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DTSTART;TZID=Europe/London:20221201T180000
DTEND;TZID=Europe/London:20221201T194500
DTSTAMP:20260412T065424
CREATED:20221121T170732Z
LAST-MODIFIED:20221125T153201Z
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SUMMARY:Evolution of Free-Energy Calculations for Drug Discovery
DESCRIPTION:Christopher Ingold Building\, XLG1 Lecture Theatre \n\n\n\n\n\nFigure 1. Rendering from a 1.8-Å crystal structure for a complex with the main protease of SARS-CoV-2(PDB ID 7L11). Carbon atoms of the ligand are in yellow.\n\n\n\n\nEvolution of Free-Energy Calculations for Drug Discovery Share on X\n\n\n\n\nWilliam L. Jorgensen\, Yale University \n\n\n\nFree-energy calculations have had a revolutionary effect on computational chemistry. In conjunction with molecular dynamics and Monte Carlo simulations\, they have enabled the calculation of free energy changes for wide-ranging phenomena including fundamental solution thermodynamics\, activation barriers for reactions in solution\, host-guest binding\, and drug lead optimization. An overview of our FEP efforts beginning with the ethane to methanol calculation in 1985 and leading to recent discoveries of extraordinarily potent inhibitors of the main protease of SARS-CoV-2 will be presented. \n\n\n\nReferences \n\n\n\nComputer-Aided Discovery of Anti-HIV Agents. Jorgensen\, W. L. Bioorg. Med. Chem. 2016\, 24\, 4768-4788. \n\n\n\nRobust FEP Protocols for Creating Molecules in Solution. Cabeza de Vaca\, I.; Zarzuela\, R.; Tirado-Rives\, J.; Jorgensen\, W. L. J. Chem. Theory Comput. 2019\, 15\, 2734-2742. \n\n\n\nAbsolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Drug-like Inhibitor. Qian\, Y.; Cabeza de Vaca\, I.; Vilseck\, J. Z.; Cole\, D. J.; Tirado-Rives\, J.; Jorgensen\, W. L. J. Phys. Chem. B 2019\, 123\, 8675-8685. \n\n\n\nIdentification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. Ghahremanpour\, M.; Tirado-Rives\, J.; Deshmukh\, M.; Ippolito\, J. A.; Zhang\, C.-H.;Cabeza de Vaca\, I.; Liosi\, M.-E.; Anderson\, K. S.; Jorgensen\, W. L. ACS Med. Chem. Lett. 2020\, 11\, 2626-2533. \n\n\n\nPotent non-covalent inhibitors of the main protease of SARS-CoV-2 from molecular sculpting of the drug parampanel guided by free-energy perturbation calculations.Zhang\, C.-H.; Stone\, E. A.; Deshmukh\,M.; Ippolito\, J. A.; … Anderson\, K. S.; Jorgensen\, W. L. ACS Central Sci. 2021\, 7\, 467-475.
