BEGIN:VCALENDAR VERSION:2.0 PRODID:-//THOMAS YOUNG CENTRE - ECPv6.15.17//NONSGML v1.0//EN CALSCALE:GREGORIAN METHOD:PUBLISH X-WR-CALNAME:THOMAS YOUNG CENTRE X-ORIGINAL-URL:https://thomasyoungcentre.org X-WR-CALDESC:Events for THOMAS YOUNG CENTRE REFRESH-INTERVAL;VALUE=DURATION:PT1H X-Robots-Tag:noindex X-PUBLISHED-TTL:PT1H BEGIN:VTIMEZONE TZID:Europe/London BEGIN:DAYLIGHT TZOFFSETFROM:+0000 TZOFFSETTO:+0100 TZNAME:BST DTSTART:20210328T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0100 TZOFFSETTO:+0000 TZNAME:GMT DTSTART:20211031T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0000 TZOFFSETTO:+0100 TZNAME:BST DTSTART:20220327T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0100 TZOFFSETTO:+0000 TZNAME:GMT DTSTART:20221030T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0000 TZOFFSETTO:+0100 TZNAME:BST DTSTART:20230326T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0100 TZOFFSETTO:+0000 TZNAME:GMT DTSTART:20231029T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0000 TZOFFSETTO:+0100 TZNAME:BST DTSTART:20240331T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0100 TZOFFSETTO:+0000 TZNAME:GMT DTSTART:20241027T010000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;TZID=Europe/London:20230713T130000 DTEND;TZID=Europe/London:20230713T143000 DTSTAMP:20260410T110547 CREATED:20230608T162927Z LAST-MODIFIED:20230615T135350Z UID:4093-1689253200-1689258600@thomasyoungcentre.org SUMMARY:Virtual tutorial on Theoretical Electrochemistry - Jun Cheng\, XMA DESCRIPTION:Home » Events » Page 8\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:20260410T110548 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:20260410T110548 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:20260410T110548 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:20260410T110548 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:20260410T110548 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:20260410T110548 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:20260410T110548 CREATED:20230323T205931Z LAST-MODIFIED:20230427T101632Z UID:3912-1683032400-1683039600@thomasyoungcentre.org SUMMARY:TYC Early Career Researchers' Forum: Mustafa Abbas DESCRIPTION:Home » Events » Page 8\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:20260410T110548 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 8\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:20260410T110548 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:20260410T110548 CREATED:20230222T150224Z LAST-MODIFIED:20230417T155858Z UID:3759-1682085600-1682096400@thomasyoungcentre.org SUMMARY:Data Driven Materials Design DESCRIPTION:Home » Events » Page 8\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:20260410T110548 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 8\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:20260410T110548 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:20260410T110548 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:20260410T110548 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:20260410T110548 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:20260410T110548 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 8\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:20260410T110548 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:20260410T110548 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:20260410T110548 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:20260410T110548 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:20260410T110548 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 END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20221214T090000 DTEND;TZID=Europe/London:20221216T170000 DTSTAMP:20260410T110548 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:20221207T140000 DTEND;TZID=Europe/London:20221207T160000 DTSTAMP:20260410T110548 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 END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20221202T150000 DTEND;TZID=Europe/London:20221202T173000 DTSTAMP:20260410T110548 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 END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20221201T180000 DTEND;TZID=Europe/London:20221201T194500 DTSTAMP:20260410T110548 CREATED:20221121T170732Z LAST-MODIFIED:20221125T153201Z UID:3459-1669917600-1669923900@thomasyoungcentre.org 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:20221027T160000 DTEND;TZID=Europe/London:20221027T180000 DTSTAMP:20260410T110548 CREATED:20221010T150421Z LAST-MODIFIED:20221019T162816Z UID:3288-1666886400-1666893600@thomasyoungcentre.org SUMMARY:TYC Highlight Seminar: A Tale of Two Particles: Hot-carrier transfer and Designing of Alloy Nanostructures for Optical Sensing DESCRIPTION:SAFB G34 plus the mezzanine on Level 1\, Alexander Fleming\, Imperial College London \n\n\n\n\n\n\n\n\n\n\nTYC Highlight Seminar: A Tale of Two Particles: Hot-carrier transfer and Designing of Alloy Nanostructures for Optical Sensing Share on X\n\n\n\n\nProf. Paul Erhart\, Chalmers University of Technology \n\n\n\nIn the first part of this talk\, I will discuss atomic scale simulations of plasmon-induced hot carrier generation and transfer. Metal nanoparticles are attractive for plasmon-enhanced generation of hot carriers\, which may be harnessed in photochemical reactions. \n\n\n\nWhile direct hot-carrier transfer can in principle be particular efficient for increasing photo-catalytic activity\, it is difficult to discern experimentally and competes with several other mechanisms. In our work\, we analyze the coherent femtosecond dynamics of photon