This is a proof of concept of a live simlation of actin threadmilling using Mike Bostock D3 javascript library.
Dark monomers (and left pool)a re ADP actin, light monomer (and right pool) are APT actin. Middle pool should be ATP + profiline, that for now only participate on the regeneration of ATD into ATP.
The simulation is quite fast, but one should still be able to see rare addition of monomer to the pointed end, and monomer detaching from the pointed end.
| <!DOCTYPE html> | |
| <meta charset="utf-8"> | |
| <style> | |
| .node { | |
| stroke-width: 1.5px; | |
| } | |
| </style> | |
| <body> | |
| <script src="http://d3js.org/d3.v3.min.js"></script> | |
| <script> | |
| var width = 900, | |
| height = 500, | |
| spf =400, | |
| kalapha = 2, | |
| totalmonomer = 140; | |
| var fill = d3.scale.category10(); | |
| var delta = 300; | |
| var nodes = [], | |
| foci = [{x: width/2-delta, y: 100}, {x: width/2+delta, y: 100}, {x: width/2, y: 350}, | |
| {x: width/2, y:20} ]; | |
| pools = { | |
| 'a': { | |
| x:100, | |
| y:100, | |
| pool : [] | |
| }, | |
| 'b': { | |
| x:150, | |
| y:150, | |
| pool : [] | |
| }, | |
| 'c': { | |
| x:250, | |
| y:250, | |
| pool : [] | |
| }, | |
| } | |
| var ft = function(from,to){ | |
| var monom = pools[from].pool.shift(); | |
| if(!monom) return | |
| monom.id = to | |
| pools[to].pool.push(monom) | |
| } | |
| var svg = d3.select("body").append("svg") | |
| .attr("width", width) | |
| .attr("height", height); | |
| var force = d3.layout.force() | |
| .nodes(nodes) | |
| .links([]) | |
| .linkStrength(function(){return 0}) | |
| .chargeDistance(100) | |
| .charge(function(o,i){return (o.id==factinid)? -0: -15}) | |
| .gravity(-0.0) | |
| .size([width, height]) | |
| .on("tick", tick); | |
| var node = svg.selectAll("rect"); | |
| function tick(e) { | |
| var k = .035 * kalapha* e.alpha; | |
| // Push nodes toward their designated focus. | |
| nodes.forEach(function(o, i) { | |
| var dx=o.dx||0; | |
| var dy=o.dy||0; | |
| if(o.id == factinid){ | |
| //k= 0.1*e.alpha | |
| } | |
| try{ | |
| ddy = (foci[o.id].y+dy - o.y) * k; | |
| ddx = (foci[o.id].x+dx - o.x) * k; | |
| //dmax = 0.60 | |
| //if(Math.abs(ddy) > dmax){ ddy = ddy/Math.abs(ddy)*dmax} | |
| //if(Math.abs(ddx) > dmax){ ddx = ddx/Math.abs(ddx)*dmax} | |
| o.y += ddy; | |
| o.x += ddx; | |
| } catch (e){ | |
| } | |
| }); | |
| node | |
| .attr("x", function(d) { return d.x; }) | |
| .attr("y", function(d) { return d.y; }) | |
| .style("fill", function(d) { | |
| if (d.atp){ | |
| return d3.rgb(fill(d.id*0)).brighter(1); | |
| } else { | |
| return d3.rgb(fill(d.id*0)).darker(0.5); | |
| } | |
| } | |
| ) | |
| .style("stroke", function(d) { return d3.rgb(fill(d.id)).darker(2); }); | |
| } | |
| var subset = [[],[],[]] | |
| actinpool = []; | |
| adppool = []; | |
| adpid = 0; | |
| atppool = []; | |
| atpid = 1; | |
| factinid = 2; | |
| profilinepool = []; | |
| profilineid = 3; | |
| var renumberThreadmill = function(actin){ | |
| actin.forEach(function(o,i){ | |
| o.dx=(i-actin.length/2)*8; | |
| o.dy=o.parity*5 | |
| }) | |
| } | |
| var hydrolyse = function(monomer){ | |
| monomer.atp=false; | |
| } | |
| var addToBarbedEnd = function(monomer){ | |
| if(!monomer) return | |
| monomer.id = factinid; | |
| var lastm = actinpool[actinpool.length-1]||{} | |
| monomer.parity = (lastm.parity==-1)?1:-1 | |
| actinpool.push(monomer) | |
| renumberThreadmill(actinpool) | |
| } | |
| var addToPointedEnd = function(monomer){ | |
| if(!monomer) return | |
| monomer.id = factinid; | |
| var firstm = actinpool[0]||{} | |
| monomer.parity = (firstm.parity==1)?-1:1; | |
| actinpool.unshift(monomer) | |
| renumberThreadmill(actinpool) | |
| } | |
| //setInterval(function(){ | |
| //console.log('>>>>> ', actinpool.length+ adppool.length+ atppool.length) | |
| //},100) | |
| var removeBarbedEnd = function(){ | |
| var monomer = actinpool.pop(); | |
| if(!monomer) return; | |
| monomer.dx = 0 | |
| monomer.dy = 0 | |
| if(monomer.atp){ | |
| monomer.id = atpid | |
