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DTSTART;TZID=Europe/London:20231030T160000
DTEND;TZID=Europe/London:20231030T180000
DTSTAMP:20260410T052445
CREATED:20230920T130341Z
LAST-MODIFIED:20230926T092919Z
UID:4383-1698681600-1698688800@thomasyoungcentre.org
SUMMARY:TYC Seminar: Moving in a dynamically changing free energy landscape: strain\, heterostructure and optical control of the correlation-driven metal-insulator transition
DESCRIPTION:Andrew (Andy) Millis\, Director of the CCQ center\, Columbia University and CCQ\, the Flatiron Institute  \n\n\n\nVenue: K2.40\, King’s College London (https://www.kcl.ac.uk/core-assets/maps/floor-plans/strand-campus/kings-building/kings-building-gf-d.pdf) \n\n\n\n\n\n\n\n\n\n\n\n\nTYC Seminar: Moving in a dynamically changing free energy landscape: strain\, heterostructure and optical control of the correlation-driven metal-insulator transition Share on X\n\n\n\n\n \n\n\n\nAbstract: A theory [1] of energy landscape in the space of electronic and lattice degrees of freedom is formulated for  “Mott” metal-insulator materials is formulated and argued to resolve the long-standing question of the relative importance of electronic and lattice contributions in the Mott metal insulator transition. Moving beyond equilibrium\,  the theory is used to understand the physics of optically driven metal-insulator transitions. Atomic scale calculations at equilibrium and short times are used to define an energy landscape and the initial evolution of order parameters;  longer times are accessed in terms of time dependent Ginzburg-Landau theories. The importance of the  time dependence of the landscape is highlighted via modeling of experiments on photo induced superconductivity in the LBCO system [2\,3] and the importance of electronic bottlenecks and of electron-lattice effects [4] are explored in the context of a study of  ithe dynamics of the photo induced metal transition in Ca2RuO4 \n\n\n\n[1] A. Georgescu and A. J. Millis\, Communications Physics 5\,  135 (2022)[2] K. A. Cremin\, J. Zhang\, C. C. Homes\, G. D. Gu\, Z. Sun\, M. M. Fogler\, A. J. Millis\, D. N. Basov\, and R. D. Averitt\, Proceedings of the National Academy of Sciences 116\, 19875 (2019).[3] Z. Sun and A. J. Millis\, Phys. Rev. X 10\, 021028 (2020)[4] A. Verma\, D. Golez\,…A. J. Millis and  A. Singer arXiv:2304:02149 \n\n\n\nBio: Andrew Millis was educated at Harvard\, Cambridge University  and MIT. He currently serves as Professor of Physics at Columbia University\, and as the co-Director of the Center for Computational Quantum Physics at the Simons foundation’s Flatiron Institute\, where he is also Managing Director.  He is a Fellow of the American Physical Society and of the American Association for the Advancement of Science and a member of the U.S. National Academy of Sciences. He was awarded the 2017 Hamburg Prize in Theoretical Physics.
URL:https://thomasyoungcentre.org/event/tyc-seminar-andrew-millis-ccq-centre-columbia-university/
CATEGORIES:Main event
ORGANIZER;CN="George Booth":MAILTO:george.booth@kcl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20231020T150000
DTEND;TZID=Europe/London:20231020T163000
DTSTAMP:20260410T052445
CREATED:20230925T155243Z
LAST-MODIFIED:20231009T102130Z
UID:4421-1697814000-1697819400@thomasyoungcentre.org
SUMMARY:CANCELLED: TYC Seminar: What can CHARMM-GUI do for you?
DESCRIPTION:Wonpil Im. Soyeon Yoo – Lehigh University \n\n\n\nVenue: Physics E7 – Grd Floor\, Physics Building\, UCL \n\n\n\n\n\n\n\n\n\n\n\n\nTYC Seminar: What can CHARMM-GUI do for you? Share on X\n\n\n\n\nAbstract: Since its original development in 2006\, CHARMM-GUI has proven to be an ideal web-based platform to interactively build complex molecular systems and prepare their simulation inputs with well-established and reproducible simulation protocols for state-of-the-art molecular simulations using widely used simulation packages. The CHARMM-GUI development project has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of molecular simulation systems. Our philosophy in CHARMM-GUI development is less about providing the nuts and bolts of molecular modeling\, but instead focused on helping users to achieve a task\, such as building a membrane system or solvating a protein\, by providing a streamlined interface. This design principle helps us to think of the workflow critically when designing the interface\, which leads CHARMM-GUI to be accessible to users with little experience in modeling tools and remains useful to experts\, especially for batch generation of systems. The CHARMM-GUI development project is still ongoing. CHARMM-GUI will continue to help expert and non-expert researchers from a broader range of the modeling and simulation community to build the complex molecular systems of their interest and prepare the input files for any general and advanced modeling and simulation through the large and unique scope of CHARMM-GUI functionality\, allowing the research community to carry out innovative and novel molecular modeling and simulation research. In this talk\, I will present the past\, present\, and future of the CHARMM-GUI development project\, and some applications for specific modules will be also discussed. \n\n\n\nBio: Wonpil Im received in bachelor’s and master’s degrees from Hanyang University in Seoul. He then earned his Ph.D. in Biochemistry from Cornell University. He did his post-doctoral research at the Scripps Research Institute in La Jolla\, California. In 2005\, he was hired as an assistant professor in the Center for Computational Biology and Department of Molecular Biosciences at the University of Kansas\, Lawrence.  In 2011\, he was promoted to associate professor and then professor in 2015. In 2016\, he joined the Faculty in Departments of Biological Sciences and Bioengineering at Lehigh University\, and he has been named the Presidential Endowed Chair in Health – Science and Engineering. Wonpil was awarded the Alfred P. Sloan Research Fellowship (2007)\, ACS HP Outstanding Junior Faculty Award (2011)\, J. Michael Young Undergrad Advisor Award (2011)\, Meredith Docking Scholar (2013)\, and University Scholarly Achievement Award (2015). the Friedrich Wilhelm Bessel Research Award from the Humboldt Foundation (2017)\, Lehigh CAS Dean’s Research Award (2019)\,  Libsch Research Award (2021)\, and was named a KIAS Scholar from the Korea Institute for Advanced Study (2016). \n\n\n\nResearch in his lab is focused on the applications of theoretical/computational methods to chemical and physical problems in biology and material sciences. In particular\, he is interested in modeling and simulations of biological membranes and associated proteins\, glycoconjugates\, and protein-ligand (drug) interactions. In addition\, his lab has been developing CHARMM-GUI for the biomolecular modeling and simulation community. 
URL:https://thomasyoungcentre.org/event/tyc-seminar-developing-charmm-gui/
CATEGORIES:Main event
ORGANIZER;CN="Edina Rosta":MAILTO:e.rosta@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20231012T110000
DTEND;TZID=Europe/London:20231012T140000
DTSTAMP:20260410T052446
CREATED:20230921T160506Z
LAST-MODIFIED:20240531T141608Z
UID:4401-1697108400-1697119200@thomasyoungcentre.org
SUMMARY:TYC Welcome Day 2023
DESCRIPTION:Venue: Nyholm Room\, Christopher Ingold Building\, UCL \n\n\n\n\n\n\n\n\n\n\nTYC Welcome Day 2023 Share on X\n\n\n\n\nWe encourage you to attend our in-person TYC Welcome Event which is the perfect opportunity to begin networking with your peers\, and to hear about the fantastic benefits of being affiliated to this active and exciting institute.  Our Interest Group Leads will talk to you about the hot topics they are working on\, and a panel of TYC students and postdocs will be on hand to answer your questions\, providing an overview of TYC activities and opportunities. \n\n\n\nLunch will be provided. \n\n\n\nTell us your PhD topic\, plus one (or more) burning question/s you have for the current TYC PhD students and postdocs\, to enable the panel to cover topics which are relevant to you. Ask them anything – from student life in London and at the TYC\, to what it’s like to undertake a PhD.  Questions will be answered anonymously. \n\n\n\nWe’ll need your confirmation by email to register you\, and send out details.  Don’t forget to include your question/s! Email Karen at tyc-administrator@ucl.ac.uk \n\n\n\n11:05 Introduction to the TYC – Rachel Crespo-Otero\, UCL Chemistry \n\n\n\nInterest Group spokespeople present TYC Interest Groups\, and their ‘hot topics’11:15 – Edina Rosta\, UCL Physics – Soft and Biological Matter (biochemistry\, biophysics\, biomaterials\, statistical mechanics)11:25 – Devis Di Tommaso\, QMUL SPCS – Structural materials (dislocations\, rheology\, chemimechanics\, tribology)11:35 – Martijn Zwijnenburg\, UCL Chemistry – Functional Materials & Devices (Light-Matter interactions\, spectroscopy\, excited states\, photonics\, plasmonics\, solar energy conversion\, electronic\, thermal and ionic transport)11:45 – Clotilde Cucinotta\, Imperial Chemistry – Surfaces & Interfaces (catalysis\, electrochemistry\, nanostructures)11:55 – Jan Tomczak\, King’s Physics – IG1: Methods and Formalisms for simulating materials \n\n\n\n12:15 – Student Q&A panelRashid Al-Heidous – ImperialMargherita Buraschi – ImperialTeo Cobos – UCLVas Fotis – UCLAraf Haque – King’sKit Joll – UCL \n\n\n\n13:00 – Lunch social \n\n\n\n14:00 – End
URL:https://thomasyoungcentre.org/event/tyc-welcome-day-2023/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230927T160000
DTEND;TZID=Europe/London:20230927T170000
DTSTAMP:20260410T052446
CREATED:20230814T102131Z
LAST-MODIFIED:20230927T102116Z
UID:4291-1695830400-1695834000@thomasyoungcentre.org
SUMMARY:*CANCELLED due to illness* TYC Highlight Seminar: Photophysics of two-dimensional materials and moiré structures
DESCRIPTION:Venue: G20 in the Royal School of Mines (Dept of Materials)\, Imperial College London \n\n\n\n\n\n\n\n\n\n\n*CANCELLED due to illness* TYC Highlight Seminar: Photophysics of two-dimensional materials and moiré structures Share on X\n\n\n\n\nSteven G. Louie – University of California at Berkeley\, and Lawrence Berkeley National Lab \n\n\n\nAbstract: Enhanced many-electron interactions\, strong spatial/environmental-dependent screening\, as well as distinct topology in reduced-dimensional systems often lead to novel phenomena of fundamental and technological interests. In this talk\, I present some recent progress along this direction in the photophysics of some systems of current interest\, including atomically thin two-dimensional (2D) materials and their moiré structures. Different measurements and phenomena entail different levels of conceptual/theoretical treatments. Their understanding and prediction are a challenging quantum many-body problem. We address this problem employing an ab initio interacting n-particle Green’s function approach. \n\n\n\nSome fascinating phenomena discovered in recent studies are presented – e.g.\, strongly bound excitons (electron-hole pairs) with highly unusual level structures and optical selection rules; unique moiré excitons in van der Waals heterostructures; tunable magneto-optical & plasmonic properties; prominent correlated 3- and 4-particle excitations; exciton enhanced nonlinear optical responses; remarkable field-driven nonequilibrium and time-dependent effects in pump-probe measurements\, etc. Our latest ab initio field-driven studies lead to the discovery of a self-driven exciton-Floquet effect as well as the discovery of a strikingly new phenomenon of formation of light-induced shift current vortex crystals in van der Waals moiré systems. The richness of the photophysics of these materials add to their promise for exploration of new science and valuable applications. \n\n\n\nBio: Steven G. Louie received his Ph.D. in physics from the University of California at Berkeley in 1976.  After having worked at the IBM Watson Research Center\, Bell Labs\, and U of Penn\, he joined the UC Berkeley faculty in 1980\, where he is Distinguished Professor of Physics and a Senior Faculty Scientist at the Lawrence Berkeley National Lab.  He is an elected member of the National Academy of Sciences\, the American Academy of Arts & Sciences\, the Academia Sinica (Taiwan)\, and a foreign member of the Chinese Academy of Sciences\, as well as a fellow of the American Physical Society (APS)\, the American Association for the Advancement of Science\, and the Materials Research Society (MRS). \n\n\n\nHe is a recipient of the APS Aneesur Rahman Prize\, the APS Davisson-Germer Prize\, the MRS Materials Theory Award\, the Foresight Institute Richard Feynman Prize\, the DoE Award for Sustained Outstanding Research in Solid State Physics\, as well as named Jubilee Professor of Chalmers University of Technology\, Ørsted Lecturer of Technical University of Denmark\, and Benjamin Lee Professor Award of the Asia Pacific Center for Theoretical Physics\, among others.  Louie’s research spans a broad spectrum of topics in condensed matter physics and nanoscience.  He is known for his pioneering development of the ab initio GW method and for his studies of novel bulk and reduced-dimensional systems.
