Computer Simulation Meets Molecular Biology

Author(s):  
Volkhard Helms ◽  
Christian Gorba ◽  
Markus Lill
1994 ◽  
Vol 02 (01) ◽  
pp. 55-72 ◽  
Author(s):  
CLAIRE MARTINET-EDELIST

The molecular biology of viruses can be effectively described by kinetic logic, even in its so-called “naïve” version, since feedback loops are implicated in all viral cycles and viral proteins generally display several functions. A general method for the evolution of systems involving feedback loops using this modelling is presented. It can be summarized as follows: (i) description of the system through boolean equations, (ii) identification of the steady states (is there a good agreement between the observations and the logical description?), (iii) experimental determination of several parameters, (iv) computer simulation of viral cycles, (v) predictions and their relation to the biological facts. This survey of oscillation between experimentation and logical description was applied to the study of rhabdovirus cycles and allowed us to describe some aspects of their gene expression.


ChemInform ◽  
2010 ◽  
Vol 22 (10) ◽  
pp. no-no
Author(s):  
J. M. GOODFELLOW

Author(s):  
Cecil E. Hall

The visualization of organic macromolecules such as proteins, nucleic acids, viruses and virus components has reached its high degree of effectiveness owing to refinements and reliability of instruments and to the invention of methods for enhancing the structure of these materials within the electron image. The latter techniques have been most important because what can be seen depends upon the molecular and atomic character of the object as modified which is rarely evident in the pristine material. Structure may thus be displayed by the arts of positive and negative staining, shadow casting, replication and other techniques. Enhancement of contrast, which delineates bounds of isolated macromolecules has been effected progressively over the years as illustrated in Figs. 1, 2, 3 and 4 by these methods. We now look to the future wondering what other visions are waiting to be seen. The instrument designers will need to exact from the arts of fabrication the performance that theory has prescribed as well as methods for phase and interference contrast with explorations of the potentialities of very high and very low voltages. Chemistry must play an increasingly important part in future progress by providing specific stain molecules of high visibility, substrates of vanishing “noise” level and means for preservation of molecular structures that usually exist in a solvated condition.


Author(s):  
Kiyomichi Nakai ◽  
Yusuke Isobe ◽  
Chiken Kinoshita ◽  
Kazutoshi Shinohara

Induced spinodal decomposition under electron irradiation in a Ni-Au alloy has been investigated with respect to its basic mechanism and confirmed to be caused by the relaxation of coherent strain associated with modulated structure. Modulation of white-dots on structure images of modulated structure due to high-resolution electron microscopy is reduced with irradiation. In this paper the atom arrangement of the modulated structure is confirmed with computer simulation on the structure images, and the relaxation of the coherent strain is concluded to be due to the reduction of phase-modulation.Structure images of three-dimensional modulated structure along <100> were taken with the JEM-4000EX high-resolution electron microscope at the HVEM Laboratory, Kyushu University. The transmitted beam and four 200 reflections with their satellites from the modulated structure in an fee Ni-30.0at%Au alloy under illumination of 400keV electrons were used for the structure images under a condition of the spherical aberration constant of the objective lens, Cs = 1mm, the divergence of the beam, α = 3 × 10-4 rad, underfocus, Δf ≃ -50nm and specimen thickness, t ≃ 15nm. The CIHRTEM code was used for the simulation of the structure image.


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