 Well, I'm the next speaker. Let me close that. Okay, so I hope you can all hear me clearly. So good morning. My name is Ali Hassan Ali. And what I'm going to tell you about today is sort of a different topic from the first one, but complimentary. And the theme of the talk is why the solvent bath matters in biology. Actually, this was an affirmation. I should be asking the question, does the solvent bath matter in biology? And hopefully I can convince you of that by the end of this talk. And so, Angelo, nice to introduce some of the beginning of what constitutes biological systems, biological matter. And so we're all very familiar in this audience with biological function being attributed to proteins, to DNA and other types of biomolecules. And I took this picture from Rob Phillips' textbook, Physical Biology of the Cell, which shows a cartoon of how a cell is depicted to look like. And what you wanna take away from this picture is that often these pictures of cells are shown, sometimes in very isolated conditions. So you see single protein, single DNA. But in actuality, they're of course very crowded. And they're crowded with a lot of organic matters, somehow like an organic soup. And the soup is actually what I'm going to talk about to tell you about today, which is that the environment in which biological materials live in is an aqueous solution. It's made up of water and ions. And the water and the ions play a very, very important role in biological. And so just to give you a sense of the numbers and why it matters to think about the environment in terms of the water of biomolecules. These are sort of typical numbers of the number of proteins, the number of ions and the number of water molecules in a single cell. And if you do a very simple calculation, what you would see is that the typical spacing between proteins, for example, is on the order of 10 nanometers, which is not large. And in between those 10 nanometers is water and ions. And so biomolecules, even though you may see them as dry in the gas phase are actually hydrated and water can play a role in many different ways. So just to give you some examples to motivate this a bit better. So our ultimate destiny is this picture on the left here of going back to bones. And it turns out that as you, of course, age, the strength, the elasticity of your bones changes. And if you were to take a bone and you would break it down and go all the way to the nanometer length scale, you would find water molecules and different levels of this architecture. And so bones are made up of an important protein and a mineral. So the protein is called collagen with a mineral called hydroxyapatite is a calcium phosphate mineral and intercalating this collagen and mineral are these things known as structural water molecules. So these are water molecules that stabilize the structure. They help lubricate the bone proteins. And that's sort of the general sort of accepted idea now of the role of water is that it acts as a very important lubricant. And this changes both the thermodynamics of your system as well as the dynamics. I just wanna point out one thing here. There's these words that are used here is loosely bound water and tightly bound water. And so loosely refer to the strength of the interactions between the water and the biomolecule. And there's been a lot of discussion in the literature in the field as to how much water is affected by biomaterials. And so one of the questions that I will try to address and show you some data on is by how much does water slow down near biomaterials? Are there some general rules? Is it the same around different types of biomolecules? And does this slow down have any possible biological implications? So that's a first example of where water plays an important role in the architecture of bones. Another one that's interesting to think about is what's inside your brain? And so this is an example of two pictures of a brain. On the left side, it's a normal brain. On the right side, it's a brain of a patient who suffers from a neurodegenerative disease called Alzheimer's. And it's well appreciated that these neurodegenerative diseases are somehow linked to the aggregation of biomolecules or proteins. And when they aggregate together, they form these fiber-like objects and that are often stabilized by these beta sheet-like structures. And what is often found also in these fibrillar or architectures are water molecules. And so one of the important messages that I want to give you here is that many of these biological architectures, biological machineries that we talk about, we see are actually involved a combination of both water and peptide or protein-hydrogen bond networks. Okay, so because water has attracted a lot of interest from people from different fields over a century, it has also been subject to a lot of controversy. And so I like to ask this rhetorical question, which is, you know, water, is it mythology or really a weird liquid? And I'm just showing you a couple of examples here of let's say relatively recent articles on the left side. These are more, let's say less biological, more physical chemistry-oriented topics related to water where there's a big debate right now on what is the pH, if that's even a valid concept for an interface, what is the pH of the surface of water? And you see this from these two different titles. So there's a lot of controversy of understanding the dielectric properties of the air-water interface. So the surface of water. And