Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Simulation: Difference between revisions
(Finishing up random walk section with some results of simulation) |
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==MATLAB Code== | ==MATLAB Code== | ||
At the core of the simulation is a function which runs runs one random walk on an origami of specified size. It can run in both a cargo-bearing (one-cargo one-goal) and a purely random-walk mode. The former has cargo positions corresponding to our particular origami pre-programmed and starting with multiple (specified by user) walkers at random locations on the origami, and terminates when all of the cargos have been "sorted" to the goal location (the x axis). The latter runs one walker starting at a specified location, and terminates when that walker reaches the specified irreversible track location. The function returns a log reporting when cargos were picked up and dropped off, and a count of the number of steps the simulation took. This function is utilized by separate cargo-bearing and random-walk data collection programs that call the function many times over a range of parameters. | At the core of the simulation is a function which runs runs one random walk on an origami of specified size. It can run in both a cargo-bearing (one-cargo one-goal) and a purely random-walk mode. The former has cargo positions corresponding to our particular origami pre-programmed and starting with multiple (specified by user) walkers at random locations on the origami, and terminates when all of the cargos have been "sorted" to the goal location (the x axis). The latter runs one walker starting at a specified location, and terminates when that walker reaches the specified irreversible track location. The function returns a log of all walkers positions over time, a log reporting when cargos were picked up and dropped off, and a count of the number of steps the simulation took. This function is utilized by separate cargo-bearing and random-walk data collection programs that call the function many times over a range of parameters. | ||
The function code (saved as randomWalkFunction.m): | The function code (saved as randomWalkFunction.m): | ||
<code><pre> | <code><pre> | ||
function [cargoLog, steps] = randomWalkFunction(x, y, length | function [log, cargoLog, steps] = randomWalkFunction(x, y, length, ... | ||
startPos, endPos, cargoBearing, restricted) | numWalkers, startPos, endPos, cargoBearing, restricted, error) | ||
%x: Width y: Height | %x: Width y: Height | ||
%length: max # of steps to run simulation | %length: max # of steps to run simulation | ||
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%cargoBearing = running cargoBearing (1) vs randomWalking (0) | %cargoBearing = running cargoBearing (1) vs randomWalking (0) | ||
%restricted = whether we're paying attention to borders | %restricted = whether we're paying attention to borders | ||
%error = the chance of the failure of any single track | |||
%Random walking cargo pickup/dropoff simulation | %Random walking cargo pickup/dropoff simulation | ||
Line 42: | Line 44: | ||
% 20110616: Modified to be a random walk function, to be | % 20110616: Modified to be a random walk function, to be | ||
% called in a data accumulator program | % called in a data accumulator program | ||
% 20110628-30: Modified to take into account omitted positions | |||
% , new probe layout, and automatic halting when | |||
% starting on impossible positions. | |||
% 20110706: Fixed walker collision. It detects collisions properly | |||
% now. | |||
% 20110707: Adding support for errors -- cycles through and | |||
% omits each track position at an input error rate | |||
%Initialize some things: | |||
%Cargo positions: | |||
cargoPos = [[3, 5]; [9, 5]; [15, 5]; [7, 7]; [11, 7]]; | |||
filledGoals = []; | |||
omitPos = [[3, 6]; [7, 8]; [8, 5]; [11, 8]; [15, 6]]; | |||
steps = 0; | |||
hasCargo = zeros(numWalkers); | |||
sorted = 0; | |||
trackAPoss = [0, 1; 0, -1; 1, 0; -1, -1]; %Movement rules, even column | |||
trackBPoss = [0, 1; 0, -1; -1, 0; 1, 1]; %'', odd column | |||
log = zeros(length, 2*numWalkers + 1); | |||
