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Yusuf Hamied Department of Chemistry

 

Recent Publications from the Theory Research Interest Group

Optimal dimensionality reduction of Markov chains using graph transformation.
D Kannan, DJ Sharpe, TD Swinburne, DJ Wales
– The Journal of chemical physics
(2020)
153,
244108
(DOI: 10.1063/5.0025174)
Energy Landscapes for Electronic Structure
HGA Burton, DJ Wales
– Journal of chemical theory and computation
(2020)
acs.jctc.0c00772
(DOI: 10.1021/acs.jctc.0c00772)
Systematic analysis of protein targets associated with adverse events of drugs from clinical trials and postmarketing reports
IA Smit, AM Afzal, CHG Allen, F Svensson, T Hanser, A Bender
– Chemical research in toxicology
(2020)
acs.chemrestox.0c00294
(DOI: 10.1021/acs.chemrestox.0c00294)
Systematic Evaluation of ReaxFF Reactive Force Fields for Biochemical Applications.
E Moerman, D Furman, DJ Wales
– Journal of chemical theory and computation
(2020)
17,
497
(DOI: 10.1021/acs.jctc.0c01043)
New Associations between Drug-Induced Adverse Events in Animal Models and Humans Reveal Novel Candidate Safety Targets.
KA Giblin, D Basili, AM Afzal, L Rosenbrier-Ribeiro, N Greene, I Barrett, SJ Hughes, A Bender
– Chem Res Toxicol
(2020)
acs.chemrestox.0c00311
(DOI: 10.1021/acs.chemrestox.0c00311)
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 discovery today
(2020)
(DOI: 10.1016/j.drudis.2020.12.009)
Electronic correlations and magnetic interactions in infinite-layer NdNiO2
VM Katukuri, NA Bogdanov, O Weser, J Van Den Brink, A Alavi
– Physical Review B
(2020)
102,
241112
(DOI: 10.1103/PhysRevB.102.241112)
The adaptive shift method in full configuration interaction quantum Monte Carlo: Development and applications
K Ghanem, K Guther, A Alavi
– The Journal of Chemical Physics
(2020)
153,
224115
(DOI: 10.1063/5.0032617)
Electric field based Poisson-Boltzmann: Treating mobile charge as polarization
M Sprik
– arxiv.org/abs/2012.02988
(2020)
Numerical method for computing the free energy of glasses
HA Vinutha, D Frenkel
– Physical Review E
(2020)
102,
063303
(DOI: 10.1103/PhysRevE.102.063303)
A Stochastic Approach to Unitary Coupled Cluster
M-A Filip, AJW Thom
– The Journal of chemical physics
(2020)
153,
214106
(DOI: 10.1063/5.0026141)
The color center singlet state of oxygen vacancies in TiO2.
J Chen, NA Bogdanov, D Usvyat, W Fang, A Michaelides, A Alavi
– J Chem Phys
(2020)
153,
204704
(DOI: 10.1063/5.0030658)
Continuum model of the simple dielectric fluid: Consistency between density based and continuum mechanics methods
M Sprik
– arxiv.org/abs/2011.05052
(2020)
Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions
S Farr, E Woods, J Joseph, A Garaizar, R Collepardo-Guevara
(2020)
(DOI: 10.1101/2020.11.23.391599)
Eliminating the wave-function singularity for ultracold atoms by a similarity transformation
P Jeszenszki, U Ebling, H Luo, A Alavi, J Brand
– Physical Review Research
(2020)
2,
043270
(DOI: 10.1103/physrevresearch.2.043270)
Towards a Holomorphic Density Functional Theory
RA Zarotiadis, HGA Burton, AJW Thom
– J Chem Theory Comput
(2020)
16,
7400
(DOI: 10.1021/acs.jctc.0c00822)
Extraction and Integration of Genetic Networks from Short-Profile Omic Data Sets
J Iacovacci, A Peluso, T Ebbels, M Ralser, RC Glen
– Metabolites
(2020)
10,
435
(DOI: 10.3390/metabo10110435)
Quantum-mechanical exploration of the phase diagram of water
A Reinhardt, B Cheng
– Nature Communications
(2020)
Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence
S Lichtinger, A Garaizar, R Collepardo-Guevara, A Reinhardt
– bioRxiv
(2020)
(DOI: 10.1101/2020.10.20.347542)
DNA binds to a specific site of the adhesive blood-protein von Willebrand factor guided by electrostatic interactions
A Sandoval-Pérez, RML Berger, A Garaizar, SE Farr, MA Brehm, G König, SW Schneider, R Collepardo-Guevara, V Huck, JO Rädler, C Aponte-Santamaría
– Nucleic Acids Res
(2020)
48,
gkaa988-
(DOI: 10.1093/nar/gkaa988)

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