at the same time, there's been a lot of debate and controversies about the actual structure of water itself, as you can see from this rather provocative title from the Goddard group. So on the right side, or my right side, I'm showing you a couple of papers related to controversies about how water is different near biological systems. And this is why there's been a lot of interest in this area. So this is a notion that was introduced by Ahmed Zewail. So Ahmed Zewail was the late Ahmed Zewail Goddard, the Nobel Prize in Chemistry for his work on femtosecond spectroscopy. And he introduced this notion of biological water. So water near a protein was named biological because it was very, very different from that in the bulk. And there's been a lot of debate about whether this is true. And this is a nice perspective that I subscribe to more, which is written by Pavel Youngworth on whether they should be thought of as biological water or rather water in biology. And what I will hopefully try and show you is something that rests more on the latter side, which is rather water in biology compared to biological water. Okay, so there we go. So before I get into some specifics about what I wanna tell you about, I thought it would be useful to kind of build our intuitions a bit about why this is an interesting problem and what are the questions and things one thinks about when you put molecules in water. And so I've been interested for a long time in trying to understand the physical chemistry of dissolving molecules in water. So if we think of taking something at a macroscopic scale like the surface of the sea in contact with the air and you want to put or take a gas like carbon dioxide and bring it from the air through the interface into the water and you want to understand things like the thermodynamics associated with the kinetics of this process. Molecular dynamics simulations have played a very, very important role in trying to understand this. And so there are several processes that happen when you want to actually have to think about when you put a molecule in water. The first one is of course, for example, in a molecule like carbon dioxide, the oxygen and the carbon atoms will interact very differently with the water because of their different electronegativities. And so that will determine the type of the strengths of the relative interactions that water molecules will make with that solute. And another thing is that if you want to put a molecule like CO2 into water, possibly this would be more important for bigger molecules like proteins, something has to happen around the protein or the solute in order to accommodate that molecule to sit inside it. So you have to create some space inside and then you have to turn on or change the interactions that exist between the solute and the water. And so MD simulations and the entire MD, let's say, culture of doing numerical simulations has played a very instrumental role in trying to understand these processes. Now, why is it, what's the challenge? What's interesting and what are the kind of the open, let's say, questions? So if you go back to this, I showed you this trajectory of a, this is a short trajectory of an MD simulation of water molecules, the building block of those water molecules are these things known as hydrogen bonds, which I'm sure you're all familiar with and what makes the hydrogen bond a very interesting object and also a challenging object to understand is that it is, while it is mostly, or let's say 70 to 80% of it is driven by classical electrostatics, it has a non-insignificant contribution of quantum mechanical effects in evolving both the electrons and the nuclei. And so this is another point I just wanted to stress is that sometimes in biological systems, we forget that, of course, biological assemblies, water are all made up of electrons and protons. And so this opens up a very different angle on sort of interesting areas and open questions on the electronic and nuclear properties of hydrogen bonded systems. And so what makes understanding fluctuations of hydrogen bond networks in water interesting and challenging, which I've been interested in for a while is that it involves the coupling of several different things. There are density fluctuations occurring on different length scales because the hydrogen bond is a directed interaction. So, and it's directed because of the position of where the proton sits relative to the two waters. It's a directed interaction. So it can form a very complex, dynamically evolving topology. And coupled to that is electronic and nuclear fluctuations. And so the electrons and the protons can also respond and fluctuate in non-trivial ways. And so if you're a physical chemist or if you're not, you've maybe encountered ideas and notions of things like reorganization energy in Marcus theory, solving reorganization in hydrophobic salvation. And so these are notions and ideas that we've known about for decades, right? But one of the big challenges in this field that still remains is trying to understand the molecular origins of these fluctuations and one of the big challenges is that, of course, there are many of these processes that are entropic effects and quantifying many body entropic effects from the solvent are extremely difficult, okay? Okay, so one last point on the introduction side. So you're going to hear maybe a bit about this in some of the other talks. There are let's say two classes of molecular dynamics, broadly speaking, the