Team:Paris Bettencourt/Modeling/Assisted diffusion

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<h1>Assisted diffusion</h1>
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== Introduction to the model ==
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<h2>Introduction to the model</h2>
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The diffusion through the nanotubes is a fast process. This speed can be partially explained by the passive diffusion through the tubes. But what if it is faster?
 
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The article from Dubey and Ben-Yehuda suggests that the diffusion is an active process. Several points can be opposed to this statement:
 
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* First, the diffusion is happening with molecule of different natures, that have nothing to do with the natural compoments of a cell
 
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* Unlike the mamalian cells, the tube seems not to have no "railroad" design for such a transport
 
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The question is: can we immagine a process that is faster than passive diffusion but does not rely on specific interractions?
 
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The answer is probably yes, and in this page we propose a new model, really challenging for the mind, but that can play a role in the diffusion process through the nanotubes.
 
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== General physical concepts and Hypothesis ==
 
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=== Starting from an analogy ===
 
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Immagine two bottles of gaz connected by a tube. The fist one have an higher pressure than the second one. In the first one, diluted in the gaz, there are a few molecules of another nature. We follow the destiny of these molecules.
 
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When you open the tape, the bottle with a higher pressure will equillibrate with the other one my moving a certain quantity of it's particles through the tube in the direction of the second bottle. These moving molecules will drag with them the copoment diluted in the gaz and a few of these molecules will be transported to the other bottle.
 
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=== From the analogy to the biology ===
 
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Of cource, the cell is not a bag of liquid under pressure. The water is equillibrated at both sides of the exterior membrane. The pressure we are dealing with is not related to water or osmotic pressure (that is a "passive diffusion thermodynamical pressure"). There is a part of the cell we are not used to think about that undergo a huge variablilty of pressure: the phospholipid membrane!
 
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Let's evaluate the constraints that the membrane underdo. First, as it is a Gramm positive bacteria, the external sugar envelopp impose the shape of the bacteria. On the other hand, the osmotic pressure is pushing the membrane against the sugar wall. Inside the membrane, the number of phospho-lipids is fixed by the state of division on the cell.
 
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Though, a phospholipid is somehow behaving as a gaz trapped in a bottle. The ospotic pressure and the sugar layer are the bottle, and the number of particle trapped is giving the pressure. This variation of pression can be important if the cell has just devide or if the cell is about to devide.
 
