelling   Molecular modelling of structure and dynamics (FVM cube method)
      Simulation   Simulation of kinetic, structure and origin of live experiments
    DataConcept Data structure concepts for programs and files
      File formats   Structured file formats for complex kinetic and structure experiments
      Hardware   Hardware for experiment control and data aquisition
    Control Software for experiment control and data aquisition

    Data evaluation
Available data evaluation programs :
  Kinex   Universal evaluation program with interactive graphics for kinetic and other experiments 
  PicView   Inspection and simple evaluation of X-ray, neutron or optic camera data (scattering ...)
  Scate   Evaluation program for single small angle scattering experiments (1D-data)
  Tabula   Universal evaluation program for single experiments (1D-data), scientific table calculator 
  QuiDas   Library and open system for program design
pH-Jump Evaluation of pH-jump experiments with dye entrapped liposomes and time resolved optical spectra
All our current evaluation programs are designed for the use with PC's. The elder Fortran programs for small angle scattering data evaluation under VMS and MULTICS (the ancient UNIX-parent) are no longer supported. The data evaluation programs are available as 1.x versions for DOS or DOS-Window of Windows. Versions 2.x for Windows9x / NT are in the beta-state (under construction and test). The 1.x versions run also on simple PC's (requirements: 486/386-CPU with arithmetic coprocessor, standard VGA).
The interactive graphics of Kinex and Scate allows the evaluation of data  tables by selection of a region of interest on the graphics display. The region of interest (ROI) may consist of up to 20 sub-areas, which may overlap. Each is defined by a start and endpoint selected by the graphics cursor control. The evaluation function, e.g. a last square fit straight line, is applied to the region of interest only, which is available as a special copy dataset. The evaluation by a special function is done in two steps: 1) Convert the data to the special representation in the numerics function menu or in a specialized application function menu, e.g. Guinier-plot or Arrhenius representation. This generates a special data set in parallel to the unchanged original data. 2) Apply the interactive evaluation to the special representation. The evaluation can be done as a multistage process subsequently to the same dataset or by storage of  intermediate results in separate datasets (up to 10 datasets are held in the memory in parallel).
Versions 1.x allow only the direct manipulation of the data by user-control, and the data storage in the SF3 or ASCII file format. Version 2.x of Kinex can apply command-files (scripts) to the data by evaluation with an "engine" instead of direct command processing. Thus huge data structures, as result from kinetic experiments (structural films), can be controlled and evaluated automatically. The command files as well as the data can be part of a structured file, if the SF4 file format is used (strutured data format 4, suitable of storage of structural film with all additional data).
Versions 1.x of Kinex, Scate, Tabula and Quidas are written with the Microsoft "Professional Basic Developmemt Sytstem" PDS7.1 optimizing compiler, which uses "labeled common data" structures as Fortran. This is used for the data transfer between the program modules in the QuiDas propgramming system as a "software bus structure". The 2.x versions are written with Microsoft "Visual Basic" and "Visual C++" (final versions of fast subroutines only). The pH-Jump1 program was written by Dr. K. Zwicker (PhD thesis: T15, T7) using Borlands "Turbo Pascal" compiler.
Quidas is an open system and subroutine library designed for program development of distributed programmers. The concept requires that the source code and the concepts are available for every interest (as LINUX). You are free of using any part for scientific (non commercial) purpose. If you write further moldules, please send the code and description for completion of this WEB-site by email to Please indicate your name and the date of last change as a comment (') in the second line.

    Molecular modelling
Available molecular modelling program :
  Finix   Molecular modelling of structure, dynamics and surface of macromloecules using the FVM cube method; Interpretation of small angle scattering data, surface photo labeling and photo crosslinking experiments; Simulation of molecular motions.

Available simulation programs :
  Finix   Simulation of molecular motions; molecular modelling of structure, dynamics and surface of macromolecules using the FVM cube method; Interpretation of small angle scattering data, photo-labeling and photo crosslinking experiments.
  Impact   Simulation of a meteorite fall on earth from the interstellar space: Calculation of energy and temperature, estimation of light radiation dose obtained during the journey. This case might have contributed to the origin of life on earth.
  PolySim   Simulation of the formation of a polymer from amino acids by a Monte Carlo algorthim. Simulation of a possible way for the origin of life by chemical evolution based on polycondensation kinetics experiments. 


