Molecular animation – Tech Talk by Drew Berry wehi.tv (2022)

Molecular animation – Tech Talk by Drew Berry wehi.tv (2022) WEHImovies 213K subscribers From a validated medical research institute in Australia Learn how health sources are defined by the World Health Organization 72,596 views Aug 9, 2022 Animation Tech Talk by Drew Berry wehi.tv – AMI.org 23 July 2022 "How to Stop your Molecules Looking Like They ‘Know’ Where to Go – The Problem of Agency in Molecular Animation" A problem that plagues many 3D molecular animations is the way molecules are presented moving around the cell – flying straight to their enzyme destinations as if they know where to go. Drew Berry will present a few of his considerations, tricks and techniques to reduce the appearance of molecular agency, while delivering stochastic-looking moving molecules that are fully under animator control for choreography and storytelling. Session Takeaways: 1. Wrangling time scales at a quadrillionth of a second while making molecules meaningful to watch 2. Wandering randomly while getting there on time Key moments View all Transcript Follow along using the transcript. Show transcript Transcript Search in video 0:00 my name is drew berry and i'm a biomedical animator uh at the walter elizabeth institute of medical research 0:05 which you're seeing in the image just behind me it's australia's leading flagship for 0:12 biomedical research into various diseases such as cancer infection diseases like malaria and 0:18 autoimmune diseases like diabetes i'm going to briefly talk just for a few minutes about my background and 0:25 motivations behind my work and i'm going to show you some examples of my most recent productions and show you some of 0:32 the techniques considerations and technology we're using to build our current animations 0:39 i began my career in science as a cell biologist and microscopist 0:44 where i was fortunate to work in the lab of professor jeremy pickett heaps who specialize in filming single-celled 0:51 organisms using various forms of microscope and time-lapse microscopy 0:56 these are some of the organisms we were studying these are all common all around the world uh in damp soils or in lakes and 1:04 rivers or even in the gutter after a rain these sorts of organisms are everywhere 1:09 and they're all mind-blowing in so many different ways and so this was my initial inspiration and still driving 1:16 passion behind the work that i do is studying and investigating all the 1:21 living life at the cellular level 1:27 part of my background i was also of the first generation that grew up with a 1:32 personal computer in the 1980s late 1980s and early 1990s 1:38 i had access to this machine which is the pivotal machine that changed my life uh called the amiga 1:44 the amiga was way ahead of its time for graphics and sound um and i just became 1:51 totally enthralled with what it was capable of doing most particularly in playing video games 1:57 i loved games like this and exploring how they were recreating these incredible visuals 2:04 i remember when xenon 2 it's a mega blast came out it had all these little uh organic life 2:09 forms and just incredible graphics and also sound as the soundtrack was unbelievable 2:15 i really became very interested in how they were creating these graphics and cracked open 2:21 the game and learnt all the different techniques that the game designers were using at the time 2:27 i remember when shadow of the beast came out i had like an electric shock through me i couldn't believe how realistic and 2:34 3d these graphics were i couldn't imagine graphics getting any better than this 2:40 what i also want to reference is the running loops the the loop of animation that's being used 2:46 for this running character using loops and or seamless loops and endless play is a key feature in video 2:53 game graphics and it's very much something i've always employed in my animation and i'll be referencing that 2:59 in my contemporary work that you'll be seeing in a moment when i first joined wehi i was hired as 3:05 their photoshop guy where i was jazzing up images from the labs and preparing them for scientific journals 3:12 because of my skills in computer graphics i was very very fast and efficient at this kind of work and so i had a lot of spare time on my hands and 3:19 started developing under my own interests uh computer animations that would help reveal and explain some of 3:25 the scientific discoveries that were being made at the institute so the animations i'm going to present 3:31 to you today are on the topic of respiration classic 101 biology topics 3:36 that are usually dreaded by high school and university students and is one that i wanted to transform into a visual 3:43 story where you could see all of the enzymes in action all the way from the sugar molecule glucose 3:49 broken down through glycolysis the citric acid cycle the electron transport chain 3:56 crafted as a visual review of aerobic respiration for high school and university biology education 4:03 topics explored in the animation include glycolysis the citric acid cycle the 4:08 electron transport chain and atp meticulously reconstructed for more than 4:14 100 x-ray crystallography models cryo-electron microscopy molecular 4:20 dynamics simulation and animation respiration reveals step-by-step the 4:26 complete enzyme reaction pathway from glucose to atp 4:34 this work presents the first generation of our gpu gain engine pipeline for 4:40 production of cinematic molecular animation and real-time interactive visualizations 4:48 running real time on a normal gaming pc our pipeline was initially constructed 4:53 to solve the challenge of producing 8k 3d immersive experiences for an advanced 5:00 360 degree dome theater in worshiping sweden 5:06 the same animation pipeline natively supports production of vr and interactive molecular dioramas for 5:12 augmented reality on mobile devices we've exploited the incredible advances 5:19 of video game technology to generate vast molecular landscapes upon a 5:24 foundation of detailed scientific research enabling interactive exploration of 5:30 molecular biology in ultra high resolution detail 5:35 our system brings together scientific models and molecular dynamics simulation 5:40 into autodesk maya software for integration and animation 5:46 then exported to unity game engine for generation of multi-scale animated 5:51 molecular landscapes i'm not going to get too bogged down in 5:57 the details of how our pipeline works except to just give you an outline of the different steps 6:02 that we use for our productions uh the biggest part and most important