URL:https://thomasyoungcentre.org/event/evolution-of-free-energy-calculations-for-drug-discovery/
CATEGORIES:Main event
ORGANIZER;CN="Edina Rosta":MAILTO:e.rosta@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20221202T150000
DTEND;TZID=Europe/London:20221202T173000
DTSTAMP:20260412T065424
CREATED:20221014T170757Z
LAST-MODIFIED:20221104T121626Z
UID:3327-1669993200-1670002200@thomasyoungcentre.org
SUMMARY:Thomas Young Centre Early Career Award Symposium
DESCRIPTION:B10 Materials Sciences Research Hub (MSRH)\, White City Campus\, Imperial College London \n\n\n\n\n\n\n\n\n\n\n\n\nThomas Young Centre Early Career Award Symposium Share on X\n\n\n\n\nThe TYC Early Career Prize\, established in 2022 will be awarded to an early career researcher in recognition of their original published research in the theory and/or simulation of materials or (bio)moleculesShortlisted applicants are invited to give an oral presentation of their research work at this special in-person Symposium. \n\n\n\nAttendance is free but we kindly ask you to register here \n\n\n\n\n\n\n\nChristoph Schran\, Cambridge – Understanding complex aqueous systems with machine learning \n\n\n\nAbstract: Simulation techniques based on accurate and efficient representations of potential energy surfaces are urgently needed for the understanding of complex systems such as solid-liquid interfaces.In this talk\, we present our recent methodological advances for machine learning potentials enabling the efficient development and validation of models for complex aqueous systems.[1\,2]Building on the seminal work by Behler and Parrinello\, we make use of committee models providing accuracy improvements\, measures of uncertainty\, and strategies for active learning.[1]These features enable the streamlining of the development of new models in an end-to-end framework to tackle complex aqueous systems.[2]Finally\, we demonstrate the capability of these approaches for providing insight into the water flow in single-wall nanotubes[3] as well as the complex phase behaviour of mono-layer confined water[4].[1] C. Schran\, K. Brezina\, O. Marsalek\, J. Chem. Phys.\, 2020\, 153\, 104105[2] C. Schran\, F. L. Thiemann\, P. Rowe\, E. A. Müller\, O. Marsalek\, A. Michaelides\, Proc. Nat. Acad. Sci.\, 2021\, 118 (38)\, e2110077118[3] F. L. Thiemann\, C. Schran\, P. Rowe\, E. A. Müller\, A. Michaelides\, ACS Nano\, 2022\, 16\, 7\, 10775–10782[4] V. Kapil\, C. Schran\, A. Zen\, J. Chen\, C. J. Pickard\, A. Michaelides\, Nature\, 2022\, 609\, pages 512–516 \n\n\n\n\n\n\n\nZsuzsanna Koczor-Benda\, UCL – Computational molecular design for terahertz detection and surface-enhanced applications \n\n\n\nMolecules interacting with electromagnetic fields confined in nanometre-sized structures experience an extreme enhancement of their spectral intensities\, which can be utilized in new technologies e.g.\, for biosensing\, security scanning\, and wireless communication. These emerging technologies need molecules with highly specialized and optimized properties to achieve high efficiency. \n\n\n\nWe investigate a promising new terahertz detection technique based on frequency upconversion in nanoantennas through molecular vibrations. We present a computational methodology using quantum chemistry calculations and machine learning tools to find molecules with optimal properties for terahertz detection. By screening databases containing millions of molecules\, we achieve a two-orders-of-magnitude improvement of spectral intensity and identify highly active functional groups. \n\n\n\nAdditionally\, we introduce an open-access interactive online database and toolbox\, Molecular Vibration Explorer\, that enables exploring and screening thousands of molecules specifically for surface-enhanced applications. Based on accurate quantum chemistry calculations and comprehensive numerical tools\, this platform enables customized visualization of vibrational spectroscopic properties for applications in e.g. SERS tags\, vibrational strong coupling\, and toxic substance detection by frequency upconversion. \n\n\n\n\n\n\n\nRomain Reocreux\, UCL – What makes Single-Atom Alloys so Special? Active Site Miniaturisation for Boosted Catalytic Performance \n\n\n\nSingle-Atom Alloys (SAAs) are emerging materials with outstanding catalytic performance. They consist of active