one can do one where you treat the particles as classical particles and you also ignore the electronic degrees of freedom and you just evolve the particles with Newtonian equations of motion. And on the other side, you can also do ab initio approaches. So where you treat the many body electronic and nuclear wave function. So you can study quantum mechanical effects. And I just wanted to make a brief comment here that this is an example of a simulation of a DNA. So this is a DNA dimer that is initially spurious. So it has two covalent bonds attached to each other and then there's some chemistry that happens, okay? Don't worry about the details of the chemistry just two bonds break. And one of the things that has grown in appreciation a lot over the last decade is that a lot of the chemistry that happens to biomolecules happens because it is facilitated by fluctuations of the solvent. And these fluctuations of the solvent are collective. And this is why there's a lot of interest in trying to understand how these free energy landscapes of these many body systems look like. And I think you're gonna hear a bit about some of this later on during the week. Okay, so basically the outline of what I want to tell you about today with that brief introduction is the following. So how does the question is the following? So I have a biomaterial. I have water in contact with that biomaterial. And the question is what happens to the water molecules in this vicinity here close to the biomaterial? So there are two questions. The first one is what is the magnitude of that slowdown if there is a slowdown that I alluded to earlier in the talk. And secondly, what is the spatial extent of that slowdown? So that's number one. Number two, are there some interesting unexpected dielectric properties that can occur at these interfaces? So the first system, so this was a work with a former PhD student, CISA actually was in the condensed matter group, Noaz Keisarani and I was a postdoc at Mines. And so we were interested in trying to understand how does water change near glutamine, so glutamine amino acid surfaces. And so these are the three crystallographic surfaces, the 1000010 and 001 of glutamine. And these are nice model system because they're crystals and one can sort of isolate without dealing with the fluctuations of the protein itself how the water dynamics changes. So this is on the more practical side, on the biological side, again, these aggregates have been noted down as playing a role in triggering neurodegenerative diseases. So we did some classical molecular dynamic simulations and what I'm showing you here are, I want you to focus on the black solid curves. The black solid curves are the water densities near each surface. And so far away from the surface you have bulk water but as you come close to the interface you see that there's some, there are oscillations, there's structuring. And so near most biological interfaces if you would look at the density of water near any surface actually you would see some structuring going on because the interface introduces, perturbs the density. And but what's interesting here that I want you to take note of is that there's a lot of water that penetrates into the crystal, okay? And this is seen by these, in these first peaks of the water density profile. So how does this trapped or how does this water structuring affect the dynamics? And so what you're seeing here on the left is are basically residence time correlation functions. So these measure how long it takes for how long does a water molecule continuously remain in the near the surface? And so what's interesting here is you see that all the three surfaces have very different water dynamics and one in particular this one here that one in black has very, very long turnover times. So water molecules remain trapped. They get intercalated into the surface of the crystal on very, very long time scales and they resemble, not exactly that but they resemble very glassy and what you'd expect from very glassy dynamics. Now, what, who cares? Why, so what's the big deal if water is trapped near the interface? Well, there've been the two points that I want you to keep in mind on the broader implications. One is that, you know, trapped water does have an implication on how drugs can bind to proteins especially if you have these long lived residence time for waters. And number two is if you were thinking about nucleation of an interface, having water molecules that are moving on a very slow time scale can change sort of the rate limiting step that's needed before you can grow an interface or aggregate two systems in solution. So we started talking to one of my colleagues here at ICDP who's an expert in stochastic thermodynamics at Garoldon. And one of the things we were interested is well, can we look at the dynamics of water around one of these surfaces and use that as an imaging to say something about how the surface looks like. And so in stochastic thermodynamics or stochastic, I should say stochastic theory, there's a well-established idea of something known as a first passage time statistics. And the idea is if you have a surface and you've got, you think of your water molecules as random walkers moving as you move away from the surface, one can turn on a clock depending on where you're starting pointers and where you're ending pointers. And you can look at the statistics of these water molecules diffusing away from that interface. And so, and you can also then recast