part is always the research at the beginning and 6:09 gathering all the various forms of data that are available in the published literature uh from the pdb of course 6:15 from the 3d models of proteins molecular dynamic stimulation cryo electron microscopy tomography 3d reconstructions 6:23 and and all the various forms of microscopy these all these different kinds of data we're able to bring together into 6:31 our 3d animation package which in my case is autodesk maya um it's the one 6:36 i've been using since the year 2000 and it is of course very capable if you 6:42 though are looking to get into 3d animation and haven't yet made your choice i would personally recommend you 6:48 have a good look at blender it is uh every bit as capable as far as i can tell as what my autodesk maya goes but 6:55 um i'm really more focused and passionate about the science and the data sets and our pipeline works so not 7:02 currently looking to change once all we've done integration and model building with these data sets in 7:09 autodesk maya we then export to a game engine in our case is unity um 7:16 there are many game engines out there we find unity between very productive and excellent um and 7:22 the animations or the the whole rigs the worlds we're building the molecular worlds we're building then play in real 7:28 time on a normal gaming pc in unity and we can make all sorts of decisions at 7:35 that point about how it's all looking and lighting and so on all in real time and it's just a matter of then capturing 7:41 with a virtual camera what we're seeing in game engine uh with uh to to create a 7:47 either a movie or uh also an animation like a traditional animation or to export to augmented 7:53 reality and virtual reality still linear videos are still my 7:59 personal preference and passion um that's what i enjoy creating as an artist but i do see totally the future 8:05 is real time endless playback of augmented reality and and playing things on game engine 8:13 so one of the key forms of data that we import into uh animation production is 8:18 molecular dynamic simulation um and a person i've long time collaborator of mine is dr mike kuiper uh he is a he 8:28 specializes in molecular dynamic stimulations uh here in melbourne and this these are some of the simulations 8:33 that he's created for me of small molecules so on the left hand side you can see it's atp the molecule atp in a 8:41 molecular dynamics delay simulation surrounded by water molecules and this what i'm on the right hand side 8:48 here is i'm able to extract the atp out of the simulation and i've colorized it 8:53 and prepared it for animation production but all the small molecules you'll be seeing in my animations are have gone 9:00 through a process of molecular dynamic stimulation such as this one to get the 9:06 to capture the way the molecule moves and and exists and vibrates uh 9:12 in in its native environment in the molecular world and use that to populate my animated 9:18 worlds so the animation topic we're going to focus on today is the electron transport 9:24 chain um this is my favorite figure flip my i think what i think is the best illustration out there of the electron 9:31 transport chain and what it shows is the various enzyme complexes involved in 9:36 this this particular pathway these enzymes are embedded in the inner 9:42 mitochondrial membrane which is represented by this blue band here and each of these structures are from 9:49 the protein data bank so they're accurate models of each of these enzyme complexes but what they've done 9:56 in this figure is overlaid the various reactions that are happening throughout these enzymes 10:02 as part of the text here and it really was my job to 10:07 look at each of these steps each of each of these reaction steps and to work out what would those look what would it look 10:13 like so i was using like this figure the protein data bank models for the complexes but i wanted to 10:21 re recreate the location of where these enzymes are placed and to 10:28 reconstruct what each of these chemical reactions would actually look like if we were able to see them 10:34 so i'll begin at the end of this particular pathway with the enzyme on the right hand side there which is the 10:41 classic atp synthase and immensely probably the most popular enzyme for animators to tackle for re 10:49 for creating molecular animation so this is the first bit of data that i went into building my animation this is from 10:56 a paper where they're investigating the 3d structure and conformational changes 11:02 of atv synthase as it's found inside a e coli 11:07 so this is from their figure where on the left hand side is their illustration of what atp synthase all the different 11:14 enzyme parts and on the right hand side is their animated model where they are able to 11:21 capture the atp synthase in three different conformational states of process and then they're morphing 11:28 between each of those different conformational states so i'm able to access this data directly and build 11:36 begin my animation model building with this data at the next level of data 11:42 that goes into building in the animation is something like this this is from a paper where they're using an electron 11:49 microscope to directly observe the atp synthase and what's quite clear from this figure 11:54 is that atp synthase forms in pairs they enter interlocking pairs that are 11:59 embedded in the membrane uh and causes sort of a kink a pinch in the 12:05 inner mitochondrial membrane the measurements and the the all the sort of the details of how the atp 12:12 synthase are getting together uh go directly into building my animation 12:17 at the next scale of data uh this is from a beautiful paper where they're looking at those atp synthase pairs and 12:26 using electron microscope they can see that the atp synthase pairs are forming 12:31 rows along the inner mitochondrial membrane this figure is comparing different organisms 12:38 at the at the bottom you're seeing bottom left is a cow uh atp synthase pears the middle three are of different 12:46 species of yeast and the right hand one is of a potato uh what they're showing is there's various variations in the 12:53 precise positioning and orientations of atp synthase i love those kind of details that include them wherever i can 12:59 in my visualizations so this is my animation of the atp synthase pairs 13:09 it's now animated i'm also mixing in the reactants the the the different 13:14 components the chemistry that's coming in and reacting within the enzyme this is my single model of atp synthase and 13:22 it's all operating on a