 Okay I introduce myself it's very difficult to pronounce I know okay let's share my window my screen are you seeing my presentation yes can you see my okay that's good my name is Muhammad Rizad you can people call me Rizal that's much simpler and I first of all I would like to thank Edgar Ali and Ali for organizing this interesting conference I'm going to use my time to give an overview of some projects that we are dealing with right now of course I will not go very deep on this project because the number of the project that's and time that I have but I would like to introduce my group that's soft condensed matter group at Shariff University of Technology and where we are interested to anything soft from molecules to human and just starting from the molecules I have to say that's mostly we do molecular dynamic simulation of biological systems and for the just I would like to give a short advertisement for the treat presentation that's my group we'll have in the next days the starting from from the net us work that is thermal conductivity of the cell membrane that's in somehow if we're looking at the title of the conference this seems most relevant work of my group to the conference it has water heat noise and is important to the life as we know that the temperature is very important and to the life and if the temperature is important then the temperature difference is important and then the thermal conductivity is important and is going to talk about the important how thermal conductivity of the membranes can be affected by presence of the other kind of the molecules then the next talk is Najla's work that's he she will say us about the how we should we care about the change of the environment when we are calculating free energy in when a molecule is going to pass through the membrane that's a very important process because for example if the some draw if some drives are going to reach the internal space of the cell it has to pass from the membrane then it feels a barrier free energy barrier when passing the membrane and the question is when we are trying to calculate the free energy of this of such kind of the process and the molecule the drug is starting to move in a water environment and then goes inside the membrane the environment is changing then the partial chart it's passing is changing during the simulations but usually people are not care about the this partial chart and Najla will say us how we can switch from one force field to other force field along the simulation the third type is giving is to is being by Maryam Azimzadeh she was my postdoc in the group and right now assistant professor in Shahid Bayesh University and Maryam is going to say how sugar and glycan are important in immune system of human body that's all of these talks has been scheduled to be presented in on friday and just know i would like to go to the other researchers of the other researchers that our current here is doing in the group starting with Zahra's Zahra is a PhD student senior PhD students is going she's going to defend in couple of the month and she's working in a statistical mechanics of linear catenines when we say the catenines that means talking about a chain of some rings polymers that are connected to each other and the number of the chain rings if is n we call that linear n catenines in sometimes you can have branched catenines and the question that Zahra is trying is answered is how radius of the gyration of this kind of the chain are scaled by m the number of the beads inside in any ring and then n the number of the rings along the chain and well with a florida type theory she could find that the exponents are different for m and n mu and nu 0.64 for m and 0.6 for n and with huge simulations she could show that the results of the simulation is good agreement with the this story that this simple Ferrari approximation that we have for the catenines and here you can see that's the difference of the radius of gyration in terms of changing the m and also n and here you can see that's a synthetic values as approaching these numbers that is very good in good agreement with approximation also she looked at the effect of solvent quality the lambda parameter here is a parameter that's controlling the interaction between the then our Jones interaction between the particles in somehow it's presenting quality of solvent and she could find the theta transition and look at the look at the behavior of the chain around this data point. What do you mean by quality? Why do you call it quality of the solvent? Actually we in this simulation is a coarse current simulation that's here we don't have water and all of the effect of the water and the solvent comes in just with the interaction that we have between the effective interaction that we have between the okay just we control in the board and the distance parameter and okay that's okay and also there are some other results in this paper that she published in soft matter recently if you are interested in that point. The other research of the group that we are dealing with that for a long time is a model that we call that virtual cell model starting with the work of the summer students few years ago and now Ali Farno the PhD student of the group she's the main person in developing the model and also the software and we have introduced the model in this paper in 2017 that show that's how this virtual cell that we have introduced is able to show elasticity and deformation of the cells when it's sitting in different kinds of the substrate and there is a github right now for for the software that is available for anybody but the model it has not actually the software has not been released officially yet and the model is consists of the different components of the cell membrane that's we have two membranes one external membrane one necklace membrane and a viscoelastic media that fills the space between two membranes and that is representing cytoskeleton of the cell and some chains that's our camp are sitting inside the necklace representing the neclosomes structure inside the cell and if you put all together then we have a virtual cell that's with considering a substrate that's representing ECM we can look at the interaction of the cell with the different kind of the surfaces for example here you can see how it changes the shape when it's sitting on a hard or soft substrate and I'm not sure that the movie are seeing well that's because of the can you see the movie yes okay yeah okay it's good and also the model is good in prediction of the seam cell structure a shape when we put the cell above a different kind of the substrate with the different topology that's people are able to do that in the experiments and we have shown that the model is in good agreement with the experiments in such a way now we are doing with these models a few projects chromatin dynamics inside the necklace is the main project of alipharno these in collaboration it's in collaboration with alphe ever as in leon cell mobility is the something that's such a sort of my mastery students is introducing to the model that's the model this object can move in the according to the some difference in the properties of the substrate or some chemical arounds that so we can it can show the chemotaxis or neurotaxis or topotaxis or something like that and why virus budding is something that's what she used that did as the mastery students and now two undergrads are going to continue that's for all is doing all for all these projects we use this virtual simulator