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Yusuf Hamied Department of Chemistry

 

Recent Publications from the Theory Research Interest Group

Towards understanding antimicrobial activity, cytotoxicity and the mode of action of dichapetalins A and M using in silico and in vitro studies.
MA Chama, D Modos, LH Mervin, KB-A Owusu, DM Ayine-Tora, B Egyir, L Paemka, G Yankson, M Ohashi, AM Afzal, A Bender
– Toxicon : official journal of the International Society on Toxinology
(2021)
193,
28
(DOI: 10.1016/j.toxicon.2021.01.002)
Computational Amperometry of Nanoscale Capacitors in Molecular Simulations
T Dufils, M Sprik, M Salanne
– arXiv.org/abs/2104.03177v1
(2021)
Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model.
JA Joseph, JR Espinosa, I Sanchez-Burgos, A Garaizar, D Frenkel, R Collepardo-Guevara
– Biophysical Journal
(2021)
120,
1219
(DOI: 10.1016/j.bpj.2021.01.031)
Microscopic Kinetics Pathway of Salt Crystallization in Graphene Nanocapillaries
L Wang, J Chen, SJ Cox, L Liu, GC Sosso, N Li, P Gao, A Michaelides, E Wang, X Bai
– Physical Review Letters
(2021)
126,
136001
(DOI: 10.1103/physrevlett.126.136001)
Computation of the chemical potential and solubility of amorphous solids
HA Vinutha, D Frenkel
– J Chem Phys
(2021)
154,
124502
(DOI: 10.1063/5.0038955)
Routes to cubic ice through heterogeneous nucleation
MB Davies, M Fitzner, A Michaelides
– Proceedings of the National Academy of Sciences
(2021)
118,
e2025245118
(DOI: 10.1073/pnas.2025245118)
Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions
M-A Trapotsi, LH Mervin, AM Afzal, N Sturm, O Engkvist, IP Barrett, A Bender
– Journal of Chemical Information and Modeling
(2021)
61,
1444
(DOI: 10.1021/acs.jcim.0c00864)
Structure-based identification of dual ligands at the A<sub>2A</sub>R and PDE10A with anti-proliferative effects in lung cancer cell-lines.
L Kalash, I Winfield, D Safitri, M Bermudez, S Carvalho, R Glen, G Ladds, A Bender
– J Cheminform
(2021)
13,
17
(DOI: 10.1186/s13321-021-00492-5)
Development of ReaxFF Reactive Force Field for Aqueous Iron-sulfur Clusters with Applications to Stability and Reactivity in Water
E Moerman, D Furman, DJ Wales
– Journal of chemical information and modeling
(2021)
61,
1204
(DOI: 10.1021/acs.jcim.0c01292)
Structural and electronic properties of solid molecular hydrogen from many-electron theories
K Liao, T Shen, XZ Li, A Alavi, A Grüneis
– Physical Review B
(2021)
103,
054111
(DOI: 10.1103/PhysRevB.103.054111)
Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions.
G Krainer, TJ Welsh, JA Joseph, JR Espinosa, S Wittmann, E de Csilléry, A Sridhar, Z Toprakcioglu, G Gudiškytė, MA Czekalska, WE Arter, J Guillén-Boixet, TM Franzmann, S Qamar, PS George-Hyslop, AA Hyman, R Collepardo-Guevara, S Alberti, TPJ Knowles
– Nat Commun
(2021)
12,
1085
(DOI: 10.1038/s41467-021-21181-9)
Valency and binding affinity variations can regulate the multilayered organization of protein condensates with many components
I Sanchez-Burgos, JR Espinosa, JA Joseph, R Collepardo-Guevara
– Biomolecules
(2021)
11,
278
(DOI: 10.3390/biom11020278)
Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions
G Krainer, TJ Welsh, JA Joseph, P St George-Hyslop, AA Hyman, R Collepardo-Guevara, S Alberti, TPJ Knowles
– BIOPHYSICAL JOURNAL
(2021)
120,
28A
(DOI: 10.1101/2020.05.04.076299)
Deep diversification of an AAV capsid protein by machine learning.
DH Bryant, A Bashir, S Sinai, NK Jain, PJ Ogden, PF Riley, GM Church, LJ Colwell, ED Kelsic
– Nat Biotechnol
(2021)
1
(DOI: 10.1038/s41587-020-00793-4)
Collective motion in large deviations of active particles.
Y-E Keta, É Fodor, F van Wijland, ME Cates, RL Jack
– Physical review. E
(2021)
103,
022603
(DOI: 10.1103/physreve.103.022603)
Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 1: Ways to make an impact, and why we are not there yet.
A Bender, I Cortés-Ciriano
– Drug Discov Today
(2021)
26,
511
(DOI: 10.1016/j.drudis.2020.12.009)
Comparison of Cellular Morphological Descriptors and Molecular Fingerprints for the Prediction of Cytotoxicity- And Proliferation-Related Assays
S Seal, H Yang, L Vollmers, A Bender
– Chem Res Toxicol
(2021)
34,
422
(DOI: 10.1021/acs.chemrestox.0c00303)
Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 2: a discussion of chemical and biological data used for AI in drug discovery
A Bender, I Cortes-Ciriano
– Drug Discovery Today
(2021)
(DOI: 10.1016/j.drudis.2020.11.037)
Quantum-mechanical exploration of the phase diagram of water.
A Reinhardt, B Cheng
– Nat Commun
(2021)
12,
588
(DOI: 10.1038/s41467-020-20821-w)
A demonstration of improved constraints on primordial gravitational waves with delensing
PAR Ade, Z Ahmed, M Amiri, AJ Anderson, JE Austermann, JS Avva, D Barkats, RB Thakur, JA Beall, AN Bender, BA Benson, F Bianchini, CA Bischoff, LE Bleem, JJ Bock, H Boenish, E Bullock, V Buza, JE Carlstrom, CL Chang, JR Cheshire, HC Chiang, TL Chou, R Citron, J Connors, CC Moran, J Cornelison, TM Crawford, AT Crites, M Crumrine, A Cukierman, T De Haan, M Dierickx, MA Dobbs, L Duband, W Everett, S Fatigoni, JP Filippini, S Fliescher, J Gallicchio, EM George, TS Germaine, N Goeckner-Wald, DC Goldfinger, J Grayson, N Gupta, G Hall, M Halpern, NW Halverson, S Harrison, S Henderson, JW Henning, SR Hildebrandt, GC Hilton, GP Holder, WL Holzapfel, JD Hrubes, N Huang, J Hubmayr, H Hui, KD Irwin, J Kang, KS Karkare, E Karpel, S Kefeli, SA Kernasovskiy, L Knox, JM Kovac, CL Kuo, K Lau, AT Lee, EM Leitch, D Li, A Lowitz, A Manzotti, JJ McMahon, KG Megerian, SS Meyer, M Millea, LM Mocanu, L Moncelsi, J Montgomery, A Nadolski, T Namikawa, T Natoli, CB Netterfield, HT Nguyen, JP Nibarger, G Noble, V Novosad, R O'Brient, RW Ogburn, Y Omori, S Padin, S Palladino, S Patil, T Prouve, C Pryke, B Racine, CL Reichardt
– Physical Review D
(2021)
103,
022004
(DOI: 10.1103/physrevd.103.022004)

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