transition metal atoms dispersed\, as single-atom dopants\, at the surface of a more inert coinage metal host (see Figure). This miniaturisation of the active site\, from an extended surface in traditional catalysts to single atoms\, offers the possibility to explore new chemistries unattainable with traditional catalysts (1). \n\n\n\nUsing Density Functional Theory (DFT) calculations\, we first computed the activation and reaction energies of a series of catalytically relevant elementary steps (C-H\, N-H\, O-H\, H-O and C=O dissociations) (2). We showed that SAAs could activate chemical bonds more efficiently than pure transition metal nanoparticles. Combining further DFT calculations with high-fidelity kinetic Monte-Carlo simulations\, we revealed properties unique to SAA heterogeneous catalysts: they can perform C-C coupling reactions between sp3-carbons via a mechanism that involves spectator species\, similarly to homogeneous catalysts (3\, 4). This knowledge gained over the years allowed us to computationally identify RhCu SAA as a potential catalyst for alkane activation (5). Experiments later confirmed this prediction. This achievement has showed that the in-silico design of catalysts in now at reach\, albeit rare because of our lack of understanding of the fundamental principles underpinning the interaction of species with the active sites of SAAs. \n\n\n\nTo address this knowledge gap\, we have recently conducted two high throughput studies that have delivered a theoretical framework explaining the binding and reactivity trends on SAAs (6\, 7). The dopant charge and the number of valence electrons (10-electron rule) are key descriptors for the binding of adsorbates on SAAs. This can be rationalised using molecular orbitals rather than the traditional d-band model. This significant step forward goes beyond the now-widespread use of DFT to understand problems in catalysis and will support the development of more efficient technologies for the sustainable production of chemicals and energy. \n\n\n\n1.             R. Réocreux\, M. Stamatakis\, Acc. Chem. Res. 55\, 87–97 (2022).2.             M. T. Darby\, R. Réocreux\, E. C. H. Sykes\, A. Michaelides\, M. Stamatakis\, ACS Catal. 8\, 5038–5050 (2018).3.             R. Réocreux et al.\, Chem. Commun. 55\, 15085–15088 (2019).4.             P. Kress et al.\, J. Chem. Phys. 154\, 204701 (2021).5.             R. T. Hannagan et al.\, Science. 372\, 1444–1447 (2021).6.             R. Réocreux\, E. C. H. Sykes\, A. Michaelides\, M. Stamatakis\, J. Phys. Chem. Lett. 13\, 7314–7319 (2022).7.             J. Schumann\, A. Stamatakis\, A. Michaelides\, R. Réocreux\, \, doi:10.26434/chemrxiv-2022-d5hhf. \n\n\n\n\n\n\n\nWhiteCityCampus_mapDownload\n\n\n\nOrganiser: Jochen Blumberger (UCL) j.blumberger@ucl.ac.uk
URL:https://thomasyoungcentre.org/event/thomas-young-centre-early-career-award-symposium/
LOCATION:Imperial College London
CATEGORIES:Main event
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BEGIN:VEVENT
DTSTART;TZID=Europe/London:20221207T140000
DTEND;TZID=Europe/London:20221207T160000
DTSTAMP:20260412T065424
CREATED:20221128T150120Z
LAST-MODIFIED:20221128T150122Z
UID:3517-1670421600-1670428800@thomasyoungcentre.org
SUMMARY:TYC Festive Gathering
DESCRIPTION:UCL Physics E3/7 \n\n\n\n\n\n\n\n\n\n\nTYC Festive Gathering Share on X\n\n\n\n\nThe Thomas Young Centre invites you all to our annual Festive Celebration event for snacks & drinks\, mulled wine (and non-alcoholic alternatives)\, optional games and Christmas crafts\, and the opportunity to win prizes at the highly anticipated TYC Quiz of Year! \n\n\n\nTime and place: 2-4pm\, Wednesday 7th December\, room E3/7\, Ground Floor\, Physics Building\, Gower St\, London\, WC1E 6BT  \n\n\n\nWait\, there’s more! The TYC will be providing tickets to Winter Wonderland in Hyde Park\, leaving from E3/7 directly after the afternoon’s activities.  \n\n\n\nIf you would like to come to these events\, please let us know by filling out this form: https://forms.office.com/r/bLWB7VUGmj \n\n\n\nIf you would like to be included in the visit to Winter Wonderland\, please register by Monday 28th November. \n\n\n\nIf you would like to attend the Christmas Party only\, please register by Friday 2nd December.  \n\n\n\nPlease join us for festive drinks\, fun and a trip Winter Wonderland!