URL:https://thomasyoungcentre.org/event/tyc-highlight-seminar-photophysics-of-two-dimensional-materials-and-moire-structures/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230920T093000
DTEND;TZID=Europe/London:20230922T170000
DTSTAMP:20260410T052446
CREATED:20230330T135633Z
LAST-MODIFIED:20230920T182334Z
UID:3961-1695202200-1695402000@thomasyoungcentre.org
SUMMARY:Twistronics of 2D materials: from modelling to real systems
DESCRIPTION:Twistronics of 2D materials: from modelling to real systems Share on X\n\n\n\n\nVenue: National Graphene Institute of the University of Manchester (in-person\, talks can be attended remotely via zoom) \n\n\n\nStacked van der Waals multilayers exhibit a moiré pattern if the constituent monolayers have different lattice constants or are twisted relative to each other. These moiré patterns give rise to fascinating new properties\, including correlated insulator states\, unconventional superconductivity\, flat electron and phonon bands\, moiré excitons as well as topological states. Example systems include twisted bilayer graphene or twisted bilayers of transition metal dichalcogenides. Despite many advances\, these moiré materials remain challenging to study from a theoretical point of view because they combine two unique challenges: (i) the unit cells of moiré materials are extremely large often containing thousands of atoms and (ii) electrons in these materials are strongly correlated. As a consequence\, there are no “off-the-shelf” methods and computer codes available for the modelling of these materials. \n\n\n\nOur workshop aims to bring together researchers from different modelling communities (including those using atomistic ab initio approaches\, continuum approaches\, emergent moiré lattice models\, topological methods\, strong correlation as well as excited state and non-equilibrium techniques) as well as experimentalists to identify synergies and possible ways forward. \n\n\n\nTo make the workshop accessible for students\, we will begin each topical session with a tutorial talk that introduces the relevant concepts. \n\n\n\nThe workshop will be run jointly by the UK’s National Graphene Institute (Manchester)\, the Thomas Young Centre for Theory and Simulation of Materials (London)\, and the Sir Henry Royce Institute and has received funding from the Psi-k Charity (http://psi-k.net/)\, CCP9 and the Institute of Physics. \n\n\n\n \n\n\n\nRegistration fee: attendance of the workshop is free \n\n\n\n \n\n\n\n\nRegister here\n\n\n\n\n\n\n\n\nWednesday\, September 20  \n\n\n\n09.30: Arrival\, registration\, coffee10.00: Welcome (Vladimir Falko) \n\n\n\n10.10: Session 1: Twisted graphene materials I (Chair: Nicholas Hine)10.10: Tim Kaxiras (invited): Twisted bilayer graphene revisited: where is the “magic”?10.40: Niels Walet (contributed): Electronic structure inside the domain walls of twisted and strained graphene layers11.00: Alessandro Principi (contributed): Interlayer electron-hole friction in tunable twisted bilayer graphene semimetal11.20: Angelika Knothe (invited): Regular and chaotic electron dynamics in ballistic (twisted) bilayer graphene cavities11.50: Darryl Foo (contributed): Extended magic phase in twisted graphene multilayers \n\n\n\n12.10: Lunch & Poster session \n\n\n\n13.30: Session 2: Twisted graphene materials II (Chair: Dahlia Klein)13.30: Sid Parameswaran (invited): A Spiral Twist to the “Normal” State of Moiré Graphene14.00: Sankalpa Ghosh (contributed): Moiré fractals in twisted graphene layers14.20: Irina Grigorieva (invited): Magnetic-field induced phase transition in heterostructures based on unconventional superconductor PdBi214.50: Mohammed Al Ezzi (contributed): Topological Flat Bands in Graphene Super-moiré Lattices \n\n\n\n15.10: Coffee break \n\n\n\n15.30: Session 3: Twisted graphene materials III (Chair: Kristian Thygesen)15.30: Artem Mishchenko (invited): Moiré effects in thick graphitic films with surface layer aligned with hBN 16.00: Mei-Yin Chou (contributed): Origin of Magic Angles in Twisted Bilayer Graphene: The Magic Ring16.20: Maxim Trushin (contributed): Electron pairing across a band intersection may create a highly conductive state16.40: Francesco Guinea (invited): Superconductivity in graphene stacks. \n\n\n\nThursday\, September 21 \n\n\n\n09.20: Session 1: Twisted TMDs I (Chair: Neil Drummond)09.20: Steven Louie (invited): Excitons and photophysics of 2D van der Waals structures09.50: Sufei Shi (invited): Valley-polarized Exitonic Mott Insulator in WS2/WSe2 Moiré Superlattices \n\n\n\n10.20: Coffee break \n\n\n\n10.40: Session 2: Twisted TMDs II (Chair: Sid Parameswaran)10.40: Brian Gerardot (invited): Optically probing correlated states in mult-orbital moiré systems11.10: Andres Grandos del Aguila (contributed): Ultrafast exciton fluid flow in an atomically-thin MoS2 semiconductor11.30: Guang-Yu Guo (contributed): Ab initio studies of nonlinear optical responses of 2D semiconductors11.50: Samuel Magorrian (contributed): One-dimensional confinement in moiré superlattices of twisted 1T’-WTe2 bilayers12.10: Sergey Slizovskiy (contributed): Kagome quantum oscillations in graphene superlattices \n\n\n\n12.30: Lunch & Poster session \n\n\n\n13.30: Session 3: Twisted TMDs III (Chair: Angelika Knothe)13.30: Adina Luican-Mayer (invited): Scanning Tunneling Microscopy of twisted 2D semiconductors14.00: Andor Kormanyos (contributed): Induced spin-orbit coupling in twisted graphene-TMDC heterobilayers14.20: Kristian Thygesen (invited): Emergent properties of van der Waals bilayers revealed by computational stacking \n\n\n\n14.50: Coffee break \n\n\n\n15.10: Session 4: Twisted TMDs IV (Chair: Sarah Haigh)15.10: Nicholas Hine (invited): Combining Large Scale DFT and Machine Learned Interatomic Potentials to Simulate Twisted Bilayers\, Heterostructures and Alloys of 2D Materials15.40: Pierre Pantaleon-Peralta (contributed): Designing Moiré Patterns by Strain16.00: Aitor Garcia-Ruiz (contributed): FE polarization in mixed-stacking graphene tetra layers \n\n\n\nFriday\, September 22 \n\n\n\n09.20: Session 1: (Chair: Sufei Shi)09.20: Sarah Haigh (invited): Understanding Twisted 2D material heterostructures Using Scanning Transmission Electron Microscopy09.50: Neil Drummond (invited): Adhesion of Graphene to Hexagonal Boron Nitride \n\n\n\n10.20: Coffee break \n\n\n\n10.40: Session 2: (Chair: Brian Gerardot)10.40: Dahlia Klein (invited): Atomic SET: a new technique for high-resolution potential imaging11.10: Lorenzo Sponza (contributed): Electronic structure and optical response of twisted boron nitride bilayers11.30: Sushant Kumar Behera (contributed): Engineering Moiré Potential Induced Electronic Structure in van der Waals heterostructure11.50: Allan MacDonald (invited): Magic Angles and Fractional Chern Insulators in Twisted Homobilayer TMDs12.20: Closing (Johannes Lischner) \n\n\n\nOrganizers:Johannes Lischner (Imperial College London\, j.lischner@imperial.ac.uk)Vladimir Falko (University of Manchester\, Vladimir.Falko@manchester.ac.uk) \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nhttps://www.royce.ac.uk/events/twistronics-of-2d-materials-from-modelling-to-real-systems/
URL:https://thomasyoungcentre.org/event/twistronics-of-2d-materials-from-modelling-to-real-systems/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230919T130000
DTEND;TZID=Europe/London:20230919T143000
DTSTAMP:20260410T052446
CREATED:20230712T114240Z
LAST-MODIFIED:20230808T123932Z
UID:4153-1695128400-1695133800@thomasyoungcentre.org
SUMMARY:MMM Hub Software Spotlight: CASTEP on the GPU - A crossover Tier-2 HPC virtual training event
DESCRIPTION:Venue: ONLINE \n\n\n\n\n\n\n\n\n\n\nMMM Hub Software Spotlight: CASTEP Share on X\n\n\n\n\nSpeaker: Phil Hasnip\, University of York \n\n\n\nWe are excited to announce a ‘software spotlight’ event across the MMM Hub\, N8\, and CSD3 Tier-2 consortia\, to showcase a brand new release of the popular ‘CASTEP’ materials modelling package\, which now features significant GPU acceleration. We welcome Phil Hasnip from York\, who will showcase the capabilities of the CASTEP package from a research perspective and will use live demonstrations to show how the code can be efficiently run in practice – in particular multinode and new GPU acceleration capabilities on the ‘Young’ HPC infrastructure. \n\n\n\nWith demand for GPUs at historic highs (HPE leadtimes on new GPUs are at 52 weeks)\, we are very lucky to have access to the A100 GPUs on Young\, which provide large amounts of RAM and compute enabling large simulations. This talk will provide an opportunity for CASTEP users to switch from a CPU implementation to use these currently underused GPU resources. \n\n\n\nJoin Zoom Meetinghttps://ucl.zoom.us/j/99746496587?pwd=UUJHeFBzU3p1a0crTEh2T1lrNUFrUT09 \n\n\n\nMeeting ID: 997 4649 6587Passcode: TYCSWS
URL:https://thomasyoungcentre.org/event/mmm-hub-software-spotlight-castep/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230724T140000
DTEND;TZID=Europe/London:20230724T150000
DTSTAMP:20260410T052446
CREATED:20230711T105001Z
LAST-MODIFIED:20230731T143219Z
UID:4142-1690207200-1690210800@thomasyoungcentre.org
SUMMARY:TYC Seminar: Understanding the action of pore forming proteins: Insights from molecular dynamics simulations\, single molecule experiments and oligomerization kinetics - K Ganapathy Ayappa\, Indian Institute of Science