loop so very much like that video game i was showing earlier 13:28 all of this is built with looping technology so this is now showing the individual 13:34 enzyme and the active site of where the chemistry is being pressed together to form a bond um this is the inner 13:41 rotational motor that is the driving force of the conformational changes of 13:47 atp synthase so this model is now in game engine and i'm 13:52 now able to build the whole world around this particular animation 13:58 for atp synthase i wanted to see if we could take this topic to the next level 14:05 to make it accessible to a wide public but i also wanted the animation to resonate with 14:11 the target audience which is high school kids so i wanted it to be voiced by someone of their age and i also wanted 14:19 to include uh artistic elements which uh are there for to to to 14:25 create a sense of engagement and wonder and a big part of that was the sound design uh for the animation about the play we 14:32 not only use uh foley sound effects we also used uh the middle school choir at 14:38 the school high school where my kids go to to create a musical score to generate a sense of awe and wonder 14:46 about these incredible mind-blowing mechanisms that we're witnessing uh all of my sound design was created by 14:53 the gentleman on the right hand side there frank titus he's been a dear friend of mine since the 1990s uh 15:01 and what you're about to hear is frank's sound design for the animation but also 15:06 a musical score to create a sense of wonder and awe about how incredible these sorts of 15:13 molecular structures are inside of our cells and so here's the final animation 15:18 production for atp synthase it incorporates many different forms of data including microscopy and i'm trying 15:25 to make it accessible engaging for high school students and university level students 15:34 all life on earth depends on this tiny energetic molecule adenosine triphosphate or atp 15:43 atp drives biochemical activity inside your living cells 15:48 and is a key building block of dna and rna 15:54 generating atp for your living cells are mitochondria electrochemical batteries that converts 16:00 energy from the food you eat and oxygen from the air you breathe into atp 16:07 so where does your atp come from 16:12 deep inside your mitochondria rows of molecular motors generate atp 16:18 the molecule essential to all life on earth 16:26 enzymes bring together reactants to form a chemical bond converting mechanical energy into 16:32 chemical energy a ring of enzymes work in step creating 16:40 three molecules of atp with each cycle 16:50 inside the molecular motor a rotating axle powers the sequence 16:57 the axle is attached to a rotary molecular motor moved by the force of protons pushing from the other side of 17:04 the membrane a difference in proton concentration 17:11 propels the molecular mechanism [Music] 17:20 synthesis of atp [Music] 17:25 [Applause] atp drives biochemical activity inside your living cells and is a key building 17:33 block of dna and rna 17:48 so i'm now going to describe to you some of the techniques and considerations that went into 17:54 building this particular animation um all of this was done in game engine so it plays real time on the gaming pc 18:02 uh the way we actually create the animations just creating a virtual camera and saving what the camera is 18:08 seeing um so the slow part is just the file save the rendering is is well beyond real time 18:14 all of this is built using gaming technology principles so everything runs 18:20 on a seamless loop and in fact this entire animation with the camera move everything is a 18:26 seamless loop and can play endlessly um part of crafting this animation is 18:34 how do you represent the brownian stochastic randomness of the molecular soup 18:40 and also make it watchable to a human audience so you have to do some 18:47 manipulations of time obviously but also density so that stuff can be seen otherwise this would be 18:54 a thick soup of extremely fast moving stuff that would be impossible to understand 18:59 um but with building this as a loop on loops what i found was that you can't 19:05 have it being too random too messy too realistic because for the audience it becomes very 19:11 difficult to interpret what you're looking at so there has to be some level of 19:17 of beats of repetition that just humans are able to isolate out of a complex and busy image 19:24 like this uh so you have to it has to be a balance between true realism of 19:29 brownian stochastic behavior and somewhat repetitive um 19:37 watchable type content um all of these structures uh the 19:42 the enzyme itself are from conformational changes uh from the published literature um but then i have 19:49 uh the reactant molecules coming in and having to dock and i'm going to show you the techniques i use to get them to move 19:55 in a brownian style movement like this but then to come in and land at the appropriate time 20:02 and undergo the reactions under a way in a way that is controllable by me to help tell and move the story forward 20:11 so the next enzyme we're going to look at in animation is for enzyme complex 2 20:16 of the electron transport chain this enzyme is also step 6 of the citric acid cycle so it links those two 20:23 pathways this enzyme is embedded in the inner mitochondrial membrane 20:29 and what i'm going to do what i attempt to do with this particular animation is to reveal what all the 20:35 different the different locations of where the chemistry is happening uh but most particularly this activity inside 20:41 the membrane so versus what's shown here in this illustration uh where a chemical 20:47 reaction is just depicted by an arrow from q to qh2 uh i wanted to show what 20:52 that chemistry would look like and what the molecules look like and where precisely the active the chemical 20:59 reactions occurring what that's referring to the letter q is coenzyme q it's a molecule that lives 21:05 inside the membrane but versus the way this is represented here just sort of a mysterious reaction 21:11 depicted by an arrow i wanted to see what that reaction looked like what do these molecules look like and how does 21:16 coenzyme q exist in the membrane so this is a molecular dynamic 21:22 simulation of coenzyme q in a lipid membrane created by dr mike kuiper as a molecular 21:29 dynamic stimulation coenzyme q is represented here as a bollin stick model embedded in the 21:35 membrane and aligns itself all over lipids so it reverses the the lipid membrane 21:42 i of course was able to extract out the behavior of the coenzyme q here and 21:47 