URL:https://thomasyoungcentre.org/event/tyc-festive-gathering/
CATEGORIES:Main event
ORGANIZER;CN="Katherine Milton":MAILTO:katherine.milton.20@ucl.ac.uk
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BEGIN:VEVENT
DTSTART;TZID=Europe/London:20221214T090000
DTEND;TZID=Europe/London:20221216T170000
DTSTAMP:20260412T065424
CREATED:20220503T121142Z
LAST-MODIFIED:20230103T154146Z
UID:2893-1671008400-1671210000@thomasyoungcentre.org
SUMMARY:TYC 6th Energy Materials workshop: Modelling Energy Interfaces
DESCRIPTION:TYC 6th Energy Materials workshop: Modelling Energy Interfaces Share on X\n\n\n\n\nSponsored in part by the EPSRC-JSPS Core-to-Core Collaborations in Advanced Functional Materials: EP/R034540/1 Defect Functionalized Sustainable Energy Materials: From Design to Devices Application  \n\n\n\nand  \n\n\n\nEPSRC grant: Discovering twisted bilayer materials with strong electron correlations: EP/S025324/1 \n\n\n\nFormat: in-person \n\n\n\nVenue: Wellcome Collection\, 183 Euston Road\, London\, NW1 2BE \n\n\n\nRegistration: Early-bird registration deadline: 15 October 2022\, registration fee: 150 pounds; regular registration deadline: 30 November 2022\, registration fee: 200 pounds.  Registration covers lunches on Dec. 14/15/16\, dinner & drinks at the poster session as well as refreshments during breaks; register via the ‘Register’ button below: \n\n\n\n\n            Register            \n\n\n\n\n\n\n\n\nAbstract submission: deadline for poster abstract submissions is 15 October; submit your abstracts via this link: \n\n\n\n\nSubmit your abstract\n\n\n\n\n\n\n\n\nDeveloping an efficient and sustainable energy technology remains one of the key global challenges\, but this requires advances in the understanding of energy materials. Materials modelling can provide atomic-scale insights\, but applying these techniques to realistic in-operando interfaces is challenging.  \n\n\n\nIn this workshop\, we bring together leading theorists and experimentalists for three days of invited and contributed talks and poster sessions\, to discuss the current state-of-the-art in modelling interfaces and outline future directions guided by experimental and technological needs.  \n\n\n\nThe workshop will take a place at the Wellcome Collection located in the heart of London\, a beautiful venue which also hosts a famous museum (https://wellcomecollection.org/) exploring the history of medical artefacts.   \n\n\n\nDirections to the Wellcome Collection \n\n\n\nPreliminary programme: \n\n\n\nWednesday 14 December \n\n\n\n9.00 am: welcomeSession 1: Tutorials9.30 am: Kirk Bevan (McGill University) – The Physics of Electrochemical Interfaces10.30 am: coffee & snacks11.00 am: Michiel Sprik (University of Cambridge) – The relation and distinction between redox potentials\, electrode potentials and Fermi levels \n\n\n\n12.00 pm: lunch \n\n\n\nSession 2: structure & stability of interfaces1.30 pm: Karsten Reuter (Fritz-Haber Institute) – Out of the crystalline comfort zone: atomistic modelling of operando energy conversion systems2.10 pm: Chiara Gattinoni (London South Bank University) – Strain-driven dissociation of water (incipient) ferroelectrics2.35 pm: coffee & snacks3.00 pm: Bilge Yildiz (MIT) – Atomic and electronic structure and hydrogen interactions at the Al2O3/Al interface quantified by ab initio grand canonical Monte Carlo3.40 pm: Stefan Bromley (University of Barcelona/ICREA) – An unconstrained approach to systematic structural and energetic screening of materials interfaces4.05 pm: short break4.30 pm: panel discussion led by Jochen Blumberger (UCL)5.30 pm: poster session including dinner & drinks \n\n\n\nThursday 15 December \n\n\n\nSession 3: modelling electrified interfaces9.00 am: Jan Rossmeisl (University of Copenhagen) – Electrocatalysis on high entropy alloys9.40 am: Margherita Buraschi (Imperial College London) – Efficient