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DTSTART;TZID=Europe/London:20221202T150000
DTEND;TZID=Europe/London:20221202T173000
DTSTAMP:20260410T144605
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:20260410T144605
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:20260410T144605
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:20260410T144605
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:20260410T144605
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:20260410T144605
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
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220919T090000
DTEND;TZID=Europe/London:20220923T180000
DTSTAMP:20260410T144605
CREATED:20220721T133654Z
LAST-MODIFIED:20220721T134016Z
UID:3124-1663578000-1663956000@thomasyoungcentre.org
SUMMARY:MSSC2022 - Ab initio Modelling in Solid State Chemistry
DESCRIPTION:MSSC2022 – Ab initio Modelling in Solid State Chemistry Share on X\n\n\n\n\nThe Department of Chemistry and the Thomas Young Centre at Imperial College London and the Theoretical Chemistry Group of the University of Torino\, in collaboration with the Computational Materials Science Group of the Science and TechnologyFacilities Council (STFC)\, are organising the 2022 MSSC Summer School on the “ab initio modelling of crystalline and defective solids with the CRYSTAL code”. \n\n\n\nThe MSSC2022 will be a virtual workshop\, the morning and the afternoon sessions will be run remotely. \n\n\n\nThe week long school is designed for new users of CRYSTAL\, PhD students\, Post-Docs and researchers with interests in solid state chemistry\, physics\, materials science\, surface science\, catalysis\, magnetism and nano-science. It will provide an introduction to the capabilities of quantum mechanical simulations and to the practical use of CRYSTAL. \n\n\n\nCRYSTAL is a general-purpose program for the study of periodic systems. It uses a local basis set comprised of Gaussian type functions and can be used to perform calculations at the Hartree-Fock\, density functional or global andrange-separated hybrid functionals (e.g. B3LYP\, HSE06)\, double hybrid levels of theory. \n\n\n\nAnalytical first derivatives with respect to the nuclear coordinates and cell parametersand analytical derivatives\, up to fourth order\, with respect to an applied electric field (CPHF/CPKS) are available. \n\n\n\nThe programme is available:https://www.imperial.ac.uk/mssc/mssc2022/programme/ \n\n\n\nYou can register at:https://www.imperial.ac.uk/mssc/mssc2022/registration/
URL:https://thomasyoungcentre.org/event/mssc2022-ab-initio-modelling-in-solid-state-chemistry/
CATEGORIES:Main event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220905T090000
DTEND;TZID=Europe/London:20220909T170000
DTSTAMP:20260410T144605
CREATED:20220516T094529Z
LAST-MODIFIED:20220609T145454Z
UID:2941-1662368400-1662742800@thomasyoungcentre.org
SUMMARY:Sargent Centre Summer School on Data-Driven Optimization
DESCRIPTION:Venue: Lecture Theatre 1\, ACE Extension\, South Kensington Campus\, Imperial College London \n\n\n\nTickets: £250 \n\n\n\nTo Register: Sargent Centre Summer School on Data-Driven Optimization | Events | Imperial College London \n\n\n\nThe Summer School will include tutorials and workshops by leading researchers on areas such as Reinforcement Learning\, Machine Learning\, Bayesian Optimisation\, Hybrid Modelling\, and other exciting topics. It will also allow participants to interact with speakers and peers to build a community around the topic and its applications.  The school is targeted at PhD students\, Postdocs and early career researchers in general.   \n\n\n\nThe summer school will be followed by a PSE@ResearchDay (9th of September)\, where the attendees will be able to present their work either in an oral presentation or poster format. The idea is that this will foster more interaction between participants and their research. This is of course optional but included with the Summer School. 
URL:https://thomasyoungcentre.org/event/summer-school-on-data-driven-optimization/
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2022/05/CPSE-Centre-for-Process-Systems-Engineering.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220706T090000
DTEND;TZID=Europe/London:20220707T170000
DTSTAMP:20260410T144605
CREATED:20220331T132010Z
LAST-MODIFIED:20220624T114136Z
UID:2766-1657098000-1657213200@thomasyoungcentre.org
SUMMARY:Fundamentals of the Electrochemistry of the Metal/Electrolyte Interface Symposium
DESCRIPTION:Venue: Anatomy Lecture Theatre\, 6th Floor\, King’s Building\, Strand campus\, King’s College London  \n\n\n\n\n\nThis symposium is supported by the TYC and is the third meeting organised by the partners of the EPSRC project on quantum corrosion. The symposium will focus on the fundamentals of electrochemistry of the metal/electrolyte interface\, and will bring together theorists and experimentalists to discuss the latest developments. As well as the talks\, there is a poster session and a concluding discussion session. \n\n\n\nRegistration is now open and will close once we have 50 attendees.To register please click here  \n\n\n\nProgramme: \n\n\n\nDay 1 – Wednesday 6th July 0930 – 0955Tea and Coffee0955 – 1000Introduction Professor Bashir M. Al-Hashimi CBE FREng Executive Dean\, Faculty of Natural Mathematical & Engineering Sciences\, KCL1000 – 1100Structure and stability of surface oxides on metals Philippe Marcus (Centre National de la Recherche Scientifique)1100 – 1200Atom probe tomography and its applications in understanding corrosion of metalsStella Pedrazzini (Imperial College London)1200 – 1300  Lunch1300 – 1400Time-resolved ATR-SEIRAS studies of electrocatalytic reactions Angel Cuesta Ciscar (The University of Aberdeen)1400 – 1500 Vibrational sum frequency generation spectroscopy at the solid/liquid interface Ellen Backus (University of Vienna)1500 – 1520Break1520 – 1620Vibrational spectroscopy of water interfaces from ab initio molecular dynamicsMarialore Sulpizi (Bochum University)1620 – 1720Electrode models for computational electrochemistry Mathieu Salanne (Sorbonne Université)1730Reception\n\n\n\nDay 2 – Thursday 7th July0900 – 0930Tea and Coffee0930 – 1030Using Electrochemical Noise for Improving Current Understanding on the Transition of Pitting into SCC Helmut Sarmiento-Klapper (Baker Hughes)1030 – 1130Insights on the hydrogen pick up mechanisms of a Nb-containing Zr alloy (M5Framatome) during its corrosion in PWR primary water: an experimental study of the media/oxide/alloy system and its modelling Frantz Martin (Atomic Energy and Alternative Energies Commission\, CEA)1130 – 1230Correlative imaging of lithium ion diffusion in 3D structures inside operating batteries Ann Huang (Imperial College London)1230 – 1330Lunch 1330 – 1430Ab initio insights into processes at solid/liquid interfaces Mira Todorova (Max-Planck-Institut für Eisenforschung)1430 – 1530Electro-chemo-mechanical phase field models for predicting pitting and stress corrosion cracking Emilio Martínez-Pañeda (Imperial College London)1530 – 1550Break1550 – 1650Discussion: Chair Alexei Kornyshev\, Imperial College London1650 – 1700Close\n\n\n\nOrganisers \n\n\n\nClotilde Cucinotta (Imperial College London)Andrew Horsfield (Imperial College London & King’s College London)Tony Paxton (Imperial College London)Hafiza Bibi (Imperial College London)
URL:https://thomasyoungcentre.org/event/fundamentals-of-the-electrochemistry-of-the-metal-electrolyte-interface/
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/11/cropped-TYC-Logo_blue_on_white_2.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220623T113000
DTEND;TZID=Europe/London:20220623T140000
DTSTAMP:20260410T144605
CREATED:20220428T101830Z
LAST-MODIFIED:20220623T094437Z
UID:2847-1655983800-1655992800@thomasyoungcentre.org
SUMMARY:Atomistic view on structures and processes in electrochemical energy conversion and storage from first principles
