∞ generated on 2023.05.19 and updated on 2023.10.03 ∞
How many steps until a phage physically encounters a bacterium?
Please cite as:
Stephen T. Abedon
Why R?
encounter.phage.org
Click here for calculator or see immediately below for further explanation and discussion.
| The goal of this calculator is to explore the validity of the theory presented by Schlesinger (1932) considering the kinetics of phage adsorption. Specifically, that theory is based on the ideas of Smoluchowski (1917) regarding "the coagulation kinetics of The bacterium can be either a circle or a square, for which phages conduct a two-dimensional (2D) search – a random walk – where that bacterium is found approximately in the center of a larger 2D square. The larger 2D square should be at least twice the width of the bacterium, but ideally much larger than that. These 2D simulations take much less time to run but are less realistic in terms of output. Alternatively are 3D spheres and cubes, or for the latter elongated cubes (rectangular cuboids with square perpendicular cross sections), which serve as approximations of bacilli. These 3D searches will take much longer to run than 2D searches for the same-width search environment. Note that a bacterium of size 1 is basically the size of a phage, while a square with an edge of length, 10, is 100-times that area, while 40 times the 'surface' (perimeter) size. Note also that the phage's intial position is that of the 0,0 or 0,0,0 corner of the grid. For long simulation runs, start by refreshing the window (ctrl-shift-R), setting 'Popup' to 1, and make sure that you close any previous pop-up windows (you might also need to tell your browser to allow pop-up windows to come from phage.org; these explicitly are not ads!!!). If your browser asks you if you are to continue waiting, tell it that you do want to (or just do nothing) as these runs can take a very long time. If you navigate away from a running page it may be blank when you return (an indication that the program is still running), but don't worry about that as the page will reappear when the run is (but don't otherwise leave of refresh this page while you are waiting, unless you want to start over). Note that the provied linear regression summaries (m = slope, b = y-intercept, and r = correlation coefficient) are based upon x and y axes presented as percentages of the results from the smallest cell looked at, e.g., one that is 10 units in radius. These are based the graphing of average number of steps (as a percentage) as a function of either 1/R1 or 1/R2, again as a percentage of the smallest radius looked at. Thus, e.g., [% number of steps] vs. [1/R also as a percentage] When the pop-up window appears, click on it, then use ctrl-A to highlight all of the text, then ctrl-C to copy all of the text, then insert the text into Excel using ctrl-V. This data then needs to be deliminated in Excel (sorry about needing to do that). This is accomplished by going to the Data tab, clicking on 'Text to Columns', then choosing 'Delimited', then pressing 'Next', then clidking 'Space', again pressing 'Next', and then pressing 'Finish'. Work your way up to longer runs – such as by starting using fewer technical repeats – so that you can be sure that runs really will eventually conclude for you. Ultimately, it probably would be good to run 100 or more technical repeats, though this may take your computer a long time (hours?) to accomplish. Also, this is all running on your computer, i.e., as JavaScript app, rather than on a server. |