DESCRIPTION:View the recording HERE \n\n\n\n\n\n\n\n\n\n\n\n\nTYC Seminar: Understanding the action of pore forming proteins: Insights from molecular dynamics simulations\, single molecule experiments and oligomerization kinetics – K Ganapathy Ayappa\, Indian Institute of Science Share on X\n\n\n\n\n \n\n\n\nVenue: Harrie Massey LT\, UCL and Zoom \n\n\n\nAbstract:The  plasma membrane of our cells form the first line of defence to external threats. Protein-membrane interactions dominate this landscape\, playing an important role in our understanding of a myriad of bacterial and viral infections. Phenomena range from membrane-assisted protein aggregation\, oligomerization and folding. Pore-forming toxins a subclass of proteins expressed by bacteria form their primary arsenal responsible for over 30 % of  bacterial infections. Pore forming proteins/toxins expressed in a water-soluble form bind to the target cellular membrane and self-assemble to form multimeric transmembrane pore complexes to eventually kill the cell.  In this talk I will summarize our understanding of the pore forming toxin cytolysin A (ClyA) – a 34 kDa protein expressed by E. coli and known to undergo one of the largest conformational transitions during pore formation. \n\n\n\nWe use large scale molecular dynamics simulations at atomistic and coarse grained levels and enhanced free energy sampling methods in combination with experiments on supported bilayer and vesicle platforms to unravel the process of membrane insertion and kinetics of pore formation.  Each of the different techniques offers unique insights at different length and time scales into membrane binding\, influence of lipid composition as well as the inherent conformational changes that the protein undergoes during the  pore formation process. We connect membrane insertion and ensuing conformational changes with recent superresolution and single molecule microscopy data to provide molecular insights into the pore forming pathway. \n\n\n\nBio:Professor Ayappa obtained his Bachelors degree in Chemical Engineering from Mangalore University\, India in 1984\, and an MS and PhD in Chemical Engineering with a Minor in Mathematics from the Department of Chemical Engineering  and Materials Science at the  University of Minnesota\, in 1992. Professor Ayappa has held visiting positions at the University of North Carolina\, the James Franck Institute at the University of Chicago and Department of Materials at ETH Zurich. He is a fellow of the Indian National Academy of Engineers and the National Science Academy. His interests lie in developing a molecular understanding of structure and dynamics of molecules at the nanoscale using molecular simulations and statistical mechanics. Current research interests lie in the area of biological membranes\, membrane-protein interactions implicated in bacterial and viral infections\, cellular signalling and dynamics at the nanoscale.
URL:https://thomasyoungcentre.org/event/tyc-seminar-biological-membranes-k-ganapathy-ayappa-indian-institute-of-science/
CATEGORIES:Main event
ORGANIZER;CN="Edina Rosta":MAILTO:e.rosta@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230720T150000
DTEND;TZID=Europe/London:20230720T170000
DTSTAMP:20260410T052446
CREATED:20230608T140752Z
LAST-MODIFIED:20230720T140145Z
UID:4079-1689865200-1689872400@thomasyoungcentre.org
SUMMARY:TYC Highlight Seminar: Enhanced sampling simulations in drug design – Alessio Lodola\, University of Parma
DESCRIPTION:Join Zoom Meetinghttps://ucl.zoom.us/j/91379186134 \n\n\n\nMeeting ID: 913 7918 6134 \n\n\n\n\n\n\n\n\n\n\n\n\nTYC Highlight Seminar: Enhanced sampling simulations in drug design – Alessio Lodola\, University of Parma Share on X\n\n\n\n\nAlessio Lodola\, Department of Food & Drug\, University of Parma\, Italy; alessio.lodola@unipr.itLODOLA Alessio | Teaching staff (unipr.it)Enhanced sampling methods are becoming increasingly important in modern computational medicinal chemistry\, flanking standard approaches such as protein-ligand docking and molecular dynamics (MD). This is due to the impressive progresses made with GPU cards in term of performance as well as with the development of improved codes. These progresses are making possible the exhaustive exploration of relevant degrees of freedom of protein-ligand complexes\, with the possibility to simulate unbinding/binding events\, accounting for conformational rearrangements and solvation effects. In these favorable conditions\, the reconstruction of the free-energy surface (FES) of binding has become possible also on desk computers in less than a week of calculations\, with an accuracy depending on the quality of the potential employed and on the approximations made in the definition of the virtual model under investigation. The FES of binding is of pivotal interest for rational drug design as its knowledge can allow to identify productive binding schemes for a small molecule to its target and to rank different ligands targeting the same receptor on a free–energy scale. In the present talk\, I’ll describe our recent experiences regarding the retrospective and perspective application of enhanced sampling in drug design. \n\n\n\nReferences \n\n\n\nCavalli et al\, Acc Chem Res\, 2015\, 48\, 277. \n\n\n\nLodola et al\, J Med Chem\, 2017\, 60\, 4304. \n\n\n\nCastelli et al\, J Med Chem 2020\, 63\, 1261. \n\n\n\nGalvani et al\, submitted. \n\n\n\nShort bioAlessio Lodola received his PhD in medicinal chemistry 2006 working at the University of Parma. After a stint at the University of Bristol (UK) and at the Italian Institute of Technology (IIT) in Genoa\, in 2014 Dr. Lodola became Associate Professor at the University of Parma where is currently working.  \n\n\n\nDr. Lodola’s research focuses on the use of multiscale simulations for the design of endocannabinoid modulators\, inhibitors of kinases\, and protein-protein interaction antagonists.
URL:https://thomasyoungcentre.org/event/tyc-highlight-seminar-enhanced-sampling-simulations-in-drug-design-alessio-lodola-university-of-parma-keep/
CATEGORIES:Main event
ORGANIZER;CN="Edina Rosta":MAILTO:e.rosta@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230713T130000
DTEND;TZID=Europe/London:20230713T143000
DTSTAMP:20260410T052446
CREATED:20230608T162927Z
LAST-MODIFIED:20230615T135350Z
UID:4093-1689253200-1689258600@thomasyoungcentre.org
SUMMARY:Virtual tutorial on Theoretical Electrochemistry - Jun Cheng\, XMA
DESCRIPTION:Home » Events » Page 7\n\n\nZoom \n\n\n\n\n\n\n\n\n\n\n\n\nVirtual tutorial on Theoretical Electrochemistry – Jun Cheng\, XMA Share on X\n\n\n\n\nAbstract: Electrochemical interfaces are the place where matters and energy transform through electrochemical reactions\, and by far the most important and difficult to study in a wide range of electrochemical applications including batteries and electrocatalysis. In the past two decades or so\, ab initio methods have been extensively applied to model electrochemical interfaces. The first hurdle to overcome is how to compute and account for electrode potential in the simulations. I will discuss how it is treated using ab initio molecular dynamics (AIMD) and then extend to modeling of electric double layers\, enabling us to elucidate the dynamic change of microscopic structures and capacitive response to applied potential. The high computational cost of AIMD however limits its application to small model systems consisting of hundreds of atoms at timescale of tens of ps. While\, the latest development of AI accelerated AIMD (AI^2MD) significantly increases the size and timescale\, showing great promise for in situ modeling of realistic electrochemical systems. \n\n\n\n Join Zoom Meeting  \n\n\n\nhttps://ucl.zoom.us/j/96878861727 \n\n\n\nMeeting ID: 968 7886 1727 
URL:https://thomasyoungcentre.org/event/virtual-tutorial-on-theoretical-electrochemistry-jun-cheng-xma/
CATEGORIES:Main event
ORGANIZER;CN="Clotilde Cucinotta":MAILTO:c.cucinotta@imperial.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230622T110000
DTEND;TZID=Europe/London:20230622T123000
DTSTAMP:20260410T052446
CREATED:20230608T135802Z
LAST-MODIFIED:20230608T141217Z
UID:4075-1687431600-1687437000@thomasyoungcentre.org
SUMMARY:TYC Seminar: Interactions of Coronavirus Virions as Biological Nanoparticles with Respiratory Environment: Insight from Multiscale Molecular Simulations - Alex Neimark\, Rutgers University
DESCRIPTION:Room RODH 617 – Sargent Center Seminar room\, Imperial  \n\n\n\n\n\n\n\n\n\n\n\n\nTYC Seminar: Interactions of Coronavirus Virions as Biological Nanoparticles with Respiratory Environment: Insight from Multiscale Molecular Simulations – Alex Neimark – Rutgers University Share on X\n\n\n\n\nCOVID-19 pandemic has triggered broad research activities aiming at preventing and curing coronavirus disease. COVID-19 is transmitted by inhaling airborne SARS-CoV-2 virions\, which represent biologically active nanoparticles of ~ 120 nm enveloped by a lipid bilayer decorated by a “crown” of Spike protein protrusions. In the respiratory tract\, coronavirus virions interact with surfactant films composed of phospholipids and cholesterol that coat lung airways. Active clinical search is underway for physiological and exogenous surfactants that may adsorb on Spike proteins or dilute the lipid envelope affecting the virion ability to bind and penetrate the cells. While the knowledge on the biochemical structure\, pathology\, and antibody/drug interactions of SARS-CoV2 and its variants is quickly growing\, the physico-chemical aspects of the virion interactions with the respiratory system environment and specifically with adsorbing surfactants have been sparsely addressed and are poorly understood. \n\n\n\nWe explore by using coarse-grained molecular dynamics simulations the physico-chemical mechanisms of adsorption of selected pulmonary surfactants\, zwitterionic dipalmitoyl phosphatidyl choline and cholesterol\, and exogeneous anionic surfactant\, sodium dodecyl sulfate\, on the S1-domain of the Spike protein.  We show that surfactants form micellar aggregates that selectively adhere to the specific regions of the S1-domain that are responsible for binding with ACE2 receptors. We find distinctly higher cholesterol adsorption and stronger cholesterol-S1 interactions in comparison with other surfactants\, that is consistent with the experimental observations of the effects of cholesterol on COVID-19 infection.  Distribution of adsorbed surfactant along the protein residue chain is highly specific and inhomogeneous with preferential adsorption around specific amino acid sequences.  We observe preferential adsorption of surfactants on cationic arginine and lysine residues in the receptor-binding domain (RBD) that play an important role in ACE2 binding and are present in higher amounts in Delta and Omicron variants\, which may lead to blocking direct Spike-ACE2 interactions. Our findings of strong selective adhesion of surfactant aggregates to of Spike proteins have important implications for informing clinical search for therapeutic surfactants for curing and preventing COVID-19 caused by SARS-CoV-2 and its variants.