cargoLog = []; | |||
collisionLog = []; | |||
%Walkers: | %Walkers: | ||
Line 49: | Line 73: | ||
currentPos = zeros(numWalkers, 2); | currentPos = zeros(numWalkers, 2); | ||
for i=1:numWalkers | for i=1:numWalkers | ||
currentPos(i, :) = [randi(x, 1), randi(y, 1)]; | done = 0; | ||
while done ~= 1 | |||
currentPos(i, :) = [randi(x, 1), randi(y, 1)]; | |||
done = checkPossible(numWalkers, currentPos, omitPos, ... | |||
cargoPos); | |||
end | |||
end | end | ||
else | else | ||
numWalkers = 1; %Want to make sure this is one for this case | |||
currentPos = startPos; | currentPos = startPos; | ||
numWalkers = 1; | if checkPossible(numWalkers, currentPos, omitPos, ... | ||
cargoPos) ~= 1 | |||
'Invalid start position.'; | |||
cargoLog = []; | |||
steps = -1; | |||
return | |||
end | |||
end | end | ||
%Error: If there's a valid error rate, go omit some positions: | |||
if error > 0 | |||
for xPos=1:x | |||
for yPos=1:y | |||
%Only omit if it's not already blocked by something | |||
if checkPossible(0, [xPos, yPos], omitPos, cargoPos) | |||
if rand <= error | |||
omitPos = [omitPos; [xPos, yPos]]; | |||
end | |||
end | |||
end | |||
end | |||
end | |||
%Convenience: | |||
numOmitPos = size(omitPos, 1); | |||
numCargoPos = size(cargoPos, 1); | |||
% | %Main loop: | ||
for i=1:length, | for i=1:length, | ||
for walker=1:numWalkers | for walker=1:numWalkers | ||
%Add current pos to log | %Add current pos to log | ||
log(steps + 1, 2*walker-1:2*walker) = currentPos(walker, :); | log(steps + 1, 2*walker-1:2*walker) = currentPos(walker, :); | ||
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%these are the only valid neighbors: | %these are the only valid neighbors: | ||
% (0, +1), (0, -1) | % (0, +1), (0, -1) | ||
% IF | % IF x%2 = 0: | ||
% (+1, 0), (-1, -1) | % (+1, 0), (-1, -1) | ||
% ELSE: | % ELSE: | ||
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temp = randi(4, 1); | temp = randi(4, 1); | ||
if (mod(currentPos(walker, 1),2) == 0) | if (mod(currentPos(walker, 1),2) == 0) | ||
newPos = currentPos(walker, :) + | newPos = currentPos(walker, :) + trackAPoss(temp, :); | ||
else | else | ||
newPos = currentPos(walker, :) + | newPos = currentPos(walker, :) + trackBPoss(temp, :); | ||
end | end | ||
%If we | %If we tried to move onto the bottom two spots (in terms of y) | ||
% a goal) | %on an even column (i.e. a goal), we drop off cargo if we had it | ||
if | %and there wasn't one there already. | ||
%% Specific: 8th column has no goals! It has track instead. | |||
if newPos(2) <= 2 && mod(newPos(1),2) == 0 && newPos(1) ~= 8 | |||
if cargoBearing && hasCargo(walker) == 1 | |||
%Drop cargo, increment cargo-dropped-count, but | |||
%only if there isn't already a cargo here | |||
temp = size(filledGoals); | |||
match = 0; | |||
for k=1:temp(1) | |||
if filledGoals(k, :) == newPos | |||
match = 1; | |||
break | |||
end | |||
end | |||
if match ~= 1 | |||
hasCargo(walker) = 0; | |||
cargoLog = [cargoLog; steps, walker]; | |||
sorted = sorted + 1; | |||
filledGoals = [filledGoals; newPos]; | |||
end | |||
end | |||
%Don't move | %Don't move | ||
newPos = currentPos(walker, :); | newPos = currentPos(walker, :); | ||
end | end | ||
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%Hitting cargos case: | %Hitting cargos case: | ||
for k=1:numCargoPos | |||
if cargoPos(k, :) == newPos | |||
%Remove the cargo from the list of cargos and "pick up" | |||
% if you don't already have a cargo | |||
if hasCargo(walker) == 0 && cargoBearing | |||
cargoPos(k, :) = [-50, -50]; | |||
hasCargo(walker) = 1; | |||
cargoLog = [cargoLog; steps, walker]; | |||
end | end | ||
%Anyway, don't move there | |||
newPos = currentPos(walker, :); | |||
end | end | ||
end | end | ||
% Already on irrev. cargo case: | % Already on irrev. cargo case: | ||
if (currentPos(walker, :) == endPos) | if (currentPos(walker, :) == endPos) | ||
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%Hitting other walkers case: | %Hitting other walkers case: | ||
if numWalkers > 1 | if numWalkers > 1 | ||
for k = 1:numWalkers | |||
if all(newPos == currentPos(k, :)) && k ~= walker | |||
if (currentPos( | |||