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<td><center><img src="https://static.igem.org/mediawiki/2011/8/8a/MembraneCompression.png" height=200px></center></td>
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<td><center><img src="https://static.igem.org/mediawiki/2011/d/d3/MembraneExtension.png" height=250px></center></td>
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<img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/b/b9/Active-diff-button.png">
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<td><p><center><u><b>Fig2:</b></u> When the cell is about to devide, there is an excess of phospholipids. The membrane is under compression<p></td>
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<p> Inspired by the experiments of Dubey and Ben-Yehuda we asked ourselves several questions.  
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<td><p><center><u><b>Fig3:</b></u> When the cell is about to devide, there are not enough phospholipids. The membrane is under extension<p></td>
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When the cell enter of communication, a flow of molecule can pass from the cell that have the highest membrane pressure to the other one. To pass from one cell to another, phospholipids runs around the tube.
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The tube is small and water has its intrinsic viscosity. If the pipe is moving, the water inside will follow, pumping the water from one cell to another. The sliding will look like a Poiseuil flow. Constituents diluted in water will move from one cell to another unidirectionally and faster than simply diffusing. This is a fast process that we have named after the "active" and "passive" diffusion, the "assisted diffusion"
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What kind of process could do this molecular transfer? How can we characterize it?
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=== When membranes behave like a 2D Van der Waals fluid ===
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It could be an active process, a passive diffusion or something else.
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Trapped between the osmotic pressure and the cell wall, the phospholipids particle are moving in a double layered environement. Their motion is contricted into a two dimentional motion, following the shape of the membrane. At the scale of the phospholipid, the motion can be approximated to a motion in 2D. Using the formalism of the Statistical Physics, we can say that the phase space has 4 dimentions: two dimentions of impulsion and two dimentions of coordinate.
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Several arguments can be opposed to the <em>active process</em> hypothesis:
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<ul>
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Can we descripe the interraction between two phospholipids in the membrane? Well, the question is complicated, but we will demonstrate that describing properly the pholpholipid, it is reasonable to fit a Lennard-Jones potential energy to this interraction. The enery of binding is smaller and the speed of sliding of one phospholipid against another is slower than the internal vibration of the chemical bounds and the internal conformers rotation of the CH2 tails. Though, in ''Intermolecular Forces'' by Israelacviili, the author shows that a phospholipid trapped in a bilayer can be aproximated by a section of cone. The section of cones is an individual, and the others are section of cone joining the previous one. The shape of the sections are giving the shape of the global structure.
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<li>During the process, an exchange of <em>molecules of different natures</em> takes place. These molecules have nothing to do with the natural components of a cell (GFP, calcein, etc.). Thus there is <em>no specificity</em> of transport, and there should be no specific mechanism of active transport.</li>
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<li>Unlike the mammalian cells, the bacterial tubes seem to have no "railroad" to guide the transported molecules.</li>
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&nbsp; &nbsp; &nbsp; &nbsp;
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<td align="center"><img src="https://static.igem.org/mediawiki/2011/e/e9/Image_phospholipide.png" height=200px></td>
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<td align="center"><img src="https://static.igem.org/mediawiki/2011/8/82/Mod%C3%A8le_Phospholipide.png" height=200px></td>
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<td align="center"><center><b><u>Fig5:</u></b> Chemical structure of one pholpholipid</center></td>
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<td align="center"><center><b><u>Fig6:</u></b> Schematics of the cylindrical approximation made for the phospholipid</center></td>
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Speaking in term of energy, once we have these cones, it is reasonable to fit a Lennard-Jones potential to this interraction. If the cones are interpenetrating, a sterical repulsion keeps the molecules appart, and the hydropatic interraction that joins one lipid with the other act as an attractive force keeping the coherence of the mombrane. We will discuss later about the value of the two coefficients.
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<p>The question is :</p>
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<p><center><b>Can we develop a theoretical model of "active" transfer that can justify what was observed in the orignal article?</p>
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</b></center>
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[[File:LJpot.jpg|center|Lennard-Jones potential]]
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<p>We need to know if such a model can be designed starting from physical laws and if this model can explain quantitatively the transfer through the nanotubes. Due to its purely physical nature, our model can also shed some light as to the nanotube formation.</p>
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<p>We managed to come up with an idea for such a process, and in this page <em>we propose a new model</em> that can possibly explain the speed of the molecule exchange through the nanotubes.</p>
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In the liquid physics, we use to call any system behaving with a Morse-like potential a Wan der Waals fluid, because once the statistical aspect is solved, we come back to the famous thermodynamical equation of Van der Waals.
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<p>As a matter of fact, <em> the difference in membrane tension</em> between two bacteria could lead to a pressure difference. That could induce a small cytoplasmic transfer to reach internal pressure equilibrium. </p>
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<h2>Summary</h2>
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[[File:VdW_eq.jpg|center|Van der Waals equation]]
 
