THOMAS YOUNG CENTRE

MMM Hub: HPE / NVIDIA GPU Training Day
2022-03-31 09:00 - 16:00 (Europe/London)
Software solutions to the challenges of materials modelling Share on X

Software solutions to the challenges of materials modelling Share on X

09:00 – 12:00 (UK time) Technology and Partner sessions (UCL, HPE & NVIDIA) chaired by Owain Kenway – UCL

Recording: 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

13:00 – 16:00 (UK time) Materials community codes, experiences & lessons learned (invited speakers) chaired by Filippo Spiga – NVIDIA

Recording: 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

TYC Distinguished Speaker Symposium: Modelling Surfaces & Catalysis
2022-03-30 14:00 - 17:00 (Europe/London) | XLG1 Lecture Theatre, Christopher Ingold Building, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
Software solutions to the challenges of materials modelling Share on X

Software solutions to the challenges of materials modelling Share on X

Watch the Symposium here

Professor 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).

The 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.

The conclusions are also relevant for adsorption of alcohols at b-OH sites.

Professor 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.

Dynamical-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.

Increasingly, 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.

Virtual 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.

References‘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)

Biography: 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’.

Dr 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].

References:[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).

Biography: 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.

Dr 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].

Edina Rosta1, Department of Physics and Astronomy, University College London, London, WC1E 6BT, e.rosta@ucl.ac.uk

References[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

Biography: 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.

TYC Journal Club: Controlling the bias in electrochemical systems by means of hair probes methodology
2022-03-21 11:00 - 12:00 (Europe/London)
Software solutions to the challenges of materials modelling Share on X

Software solutions to the challenges of materials modelling Share on X

Join us on Monday 21 March, at 11am on Zoom.

In this meeting, Margherita will discuss her work on:“Controlling the bias in electrochemical systems by means of hair probes methodology”

Fixed 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.

Hope to see you all there!

Joining on Zoom:https://ucl.zoom.us/j/708748699?pwd=[REDACTED] Meeting ID: 708 748 699Password: [REDACTED]

TYC Lunchtime Seminar: Structural origins of the low-temperature orthorhombic-to-tetragonal phase transition in high-Tc cuprates
2022-03-07 12:00 - 12:30 (Europe/London) | Online
Christopher Keegan, Department of Materials

Click here to join the Seminar

Abstract:

The 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.

TYC Seminar: Interpreting experiments using simulations and using experiments to improve simulations of intrinsically-disordered proteins
2022-03-03 15:00 - 16:00 (Europe/London)
Software solutions to the challenges of materials modelling Share on X

Software solutions to the challenges of materials modelling Share on X

See a recording of the seminar here

Kresten Lindorff-Larsen – University of CopenhagenInterpreting experiments using simulations and using experiments to improve simulations of intrinsically-disordered proteins

Intrinsically 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.

In 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].

In 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].

References: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).

BiographyKresten 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.

https://ucl.zoom.us/j/93351179800?pwd=[REDACTED]

Meeting ID: 933 5117 9800 Passcode: [REDACTED]

TYC Soiree: Modelling mineralization process
2022-02-24 11:00 - 13:00 (Europe/London) | Online
Watch a recording of the soiree here

Paolo Raiteri – CurtinAtomistic simulations of ion-association, surface adsorption and mineral dissolution processes; pitfalls and successes

Mariette Wolthers – UtrechtHow minerals grow and dissolve: insights from simulations and experiments

Abstracts:Atomistic simulations of ion-association, surface adsorption and mineral dissolution processes; pitfalls and successes – Paolo Raiteri – Curtin

The 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.

In 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.

How minerals grow and dissolve: insights from simulations and experiments – Mariette Wolthers – Utrecht

During 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].

In 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.

References: [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.

Meeting ID: 977 4584 0071 Passcode: [REDACTED]

MMM Hub Software Spotlight event: CP2K
2022-02-17 15:00 - 16:30 (Europe/London) | Online
Watch the recording here

Abstract:

Showcasing 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.