DESCRIPTION:Atomistic view on structures and processes in electrochemical energy conversion and storage from first principles Share on X\n\n\nAxel GroßInstitute of Theoretical Chemistry\, Ulm University\, 89069 Ulm/GermanyHelmholtz Institute Ulm (HIU) Electrochemical Energy Storage\, 89081 Ulm/Germany \n\n\n\nRoom B10\, White City Campus\, Wood Lane – Imperial College London and hybrid \n\n\n\n \n\n\n\n \n\n\n\nAbstract: Electrochemical energy storage and conversion is of critical importance for our future sustainable\, environmentally friendly energy supply. Due to this importance\, significant research and development efforts are undertaken worldwide in order to improve our understanding of electrochemical processes at electrolyte/electrode interfaces and to develop more efficient electrochemical devices such as electrocatalysts\, fuel cells and batteries. Many concepts still used today in electrochemistry are rooted in insightful thermodynamical concepts developed more than one century ago. Thermodynamics is a field that deals with measurable macroscopic physical quantities\, but a full understanding of the nature of these quantities requires a connection to microscopic properties via statistical mechanics. In this talk\, I will try to illustrate this connection using recent examples of first-principles studies addressing structures and processes in electrocatalysis and batteries on the atomic level. \n\n\n\nThe atomistic modelling of electrochemical interfaces between liquid electrolytes and electrodes requires to perform appropriate statistical averages to capture the liquid nature of electrolytes. Fortunately\, due to the increase in computer power and the development of more efficient first-principles codes\, it has nowadays become possible to perform these averages based on ab initio molecular dynamics simulations. I will address the recent progress in our understanding of the interfaces between aqueous electrolytes and metal electrodes [1]\, but also present examples how stable adsorbate structures can be derived based on grand-canonical concepts [2]. \n\n\n\nIn the second part\, I will focus on structures and processes in batteries from an atomistic perspective. I will particularly use the concept of descriptors to relate materials properties to desired or undesired functional properties of these materials. It will be shown that dendrite growth in batteries might be related to the height of metal self-diffusion barriers [3]. Furthermore\, I will show that the competition between coordination and bond length that governs the ionic site preference in spinel compounds upon trigonal distortions can only be understood by also taking covalent interactions into account [4]. This has led to the identification of a descriptor for the ion mobility in crystalline battery electrodes and solid electrolytes [5]\, that combines ion radii\, oxidations states and the difference in the electronegativity of the migrating cations and the anions of the host lattice\, resulting in linear scaling relations between the height of the migration barrier and this descriptor. \n\n\n\nLiterature: \n\n\n\n[1] Axel Groß and Sung Sakong\, Chem. Rev. 2022\, DOI: 10.1021/acs.chemrev.1c00679[2] Axel Groß\, Curr. Opin. Electrochem. 2021\, 27\, 100684.[3] M. Jäckle\, K. Helmbrecht\, M. Smits\, D. Stottmeister\, A. Groß\, Energy Environ. Sci. 2018\, 11\, 3400.[4] M. Sotoudeh\, M. Dillenz\, A. Groß\, Adv. Energy Sustainability Res. 2021\, 2\, 2100113.[5] Mohsen Sotoudeh and Axel Groß\, JACS Au 2022\, 2\, 463–471
URL:https://thomasyoungcentre.org/event/atomistic-view-on-structures-and-processes-in-electrochemical-energy-conversion-and-storage-from-first-principles/
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2022/04/index.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220620T110000
DTEND;TZID=Europe/London:20220620T120000
DTSTAMP:20260410T144605
CREATED:20220615T125722Z
LAST-MODIFIED:20220616T090957Z
UID:2841-1655722800-1655726400@thomasyoungcentre.org
SUMMARY:TYC Journal Club: Impact of metastable defect structures on carrier recombination in solar cells
DESCRIPTION:TYC Journal Club: Impact of metastable defect structures on carrier recombination in solar cells  Share on X\n\n\n\n\nJoin us on Monday 20 June at 11am on Zoom. \n\n\n\nIn this meeting\, Seán Kavanagh will discuss his work on: Impact of metastable defect structures on carrier recombination in solar cells \n\n\n\nThe main results: \n\n\n\nWe elucidate the additional pathways for electron-hole recombination (the key limiting factor for solar cell efficiencies) introduced by metastable defects in semiconductors.We show that metastable defects introduce multiple extra recombination pathways\, potentially catalysing the overall recombination rate\, depending on the individual kinetics.We analyse the general trends in behaviour for electron/hole capture by metastable defects\, determining the energetic requirements and conditions under which metastable states are likely to impact recombination.Finally\, we take tellurium interstitials in CdTe as an illustrative example of this behaviour\, where metastable defect structures transform this species from a benign defect centre to a relevant trap state.\n\n\n\nHope to see you all there! \n\n\n\nJoining on Zoom:https://ucl.zoom.us/j/708748699?pwd=MU50Wi9Dc1IyTkcxenRBalY5dm9rZz09 Meeting ID: 708 748 699Password: TYCJC
URL:https://thomasyoungcentre.org/event/tyc-journal-club-impact-of-metastable-defect-structures-on-carrier-recombination-in-solar-cells/
CATEGORIES:Journal Club
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/11/cropped-TYC-Logo_blue_on_white_2.jpg
ORGANIZER;CN="Vasileios Fotopoulos Fotis":MAILTO:vasileios.fotis.19@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220608T085500
DTEND;TZID=Europe/London:20220609T163000
DTSTAMP:20260410T144605
CREATED:20220428T102829Z
LAST-MODIFIED:20220503T120508Z
UID:2842-1654678500-1654792200@thomasyoungcentre.org
SUMMARY:Software solutions to the challenges of materials modelling
DESCRIPTION:Carbon cluster and fullerene formation from molecular dynamics simulations\, performed using the GAP-20 machine learning model. Credit: Patrick Rowe\n\n\n\n\nSoftware solutions to the challenges of materials modelling Share on X\n\n\n\n\nSatellite meeting organised by Professor Scott Woodley\, Professor Sir Richard Catlow FRS\, Professor Nora H de Leeuw and Professor Angelos Michaelides. \n\n\n\nOverview\n\n\n\nSatellite meeting organised by Professor Scott Woodley\, Professor Sir Richard Catlow FRS\, Professor Nora H de Leeuw and Professor Angelos Michaelides. \n\n\n\nIn the Discussion meeting the aim is to discuss the challenges and achievements in materials modelling that will and have been enabled by High End Computer (HEC) resources. The Satellite meeting will move on to the software solutions recently developed and still required in order to effectively exploit HEC to address the scientific challenges identified during the Discussion meeting. \n\n\n\nMore information about the schedule of talks and speaker biographies will be available soon. Speaker abstracts will be available closer to the meeting date.  \n\n\n\nPoster session/talk submission\n\n\n\nThe event will feature a poster session on 8 June 2022. The organisers would like to invite submissions for short talks and posters. The talks should cover research in the area of the meeting and are expected to be 25 minutes. If you are interested in submitting a talk or poster abstract for consideration please send a title and a 200-word abstract\, in the third person with no references nor pictures\, to scientific.meetings@royalsociety.org with subject line ‘Software solutions to the challenges of materials modelling’ by 25 April 2022. Please note you should register to attend the event before submitting a talk or poster abstract. \n\n\n\nAttending this event\n\n\n\nThis meeting is intended for researchers in relevant fields. \n\n\n\nFree to attend (attendees can only join in-person)Limited places\, advance registration essential (more information about registration will be available soon)\n\n\n\nEnquiries: contact the Scientific Programmes team. \n\n\n\nhttps://royalsociety.org/science-events-and-lectures/2022/06/materials-modelling/
URL:https://thomasyoungcentre.org/event/software-solutions-to-the-challenges-of-materials-modelling/
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2022/04/Supercomputer-event-June-22.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220606T120000
DTEND;TZID=Europe/London:20220606T123000
DTSTAMP:20260410T144605
CREATED:20220601T122408Z
LAST-MODIFIED:20220601T122413Z
UID:2961-1654516800-1654518600@thomasyoungcentre.org
SUMMARY:TYC Lunchtime Seminar: Engineering and predicting the electronic and optical properties of porphyrin-based structures
DESCRIPTION:Victor H Posligua HernandezDeaprtment of Chemistry \n\n\n\nAbstract: Metal-organic frameworks (MOFs) are promising photocatalytic materials due to their high surface area and tuneability of their electronic structure. We  will discuss how to engineer the band structures and optical properties of a family of two-dimensional porphyrin-based MOFs\, consisting of M-tetrakis(4-carboxyphenyl)porphyrin structures (M-TCPP\, where M = Zn or Co) and metal (Co\, Ni\, Cu or Zn) paddlewheel clusters\, with the aim of optimising their photocatalytic behaviour in solar fuel synthesis reactions (water-splitting and/or CO2 reduction). Based on density functional theory (DFT) and time-dependent DFT simulations with a hybrid functional\, three types of composition/structural modifications were studied: (a) varying the metal centre at the paddlewheel or at the porphyrin centre to modify the band alignment; (b) partially reducing the porphyrin unit to chlorin\, which leads to stronger absorption of visible light; and (c) substituting the benzene bridging between the porphyrin and paddlewheel\, by ethyne or butadiyne bridges\, with the aim of modifying the linker to metal charge transfer behaviour. Our work offers new insights on how to improve the photocatalytic behaviour of porphyrin- and paddlewheel-based MOFs.