absorption\, plasmon formation\, and subsequent hot-carrier generation through plasmon dephasing using first-principles simulations [1]. I will show how we can predict the energetic and spatial hot-carrier distributions in small metal nanoparticles and how they vary with particle size and shape. The distribution of hot carriers on a surface is\, however\, only one part in the transfer process\, the other part being the receiving molecule (or semiconductor) [2]. In this context\, I will discus how the dependence of the hot-carrier transfer probability on the nanoparticle-molecule distance and configuration. Our simulations show that hot-electron transfer can even be effective at long distances\, well outside the region of chemisorption; hot-hole transfer on the other hand is limited to shorter distances. These observations can be explained by the energetic alignment between molecular and nanoparticle states as well as the excitation frequency. The hybridization of the molecular orbitals is the key predictor for hot-carrier transfer in these systems\, emphasizing the need to include the effects of ground state hybridization for accurate predictions. Finally\, I will show a non-trivial dependence of the hot-carrier distribution on the excitation energy\, which could be exploited when optimizing photo-catalytic systems. \n\n\n\nIn the second part I will present recent results pertaining to the computational design of Pd nanoalloy structures for hydrogen sensing. Pd nanoalloys show great potential as hysteresis-free\, reliable hydrogen sensors. Changes in hydrogen pressure translate to changes in hydrogen content and eventually the optical spectrum. Recently\, we employed a multi-scale modeling approach to determine optimal conditions for optical hydrogen sensing using Pd-Au alloys. To this end\, we combined electronic structure calculations of the dielectric response [3] with atomic scale simulations of the alloy thermodynamics [4] and electrodynamic simulations [5]. We carefully compare the simulation results with experimental data and assess potential sources for discrepancies. Invariably\, the results suggest that there is an upper bound to the “optical” sensitivity that cannot be overcome by engineering composition and/or geometry. While the alloy composition has a limited impact on optical sensitivity\, it can\, however\, strongly affect H uptake and consequently the “thermodynamic” sensitivity. Specifically\, I will show how the latter can be improved by compositional engineering and even substantially enhanced via the formation of an ordered phase that can be synthesized at higher hydrogen partial pressures.  \n\n\n\n[1] T. P. Rossi\, P. Erhart\, and M. Kuisma\, “Hot-Carrier Generation in Plasmonic Nanoparticles: The Importance of Atomic Structure”\, ACS Nano 14\, 9963 (2020)  \n\n\n\n[2] J. Fojt\, T. P. Rossi\, and P. Erhart\, “Hot-carrier transfer across a nanoparticle-molecule junction: The importance of orbital hybridization and level alignment”\, Nano Letters\, accepted (2022) \n\n\n\n[3] J. M. Rahm et al.\, “A Library of Late Transition Metal Alloy Dielectric Functions for Nanophotonic Applications”\, Advanced Functional Materials 30\, 2002122 (2020) \n\n\n\n[4] J. M. Rahm et al.\, “A tale of two phase diagrams: Interplay of ordering and hydrogen uptake in Pd-Au-H “\, Acta Materialia 211\, 116893 (2021)  \n\n\n\n[5] P. Ekborg-Tanner et al.\, “Computational Design of Alloy Nanostructures for Optical Sensing of Hydrogen”\, ACS Appl. Nano Mater. 2022\, 5\, 8\, 10225–10236 \n\n\n\n\n\n\n\nOrganiser: Johannes Lischner URL:https://thomasyoungcentre.org/event/tyc-highlight-seminar-a-tale-of-two-particles-hot-carrier-transfer-and-designing-of-alloy-nanostructures-for-optical-sensing-2/ CATEGORIES:Main event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20221020T120000 DTEND;TZID=Europe/London:20221020T140000 DTSTAMP:20260410T110548 CREATED:20221014T181312Z LAST-MODIFIED:20230123T212811Z UID:3335-1666267200-1666274400@thomasyoungcentre.org SUMMARY:MMM Hub Software Spotlight - VASP (Vienna ab initio simulation package) DESCRIPTION:MMM Hub Software Spotlight – VASP (Vienna ab initio simulation package Share on X\n\n\n\n\nThe format of these events are in two parts:1. Scientific motivation\, and research highlights using results obtained from the code being presented 2. Discussion of the code functionality and capabilities\, with a tutorial on technical aspects of using the code\, including input/output\, recommended job sizes\, common problems\, etc with a live demo running on ‘Young’/Tier-2 HPC architectures using the module environment. \n\n\n\nBonan Zhu has been invited to showcase the capabilities of VASP 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\, LAMMPS\, Casino and include some emerging technologies such as machine learning with Keras\, Tensorflow and Torch URL:https://thomasyoungcentre.org/event/mmm-hub-software-spotlight-vasp-vienna-ab-initio-simulation-package/ CATEGORIES:Main event ORGANIZER;CN="George Booth":MAILTO:george.booth@kcl.ac.uk END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20220930T143000 DTEND;TZID=Europe/London:20220930T163000 DTSTAMP:20260410T110548 CREATED:20220706T125401Z LAST-MODIFIED:20220929T163647Z UID:3045-1664548200-1664555400@thomasyoungcentre.org SUMMARY:Latest Developments in Density Functional Methodology Symposium DESCRIPTION:River Room\, Strand campus\, King’s College London \n\n\n\n\n\n\n\n\nLatest developments in Density Functional Methodology symposium Share on X\n\n\n\n\nPushing the frontiers of density functional theory using machine learning – Aron Cohen\, Google DeepmindWe will highlight the use of machine learning to the exchange-correlation functional\, where numerous hand-crafted functional forms have already achieved great success in calculations throughout chemistry and physcis. In our recent DM21 functional (Kirkpatrick et al.