URL:https://thomasyoungcentre.org/event/tyc-seminar-interactions-of-coronavirus-virions-as-biological-nanoparticles-with-respiratory-environment-insight-from-multiscale-molecular-simulations-2/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230526T100000
DTEND;TZID=Europe/London:20230526T120000
DTSTAMP:20260410T052446
CREATED:20230417T162350Z
LAST-MODIFIED:20230417T162913Z
UID:3985-1685095200-1685102400@thomasyoungcentre.org
SUMMARY:Theory and Machine Learning for Crystal Growth lecture (3/3)
DESCRIPTION:Venue: Online \n\n\n\n\n\n\n\n\nTheory and Machine Learning for Crystal Growth lecture (1/3) Share on X\n\n\n\n\nProf. Akira Kusaba from Kyushu University\, Japan will present an online course of 3 lectures on Theory and Machine Learning for Crystal Growth \n\n\n\nLectures will take place on Fridays\, May 12\, 19\, 26 at 10 am – 12 noon on Zoom at the following link:  \n\n\n\nJoin Zoom Meetinghttps://ucl.zoom.us/j/95072055014 \n\n\n\nMeeting ID: 950 7205 5014 \n\n\n\nThis lecture course aims to introduce students to theory and machine learning for crystal growth. It contains two complementary parts: qualitative understanding and quantitative prediction of the phenomena. In the first part\, students will learn how classical and analytical theories can be used to understand crystal growth phenomena. After introducing the concept of rate-limiting processes\, the formulas for the growth rates limited by nucleation\, step flow and mass transport are derived. Also\, the need to consider surface reconstruction is discussed. In the second part of machine learning\, students will learn how machine learning can improve crystal growth experiments. Emphasis is on the use of machine learning from the perspective of material scientists and material process engineers. \n\n\n\nSyllabus: \n\n\n\nPart 1: Theory for Crystal Growth \n\n\n\n\nBasic Concept and Early Stage of Growth (Elementary Processes\, Thermodynamics\, Supersaturation\, Nucleation)\n\n\n\nAtomic Models (Surface Energy\, Surface Reconstruction\, Surface Phase Diagram\, First-principle Calculations\, Statistical Mechanics)\n\n\n\nMesoscopic Models (BCF Theory\, Interplane Diffusion\, Monte Carlo Simulations)\n\n\n\nMacroscopic Models (Thermodynamic Analysis\, Driving Force for Growth\, Alloy Composition)\n\n\n\n\nPart 2: Machine Learning for Crystal Growth \n\n\n\n\nBasic Concept (Regression\, Classification\, Dimensionality Reduction\, Clustering)\n\n\n\nBayesian Optimization: After understanding how Bayesian optimization works\, we will consider how it can be utilized in our research.\n\n\n\nMulti-objective Optimization (and Data Assimilation): through examples\, we will learn how to use multi-objective optimization in materials process engineering and how data assimilation\, in which experimental data improves the predictive performance of simulations\, can be used.\n\n\n\nSummary\, Advanced models and Applications: will introduce more advanced and recent models and my own research applying crystal growth theory and machine learning.
URL:https://thomasyoungcentre.org/event/theory-and-machine-learning-for-crystal-growth-lecture-3-3/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230525T100000
DTEND;TZID=Europe/London:20230525T180000
DTSTAMP:20260410T052446
CREATED:20230327T123227Z
LAST-MODIFIED:20230518T113944Z
UID:3927-1685008800-1685037600@thomasyoungcentre.org
SUMMARY:TYC Postgraduate Student Day 2023
DESCRIPTION:Venue: Jeremy Bentham Room\, Wilkins Building\, University College London \n\n\n\n\n\n\n\n\n\n\nTYC Postgraduate Student Day 2023 Share on X\n\n\n\n\nSubmit your abstract and register here: \n\n\n\n\nRegister\n\n\n\n\n\n\n\n\nThere will be 12 talks and almost 40 posters on display from across the four London TYC colleges\, LSBU and Brunel\, at the TYC Student Day.This year coincides with the 250th anniversary of the birth of Thomas Young – there will be cake!  We are very pleased to welcome Andrew Robinson\, author of Thomas Young: The Last Man Who Knew Everything. \n\n\n\nAbstract: The blue plaque on Thomas Young’s house in central London labels him simply ‘Man of Science’\, 1773-1829. There was no space to mention he was a physicist\, physiologist and physician; a classicist\, Egyptologist and philologist; and a prolific writer—probably the greatest polymath since Leonardo da Vinci. Young proved—contra Isaac Newton’s corpuscular theory of light—that light is a wave\, through his inspirational ‘double-slit’ experiment; he also explained elasticity—the ratio between stress and strain in materials—through Young’s modulus. He revealed how the human eye focuses\, perceives colours and suffers from astigmatism. As a Fellow of the Royal College of Physicians\, he practiced medicine for three decades. He launched the decipherment of the hieroglyphic and demotic scripts on Egypt’s Rosetta Stone. He compared 400 languages and coined the term ‘Indo-European’. His numerous articles and books included more contributions to the Encyclopaedia Britannica than any other contributor in its history. This talk on his 250th birth anniversary will introduce his life and work\, and consider why polymathy still matters in a world of specialization. For example\, his physician’s investigation of vision triggered his fascination with the physics of light. Not long before his death\, Young said: ‘It is probably best for mankind that the researches of some investigators should be conceived within a narrow compass\, while others pass more rapidly through a more extensive sphere of research.’ \n\n\n\n(The Last Man Who Knew Everything. 2023 edition: https://www.openbookpublishers.com/books/10.11647/obp.0344.) \n\n\n\nWe also welcome a team from Ab Initio Software Ltd. to discuss careers within their company\, and who are generously sponsoring cash prizes for the ‘Best Talk’ and ‘Best Poster’ awards. \n\n\n\n\nAb Initio’s customers use our enterprise software platform to build applications that tackle the largest and most complex data processing challenges. These applications are some of the most complex operational and analytical systems in the world – mission critical applications with demanding performance requirements.  The characteristics of these applications include the processing of huge volumes of data (petabytes are not uncommon); low latency real-time applications; applications that dynamically reconfigure themselves based on their data and applications that scale as data volumes increase. \n\n\n\nAb Initio has grown through reference rather than marketing\, so you may not have heard of us\, but our customers are among the largest companies in the world in industries such as financial services\, retail\, telecommunications\, transportation\, healthcare and high tech.  We are headquartered in Boston\, Massachusetts and have offices all over the world. Our UK office is in Weybridge\, Surrey.
URL:https://thomasyoungcentre.org/event/tyc-postgraduate-student-day-2023/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230519T100000
DTEND;TZID=Europe/London:20230519T120000
DTSTAMP:20260410T052446
CREATED:20230417T162247Z
LAST-MODIFIED:20230420T091922Z
UID:3983-1684490400-1684497600@thomasyoungcentre.org
SUMMARY:Theory and Machine Learning for Crystal Growth lecture (2/3)
DESCRIPTION:Venue: Online \n\n\n\n\n\n\n\n\nTheory and Machine Learning for Crystal Growth lecture (2/3) Share on X\n\n\n\n\nProf. Akira Kusaba from Kyushu University\, Japan will present an online course of 3 lectures on Theory and Machine Learning for Crystal Growth \n\n\n\nLectures will take place on Fridays\, May 12\, 19\, 26 at 10 am – 12 noon on Zoom at the following link:  \n\n\n\nJoin Zoom Meetinghttps://ucl.zoom.us/j/95072055014 \n\n\n\nMeeting ID: 950 7205 5014 \n\n\n\nThis lecture course aims to introduce students to theory and machine learning for crystal growth. It contains two complementary parts: qualitative understanding and quantitative prediction of the phenomena. In the first part\, students will learn how classical and analytical theories can be used to understand crystal growth phenomena. After introducing the concept of rate-limiting processes\, the formulas for the growth rates limited by nucleation\, step flow and mass transport are derived. Also\, the need to consider surface reconstruction is discussed. In the second part of machine learning\, students will learn how machine learning can improve crystal growth experiments. Emphasis is on the use of machine learning from the perspective of material scientists and material process engineers. \n\n\n\nSyllabus: \n\n\n\nPart 1: Theory for Crystal Growth \n\n\n\n\nBasic Concept and Early Stage of Growth (Elementary Processes\, Thermodynamics\, Supersaturation\, Nucleation)\n\n\n\nAtomic Models (Surface Energy\, Surface Reconstruction\, Surface Phase Diagram\, First-principle Calculations\, Statistical Mechanics)\n\n\n\nMesoscopic Models (BCF Theory\, Interplane Diffusion\, Monte Carlo Simulations)\n\n\n\nMacroscopic Models (Thermodynamic Analysis\, Driving Force for Growth\, Alloy Composition)\n\n\n\n\nPart 2: Machine Learning for Crystal Growth \n\n\n\n\nBasic Concept (Regression\, Classification\, Dimensionality Reduction\, Clustering)\n\n\n\nBayesian Optimization: After understanding how Bayesian optimization works\, we will consider how it can be utilized in our research.\n\n\n\nMulti-objective Optimization (and Data Assimilation): through examples\, we will learn how to use multi-objective optimization in materials process engineering and how data assimilation\, in which experimental data improves the predictive performance of simulations\, can be used.\n\n\n\nSummary\, Advanced models and Applications: will introduce more advanced and recent models and my own research applying crystal growth theory and machine learning.