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== Let's start the Maths ==
 
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In stastical physics, in the canonic ensemble, the partition function for a classical particule is given by:
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<div id="assisted_diff" style="margin-left:50px;">
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<div class="assisted_diff_link" style="position:relative; left:80px; top:30px;"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Assisted_diffusion/Membrane_tension"><img src="https://static.igem.org/mediawiki/2011/7/7b/Select_bilayer.png" /></a></div>
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<div class="assisted_diff_link" style="position:relative; left:375px; top:19px;"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Assisted_diffusion/Tube_formation"><img src="https://static.igem.org/mediawiki/2011/8/8f/Select_formation.png" /></a></div>
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<div class="assisted_diff_link" style="position:relative; left:339px; top:94px;"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Assisted_diffusion/From_membrane_tension_to_liquid_flux"><img src="https://static.igem.org/mediawiki/2011/4/47/Select_pressure.png" /></a></div>
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</div>
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<center><h4>Click on the circles on the above picture to discover our assisted diffusion model in details</h4></center>
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Where H(p,r) is the Hamiltonian of the system, given by:
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<p>
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Model description in few words :
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</p>
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where LJ(r1,r2) is the potential energy given by the Lennard Jones formulea. As usual in statiscical physics, we devide the total potential energy of the system into the pair-to-pair interraction between particles.
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<p>
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Once calculated, the partition function has the form of:
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We do not know what is the mechanism behind nanotube formation. We can suppose they are made of lipid membrane within a cell-wall like matrix, as suggested by the original electron microscopy experiment. When the membrane of the two cells fuse, there might be a <em>difference of tension between the two phospholipid bilayers</em>. This phenomenon might lead to a <em>movement of lipids</em> from one membrane to the other. The newly arrived phospholipids change the membrane tension of the bacterium. As a consequence, they change the internal Laplace pressure <i>ΔP<sub>Lap</sub></i> of the bacterium.
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</p>
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The next step is to calculate the free-energy associated with the partition function. Free energy is the value that links the statiscical physics to classical thermodynamics. The classical formulea is:
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<p>
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<center>
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<img src='https://static.igem.org/mediawiki/2011/7/7d/Laplacian_pressure.png' style="height:45px">
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</center>
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</p>
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Which, once applicated to our system gives:
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<p>
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where τ is membrane tension, R is a radius of bacterium.
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</p>
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<p>
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A simple analogy of clothesline can help to understand what is happening. You need to pull more your clothesline to put more clothes on it. When you pull the rope by two ends you create a tension. The bigger the tension, the more weight (pressure) you can put on the rope.
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</p>
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The pressure of the membrane, that correspond to the tension, is given by the formulea
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<p>
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All of this will lead to establishing the pressure difference at the tube extremities and we will get a Poiseuille's flow. Constituents diluted in water will move from one cell to another unidirectionally and faster than by simple diffusion. This is a fast process that we have named the <em>"assisted diffusion"</em>.
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</p>
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...
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<div style="margin-left:50px; margin-right:50px; padding: 5px; border:2px solid black;"><b><p>The assisted diffusion model in 3 bullet points:
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...
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<ul>
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    <li>Characteristic time of the process is about 100 ns</li>
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    <li>The effect strongly depends on the initial phospholipid distribution on the membrane of two connected bacteria</li>
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    <li>The phenomenon predicts the flux of only 0.1 % of the cytoplasme, not enough to explain the GFP experiment of the original paper</li>
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</ul></p></b></div>
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And so on Oleg !!!
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<p>
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We have done a <a href='https://2011.igem.org/Team:Paris_Bettencourt/Modeling/Assisted_diffusion/Back_of_the_envelope_calculation'>back of the envelope calculation</a> to see whether an order of magnitude is acceptable.</p>
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...
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...
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<div id="citation_box">
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<p id="references">References</p>
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Which gives a tension that is a function of the radius of the vesicle (R), the number of lipids (N) and the temperature (T)
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<ol>
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<li><i>Intercellular Nanotubes Mediate Bacterial Communication</i>, Dubey and Ben-Yehuda, Cell, 2011, available <a href="http://bms.ucsf.edu/sites/ucsf-bms.ixm.ca/files/marjordan_06022011.pdf">here</a></li>
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== Back to the classical physics ==
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<li><i>BioNumbers</i> <a href="http://bionumbers.hms.harvard.edu/">here</a></li>
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</ol>
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Now that we can calculate the tension of the membrane (i.e. the pressure of the Wan der Waals fluid), we can start calculating the equential equation of the relaxation of the membrane. As it is a fluid with an intrinsic viscosity, we will use the Navier-Stokes equation.
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[[File:NavierStokes.jpg|center|Navier Stokes equation]]
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Let's first choose a point of view of considering the flux. There is the Bernouilli point of view in which we track the fluid particule destiny and the stokes point of view in which we are fixed in one point and watch the flux of fluid particle. The second point of view is easier for us, because, we want to count in the end the a certain quantity of phopholipids that have passed through the tubes, and link that to the quantity of water.
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Let's imagine that we are an observer sitting at the entrance of the nanotube. He watch the liquid passing between his legs, and canlculate the flux.
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...
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Your job agains Oleg, the games get it's tracks!!
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...
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Finally with a difference of pressure P2-P1, we can estimate the caracteristical time of the relaxation to be:
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where...
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== Getting back to the quantity of water ==
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We are in the situation where a tube, that have good hydrophilic properties is moving, the tube is small and the liquid viscuous (the density of the cytoplasm over the tensity of water is about 3.2). Water will be dragged in the tube.The fluid will undergo a Poiseuille flow, but this time the tube is moving and the water following.
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[[File:Poiseuille.jpg|center|a Poiseuille flow inside a tube]]
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...
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Going down the Poiseuille equation you will estimate the total flux dragged for a certain quantity of phospholipids that have passed bhy depending on the size of the tube, the viscosity of water...
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== Getting the good parameters ==
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It will take some time, but once you have the equation, from the size of a vesible in equillibium, when we know the number of phospholipids. The viscosity has probably been estimated by FRAP techniques. For the rest, we will find out.
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== Analysing the results ==
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== Can this process be an efficient way for passing molecules?? ==
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== Conclusion ==
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Latest revision as of 02:14, 29 October 2011

