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

WEHImovies

9 Aug 202237:25

EducationalLearning

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TLDRDrew Berry, a biomedical animator at the Walter and Elizabeth Institute of Medical Research, shares his journey from cell biology to creating stunning molecular animations. He discusses the techniques and technology used to bring complex biological processes to life, including the use of gaming technology and molecular dynamics simulations. Berry's work aims to transform difficult scientific concepts, such as the electron transport chain and ATP synthesis, into visually engaging stories for education and public understanding.

Takeaways

🎨 Drew Berry is a biomedical animator at the Walter and Elizabeth Institute of Medical Research, Australia's leading biomedical research center.
🔬 His work focuses on creating animations that visually explain complex biological processes, such as cancer, malaria, and diabetes, to enhance scientific understanding.
🌿 Berry's initial inspiration came from his background in cell biology and microscopist, studying single-celled organisms with Professor Jeremy Pickett-Heaps.
📺 He began his career as a Photoshop specialist, enhancing lab images for scientific journals, and later developed his own computer animations to illustrate scientific discoveries.
🎮 Berry's interest in graphics and sound from his early exposure to the Amiga computer and video games influenced his approach to biomedical animation.
🖥️ He uses a combination of X-ray crystallography, cryo-electron microscopy, molecular dynamics simulation, and other data sources to create accurate molecular models for his animations.
🎬 The animations are produced using a GPU-based pipeline for cinematic molecular animation and real-time interactive visualizations, compatible with VR and AR platforms.
🔧 The production process involves extensive research, data gathering, model building in Autodesk Maya, and final animation in Unity game engine.
🎓 The animations aim to transform complex biology topics, like respiration, into visually engaging stories for educational purposes, especially for high school and university students.
🎼 Artistic elements, such as sound design and music, are incorporated to create a sense of engagement and wonder in the animations.
🏆 The use of AI-driven predictive models like AlphaFold is seen as a game-changer for Berry's work, potentially saving significant time in reconstructing complex molecular models.

Q & A

What is Drew Berry's profession and where does he work?
-Drew Berry is a biomedical animator at the Walter and Elizabeth Institute of Medical Research in Australia.
What are some of the diseases that the institute researches?
-The institute researches various diseases including cancer, infectious diseases like malaria, and autoimmune diseases like diabetes.
How did Drew Berry's early career as a cell biologist and microscopist influence his current work?
-Drew Berry's early career in cell biology and microscopist, particularly his work with Professor Jeremy Pickett-Heaps on filming single-celled organisms, inspired his passion for studying life at the cellular level, which drives his current work in biomedical animation.
What role did video games play in shaping Drew Berry's interest in graphics and animation?
-Drew Berry's fascination with video games, especially their graphics and sound, sparked his interest in how these visuals were created. He was particularly inspired by the graphics in games like Xenon 2 and Shadow of the Beast, and the running loops used in video game animations, which he later incorporated into his own work.
What is the significance of the Amiga computer in Drew Berry's life?
-The Amiga computer was a pivotal machine in Drew Berry's life as it introduced him to advanced graphics and sound capabilities, which were ahead of its time. It sparked his interest in the possibilities of computer graphics and laid the foundation for his career in animation.
How does Drew Berry's animation on the electron transport chain contribute to education?
-Drew Berry's animation on the electron transport chain is designed to transform a typically dreaded biology topic into a visual story, allowing students to see all the enzymes in action from glucose breakdown to ATP production. It serves as a crafted visual review of aerobic respiration for high school and university biology education.
What technologies and techniques are used in creating Drew Berry's animations?
-Drew Berry uses a combination of scientific research, X-ray crystallography models, cryo-electron microscopy, molecular dynamics simulation, and animation software such as Autodesk Maya. The animations are then exported to the Unity game engine for real-time interactive visualizations.
How does Drew Berry's team integrate scientific models and molecular dynamics simulation into their animations?
-The team integrates scientific models and molecular dynamics simulation into Autodesk Maya software for animation. They then export these to the Unity game engine to create multi-scale animated molecular landscapes that can be explored in real-time.
What is the role of molecular dynamics simulation in Drew Berry's animation production?
-Molecular dynamics simulation plays a key role in Drew Berry's animation production by providing data on how molecules move, exist, and vibrate in their native environment. This data is used to accurately represent the behavior of molecules in the animated world.
How does Drew Berry address the challenge of representing Brownian motion in his animations?
-Drew Berry addresses the challenge of representing Brownian motion by creating a balance between true realism and watchable content. He manipulates time and density to make the molecular motion interpretable by the human eye, using techniques that allow for controllable randomness in the animations.
What new technology does Drew Berry mention as having the potential to radically change molecular animation production?
-Drew Berry mentions AI-driven predictive models, such as AlphaFold, as a new technology that could radically change molecular animation production by filling in the gaps in the protein data and saving significant time in reconstructing complex models.
How does Drew Berry's team ensure that their animations are accessible and engaging for their target audience?
-Drew Berry's team ensures that their animations are accessible and engaging by using a combination of scientific accuracy, artistic elements, and sound design. They also consider the target audience, such as high school students, and aim to make the complex topics understandable and visually captivating.