CP2K (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

TYC Symposium: Modelling of Materials for Quantum Technologies
2022-02-10 15:00 - 17:00 (Europe/London) | Online
See the recording of the event here

Audrius Alkauskas FTMC LithuaniaAndrew Fisher, UCLAdam Gali, Budapest

Abstract:

Photoionisation 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.

Deterministically 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.

Theoretical 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)

Meeting ID: 933 5117 9800 Passcode: [REDACTED]

TYC Highlight Seminar: Jonathan Yates, University of Oxford
2022-01-27 15:00 - 16:00 (Europe/London) | Online
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.

Meeting ID: 933 5117 9800 Passcode: [REDACTED]

TYC Highlight Seminar: Intranuclear phase separation, and its role in transcription and gene regulation
2021-12-09 15:00 - 17:00 (Europe/London)
avide Marenduzzo, University of Edinburgh

The recording of the seminar can be found here

Abstract: 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.

Specifically, 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.

Mini symposium: Beyond density functional theory for predictive excitations
2021-12-02 15:00 - 17:00 (Europe/London)
A description of the electronic excitations in materials and molecules is central to understanding the key optical, transport and reactive properties. While density functional theory often describes ground state energetics to reasonable accuracy, it will often more qualitatively fail in its description of these excitations, and therefore methodological development which can go beyond DFT is of central importance for a theorists toolkit. In this mini-symposium, we will hear from three researchers at the cutting edge of this field, developing approaches for ‘Beyond density functional theory for predictive excitaitons’: Neepa Maitra (Rutgers University), Marc Dvorak (Aalto University), Fillipp Furche (UC Irvine).

TYC 15th Anniversary Event
2021-11-09 15:00 - 18:00 (Europe/London) | Queen’s Tower Rooms, Imperial College London, 7 Imperial College Road, South Kensington, London, SW7 2AZ
The Thomas Young Centre (TYC) is a dynamic and interdisciplinary alliance of London researchers operating at the forefront of science to address the challenges of society and industry through the theory and simulation of materials and molecules, or materials and molecular modelling.

The TYC is made up of around 100 research groups from four London Colleges: Imperial College London, King’s College London, QMUL (Queen Mary University London) and UCL (University College London). The academic departments involved include Physics, Materials, Chemistry, Earth sciences, Biology, and several branches of engineering.

Now in its fifteenth year, the Thomas Young Centre remains a renowned London-based interdisciplinary research network which brings together a range of groups across the capital whose research involves materials and molecular modelling and theoretical chemistry. To celebrate the 15th year of the Thomas Young Centre, past, present and future influencers of the TYC Michele Parinello, Mike Finnis and next-generation speaker Rachel Crespo-Otero will provide an afternoon of fascinating talks.

The event will be followed with a long-awaited in-person reception with wine and nibbles.

TYC Student Welcome Event 2021
2021-10-21 15:00 (Europe/London) | Airmeet
The TYC is looking forward to welcoming new PhD students to our centre, from across the four London colleges. It is a brilliant opportunity to meet your peers (virtually), and to hear about the fantastic benefits of being affiliated to this active and exciting institute. We will hear from our Interest Group Leaders about the hot topics they are currently working on, and a panel of existing TYC students will be on hand to answer questions and provide an overview of TYC activities and the opportunities available to members. These include details of our Highlight and Seminar Series, tailor-made materials modelling course, TYC Journal Club, Mentoring Scheme and fortnightly newsletter advertising events, job opportunities and news.

CECAM Psi-k Research Conference on New Horizons in Nucleation: a playground classical and ab initio simulation methods
2021-09-20 13:15 - 2021-09-24 17:15 (Europe/Paris)
https://www.cecam.org/workshop-details/7#program-7