Team IGEM Paris 2011

Assisted diffusion

Introduction to the model

Inspired by the experiments of Dubey and Ben-Yehuda we asked ourselves several questions. What kind of process could do this molecular transfer? How can we characterize it? It could be an active process, a passive diffusion or something else. Several arguments can be opposed to the active process hypothesis:

  • During the process, an exchange of molecules of different natures takes place. These molecules have nothing to do with the natural components of a cell (GFP, calcein, etc.). Thus there is no specificity of transport, and there should be no specific mechanism of active transport.
  • Unlike the mammalian cells, the bacterial tubes seem to have no "railroad" to guide the transported molecules.
       

The question is :

Can we develop a theoretical model of "active" transfer that can justify what was observed in the orignal article?

We need to know if such a model can be designed starting from physical laws and if this model can explain quantitatively the transfer through the nanotubes. Due to its purely physical nature, our model can also shed some light as to the nanotube formation.

We managed to come up with an idea for such a process, and in this page we propose a new model that can possibly explain the speed of the molecule exchange through the nanotubes.

As a matter of fact, the difference in membrane tension between two bacteria could lead to a pressure difference. That could induce a small cytoplasmic transfer to reach internal pressure equilibrium.

Summary

Click on the circles on the above picture to discover our assisted diffusion model in details

Model description in few words :

We do not know what is the mechanism behind nanotube formation. We can suppose they are made of lipid membrane within a cell-wall like matrix, as suggested by the original electron microscopy experiment. When the membrane of the two cells fuse, there might be a difference of tension between the two phospholipid bilayers. This phenomenon might lead to a movement of lipids from one membrane to the other. The newly arrived phospholipids change the membrane tension of the bacterium. As a consequence, they change the internal Laplace pressure ΔPLap of the bacterium.

where τ is membrane tension, R is a radius of bacterium.

A simple analogy of clothesline can help to understand what is happening. You need to pull more your clothesline to put more clothes on it. When you pull the rope by two ends you create a tension. The bigger the tension, the more weight (pressure) you can put on the rope.

All of this will lead to establishing the pressure difference at the tube extremities and we will get a Poiseuille's flow. Constituents diluted in water will move from one cell to another unidirectionally and faster than by simple diffusion. This is a fast process that we have named the "assisted diffusion".

The assisted diffusion model in 3 bullet points:

  • Characteristic time of the process is about 100 ns
  • The effect strongly depends on the initial phospholipid distribution on the membrane of two connected bacteria
  • The phenomenon predicts the flux of only 0.1 % of the cytoplasme, not enough to explain the GFP experiment of the original paper

We have done a back of the envelope calculation to see whether an order of magnitude is acceptable.

References

  1. Intercellular Nanotubes Mediate Bacterial Communication, Dubey and Ben-Yehuda, Cell, 2011, available here
  2. BioNumbers here



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