incorporate that directly into the animation but already it informed me as to 21:53 how this reaction is uh going where it's located and how this this molecule and 21:59 how the lipids are behaving uh with this chemical reaction part of the 22:04 challenge in representing brownian motion is the time scale 22:10 that a lot of the key events happen at this animation is from a molecular dynamic simulation 22:17 of atp coming in and docking at an active site of a kinesin molecular motor 22:22 and the reason i'm showing it to you is as it's to illustrate the challenge of representing 22:28 true molecular motion and activity the time scales are unimaginably short 22:34 uh this is happening at nanosecond time scales one billionth of a second time steps uh but even at that scale you 22:41 although you can see the atp and how it's behaving and how it's wandering around um you have to wait quite a long 22:48 time for it to actually arrive at the location where it's going to do its reaction 22:54 but if you went for bigger time scales you wouldn't get all these sorts of details so in representing this in animation i'm 23:02 certainly influenced and trying to emulate this look and feel of molecular activity 23:08 but i'm also wanting this the reactions to happen in a timely manner so it's a 23:13 compromise a balance so this is my animation of 23:19 enzyme complex 2 of the electron transport chain or step 6 of the citric acid cycle 23:25 the enzyme itself is embedded in the mitochondrial membrane the enzyme is from x-ray crystallography 23:32 from the pdb the membrane itself is derived from 23:38 molecular dynamics simulation by dr mike kuiper and i've taken his 23:43 molecular dynamic simulations of coenzyme q the pale green molecule in the membrane 23:49 and overlaid or added my own animated uh behavior for how it would traverse and 23:54 travel around inside the membrane i'm also trying to reconstruct the small molecules and give a sense of the 24:00 molecular soup that would be around this enzyme the yellow molecule is succinate this is 24:07 the reactant that's going to come in come arriving from the the citric acid cycle and it undergoes a reaction at the 24:13 top of this enzyme in the circle as you see in the circle here the reaction strips off two electrons 24:20 that then hop through this enzyme to coenzyme q waiting in within the 24:25 membrane so this animation's incorporating various forms of data but i'm really trying to show the location 24:32 and where these reactions are occurring and to give a sense of the the how this 24:38 this enzyme complex works so like my earlier animations this was 24:44 built in game engine with seamless loops so this animation is only actually 10 24:50 seconds long but plays seamlessly so it can work in a classroom situation for a 24:57 teacher to present or for a student to learn from and take the time they need to understand all the various activities 25:02 and reactions that are going on here i'm now going to describe for you the techniques i used for 25:10 controlling this browning behavior of the reactants of succinate coming in and landing it in location where the 25:16 reactions are going to occur and then releasing the products uh this had to i wanted to to have the look and feel of 25:23 molecular dynamics but i needed to happen in a controllable way 25:28 that didn't look like the molecules were directed knew where they would go it looked it looked like it was random 25:34 but it is actually under animated control now the techniques i'm using because i'm a dinosaur um really haven't 25:41 changed too much since the 1990s but they work they're techniques that i know 25:46 all the animation packages can have um so i hope that you can take inspiration and use these own these techniques for 25:53 your own productions so this is um how it looks in maya in my animation 26:00 software uh where our reactants are coming in and landing at the letter n here um so they are um wandering around 26:08 by all arriving in a reasonable amount of time and reacting together and then be released and the arrival and the 26:14 departure of these molecules has the same look and feel that's sort of critical 26:20 for these sorts of visualizations there are a number of techniques i've used over the years to achieve this but the 26:25 simplest is the best so this is the trick i'm using to build these animated rigs 26:31 for making molecules move around in a random brownian style movement but be fully controllable and this technique is 26:38 totally applicable to all the animation packages such as blender or houdini or cinema 4d or indeed maya in maya i'm 26:45 using paint effects it's their tool set for creating random structures and curves and what's really 26:52 nice about paint effects is that it's uh somewhat like a fractal where you can change a seed value and a 26:58 completely new curve is spontaneously generated so what i'm doing is having 27:04 the molecules that be attached to those these these curves as uh motion paths they then travel along through keyframes 27:11 i control they're moving along those paths and then change the seed value to change the path out for the molecule 27:18 versus the path in what i found over the years is that you have to balance your messy random 27:26 looking behavior with some repetition some 27:31 repeats that of some cycles that makes this watchable and interpretable by humans so 27:37 it's it has to be a balance between something that's watchable and something that's truly brownian and messy random 27:42 random behavior the next animation rig i'm going to 27:49 describe for you is for this beast a massive enzyme complex called pyruvate 27:54 dehydrogenase and it connects it does a number of reactions that connect glycolysis with the citric acid 28:01 cycle this was a particularly difficult and challenging animation to build or animation rigged 28:07 to build because of the science it was very fragmentary in the structures and what we knew about 28:13 the structures because it involved lots of different flexible regions which don't usually appear in the data 28:19 my favorite part of building any of these sorts of animations is actually the research stage where i'm learning 28:25 uh what it is these molecules are doing and how they get together and do what they do and it's always a delight for me a 28:33 relief for me if david goodsell has visited this topic before because 28:39 he just always lays it out what these uh molecules are like and how they're interacting to build these complex 28:45 systems in this illustration david goodsell has laid out a roadmap of how this enzyme 28:53 complex comes together