Outlines

00:00

🎨 Introduction to Drew Berry's Biomedical Animation Journey

Drew Berry, a biomedical animator at the Walter and Elizabeth Institute of Medical Research in Australia, introduces himself and provides an overview of his work. He discusses his background in cell biology and microscopy, his early fascination with computer graphics and video games, and his transition into creating animations that visualize complex biological processes. Berry emphasizes his passion for exploring cellular life and his innovative use of technology to enhance scientific communication.

05:00

🚀 Harnessing Video Game Technology for Molecular Animation

Berry explains how his team utilizes video game technology to create detailed and interactive molecular animations. He describes their pipeline, which integrates scientific research, molecular dynamics simulations, and 3D modeling to produce animations that can be viewed in real-time on gaming PCs. The animations are designed to be immersive and educational, with applications in VR and AR platforms, and are used to illustrate fundamental biological processes such as respiration and the electron transport chain.

10:01

🧬 Crafting the Animation: ATP Synthase and the Electron Transport Chain

Berry delves into the process of creating an animation about ATP synthase, a crucial enzyme in cellular energy production. He discusses the use of molecular dynamics simulations, X-ray crystallography, and electron microscopy to accurately model the enzyme's structure and function. The animation aims to make complex biological mechanisms accessible and engaging for students by incorporating artistic elements, such as sound design and music, to evoke a sense of wonder and awe.

15:01

🎞️ Techniques and Considerations in Molecular Animation

Berry shares the technical aspects of creating molecular animations, focusing on the representation of Brownian motion and the challenge of balancing realism with watchability. He explains the use of gaming technology to build seamless loops that allow the animations to run indefinitely, and the importance of controlling the randomness to make the molecular interactions understandable to the audience. Berry also discusses the use of different data sources, including published literature and molecular simulations, to inform the animation process.

20:02

🧬 Enzyme Complex 2 and the Citric Acid Cycle

Berry describes his approach to animating enzyme complex 2, which is involved in both the electron transport chain and the citric acid cycle. He aims to depict the precise locations and mechanisms of the chemical reactions occurring within the enzyme, using molecular dynamics simulations and other data to inform the animation. The goal is to provide a clear and engaging visual representation of the enzyme's function, despite the complexity and the challenges of representing molecular motion at such a small scale.

25:03

🧬 Pyruvate Dehydrogenase: A Complex Animation Challenge

Berry discusses the challenges of animating the pyruvate dehydrogenase enzyme complex, which connects glycolysis with the citric acid cycle. He highlights the difficulties in reconstructing the enzyme's structure due to its large size and flexible regions. Berry uses various historical and contemporary scientific data, including electron micrographs and cryo-EM tomography, to build a detailed model for the animation. He also expresses excitement about the potential of AI-driven predictive models to streamline the animation process and improve the accuracy of molecular representations.

30:03

🌟 The Future of Molecular Animation with AI

Berry concludes by reflecting on the impact of AI-driven predictive modeling tools, such as AlphaFold, on the future of molecular animation. He shares his experience using AlphaFold to quickly and accurately model complex enzyme structures, which significantly reduces the time and effort required for manual reconstruction. Berry is optimistic about the possibilities these tools open up for creating more accurate and efficient animations, enhancing the educational and scientific value of his work.

Mindmap

Keywords

💡Biomedical Animation

Biomedical Animation refers to the creation of visual representations of biological processes, structures, or mechanisms using computer graphics. In the video, Drew Berry uses this technique to illustrate complex biological concepts such as cellular respiration and the function of enzymes, making them accessible and understandable to a wider audience.

💡Walter and Elizabeth Institute of Medical Research

The Walter and Elizabeth Institute of Medical Research is a leading biomedical research institution in Australia. It is the workplace of Drew Berry, where he applies his skills in biomedical animation to visualize scientific research and discoveries.

💡Cell Biology

Cell Biology is the study of cell structure, function, and behavior, which is a fundamental aspect of biology. In the context of the video, Berry's background in cell biology and microscopist work informs his approach to creating detailed and accurate animations of cellular processes.