Nucleation from liquids is a phenomenon encountered in countless natural and industrial processes. Nucleation is the initial step in the formation of a new, usually thermodynamically stable phase, from a parent, metastable phase. Phenomena that range from the formation of ice particles in the atmosphere, to the obstruction of oil pipelines by gas hydrates, including the synthesis of advanced functional materials and the controlled precipitation of specific polymorphs of active pharmaceutical ingredients crucially depend on nucleation. Understanding and learning how to control nucleation is therefore a fundamental problem with far reaching practical ramifications. Nucleation is a process that takes place on nanometer-length and picosecond-time scales that challenge direct experimental observations. By providing a natural description of the molecular scale, where the embryo of a new phase is formed, molecular simulations of crystal nucleation have historically played a pivotal role in improving our understanding of nucleation fundamentals [1]. For instance, molecular simulations have enabled the development of a detailed understanding of nucleation in simple model systems, such as hard-spheres and Lennard-Jones fluids [2, 3], and have decisively contributed to uncover and corroborate complex collective phenomena such as two-step nucleation [4]. With the steady development of both algorithms and computational power, molecular simulation methods are nowadays starting to be applied to problems and systems of increasing complexity, nearing experimental conditions. For instance, in the last few years simulation studies on heterogeneous nucleation [5], nucleation in multi-component liquids [6], or nucleation in biological systems [7] have appeared in the literature, providing unprecedented insight into nucleation fundamentals [8]. Despite the tremendous progress, molecular simulations of nucleation still face a number of challenges, some of which are determined by intrinsic modeling limitations, associated with e.g. the use of classical, semiempirical forcefields, sampling efficiency, system size, and the inherent complexity of the experimental conditions in which nucleation takes place [1]. For instance, a key challenge in the field is to simultaneously provide accurate (ab inito quality) energies and extensive sampling in realistic systems, which include interfaces, defects, and disordered domains. With this in mind a key aim of this meeting will be to bring the electronic structure, classical molecular dynamics, and nucleation theory communities together. Simultaneously we will promote an all-around perspective on the wide range of contexts in which nucleation plays a dominant role, discussing applications in pharmaceutical processes, biomolecular systems, and active matter.

Objectives. With the CECAM/Psi-k research conference on “New Horizons in Nucleation” we aim to:

• Understand and review the current state of the art of the field.

• Discuss and set some guidance for future directions for the field.

• Bring together the disparate communities with expertise in nucleation, including the molecular dynamics, ab initio, and industrial communities with a view to developing new techniques and applying our techniques to the most relevant problems.

• Possibly producing a perspective road-map style article.

Themes. In the research conference we will encourage participation and stimulate an open discussion in the following areas:

• An overview on current challenges in nucleation modelling

• Recent advances in modelling heterogeneous nucleation

• Predicting nucleation kinetics

• Accuracy across length and time scales: a challenge to ab-initio calculations and machine learning methods

• Nucleation and self-assembly in out-of-equilibrium conditions

• Nucleation theory and mesoscale modelling methods (classical DFT, DDFT, Phase Field)

• Nucleation in glasses

• Nucleation in reactive systems

• Nucleation and self-assembly in biomolecular systems

• Nucleation of active pharmaceutical ingredients

• Nucleation in active and biogenic materials

We envisage this research conference as an important meeting for the development of PhD students and Early Career Researchers (ECRs) directly involved in simulations of nucleation processes or interested in broadening their perspective on this topic.

References

[1] G. Sosso, J. Chen, S. Cox, M. Fitzner, P. Pedevilla, A. Zen, A. Michaelides, Chem. Rev., 116, 7078-7116 (2016)[2] S. Auer, D. Frenkel, Nature, 409, 1020-1023 (2001)[3] P. ten Wolde, M. Ruiz-Montero, D. Frenkel, Phys. Rev. Lett., 75, 2714-2717 (1995)[4] P. Wolde, D. Frenkel, Science, 277, 1975-1978 (1997)[5] M. Fitzner, G. Sosso, S. Cox, A. Michaelides, J. Am. Chem. Soc., 137, 13658-13669 (2015)[6] N. Zimmermann, B. Vorselaars, J. Espinosa, D. Quigley, W. Smith, E. Sanz, C. Vega, B. Peters, The Journal of Chemical Physics, 148, 222838 (2018)[7] A. Šarić, A. Buell, G. Meisl, T. Michaels, C. Dobson, S. Linse, T. Knowles, D. Frenkel, Nature. Phys., 12, 874-880 (2016)[8] E. Sanz, C. Vega, J. Espinosa, R. Caballero-Bernal, J. Abascal, C. Valeriani, J. Am. Chem. Soc., 135, 15008-15017 (2013)

