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for i = 2:numSteps %define the space over which to simulate for n = 1:clutchNum %loop over each individual clutch if clutchState(n) == 0% !! clutch is unbound pBind = 1-exp(-clutchOn*timeStep);% !! probability of binding within the given time step temp = rand; % !! generate random number if temp <= pBind %determine if the event is executed or not clutchState(n) = 1; % !! clutch is now bound end elseif clutchState(n) == 1 % !! clutch is bound %% unbinding rate is now depending on the loading force clutchOff_prime = clutchOff*exp(clutchForce(n)/bondForce); % !! from Eq. 7, calculate the loaded dissociation rate pUnbind = 1-exp(-clutchOff_prime*timeStep); % new probability of unbinding within the given time step temp = rand; % !! generate random number if temp <= pUnbind % !! determine if the event is executed or not clutchState(n) = 0; % !! clutch is now unbound end end end csArray(i) = sum(clutchState); %record the total number of bound clutches %balance the forces to determine the substrate position sumClutchPos = sum(clutchPos(clutchState==1)); %summation from numerator of Eq. 5, do not change (note: this is only the summation, not complete numerator) subPos(i) = (clutchKs*sumClutchPos)/(subKs+(csArray(i)*clutchKs)); % !! from Eq. 5, solve for the substrate position %% solve for the actin flow rate based on the load Fstall = motorNum*motorForce; % from Eq. 10, calculate the total stall force actinFlow(i) = motorVel*(1-((subKs*subPos(i))/Fstall)); % !! from Eq. 9, determine the actin flow rate %% forces have been added. loop through each clutch, update position and calculate force for n = 1:clutchNum if clutchState(n) == 0% !! clutch is unbound clutchPos(n) = subPos(i); %unbound clutches are set at the substrate position clutchForce(n) = (clutchPos(n)-subPos(i)); % !! from Eq. 8, determine the force on the individual clutch elseif clutchState(n) == 1 % !! clutch is bound clutchPos(n) = clutchPos(n) + actinFlow(i)*timeStep; % !! position moves at velocity of actin flow clutchForce(n) = clutchKs*(clutchPos(n)-subPos(i)); % !! from Eq. 8, determine the force on the individual clutch end end timeArray(i) = timeArray(i-1)+timeStep; %record the current time end

%%%%%%%%%%%%%%%%submit this section of code to the Synapse page%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% for i = 2:numSteps %define the space over which to simulate for n = 1:clutchNum %loop over each individual clutch if clutchState(n) == 0% !! clutch is unbound pBind = 1-exp(-clutchOn*timeStep);% !! probability of binding within the given time step temp = rand; % !! generate random number if temp <= pBind %determine if the event is executed or not clutchState(n) = 1; % !! clutch is now bound end elseif clutchState(n) == 1% !! clutch is bound %% unbinding rate is now depending on the loading force clutchOff_prime = clutchOff*exp(clutchForce(n)/bondForce); % !! from Eq. 7, calculate the loaded dissociation rate pUnbind = 1-exp(-clutchOff_prime*timeStep); % new probability of unbinding within the given time step temp = rand; % !! generate random number if temp <= pUnbind % !! determine if the event is executed or not clutchState(n) = 0; % !! clutch is now unbound end end end csArray(i) = sum(clutchState); %record the total number of bound clutches %balance the forces to determine the substrate position sumClutchPos = sum(clutchPos(clutchState==1)); %summation from numerator of Eq. 5, do not change (note: this is only the summation, not complete numerator) subPos(i) = (clutchKs*sumClutchPos)/(subKs+(csArray(i)*clutchKs)); % !! from Eq. 5, solve for the substrate position %% solve for the actin flow rate based on the load Fstall = motorNum*motorForce; % from Eq. 10, calculate the total stall force actinFlow(i) = motorVel*(1-((subKs*subPos(i))/Fstall)); % !! from Eq. 9, determine the actin flow rate %% forces have been added. loop through each clutch, update position and calculate force for n = 1:clutchNum if clutchState(n) == 0 % !! clutch is unbound clutchPos(n) = subPos(i); %unbound clutches are set at the substrate position clutchForce(n) = clutchKs*(clutchPos(n)-subPos(i)); % !! from Eq. 8, determine the force on the individual clutch elseif clutchState(n) == 1% !! clutch is bound clutchPos(n) = clutchPos(n)+actinFlow(i)*timeStep; % !! position moves at velocity of actin flow clutchForce(n) = clutchKs*(clutchPos(n)-subPos(i)); % !! from Eq. 8, determine the force on the individual clutch end end timeArray(i) = timeArray(i-1)+timeStep; %record the current time end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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