💡Molecular Dynamics Simulation

Molecular Dynamics Simulation is a computational method that allows for the study of the physical movements of atoms and molecules over time. It is used in the video to create realistic animations of how molecules interact and move within their environment, providing a dynamic and accurate representation of molecular behavior.

💡Autodesk Maya

Autodesk Maya is a 3D computer graphics software used for creating animations, visual effects, and 3D models. In the video, Berry uses Maya as his primary tool for integrating scientific data and creating the 3D animated visualizations of molecular processes.

💡Unity Game Engine

The Unity Game Engine is a platform used to create and develop video games and interactive content. In the video, Berry's team uses Unity to export and run their animations in real-time, allowing for the creation of immersive and interactive experiences for educational purposes.

💡ATP Synthase

ATP Synthase is a molecular machine within the mitochondria that synthesizes ATP (adenosine triphosphate), the energy currency of the cell. In the video, Berry focuses on animating the process of ATP synthase to illustrate the mechanism by which cells generate energy from glucose and oxygen.

💡Electron Transport Chain

The Electron Transport Chain (ETC) is a series of protein complexes located in the inner mitochondrial membrane that transfers electrons from one protein to another, ultimately producing ATP. In the video, Berry's animation of the ETC aims to visually explain the complex series of reactions that occur within this chain.

💡Cryo-Electron Microscopy

Cryo-Electron Microscopy (cryo-EM) is a technique used to image biological samples at near-atomic resolution. It is particularly useful for determining the 3D structures of proteins and other macromolecules. In the video, Berry uses data from cryo-EM to inform the accurate modeling of enzymes and their interactions within his animations.

💡Augmented Reality (AR)

Augmented Reality (AR) is a technology that overlays digital information, such as images or animations, onto the real world through a device like a smartphone or tablet. In the video, Berry discusses the potential of using AR to create interactive molecular dioramas, allowing users to explore molecular biology in an engaging and immersive way.

💡AlphaFold

AlphaFold is an AI system developed by DeepMind that predicts the 3D structures of proteins. It has revolutionized the field of protein structure prediction by providing highly accurate models where experimental data may be lacking. In the video, Berry expresses excitement about the potential of AlphaFold to streamline the process of creating animations of complex molecular systems.

Highlights

Drew Berry is a biomedical animator at the Walter and Elizabeth Institute of Medical Research, Australia's leading biomedical research center.

Berry's work focuses on diseases like cancer, malaria, and autoimmune diseases like diabetes.

He began his career as a cell biologist and microscopist, studying single-celled organisms with Professor Jeremy Pickett-Heaps.

Berry's passion for animation was sparked by his early exposure to the Amiga computer and its advanced graphics capabilities.

He was initially hired at WEHI as a Photoshop specialist to enhance lab images for scientific journals.

Berry's animations aim to transform complex biological processes into visual stories, like his work on the electron transport chain.

His animations use a combination of X-ray crystallography, cryo-electron microscopy, and molecular dynamics simulation.

Berry's team has developed a GPU-based animation pipeline for creating cinematic molecular animations and real-time interactive visualizations.

The pipeline was initially built for 8K 3D immersive experiences in a dome theater in Sweden.

The animations are produced using gaming technology, allowing them to run in real-time on standard gaming PCs.

Berry's work includes meticulous reconstruction of ATP synthase, a crucial enzyme in cellular energy production.

The animations incorporate molecular dynamics simulations to capture the movement and vibration of molecules in their native environment.

Berry's team includes Justin Muir, with 20 years in the gaming industry, and Atsuko Uno, who has been with WEHI TV for 14 years.

The new AI-driven predictive models like AlphaFold are expected to greatly enhance the creation of complex molecular animations by filling in gaps in the Protein Data Bank.

Berry's animations are designed to be engaging and accessible for high school and university students, incorporating artistic elements and sound design.

The animations are built using gaming technology principles, allowing for seamless looping and endless playback.

Berry's approach to representing molecular motion involves a balance between true randomness and watchability for the audience.

The pyruvate dehydrogenase enzyme complex animation was particularly challenging due to the fragmentary structures and flexible regions.

Berry's animations are crafted to be both educational and visually captivating, aiming to resonate with the target audience.

The use of molecular dynamics simulations in the animations helps to accurately depict the behavior and location of chemical reactions within enzymes.

Berry's work represents a significant contribution to the field of scientific visualization, making complex biological processes understandable and engaging.

Transcripts

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Related Tags

Biomedical Animation Walter Elizabeth Institute Cellular Research Gaming Tech Educational Visuals Molecular Dynamics 3D Modeling ATP Synthase Electron Transport Pyruvate Dehydrogenase