MSSC2021@London - Virtual Ab initio Modelling in Solid State Chemistry
2021-09-20 09:00 - 2021-09-24 17:00 (Europe/London)
Virtual Edition (New Users)

Discovering quantum-mechanical simulations with CRYSTAL

Directors: S. Casassa – A. Erba – N.M. Harrison – G. Mallia

https://www.imperial.ac.uk/mssc/mssc2021/

The 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 Technology Facilities Council (STFC), are organising the 2021 MSSC Summer School on the “ab initio modelling of crystalline and defective solids with the CRYSTAL code”.

The MSSC2021 will be a virtual workshop.

The morning and the afternoon sessions will be run remotely.

The 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.

CRYSTAL is a general-purpose program for the study of periodic solids. 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 and range-separated hybrid functionals (e.g. B3LYP, HSE06), double hybrid levels of theory. Analytical first derivatives with respect to the nuclear coordinates and cell parameters and analytical derivatives, up to fourth order, with respect to an applied electric field (CPHF/CPKS) are available.

Programme: https://www.imperial.ac.uk/mssc/mssc2021/programme/

Registration: https://www.imperial.ac.uk/mssc/mssc2021/registration/

MMM Hub++ Conference 2021
2021-09-14 09:30 - 2021-09-15 16:00 (Europe/London)
This virtual conference brings together researchers working in all aspects of theory and simulation of materials and molecular systems and is jointly organised by the UK’s Materials and Molecular Modelling Hub, the Thomas Young Centre, CCP9, CCP5, CCPBioSim, the Materials Chemistry Consortium and the UK Car-Parrinello Consortium. The conference will cover topics including, but not limited to, biological and technological soft matter, functional materials and devices, structural materials, surfaces and interfaces and methods and method development.

Pre-recorded flash presentationsInstead of a traditional poster session, we will take advantage of the virtual format to invite participants, particularly graduate students, to contribute short (max. 3 minute) pre-recorded flash presentations about their research. These videos will be made available to conference participants both in advance and during the conference and we will make virtual spaces available during the conference for participants and presenters to meet to discuss.

14th September 2021Designing molecular models by machine learning and experimental data – Cecilia Clementi, Free University of Berlin

Biomolecules and Biological Soft MatterBiomolecular simulations with large scale density functional theory – Chris-Kriton Skylaris, University of SouthamptonHow carbon monoxide dehydrogenase converts CO2 to CO – Umberto Terranova, University of Buckingham

Functional Materials & DevicesFunctional 2D materials – Kristian Thygesen, Technical University of DenmarkBandgap engineering in strained monolayer and few layer MoS2 – Alex Armstrong, University of York

Methods & Method DevelopmentData-enhanced multi scale theory of operando energy conversion systems – Karsten Reuter, FHI BerlinRecent theoretical development of Py-chemshell for calculating vibrational properties of transition metal containing zeolites – Jingcheng Guan, University College London

Biomolecules and Biological Soft MatterInterscale simulations: a novel combined methodology to bridge between scales and methods – Andrey Brukhno, STFCHigh-performance computing and disordered elastic systems theory as a framework to study collective cell migration – Nirvana Cabellero, University of GenevaSmart Droplets: can you fragment and deliver? – Francois Sicard, University College LondonFunctional Materials & DevicesExternal stimuli driven spin transitions and piezochromism in metal organic complexes – Hrishit Banerjee, University of CambridgeMolecular Dynamics modelling of polymeric nanocomposites – Jacob Earnshaw, Sheffield Hallam UniversityQuantifying polaronic effects on charge-carrier scattering and mobility in lead halide perovskites – Lewis Irvine, University of Bath

