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Yusuf Hamied Department of Chemistry

 

Recent Publications from the Theory Research Interest Group

Instantons and the quantum bound to chaos
VG Sadhasivam, L Meuser, DR Reichman, SC Althorpe
– Proc Natl Acad Sci U S A
(2023)
120,
e2312378120
(DOI: 10.1073/pnas.2312378120)
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data
K Handa, MC Thomas, M Kageyama, T Iijima, A Bender
– J Cheminform
(2023)
15,
112
(DOI: 10.1186/s13321-023-00781-1)
Optimised Baranyai partitioning of the second quantised Hamiltonian
B Csakany, AJW Thom
(2023)
A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals
A Reinhardt, PY Chew, B Cheng
– The Journal of chemical physics
(2023)
159,
184110
(DOI: 10.1063/5.0173341)
Predicting multiple conformations via sequence clustering and AlphaFold2
HK Wayment-Steele, A Ojoawo, R Otten, JM Apitz, W Pitsawong, M Hömberger, S Ovchinnikov, L Colwell, D Kern
– Nature
(2023)
1
(DOI: 10.1038/s41586-023-06832-9)
Many-Body Methods for Surface Chemistry Come of Age: Achieving Consensus with Experiments.
BX Shi, A Zen, V Kapil, PR Nagy, A Grüneis, A Michaelides
– J Am Chem Soc
(2023)
145,
25372
(DOI: 10.1021/jacs.3c09616)
Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.
ML Boby, D Fearon, M Ferla, M Filep, L Koekemoer, MC Robinson, COVID Moonshot Consortium‡, JD Chodera, AA Lee, N London, A von Delft, F von Delft, H Achdout, A Aimon, DS Alonzi, R Arbon, JC Aschenbrenner, BH Balcomb, E Bar-David, H Barr, A Ben-Shmuel, J Bennett, VA Bilenko, B Borden, P Boulet, GR Bowman, L Brewitz, J Brun, S Bvnbs, M Calmiano, A Carbery, DW Carney, E Cattermole, E Chang, E Chernyshenko, A Clyde, JE Coffland, G Cohen, JC Cole, A Contini, L Cox, TI Croll, M Cvitkovic, S De Jonghe, A Dias, K Donckers, DL Dotson, A Douangamath, S Duberstein, T Dudgeon, LE Dunnett, P Eastman, N Erez, CJ Eyermann, M Fairhead, G Fate, O Fedorov, RS Fernandes, L Ferrins, R Foster, H Foster, L Fraisse, R Gabizon, A García-Sastre, VO Gawriljuk, P Gehrtz, C Gileadi, C Giroud, WG Glass, RC Glen, I Glinert, AS Godoy, M Gorichko, T Gorrie-Stone, EJ Griffen, A Haneef, S Hassell Hart, J Heer, M Henry, M Hill, S Horrell, QYJ Huang, VD Huliak, MFD Hurley, T Israely, A Jajack, J Jansen, E Jnoff, D Jochmans, T John, B Kaminow, L Kang, AL Kantsadi, PW Kenny, JL Kiappes, SO Kinakh, B Kovar, T Krojer, VNT La, S Laghnimi-Hahn, BA Lefker, H Levy, RM Lithgo, IG Logvinenko, P Lukacik, HB Macdonald, EM MacLean, LL Makower, TR Malla, PG Marples, T Matviiuk, W McCorkindale, BL McGovern, S Melamed, KP Melnykov, O Michurin, P Miesen, H Mikolajek, BF Milne, D Minh, A Morris, GM Morris, MJ Morwitzer, D Moustakas, CE Mowbray, AM Nakamura, JB Neto, J Neyts, L Nguyen, GD Noske, V Oleinikovas, G Oliva, GJ Overheul, CD Owen, R Pai, J Pan, N Paran, AM Payne, B Perry, M Pingle, J Pinjari, B Politi, A Powell, V Pšenák, I Pulido, R Puni, VL Rangel, RN Reddi, P Rees, SP Reid, L Reid, E Resnick, EG Ripka, RP Robinson, J Rodriguez-Guerra, R Rosales, DA Rufa, K Saar, KS Saikatendu, E Salah, D Schaller, J Scheen, CA Schiffer, CJ Schofield, M Shafeev, A Shaikh, AM Shaqra, J Shi, K Shurrush, S Singh, A Sittner, P Sjö, R Skyner, A Smalley, B Smeets, MD Smilova, LJ Solmesky, J Spencer, C Strain-Damerell, V Swamy, H Tamir, JC Taylor, RE Tennant, W Thompson, A Thompson, S Tomásio, CWE Tomlinson, IS Tsurupa, A Tumber, I Vakonakis, RP van Rij, L Vangeel, FS Varghese, M Vaschetto, EB Vitner, V Voelz, A Volkamer, MA Walsh, W Ward, C Weatherall, S Weiss, KM White, CF Wild, KD Witt, M Wittmann, N Wright, Y Yahalom-Ronen, NK Yilmaz, D Zaidmann, I Zhang, H Zidane, N Zitzmann, SN Zvornicanin