not only including the various structures we do know of the 28:59 the core enzyme parts but also the flexible regions which don't actually appear in the protein databank 29:06 so he's really laid out how these which bits of the which enzyme are connected to which and 29:12 also gives you a sense of the flexible regions the dynamic moving regions which 29:17 wouldn't otherwise appear in the pdb the pyruvate dehydrogenase enzyme 29:24 complex has been a focus of research for many many many decades this is from a paper in 1964 29:32 where they're looking using electron microscope to observe the pyruvate complex 29:39 within an e coli bacterium so on the left you have an electron micrograph image of this complex and you 29:46 can sort of get a sense of it has many parts that are coming together and on the right they have 29:52 created an illustration of uh how they the different enzymes and how they think they're coming together 29:58 to form this this spherical complex moving forward to 1979 we're looking at 30:06 better quality electron micrographs of the the enzyme complex and a more 30:12 advanced model uh through this illustration showing how these enzymes are attached 30:18 to each other and how they come together moving forward to 2001 30:24 this is from a paper where they're using cryo-em tomography to reconstruct the 3d 30:30 shape of this complex on the left-hand side you see a figure where they're able to identify 30:38 where each of the enzymes are located in in the interior of the enzyme complex as well as the exterior 30:44 but also in the bottom of this figure i figure c this is a important part of the paper 30:50 where they're showing the domains or the parts we know the 3d structures and then having these flexible tethers uh which 30:57 don't appear in the protein databank so this is really critical for written for reconstructing my own model of what 31:04 this enzyme complex would look like and how these different enzyme enzymes would interact 31:11 so now i will play for you my animation of the pyruvate dehydrogenase enzyme complex in action 31:18 the story begins on the exterior of a mitochondria at the very end of glycolysis the product of glycolysis 31:26 with a pyruvate molecule of a particular note is the challenge the compromise i 31:32 had to make in trying to keep the look and feel of browning behaviors particularly all the 31:37 different individual chemical reactions that are occurring uh the messy nature of that 31:42 while also keeping it in a happening all the different reactions happening in a timely and quite frankly repetitive 31:50 manner so that it was watchable and interpretable for students learning this topic 32:01 the product of glycolysis the pyruvate molecule is the source of 32:06 carbon and electrons or aerobic respiration reactions inside your 32:12 mitochondria pyruvate enters pores on the 32:17 mitochondria membrane and is transported into the interior 32:26 the reactions linking pyruvate with aerobic respiration 32:32 are performed by a huge protein complex made with multiple copies 32:39 of three types of enzyme 32:51 the first enzyme catalyzes decarboxylation transforming three carbon pyruvate 32:58 into a two carbon acetyl group generating carbon dioxide as waste 33:06 the acetyl group is then grabbed by the second enzyme using flexible arms to efficiently 33:13 transfer the product between reaction sites 33:24 in the active site of the second enzyme the acetyl group is attached to coenzyme 33:30 a generating acetyl-coa fuel for the citric acid cycle 33:41 two electrons from pyruvate oxidation are retained by the second enzyme 33:49 before passing them to coenzyme nadh catalyzed by the third enzyme 33:57 coenzyme nadh travels through the matrix delivering electrons for the electron 34:04 transport chain 34:19 in a sequence of reaction steps the pyruvate dehydrogenase enzyme complex 34:26 generates fuel for aerobic respiration reactions of the citric acid cycle and 34:32 the electron transport chain 34:42 since the time i completed these animations last year there's been a new technology that's come out that i think is going to 34:49 radically change what is possible and the way we produce these kinds of animations and that is the new tool sets 34:56 of ai driven data data sources of predictive models uh that fill in all 35:03 the gaps that the protein data bank currently doesn't doesn't touch um 35:08 for this particular animation on the pyruvate complex that enzyme with the flexible tethers took me many weeks to 35:14 reconstruct uh exactly and make by hand what that model would look like that i 35:20 reconstructed in in animation software alpha fold was announced i ran 35:26 the second enzyme that won with the flexible tethers in alpha fold and this is the result that came out 35:34 on the right is my animated model of enzyme complex ii and on the left here is an alpha fold 35:42 the alpha fold model is much much as far superior to my own model uh and it's 35:48 revealed a number of details that i'd missed in reconstructing it from this this this enzyme from literature uh this 35:56 is just so exciting um this will save me weeks and weeks of time per animation uh 36:02 trying to reconstruct these sorts of complex models uh just go in and like a google search um or in a protein 36:08 databank search and to get this sort of complete model uh generated and it's certainly 36:13 sufficiently high quality for my productions um very very exciting and i think this is 36:20 opens up so many possibilities for the future in in building these kinds of complex molecular systems 36:28 uh so with that i hope uh i've given you some insight to uh the work that i've been 36:33 producing and my team's producing uh this is my team uh there's three of us currently at wehi tv justin muir in the 36:41 middle there he's been with us for three or four years he comes from 20 years in the games industry he was part of the 36:47 team that created mortal kombat fear and a number of other blockbuster video games um and he is one 36:55 who's really implemented our brought in uh gaming technology and create he is 37:00 correct programming our current uh pipeline on the right hand side there is atsuko 37:05 uno who's been with wehi tv now for 14 years and etsuko is the one who's 37:11 creating animations specific to the research focus at wehi 37:24 you WEHImovies 213K subscribers Videos About Facebook Twitter Instagram LinkedIn 135 Comments rongmaw lin Add a comment... @unusualfabrication9937 2 years ago these are, and always will be, my FAVORITE animations for learning and exploring molecular biology. you are a legend, Drew Berry! thank you for these masterpieces 80 Reply 1 reply @johnlee4897 1 year ago (edited) Drew's animations are just staggering and reflects on his extraordinary ability to collate literally decades worth of molecular research. Indeed built on the shoulders of Nobel giants. Drew often references Brownian motion to basically move the "soup" around to instigate enzymatic reactions within the cell and this has puzzled me whether it's sufficient. Which led me to latest research from Harvard that the cummulative movement of all of the molecular motors such as dynein and kinesin produce waves in the soup so that it aids reactions. Totally fascinating from my humble I.T. background that I can view in my life time the intricate level of life itself. Please do not stop showing us such molecular marvels. I'd personally vote Drew for a knighthood for his contribution to understanding biological functions. 