We prefer to use the terminology “reaction cycle” that represents better the conformational and functional dynamics than the more spectroscopic term “photocycle”. The time scales at which the different light-induced intermediates of the reaction cycle occur, span from femtoseconds to milliseconds and have been studied by spectroscopy and structural methods 2, 3, 4, 5, 6. This event starts a cascade of reactions that lead to H +-release on the extracellular side and cytoplasmic H +-uptake 2, 3, thus H +-pumping that establishes an electrochemical H +-gradient that powers ATP-production. Photon absorption induces the isomerization of the retinal from all- trans to 13- cis. With increasing experience you will learn how to handle the software in its best way possilbe and how to avoid running into bugs or error messages, as I could follow this processes for my collegues and myself.Bacteriorhodopsin (bR) is a membrane protein and member of the microbial rhodopsin family, a light-driving proton (H +) pump formed by seven transmembrane helices (TMHs) and a covalently bound retinal chromophore 1. Since I am only a semi-professional programmer, this code is not 100% bug-free. All created new wave types follow the nameing principles of Asylum Research (ONLY NAMES).Additionally, some command-window only procedures ("folder_info2XXX") are supplied to extract every kind of information wanted.When extracting informations a corresponding overview wave for the currentfolder will be generated to sum up the results. Modifying the raw data will create new results waves.These automated zoom-in ranges can be adjusted only within the source-code. This will trigger certain zoom-in processes to simplify checking the results after processing. The displayed 'kind' of curve (raw deflection vs raw piezomovement, force vs deformation/separation and so on) can be adjusted by checkboxes. It includs a graphical display of the current force distance measurement. Almost all interactions with this software are handled through the graphical user interace.Additionally, further smaller scripts are available for other kind of interaction forces, BUT they are not yet perfected since they were not used to same excess as the ones mentioned above.Fitting panels for polymer brush measurements based on a mean-field theory and the Alexander deGennes model.This mechanics panel supports a great varity of adjustable variables to adjust the fitting algorithm to experimental data in regard to size, geometry, fitting ranges and many others. Mechanical interpretation of force-deformation curves: available contact mechanics theorys are Hertz-Model, 'regular' Johnson-Kendal-Roberts theory, '2 point' Johnson-Kendal-Roberts theory, Derjaguin-Muller-Toporov theory, Reissner theory for thin-shell capsuls, Maugis-Dugdale theory in the approximation of Carprick and others.Determination of load and dissipated energy. Calculation of "advanced" adhesion properties based on JKR and DMT theory for different contact geometries.General processing features include: determination of baseline tilt angle and its correction to be flat "easy" calculation of the adhesion force (lowest force value while retracting) determination of the contact point: 5 different algorithm adjustable through different input values conversion from raw deflection and piezo movement to force versus deformation/separation.All systems constants like cantilever spring constant, sensitivity, probe radius etc.All curves can be processed and visualizied in graph indiviually or all at once. The procedure first indexes all force-distance curves in a specified Igor Pro Folder.Only 'name style' of the measurements must follow the principles of Asylum Research.(everything is explained in 'Naming_principles') No header-information from waves are used. Therefore, it is suitable for measurements collected at any atomic force microscope, provided the data is importable to Igor Pro. This software processes raw detector deflection signals in voltage vs raw piezo movement waves in meter.All code is commented to ease understanding the tasks and ideas behind commands used.In particular for hydrogel and polymer mechanics and adhesion, capsule mechanics and polymer brush interactions. The reliablity and variability of the code was tested and improved over a time period of ~5 years by my collegues and me in the field of soft matter research. All processes and interactions with this software are handled through a graphical user interface (GUI, see picture) to ease the handeling. I have written these IGOR Pro procedures to process, analyze and evalute collected AFM force-distance curve during my PhD thesis. The licence for the code in this repository is contained in the included license.md file. An Igor Pro toolkit to process and evaluate Atomic Force Microscopy Force-Distance Measurements
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