electron open boundaries for electrochemical applications10.05 am: Romain Reocreux (University College London) – Ten-Electron Count Rule for the Reactivity of Single-Atom Alloy Catalysts10:30 am: Tea / coffee break 11.00 am: Marc Koper (Leiden University) – New models for the platinum-electrolyte interface11.40 am: Matthew Darby (Imperial College London – Towards the development of a realistic model of the electrified Pt-water interface12.05 am: Nicodemo Di Pasquale (Brunel University London) – A coupled constant potential/quantum mechanical/molecular dynamics simulation for the description of the graphite-electrolyte double layer \n\n\n\n12.30 pm: lunch \n\n\n\nSession 4: chemical reactions at interfaces1.30 pm: Kristina Tschulik (Ruhr-Universitaet Bochum) – Exploring the metal/electrolyte interface by single nanoparticle electrochemistry2.10 pm: Philip Schienbein (University College London) – Solvation Dynamics at the hematite/liquid water interface2.35 pm: coffee & snacks2.55 pm: Karoliina Honkala (University of Jyväskylä) – Influence of reaction conditions on modeling electrocatalysis3.35 pm: Masaaki Kitano (Tokyo Institute of Technology) – Oxynitride-Hydrides as catalysts for ammonia synthesis4.00 pm: panel discussion led by Alexei Kornyshev (Imperial) and Clotilde Cucinotta (Imperial) \n\n\n\nFriday 16 December \n\n\n\nSession 5: electronic excitations at interfaces9.00 am: Santosh Kumar (Diamond Light Source): Development of liquid and electrochemical cells for in-situ NAP XPS/NEXAFS investigation9.40 am: Jack Strand (University College London) – Charging and Degradation of Amorphous Oxide Films in Electronic Devices10.05 am: Simone Piccinin (Instituto Officina dei Materiali\, Trieste) – Surface hole accumulation drives multielectron water oxidation on hematite photoanodes10.30 am: coffee & snacks10.50 am: Alfredo Pasquarello (EPFL) – Band alignment\, surface coverage and charge transfer at semiconductor-water interfaces11.30 am: Chengcheng Xiao (Imperial College London) – Fantastic Electrides and Where to Find Them11.55 am: Hideo Hosono (Tokyo Institute of Technology) – Extension of electride concept: electro-active space in crystals \n\n\n\n12.35 pm: lunch \n\n\n\nSession 6: energy conversion with 2D and layered materials1.50 pm: Cecilia Mattevi (Imperial) – A platform of 3D printed energy storage devices to power wearable sensors1:15 pm A.K. Thakur (Indian Institute of Technology Patna) – Doped Graphene Anode for Energy Storage Applications2.40 pm: coffee & snacks3.00 pm: Arkady Krasheninnikov (Helmholtz Zentrum Dresden-Rossendorf) – Single and multi-layers of alkali metal atoms inside graphene and MoS2 bilayers as well as their heterostructures: a systematic first-principles study3.40 pm: end of conference \n\n\n\nContact:Johannes Lischnerj.lischner@imperial.ac.uk \n\n\n\nOrganisers:Clotilde Cucinotta – Imperial College LondonJohannes Lischner – Imperial College LondonAlex Shluger – University College LondonKaren Stoneham – University College LondonMartijn Zwijnenburg – University College London \n\n\n\n\n\n\n\nSuggested hotels: \n\n\n\nGrange Hotels: The ClarendonThe BeauchampThe PortlandThe BuckinghamBlooms HotelThe White Hall HotelHoliday Inn London – BloomsburyHoliday Inn Regents Park HotelThe Academy HotelAmbassadors Bloomsbury HotelRadisson EdwardianKenilworth HotelThistle Bloomsbury Park
URL:https://thomasyoungcentre.org/event/6th-tyc-energy-materials-workshop-modelling-energy-interfaces/
CATEGORIES:Main event
ATTACH;FMTTYPE=image/bmp:https://thomasyoungcentre.org/wp-content/uploads/2022/05/figure4.bmp
ORGANIZER;CN="Scott Woodley":MAILTO:scott.woodley@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20221219T104500
DTEND;TZID=Europe/London:20221220T160000
DTSTAMP:20260412T065424
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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