URL:https://thomasyoungcentre.org/event/theory-and-machine-learning-for-crystal-growth-lecture-2-3/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230512T100000
DTEND;TZID=Europe/London:20230512T120000
DTSTAMP:20260410T052446
CREATED:20230417T162035Z
LAST-MODIFIED:20230417T163126Z
UID:3980-1683885600-1683892800@thomasyoungcentre.org
SUMMARY:Theory and Machine Learning for Crystal Growth lecture (1/3)
DESCRIPTION:Venue: Online \n\n\n\n\n\n\n\n\nTheory and Machine Learning for Crystal Growth lecture (1/3) Share on X\n\n\n\n\nProf. Akira Kusaba from Kyushu University\, Japan will present an online course of 3 lectures on Theory and Machine Learning for Crystal Growth \n\n\n\nLectures will take place on Fridays\, May 12\, 19\, 26 at 10 am – 12 noon on Zoom at the following link:  \n\n\n\nJoin Zoom Meetinghttps://ucl.zoom.us/j/95072055014 \n\n\n\nMeeting ID: 950 7205 5014 \n\n\n\nThis lecture course aims to introduce students to theory and machine learning for crystal growth. It contains two complementary parts: qualitative understanding and quantitative prediction of the phenomena. In the first part\, students will learn how classical and analytical theories can be used to understand crystal growth phenomena. After introducing the concept of rate-limiting processes\, the formulas for the growth rates limited by nucleation\, step flow and mass transport are derived. Also\, the need to consider surface reconstruction is discussed. In the second part of machine learning\, students will learn how machine learning can improve crystal growth experiments. Emphasis is on the use of machine learning from the perspective of material scientists and material process engineers. \n\n\n\nSyllabus: \n\n\n\nPart 1: Theory for Crystal Growth \n\n\n\n\nBasic Concept and Early Stage of Growth (Elementary Processes\, Thermodynamics\, Supersaturation\, Nucleation)\n\n\n\nAtomic Models (Surface Energy\, Surface Reconstruction\, Surface Phase Diagram\, First-principle Calculations\, Statistical Mechanics)\n\n\n\nMesoscopic Models (BCF Theory\, Interplane Diffusion\, Monte Carlo Simulations)\n\n\n\nMacroscopic Models (Thermodynamic Analysis\, Driving Force for Growth\, Alloy Composition)\n\n\n\n\nPart 2: Machine Learning for Crystal Growth \n\n\n\n\nBasic Concept (Regression\, Classification\, Dimensionality Reduction\, Clustering)\n\n\n\nBayesian Optimization: After understanding how Bayesian optimization works\, we will consider how it can be utilized in our research.\n\n\n\nMulti-objective Optimization (and Data Assimilation): through examples\, we will learn how to use multi-objective optimization in materials process engineering and how data assimilation\, in which experimental data improves the predictive performance of simulations\, can be used.\n\n\n\nSummary\, Advanced models and Applications: will introduce more advanced and recent models and my own research applying crystal growth theory and machine learning.
URL:https://thomasyoungcentre.org/event/theory-and-machine-learning-for-crystal-growth-lecture-1-3/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230504T160000
DTEND;TZID=Europe/London:20230504T180000
DTSTAMP:20260410T052446
CREATED:20230323T170552Z
LAST-MODIFIED:20230418T132951Z
UID:3901-1683216000-1683223200@thomasyoungcentre.org
SUMMARY:TYC Highlight Seminar: The Molecular Simulation Design Framework (MoSDeF): Capabilities and Applications
DESCRIPTION:Peter Cummings\, Heriot-Watt University \n\n\n\n\n\nVenue: G20\, Department of Materials\, Imperial College London \n\n\n\n\n\n\n\n\n\n\nTYC Highlight Seminar: The Molecular Simulation Design Framework (MoSDeF): Capabilities and Applications – Peter Cummings\, Heriot-Watt University Share on X\n\n\n\n\nMolecular simulation plays an important role in many sub-fields of chemical engineering\, just as it does in science and engineering in general. Soft matter systems (those easily deformed at room temperature – e.g.\, liquids\, polymers\, foams\, gels\, colloids\, and most biological materials) are ubiquitous in chemical engineering\, but they pose particular computational challenges since the differences in potential energy between distant configurations are on the same order as the thermal motion\, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Furthermore\, performing a molecular simulation of a soft matter system involves multiple steps\, which have traditionally been performed by researchers in a “bespoke” fashion. The result is that many soft matter simulations published in the literature are not reproducible based on the information provided in the publication\, and large-scale screening (as envisaged in the Materials Genome Initiative) of soft materials systems is a formidable challenge. \n\n\n\nTo address the issues of reproducibility and computational screening capability\, we have been developing the Molecular Simulation and Design Framework (MoSDeF) software suite\, including the open­source mBuild (https://github.com/mosdef­hub/mbuild) and Foyer (https://github.com/mosdef­hub/foyer) packages. We will introduce MoSDeF and its capabilities in this presentation. We will also illustrate how\, by combining with the Glotzer group’s Signac­flow workflow manager (https://bitbucket.org/glotzer/signac­flow)\, we have facilitated screening of soft matter systems over chemical/structural parameter spaces. \n\n\n\nWe will report results for two timely applications: lubrication of nanoscale devices featuring surfaces functionalized by monolayers in sliding contact\, and understanding diffusion of ionic liquids in organic solvents (related to energy storage devices). In both cases\, automation of the simulation through use of the MoSDeF tools enables screening and reproducibility.
URL:https://thomasyoungcentre.org/event/tyc-highlight-seminar-peter-cummings-2/
CATEGORIES:Main event
ORGANIZER;CN="Johannes Lischner":MAILTO:j.lischner@imperial.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230502T130000
DTEND;TZID=Europe/London:20230502T150000
DTSTAMP:20260410T052446
CREATED:20230323T205931Z
LAST-MODIFIED:20230427T101632Z
UID:3912-1683032400-1683039600@thomasyoungcentre.org
SUMMARY:TYC Early Career Researchers' Forum: Mustafa Abbas
DESCRIPTION:Home » Events » Page 7\n\n\nVenue: UCL Physics E3/7 \n\n\n\n\n\n\n\n\n\n\nTYC Early Career Researchers' Forum: Mustafa Abbas Share on X\n\n\n\n\nMustafa Abbas\, visitor of Alex Shluger and Sir Richard Catlow\, talking about the challenges of research at his university in Sudan. \n\n\n\nMustafa is visiting the Thomas Young Centre to learn how to confidently use Quantum Mechanics and Molecular Dynamics software tools and learn about the potential insight those software packages can provide. He works in the following areas: Catalysis\, crystallization\, adsorption\, and photovoltaics.  \n\n\n\nAbstractA Sudanese academic presents an overview of the challenges facing researchers in the midst of political and economic instability as well as years of civil wars\, revolutions and ongoing military conflicts. Based on the UNESCO report he conducted on nanotechnology challenges\, in addition to his 15 years of personal experience\, he presents the difficulties facing researchers in his country. He also shares inspiring success stories of his PhD students who have persevered against all odds. Despite the challenging circumstances\, the presentation highlights the importance of scientific progress and the potential for innovation to positively impact the future of Sudan. \n\n\n\nBiographyDr. Mustafa Abbas Mustafa is the Chair holder of the UNESCO Chair on Materials and Nanotechnology at the University of Khartoum\, Sudan. He is currently on sabbatical leave and is hosted by Prof. Alex Shluger and Prof Sir Richard Catlow. He has extensive research experience in Process Systems Engineering and Nanotechnology\, with applications in areas including the Oil and Gas Industry\, Bio-refineries and water/waste treatment. He has published extensively in top journals as well as received numerous awards for his scientific research excellence. He is a member of various professional bodies including the UKRI International Development Peer Review College. Furthermore\, he has also provided consultancy services to a number of national and international bodies\, including UNESCO and Hydro Industries Ltd (UK).