Methods & Method DevelopmentBayesian optimization of atomic structures with gradient-enhanced Gaussian processes – Sami Kaapa, Technical University of DenmarkLinear atomic cluster expansion force fields for organic molecules – David Kovajcs, University of CambridgeEncoding of distortions in perovskites for machine learning applications – Kazuki Morita, Imperial College LondonEarly Career Invited talksPhonon screening of electron-hole interactions in lead-halide perovskite semiconductors and beyond – Marina Filip, University of OxfordModelling electrified interfaces from first principles – Clotilde Cucinotta, Imperial College LondonMolecular structure at an interface – Ed Smith, Brunel University LondonIn-silico photochemical experiments with non-born-Oppenheimer Molecular Dynamics – Basile Curchod, University of DurhamEnvironmental sorptive materials at molecular level – Valentina Erastova, University of EdinburghInvited Day 2Current landscape of UKRI activities – Billy McGregor – EPSRC, UKRIPlenary Day 2Searching for excitons: a fresh point of view – Lucia Reining, École Polytechnique Palaiseau, ParisSurfaces & InterfacesExploring Fuel Cell cathode materials: Towards more representative models – Misbah Sarwar, Johnson MattheyMachine Learning for Polarisable Force-Fields: Neural-Network models for Graphene-Electrolyte interfaces – Nicodemo Di Pasquale, University of ManchesterFunctional Materials & DevicesAccurate multi-scale simulations for advanced functional materials – Otello Roscioni, MaterialX LtdMonte Carlo Simulations for Fitting Neurton Diffraction Data – Camilla Di Mino, UCL

Methods & Method DevelopmentSolving the many-electron Schrodinger equations using deep neural networks – Matthew Foulkes, Imperial College LondonSystematically Improvable Quantum Embedding for Real Materials – Max Nusspickel, King’s College London

Surfaces & InterfacesUnveiling novel properties and phases of mono-layer confined water – Venkat Kapil, University of CambridgePursuit of accurate moelling to reproduce experimental properties of mono- and bi-metallic surfaces – Lara Kabalan, Cardiff UniversityInfluence of Water Models on the Prediction of Desalination Properties of a Nanoporous Membrane – Aziz Ghoufi, University of Rennes

Functional Materials & DevicesTheoretical modelling of the electrochemical behaviour of the graphene and graphene-based materials – Natalia Martsinovich, University of SheffieldCatalytic formation of oxalic acid on the partially oxidised greigite Fe3S4 (001) surface – David Santos-Carballal, University of LeedsDefect-dependent corrugation in graphene – Fabian Thiemann, University College London

Methods & Method DevelopmentDensity functional embedded scheme for molecules and periodic systems – Manas Sharma, Friedrich-Schiller University of JenaAccelerating Path Integral Calculations of Vibrational Spectra – David Wilkins, Queen’s University BelfastImportance of long-ranged electron interactions for the magnetic phase diagram of twisted bilayer graphene – Zachary Goodwin, Imperial College London

Surfaces & InterfacesTowards the elucidation of the mechanism of hydrothermal synthesis of zeolites – Valeria Molinero, The University of UtahEvaluation of methods for viscosity simulations of lubricants at different operational conditions – Dimitrios Mathas, University of Southampton

Structural MaterialsCoarse-grained modelling of cement hydrates – Katerina Ioannidou, University of MontpellierCo-substituted BiFiO3: thermodynamic, electronic and ferroelectric properties from first principles – Shivani Grover, University of Reading

Methods & Method DevelopmentChromonic liquid crystals: insights from simulations at multiple scales – Mark Wilson, University of DurhamMolecular-scale thermoelectricity: as simple as ABC – Ali Ismael, Lancaster University

Surfaces & InterfacesModelling Organic-Inorganic interfaces of Urinary Calculi – Rhiannon Morris, University of LeedsPredictive model for adsorption of molecules through ab initio simulations – Paolo Restuccia, Imperial College LondonPentacene meets transition metal dichalcogenides for solar energy conversion – Juliana Morbec, Keele University

Structural MaterialsStructural MaterialsPolytypism of inorganic lead halide perovskite – Zhenzhu Li, Yonsei UniversitySimulating the Charring of Phenol-Formaldehyde Resins with Reactive Molecular Dynamics – Marcus Purse, University of SurreyElectronically Driven Cooperative Diffusion in Simple Cubic Calcium – Andreas Hermann, University of Edinburgh