| atppool.push(monomer) | |
| } else { | |
| monomer.id = adpid | |
| adppool.push(monomer) | |
| } | |
| renumberThreadmill(actinpool) | |
| return monomer | |
| } | |
| setInterval(removeBarbedEnd, 1.907*spf) | |
| var removePointedEnd = function(){ | |
| if(Math.random() < 0.10) { | |
| var rd= Math.random()*atppool.length | |
| if (rd > 4*totalmonomer/5){ | |
| addAtpToPointedEnd(); | |
| } else if (rd > 3*totalmonomer/5){ | |
| addAdpToPointedEnd(); | |
| } | |
| return | |
| } | |
| var monomer = actinpool.shift(); | |
| if(!monomer) return; | |
| monomer.dx = 0 | |
| monomer.dy = 0 | |
| if(monomer.atp){ | |
| monomer.id = atpid | |
| atppool.push(monomer) | |
| } else { | |
| monomer.id = adpid | |
| adppool.push(monomer) | |
| } | |
| renumberThreadmill(actinpool) | |
| return monomer | |
| } | |
| var fromPoolToPool = function(from, to, proba, transform){ | |
| var rnd = Math.random() | |
| if(rnd < proba*from.length){ | |
| monomer = from.shift(); | |
| if(!monomer) return; | |
| transform(monomer); | |
| to.push(monomer) | |
| } | |
| } | |
| // slow atp regeneration | |
| reg = function(){fromPoolToPool(adppool, atppool, 0.00, function(m){m.id=atpid, m.atp=true });} | |
| setInterval(reg, 1.0*spf) | |
| // fast atp regeneration | |
| reg = function(){fromPoolToPool(adppool, profilinepool, 41.0/1000, function(m){m.id=profilineid});} | |
| setInterval(reg, 1.0*spf) | |
| reg = function(){fromPoolToPool(profilinepool, atppool, 20.0/1000, function(m){m.id=atpid, m.atp=true});} | |
| setInterval(reg, 1.0*spf) | |
| reg = function(){fromPoolToPool(atppool, adppool, 0.00, function(m){m.id=adpid, m.atp=false });} | |
| setInterval(reg, 1.0*spf) | |
| //slow atp hydrolysis | |
| setInterval(function(){ | |
| return | |
| var rd = Math.random()*atppool.length; | |
| if(rd > 0.25*totalmonomer){ | |
| var matp = atppool.shift() | |
| matp.atp=false; | |
| matp.id = adpid; | |
| adppool.push(matp); | |
| } | |
| }, 0.3*spf) | |
| setInterval(function(){ | |
| var rd = Math.random()*atppool.length; | |
| if(rd > totalmonomer/20){ | |
| var monomer = atppool.shift(); | |
| addToBarbedEnd(monomer) | |
| } | |
| }, 0.45*spf) | |
| setInterval(function(){ | |
| monomer = removePointedEnd() | |
| }, 1.00*spf) | |
| // fast hydrolyse in actin filament | |
| setInterval(function(){ | |
| var index = ~~(Math.random() * actinpool.length-7) | |
| for(var i= index; i>0; i--){ | |
| if(actinpool[index] && actinpool[index].atp==true){ | |
| hydrolyse(actinpool[index]) | |
| return | |
| } | |
| } | |
| },0.36*spf) | |
| // addAtpPointed | |
| var addAtpToPointedEnd = function(){ | |
| var monomer = atppool.shift(); | |
| console.log('adding to pointed end'); | |
| addToPointedEnd(monomer); | |
| } | |
| // adddtpPointed | |
| var addAdpToPointedEnd = function(){ | |
| var monomer = adppool.shift(); | |
| console.log('adding to pointed end (ADP)'); | |
| addToPointedEnd(monomer); | |
| } | |
| //setInterval(addAtpToPointedEnd, 4*1000); | |
| var addmon = function(){ | |
| var monom = {id: ~~(Math.random() * foci.length), atp:true, weight:0} | |
| //nowhere.push(monom) | |
| nodes.push(monom); | |
| var roll = Math.random(); | |
| if(roll < 0.3){ | |
| monom.atp=true; | |
| monom.id = atpid; | |
| atppool.push(monom); | |
| } else if( roll < 0.6){ | |
| addToBarbedEnd(monom); | |
| } else { | |
| monom.atp=false; | |
| monom.id = adpid; | |
| adppool.push(monom); | |
| } | |
| force.start(); | |
| node = node.data(nodes); | |
| node.enter().append("rect") | |
| .attr("class", "node") | |
| .attr("width", 18) | |
| .attr("height", 8) | |
| .attr("x", function(d) { return d.x; }) | |
| .attr("y", function(d) { return d.y; }) | |
| .style("fill", function(d) { return fill(d.id); }) | |
| .style("stroke", function(d) { return d3.rgb(fill(d.id)).darker(2); }) | |
| .call(force.drag); | |
| }; | |
| setInterval( function(){force.start()} , 600) | |
| for( var i=0; i<totalmonomer; i++){ | |
| addmon(); | |
| } | |
| setTimeout(function(){ location.reload()}, 60*1000) | |
| </script> |