 speaker. He's from ICTP and he has the longest title of the talk in the workshop. Navas please. Thank you Ali and thank you all. So yeah it's pretty long so I will try to make you understand better during the talk. So I will talk about today most of the my PhD work carried out at ICTP under the supervision of Ihasan Ali and Ralf Kapavar and a couple of slides I will talk about with my work that is done in my post PhD studies with lab of Edgar Olden. So why glutamine? So I have to build a bit of motivation. So from almost one and a half decades there is an interesting field of research which are trying to understand the intrinsic fluorescence of protein. So actually if you shine a light on protein and it intrinsically glow it means that it contain intrinsic chromophore which are the three amino acid out of the 20 and these amino acids are aromatic in nature and they have the density to absorb in near UV and emit in the visible. So this picture was true till 2004 but later on in the lab of Gupta Sharma lab when the Shukla and the co-worker also see intrinsic fluorescence of crystals of lysosine which even don't contain the aromatic amino acid. So this unconventional emission protein really puzzled many people and later on people try to understand what is the origin of this fluorescence and interestingly this kind of fluorescence emerging like during aggregation process and it is if you see like it is a function of aggregation time the fluorescence intensity increase and this observe also in other complex system like amyloid fibrils. These are those architecture which are involved in neurodegenerative diseases and they have also similar kind of emission which is non-aromatic. So the commonality in this kind of structure which emit this non-aromatic fluorescence is the presence of dense network of hydrogen bond. So then our collaborator in the Cambridge came up with some really simple system like glutamine. So in its crystalline form glutamine contain four amino acid which are connected through hydrogen bond and they try to do experiment fluorescence experiment on this simple system. While during the incubation they observe one interesting thing like the algalutamine actually chemically transform into a new structure which was unknown before which has completely different chemistry than the glutamine. It contain very very short hydrogen bond which is complex with ammonia mine and it also has crystalline form and its fluorescence characteristic is similar to what I showed you before for the complex other protein architecture. So this impose a very interesting question like a chemically different structure show similar photophysics why. So then my PhD project is now actually work in two direction. In one direction I was applying theoretical tool to understand the molecular origin of the non-aromatic fluorescence and using the glutamine aggregates because the data we have from our Cambridge colleagues. So this needs a lot of a lot of tools like to discuss the ground state properties excited state and then see what are the role of hydrogen bond network and if there is some other nuclear interaction coordinate which are involved in making electronic excitations such as proton transfer. So this is one part of my work and today I'm not talking at all about this and if someone is interested to this we can discuss maybe in emails or in Skype but I will do another part because this aggregation mechanism happen in accurate solution. So what is the role of solvent modulating the structural properties of this system are in journal to proteins. So today I will talk about this. So I look at the structure dynamics and interactions of water at these glutamine interfaces as these are very simple system like their single amino acid same kind of species. So it provides an excellent system to study the interfacial property. So what kind of the questions that one can answer for example water in a in a neat water it's like a homogeneous system it has many different types of dynamics such as like vibrations liberations and stretches and how these different dynamical modes of the time scale associated with the dynamics will change when the water is in the hydration shell in the complex biomolecules such as protein, DNA, and lipids. Okay so we use the glutamine surfaces so we just periodically repeat the units are left glutamine in three different production to generate three different surface and we so we face one face of the glutamine to the water and run long simulations using a Gromax package and try to understand how the different surface which are different in their chemical nature and also the geometry so how this alter the structure and the dynamics of the water. So first quick thing is to look what also the Ricardo was showing for his system to see some static quantities such as like density profile or the charge of the mass density profile. So due to the different chemistry and the feature of each surface so water attain a complete different structure which you can see from the density profile for example in the surface too you have a double layer of water at the interface also the surface three has a sharp shoulder double layer shoulder and surface one is have completely different structure. Similarly the water exchange dynamics when it's in the hydration shell are also completely different and they are slave also to the heterogeneous environment which a surface provide to the water so we compute residence time so the residence time of water like how long a water continuously stay in the hydration shell of each surface and then we fit these residence time curves with the function shown here which contain like three exponential one spatch exponential and the two normal exponential so it shows that they are different timescale associated with the water exchange dynamics sorry for the gamma it is in the exponent so gamma is tell you like how heterogeneous is the decay so if the gamma value is less than one so it is like a glassy type of environment and if it is equal to one it's like a normal decay so each surface actually provide a glassy heterogeneous environment with different type of gamma and as you see like these glutamine surface sorry they are very hydrophilic so the timescale of the exchange dynamics they are quite long so we also check like other things rotational dynamics or translational dynamics and the surface has like some highly hydrophilic pockets where water can trap and it's rotationally frozen very long time to make rotational flicks so we also look at the rotational dynamics and we fit the curve with also stretch exponential and there is also a degree of heterogeneity heterogeneity in the in the rotational dynamics of the water so from now actually I want to add a few slides on top of the roman talks that you listened yesterday on