Methods and Method DevelopmentTowards an effective Hamiltonian for a proton transfer ferroelectric – Matthew Okenyi, Imperial College LondonA machine learning description of excited states of functional organic molecules – Julia Westermayr, University of WarwickMachine learning potentials for complex aqueous systems made simple – Christoph Schran, University of Cambridge

Scientific Advisory Committee

George Booth, King’s College London Richard Catlow, University College London Georgina Ellis, OCF Ltd Nicholas Harrison, Imperial College London John Harding, University of Sheffield Kim Jelfs, Imperial College London Chris Lorenz, King’s College London Angelos Michaelides, University of Cambridge Carla Molteni, King’s College London Mark House, HPE Matt Probert, UKCP & University of York Andela Saric, University College London Alex Shluger, University College London David Wilkins, Queen’s University Belfast

Organising Committee Hafiza Bibi, Imperial College LondonPaola Carbone, University of Manchester Stewart Clark, University of Durham Alin Marin Elena, Science and Technology Facilities Council Arash Mostofi, Imperial College London Catherine O’Sullivan, Imperial College London Edina Rosta, University College London Marco Sacchi, University of Surrey Karen Stoneham, University College London Scott Woodley, University College London

Moire-Twistronics workshop
2021-08-09 13:30 - 2021-08-13 16:30 (Europe/London) | Online
The online Moiré-Twistronics workshop is dedicated to recent developments in theory and experiments on twisted bilayer materials. The workshop will be run jointly by the UK’s National Graphene Institute (Manchester), the Thomas Young Centre for Theory and Simulation of Materials (London), and the Sir Henry Royce Institute.

Workshop attendance is free of charge.

Programme

BST UK Time

Monday (Aug 9)

1.30pm: Allan MacDonald (UT Austin): Known knowns and known unknowns in magic angle twisted bilayer graphene

2.00pm: Folkert de Vries (ETH Zurich): Superconducting Devices in Magic-Angle Twisted Bilayer Graphene

2.15 pm: Tommasso Cea (IMDEA): Coulomb interaction, phonons, and superconductivity in twisted bilayer graphene

2.30pm: Kevin Nuckolls (Princeton University): Spectroscopic Signatures of Unconventional Superconductivity and Correlated Chern Insulators in Magic-Angle Twisted Bilayer Graphene

2.45pm: break

3.00pm: Zachary Goodwin (Imperial College London): Importance of long-ranged Coulomb interactions for the magnetic phase diagram of twisted bilayer graphene

3.15pm: Youngjoon Choi (Caltech): Interaction-driven Band Flattening and Correlated Phases in Twisted Bilayer Graphene

3.30pm: Jeanie Lau (Ohio State University): Strange metal behavior and Superconducting Critical Current in twisted bilayer graphene

4.00pm: break-out room discussions

Tuesday (Aug 10)

1.30pm: Wang Yao (The University of Hong Kong): Layer pseudospin texture and Berry phase effects in Moiré superlattices of twisted homobilayers

2.00pm: Brian Gerardot (Herriot-Watt University): Quantum Light and Strongly Correlated Electronic States in a Moiré Heterostructure

2.30pm: Benjamin Remez (Cambridge University): Dark and Leaky Exciton Condensates in Transition Metal Dichalcogenide Twisted Bilayers

2.45pm: break

3.00pm: Indrajit Maity (Imperial College London): Chiral phonons in twisted TMDs

3.15pm: Vladimir Enaldiev (The University of Manchester): Piezoelectric and weak ferroelectric networks and band-energy landscapes in twistronic TMD bilayers

3.30pm: Jie Shan (Cornell University): Quantum anomalous Hall effect in semiconductor moiré structures

4.00pm: break-out room discussions

Wednesday (Aug 11)

1.30pm: Philipp Kim (Harvard University): Ferroelectric polar domain dynamics in twisted bilayer transition metal dichalcogenides

