 |
Membrane Pharmacy Structure Dynamics
Research group : Priv.Doz. Dr. Thomas NawrothComputing
|
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 nawroth@mail.uni-mainz.de. 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. |
......
Simulation
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)
Hardware
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.
email to: nawroth@MPSD.de
update : 15.10.2012