this problem as a one-dimensional Smolakowski equation for inhomogeneous diffusion. And there's a nice relationship between the first passage time and the local diffusion constant. And so this is what we get for one of the surfaces. So the gray curve here is the free energy profile of the solvent. So it comes from the density minus KBT log of the density. And the blue here is the inferred diffusion constant. And what you should take away from this is that the diffusion constant changes from the bulk right to the surface on a length scale of about one nanometers. So there's this one nanometer region near the surface where the diffusion constant gets slowed down by a factor of two to three, let's say roughly. And this tends to be the, let's say the recurring pattern across a range of different biological systems. So the slowdown of the diffusion constant roughly is about a factor of two to three. And is in a region that's roughly about a nanometer. Of course, this is not a general rule, but at least with many of the systems we've looked at, that's what we find. Okay, so maybe I'll skip this because just to be in the interest of time, I'll just mention one last thing about this. So I mentioned structural water molecules when I was talking about the bones. And so structural water molecules in trapped in these architectures in these aggregates can also play a very important role in changing protonation state. As an example of a situation where you have a water molecule trapped in a structure and this changes the zwitterionic state of the two termini that are interacting. Okay, so I guess in the interest of time, I will try to quickly go through the second part. And so I just wanna give you an example of, so in this previous work, that's a very little contact with the experiments. And I think it's useful to see an example where simulation experiments can actually go hand in hand and work very well together. And so this is a project related to understanding the chemistry of soap films, okay? So this is a soap film basically looks like something like this. So you have a layer of water and you have surfactant. So you have these amphiphilic molecules. So amphiphilic molecules are things that have a hydrophobic and a hydrophilic side. And so we were interested in understanding the structure and dynamics of these surfactant water interfaces. And in particular, to see if one can do any interesting chemistry at these interfaces. So I will skip the validation. So we can compare things like surface tensions compared to an X-ray. We get a reasonably good agreement between the theory and experiment. These are the type of cartoons that maybe some of you have seen of how surfactant water interfaces or soap films look like they're often drawn like this. But one of the things that we find for this particular surfactant that we use is that there's a lot of co-penetration of water into the surfactant. So it's very heterogeneous. It's a very fluxional object. And so that's why this is the water density here shown together with the hydrophobic groups and the hydrophilic groups. So a lot of water penetrates into the surfactant. Our collaborators, we have some collaborators at Amalf in the Netherlands who do vibrational spectroscopy. And so without, it would take another lecture to give you a review on vibrational spectroscopy. But basically this is these spectra, focus on the one on the top here, tell you about the strength of hydrogen bond interactions. So when you go from water, so the air-water interface, so without surfactant to something with the surfactant, you see that there's a big red shift, a red shift in the frequency. And so this means that there are strong interactions forming between the water and the surfactant. And so we can go to our simulations and try to understand this. And what you find is that the water because it's penetrating into the surfactant, you know, forms very stable, a very stable hydrogen bond network together with the surfactant molecules consistent with what is seen in the experiment. So the thing I actually wanted to tell you about the most is in this particular topic is sort of very interesting dielectric properties at these interfaces. And so this is a very heavy slide. You can, all we need to focus on is on this middle panel here. So this middle panel here looks at the electric field. So the net electric field at the interface at the air-water interface, so without surfactant. And that's on the right side, on the left side, it's the electric field at the surfactant water interface. And what you see is that at an interface, as you, no surprise, of course, because of symmetry breaking there's a, you might expect there to be a net electric field, but it's quite large. So in the order of one volt per nanometer, that's just without the surfactant. And with the surfactant, the electric field is also of similar strength, the net electric field, but it comes from the contribution of polarized water molecules as well as surfactant. So the surfactant also contributes to the electric field. And so of course, these are predictions from a simulation. And so we wanted to see what, how do we know that this is true? And so again, we turned to our experimental collaborators who do something known as Kelvin probe experiments. So these are experiments where you come with an electrode and you can measure the surface potential at the interface. And so the agreement is modest between the experiments and the simulation. But the interesting