2.00pm: Roman Gorbachev (The University of Manchester): Controlling optoelectronic properties of 2D semiconductors: band engineering and moiré superlattices

2.30pm: Efthimios Kaxiras (Harvard University): Twistronics: Atomic relaxation in moiré layered structures and its effect on electron localization

3.00 pm: break

3.15pm: poster session

Thursday (Aug 12)

1.30pm: Leni Bascones (Madrid): Correlated states in ABC trilayer graphene on hBN

2.00pm: Abhay Pasupathy (Columbia University): Twistons in the magic sea

2.30pm: QuanSheng Wu (EPFL): Chiral Decomposition of Twisted Graphene Multilayers with Arbitrary Stacking

2.45pm: break

3.00pm: Lennart Klebl (RWTH Aachen): Atomistic View on Correlations in Moire Heterostructures

3.15pm: Giulia Zheng (ETH Zurich): Farby-Pérot Cavities Using Different Dispersions in Twisted Double Bilayer Graphene

3.30pm: Senthil Todadri (MIT): Re-entrant superconductivity in twisted trilayer graphene

4.00pm: break-out room discussions

Friday (Aug 13)

1.30pm: Alexander Tartakovskii (University of Sheffield): Resonant electronic and excitonic hybridisation in heterobilayers of transition metal dichalcogenide alloys

2.00pm: Mariya Romanova (UC Santa Barbara): Stochastic many-body calculations of moiré states in twisted bilayer graphene at high pressures

2.15pm: Nicholas Hine (University of Warwick): Linear-Scaling DFT and Spectral Function Unfolding applied to 2D Heterostructures

2.30pm: break

2.45pm: Danny Bennett (University of Cambridge): Electrically tunable stacking domains in Moiré superlattices

3.00pm: Louk Rademaker (Universite de Geneve): Spin-valley symmetry breaking and Chern insulators in twisted graphene structures

3.15pm: Jose Lado (Aalto University): Designing correlated quantum matter with magnetic twisted van der Waals heterostructures

3.45pm: break-out room discussions.

Modelling phase separation
2021-07-08 15:00 - 17:00 (Europe/London) | Zoom
Jeremy Schmit – Kansas State University

Thomas Michaels – UCL (previously ETHZ, Cambridge, Harvard)

Jerelle Joseph – University of Cambridge

Time: 15:00 BST

Venue: Zoom

Contact: Andela Saric

Email: tyc-administrator@ucl.ac.uk

MMM Hub Software Spotlight: ONETEP
2021-07-02 15:00 - 16:00 (Europe/London)
Venue: Join Zoom Meeting https://ucl.zoom.us/j/99746496587?pwd=[REDACTED]

Meeting ID: 997 4649 6587 Passcode: [REDACTED]

Contact: George BoothEmail: george.booth@kcl.ac.uk

In the second of the MMM Hub/TYC ‘Software Spotlight’ event series, we will be looking at the ONETEP package for linear-scaling density functional theory calculations with controllable accuracy.

The favourable scaling of this package has allowed it to be pushed out to fully quantum applications in biology, surfaces, nanostructures and defects. It has excellent parallelism for large scale calculations with thousands of cores on both ARCHER2 and Tier-2 infrastructure, and is developed by a number of researchers across the UK.

In this event, Professor Chris-Kriton Skylaris will be talking about the capabilities and impact that the software has had on the field, alongside Dr Jacek Dziedzic and Arihant Bhandari, all at the University of Southampton, presenting the anatomy of a ONETEP calculation and demonstrating the range of capabilities of this powerful code.

IWOM 2021: International Workshop on Charge Transport and Excited State Processes in Organic Materials
2021-06-21 14:00 - 2021-06-25 17:00 (Europe/London) | Zoom
Time: 2-5pm (GMT +1) daily

The scope of this workshop is to bring together theorists, computational and experimental scientists working in the area of organic materials for electronic applications. The content will cover approaches across different length scales (from molecular to device-level) towards the understanding of phenomena and mechanisms inherent to the function of organic semiconducting materials. Our aim is to provide a comprehensive overview of current state-of-the-art advances in this research field, covering key issues such as: electronic structure methods for excited states calculations, charge transport mechanisms in bulk and nanostructured interfacial systems, energy conversion through light harvesting, and light generation via recombination processes.