URL:https://thomasyoungcentre.org/event/tyc-lunchtime-seminar-engineering-and-predicting-the-electronic-and-optical-properties-of-porphyrin-based-structures/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220606T090000
DTEND;TZID=Europe/London:20220607T170000
DTSTAMP:20260410T144605
CREATED:20220428T105119Z
LAST-MODIFIED:20220503T120555Z
UID:2864-1654506000-1654621200@thomasyoungcentre.org
SUMMARY:Supercomputer modelling of advanced materials
DESCRIPTION:Water droplet on graphene simulated by first-principle quality machine learning potentials. Image credit: Christoph Schran.\n\n\n\n\nSupercomputer modelling of advanced materials Share on X\n\n\n\n\nScientific discussion meeting organised by Professor Scott Woodley\, Professor Sir Richard Catlow FRS\, Professor Nora H de Leeuw and Professor Angelos Michaelides. \n\n\n\nThe development of advanced materials is of central importance in key scientific and industrial areas\, including energy\, catalysis and quantum technologies. High end computing and data science offer unprecedented opportunities for predictive modelling of complex materials. The meeting will explore the scientific and methodological challenges in the field\, focusing on structure prediction\, nucleation and crystal growth\, biomaterials and catalysis. \n\n\n\nThe schedule of talks and speaker biographies will be available soon. Speaker abstracts will be available closer to the meeting date. Meeting papers will be published in a future issue of Philosophical Transactions of the Royal Society A. \n\n\n\nPoster session\n\n\n\nThis event will feature a poster session on 6 June 2022. The posters will be selected by the organisers of the meeting. If you are interested in submitting a poster for consideration please send a title\, list of authors and a 200-word abstract\, in the third person with no references nor pictures\, to scientific.meetings@royalsociety.org with subject line ‘Supercomputer modelling of advanced materials – poster abstract’ by 13 May 2022. Please note the poster presenters should register to attend the meeting before they send us a poster abstract. \n\n\n\nAttending this event\n\n\n\nThis meeting is intended for researchers in relevant fields. \n\n\n\nFree to attendBoth in-person and online attendance availableLimited places\, advance registration essential\n\n\n\nEnquiries: contact the Scientific Programmes team. \n\n\n\nhttps://royalsociety.org/science-events-and-lectures/2022/06/supercomputer-modelling/
URL:https://thomasyoungcentre.org/event/supercomputer-modelling-of-advanced-materials-2/
CATEGORIES:Main event
ATTACH;FMTTYPE=image/png:https://thomasyoungcentre.org/wp-content/uploads/2022/04/Supercomputer-event-June-22.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220523T120000
DTEND;TZID=Europe/London:20220523T123000
DTSTAMP:20260410T144605
CREATED:20220517T125705Z
LAST-MODIFIED:20220517T125707Z
UID:2949-1653307200-1653309000@thomasyoungcentre.org
SUMMARY:TYC Lunctime Seminar: Electronic structure of twisted bilayer materials
DESCRIPTION:Click here to join the Seminar \n\n\n\nKemal AtalarDepartment of Materials\, ICL \n\n\n\nAbstract: The discovery of correlated and superconducting states in magic-angle twisted bilayer graphene has generated interest in twisted heterostructures composed of other 2D materials. For example\, signatures of superconductivity and exotic optical behaviour have been observed recently in twisted bilayers of transition metal dichalcogenides (TMDs). The theoretical and computational study of these materials using first-principles methods\, however\, remains challenging due to their large Moiré superlattice sizes at small twist angles. In this work\, accurate and efficient tight-binding models for predicting and understanding the electronic structure of twisted TMD heterostructures are developed. The first-principles TMD tight-binding model of Fang et al. is extended to twisted and hetero-bilayer structure and additional interlayer interactions between pz and dz2 orbitals are included. Finally\, the band structures and effect of twisting in various Moiré heterostructures of TMDs are demonstrated.
URL:https://thomasyoungcentre.org/event/tyc-lunctime-seminar-electronic-structure-of-twisted-bilayer-materials/
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/11/cropped-TYC-Logo_blue_on_white_2.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220516T120000
DTEND;TZID=Europe/London:20220516T123000
DTSTAMP:20260410T144605
CREATED:20220511T101519Z
LAST-MODIFIED:20220512T134654Z
UID:2912-1652702400-1652704200@thomasyoungcentre.org
SUMMARY:Death Spikes and Healthy Bumps: Nanostars for drug delivery
DESCRIPTION:William Morton\, Department of Materials  \n\n\n\nVenue: G20\, Royal School of Mines  \n\n\n\nClick here to join the Seminar \n\n\n\nAbstract: Understanding how nanoparticles navigate biological barriers is crucial for determining their use as drug delivery agents. Cellular uptake has thus far been the main metric of determining the design of a successful nanoparticle. A mechanistic understanding of how nanoparticles enter cells\, and what the limitations are\, has been thoroughly developed over the past decade. However\, a particle class that has been overlooked in this study is nanostars (nano-urchins\, virus-like nanoparticles\, etc.). Using a specialised experimental data set\, the theoretical work presented demonstrates different pathways for diffusion of nanostars\, compared to nanospheres. Specifically\, interest lies in densely packed cellular environments\, similar to those found in the blood brain barrier. Geometrical effects alone can promote drug delivery in difficult to reach areas of the body by avoiding endocytosis in densely packed areas. 
URL:https://thomasyoungcentre.org/event/death-spikes-and-healthy-bumps-nanostars-for-drug-delivery/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220510T100000
DTEND;TZID=Europe/London:20220510T160000
DTSTAMP:20260410T144605
CREATED:20220315T094953Z
LAST-MODIFIED:20220509T101954Z
UID:2676-1652176800-1652198400@thomasyoungcentre.org
SUMMARY:TYC Student Day 2022
DESCRIPTION:TYC Student Day 2022 Share on X\n\n\n\n\nAfter the long hiatus we are looking forward to seeing you in-person at the TYC Student Day 2022.  It will be great to see your faces again\, old and new! \n\n\n\nWe would like to invite all TYC students to submit abstracts to present a poster of their research\, and final year students to submit abstracts for talks.  ~12 talks will be selected\, and all of the posters from across the four TYC colleges will be on display at a poster presentation during lunch and at a drinks reception at the end of the day.We are also looking forward to hosting external speakers from DeepMind and the UK Atomic Energy Authority (UKAEA) to talk about careers.Best Talk’ and ‘Best Poster’ will be awarded prizes. \n\n\n\nA copy of the abstract booklet can be downloaded here  \n\n\n\nSchedule: \n\n\n\n10:00 – 10:05 Introduction  (Session 1) –  chaired by Kemal Atalar10:05 – 10:20 Christopher Keegan 10:20 – 10:35 Amir Sidat 10:35 – 10:50 Luisa Herring Rodriguez 10:50 – 11:05 Yao Wei 11:05 – 11:20 Refreshments  (Session 2) – chaired by William Morton11:20 – 11:35 Christian Ahart 11:35 – 11:50 Robert Michael Jones 11:50 – 12:20 Sam Tippetts – UKAEA 12:20 – 14:00 Lunchbreak  (Session 3) – chaired by Chengcheng Xiao14:00 – 14:15 Fiona Sander 14:15 – 14:30 Nicholas Siemons 14:30 – 14:45 Fabian Thiemann 15:00 – 15:15 Mario Zauchner 15:15 – 15:30 Refreshments  (Session 4) – chaired by Robert Michael Jones15:30 – 16:00 Lara Roman Castellanos – DeepMind 16:00 – 16:15 Yannic Rath 16:15 – 16:30 Camilla Di Mino 16:30 – 16:35 Closing remarks 16:35 – 17:00 Posters 17:00 – 17:05 Winning poster / talk announcement 17:05 – 18:00 Drinks reception 
URL:https://thomasyoungcentre.org/event/tyc-student-day-2022/
LOCATION:The Octagon\, Queens’ Building\, Queen Mary University of London\, Mile End Road\, London\, E1 4NS\, United Kingdom
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2022/03/Student-Day-image.jpg
ORGANIZER;CN="Karen Stoneham / Hafiza Bibi":MAILTO:tyc-administrator@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220509T120000
DTEND;TZID=Europe/London:20220509T123000
DTSTAMP:20260410T144605
CREATED:20220329T092643Z
LAST-MODIFIED:20220428T111214Z
UID:2743-1652097600-1652099400@thomasyoungcentre.org
SUMMARY:TYC Lunctime Seminar: FCIQMC Simulations of Solids
DESCRIPTION:Click here to join the Seminar \n\n\n\nChristopher BradleyDepartment of Physics\, ICL \n\n\n\nAbstract:Quantum Monte Carlo (QMC) refers to a set of stochastic methods used in solving quantum many-body problems. They have a rich history in solid-state physics\, for instance in the production of very accurate benchmarks for better scaling methods like DFT. One such method is Full Configuration Interaction QMC (FCIQMC)\, which solves for the ground state of a system by evolving a population of walkers in a Hilbert space of Slater determinants. Unlike more popular Monte Carlo methods (e.g. Variational QMC\, Diffusion QMC)\, it is not dependent upon the quality of an initial trial function nor does it rely on uncontrolled approximations. This has led to its success in energy calculations of molecular systems as well as in the uniform electron gas. \n\n\n\nIn this talk\, I will give a brief summary of FCIQMC before going on to discuss its application to solids and its performance relative to other methods.