URL:https://thomasyoungcentre.org/event/tyc-early-career-researchers-forum-mustafa-abbas-2/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230427T140000
DTEND;TZID=Europe/London:20230427T170000
DTSTAMP:20260410T052446
CREATED:20230315T162333Z
LAST-MODIFIED:20230420T083559Z
UID:3849-1682604000-1682614800@thomasyoungcentre.org
SUMMARY:TYC Inaugural Lecture: Thomas Keal - Scaling up computational chemistry: from small molecules to complex systems
DESCRIPTION:Home » Events » Page 7\n\n\n\n\n\n\nVenue: Ramsay Lecture Theatre\, followed by a reception in the Nyholm Room\, Christopher Ingold Building \n\n\n\n\n\n\n\n\n\n\nTYC Inaugural Lecture: Thomas Keal – Scaling up computational chemistry: from small molecules to complex systems Share on X\n\n\n\n\n14:00 Michael Buehl\, St Andrews – Enzymology in silico Enzymes with their well-defined active sites are targets for QM/MM applications par excellence. Two case studies of such applications will be discussed\, where insights into enzyme function have been obtained from DFT/Charmm calculations. The first one is on the origin of the oxidative power of ligninolytic enzymes\, believed to be at the heart of their ability to degrade lignin.1 Trends in redox potentials across a series of heme-based peroxidases (Figure 1a)\, as well as their high sensitivity to pH\, are well captured computationally\, but contrary to earlier proposals\,1a no simple rationalisation of these findings is emerging.1b The second case study involves explores the reaction mechanism of Is-PETase\, a recently discovered enzyme capable of degrading PET. Surprisingly low activation barriers for serine protease-type hydrolysis steps are computed (Figure 1b)\,2 suggesting that other steps\, notably substrate binding and/or product release\, to be rate lomiting.References1. a) L. Castro\, L. Crawford\, A. Mutengwa\, J. Götze\, M. Bühl\, Org. Biomol. Chem. 2016\, 14\, 2385; b) J. D. Colburn\, M. Bühl\, unpublished.2. E. Shrimpton-Phoenix\, J. B. O. Mitchell\, M. Bühl\, Chem. Eur. J. 2022\, 28\, e202201728. \n\n\n\n2.45 Kakali Sen\, STFC – Modelling enzyme reactivity with QM/MM simulationsCopper nitrite reductases are enzymes occurring in a wide range of bacteria and fungi and perform a vital role in the denitrification pathway of the nitrogen cycle. The functional core of these enzymes consists of two different copper sites\, one of which is involved in electron transfer and one that is the catalytic site where nitrite binds and reduction to nitric oxide occurs. The recently developed multiple structures from one crystal (MSOX) serial crystallography method can be used to provide multiple snapshots of the progress of the reduction reaction as it takes place in a protein crystal [1]. These snapshots can be used as a reference for combined quantum mechanical/molecular mechanical (QM/MM) simulations of enzyme reactivity within the crystal\, which can be used to identify details of reference states that cannot be directly observed by X-ray diffraction experiments\, such as protonation and oxidation states\, and identify preferred reaction paths. Through a combination of MSOX experiments and QM/MM calculations we propose a mechanism for the reduction reaction in Achromobacter cycloclastes copper nitrite reductase\, starting from the initial binding of nitrite to the final NO-bound structure [2]. The results are compared with QM/MM simulations performed in a solvated environment. \n\n\n\n[1] S. Horrell\, S. V. Antonyuk\, R. R. Eady\, S. S. Hasnain\, M. A. Hough and R. W. Strange\, IUCrJ 3\, 271 (2016).[2] K. Sen\, M.A. Hough\, R.W. Strange\, C. Yong and T.W. Keal\, J. Phys. Chem. B 125\, 9102−9114 (2021). \n\n\n\n3.05 Xingfan Zhang\, UCL – Combining QM/MM with other Theoretical Approaches for A Comprehensive Understanding of CeO2We combined polarisable-shell-model (PSM)-based Mott-Littleton defect calculations\, electrostatic analysis\, hybrid quantum mechanics/molecular mechanics (QM/MM) embedded-cluster approaches\, and plane-wave DFT calculations in developing a thorough understanding of several properties of CeO2. PSM interatomic potentials are widely used for modelling charged defects in solids. However\, at the pure MM level of theory\, the calculated defect energetics may not satisfy the requirement of quantitative predictions and are usually limited to certain charged states. We proposed a strategy that employs accurate ionic polarisabilities\, defect structures\, and formation energies calculated by the QM/MM approach in developing a robust PSM potential for CeO2.1 The new potential not only reproduces a wide range of physical properties\, but also unifies the predictions of intrinsic charged defects based on the MM Mott–Littleton approach and QM/MM calculations. \n\n\n\nThe ionisation potential (IP)\, which is the energy required to remove an electron from a solid\, provides valuable information about the electronic\, optical\, and transport properties. While molecules have well-defined IPs\, assessing the absolute IP of solid-state materials is much more challenging. CeO2 is an exceptionally interesting case where previous experiments observed significant differences in the IP ranging from 5.5 eV to 9.1 eV. To understand the origin\, we employed several theoretical approaches to separate the bulk and surface contributions to the IP of CeO2. Using the QM/MM approach with complete cancellation of surface effects\, we determined a theoretical bulk IP of only 5.38 eV for CeO2. Changing surface orientations can vary the IP of CeO2 from 4.2 eV to 8.2 eV\, as revealed by plane-wave DFT calculations and PSM-based electrostatic analysis. These conclusions were further extended to other high-dielectric-constant MO2-type oxides such as TiO2\, ZrO2\, and HfO2\, bridging the gap between theory and experiment. Finally\, a relationship was built to correlate bulk and surface contributions to the IP with cation properties in metal oxides. \n\n\n\nReferences:1. X. Zhang\, L. Zhu\, Q. Hou\, J. Guan\, Y. Lu\, T. W. Keal\, J. Buckeridge\, C. R. A. Catlow and A. A. Sokol\, Chem. Mater.\, 2023\, 35\, 207-227. \n\n\n\n3.25 Keith Butler\, QMUL – Scratching the surface: atomistic modelling\, chemical heuristics and machine learning for designing interfaces in energy materialsMaterials for energy-related applications\, which are crucial for a sustainable energy economy\, rely on combining materials that form complex heterogenous interfaces. Simultaneously\, progress in computational materials science for describing complex interfaces is critical for improving the understanding and performance of energy materials. In this presentation I will give an overview of computational approaches for understanding and tailoring interfaces for renewable energy applications. Density functional theory (DFT) has been a crucial tool for understanding the atomic and electronic structure of surfaces and interfaces and I will show how insights from DFT calculations have allowed us to propose new designs to tailor interfaces for bespoke applications. Computational screening also offers the possibility of virtual selection of materials where optimal pairs satisfy different criteria\, I will present a scheme that allows rapid searching of known materials to identify mechanically stable and electronically optimal interfaces for photovoltaics. One of the limiting factors for virtual screening of interfaces is the lack of data on electronic energy levels. Recent advances in machine learning promise the ability to predict properties in a fraction of the time required for DFT calculations\, thereby facilitating virtual screening\, but the lack of reliable data hinders the training of such models. I will consider two approaches to overcoming this problem\, first using simple chemical heuristics to estimate energy levels and second developing active learning techniques that can facilitate the generation of sparse yet representative databases of interface properties. \n\n\n\n3.45 Tea  \n\n\n\n4.15 Thomas Keal\, STFC/UCL – Scaling up computational chemistry: from small molecules to complex systemsAs computers grow more powerful\, they become ever more important tools for understanding chemistry. But solving the underlying mathematical equations that govern chemical processes is a struggle for even the world’s largest supercomputers. This lecture will give a personal perspective on some of the challenges we encounter when we try to simulate chemistry\, and how in practice we can balance a desire for accuracy with the reality of limited computational resources. \n\n\n\nBeginning in the realm of small molecules\, we see how the properties of even the simplest chemical systems can be difficult to calculate\, and how “one weird trick” makes a big difference for calculating the magnetic properties relevant to nuclear magnetic resonance spectroscopy. Next\, we see how interactions with light make the challenge of simulating chemistry still more daunting\, and how in practice we can model the ultrafast chemical processes that detect light in the eye. \n\n\n\nComplex chemical systems provide a special challenge for simulation\, as calculations rapidly become prohibitively expensive as the size of the model increases. In order to simulate chemistry in realistic environments\, we develop methods that divide complex systems into regions which are calculated at different levels of approximation. The power and flexibility of these “multiscale” methods is illustrated with applications including the surfaces that can transform inert greenhouse gases into activated reactants\, the use of spectroscopy to fingerprint gas-sensing proteins\, and porous materials that can remove harmful nitrogen oxide compounds from diesel exhaust fumes. \n\n\n\nFinally\, future directions for modelling complex chemical systems will be considered\, including combined computational and experimental techniques for enzyme engineering\, advanced modelling methods for designing new forms of catalysts\, the promise of the exascale computing era for chemical simulation\, and the potential for computational chemistry to be a “killer app” for quantum computing. \n\n\n\n5.15 Reception – Nyholm Room
URL:https://thomasyoungcentre.org/event/tyc-inaugural-lecture-thomas-keal/
CATEGORIES:Main event
ORGANIZER;CN="Professor Sir Richard Catlow":MAILTO:tyc-administrator@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230425T130000
DTEND;TZID=Europe/London:20230425T141500
DTSTAMP:20260410T052446
CREATED:20230323T173014Z
LAST-MODIFIED:20230418T112020Z
UID:3905-1682427600-1682432100@thomasyoungcentre.org
SUMMARY:MMM Hub Software Spotlight: Chemshell
DESCRIPTION:Venue: ONLINE \n\n\n\n\n\n\n\n\n\n\nMMM Hub Software Spotlight: Chemshell Share on X\n\n\n\n\nTo coincide with Thomas Keal’s Inagural Lecture on 27th April 2023\, You Lu from STFC has been invited to showcase the capabilities of the ChemShell package from a research perspective\, as well as spending time looking at exactly how the code can be efficiently run in practice – in particular multinode jobs on Young.   \n\n\n\nFuture talks aim to include commonly codes used on Young\, such as Quantum ESPRESSO and Casino and include some emerging technologies such as machine learning with Keras\, Tensorflow and Torch \n\n\n\nJoin Zoom Meeting \n\n\n\nhttps://ucl.zoom.us/j/99746496587?pwd=UUJHeFBzU3p1a0crTEh2T1lrNUFrUT09
URL:https://thomasyoungcentre.org/event/mmm-hub-software-spotlight-chemshell/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230421T140000
DTEND;TZID=Europe/London:20230421T170000
DTSTAMP:20260410T052446
CREATED:20230222T150224Z
LAST-MODIFIED:20230417T155858Z
UID:3759-1682085600-1682096400@thomasyoungcentre.org
SUMMARY:Data Driven Materials Design
DESCRIPTION:Home » Events » Page 7\n\n\n\n\n\n\nVenue: DERI – Digital Environment Research Institute\, 67 New Road\, London\, E1 1HH \n\n\n\n\n\n\n\n\n\n\nData Driven Materials Design – Volker Deringer\, Oxford Share on X\n\n\n\n\nData driven materials design is a series of seminars showcasing the latest in machine learning an informatics techniques applied to materials simulation. In recent years there has been an explosion of available materials science data\, and machine learning has become an increasingly important tool for simulating and designing materials. The seminar series highlights the latest work in this area covering the field from high-throughput data generation\, to method developments in machine learning\, to the latest applications of machine learning to materials design. The seminars will feature a keynote talk as well as the latest research updates from early career researchers. \n\n\n\nVolker Deringer – Oxford  \n\n\n\nXia Liang – Imperial   \n\n\n\nPhilipp Schienbein – UCL  \n\n\n\nDue to limited capacity at the venue we kindly ask that you register here:  \n\n\n\nhttps://www.eventbrite.com/e/data-driven-materials-design-with-volker-deringer-tickets-592291207947
URL:https://thomasyoungcentre.org/event/data-driven-materials-design/
CATEGORIES:Main event
ORGANIZER;CN="Keith Butler":MAILTO:k.butler@qmul.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230413T150000
DTEND;TZID=Europe/London:20230413T170000
DTSTAMP:20260410T052446
CREATED:20230131T150937Z
LAST-MODIFIED:20230316T101506Z
UID:3734-1681398000-1681405200@thomasyoungcentre.org
SUMMARY:TYC Symposium: The large system limit: How big can we go in our simulations...? 