Keynote speakers

Irene Burghardt, Goethe University Frankfurt, GermanySir Richard Friend, University of Cambridge, UKHenning Sirringhaus, University of Cambridge, UKWeitao Yang, Duke University, USA

Invited Speakers

David Beljonne, University of Mons, BelgiumAntoine Carof, University of Lorraine, FranceRachel Crespo-Otero, Queen Mary University of London, UKMarcus Elstner, Karlsruhe Institute of Technology, GermanySimone Fratini, CNRS, FranceJenny Nelson, Imperial College London, UKHarald Oberhofer, Technical University Munich, GermanyJean-Hubert Olivier, University of Miami, USAFrank Ortmann, Technical University Munich, GermanyVitaly Podzorov, Rutgers University, USAOleg Prezhdo, University of Southern California, USASergei Tretiak, Los Alamos National Laboratory, USATroy Van Voorhis, Massachusetts Institute of Technology, USA

Contact: tyc-administrator@ucl.ac.uk

CCP5++ Software Seminar Series: Sampling, detecting, and analysing collective arrangements in atomistic simulations
2021-06-14 14:00 - 17:00 (Europe/London) | Online
Matteo Salvalaglio

Thomas Young Centre and Department of Chemical Engineering, University College London

Abstract: The synthesis of crystalline materials by precipitation from solution is a phenomenon at the heart of many technological and natural processes, ranging from biomineralisation to the production of active pharmaceutical ingredients. The properties of macroscopic crystals are inherently determined by their structure and morphology, two products of the atomistic-scale arrangement of building blocks emerging and propagating during crystal nucleation and growth. Molecular dynamics simulations offer a direct insight into the fundamental processes underpinning the assembly of building blocks (atoms or molecules) and into the stability of the structures emerging from such assembly. However, to exploit the potential of atomistic simulations, it is critical to overcome the timescale limitations associated with rare events, perform simulations in conditions resembling macroscopic systems (i.e. constant driving force), and systematically identify the structure of assemblies emerging from simulation.

In this seminar, I will discuss methods to sample, detect, and analyse the collective arrangement of crystal building blocks based on the definition of collective variables and on the application of clustering algorithms. To this aim, I will illustrate two applications, both featuring prominent use of PLUMED [Tribello et al. Computer Physics Communications 185 (2), 604-613, 2014], including i. the characterisation of dense liquid-like clusters at graphite-NaCl(aq) interfaces [Finney et al. arXiv 2021, https://arxiv.org/abs/2104.11773], and ii. the systematic application of enhanced sampling and clustering algorithms to improve the prediction of polymorphism in molecular crystals [Francia et al. Crystal Growth and Design, 2020Registration required, and please help us by feeling in the optional survey.

NEW: TYC Careers Talks - Engineering Analysis and High-Performance Computing (HPC) at UKAEA
2021-05-24 12:00 (Europe/London) | Online
The Thomas Young Centre and UCL Women in Physics & Astronomy group are very excited to bring you the first in a set of careers talks. To kick of the series we are very pleased to host a panel of representatives from the UK Atomic Energy Authority (UKAEA). We encourage all of our TYC members to attend, and particularly those members from less well-represented groups.

Fusion energy is entering a golden age, with more public and private reactors being built than ever before, and the United Kingdom Atomic Energy Authority (UKAEA) is at the forefront of international research and development.

We operate two world leading experiments, JET and MAST Upgrade, that are paving the way for future fusion power plants, and are both undergoing the most exciting phases of their operational histories.

Fusion research and development is heavily dependent on the two related disciplines of Engineering Analysis and High-Performance Computing (HPC), and with this online event we will be showcasing the work of our specialists in these areas, as well as discussing the benefits of working at UKAEA. There will be opportunity to ask questions of our panellists and to get into contact for careers information.

Topic: TYC Careers Talks

Meeting ID: 991 4638 9027Passcode: [REDACTED]