URL:https://thomasyoungcentre.org/event/tyc-lunctime-seminar-fciqmc-simulations-of-solids/
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/11/cropped-TYC-Logo_blue_on_white_2.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220412T120000
DTEND;TZID=Europe/London:20220412T130000
DTSTAMP:20260410T144605
CREATED:20220407T135808Z
LAST-MODIFIED:20220407T135811Z
UID:2808-1649764800-1649768400@thomasyoungcentre.org
SUMMARY:New catalytic mechanisms in carbohydrate-active enzymes (CAZymes) unveiled by computer simulation
DESCRIPTION:Professor Carme RoviraDepartment of Inorganic and Organic Chemistry & Institute of Computational and Theoretical Chemistry (IQTCUB)\, University of Barcelona \n\n\n\nJoin the Seminar here  \n\n\n\nAbstract: \n\n\n\nCarbohydrate-active enzymes (CAZymes)\, such as glycoside hydrolases and glycosyltransferases\, constitute the main machinery for the degradation\, synthesis and modification of carbohydrates in nature. They have a myriad of industrial and biotechnological applications\, ranging from biofuel production to biotherapeutics. Understanding how carbohydrate are processed by CAZymes\, identifying the catalytic residues\, the role of enzyme conformational transitions and the conformation of the substrate at the transition state of the chemical reaction\, can guide inhibitor design.  Using state-of-art simulation techniques such as ab initio quantum mechanics/molecular mechanics (QM/MM) and metadynamics [1-3] we have contributed to answer these questions\, providing an atomistic view of enzyme action. In this talk I will describe some of the CAZyme mechanisms that we have recently investigated [4-6]\, in a collaborative work with research groups of structural and chemical biology. \n\n\n\n[1] Laio\, A.; Parrinello\, M. Proc. Nat. Acad. Sci. U.S.A. 2002\, 99\, 12562-12566. \n\n\n\n[2] Ardèvol\, A.; Rovira\, C. J. Am. Chem. Soc. 2015\, 137\, 7528-7547. \n\n\n\n[3] J. Coines\, L. Raich\, C. Rovira. Curr. Opin. Chem. Biol. 2019\, 53\, 183-191. \n\n\n\n[4]  L. F. Sobala\, G. Speciale\, S. Zhu\, L. Raich\, N. Sannikova\, A. J. Thompson\, Z. Hakki\, D. Lu\, Y. Zhang\, S. S. K. Abadi\, A. R. Lewis\, V. Rojas-Cervellera\, G. Bernardo-Seisdedos\, O. Millet\, J. Jiménez-Barbero\, A. J. Bennet\, M. Sollogoub\, C. Rovira\, G. J Davies\, S. J. Williams\, ACS Cent. Sci. 2020\, 6\, 760–770. \n\n\n\n[5] M. K. Bilyard\, H. Bailey\, L. Raich\, M. Gafitescu\, T. Machida\, J. Iglesias-Fernández\, S. S. Lee\, C. D. Spicer\, C. Rovira\, W. W. Yue\, B. G. Davis\, Nature 2018\, 563\, 235–240. \n\n\n\n[6] M. A. B. Morais\, J. Coines\, M. N. Domingues\, R. A. S. Pirolla\, C. C. C. Tonoli\, C. R. Santos\, J. B. L. Correa\, F. C. Gozzo\, C. Rovira\, M. T. Murakami. Nat. Commun. 2021\, 12\, 367.
URL:https://thomasyoungcentre.org/event/new-catalytic-mechanisms-in-carbohydrate-active-enzymes-cazymes-unveiled-by-computer-simulation/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220404T110000
DTEND;TZID=Europe/London:20220404T120000
DTSTAMP:20260410T144605
CREATED:20220324T130359Z
LAST-MODIFIED:20220324T131245Z
UID:2719-1649070000-1649073600@thomasyoungcentre.org
SUMMARY:TYC Journal Club: Moiré materials and flat bands: the case of twisted transition metal dichalcogenides bilayers
DESCRIPTION:Software solutions to the challenges of materials modelling Share on X\n\nSoftware solutions to the challenges of materials modelling Share on X\n\n\n\n\nJoin us on Monday 4 April at 11am on Zoom. \n\n\n\nIn this meeting\, Valerio Vitale will discuss his work on:Moiré materials and flat bands: the case of twisted transition metal dichalcogenides bilayers. \n\n\n\nIntro to the physics of moiré materials and the field of twistronicsFlat bands and electron correlation Twisted transition metal dichalcogenides (TMDs) bilayers as a realisation of moiré materialsChallenges in modelling the atomic and electronic structure of moiré materialsOur multiscale approach: Classical force fields and ab initio tight-bindingResultsConclusions\n\n\n\nHope to see you all there! \n\n\n\nJoining on Zoom:https://ucl.zoom.us/j/708748699?pwd=MU50Wi9Dc1IyTkcxenRBalY5dm9rZz09 Meeting ID: 708 748 699Password: TYCJC
URL:https://thomasyoungcentre.org/event/tyc-journal-club-moire-materials-and-flat-bands-the-case-of-twisted-transition-metal-dichalcogenides-bilayers/
CATEGORIES:Journal Club
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/11/cropped-TYC-Logo_blue_on_white_2.jpg
ORGANIZER;CN="Vasileios Fotopoulos Fotis":MAILTO:vasileios.fotis.19@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220331T090000
DTEND;TZID=Europe/London:20220331T160000
DTSTAMP:20260410T144605
CREATED:20220307T104950Z
LAST-MODIFIED:20220404T154009Z
UID:2632-1648717200-1648742400@thomasyoungcentre.org
SUMMARY:MMM Hub: HPE / NVIDIA GPU Training Day
DESCRIPTION:Software solutions to the challenges of materials modelling Share on X\n\nSoftware solutions to the challenges of materials modelling Share on X\n\n\n\n\n \n\n\n\n09:00 – 12:00 (UK time) Technology and Partner sessions (UCL\, HPE & NVIDIA) chaired by Owain Kenway – UCL \n\n\n\nRecording: Introduction to the MMM Hub GPU Training Day – Owain Kenway\, UCLRecording: HPE HPC/AI EMEA Research Lab – Tim Dykes\, HPERecording: Overview of the new MMM Hub system – Owain Kenway\, UCLRecording: HPE CRAY Programming Environment – Tim Dykes\, HPERecording: Multi-GPU programming with MPI and NCCL – Jiri Kraus\, NVIDIARecording: Developer Tools: Nsight Product Review – Sanjiv Satoor\, NVIDIA \n\n\n\n13:00 – 16:00 (UK time) Materials community codes\, experiences & lessons learned (invited speakers) chaired by Filippo Spiga – NVIDIA \n\n\n\nRecording: Tools and Techniques to port codes on GPU – Introduction by Filippo Spiga\, NVIDIARecording: Tools & Techniques to port CASTEP – Phil Hasnip\, YorkRecording: Lessons learned from porting VASP to GPUs – Stefan Maintz\, NVIDIARecording: Current state of CP2K on GPU – Matthieu Talletumier\, CSCSRecording: Challenges and lesons from using GPUs in GSGW – Dimitar Pashov\, King’s College LondonRecording: Getting QMCpack ready to model material properties at Exascale – Ye Luo\, Argonne National Laboratories
URL:https://thomasyoungcentre.org/event/mmm-hub-hpe-nvidia-gpu-training-day/
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2022/01/MMM-no-description.jpg
ORGANIZER;CN="Dr Owain Kenway":MAILTO:o.kenway@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220330T140000
DTEND;TZID=Europe/London:20220330T170000
DTSTAMP:20260410T144605
CREATED:20220218T161617Z
LAST-MODIFIED:20220404T093632Z
UID:2494-1648648800-1648659600@thomasyoungcentre.org
SUMMARY:TYC Distinguished Speaker Symposium:  Modelling Surfaces & Catalysis
DESCRIPTION:Software solutions to the challenges of materials modelling Share on X\n\nSoftware solutions to the challenges of materials modelling Share on X\n\n\n\n\nWatch the Symposium here\n\n\n\nProfessor Dr Joachim Sauer – Humboldt Universität zu BerlinNext Generation Quantum Chemistry of Water in Acidic ZeolitesWater plays a ubiquitous role in the synthesis\, post-synthesis treatment and reactivity of zeolite catalysts. We consider the local structure of bridging OH groups (b-OH) and their interaction with water molecules for Al-O(H)-Si sites in different zeolite frameworks and at different locations.A review of past work is followed by next generation studies which go beyond previous work in several respects:(1) Structure optimizations are performed at the MP2 level using our hybrid MP2(cluster model):DFT-D(periodic) method.(2) Special attention is paid to sites with internal H-bonds across rings of corner-sharing TO4 tetrahedra to a Si-O-Si acceptor site (Fig.\, left).(3) In addition to the H-bond approach of H2O to the b-OH site (Fig.\, right)\, we consider Lewis attack to the AlO4 tetrahedron in anti-position to the b-OH site (Fig.