kind of result from this is you can think of this, the dipoles created by the surfactant with this underlying potential in a dielectric continuum model. And what you infer from this with these potentials and with the sudden dipole moment of the surfactant is that the dielectric constant at the interface is very small, okay? And so this is an effective model, but what it tells you is that you have a very polarized medium at the interface that's very different from bulk water. Okay, so I think I'm going to stop here. So basically there may be two or three take home messages that I want to say. The first one is that the first one is basically that water slows down near most biological interfaces. The extent of that slowdown varies depending on the chemistry, but it's not the type of slowdown that has originally thought with some ideas of biological water where people thought there was like a frozen iceberg of water near proteins. So that's the first thing I wanted to tell you about. The second thing is, although I went rather quickly through this, there's a lot of interesting physics and chemistry of understanding how dielectric properties change at interfaces. I focus on a very, very simple system. It's just surfactant water but you can imagine that when you're dealing with more complex proteins, membranes, things get much more interesting and more complicated. And the final message that I wanted to give is that, I think there's a lot of new and interesting chemistry and physics emerging that you are allowed to explore combining and relations as well as advanced data science techniques which you will hear about probably maybe tomorrow. Okay, so that's it for me. I'm happy to take questions now or later on in the afternoon. I guess we have maybe six or seven minutes left. Thank you, Ali. So if you have questions, people, I think there is a question in the chat, Ali. So when you set up an MD simulation of a solid water such as what's a HAP, maybe a hydro, I don't know. What are the important things to consider when energy minimizing and equilibrating the system? Okay, so hydroxyapatite, okay. So well, hydroxyapatite is a rather complicated beast because of all the charges that you're dealing with. So the first thing that's challenging in that system is the force field. So the interaction potentials. And so one has to have a very good control over validating those interaction potentials between water and hydroxyapatite. The other thing to consider is, of course, as far as I remember, the collagen hydroxyapatite system is a very complex, large-scale polymer. So you have to try to, depending on the type of simulation that you use, if you want to do atomistic MD, you have to have a reasonably sized system that one can do. The other thing that comes to mind, when it comes to, I don't know, setting up, equilibrating a system like that again is that you can imagine that in hydroxyapatite, there's a lot of trapped water molecules in the structure. And so that can obviously play a big role in something known as sampling, which you're going to hear about next from Alessandro Lio. So it may take a long time to equilibrate that system. So I would say that the biggest challenge in half water is perhaps the quality of the force fields, because you're dealing with highly very particular electrostatic interactions at the interface. So yeah. So there's another question in the chat. How do you suggest to implement pH of a water solution in biological systems? This is a great question. And my suggestion is not to, no, I'm just kidding. So I think it depends a bit on what you mean by implementing pH. So if you're interested in the thermodynamics of pH, then, and for example, if you're dealing with amino acids, you can, if you know the pH that you're interested in, you know the pKa's of the groups that you're interested in, you can account effectively for the pH in a thermodynamic sense by changing the charge of the protonation states of the system. Now, this can be done in a static way. So where that's kept constant for the whole run, or even better, I believe they are implementations where people have done things on this constant pH simulations. So you can do things from the thermodynamic point of view. From the dynamic point of view, I think it's basically impossible at the moment. And unless you're dealing with very low or very high pH, it's probably not so burdened for protons, because, you know, for example, at pH seven, two protons will be, the concentration is so low that you can essentially get away with just using a box of neutral water molecules. So okay, so maybe I'll just take this last question. So how do you deal with ionization caused by electric field? That's another great question I don't personally. In order to deal with ionization, you need to have a model where you explicitly allow for dissociation. So you allow for protons to dissociate. I think that was probably what you were thinking about when you were thinking about ionization. And so you need either a dissociative water model, which is very, very difficult to have it develop. There are some around, or you have to do something known as ab initio molecular dynamics or Carpenello, yeah, Born-Aupenheimer molecular dynamics, which way you can account for these effects. But in our simulations, we didn't really do that. Okay. I think I'm basically out of time. So please keep these questions for the Q and A later on this afternoon. So I think the next speaker is Alessandro. Alessandro, yes.