the first passage time so for these surfaces we also look at the first passage time of the water and here actually I will go slowly maybe you are seeing the movie so the roman showed you the picture on the right so the first passage time of the water is like the when a water hit a boundary first time so not it's time and in a real system you see like on the left where I show you a movie so it's a complex surface and we assign clock to each water molecule and the roman built a way to infer the diffusion which he showed you yesterday on the on the basis of the first passage point first passage time statistic but what did he tell you 8 minutes left yeah okay so what he didn't explain is that like this first page in first passage time statistics give you much more particularly like it can probe the surface chemistry and geometry of the underlying surface so you see like down the x and the y skin so we look at the first passage time along the x and the y in the columns and you see it's beautifully capture the periodicity of the of the surface and also the chemistry for example the peaks you can see here in the x skin like the large peaks that corresponding to those pockets where you see strong charge groups are there and similar it's repeat itself and similar into the y axis so you can see there is a pattern which is completely captured by this dynamical dynamical matrix so we used here only the translational degrees of freedom so we just look at the water translational motion but this could be much more rich for example we didn't look at all means if there are fingerprints of rotational dynamics over the time scale where water can make flips and it's also captured some kind of surface chemistry or some kind of it's topography there's also maybe at very very short time scale there are also water vibrational modes and one can assign also clock to the water vibrational modes so this is very very very like a rich problem but the appreciation is like that these are we are looking at like picoseconds and a few angstrom the length scales are few so this is the resolution at like the few angstrom like hydrogen bond distance and the time scales like they are in picosecond so that is one thing that I add on top of the roman talk that we did yesterday and you can see now here for example for the three surfaces how the first passage time actually captured the feature of the underlying surface so on the on the left side you see the 2d density okay it is a static metric you take many many snapshot and average your time so it will tell you what are the underlying surface is but under on the right you the column you can see it is the mean first passage time which you can see so it's tell you a bit more detail about the about the underlying surface so the conclusion is like that the statistics of the m mfpt the mean first passage time of water molecule can provide the fingerprints of the underlying surface it's periodicity or it's chemistry and there are much more to look about it for example in this work we only we only did like 1d and I think 2d escape of water but one can also look at for example the first passage time in a cage or in a sphere we didn't do it yet maybe it will be more more interesting and also for example I have a question is there an experimental evidence for mfpt measurement or so not yet for this resolution for example this atomic i'd say resolution or this picosecond times but I don't know for other complex system like a big micro system and long time scale it may be an active matter there are some experiment but not not yet so how do you validate your result is there any it's a question and actually we discuss it a lot I don't know at the moment means how it experimentally can be probed maybe there's some new transcaping experiment can do it but I'm not sure like what is the method to do this maybe Ali Ali as an Ali can add some comments in this okay so yeah so with this actually I'm done and thank you for your patience okay thank you very much to be on time and for your interesting talk so we have time to ask two questions I have one question yes now what can you come back to your slide nine slide number nine yeah yeah yeah here you show very nice pictures of the formation of water near the tree surfaces but I didn't get the point that what's the difference between the structures of these aggregations that yeah so okay this is just for I so I am showing you here water within say 3.5 angstrom or 5 angstrom because a snapshot but it is like the actual profile the density profile is above so you where you can see like how as a function of sea the water density is is changing so this is just an illustration like how water actually adopt the first few layers of water actually adopt what is the topography of the surface for example if you see the surface three you have like you can see that the water has a current way because it's a feature of the surface and in the surface two you can see a little more penetration of the water which you can also appreciate with this double layer on the top so it's just for you know showing you like okay what is the resolution of I mean the s-lice the thickness of the s-lice yeah okay okay so I use like a half angstrom half angstrom yeah so the box is like say is I just want to remember how much 120 angstrom I think so I make like 240 slices and when you go to smaller size you probably I did check this but I yeah I try first one angstrom so it was too smooth and then I go with slowly to 0.8 to then 0.5 and I think I check a bit more and then it's much more noise so I then I stick with 0.5 and yeah and as Neda said it seems that the water between two proteins are very well structured yeah yeah as I told you it's very hydrophilic and it's it's depend upon like how the surface host means what are the pockets are there what is the geometrical feature so the first few water layer what I'm showing they almost adopt the same feature of the surface okay thank you any more question no thank you very much yes please I have a question what do you choose glutamine just due to aggregation or no okay the aggregation mechanism actually that is done on the experiment that I told you before and that is for that their fluorescence experiment we also tried not aggregation but we use also like concentrated solution of of the glutamine to probe like a pre-nucleation condition and the result I don't have here we can discuss it later where you can see that with water there is also glutamine in the solution which diffuse into the hydration shell and form like a complex jelly type of interface which which is like a cloudy environment for water and we look at the same density and exchange dynamics of water in the cloudy system so we can discuss it if you want okay great thank you okay thank you thank you very much now was uh so