newPos = currentPos(walker, :); | newPos = currentPos(walker, :); | ||
collisionLog = [collisionLog; newPos, walker]; | collisionLog = [collisionLog; newPos, walker, k]; | ||
end | end | ||
end | end | ||
end | |||
%Hitting the omitted positions case: | |||
%If we have any position matches with "omitted" list | |||
%, just don't go there. | |||
match = 0; | |||
for k=1:numOmitPos | |||
if omitPos(k, :) == newPos | |||
match = 1; | |||
end | |||
end | |||
if match == 1 | |||
newPos = currentPos(walker, :); | |||
end | end | ||
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end | end | ||
return | |||
%%Checks if a position is a possible place for a walker to be: | |||
function [possible] = checkPossible(numWalkers, currentPos, ... | |||
omitPos, cargoPos) | |||
% If we're starting on an omitted position, or a goal, a cargo, | |||
% or another walker, just give up immediately, and return a -1: | |||
numOmitPos = size(omitPos, 1); | |||
numCargoPos = size(cargoPos, 1); | |||
possible = 1; | |||
for walker = 1:numWalkers | |||
thisWalkerPos = currentPos(walker, :); | |||
% Only run this for this walker if it's placed somewhere | |||
% valid (i.e. not waiting to be placed, x,y = 0,0) | |||
if all(thisWalkerPos) | |||
%Omitted positions: | |||
for k=1:numOmitPos | |||
if omitPos(k, :) == thisWalkerPos | |||
possible = 0; | |||
return | |||
end | |||
end | |||
%Cargo positions: | |||
for k=1:numCargoPos | |||
if cargoPos(k, :) == thisWalkerPos | |||
possible = 0; | |||
return | |||
end | |||
end | |||
%Other walkers: | |||
for k=1:numWalkers | |||
if (all(currentPos(k, :) == thisWalkerPos)) && ... | |||
(k ~= walker) | |||
possible = 0; | |||
return | |||
end | |||
end | |||
%Goal positions: | |||
if mod(thisWalkerPos(1), 2)==0 && thisWalkerPos(1) ~= 8 ... | |||
&& thisWalkerPos(2) <= 2 | |||
possible = 0; | |||
return | |||
end | |||
end | |||
end | |||
return | return | ||
</pre></code> | </pre></code> | ||
Line 172: | Line 284: | ||
% Gregory Izatt & Caltech BIOMOD 2011 | % Gregory Izatt & Caltech BIOMOD 2011 | ||
% 20110616: Initial revision | % 20110616: Initial revision | ||
% | % 20110624: Updating some documentation | ||
% 20110701: Updating to use new, updated randomWalkFunction | |||
% 20110707: Updated to use new error-allowing randomWalkFunction | |||
%% Dependency: makes calls to randomWalkFunction.m | %% Dependency: makes calls to randomWalkFunction.m | ||
Line 179: | Line 293: | ||
xMax = 16; %Scale of platform for test | xMax = 16; %Scale of platform for test | ||
yMax = 8; | yMax = 8; | ||
stopPos = [ | stopPos = [15, 7]; %Stop position | ||
averages = zeros(xMax, yMax); %Init'ing this | averages = zeros(xMax, yMax); %Init'ing this | ||
trash = []; %Trash storing variable | trash = []; %Trash storing variable | ||
Line 189: | Line 303: | ||
temp = zeros(iterations, 1); | temp = zeros(iterations, 1); | ||
parfor i=1:iterations | parfor i=1:iterations | ||
[trash, temp(i)] = randomWalkFunction(xMax, yMax | [trash, trash2, temp(i)] = randomWalkFunction(xMax, yMax, ... | ||
1, [x, y], stopPos, 0, 1); | 10000, 1, [x, y], stopPos, 0, 1, 0.0); | ||
end | end | ||
stdDev(x, y) = std(temp); | stdDev(x, y) = std(temp); |
Revision as of 14:44, 7 July 2011
Tuesday, March 19, 2024
|
SimulationsOverviewOur proposed sorting mechanism depends very heavily on a particular random-walking mechanism that has not been demonstrated in literature before. The verification of this mechanism is thus a vital step in our research. Verification of the random walk in one dimension is fairly straightforward: as discussed in <LINK TO THE EXPERIMENTAL DESIGN SECTION>, a one-dimensional track is easy to construct, and will behave like a standard 1D random walk, showing an average translation on the order of [math]\displaystyle{ n^{\frac{1}{2}} }[/math] after n steps. Thus, we should expect the time it takes to get to some specific level of fluorescence to be proportional to the square of the number of steps we start the walker from the irreversible substrate. If we can, in an experiment, record the fluorescence over time when the walker is planted at different starting points and show that that fluorescence