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Yusuf Hamied Department of Chemistry

 

Recent Publications from the Theory Research Interest Group

Combined unitary and symmetric group approach applied to low-dimensional Heisenberg spin systems
W Dobrautz, VM Katukuri, NA Bogdanov, D Kats, G Li Manni, A Alavi
– Physical Review B
(2022)
105,
195123
(DOI: 10.1103/physrevb.105.195123)
Long-Range Ionic and Short-Range Hydration Effects Govern Strongly Anisotropic Clay Nanoparticle Interactions.
A Zen, T Bui, TT Bao Le, WJ Tay, K Chellappah, IR Collins, RD Rickman, A Striolo, A Michaelides
– Journal of Physical Chemistry C
(2022)
126,
8143
(DOI: 10.1021/acs.jpcc.2c01306)
<p>Can molecular simulations reliably compare homogeneous and heterogeneous ice nucleation?</p>
D Atherton, A Michaelides, SJ Cox
– J Chem Phys
(2022)
156,
164501
(DOI: 10.1063/5.0085750)
Designing multiphase biomolecular condensates by coevolution of protein mixtures
PY Chew, J Joseph, R Collepardo-Guevara, A Reinhardt
– bioRxiv
(2022)
(DOI: 10.1101/2022.04.22.489187)
On the capacity and superposition of minima in neural network loss function landscapes
MP Niroomand, JWR Morgan, CT Cafolla, DJ Wales
– Machine Learning: Science and Technology
(2022)
3,
025004
(DOI: 10.1088/2632-2153/ac64e6)
Making the most of data: Quantum Monte Carlo Post-Analysis Revisited
T Ichibha, VA Neufeld, K Hongo, R Maezono, AJW Thom
– Physical Review E
(2022)
105,
045313
(DOI: 10.1103/PhysRevE.105.045313)
Energy Landscapes for Base-Flipping in a Model DNA Duplex.
Nicy, D Chakraborty, DJ Wales
– The journal of physical chemistry. B
(2022)
126,
3012
(DOI: 10.1021/acs.jpcb.2c00340)
Prediction of in Vivo Pharmacokinetic Parameters and Time-Exposure Curves in Rats Using Machine Learning from the Chemical Structure
O Obrezanova, A Martinsson, T Whitehead, S Mahmoud, A Bender, F Miljković, P Grabowski, B Irwin, I Oprisiu, G Conduit, M Segall, GF Smith, B Williamson, S Winiwarter, N Greene
– Molecular Pharmaceutics
(2022)
19,
1488
(DOI: 10.1021/acs.molpharmaceut.2c00027)
Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers
A Cumberworth, D Frenkel, A Reinhardt
(2022)
Energy Landscapes of Carbon Clusters from Tight-Binding Quantum Potentials
D Furman, F Naumkin, DJ Wales
– The journal of physical chemistry. A
(2022)
126,
2342
(DOI: 10.1021/acs.jpca.2c00834)
Multiscale modelling of chromatin organisation: Resolving nucleosomes at near-atomistic resolution inside genes.
J Huertas, EJ Woods, R Collepardo-Guevara
– Current Opinion in Cell Biology
(2022)
75,
102067
(DOI: 10.1016/j.ceb.2022.02.001)
Ageing critically transforms the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it
A Tejedor, I Sanchez-Burgos, M Estevez-Espinosa, A Garaizar, R Collepardo-Guevara, J Ramirez, J Espinosa
(2022)
(DOI: 10.1101/2022.03.30.486367)
Full configuration interaction quantum Monte Carlo treatment of fragments embedded in a periodic mean field.
EM Christlmaier, D Kats, A Alavi, D Usvyat
– Journal of Chemical Physics
(2022)
156,
154107
(DOI: 10.1063/5.0084040)
General embedded cluster protocol for accurate modeling of oxygen vacancies in metal-oxides.
BX Shi, V Kapil, A Zen, J Chen, A Alavi, A Michaelides
– Journal of Chemical Physics
(2022)
156,
124704
(DOI: 10.1063/5.0087031)
Latent Variables Capture Pathway-Level Points of Departure in High-Throughput Toxicogenomic Data.
D Basili, J Reynolds, J Houghton, S Malcomber, B Chambers, M Liddell, I Muller, A White, I Shah, LJ Everett, A Middleton, A Bender
– Chem Res Toxicol
(2022)
35,
670
(DOI: 10.1021/acs.chemrestox.1c00444)
Same and interconvertible high-pressure ice phases
A Reinhardt, M Bethkenhagen, F Coppari, M Millot, S Hamel, B Cheng
(2022)
Kinetic interplay between droplet maturation and coalescence modulates shape of aged protein condensates.
A Garaizar, JR Espinosa, JA Joseph, R Collepardo-Guevara
– Scientific Reports
(2022)
12,
4390
(DOI: 10.1038/s41598-022-08130-2)
Deriving waveform parameters from calcium transients in human iPSC-derived cardiomyocytes to predict cardiac activity with machine learning
H Yang, W Stebbeds, J Francis, A Pointon, O Obrezanova, KA Beattie, P Clements, JS Harvey, GF Smith, A Bender
– Stem Cell Reports
(2022)
17,
556
(DOI: 10.1016/j.stemcr.2022.01.009)
Using deep learning to annotate the protein universe.
ML Bileschi, D Belanger, DH Bryant, T Sanderson, B Carter, D Sculley, A Bateman, MA DePristo, LJ Colwell
– Nat Biotechnol
(2022)
1
(DOI: 10.1038/s41587-021-01179-w)
Temperature protocols to guide selective self-assembly of competing structures.
A Bupathy, D Frenkel, S Sastry
– Proceedings of the National Academy of Sciences
(2022)
119,
e2119315119
(DOI: 10.1073/pnas.2119315119)

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