\, middle). \n\n\n\n\n\n\n\nThe MP2-quality results for OH vibrational frequencies and 1H-NMR chemical shifts of different types of bridging OH groups and their interaction with one and two water molecules are compared with experimental spectroscopic results and heats of adsorption. \n\n\n\nThe conclusions are also relevant for adsorption of alcohols at b-OH sites. \n\n\n\n\n\n\n\nProfessor Adrian Mulholland – University of BristolMultiscale modelling of biocatalysts for enzyme design\, evolution and engineeringSimulations are revealing biomolecular mechanisms relevant to function\, and are contributing to catalyst and inhibitor design. Simulations can be used as computational ‘assays’ of biological activity\, e.g. to predict drug resistance or effects of mutation. Combined quantum mechanics/molecular mechanics (QM/MM) methods allow modelling of reactions in proteins: they can identify mechanisms of reaction (e.g. for targeted covalent inhibitors such as ibrutinib\, and for the SARS-CoV-2 main protease) determinants of catalytic activity and predict the activity of bacterial enzymes against antibiotics. \n\n\n\nDynamical-nonequilibrium molecular dynamics (D-NEMD) simulations show coupling between allosteric sites and the active site in beta-lactamase enzymes; the pathways identified contain positions that differ between clinically relevant variants\, indicating that allosteric effects modulate the spectrum of activity of these antibiotic resistance enzymes. The D-NEMD approach can effectively combine cloud-based and other HPC resources. \n\n\n\nIncreasingly\, simulations are contributing to the engineering of natural enzymes and de novo biocatalysts. Simulations are also contributing to the emerging evidence that activation heat capacity is an important factor in enzyme evolution and thermoadaptation. Directed evolution of a designed Kemp eliminase unexpectedly introduced curvature into the temperature dependence of reaction\, showing the emergence of an activation heat capacity. Simulations identify the dynamical networks involved\, which may provide useful targets for mutation and directed evolution experiments. \n\n\n\nVirtual reality offers new ways interact with simulations\, and new ways to collaborate. Interactive MD simulation in virtual reality (iMD-VR) allows manipulation of biological macromolecules\, going beyond mere visualization to allow e.g. fully flexible docking of drugs into protein targets. The COVID-19 pandemic has highlighted the need for effective tools for virtual collaboration. Groups of researchers can work together\, using iMD-VR for molecular problems such as catalyst and structure-based drug design. Using the cloud\, researchers in different physical locations can work together in the same virtual molecular environment. Simulations\, including iMD-VR\, with collaborative sharing of models and data\, have been brought together to design peptide inhibitors of the SARS-CoV-2 main protease. \n\n\n\nReferences‘Evolution of dynamical networks enhances catalysis in a designer enzyme HA Bunzel\, JL Anderson\, D Hilvert\, VL Arcus\, MW van der Kamp & AJ Mulholland Nature Chemistry 13\, 1017-1022 (2021)‘Designing better enzymes: Insights from directed evolution’ HA Bunzel\, JLR Anderson & AJ Mulholland Current Opinion in Structural Biology 67\, 212-218 (2021)‘Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems ASF Oliveira\, G Ciccotti\, S Haider\, AJ Mulholland The European Physical Journal B 94\, 1-12 (2021)‘Discovery of SARS-CoV-2 M pro peptide inhibitors from modelling substrate and ligand binding H. Chan et al. Chemical Science 12\, 13686-13703 (2021) \n\n\n\nBiography: Adrian Mulholland is a Professor of Chemistry\, University of Bristol\, UK. Following his first degree at Bristol\, he worked in a wine merchant and for ICI Pharmaceuticals before doctoral studies with Graham Richards (Oxford) and postdoctoral work with Martin Karplus (Harvard). His research focuses on mechanisms of enzyme catalysis\, biomolecular dynamics and function. He develops and applies biomolecular simulation methods to problems in antimicrobial resistance\, drug metabolism\, biocatalysis and enzyme design and evolution. He has published over 200 papers\, attracting over 10\,000 citations. He was awarded the 2020 John Meurig Thomas Medal ‘for outstanding and innovative work in catalytic science’. \n\n\n\n\n\n\n\nDr Thomas Keal – Science and Technology Facilities Council (STFC)Recent developments in QM/MM modelling with ChemShellChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. The QM/MM approach is well suited to studying catalysis in both biomolecular systems and materials\, where the reactive region can be treated at the QM level and the environment with classical methods. QM/MM is particularly useful when coupled with serial crystallography experiments\, as is highlighted by a case study of the mechanism of nitrite reduction in a copper nitrite reductase enzyme [1]. Recent work in QM/MM modelling of materials chemistry will also be discussed\, as well as the redevelopment of ChemShell as an open source\, python-based package\, which offers a modern platform for multiscale modelling with an emphasis on high performance computing platforms [2]. \n\n\n\nReferences:[1] K. Sen\, M.A. Hough\, R.W. Strange\, C. Yong and T.W. Keal\, J. Phys. Chem. B\, 125\, 9102 (2021).[2] Y. Lu\, M.R. Farrow\, P. Fayon\, A.J. Logsdail\, A.A. Sokol\, C.R.A. Catlow\, P. Sherwood and T.W. Keal\, J. Chem. Theory Comput.\, 15\, 1317 (2019). \n\n\n\nBiography: Thomas Keal is a Principal Scientist in the Computational Chemistry Group at STFC Daresbury Laboratory\, with responsibility for QM/MM methods development. He completed his PhD in 2005 in the group of David Tozer at Durham University\, focussing on the development of new exchange-correlation functionals for density functional theory. He then moved to a postdoctoral position in the group of Walter Thiel in Mülheim an der Ruhr\, Germany\, working on methods for excited state optimisation and dynamics of biomolecules. He joined Paul Sherwood’s group at Daresbury in 2008 to continue work on methods development in the ChemShell software package\, and now leads the team developing ChemShell. His research interests are in QM/MM methodology and its application to problems in biochemistry and materials chemistry. \n\n\n\n\n\n\n\nDr Edina Rosta – University College LondonDynamics\, function and mechanism of phosphate processing enzymesPhosphate catalytic enzymes are essential and ubiquitous to all forms of life. While structures of these proteins are typically readily available\, prediction and design of their function and activity is a key current challenge. Here we review free energy calculation methods and applications for prototype examples including HIV-1 RNase H [1]. Our work highlights the important role of coupled proton transfer steps in the catalytic mechanism using the finite-temperature string method. This allows us to use multiple collective variables that govern the reaction path. Identification of these collective variables in complex processes presents a major problem. We offer promising AI-driven algorithms to help identify essential reaction coordinates in biomolecular processes [2]. \n\n\n\nEdina Rosta1\, Department of Physics and Astronomy\, University College London\, London\, WC1E 6BT\, e.rosta@ucl.ac.uk \n\n\n\nReferences[1] S. Dürr\, O. Bohuszewicz\, R. Suardiaz\, P. G. Jambrina\, C. Peter\, Y. Shao\, and E. Rosta\, ACS Catalysis\, 10.1021/acscatal.1c01493\, 2021[2] M. Badaoui\, P. J. Buigues\, D. Berta\, G. M. Mandana\, H. Gu\, T. Földes\, C. J. Dickson\, V. Hornak\, M. Kato\, C. Molteni\, S. Parsons\, and E. Rosta\, J. Chem. Theory Comput. 10.1021/acs.jctc.1c00924\, 2022 \n\n\n\nBiography: Dr. Edina Rosta is an Associate Professor in Computational Materials Modelling at UCL. After completing her PhD at USC in the group of Arieh Warshel (2013 Chemistry Nobel Prize Laureate)\, she joined the Hummer lab as a Postdoctoral Research Fellow at the NIDDK\, NIH. She took up a lecturer position at KCL Chemistry in 2012. In 2020 she joined UCL Physics. Current research in her group focuses on atomistic molecular modeling\, including hybrid quantum mechanics/molecular mechanics (QM/MM) simulations. To quantitatively and accurately assess how enzymes achieve their extraordinary efficiency and specificity in performing chemical reactions\, she develops modern enhanced sampling methods including novel algorithms to calculate molecular kinetics from biased molecular simulations using the theoretical framework of kinetic networks. Applications of her work focus on the most prominent chemical reactions of living organisms: phosphate transfer and cleavage. She studies the key functional roles of Mg2+ cofactors in phosphate catalytic reactions.
