Stretching a polymer (with optical tweezers)

Description

Freely jointed chain model of a polymer. Attach on both sides to two big beads. That are attach to optical tweezer. The polymer is pulled at several temperature and force extension curve is shown for each temperature.

What you can do

Nothing, just watch and look at the code.

Note/Improvement

Inertia far too big.
No thermal noise applied on beads.
Applet command list.

Code

Simulations:

//*********************************************** //fonction créant une bille et deux rayons lasers function OT(x,y,z) { newPhot(x-0.5,y-0.5,z,1,1,0); newPhot(x+0.5,y-0.5,z,-1,1,0); newBead(x,y,z,0.06,1); } //*********************************************** function stretch_measure(v,amplitude,mw,p0,rc,vc,bc) { //reinitialise le compteur N=0; // vitesse d'etirement v // Graphique force extension Npt=1000; setWindow(0,0); newGraph(Npt); setBounds(0,-2,13,4.5); g = lastGraph; colorGraph(0,0,0); setAxisX(1,0,2,0,0.1); setAxisY(1,0,0.5,0,0.1); setViewXYpG(0,-1); addLabel(1,1.5,'log(Force (~pN))'); addLabel(10,-0.5,'Length (~µm)'); // Pour le moyennage r=0; f=0; mean_w=mw; // On moyenne sur 20 pas de temps sync(abs(N*v)<amplitude) { N++; setP(2,N*v-0.5+p0,-0.5,0); setP(3,N*v+0.5+p0,-0.5,0); r=r+getPX_D-getPX_G; f=f+getTensionX; if (N % mw ==0) { // addPtGraph(r/mw,f/mw*40); addPtGraph(r/mw*10,log(f*50/20)/log(10)); r=0;f=0;} } //reinitialise le compteur pos0=N*v+p0; return pos0; } //************************************************** function move(v,amplitude,p0) { //Compteur de pas N=0; //Vitesse de rapprochement v // pour le dragging nhold=0; hasdragged=0; distdragging=0.03; dd2=distdragging*distdragging; sync(abs(N*v)<amplitude) { N++; setP(2,N*v-0.5+p0,-0.5,0); setP(3,N*v+0.5+p0,-0.5,0); } pos0=N*v+p0; //attend 20 pas de simulation N=0; sync(N<20) {N++;} // Sauvegarde la la position return pos0; } //*************************************************** print(commands); setScalablepG(1); setMovable(0); setMovablepG(1); //Debut du programme principal setViewXYpG(0,-1); // Vue centrée sur la pince setViewX(0.5); setViewY(-0.5); //nouveau polymère newFJC; //Double pince optique OT(-0.6,0,0); OT(0.6,0,0); //Attache le polymère aux billes attachG(0); attachD(1); //Propriétés d'étirement T1=0.2; T2=0.8; T3=3.2; mean_window=10; v_stretch=0.0002; v_back=0.006; A=1.1; //Amplitude // On fait 3 mesures setG(4); setT(0); pos=move(-v_back,A,0.7); writeInfo('T=0;'); pos=stretch_measure(v_stretch*7,A,mean_window,pos,1,0,0); setT(T1); pos=move(-v_back,A,pos); writeInfo('T=0.2;'); pos=stretch_measure(v_stretch*6,A,mean_window*2,pos,0,0,0); setT(T2); pos=move(-v_back,A,pos); writeInfo('T=0.8;'); pos=stretch_measure(v_stretch*5,A,mean_window*3,pos,0,0,1); setT(T3); pos=move(-v_back,A,pos); writeInfo('T=3.2;'); pos=stretch_measure(v_stretch*4,A,mean_window*4,pos,1,0,1);

Biophysics applet

Simulation

Stretching a polymer (with optical tweezers)

Description

What you can do

Note/Improvement

Code