Lennard Jones Centre: Members' Publications

Publications by members (links to full lists):

• BENDER, Andreas

  Three most recent publications:

  • Chama, MA and Modos, D and Mervin, LH and Owusu, KBA and Ayine-Tora, DM and Egyir, B and Paemka, L and Yankson, G and Ohashi, M and Afzal, AM and Bender, A (2021) Towards understanding antimicrobial activity, cytotoxicity and the mode of action of dichapetalins A and M using in silico and in vitro studies. Toxicon, 193. pp. 28-37. ISSN 0041-0101
  • Seal, S and Yang, H and Vollmers, L and Bender, A (2021) Comparison of Cellular Morphological Descriptors and Molecular Fingerprints for the Prediction of Cytotoxicity- and Proliferation-Related Assays. Chem Res Toxicol, 34. pp. 422-437.
  • Ade, PAR and Ahmed, Z and Amiri, M and Anderson, AJ and Austermann, JE and Avva, JS and Barkats, D and Thakur, RB and Beall, JA and Bender, AN and Benson, BA and Bianchini, F and Bischoff, CA and Bleem, LE and Bock, JJ and Boenish, H and Bullock, E and Buza, V and Carlstrom, JE and Chang, CL and Cheshire, JR and Chiang, HC and Chou, TL and Citron, R and Connors, J and Moran, CC and Cornelison, J and Crawford, TM and Crites, AT and Crumrine, M and Cukierman, A and De Haan, T and Dierickx, M and Dobbs, MA and Duband, L and Everett, W and Fatigoni, S and Filippini, JP and Fliescher, S and Gallicchio, J and George, EM and Germaine, TS and Goeckner-Wald, N and Goldfinger, DC and Grayson, J and Gupta, N and Hall, G and Halpern, M and Halverson, NW and Harrison, S and Henderson, S and Henning, JW and Hildebrandt, SR and Hilton, GC and Holder, GP and Holzapfel, WL and Hrubes, JD and Huang, N and Hubmayr, J and Hui, H and Irwin, KD and Kang, J and Karkare, KS and Karpel, E and Kefeli, S and Kernasovskiy, SA and Knox, L and Kovac, JM and Kuo, CL and Lau, K and Lee, AT and Leitch, EM and Li, D and Lowitz, A and Manzotti, A and McMahon, JJ and Megerian, KG and Meyer, SS and Millea, M and Mocanu, LM and Moncelsi, L and Montgomery, J and Nadolski, A and Namikawa, T and Natoli, T and Netterfield, CB and Nguyen, HT and Nibarger, JP and Noble, G and Novosad, V and O'Brient, R and Ogburn, RW and Omori, Y and Padin, S and Palladino, S and Patil, S and Prouve, T and Pryke, C and Racine, B and Reichardt, CL (2021) A demonstration of improved constraints on primordial gravitational waves with delensing. Physical Review D, 103. ISSN 2470-0010
• MORRIS, Andrew James J (Andrew)

  Three most recent publications:

  • Griffith, KJ and Seymour, ID and Hope, MA and Butala, MM and Lamontagne, LK and Preefer, MB and Koçer, CP and Henkelman, G and Morris, AJ and Cliffe, MJ and Dutton, SE and Grey, CP (2019) Ionic and Electronic Conduction in TiNb2O7. J Am Chem Soc.
  • Lisac, K and Topić, F and Arhangelskis, M and Cepić, S and Julien, PA and Nickels, CW and Morris, AJ and Friščić, T and Cinčić, D (2019) Halogen-bonded cocrystallization with phosphorus, arsenic and antimony acceptors. Nature Communications, 10. 61-.
  • Cliffe, MJ and Keyzer, EN and Dunstan, MT and Ahmad, S and De Volder, MFL and Deschler, F and Morris, AJ and Grey, CP (2019) Strongly coloured thiocyanate frameworks with perovskite-analogue structures. Chemical Science, 10. pp. 793-801. ISSN 2041-6520
• THOM, Alexander James JW (Alexander)

  Three most recent publications:

  • Izuogu, DC and Yoshida, T and Cosquer, G and Asegbeloyin, JN and Zhang, H and Thom, AJW and Yamashita, M (2020) Periodicity of Single-Molecule Magnet Behaviour of Heterotetranuclear Lanthanide Complexes across the Lanthanide Series: A Compendium. Chemistry - A European Journal, 26. pp. 6036-6049. ISSN 0947-6539
  • Yoshida, T and Ahsan, HM and Zhang, H-T and Izuogu, DC and Abe, H and Ohtsu, H and Yamaguchi, T and Breedlove, BK and Thom, AJW and Yamashita, M (2020) Ionic-caged heterometallic bismuth-platinum complex exhibiting electrocatalytic CO2 reduction. Dalton Trans.
  • Filip, MA and Thom, AJW (2020) A stochastic approach to unitary coupled cluster. Journal of Chemical Physics, 153. ISSN 0021-9606
• ALAVI, Ali

  Three most recent publications:

  • Weser, O and Freitag, L and Guther, K and Alavi, A and Li Manni, G (2021) Chemical insights into the electronic structure of Fe(II) porphyrin using FCIQMC, DMRG, and generalized active spaces. International Journal of Quantum Chemistry, 121. ISSN 0020-7608
  • Guther, K and Anderson, RJ and Blunt, NS and Bogdanov, NA and Cleland, D and Dattani, N and Dobrautz, W and Ghanem, K and Jeszenszki, P and Liebermann, N and Manni, GL and Lozovoi, AY and Luo, H and Ma, D and Merz, F and Overy, C and Rampp, M and Samanta, PK and Schwarz, LR and Shepherd, JJ and Smart, SD and Vitale, E and Weser, O and Booth, GH and Alavi, A (2020) NECI: N -Electron Configuration Interaction with an emphasis on state-of-the-art stochastic methods. Journal of Chemical Physics, 153. 034107-. ISSN 0021-9606
  • Chen, J and Penschke, C and Alavi, A and Michaelides, A (2020) Small polarons and the Janus nature of TiO2 (110). Physical Review B, 101. ISSN 2469-9950
• FRENKEL, Daniel (Daan)

  Three most recent publications:

  • Eloul, S and Frenkel, D (2021) Nano-pump based on exothermic surface reactions. Soft Matter, 17. pp. 1173-1177.
  • Joseph, JA and Espinosa, JR and Sanchez-Burgos, I and Garaizar, A and Frenkel, D and Collepardo-Guevara, R (2021) Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model. Biophys J.
  • Cheng, B and Frenkel, D (2020) Computing the Heat Conductivity of Fluids from Density Fluctuations. Physical Review Letters, 125. 130602-. ISSN 0031-9007
• WALES, David John J (David)

  Three most recent publications:

  • Moerman, E and Furman, D and Wales, DJ (2021) Systematic Evaluation of ReaxFF Reactive Force Fields for Biochemical Applications. Journal of Chemical Theory and Computation, 17. pp. 497-514. ISSN 1549-9618
  • Burton, HGA and Wales, DJ (2021) Energy Landscapes for Electronic Structure. Journal of Chemical Theory and Computation, 17. pp. 151-169. ISSN 1549-9618
  • Verpoort, PC and Lee, AA and Wales, DJ (2020) Archetypal landscapes for deep neural networks. Proceedings of the National Academy of Sciences of the United States of America, 117. pp. 21857-21864. ISSN 0027-8424
• ARTACHO, Emilio

  Three most recent publications:

  • Gu, B and Cunningham, B and Munõz Santiburcio, D and Da Pieve, F and Artacho, E and Kohanoff, J (2020) Efficient ab initio calculation of electronic stopping in disordered systems via geometry pre-sampling: Application to liquid water. Journal of Chemical Physics, 153. 034113-. ISSN 0021-9606
  • López-Durán, D and Plésiat, E and Krompiec, M and Artacho, E (2020) Gap variability upon packing in organic photovoltaics. PLoS ONE, 15. e0234115-.
  • García, A and Papior, N and Akhtar, A and Artacho, E and Blum, V and Bosoni, E and Brandimarte, P and Brandbyge, M and Cerdá, JI and Corsetti, F and Cuadrado, R and Dikan, V and Ferrer, J and Gale, J and García-Fernández, P and García-Suárez, VM and García, S and Huhs, G and Illera, S and Korytár, R and Koval, P and Lebedeva, I and Lin, L and López-Tarifa, P and Mayo, SG and Mohr, S and Ordejón, P and Postnikov, A and Pouillon, Y and Pruneda, M and Robles, R and Sánchez-Portal, D and Soler, JM and Ullah, R and Yu, VWZ and Junquera, J (2020) Siesta: Recent developments and applications. The Journal of chemical physics, 152. 204108-.
• CSANYI, Gabor