    Data structure concepts
For maintanance and storage of experiment data from structure, optics and enzyme kinetics investigations we have developed a general data structure concept. In this concept the data-sets are oraganized in subsets, which describe a group of correlated dataobjects belonging to one type of data, e.g. a film of pictures. Nevertheless a subset consists of several objects of different meaning and dimension, e.g. a film consists of the 3D-array of 2D-immages, the parameter-description of the film (1D-numeric with desclaimer), the parameter-description of each image (2D-numeric with desclaimer), the time-list (1D numeric), and text-remarks (a set of structured text blocks). Additional information may be measured and stored in different subsets in parallel, e.g. the temperature (in time = 1D), the light absorption at several wavelength in time (2D) etc.
The minimal data structure of an object requires : a text-header, a numeric parameter collection and the data-object. In our experiments on molecular motion in working proteins, e.g. working F1ATPase, we used six levels of experiments, e.g. a temperature-variation(time-resolutions(time-schemes(repetitions(films(2D-images))))). If a further parameter is varied, e.g. the concentration of substrate (ATP) or protein, this increases to seven experiment levels, each requiring the above minimal data structure. Thus the data structure has to be recursive (or fractal).
The data structure concept is beeing realized at two levels: the data structure inside the program and the data structure in the files. For our previous experiments (simpler) we have develloped programs and file formats for single experiments (programs: KINEX1, FINIX1 etc.; data format: SF3). The new extended experiments with the above structure, which may cover up to several 100-GB (!!!), require the new versions for complete evaluation (programs KINEX2, FINIX2; file format SF4).

    File formats
Our file format for single experiments SF3 (Strutured Fileformat 3) is preliminary described in thesis T20. The new recursive file format SF4 (Structured Fileformat 4) is still under development (inquire by EMail)

We use for our evaluation at the institute PC-computer under Windows (TM). For the new programs (KINEX2, FINIX2) at least 64 MB RAM are required.
The experiments at the large scientific facilities are done with:
- at the ESRF synchrotron, Grenoble - beamline ID2A (SAXS): SUN-Workstation with 640 MB RAM + VME crate (OS9), running under UNIX; similar equipment is used at ID1 (ASAXS) and ID24 (TR-EXAFS)
- at the ILL reactor, Grenoble - beamline D22 (SANS + TR-SANS) : UNIX-workstation + VME crate
- at the HASYLAB-DESY synchrotron, Hamburg, beamline B1 / JUSIFA (SAXS) : DEC-micro-VAX under VMS (will be replace by a UNIX workstation 9/2000) + CAMAC-crate; at the beamline BW4 (USAXS) : UNIX-workstation + VME-crate, evaluation-software under UNIX + IDL
- at the FRJ2-reactor of the FZ-Jülich, beamline KWS-II (SANS) : DEC-micro-VAX under VMS + CAMAC crate
- at the ELETTRA synchrotron, Trieste, beamline 5.2 (SAXS + TR-SAXS) : PC-cluster (3) under WINDOWS, evaluation-software under WINDOWS + IDL

Our time resolved experiments are done with computerized experiment controllers. The low level control is done by machine-language code in any case (required for real time applications).
For 2/3 of the time resolved X-ray and neutron experiments we have used a simple 6502-microprocessor system (CBM720) with TTL-stopped-flow controller with timing-programs developed at Mainz. The machine language program is controlled at a secondary level by PC-programs under BASIC (several version by A. Neidhardt and T. Nawroth, e.g. SFX500(TR-SAXS); SFN1200(TR-SANS)). Becaue of the hardware structure this equipment can move only one moter independently at a given time.
1998/99 we have used a commercial stepping motor controller (C142-4) form ISERT, Eiterfeld,  in collaboration with the group of PD. Dr. Hermann Heumann, MPI Biochemie, Martinsried (biophysics division). This device is controlled at a secondary level by a PC; the control program under LABVIEW (TM) was developed by Manfred Roessle, Martinsried, during his PhD thesis. Becaue of the hardware structure also this equipment can move only one moter independently at a given time.

For fast experiments with several motors in parallel we have a novel experiment controller under development. This constists of a TTL+Microprocessor controller for fast events (Z80 / 64180 chip with hardware vector interrupt enable parallel movements) and a PC under WINDOWS for slower controls, parameter delivery and data storage (Visual Basic6 and Visual C++ 6 programs). The device is required for expample for the combined temperatur-jump / stopped-flow experiments for the investigation of fast events in enzyme catalysis.

[ MAIN PAGE "Membrane Protein Structure Dynamics" (MPSD) ]
[ Impressum-Disclaimer | News | Address | Concepts | Science | Lectures | Technology | Publications | Health-Environment-Security | Thesis | Staff]
[ Structural Biology |Membrane Proteins| BioEnergetics | Molecular Motion | ATP-Synthase | Oxygen Proteins | Membrane Structure | NanoParticles ApplicationTime-Resolution | Computing | Study-Group ]

email to:   update : 15.10.2012