5 Reply @istvankovacs6705 2 years ago When I saw the stochastic movement in the videos, I knew it was something different. It's incredibly excellent work. 41 Reply @maciej1933 2 years ago One of the biggest ‘aha!’ moments in my life came form watching one of your first videos. It gave me a glimpse of understanding what we are made off and how life works in general on a molecular level. Thank your for allowing this. And as I greatly appreciate your efforts to ‘rhythm’ the movement I would also love to see the real randomness in one or your videos. Thank your for your amazing work. 24 Reply @millionsofsand 2 years ago i would pay my entire life savings for this to be a video game. imagine exploring this in VR?!! 49 Reply 2 replies @abcde_fz 1 year ago As a retired computer tech, hardware/software installation/support, I'm glad you told us a bit about your path through your career. It seems you started out around the same time as I did, and like you, I remember how computer graphics evolved, CGA, EGA, SVGA, all those things that were new to us, and growing by the minute. 4 Reply @marrrtin 2 years ago Can't get enough of this kind of animation. My favourite is the movement of pseudopodia. 5 Reply @bumpstockbilly4263 2 years ago I. LOVE. THESE. VIDEOS..! they're Art and Science and learning and fantastically-enthralling all-in-one.! YOU are APPRECIATED...... 6 Reply @lordofthecats6397 2 years ago I asked for a behind-the-scenes video, and you guys delivered! Seriously, this was exactly the kind of thing I had hoped you'd make. You are all awesome! 17 Reply @amirsafari7140 2 years ago I'm not a biologist, I'm a mechanical engineer, but it's been some years that I'm into biology and i see videos and seminars just because it's so amazing to think that there are trillions of this tiny machines inside me and every living creature and works perfectly every time, and it's more amazing to think about how this mechanism apeard on earth and evolved, it seems a very patient engineer just configred all these stuffs and tested them and optimized them. A few years ago after i learned all of these, i said to my self if someone solve the protein fold problem, a boom of research and development would initiate, and here we are with alphafold, every day i see some paper that they discovered something new with this technology 2 Reply @DavidStruveDesigns 1 year ago Honestly, the first time I ever saw an animation similar to this (it was likely based off your work or might actually have been yours) that showcased how the mitochondria powers the cell with these tiny little rotors spinning, it absolutely blew my mind. I couldn't help but make the comparison with how we make power for our human-scale use. The molecular machinery literally looks and seemingly acts just like the steam turbines of power stations, or water turbines of hydro-electric dams. And here we humans thought we invented this method first ... turns out nature just beat us by, oh about 1.45 billion years or so LOL 5 Reply @ciid6190 7 months ago Wonderful masterpiece!!! Thank 3.000 to Drew Berry and to all the collaborators!!! 1 Reply @pcsmith3119 2 years ago When a work sideline turns into new branch of molecular biology. The AI engine will create a new research tool from an illustration system. Well done Drew. Cheers Pierre 14 Reply @SS-kf4up 2 years ago These molecular biological animations are so just blowing! Awesome work Drew and Team. Thank you! 3 Reply @KristenLee 2 years ago This is fantastic Drew! Your 2006 animation of apoptosis inspired me to complete my PhD. Would love to see you do this as a Wednesday seminar. 32 Reply 1 reply @hgcleaner 1 year ago This is pure scientific gold! Thank you so much. I am a science dad too and I used your videos with my kids. They just love this! It makes them and me ask so many interesting questions❤. A game for VR wpuld be more than awesome! I imagine to look at labeled or highlighted levels of abstraction or focus like in your videos, all in a loop to explore all the reactions. A time zoom to watch true brownian motion would be the cherry on top. 3 Reply @damianpokarier2965 1 year ago New to your work guys and am blown away by the depth of understanding to present such sophisticated visual aids. Really happy and less despair in this information age that you guys rally the diligent and dedicated to show the evidence in terms comprehensible by many. Australians as a very good axample rather than cringeworthy underdone blowhards. You save lives, 54 years old and lost for life stoked by you guys. Not dead yet .. all eyes and ears. Cheers, Damo 3 Reply @5eZa 2 years ago one neat thing about alpha fold is it gives a confidence score along with the domains it predicts. i've messed around with it some, and it definitely doesn't get everything right. 9 Reply @philhooper 1 year ago Incredible work sir. But I am astounded. How can all this near infinite complexity work altogether at once, mind boggling so, multiple machines in perfect harmony and people still think it just happened. I don't have that kind of faith. I would have a better chance of jumping off the earth, getting to Jupiter and back, holding my breath the whole time and landing whole back at my starting point on earth than the common assumptions of materialism. To say it has the "appearance" of design is a death defying leap of presumption. It must take incredible, awesome faith that defies logic to think it's all by chance. 2 Reply @ervinperetz5973 1 year ago Thanks so much for taking the time to share your CAD/animation tooling and workflows. Reply @Kei-Kei 1 year ago Thanx. It’s been a deep dive on YouTube couple of off days. I watched the history of civilization, all the wars and destruction. Then I watched a couple of physics videos, I know if I keep at it I’ll get it! 