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Recent Publications from the Theory Research Interest Group

Investigating the role of boundary bricks in DNA brick self-assembly.
HK Wayment-Steele, D Frenkel, A Reinhardt
– Soft Matter
(2017)
13,
1670
research data supporting Machine Learning Landscapes and Predictions for Patient Outcomes
DJ Wales
Transforming the Energy Landscape of a Coiled-Coil Peptide via Point Mutations.
K Röder, DJ Wales
– J Chem Theory Comput
(2017)
Atomic clusters with addressable complexity.
DJ Wales
– The Journal of chemical physics
(2017)
146,
054306
Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy
RJM Weber, TN Lawson, RM Salek, TMD Ebbels, RC Glen, R Goodacre, JL Griffin, K Haug, A Koulman, P Moreno, M Ralser, C Steinbeck, WB Dunn, MR Viant
– Metabolomics : Official journal of the Metabolomic Society
(2017)
13,
12
Combining Internally Contracted States and Matrix Product States To Perform Multireference Perturbation Theory.
S Sharma, G Knizia, S Guo, A Alavi
– J Chem Theory Comput
(2017)
13,
488
Elabela/Toddler is an Endogenous Agonist of the Apelin APJ Receptor in the Adult Cardiovascular System, and Exogenous Administration of the Peptide Compensates for the Downregulation of its Expression in Pulmonary Arterial Hypertension
P Yang, C Read, RE Kuc, G Buonincontri, M Southwood, R Torella, PD Upton, A Crosby, SJ Sawiak, TA Carpenter, RC Glen, NW Morrell, JJ Maguire, AP Davenport
– Circulation
(2017)
Stochastic multi-reference perturbation theory with application to the linearized coupled cluster method
G Jeanmairet, S Sharma, A Alavi
– Journal of Chemical Physics
(2017)
146,
A fragment profiling approach to inhibitors of the orphan M. tuberculosis P450 CYP144A1
ME Kavanagh, J Chenge, A Zoufir, KJ McLean, AG Coyne, A Bender, AW Munro, C Abell
Research data supporting 'Investigating the role of boundary bricks in DNA brick self-assembly'
HK Wayment-Steele, D Frenkel, A Reinhardt
Self-assembly of two-dimensional binary quasicrystals: a possible route to a DNA quasicrystal
A Reinhardt, JS Schreck, F Romano, JPK Doye
– J. Phys.: Condens. Matter
(2017)
29,
014006
Modelling compound cytotoxicity using conformal prediction and PubChem HTS data
F Svensson, U Norinder, A Bender
– Toxicology Research
(2017)
6,
73
Machine learning prediction for classification of outcomes in local minimisation
R Das, DJ Wales
– Chemical Physics Letters
(2017)
667,
158
In silico target prediction for elucidating the mode of action of herbicides including prospective validation
RK Chiddarwar, SG Rohrer, A Wolf, S Tresch, S Wollenhaupt, A Bender
– J Mol Graph Model
(2017)
71,
70
A stress tensor eigenvector projection space for the (H2O)(5) potential energy surface
T Xu, J Farrell, R Momen, A Azizi, SR Kirk, S Jenkins, DJ Wales
– CHEMICAL PHYSICS LETTERS
(2017)
667,
25
Dynamics and thermodynamics of the coronene octamer described by coarse-grained potentials.
J Hernández-Rojas, F Calvo, S Niblett, DJ Wales
– Physical chemistry chemical physics : PCCP
(2017)
19,
1884
Probing helical transitions in a DNA duplex.
D Chakraborty, DJ Wales
– Physical chemistry chemical physics : PCCP
(2016)
19,
878
Finite field methods for the supercell modeling of charged insulator/electrolyte interfaces
C Zhang, M Sprik
– Physical Review B - Condensed Matter and Materials Physics
(2016)
94,
245309
GPU-Accelerated Exploration of Biomolecular Energy Landscapes.
RG Mantell, CE Pitt, DJ Wales
– Journal of Chemical Theory and Computation
(2016)
12,
6182
Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes
P Stadlbauer, L Mazzanti, T Cragnolini, DJ Wales, P Derreumaux, S Pasquali, J Šponer
– Journal of Chemical Theory and Computation
(2016)
12,
6077