the other thing that's now we can go through is from activity of a cell we can go to the activity of the many cells when we have many cells that are growing above the surface for example this kind of the bacteria that are growing we have the culture of this bacteria and you see that's in high concentration they are making some pneumatic phases like pneumatic phase in liquid crystals but in this case because the objects are alive and growing we have some kind of the activity they are moving and the stress is going to increase in some parts when there are more bacteria there and this kind of activity can affect the dynamics of topological defects and the is kind of the media we call it active pneumatic we actually learn from this paper that's if we would like to look at the pneumatic dynamics of the active matter active pneumatics we can start from Ericsson Leslie Torio for pneumatic dynamics of the liquid crystals three the equations are the same the diffusion equation now we just take the equation with the terms of for external pressure and internal stress that stress is defined in that such a way and a term an equation that's governing on the behavior of the pneumatic order parameter and when we are going to go from liquid crystal passive liquid crystal to active pneumatics we have to add two source terms to diffusion and stress because by growing the particles the concentration is not conserved we have a production of the particles and the when the particles are conducting the stress in that point is increasing adding these two source terms we have a more complicated usually solving the pneumatic dynamics equation is very complicated non-linear equation but having these two source terms makes the problem a little more complicated and we are doing we now have some kind of the um simulate sorry what we have some kind of a kind of different simulation that's solved to solve the equation to see that how the defects are active this is a initial condition for the system that we have and you this is for the director field and you can see some defects a political defects plus mine half plus half and minus half and minus half and here you can see the lost field of the this active media and we now see that's a how the activity can produce some kind of the movements and sometimes annihilation of the charge to political to political charges and something that's we are working at that point right now to see the activity of the defects in this kind of the active pneumatics Muhammad Fazer Zadeh and Ali Reza Hashemi are two master students working in that project excuse me can I ask a question yes of course what is the boundary condition here in this simulation here we have the fixed boundary condition but what we can do that's the same with the periodic boundary condition also okay so you see a similar thing with yes that's okay we can do we can make this is periodic but in this movie it's fixed boundary condition thanks here we come and the next one is something very close as years work that's when we have a particle moving in space and have the collective world is called that active media active matter and we are all familiar with we check model that's have a alignment term when the particle are moving any particle would like to move in the direction of the particle in the neighborhood and what the question is when they are approaching each other and what can control that's we that we avoid a crash between the particles these two birds when they are flying we don't they don't like to crash in the sky and there is some kind of the repulsion interaction that is applying to the particles in some kind of the torque that's change the direction of the movement when they are approaching each other and with this kind this model we have shown before that's the work that's Hamid Sayid al-Adid in a few years ago that's we can reproduce the structure four fold symmetry defects of swimming bacteria in confined environment in the our simulations that's something that we know we are interested if we go to the three dimensions and start with the same model in three dimensions and alitayi master is doing that we can see that and use the same model we can see that the all of the features of 2d model is preserved here again we have symmetry breaking due to velocity alignment we have flocking but in the three dimension there is something very interesting that's we can have big turn something that's us here told us that is in interest of the people working that's a kind of this model and just to see how it's a big turn this is a artistic representation of the result of Ali just you can forget the background but the particles are moving in a peric boundary condition and you can see how the big turn appears in the movement of the this particle is like remembering of the bird and just as you are seeing this movie I would like to thank our collaborators Ali Hassan Ali Ralfa Perez, Christos Likos, Mikael Loon and Murtaza Mahmoudi that's all are helping us in the different projects that I have presented here if thank you for your attention thank you very nice very much sorry thank you very much for this nice talk we have time for a couple of questions can I ask another one sorry if you go back to the 2d picture yeah this one is it like empty in the middle yes yes there is and even in the experiment you you can see that there is a low concentration in the middle okay but is there a reason for that just because because there's some kind of the alignment the particle have with the walls the walls are here we have a confinement and the particle when approaching the wall moving in the direction of the walls and always I would like they would like to stay in the borders and is now there is no reason to come inside okay yeah thank you can I ask a question it's um I I would like to know more about this virtual simulator model what is it based on and what kind of properties can we find is it only for the whole behavior of the cell membrane and or we can see some interactions between cell and something else and can you explain a little more thank you yes and as I thought that we have a triangulated membrane that has everything is doing in here we do MD simulation for the any part and nodes that we have here there is a mass for any node and we have all of the kind of the interaction that we need here for the triangulated membrane we have both bending rigidity and young modulus between the uh links and to uh present a membrane and there is some kind of the Monte Carlo jumps between the links that's produced some kind of the fluidity for the membrane for viscoelastic media we use uh you walk uh Maxwell model to to reproduce the real the correct rheology of the cell and for the uh chains that which are representing the chromatines we just have a model of the bead and the spring that's we put all together to make them chain all of the all the parameters come from the experiments for example the bending the young modulus the rheology of the cell all comes from the uh experimental data and just for the uh adhesion with the uh substrate we have some points in the between the surfaces and the membrane that's can produce can we can we can have a link or we can have a broken link between them that's all of the things that we need and we this uh interaction that we have we just let the cell sit on the surface here for example the membrane even the substrate is has some kind of the uh a stiffness here is really stiff is a software and with some kind of the viscoelastic media we represent the substrate also