🤣🤣🤣 And then I found you guys! 2 Reply @sbehnisch 5 months ago Phantastic to see these moleculs in action. Reply @adrianterruli253 2 years ago Incredibly valuable work which has greatly enriched the learning and understanding of my high school students, I look forward to seeing this in VR; and why not have a video game too!!? 9 Reply 1 reply @roidroid 2 years ago (edited) 1:55 omg, i used to play that game as a kid. I literally had to hack the game files(on PC) - copying the files from a previous level to haphazardly replace the CORRUPT final level files - to even be able to play the final level of this game (otherwise it would never complete loading!). I only learned to do that after a number of years too, some of my first experience fixing PC software problems, stay at it kids & come back to old problems! 😉 2 Reply @nixonlee3738 2 years ago 太酷了,這樣視覺化學習很容易理解神奇複雜細胞運作?" 美極了,由衷感謝! So cool! Visualization is more easier to help us to learn the amazing complexity of cell operation. Great! Thank you all. 1 Reply @Chris.Davies 2 years ago Your animations have amazed and astounded me for many years. Thank you deeply, Drew. Many of the inner workings of our bodies are no longer unimaginable, and in fact, are extremely beautiful. 3 Reply @williamwixon 1 year ago Love you and your team Mr. Barry. You guys are awesome. The videos are always mind blowing. ❤️ 2 Reply @memberwhen22 3 months ago I don't think sci-fi could come up with anything more bizarre than this.. unless given a few billion years maybe 2 Reply @margueriteoreilly2168 2 years ago Belfast Ireland 🇮🇪 So grateful for Drews Work Unbelievable For all of us Reply @chrysopylaedesign 9 months ago (edited) This video touches on so many professions, technologies & disciplines. I am an Industrial Designer; the science, information & technology shared in this video is supremely applicable to my industry. Please keep on your mission of information sharing & science education. Reply @fadeladdeeb2862 11 months ago Brilliant. PDH complex is the most astonishing enzyme. I would suggest to design animation for hemoglobin binding and releasing molecular oxygen with the conformational changes of oxy- and deoxy- Hb. Needles to say with the role of heme prosthetic group. Thank you. 1 Reply WEHImovies · 1 reply @David-pp9jw 2 years ago Thank you for your time and veracity in this journey you've taken, Berry! Great to see more recent uploads while soon to complete an AS in chemistry while transferring to university for biochem. Thanks again!! ⭐ 2 Reply @youtubeuser6067 4 months ago As AI plays a greater role in clarifying movements and interactions of these molecular processes, it becomes more important to UPDATE previous depictions so that research can be further advanced. I hope there is one website with all of these previous videos (dated) that will soon indicate AI enhancements to them. 1 Reply @reidmock2165 2 years ago Drew Berry, you are an inspiration to me 1 Reply @erik.werner 2 years ago Great work! Thank you for the insight in your workflow. The integration of game engines is a (...wait for it...) game changer ;-) and I'd love to hear more about this! 4 Reply @sidharthsamantaray8112 4 months ago Kudos to you and your team for making our life look beautiful Reply @andreashahn2429 2 years ago Understands the nature of what he depicts miraculously. He is a true Michelangelo of our time. If I could make a wish, I would like to see a short movie of a fish being eaten, digested, build in and respirated. Reply @igamerxd8450 5 months ago You are an amazing human, thank you for simplifying such a complex biological mechanical structures and mechanism to easily understandable chunks. Thank you for your work. Love your channel and your passion. Reply @wcfields4469 6 months ago So you're animation is an accurate depiction of what it really looks like Reply @bradhilton2283 2 years ago Buddy you are so awesome , you are helping to pioneer a new way of learning.Keep up the "Excellent Work!" 3 Reply @jawmamasarah 6 months ago Remember memorizing the Krebs/ Citric Acid cycle out of photocopied pages in a binder your Professor made you buy at the college bookstore for $100? Now the kids these days have this! I'm happy for the new generation though, they have more information presented in an understandable,visual learning format! 1 Reply @SteveHazel 2 years ago thankyou so much for your art! i love it. i also loved my amiga. 4 Reply @justinanthonyprochemdirect401 2 years ago Just amazing artistry. Bdellovibrio would be proud. Thank you! Reply @teigjie 2 years ago Nooooo, the réal Drew Berry??? :o You're my legend... Science has always been my big passion, and because of you I'm really fascinated by animation.. But I haven't found any project yet to practice both together... 1 Reply @WeBeGood06 2 years ago I love these animations of how these Protein Machines actually work. They are amazing. Reply @toddlawrimore3577 2 years ago Great work. Known your work for a few years, but this video allowed me to get to know you a little. Thank you. Inspirational. Reply @colincrooky 6 months ago Thank you Drew, that has answered many questions I have had over the years and we have got to know you better. Keep up the good work. Reply @gurbanik1 2 years ago (edited) Incredible job. Your animations are really showing how beautyful the life and science can be. Reply @carlospln 1 year ago Bravo, Drew! Stupendous. Reply @davidvine5846 7 months ago Congratulations on an amazing compilation of the science and art. Keep up your good work. David Vine , DDS, Miami Beach, . Reply @JohnDlugosz 2 years ago You called yourself a "dinosaur" because you learned techniques in the 90's... I attended a talk given by James Blin, a pioneer in animation who worked on the famous "Mechanical Universe" series. He wrote them in FORTRAN. 4 Reply @sthnwatch 11 months ago Very impressive, mate. Good work. 1 Reply @KumarRohitart 2 years ago Very nice sir 🙏 3 Reply @Frank-ie8dh 2 years ago It's incredible, it's all the questions I had in high school in one animation. Reply @ematise 1 year ago 40 minutes video just went by like 5 min. So amazing! Reply @ddr8993 2 months ago This should be turned into a simulation game. Imagine what discoveries and strategies the public might conjure up Reply @PS-vk6bn 2 years ago Thank you for your introduction! And keep up the nice work! 👍 2 Reply @regulate.artificer_g23.mdctlsk 2 years ago Anyone know more animators/channels that make videos like this? I want more molecular biology animations that depict Brownian Motion, with molecules modeled by atoms instead of electron surface. It's nice to see the inside of a mitochondrion; I am more interested to see the inner workings of free living or parasitic prokaryotes. 