varies by this relationship, we'll have fairly certainly verified one-dimensional random walking. Our particular case of 2D random walking, however, is not as easily understood, especially considering the mobility restrictions (ability to move to only 4 of 6 surrounding locations at any particular time) of our particular walker. As a control for the verification of 2D random walking, though, we still need to get an idea how long the random walk should take, and how that time will change as we start the walker at different points on the origami. We opt to do this by simulating the system with a set of movement rules derived from our design. We also use the same basic simulation (with a few alterations and extra features) to simulate our entire sorting system in a one-cargo, one-goal scenario, to give us some rudimentary numbers on how long sorting should take, with one vs multiple walkers. Basic parameters and assumptions:
MATLAB CodeAt the core of the simulation is a function which runs runs one random walk on an origami of specified size. It can run in both a cargo-bearing (one-cargo one-goal) and a purely random-walk mode. The former has cargo positions corresponding to our particular origami pre-programmed and starting with multiple (specified by user) walkers at random locations on the origami, and terminates when all of the cargos have been "sorted" to the goal location (the x axis). The latter runs one walker starting at a specified location, and terminates when that walker reaches the specified irreversible track location. The function returns a log of all walkers positions over time, a log reporting when cargos were picked up and dropped off, and a count of the number of steps the simulation took. This function is utilized by separate cargo-bearing and random-walk data collection programs that call the function many times over a range of parameters. The function code (saved as randomWalkFunction.m):
Random-Walk SimulationThe data we need from this simulator is a rough projection of the fluorescence response from our test of 2D random walking, which should change based on the starting location of the walker. Because this fluorescence is changed by a fluorophore-quencher interaction upon a walker reaching its irreversible track, in the case where we plant all of the walkers on the same starting track, the time it takes [math]\displaystyle{ (fluorescence_{initial} - fluorescence_{current}) }[/math] in the sample to reach some standard value should be proportional to the average time it takes the walkers to reach the irreversible substrate. As this 'total steps elapsed' value is one of the outputs of our simulation function, we can generate a map of these average walk durations by running a large number of simulations at each point on the origami and averaging the results:
ResultsResults of the bulk data collection at right show that the average random-walk duration, and thus the time for [math]\displaystyle{ (fluorescence_{initial} - fluorescence_{current}) }[/math] to reach some standard level, increases with distance, though it changes less significantly the farther out one gets. Also important to note is that the "effective distance" (in terms of steps) along the short axis of our platform is a significantly less than the same physical distance along the long axis. This difference is due to our arrangement of track A and B: as can be seen in the left half of the diagram at the end of the #Overview section, alternating tracks A and B create a straight vertical highway for the walker to follow. Horizontal movement, in contrast, cannot be accomplished by purely straight-line movement -- it requires a back-and-forth weave that makes motion in that direction slower. The disparity in "effective distances" between the vertical and horizontal dimensions is something, in particular, that we should test for; however, a simple series of tests running random walks at a variety of points across the surface, and the comparison of the resulting fluorescence data to the control provided by this simulation should be sufficient to prove that our walker can, indeed, perform a 2D random walk. |