DESCRIPTION:Home » Events » Page 7\n\n\n\n\nRiver Room\, King’s College London\, Strand\, London WC2R 2LS \n\n\n\n\n\n\n\n\n\n\n\n\n\n\nTYC Symposium: The large system limit: How big can we go in our simulations…?  Share on X\n\n\n\n\nSimulating Thousands of Atoms using Linear Scaling BigDFT – Laura Ratcliff\, University of BristolLinear-scaling formalisms of density functional theory (DFT) are becoming increasingly popular due to their ability to overcome the size limitations of standard cubic scaling implementations of DFT\, thereby enabling simulations of tens of thousands of atoms. One approach\, which is implemented in the wavelet-based BigDFT code\, uses localised support functions\, whose locality can also be further exploited for defining fragment-based approaches. In this talk I will describe how linear-scaling BigDFT and the related fragment approaches are used simulate large systems\, giving examples of the corresponding new opportunities forboth performing and analysing first principles simulations of many thousand atom systems. \n\n\n\nLarge-scale and linear scaling DFT: why we need it\, and how we do it – David Bowler\, University College LondonWe will survey the underlying theory behind the large-scale and linear scaling DFT code\, CONQUEST[1]\, which shows exceptional parallel scaling (demonstrated up to 200\,000 cores) and can be applied to up to ten thousand atoms with diagonalisation\, and millions of atoms with linear scaling.  We will give details of the representation of \n\n\n\nthe density matrix and the approach to finding the ground state\, and discuss the implementation of molecular dynamics with linear scaling.  We will give an overview of the performance of the code\, and provide examples of recent developments. \n\n\n\nWe will also discuss the recent application of CONQUEST to complex ferroelectric systems with up to 5\,000 atoms[2\,3].  We studied the local polarisation textures[2] of PbTiO3 thin films on SrTiO3.  We observed the formation of polar vortices in a thick film (9 layers)\, while thinner films (3 layers) cannot support these\, instead showing a polar wave with chiral bubbles forming at the surface; we have extended these studies using linear scaling to investigate the interaction of domain walls with surface trenches[3].   \n\n\n\n[1] A. Nakata et al.\, J. Chem. Phys. 152\, 164112  (2020) \n\n\n\n[2] J. S. Baker and D. R. Bowler\, Adv. Theory Simul. 3\, 2000154 (2020)[3] J. S. Baker and D. R. Bowler\, Phys. Rev. Lett. 127\, 247601 (2021) \n\n\n\nAtomistic simulations of materials with billions of atomic orbitals – Aires Ferreira\, University of YorkComputational modelling has become an essential tool in condensed matter physics that has propelled the understanding and discovery of novel quantum phases of matter with far-reaching applications in many fields. In this talk\, I will review recent advances in large-scale simulation of condensed matter that leverage the power of approximation theory to dramatically increase the system sizes we can treat using modern many-body approaches. My focus will be on the electronic structure and quantum transport properties of weakly-correlated materials\, for which accurate Chebyshev approximants have been developed that enable us to tackle tight-binding models of realistic complexity (e.g. graphene and Weyl semimetals)\, containing up to billions of atomic orbitals. In the final part of the talk\, some of the emerging and most exciting applications of Chebyshev approximation theory\, including the simulation of interacting quantum spin models\, will be briefly discussed.
URL:https://thomasyoungcentre.org/event/tyc-symposium-the-large-system-limit-how-big-can-we-go-in-our-simulations/
CATEGORIES:Main event
ORGANIZER;CN="George Booth":MAILTO:george.booth@kcl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230323T120000
DTEND;TZID=Europe/London:20230323T140000
DTSTAMP:20260410T052446
CREATED:20230307T120202Z
LAST-MODIFIED:20230321T144437Z
UID:3795-1679572800-1679580000@thomasyoungcentre.org
SUMMARY:TYC Highlight Seminar: Atomic-scale machine learning: what do models compute?
DESCRIPTION:Venue: B10\, Molecular Sciences Research Hub\, Imperial College London\, White City Campus \n\n\n\nDirections: https://www.imperial.ac.uk/chemistry/about/molecular-sciences-research-hub/ \n\n\n\n\n\n\n\n\n\n\nTYC Highlight Seminar: Atomic-scale machine learning: what do models compute? Share on X\n\n\n\n\n12:00 – 12:30 – Nan Wu\, PhD student\, Sophia Yaliraki Group\n\n\n\nAtomistic graph learning in allosteric processes \n\n\n\n12:30 – 13:30 – Michele Ceriotti\, EPFL\n\n\n\nAtomic-scale machine learning: what do models compute?Over the past decade\, machine learning (ML) techniques have become an indispensable tool in the atomic-scale modeling of materials – in the form of data-driven potentials\, and more generally of surrogate models for all quantities that can be obtained by an electronic-structure calculation. \n\n\n\nApplying machine-learning techniques to simulations has some interesting conceptual implications: if a ML model is to be able to predict the outcome of a physics-based calculation\, it should have sufficient flexibility\, and the appropriate mathematical structure\, to reproduce the desired physical interactions and processes. \n\n\n\nIn this talk I am going to summarize an ongoing effort to better understand the structure of a broad class of ML frameworks that are routinely used in atomistic simulations\, revealing their strengths and limitations. I will discuss how to extract physical insights from a critical analysis of the model performance\, and how to improve the performance of models by incorporating physical-chemical priors. \n\n\n\nI will punctuate this discussion with examples of recent applications of atomistic ML to different classes of materials\, such as high-entropy alloys and ferroelectrics. \n\n\n\n13:00 – 14:00 – Coffee and networking
URL:https://thomasyoungcentre.org/event/tyc-highlight-seminar-atomic-scale-machine-learning-what-do-models-compute-michele-ceriotti-epfl/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230322T110000
DTEND;TZID=Europe/London:20230322T125000
DTSTAMP:20260410T052446
CREATED:20230222T165545Z
LAST-MODIFIED:20230321T151923Z
UID:3771-1679482800-1679489400@thomasyoungcentre.org
SUMMARY:TYC Early Career Researchers' Forum: Career Focus Series
DESCRIPTION:Venue: UCL Chemistry Christopher Ingold Building\, Nyholm Room\, and ONLINEhttps://ucl.zoom.us/j/96843985604?pwd=NHNRSDc4YWRnYktEblVZeTVyVDMvQT09Meeting ID: 968 4398 5604 Passcode: TYCECR \n\n\n\n\n\n\n\nDr. Giulia Pacchioni from Nature Review Materials  \n\n\n\n\n\n\n\n\n\n\nTYC Early Career Forum: Career Focus Series Share on X
URL:https://thomasyoungcentre.org/event/tyc-early-career-forum-career-focus-series-2/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230315T110000
DTEND;TZID=Europe/London:20230315T125000
DTSTAMP:20260410T052446
CREATED:20230222T165227Z
LAST-MODIFIED:20230302T095444Z
UID:3767-1678878000-1678884600@thomasyoungcentre.org
SUMMARY:TYC Early Career Forum: Career Focus Series
DESCRIPTION:Venue: UCL Physics Room E3/7 \n\n\n\n\n\n\n\nDr. Enrico Berardo from Ab Initio Software Ltd. \n\n\n\n\n\n\n\n\n\n\nTYC Early Career Forum: Career Focus Series Share on X\n\n\n\n\nIn this conversation Enrico will be going through some of his research work from both his PhD at UCL and PostDoc at Imperial College and discuss how the skills gained during these experiences helped him transition into his role as a technical consultant at Ab Initio Software. He will give an overview about what are the current challenges in the always evolving world of tech and how as a consultant at Ab Initio he helps his customers to solve their complex challenges.
URL:https://thomasyoungcentre.org/event/tyc-early-career-forum-career-focus-series/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230307T130000
DTEND;TZID=Europe/London:20230307T150000
DTSTAMP:20260410T052446
CREATED:20230228T152644Z
LAST-MODIFIED:20230301T100820Z
UID:3786-1678194000-1678201200@thomasyoungcentre.org
SUMMARY:TYC Early Career Forum: Catalytic properties of transition metal carbides
DESCRIPTION:Venue: Physics E3/7 \n\n\n\n\n\n\n\n Dr. Hector Prats Garcia\, University College London \n\n\n\n\n\n\n\n\n\n\nTYC Early Career Forum: Career Focus Series Share on X\n\n\n\n\nTransition metal carbides (TMC) have been attracting an increasing amount of interest in the last few decades in the field of heterogeneous catalysis due to their extremely high melting points\, their high resistance to carbon deposition or sulphur poisoning\, their low economic cost\, and last but not least\, because they can exhibit catalytic activities similar to those of Pt-group metals for a wide range of reactions. Moreover\, TMC are excellent substrates to disperse metallic particles due to their strong covalent interactions between metal particles and the surface C atoms. In this talk\, I will discuss about the physical and catalytic properties of TMCs and present the results of a computational screening study on the catalytic activity of small particles on TMCs for efficient CH4 and CO2 conversion [1\,2]. \n\n\n\n[1] H. Prats and M. Stamatakis\, J. Mater. Chem. A (2022)\, 10\, 1522 \n\n\n\n[2] H. Prats and M. Stamatakis\, ChemRXiv (2022)\, available from 10.26434/chemrxiv-2023-f13jf
URL:https://thomasyoungcentre.org/event/tyc-early-career-forum-career-focus-series-3/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230209T150000
DTEND;TZID=Europe/London:20230209T170000
DTSTAMP:20260410T052446
CREATED:20230112T113214Z
LAST-MODIFIED:20230209T153708Z
UID:3671-1675954800-1675962000@thomasyoungcentre.org
SUMMARY:TYC Biological and Soft Matter Interest Group Seminar
DESCRIPTION:This event has been moved to Birkbeck Malet Street 351 and is no longer in Wilkins Garden Room \n\n\nHome » Events » Page 7\n\n\n\n\n\n\n\n\n\nTYC Biological and Soft Matter Interest Group Seminar Share on X\n\n\n\n\nZoom link to attend \n\n\n\nDeep Learning of G-Quadruplexes – Shozeb Haider\, University College London \n\n\n\nG-quadruplexes (G4) are widely distributed higher-order structures in nucleic acids.  Their potential involvement in various biological processes\, have attracted enormous interest as drug targets. G4-forming sequences are highly polymorphic. The same sequence\, under different conditions can adopt multiple\, highly stable structural topologies. However\, the core dynamics is undifferentiated between different topologies. A CVAE-based deep neural network is applied study the dynamics of multiple G4 structures.  We explain the similarities and differences between their dynamics characterized by sequence\, topology and ligands. The CVAE-based deep learning method captures characteristics of the investigated G4 structures and compresses them into a low-dimensional latent space in a discrete manner.    \n\n\n\nDynamics of binding pockets in proteins – Arianna Fornili\, Queen Mary University of London \n\n\n\nThe role of dynamics in modulating the druggability of proteins has found increasing recognition in recent years. This talk will cover the latest research in the lab (https://afornililab.wordpress.com/) on protein dynamics and how it can affect the stability\, shape and composition of small-molecule binding pockets.