URL:https://thomasyoungcentre.org/event/tyc-distinguished-speaker-symposium-modelling-surfaces-catalysis/
LOCATION:XLG1 Lecture Theatre\, Christopher Ingold Building\, 20 Gordon Street\, London\, WC1H 0AJ\, United Kingdom
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/11/TYC-Logo_blue_on_white_2.jpg
ORGANIZER;CN="Professor Sir Richard Catlow":MAILTO:tyc-administrator@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220321T110000
DTEND;TZID=Europe/London:20220321T120000
DTSTAMP:20260410T144605
CREATED:20220318T151744Z
LAST-MODIFIED:20220318T151745Z
UID:2694-1647860400-1647864000@thomasyoungcentre.org
SUMMARY:TYC Journal Club: Controlling the bias in electrochemical systems by means of hair probes methodology
DESCRIPTION:Software solutions to the challenges of materials modelling Share on X\n\nSoftware solutions to the challenges of materials modelling Share on X\n\n\n\n\nJoin us on Monday 21 March\, at 11am on Zoom. \n\n\n\nIn this meeting\, Margherita will discuss her work on:“Controlling the bias in electrochemical systems by means of hair probes methodology” \n\n\n\nFixed bias simulations with open-boundaries description of the electrons;Hair probes approach interfaced with dft calculations;Testing of the current implementation of the methodology within cp2k.\n\n\n\nHope to see you all there! \n\n\n\nJoining on Zoom:https://ucl.zoom.us/j/708748699?pwd=MU50Wi9Dc1IyTkcxenRBalY5dm9rZz09 Meeting ID: 708 748 699Password: TYCJC
URL:https://thomasyoungcentre.org/event/tyc-journal-club-controlling-the-bias-in-electrochemical-systems-by-means-of-hair-probes-methodology/
CATEGORIES:Journal Club
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/11/cropped-TYC-Logo_blue_on_white_2.jpg
ORGANIZER;CN="Vasileios Fotopoulos Fotis":MAILTO:vasileios.fotis.19@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220307T120000
DTEND;TZID=Europe/London:20220307T123000
DTSTAMP:20260410T144605
CREATED:20220302T102858Z
LAST-MODIFIED:20220302T121113Z
UID:2592-1646654400-1646656200@thomasyoungcentre.org
SUMMARY:TYC Lunchtime Seminar: Structural origins of the low-temperature orthorhombic-to-tetragonal phase transition in high-Tc cuprates
DESCRIPTION:Christopher Keegan\, Department of Materials \n\n\n\nClick here to join the Seminar \n\n\n\nAbstract:  \n\n\n\nThe La(2-x)Ba(x)CuO4 (LBCO) high-temperature superconductor exhibits a structural phase transition from a low-temperature orthorhombic (LTO) phase to a low-temperature tetragonal (LTT) phase near x = 1/8 doping\, which is correlated with a suppression of superconductivity and the concomitant formation of charge density waves. Here we study La2MgO4\, which is a structural analog of LBCO. Since La2MgO4 does not possess the strong electronic correlations that give rise to\, e.g.\, the superconductivity observed in the cuprates\, we use it to help disentangle structural and electronic mechanisms of the LTO-LTT phase transition.Using density-functional theory (DFT)\, we explore the energy landscape associated with the order parameters of the phase transition. We find that LTT becomes energetically more favourable than LTO above a critical magnitude of the order parameter. Our synthesis and characterisation of La2MgO4 using high-resolution diffraction confirms that this system also exhibits the LTO-LTT phase transition observed in LBCO. The critical octahedral tilt angle at which this phase transition is observed is in excellent agreement with the DFT calculations. Our work provides valuable insight into the origins of the complex structural behaviour observed for this family of compounds. 
URL:https://thomasyoungcentre.org/event/tyc-lunchtime-seminar-structural-origins-of-the-low-temperature-orthorhombic-to-tetragonal-phase-transition-in-high-tc-cuprates/
LOCATION:Online
ORGANIZER;CN="Hafiza Bibi":MAILTO:tyc-administrator@ic.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220303T150000
DTEND;TZID=Europe/London:20220303T160000
DTSTAMP:20260410T144605
CREATED:20220215T122659Z
LAST-MODIFIED:20220303T175459Z
UID:2481-1646319600-1646323200@thomasyoungcentre.org
SUMMARY:TYC Seminar: Interpreting experiments using simulations and using experiments to improve simulations of intrinsically-disordered proteins
DESCRIPTION:Software solutions to the challenges of materials modelling Share on X\n\nSoftware solutions to the challenges of materials modelling Share on X\n\n\n\n\nSee a recording of the seminar here \n\n\n\nKresten Lindorff-Larsen – University of CopenhagenInterpreting experiments using simulations and using experiments to improve simulations of intrinsically-disordered proteins \n\n\n\nIntrinsically disordered proteins (IDPs) and flexible regions in multi-domain proteins display substantial conformational heterogeneity. Characterizing the conformational ensembles of these proteins in solution typically requires combining data from one or more biophysical techniques with computational modelling or simulations [1\,2]. Experimental data can either be used to assess the accuracy of a computational model or to refine the computational model to get a better agreement with the experimental data. I will discuss two different approaches to integrate experiments and simulations of IDPs. \n\n\n\nIn the first approach we use experimental data to refine conformational ensembles of IDPs in a systemspecific manner. I will describe how we use our Bayesian-Maximum Entropy software to refine conformational ensembles of IDPs generated by simulations [2–6]. I will briefly touch upon a key issue regarding the so-called “forward models” that are used to calculate experimental observables from conformational ensemble and highlight how generating such models for IDPs is important but difficult [7–9]. \n\n\n\nIn the second approach we use the experimental data to refine the force field used the simulations. I will describe a Bayesian formalism we have developed and applied to optimize and parameterize force fields by targeting experimental observables [10\,11]. We have used this method to parameterize a new coarsegrained model for IDPs by targeting data from small-angle scattering experiments and nuclear magnetic resonance spectroscopy on IDPs in solution [11]. I will describe how this model enables us to study interactions between IDPs and their formation of higher-order structures in biomolecular condensates\, and discuss initial work towards improving the Martini coarse-grained model for disordered proteins [4\,12]. \n\n\n\nReferences:1. Bottaro\, Sandro\, and Kresten Lindorff-Larsen. “Biophysical experiments and biomolecular simulations: A perfect match?.” Science 361: 355-360 (2018)2. Orioli\, Simone\, et al. “How to learn from inconsistencies: Integrating molecular simulations with experimental data.” Prog Mol Biol and Transl Sci 170: 123-176 (2020)3. Bottaro\, Sandro\, Tone Bengtsen\, and Kresten Lindorff-Larsen. “Integrating molecular simulation and experimental data: A Bayesian/maximum entropy reweighting approach.” Structural Bioinformatics. Humana 219-240 (2020)4. Larsen\, Andreas Haahr\, et al. “Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution.” PLoS Comput Biol 16: e1007870 (2020)5. Ahmed\, Mustapha Carab et al. “Computing\, analyzing\, and comparing the radius of gyration and hydrodynamic radius in conformational ensembles of intrinsically disordered proteins.” Intrinsically Disordered Proteins. Humana 429-445 (2020)6. Crehuet\, Ramon\, et al. “Bayesian-maximum-entropy reweighting of IDP ensembles based on NMR chemical shifts.” Entropy 21: 898 (2019)7. Lindorff-Larsen\, Kresten\, and Birthe B. Kragelund. “On the potential of machine learning to examine the relationship between sequence\, structure\, dynamics and function of intrinsically disordered proteins.” J Mol Biol 433:167196 (2021).8. Pesce\, Francesco\, and Kresten Lindorff-Larsen. “Refining conformational ensembles of flexible proteins against small-angle X-ray scattering data.” Biophys J 120:5124–5135 (2021)9. Tesei\, Giulio\, et al. “DEER-PREdict: software for efficient calculation of Spin-Labeling EPR and NMR data from conformational ensembles.” PLoS computational biology 17: e1008551 (2021)10. Norgaard\, Anders B.