– Science (New York, N.Y.)
(2023)
382,
eabo7201
(DOI: 10.1126/science.abo7201)
Corrected density functional theory and the random phase approximation: Improved accuracy at little extra cost.
D Graf, AJW Thom
– J Chem Phys
(2023)
159,
174106
(DOI: 10.1063/5.0168569)
Mesoscale Simulations Reveal How Salt Influences Clay Particles Agglomeration in Aqueous Dispersions
TTB Le, AR Finney, A Zen, T Bui, WJ Tay, K Chellappah, M Salvalaglio, A Michaelides, A Striolo
– Journal of chemical theory and computation
(2023)
(DOI: 10.1021/acs.jctc.3c00719)
Exact hydrodynamics and onset of phase separation for an active exclusion process
J Mason, C Erignoux, RL Jack, M Bruna
– Proceedings of the Royal Society A
(2023)
479,
20230524
(DOI: 10.1098/rspa.2023.0524)
Exploring the parameter space of an endohedral atom in a cylindrical cavity
K Panchagnula, AJW Thom
– The Journal of chemical physics
(2023)
159,
164308
(DOI: 10.1063/5.0170010)
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank.
S Seal, O Spjuth, L Hosseini-Gerami, M García-Ortegón, S Singh, A Bender, AE Carpenter
(2023)
(DOI: 10.1101/2023.10.15.562398)
The limit of macroscopic homogeneous ice nucleation at the nanoscale
JA Hayton, MB Davies, TF Whale, A Michaelides, SJ Cox
– Faraday Discussions
(2023)
(DOI: 10.1039/d3fd00099k)
Necking and failure of a particulate gel strand: signatures of yielding on different length scales.
K Thijssen, TB Liverpool, CP Royall, RL Jack
– Soft Matter
(2023)
19,
7412
(DOI: 10.1039/d3sm00681f)
MAVEN: compound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny
L Hosseini-Gerami, R Hernansaiz Ballesteros, A Liu, H Broughton, DA Collier, A Bender
– BMC Bioinformatics
(2023)
24,
344
(DOI: 10.1186/s12859-023-05416-8)
Energy landscapes for proteins described by the UNRES coarse-grained potential.
PA Wesołowski, AK Sieradzan, MJ Winnicki, JWR Morgan, DJ Wales
– Biophys Chem
(2023)
303,
107107
(DOI: 10.1016/j.bpc.2023.107107)
Global analysis of energy landscapes for materials modeling: A test case for C60
G Csányi, JWR Morgan, DJ Wales
– Journal of Chemical Physics
(2023)
159,
104107
(DOI: 10.1063/5.0167857)
Energy Landscapes and Heat Capacity Signatures for Peptides Correlate with Phase Separation Propensity
Nicy, R Collepardo-Guevara, JA Joseph, DJ Wales
– QRB Discov
(2023)
4,
e7
(DOI: 10.1017/qrd.2023.5)
Editorial overview: Artificial intelligence (AI) methodology in structural biology
A Bender, C de Graaf, NM O'Boyle
– Curr Opin Struct Biol
(2023)
82,
102676
(DOI: 10.1016/j.sbi.2023.102676)
Active-passive mixtures with bulk loading: a minimal active engine in one dimension
JF Derivaux, RL Jack, ME Cates
– Journal of Statistical Mechanics: Theory and Experiment
(2023)
2023,
083212
(DOI: 10.1088/1742-5468/acecfa)

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