1 Reply @cocojeffrey8502 2 years ago Love your work... Taught me how DNA, mRNA and Epigenetics works. 3 Reply @zakirzak1494 2 years ago Amazing work … so happy that I had chance to listen to your incredible skills. Many thanks 🙏 Reply @Gabriel-wq3lh 4 months ago This is mind blowing! Just wow. Reply @sylviareinhofer8756 1 year ago Genius, mind blowing, tausend thanks Reply @margueriteoreilly2168 7 months ago Thank you so much You guys have helped me excell in my knowledge of the Cells I think Dyslexic people will get the Cells We think in puzzles I never thought in a million years I would get Cellular Biology....thanks guys Belfast Ireland 🇮🇪 Reply @NyznTvfk 2 years ago wonderful... 2 Reply @FaakLOL 1 year ago "no one can make cool stuff about biology" drew barry: 1 Reply @brianmbugua4193 1 year ago never has 37mins seemed so short 3 Reply 1 reply @waggieoreilly5714 1 year ago ur the best ....belfast ireland thank u so much Reply @OzGoober 7 months ago Great work. I loved molecular animation. Reply @ejmablekos 2 years ago Love this stuff! So mind blowing to get to see the process. Thank you!!!! Reply @iestynne 4 months ago I was wondering how these incredible animations were made - thank you so much for sharing! It would be amazing to see this running in VR. Unity has good VR support, so it would mostly depend on what kind of performance you get since VR generally requires more than 2x the compute for rendering than does a 'flat' game. Reply @oswaldcobblebot 1 year ago This is mind-blowing! Thank you for making these! Reply @rockapedra1130 1 year ago Amazing work! Thanks for sharing! Reply @waluigihentailover6926 8 months ago Oh my god it’s Drew Berry!! Reply @rendermanpro 1 year ago Absolutely amazing! Reply @SabaDhutt 1 year ago Thank you for all your hard work. Reply @carloscobian2316 1 month ago This is Fantastic! you may be able to get past that file saving bottleneck programmatically or via network transmission! Reply @hugopristauz3620 9 months ago Amazing, amazing, amazing ... Reply @mvognev 2 years ago Thanks a lot for all you doing! Reply @tomschuelke7955 2 years ago Yes i´ve been in architectural Compter visualisation for years... but this was realy awsome.. Reply @krisztiankoblos1948 8 months ago 28:23 look like a good map for a game. 1 Reply @maximkiritchenko4782 2 years ago This is beautiful. Reply @sachikokubota7864 1 year ago Love your work, thanks so much. Reply @FilterYT 9 months ago So wonderful! Reply @sw-yz1yu 2 years ago Im so impressed by this animation Reply @ForYou-eo5bs 2 years ago I am just so much in love with your work...it's amazing Reply @Portugal_Pete 9 months ago This was excellent!! -maya animator Reply @wcfields4469 6 months ago Fascinating. Thanks Reply @numericalcode 2 years ago This is educational gold! Reply @rodschmidt8952 1 year ago Why DO the molecules go to where they're supposed to go? Do they move by random diffusion, or is their motion powered? Reply @kummer45 2 years ago This is considered science? Yes of course. Is this art? INDEED. Is this architecture? Obviously. Engineering? Certainly. Computer science? Of course. But that's how our Lord works. These are his instruments. 2 Reply @epicsuper6775 1 year ago Those molecular dynamics simulations are very nice. However, besides the length scales shown on the simulations, it will be very nice if they could also have the time scale shown as well. Reply @baraskparas9559 2 years ago Great work from a famous name in graphics. Reply @batty128 2 years ago Great work 👍 Reply @krisztiankoblos1948 8 months ago thx for your work . Reply @geoffreydonaldson2984 8 months ago Brilliant! Reply @nikolaykocherygin7530 2 years ago Perfect job. Great work. Amazing videos. Like 👍🤗 Reply @edeyawilson8537 1 year ago I can only say thank you. thank you Reply @daniaspid 2 years ago Thank you,good video Reply @krisztiankoblos1948 8 months ago very good animation. Reply @stuckonearth4967 2 years ago (edited) How those molecules which form the ATP molecule know where to go to become ATP? It was mentioned in the animation "enzymes bring together reactants", but nothing more. How smooth is this process in reality? Like each cycle of the rotor creates exactly 3 molecules each time? 1 Reply 2 replies @ryanscott642 5 months ago How can I get into this with my Quest or even just on my PC? Reply @sindobrandnew 11 months ago 1:54 Bitmap brothers!! Reply @tesesaacstreli7045 2 years ago Good job! Congrats. Reply @issouamine217 2 years ago Middle school?!... I think what you are doing is one of the best things humans have ever did... After discovering theme.... Reply @chocolate_maned_wolf 1 year ago Incredible Reply @chqara 2 years ago (edited) #Cool 💖😊 Reply @veverickastromova 2 years ago Many thanks for the insightful info! Your videos keep inspiring me to try something similar and I wondered how would simulating the Brownian motion work. Never thought of using a game engine, great idea! Reply @oyenindahouse2804 2 years ago Nice work 👍 Reply @tomschuelke7955 2 years ago Wow... While i still don´t understand why you call Maya a game engine, i understand that the animations skillset of maya is on blockbusterlevel.. But do you also use tools like Unreal for the "REaltime" Part? it´s realy mesmerising.. If i was young again, this could be something for me to study too.. But now as my son studies something like this, i know how much you have to learn to get there 1 Reply WEHImovies · 1 reply @sa.8208 2 years ago this has got to be consciousness on a lower level... if we could somehow get crystal clear pics im sure this is where the aliens are. Reply @Musketeer009 2 years ago WOW! Reply @bradhilton2283 2 years ago You should start doing physics and chemistry this way ass well bud , After reading "Micro biology for dummies" incohesion with your animation it just makes thing so much easier to understand . I could deftly see the education system move this way , in a more digital fashion . Reply @pjgraham2211 1 year ago One looks like a dahlia 1 Reply @i.r.weasel7042 1 year ago We are the simulation. Reply @rendermanpro 1 year ago AI prediction doesn't mean that it is correct... especially in boi and medicine world, "prediction" is kinda scary thing... Reply @giovannamoro8564 1 year ago Who created us? 1 Reply 1 reply @boossersgarage3239 8 months ago Fan, fucking, tastic. awesome. thanks... Reply @choykage26 2 years ago 🙇🏽 Reply @DepletedUrbranium 11 months ago David Goodsell and Drew Berry - evolutionists bringing people to Jesus by the thousands :D Reply @timothyhill5140 2 years ago Whomst woke? Reply @Saed7630 10 months ago Just amazing! Repl