\, Jesper Ferkinghoff-Borg\, and Kresten Lindorff-Larsen. “Experimental parameterization of an energy function for the simulation of unfolded proteins.” Biophys J 94: 182-192 (2008)11. Tesei\, Giulio\, et al. “Accurate model of liquid-liquid phase behaviour of intrinsically-disordered proteins from optimization of single-chain properties.” Proc Natl Acad Sci 118: e2111696118 (2021).12. Thomasen\, F. Emil\, et al. “Improving the global dimensions of intrinsically disordered proteins in Martini 3.” bioRxiv (2021). \n\n\n\nBiographyKresten Lindorff-Larsen trained as a biochemist at the University of Copenhagen and Carlsberg Laboratory\, and completed his Ph.D. at the University of Cambridge in 2004 under the supervision of Prof. Christopher M. Dobson. He then moved on to become an assistant professor in Copenhagen before joining D. E. Shaw Research in New York in 2007. He returned to Copenhagen in 2011\, where he now serves as a Professor of Computational Protein Biophysics at the Linderstrøm-Lang Centre For Protein Science. He received the Danish Independent Research Councils’ Young Researchers’ Award in 2006\, was a co-recipient of the 2009 Gordon Bell Prize and has received several prestigious grants including a Hallas-Møller stipend (2011)\, a Sapere Aude starting grant (2012)\, and most recently a Novo Nordisk Foundation challenge programme grant (2019). He is the director of the Lundbeck Foundation BRAINSTRUC initiative in structural biology and the Novo Nordisk Foundation PRISM (Protein Interactions and Stability in Medicine and Genomics) centre. Current research interests include developing and applying computational methods for integrative structural biology\, and the integration of biophysics and genomics research. \n\n\n\n\n\n\n\n\n\n\n\nhttps://ucl.zoom.us/j/93351179800?pwd=bVBhNjJhZURNc05wR1piTUtTWXBVUT09 \n\n\n\nMeeting ID: 933 5117 9800 Passcode: TYCIGS
URL:https://thomasyoungcentre.org/event/tyc-seminar-interpreting-experiments-using-simulations-and-using-experiments-to-improve-simulations-of-intrinsically-disordered-proteins/
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/09/TYC-Logo-white-on-blue.jpg
ORGANIZER;CN="Edina Rosta":MAILTO:e.rosta@ucl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220224T110000
DTEND;TZID=Europe/London:20220224T130000
DTSTAMP:20260410T144605
CREATED:20220105T154239Z
LAST-MODIFIED:20220303T125935Z
UID:2116-1645700400-1645707600@thomasyoungcentre.org
SUMMARY:TYC Soiree: Modelling mineralization process
DESCRIPTION:Watch a recording of the soiree here \n\n\n\nPaolo Raiteri – CurtinAtomistic simulations of ion-association\, surface adsorption and mineral dissolution processes; pitfalls and successes \n\n\n\nMariette Wolthers – UtrechtHow minerals grow and dissolve: insights from simulations and experiments \n\n\n\nAbstracts:Atomistic simulations of ion-association\, surface adsorption and mineral dissolution processes; pitfalls and successes – Paolo Raiteri – Curtin \n\n\n\nThe diffusion of “easy” to use software is providing an attractive opportunity for scientists. In particular\, molecular dynamics is becoming an ubiquitous research tool in science\, with applications ranging from DNA and membrane permeation to energy storage materials and minerals. The ever-increasing computer power that is available through supercomputing facilities is pushing the boundaries of what can be simulated far beyond what we could have imagined a decade ago. \n\n\n\nIn this talk I will discuss some of the work we have performed in the past few years to model the growth/dissolution of minerals in water where we used classical thermodynamics and experiments to help us avoid (some of) the potential pitfalls of computational geochemistry. In particular\, I will focus on the development of thermodynamically accurate force fields for molecular dynamics and briefly discuss how we can compute the solubility of sparingly soluble salts. I will then show some recent work we have carried out on the adsorption of small molecules on calcite\, and\, if time permits\, on the use of static electric fields in periodic atomistic simulations. \n\n\n\nHow minerals grow and dissolve: insights from simulations and experiments – Mariette Wolthers – Utrecht \n\n\n\nDuring mineral growth and dissolution\, material (in the form of atoms\, molecules\, complexes\, or clusters) is transported through water to or from the mineral surface. Even in a solution that is at equilibrium with respect to a given mineral\, there is transport to and from the surface. The rate of dissolution or growth can vary locally depending on a complex interplay of the energy landscape of the mineral surface [1]\, water exchange kinetics [2] and the chemical composition and transport properties in the interfacial fluid [3]. \n\n\n\nIn this talk\, I will discuss how simulations at different time and length scales can be linked to experimental observations to unravel the influence of these local interfacial characteristics and processes on calcite dissolution and growth. \n\n\n\nReferences: [1] E.g. Koskamp et al. (2021) Minerals\, 11\, p 407; Heberling et al. (2021)\, Environ. Sci. Technol. 55\, p 12403-12413; see also Wolthers (2015)\, Science 349 (6254)\, p 1288. [2] E.g. De La Pierre et al. (2016) Cryst. Growth Des.\, vol. 16\, p 5907–5914; Wolthers et al. (2013) CrystEngComm 15\, p 27. [3] Agrawal et al. (2021) Geochim. Cosmochim. Acta\, 307\, p 338-350. \n\n\n\n\n\n\n\n\n\n\n\nMeeting ID: 977 4584 0071 Passcode: TYCSymp
URL:https://thomasyoungcentre.org/event/tyc-soiree-modelling-mineralization-process-2/
LOCATION:Online
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/11/TYC-Logo_blue_on_white_2.jpg
ORGANIZER;CN="Devis Di Tommaso":MAILTO:d.ditommaso@qmul.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220217T150000
DTEND;TZID=Europe/London:20220217T163000
DTSTAMP:20260410T144605
CREATED:20220110T125959Z
LAST-MODIFIED:20220218T114610Z
UID:2254-1645110000-1645115400@thomasyoungcentre.org
SUMMARY:MMM Hub Software Spotlight event: CP2K
DESCRIPTION:Watch the recording here \n\n\n\nAbstract:  \n\n\n\nShowcasing the capabilities of CP2K from a research perspective\, as well as spending some time looking at exactly how the code can be run in practice – especially on HPC resources\, specifically Young. \n\n\n\nCP2K (cp2k.org) is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state\, liquid\, molecular\, periodic\, material\, crystal\, and biological systems.  https://dx.doi.org/10.1063%2F5.0007045
URL:https://thomasyoungcentre.org/event/mmm-hub-software-spotlight-event-cp2k/
LOCATION:Online
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2022/01/MMM-no-description.jpg
ORGANIZER;CN="George Booth":MAILTO:george.booth@kcl.ac.uk
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/London:20220210T150000
DTEND;TZID=Europe/London:20220210T170000
DTSTAMP:20260410T144605
CREATED:20220106T140236Z
LAST-MODIFIED:20220217T101650Z
UID:2173-1644505200-1644512400@thomasyoungcentre.org
SUMMARY:TYC Symposium: Modelling of Materials for Quantum Technologies