URL:https://thomasyoungcentre.org/event/tyc-biological-and-soft-matter-interest-group-seminar/
CATEGORIES:Main event
ORGANIZER;CN="Edina Rosta":MAILTO:e.rosta@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230130T150000
DTEND;TZID=Europe/London:20230130T170000
DTSTAMP:20260410T052446
CREATED:20221208T165032Z
LAST-MODIFIED:20230117T164334Z
UID:3546-1675090800-1675098000@thomasyoungcentre.org
SUMMARY:TYC Highlight Seminar: Electron and Energy Transfer in Molecules and Materials - Troy Van Voorhis\, MIT
DESCRIPTION:TYC Highlight Seminar: Electron and Energy Transfer in Molecules and Materials – Troy Van Voorhis Share on X\n\n\n\n\nElectron and Energy Transfer in Molecules and Materials – Troy Van Voorhis – Massachusetts Institute of Technology \n\n\n\nElectronic reactions play a key role in understanding a host of physical processes – electron transfer reactions that power electrochemistry\, energy transfer reactions that drive photosynthesis and electron spin dynamics that govern magnetism\, just to name a few. In this talk\, we will discuss the utility of diabatic electronic states in qualitatively and quantitively describing these reactions. In particular\, we will highlight the development of constrained DFT as a technique for modern simulations of these fascinating systems. We will show how this picture leads to a unified description of electron transfer in photochemistry\, energy transfer in molecular films and triplet upconversion in hybrid organic/inorganic devices.  \n\n\n\nVenue: Bentham House LG17 Lecture Room\, 4-8 Endsleigh Gardens\, London WC1H 0EG \n\n\n\n\nTroy Van Voorhis
URL:https://thomasyoungcentre.org/event/tyc-highlight-seminar-electron-and-energy-transfer-in-molecules-and-materials-troy-van-hoorhis/
CATEGORIES:Main event
ORGANIZER;CN="George Booth":MAILTO:george.booth@kcl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230126T140000
DTEND;TZID=Europe/London:20230126T160000
DTSTAMP:20260410T052446
CREATED:20221209T155228Z
LAST-MODIFIED:20230110T154940Z
UID:3553-1674741600-1674748800@thomasyoungcentre.org
SUMMARY:TYC Symposium: Modelling Phonons in Materials
DESCRIPTION:TYC Symposium: Modelling Phonons in Materials Share on X\n\n\n\n\nA dynamical view of mechanochemical reactions – Adam Michalchuk\, University of Birminghamhttps://www.birmingham.ac.uk/staff/profiles/chemistry/michalchuk-adam.aspxMechanochemical transformations are phenomenally complex\, spanning many orders of magnitude in scale over length and time. At present\, mechanochemical transformations are being routinely investigated at the macroscopic scale\, but little is understood about the underlying\, elementary stages of these transformations. Using ab initio modeling we are exploring at the atomic scale how a sudden mechanical impact can cause elementary chemical reactions in crystalline solids. Our models are based on the vibrational excitation incited by dynamic mechanical stresses. Rapid redistribution of this vibrational energy is found to cause extensive (and highly transient) heating of crystals\, capable of causing chemical transformations. We will discuss these models and their implications for fundamental studies on mechanochemical transformations. \n\n\n\nThe (other) big bang theory: understanding impact sensitivities of energetic materials – Carole Morrison\, University of EdinburghImpact sensitivity – literally a measure of how hard you need to hit an energetic material to induce detonation – is an important safety metric in energetic materials research. It is a difficult measurement to reliably record\, however\, as it will fluctuate with sample purity\, crystal morphology\, humidity\, temperature and operator experience. This experimental variability motivated our work to devise a purely ab initio predictive model for impact sensitivity\, which requires knowledge of just the crystallographic unit cell\, and access to first principles (DFT) simulation. Having a predictive model is more than just an academic curiosity\, as it allows exploration of structure/property relationships at the most fundamental of levels. This means that the search for new energetics with enhanced safety metrics could be screened for computationally\, long before the synthetic chemist is tasked with making explosive molecules with unknown properties. This lecture will introduce our impact sensitivity predictor model\, and outline some glorious new insights into energetic materials that it allows us to learn. https://www.chem.ed.ac.uk/staff/academic-staff/professor-carole-morrison  \n\n\n\nUnderstanding and controlling the heat transport in thermoelectric materials – Jonathan Skelton\, University of ManchesterAround 60 % of the energy used globally is wasted as heat\, with clear implications for climate change. Thermoelectric generators (TEGs) can be used to recycle waste heat by harnessing the Seebeck effect in a thermoelectric material to extract electrical energy from a temperature gradient. An ideal TE requires a high Seebeck coefficient and electrical conductivity together with a low thermal conductivity. However\, compared to the electrical properties the heat transport through the lattice vibrations (phonons) is less well understood. The lattice thermal conductivity can be modelled using techniques such as the single-mode relaxation-time approximation\, and such calculations have proven valuable for understanding the low thermal conductivity in flagship TEs such as PbTe and SnSe. In this talk\, we will discuss how calculations can be used to establish the physical origin of the suppressed heat transport in materials with low thermal conductivity\, and we will demonstrate how this insight can be applied to identify new high-performance TEs and structural modifications to control the heat transport in existing materials.https://www.research.manchester.ac.uk/portal/jonathan.skelton.html
URL:https://thomasyoungcentre.org/event/tyc-symposium-modelling-phonons-in-materials-2/
LOCATION:XLG1 Lecture Theatre\, Christopher Ingold Building\, 20 Gordon Street\, London\, WC1H 0AJ\, United Kingdom
CATEGORIES:Main event
ORGANIZER;CN="Martijn Zwijnenburg":MAILTO:m.zwijnenburg@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230119T130000
DTEND;TZID=Europe/London:20230119T141500
DTSTAMP:20260410T052446
CREATED:20221209T154248Z
LAST-MODIFIED:20221209T172551Z
UID:3554-1674133200-1674137700@thomasyoungcentre.org
SUMMARY:MMM Hub Software Spotlight - LAMMPS
DESCRIPTION:MMM Hub Software Spotlight – LAMMPS Share on X\n\n\n\n\nJoin Zoom Meetinghttps://ucl.zoom.us/j/99746496587?pwd=UUJHeFBzU3p1a0crTEh2T1lrNUFrUT09 \n\n\n\nMeeting ID: 997 4649 6587Passcode: TYCSWS \n\n\n\nNicodemo Di Pasquale has been invited to showcase the capabilities of the LAMMPS package from a research perspective\, as well as spending time looking at exactly how the code can be efficiently run in practice – in particular multinode jobs on Young.   \n\n\n\nFuture talks aim to include commonly codes used on Young\, such as Quantum ESPRESSO and Casino and include some emerging technologies such as machine learning with Keras\, Tensorflow and Torch
URL:https://thomasyoungcentre.org/event/mmm-hub-software-spotlight-lammps/
CATEGORIES:Main event
ORGANIZER;CN="George Booth":MAILTO:george.booth@kcl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20230106T140000
DTEND;TZID=Europe/London:20230106T163000
DTSTAMP:20260410T052446
CREATED:20221129T153444Z
LAST-MODIFIED:20221208T170049Z
UID:3526-1673013600-1673022600@thomasyoungcentre.org
SUMMARY:Machine Learning for Materials: Data-driven materials design (2.0)
DESCRIPTION:G20\, Royal School of Mines\, Imperial College London \n\n\n\n\n\n\n\n\n\n\nMachine Learning for Materials: Data-driven materials design (2.0) Share on X\n\n\n\n\n14:00 Anthony Onwuli – Rapid structure prediction  \n\n\n\n14:20 Chengcheng Xiao – High-throughput screening  \n\n\n\n14:40 Yifan Wu – Bayesian optimisation   \n\n\n\n15:00 Tea and biscuits   \n\n\n\n15:30 Prof. Yousung Jung (KAIST) – Molecular and materials informatics   
URL:https://thomasyoungcentre.org/event/machine-learning-for-materials-data-driven-materials-design-2-0/
CATEGORIES:Main event
ORGANIZER;CN="Aron Walsh":MAILTO:a.walsh@imperial.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20221219T104500
DTEND;TZID=Europe/London:20221220T160000
DTSTAMP:20260410T052446
CREATED:20221129T152225Z
LAST-MODIFIED:20221129T152428Z
UID:3522-1671446700-1671552000@thomasyoungcentre.org
SUMMARY:Enhanced Sampling Methods Workshop
DESCRIPTION:Enhanced Sampling Simulation Methods for Thermodynamics\, Kinetics\, and Pathways \n\n\n\n\n\n\n\n\n\n\nEnhanced Sampling Methods Workshop Share on X\n\n\n\n\nSummary: How do ligands enter and leave buried binding sites? How do they diffuse through cell membranes? Where and what are the barriers that determine the kinetics? These are important questions that biomolecular simulations can offer unique insights into. But the timescales for these processes are often so slow that only enhanced sampling methods can make their study feasible. In this two-day workshop you will be introduced to a variety of enhanced sampling methods that can be used to predict pathways\, kinetics and thermodynamics for a wide range of different problem types. \n\n\n\nDay 1: Umbrella sampling\, finite temperature string method\, ligand unbinding simulations and machine learning-based analysis and CV identification. \n\n\n\nDay2: Enhanced sampling with information bias for pathways and kinetics: the Weighted Ensemble method. \n\n\n\nPre-requisites: understanding classical MD simulations\, basic python
URL:https://thomasyoungcentre.org/event/enhanced-sampling-methods-workshop/
CATEGORIES:Main event
ORGANIZER;CN="Edina Rosta":MAILTO:e.rosta@ucl.ac.uk
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