  Three most recent publications:

  • Rosenbrock, CW and Gubaev, K and Shapeev, AV and Pártay, LB and Bernstein, N and Csányi, G and Hart, GLW (2021) Machine-learned interatomic potentials for alloys and alloy phase diagrams. npj Computational Materials, 7.
  • Deringer, VL and Bernstein, N and Csányi, G and Ben Mahmoud, C and Ceriotti, M and Wilson, M and Drabold, DA and Elliott, SR (2021) Origins of structural and electronic transitions in disordered silicon. Nature, 589. pp. 59-64. ISSN 0028-0836
  • Liu, Y-B and Yang, J-Y and Xin, G-M and Liu, L-H and Csányi, G and Cao, B-Y (2020) Machine learning interatomic potential developed for molecular simulations on thermal properties of β-Ga2O3. J Chem Phys, 153. p. 144501. ISSN 0021-9606
• BOOTH, George Henry H (George)

  Three most recent publications:

  • Sharma, S and Yanai, T and Booth, GH and Umrigar, CJ and Chan, GKL (2014) Spectroscopic accuracy directly from quantum chemistry: Application to ground and excited states of beryllium dimer. Journal of Chemical Physics, 140. 104112-. ISSN 0021-9606
  • Booth, GH and Smart, SD and Alavi, A (2014) Linear-scaling and parallelisable algorithms for stochastic quantum chemistry. Molecular Physics. ISSN 0026-8976
  • Grüneis, A and Shepherd, JJ and Alavi, A and Tew, DP and Booth, GH (2013) Explicitly correlated plane waves: accelerating convergence in periodic wavefunction expansions. J Chem Phys, 139. 084112-.
• ELLIOTT, James Arthur A (James)

  Three most recent publications:

  • Gspann, TS and Ngern, NHH and Kiley, PJ and McKeown, PA and Bulmer, JS and Windle, AH and Tan, VBC and Elliott, JA (2020) A comparative study of the tensile failure of carbon nanotube, Dyneema and carbon fibre tows over six orders of strain rate. Carbon, 164. pp. 407-421. ISSN 0008-6223
  • Vanya, P and Elliott, JA (2020) Definitions of local density in density-dependent potentials for mixtures. Phys Rev E, 102. 013312-.
  • Bulmer, JS and Kaniyoor, A and Gspann, T and Mizen, J and Ryley, J and Kiley, P and Ratering, G and Sparreboom, W and Bauhuis, G and Stehr, T and Oudejans, D and Sparkes, M and O'Neill, B and Elliott, JA (2020) Forecasting continuous carbon nanotube production in the floating catalyst environment. Chemical Engineering Journal, 390. ISSN 1385-8947
• GOODMAN, Jonathan Michael M (Jonathan)

  Three most recent publications:

  • Goodman, JM and Wang, MWH and Allen, TEH (2021) Machine learning in predictive toxicology: Recent applications and future directions for classification models. Chemical Research in Toxicology. ISSN 0893-228X
  • Allen, TEH and Wedlake, AJ and Gelžinytė, E and Gong, C and Goodman, JM and Gutsell, S and Russell, PJ (2020) Neural network activation similarity: A new measure to assist decision making in chemical toxicology. Chemical Science, 11. pp. 7335-7348. ISSN 2041-6520
  • Plajer, AJ and Lee, S and Bond, AD and Goodman, JM and Wright, DS (2020) Charge-assisted phosph(v)azane anion receptors. Dalton Trans, 49. pp. 3403-3407. ISSN 1477-9226
• COLWELL, Lucy Jane J (Lucy)

  Three most recent publications:

  • Bryant, DH and Bashir, A and Sinai, S and Jain, NK and Ogden, PJ and Riley, PF and Church, GM and Colwell, LJ and Kelsic, ED (2021) Deep diversification of an AAV capsid protein by machine learning. Nature Biotechnology. ISSN 1087-0156
  • Norman, RA and Ambrosetti, F and Bonvin, AMJJ and Colwell, LJ and Kelm, S and Kumar, S and Krawczyk, K (2020) Computational approaches to therapeutic antibody design: Established methods and emerging trends. Briefings in Bioinformatics, 21. pp. 1549-1567. ISSN 1467-5463
  • Cervettini, D and Tang, S and Fried, SD and Willis, JCW and Funke, LFH and Colwell, LJ and Chin, JW (2020) Rapid discovery and evolution of orthogonal aminoacyl-tRNA synthetase–tRNA pairs. Nature Biotechnology, 38. pp. 989-999. ISSN 1087-0156
• PAYNE, Michael Christopher C (Michael)

  Three most recent publications:

  • Linscott, EB and Cole, DJ and Hine, NDM and Payne, MC and Weber, C (2020) ONETEP + TOSCAM: Uniting Dynamical Mean Field Theory and Linear-Scaling Density Functional Theory. Journal of Chemical Theory and Computation, 16. pp. 4899-4911. ISSN 1549-9618
  • Kuziel, AW and Milowska, KZ and Chau, PL and Boncel, S and Koziol, KK and Yahya, N and Payne, MC (2020) The True Amphipathic Nature of Graphene Flakes: A Versatile 2D Stabilizer. Advanced Materials, 32. e2000608-. ISSN 0935-9648
  • Oliveira, MJT and Papior, N and Pouillon, Y and Blum, V and Artacho, E and Caliste, D and Corsetti, F and De Gironcoli, S and Elena, AM and García, A and García-Suárez, VM and Genovese, L and Huhn, WP and Huhs, G and Kokott, S and Küçükbenli, E and Larsen, AH and Lazzaro, A and Lebedeva, IV and Li, Y and López-Durán, D and López-Tarifa, P and Lüders, M and Marques, MAL and Minar, J and Mohr, S and Mostofi, AA and O'Cais, A and Payne, MC and Ruh, T and Smith, DGA and Soler, JM and Strubbe, DA and Tancogne-Dejean, N and Tildesley, D and Torrent, M and Yu, VWZ (2020) The CECAM electronic structure library and the modular software development paradigm. Journal of Chemical Physics, 153. 024117-. ISSN 0021-9606
• SPRIK, Michiel

  Three most recent publications:

  • Jia, M and Zhang, C and Cox, SJ and Sprik, M and Cheng, J (2020) Computing surface acidity constants of proton hopping groups from density functional theory based molecular dynamics: application to SnO2(110)/H2O interface. J Chem Theory Comput.
  • Li, JQ and Meng, L and Sprik, M and Cheng, J (2020) Thermodynamic Investigation of Proton/Electron Interplay on the Pourbaix Diagram at the TiO<inf>2</inf>/Electrolyte Interface. Journal of Physical Chemistry C, 124. pp. 19003-19014. ISSN 1932-7447
  • Geiger, J and Sprik, M and May, MM (2020) Band positions of anatase (001) and (101) surfaces in contact with water from density functional theory. The Journal of Chemical Physics, 152. p. 194706. ISSN 0021-9606
• VENDRUSCOLO, Michele

  Three most recent publications:

  • Musteikytė, G and Jayaram, AK and Xu, CK and Vendruscolo, M and Krainer, G and Knowles, TPJ (2021) Interactions of α-synuclein oligomers with lipid membranes. Biochimica et Biophysica Acta - Biomembranes, 1863. 183536-. ISSN 0005-2736
  • Fani, G and Mannini, B and Vecchi, G and Cascella, R and Cecchi, C and Dobson, CM and Vendruscolo, M and Chiti, F (2021) Aβ Oligomers Dysregulate Calcium Homeostasis by Mechanosensitive Activation of AMPA and NMDA Receptors. ACS Chem Neurosci, 12. pp. 766-781.
  • Hardenberg, M and Horvath, A and Ambrus, V and Fuxreiter, M and Vendruscolo, M (2021) Widespread occurrence of the droplet state of proteins in the human proteome. Proceedings of the National Academy of Sciences of the United States of America, 117. pp. 33254-33262. ISSN 0027-8424
• FLECK, Norman Andrew A (Norman)

  Three most recent publications:

  • Shishvan, SS and Fleck, NA and Deshpande, VS (2021) The initiation of void growth during stripping of Li electrodes in solid electrolyte cells. Journal of Power Sources, 488. ISSN 0378-7753
  • Seiler, PE and Li, K and Deshpande, VS and Fleck, NA (2021) The Influence of Strut Waviness on the Tensile Response of Lattice Materials. Journal of Applied Mechanics, Transactions ASME, 88. ISSN 0021-8936
  • Li, K and Seiler, PE and Deshpande, VS and Fleck, NA (2021) Regulation of notch sensitivity of lattice materials by strut topology. International Journal of Mechanical Sciences, 192. ISSN 0020-7403
• HINE, Nicholas Daniel DM (Nicholas)

  Three most recent publications:

  • Li, JH and Zuehlsdorff, TJ and Payne, MC and Hine, NDM (2015) Identifying and tracing potential energy surfaces of electronic excitations with specific character via their transition origins: Application to oxirane. Physical Chemistry Chemical Physics, 17. pp. 12065-12079. ISSN 1463-9076
  • Goode, AE and Hine, NDM and Chen, S and Bergin, SD and Shaffer, MSP and Ryan, MP and Haynes, PD and Porter, AE and McComb, DW (2014) Mapping functional groups on oxidised multi-walled carbon nanotubes at the nanometre scale. Chem Commun (Camb), 50. pp. 6744-6747. ISSN 1359-7345
  • Murphy, ST and Hine, NDM (2014) Point Defects and Non-stoichiometry in Li2TiO3. CHEMISTRY OF MATERIALS, 26. pp. 1629-1638. ISSN 0897-4756
• NIKIFORAKIS, Nikolaos

  Three most recent publications:

  • Bakalis, G and Tang-Yuk, KC and Mi, X and Nikiforakis, N and Ng, HD (2021) Numerical simulation of deflagration-to-detonation transition via shock–multiple flame kernels interactions. Computers and Mathematics with Applications, 83. pp. 111-126. ISSN 0898-1221
  • Ioannou, E and Nikiforakis, N (2021) Multiphysics modeling of the initiating capability of detonators. I. The underwater test. Journal of Applied Physics, 129. ISSN 0021-8979
  • Ioannou, E and Nikiforakis, N (2021) Multiphysics modeling of the initiating capability of detonators. II. Booster initiation. Journal of Applied Physics, 129. ISSN 0021-8979
• BRISTOWE, Paul David D (Paul)

  Three most recent publications:

  • Evans, HA and Deng, Z and Collings, IE and Wu, Y and Andrews, JL and Pilar, K and Tuffnell, JM and Wu, G and Wang, J and Dutton, SE and Bristowe, PD and Seshadri, R and Cheetham, AK (2019) Polymorphism in M(H<inf>2</inf>PO<inf>2</inf>)<inf>3</inf> (M = V, Al, Ga) compounds with the perovskite-related ReO<inf>3</inf> structure. Chemical Communications, 55. pp. 2964-2967. ISSN 1359-7345
  • Wei, F and Deng, Z and Sun, S and Hartono, NTP and Seng, HL and Buonassisi, T and Bristowe, PD and Cheetham, AK (2019) Enhanced visible light absorption for lead-free double perovskite Cs<inf>2</inf>AgSbBr<inf>6</inf>. Chemical Communications, 55. pp. 3721-3724. ISSN 1359-7345
  • Hoye, RLZ and Eyre, L and Wei, F and Brivio, F and Sadhanala, A and Sun, S and Li, W and Zhang, KHL and MacManus-Driscoll, JL and Bristowe, PD and Friend, RH and Cheetham, AK and Deschler, F (2018) Fundamental Carrier Lifetime Exceeding 1 µs in Cs<inf>2</inf>AgBiBr<inf>6</inf> Double Perovskite. Advanced Materials Interfaces, 5.
• GLEN, Robert Charles C (Robert)

  Three most recent publications:

  • Robinson, MC and Glen, RC and Lee, AA (2020) Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction. Journal of Computer-Aided Molecular Design, 34. pp. 717-730. ISSN 0920-654X
  • Koundouros, N and Karali, E and Tripp, A and Valle, A and Inglese, P and Perry, NJS and Magee, DJ and Anjomani Virmouni, S and Elder, GA and Tyson, AL and Dória, ML and van Weverwijk, A and Soares, RF and Isacke, CM and Nicholson, JK and Glen, RC and Takats, Z and Poulogiannis, G (2020) Metabolic Fingerprinting Links Oncogenic PIK3CA with Enhanced Arachidonic Acid-Derived Eicosanoids. Cell, 181. 1596-1611.e27. ISSN 0092-8674
  • Read, C and Yang, P and Kuc, RE and Nyimanu, D and Williams, TL and Glen, RC and Holt, LJ and Arulanantham, H and Smart, A and Davenport, AP and Maguire, JJ (2020) Apelin peptides linked to anti-serum albumin domain antibodies retain affinity in vitro and are efficacious receptor agonists in vivo. Basic and Clinical Pharmacology and Toxicology, 126. pp. 96-103. ISSN 1742-7835
• NEEDS, Richard James J (Richard)

  Three most recent publications:

  • Shipley, AM and Hutcheon, MJ and Johnson, MS and Needs, RJ and Pickard, CJ (2020) Stability and superconductivity of lanthanum and yttrium decahydrides. Physical Review B, 101. 224511-. ISSN 2469-9950
  • Liu, C and Gao, H and Hermann, A and Wang, Y and Miao, M and Pickard, CJ and Needs, RJ and Wang, HT and Xing, D and Sun, J (2020) Plastic and Superionic Helium Ammonia Compounds under High Pressure and High Temperature. Physical Review X, 10.
  • Needs, RJ and Towler, MD and Drummond, ND and López Ríos, P and Trail, JR (2020) Variational and diffusion quantum Monte Carlo calculations with the CASINO code. Journal of Chemical Physics, 152. ISSN 0021-9606
• ALTHORPE, Stuart Christian C (Stuart)

  Three most recent publications:

  • Trenins, G and Willatt, MJ and Althorpe, SC (2019) Path-integral dynamics of water using curvilinear centroids. Journal of Chemical Physics, 151. ISSN 0021-9606
  • Vaillant, CL and Wales, DJ and Althorpe, SC (2019) Tunneling Splittings in Water Clusters from Path Integral Molecular Dynamics. Journal of Physical Chemistry Letters, 10. pp. 7300-7304.
  • Vaillant, CL and Althorpe, SC and Wales, DJ (2019) Path Integral Energy Landscapes for Water Clusters. Journal of Chemical Theory and Computation, 15. pp. 33-42. ISSN 1549-9618
• JENKINS, Stephen John J (Stephen)

  Three most recent publications:

  • Davidson, JA and Sacchi, M and Gorrec, F and Clarke, SM and Jenkins, SJ (2020) Halogen Bonding in Bicomponent Monolayers: Self-Assembly of a Homologous Series of Iodinated Perfluoroalkanes with Bipyridine. Langmuir, 37. pp. 627-635. ISSN 0743-7463
  • Robinson, N and Robertson, C and Gladden, LF and Jenkins, SJ and D'Agostino, C (2018) Direct Correlation between Adsorption Energetics and Nuclear Spin Relaxation in a Liquid-saturated Catalyst Material. ChemPhysChem, 19. p. 2448. ISSN 1439-4235
  • Jenkins, SJ (2018) Chirality at Solid Surfaces. UNSPECIFIED, pp. 1-355.
• ELLIOTT, Stephen Richard R (Stephen)

  Three most recent publications:

  • Alimagham, F and Winterburn, J and Dolman, B and Domingues, PM and Everest, F and Platkov, M and Basov, S and Izakson, G and Katzir, A and Elliott, SR and Hutter, T (2021) Real-time bioprocess monitoring using a mid-infrared fibre-optic sensor. Biochemical Engineering Journal, 167. ISSN 1369-703X
  • Deringer, VL and Bernstein, N and Csányi, G and Ben Mahmoud, C and Ceriotti, M and Wilson, M and Drabold, DA and Elliott, SR (2021) Origins of structural and electronic transitions in disordered silicon. Nature, 589. pp. 59-64. ISSN 0028-0836
  • Lee, TH and Elliott, SR (2021) Multi-Center Hyperbonding in Phase-Change Materials. Physica Status Solidi - Rapid Research Letters. ISSN 1862-6254