DESCRIPTION:See the recording of the event here \n\n\n\nAudrius Alkauskas FTMC LithuaniaAndrew Fisher\, UCLAdam Gali\, Budapest \n\n\n\nAbstract:  \n\n\n\nPhotoionisation and vibronic properties of isolated colour centres in diamond from first principles-calculationsAudrius AlkauskasIn this talk I will review our recent work on colour centres in diamond. These centres\, in particular the nitrogen-vacancy (NV) centre and the silicon-vacancy centre\, have become important systems to implement many protocols of quantum information processing. In the first part of the talk\, I will discuss the first-principles description of the vibrational broadening of optical absorption and emission lines. The methodology to account for the contribution of the multi-mode Jahn-Teller effect will be also presented. In the second part of the talk\, I will address the photoionization of NV centres. Spin dynamics\, which accompanies charge dynamics\, will be revealed. Computational techniques to achieve converged photoionization cross sections will be introduced. \n\n\n\nDeterministically implanted defects in semiconductors for quantum gates and quantum simulation – Andrew FisherI will introduce the technique of deterministic doping in tetrahedral semiconductors via atomic-scale lithography\, and give a survey of its use in reading out qubits and implementing quantum gates.  Then I will describe our recent work on using the dopants as quantum simulators for strongly interacting quantum lattice models.  I will show that donors generically simulate Hubbard models\, with modifications due to the long-range Coulomb interactions and the multi-valley nature of the conduction band\, while acceptors inherit strong spin-orbit coupling from the valence band and therefore simulate richer models including topological insulators where (uniquely) the relative strength of the Coulomb interactions can be tuned. \n\n\n\nTheoretical magneto-optical spectroscopy for solid state defect quantum bits – Adam GaliWe live in the era of second quantum revolution in which solid state defect quantum bits play a significant role. An exemplary solid state defect quantum bit is the nitrogen-vacancy center in diamond which can be effectively initialized and readout at room temperature. We show how theoretical magneto-optical spectroscopy on nitrogen-vacancy center explained its optical spinpolarization loop which is the key mechanism in the initialization and readout. To this end\, methods to calculate highly correlated electronic states and levels embedded in the itinerant solid state electron system with thousands of electrons has been developed [1] which is often called “quantum embedding” method or can be viewed as a multiscale method where the itinerant electron system is treated by density functional theory whereas the Coulomb-interaction between the strongly interacting orbitals in the system  is directly calculated\, i.e.\, so called configurational interaction theory. To our knowledge\, there is no rigorous theory about the interface of the two approaches\, i.e.\, the double counting term\, therefore\, we have recently started to use density matrix renormalization group wavefunction methods based on density functional theory ground state calculations which produce promising results for defect spins in hexagonal boron nitride [2\,3]. We show that understanding the optical spinpolarization loop requires the exploitation of dynamical effects due to the enhanced electron-phonon interaction. In this regard\, we show the power of Jahn-Teller theorem when combined with density functional theory calculations of few thousands of electrons system [4\,5]. In particular\, we show the extension of Herzberg-Teller theorem from the optical transition to intersystem crossing [6] which is the key of quantum bit operation of nitrogen-vacancy center and related quantum systems. We briefly touch the importance of ab initio spin-related coupling tensors in the description of defect qubits\, such as hyperfine tensors\, in understanding the qubit’s spin dephasing and spin coherence times [7]. [1] Michel Bockstedte\, Felix Stütz\, Thomas Garrat\, Viktor Ivády\, and Adam Gali\, npj Quantum Materials 3\, 31 (2018)  [2] Viktor Ivády\, Gergely Barcza\, Gergô Thiering\, Song Li\, Hanen Hamdi\, Jyh-Pin Chou\, Örs Legeza\, and Adam Gali\, npj Computational Materials 6\, 41 (2020)  [3] Gergely Barcza\, Viktor Ivády\, Tibor Szilvási\, Márton Vörös\, Libor Veis\, Ádám Gali\, and Örs Legeza\, Journal of Chemical Theory and Computation 17\, 1143 (2021)  [4] Gergő Thiering and Adam Gali\, Physical Review B 98\, 085207 (2018)  [5] Adam Gali\, Nanophotonics 8\, 1907 (2019)  [6] Gary Wolfowicz\, F. Joseph Heremans\, Christopher P. Anderson\, Shun Kanai\, Hosung Seo\, Adam Gali\, Giulia Galli & David D. Awschalom\, Nature Reviews Materials 6\, 906 (2021)  [7] A. Haykal\, R. Tanos\, N. Minotto\, A. Durand\, F. Fabre\, J. Li\, J. H. Edgar\, V. Ivady\, A. Gali\, T. Michel\, A. Dréau\, B. Gil\, G. Cassabois\, V. Jacques\, arXiv:2112.10176 (2021) \n\n\n\n\n\n\n\n\n\n\nMeeting ID: 933 5117 9800 Passcode: TYCIGS
URL:https://thomasyoungcentre.org/event/tyc-symposium-modelling-of-materials-for-quantum-technologies/
LOCATION:Online
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/11/TYC-Logo_blue_on_white_2.jpg
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DTSTART;TZID=Europe/London:20220127T150000
DTEND;TZID=Europe/London:20220127T160000
DTSTAMP:20260410T144605
CREATED:20220105T150854Z
LAST-MODIFIED:20220121T114201Z
UID:2098-1643295600-1643299200@thomasyoungcentre.org
SUMMARY:TYC Highlight Seminar: Jonathan Yates\, University of Oxford
DESCRIPTION:Atomic Espionage: Understanding the structure of materials using Computational and Experimental NMRSolid-state NMR is a powerful experimental probe of atomic scale structure and dynamics. A series of developments in electronic structure methods over the past two decades has given material scientists the ability to predict solid-state NMR parameters using codes such as CASTEP\, QE and Wien2k. These are a valuable tool for the interpretation of experimental spectra. Indeed\, it has been said that it is now hard to publish experimental solid-state NMR results without an accompanying DFT calculation.In this talk I will highlight the key methodological advances behind the prediction of NMR parameters. I will also reflect back on how an experimental community came to so completely adopt electronic structure calculations. Finally I will highlight some very recent advances which aim to increase the range of applicability of these calculations. \n\n\n\n \n\n\n\n\n\n\n\n\n\n\nMeeting ID: 933 5117 9800 Passcode: TYCIGS
URL:https://thomasyoungcentre.org/event/tyc-highlight-seminar-jonathan-yates-university-of-oxford/
LOCATION:Online
CATEGORIES:Main event
ATTACH;FMTTYPE=image/jpeg:https://thomasyoungcentre.org/wp-content/uploads/2021/09/TYC_black_on_white_orig.jpg
ORGANIZER;CN="George Booth":MAILTO:george.booth@kcl.ac.uk
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DTSTART;TZID=Europe/London:20211209T150000
DTEND;TZID=Europe/London:20211209T170000
DTSTAMP:20260410T144605
CREATED:20211216T145746Z
LAST-MODIFIED:20211216T145748Z
UID:1984-1639062000-1639069200@thomasyoungcentre.org
SUMMARY:TYC Highlight Seminar: Intranuclear phase separation\, and its role in transcription and gene regulation
DESCRIPTION:avide Marenduzzo\, University of Edinburgh \n\n\n\nThe recording of the seminar can be found here \n\n\n\nAbstract: Microscopy studies suggest that chromatin and its associated proteins often form phase separated droplets within the nucleus of eukaryotic organisms. I will describe some possible biophysical mechanisms underlying such intranuclear phase separation and microphase separation (arrested phase separation resulting in the formation of droplets of self-limiting size). I will also discuss potential functional roles of phase separation in transcription\, as active and inactive clusters are normally spatially segregated.  \n\n\n\nSpecifically\, I will show that multivalent chromatin binding mediates cooperative interactions between proteins which naturally leads to the creation of phase separated clusters (through what we call the “bridging-induced attraction”). Such clusters are strikingly similar to nuclear bodies and transcription factories found in side eukaryotic nuclei. The model also suggests a potential role of clustering for gene regulation\, and it provides potential solutions to puzzles concerning the actions of enhancers\, super-enhancers\, and expression quantitative trait loci. I will then discuss how the model can be enhanced to include the recently discovered “loop extrusion” so that it can predict 3D chromatin structure genome-wide\, and how it can be used to study the dynamics of chromatin transcription so that it can predict the effect of 3D structure on transcriptional activity in human cells.
URL:https://thomasyoungcentre.org/event/tyc-highlight-seminar-intranuclear-phase-separation-and-its-role-in-transcription-and-gene-regulation/
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