\, Science 374\, 1385 (2021)) we illustrate a path to utilise the power of machine learning to this critical problem from creating accurate data that captures large parts of chemistry to addressing some of the hardest challenges of DFT.  \n\n\n\nSmooth(er) meta-generalised gradient approximation functionals: design and applications in condensed systems – Albert Bartok-Partay\, WarwickI will present our efforts to create a regularised SCAN functional which improves on the numerical instabilities of the original. Results and benchmarks will be discussed\, focussing on structural\, energetic and NMR properties of organic and inorganic crystals. \n\n\n\nThe ABC… of extended DFT – Andrew Teale\, University of NottinghamThe universal density functional is elegantly expressed in Lieb’s convex formulation of DFT\, giving access to the tools of convex analysis. When additional variables are introduced the universal density functional can become dependent on not only the charge density but also additional variables. An example is DFT in a magnetic field B expressed in terms of a vector potential A. In this case the functional depends additionally on the paramagnetic current density. Another example is orbtial-free DFT\, in which the functional depends on the charge density and the the chemical potential. The four-way correspondence of bivariate functionals is a useful tool to understand the density functionals in these contexts. Practical implementations and applications of current-DFT and orbital-DFT will be discussed. URL:https://thomasyoungcentre.org/event/latest-developments-in-density-functional-methodology-symposium/ LOCATION:King’s College London CATEGORIES:Main event ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/06/iStock-864501518-cropped-e1623144008703.jpg ORGANIZER;CN="George Booth":MAILTO:george.booth@kcl.ac.uk END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20220921T140000 DTEND;TZID=Europe/London:20220921T160000 DTSTAMP:20260410T110548 CREATED:20220705T153353Z LAST-MODIFIED:20221103T160656Z UID:3039-1663768800-1663776000@thomasyoungcentre.org SUMMARY:History (and future) of modelling materials using interatomic potentials DESCRIPTION:Watch the recording here \n\n\n\n\n\n\n\n\nHistory (and future) of modelling materials using interatomic potentials Share on X\n\n\n\n\nInteratomic Potentials and modelling as a tool in materials science – Prof Sir Richard Catlow\, Dept. of Chemistry\, UCL; School of Chemistry\, Cardiff University; UK Catalysis Hub\, Research Complex at Harwell\, UKInteratomic potential models have played and continue to play a crucial role in in the application of simulation techniques to simulating and predicting the properties of complex real materials. We will review the development of the field and current trends\, including the growth of hybrid QM/MM and of ML based methods. We will show. how the use of modelling techniques especially in conjunction with a range of experimental methods can yield unique information on structures\, dynamics\, and mechanism in a range of functional inorganic materials. Our discussion will concentrate on the following topics and systems \n\n\n\n\nStructure modelling and prediction of inorganic materials;\n\n\n\nModelling of the structures and properties of oxide surfaces;\n\n\n\nModelling of defects in inorganic materials;\n\n\n\nModelling of nano-particles;\n\n\n\nModelling of active site structures and mechanisms of catalytic reactions.\n\n\n\n\nWe will discuss the prospects of the field in the light of developments in computer hardware\, methodologies and algorithms. \n\n\n\nInteratomic potentials: Basic historical developments\, with the Natural Intelligence of our brilliant predecessors – Prof Olivier Hardouin Duparc\, Institut Polytechnique de ParisAbstract: If one cannot use Schrödinger\, let alone Dirac\, for large sets of atoms\, one uses interatomic potentials. Interatomic potentials have been proposed ever since scientists know atoms exist and tend to gather\, without collapsing together. Attraction and repulsion\, first by pairs but also via many-body interactions when some electrons can be exchanged between atoms: I will propose a historical-pedagogical development of these ideas\, mainly focused on metals but not only (also semiconductors). \n\n\n\nInteratomic potentials for modelling the intermolecular forces between organic molecules\, pharmaceuticals and biomolecules – Prof Sally Price\, UCLAbstract: An accurate intermolecular potential should be able to predict all physical properties of a molecule in the solid\, liquid and gas. This was achieved for argon about half a century ago\, but it is arguable whether it has yet been achieved for water\, and certainly not in a form that can be used in standard molecular dynamics codes. For organic molecules\, the intermolecular potential is expressed in an atom-atom form. However\, the non-sphericity of atoms in molecules\, non-additive effects\, limited transferability and molecular flexibility may all limit the accuracy of atomistic modelling of the organic solid state for specific molecules\, such as pharmaceuticals. URL:https://thomasyoungcentre.org/event/history-of-modelling-materials-using-interatomic-potentials/ CATEGORIES:Main event ORGANIZER;CN="Martijn Zwijnenburg":MAILTO:m.zwijnenburg@ucl.ac.uk END:VEVENT END:VCALENDAR