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Recent Publications from the Theory Research Interest Group

Field-Programmable Gate Arrays and Quantum Monte Carlo: Power Efficient Co-processing for Scalable High-Performance Computing
S Cardamone, JRR Kimmitt, HGA Burton, TJ Todman, S Li, W Luk, AJW Thom
– International Journal of Quantum Chemistry
(2019)
119,
e25853
(DOI: 10.1002/qua.25853)
Preconditioning and Perturbative Estimators in Full Configuration Interaction Quantum Monte Carlo
NS Blunt, AJW Thom, CJC Scott
– Journal of chemical theory and computation
(2019)
15,
3537
(DOI: 10.1021/acs.jctc.9b00049)
Synthesis of C C, C N coupled novel substituted dibutyl benzothiazepinone derivatives and evaluation of their thrombin inhibitory activity
CP Baburajeev, CD Mohan, V Pandey, S Rangappa, N Shivalingegowda, L Kalash, S Devaraja, A Bender, PE Lobie, KS Rangappa, Basappa
– Bioorganic Chemistry
(2019)
87,
142
(DOI: 10.1016/j.bioorg.2019.03.004)
Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity.
CHG Allen, LH Mervin, SY Mahmoud, A Bender
– Journal of cheminformatics
(2019)
11,
36
(DOI: 10.1186/s13321-019-0356-5)
Using attribution to decode binding mechanism in neural network models for chemistry.
K McCloskey, A Taly, F Monti, MP Brenner, LJ Colwell
– Proceedings of the National Academy of Sciences of the United States of America
(2019)
201820657
(DOI: 10.1073/pnas.1820657116)
A novel cyclic biased agonist of the apelin receptor, MM07, is disease modifying in the rat monocrotaline model of pulmonary arterial hypertension.
P Yang, C Read, RE Kuc, D Nyimanu, TL Williams, A Crosby, G Buonincontri, M Southwood, SJ Sawiak, RC Glen, NW Morrell, AP Davenport, JJ Maguire
– British Journal of Pharmacology
(2019)
176,
1206
(DOI: 10.1111/bph.14603)
Colocalization Features for Classification of Tumors Using Desorption Electrospray Ionization Mass Spectrometry Imaging
P Inglese, G Correia, P Pruski, RC Glen, Z Takats
– Analytical Chemistry
(2019)
91,
6530
(DOI: 10.1021/acs.analchem.8b05598)
The pathway and kinetics of hierarchical assembly of ionic oligomers into a lyotropic columnar phase.
W Huang, S Wei, D Frenkel, N Huang
– Soft matter
(2019)
15,
4460
(DOI: 10.1039/c9sm00383e)
Go-Kit: A Tool To Enable Energy Landscape Exploration of Proteins
S Neelamraju, DJ Wales, S Gosavi
– Journal of Chemical Information and Modeling
(2019)
59,
1703
(DOI: 10.1021/acs.jcim.9b00007)
Unraveling the Large Deviation Statistics of Markovian Open Quantum Systems
F Carollo, RL Jack, JP Garrahan
– Phys Rev Lett
(2019)
122,
130605
(DOI: 10.1103/PhysRevLett.122.130605)
Microscopic analysis of thermo-orientation in systems of off-centre Lennard-Jones particles.
RL Jack, P Wirnsberger, A Reinhardt
– The Journal of Chemical Physics
(2019)
150,
134501
(DOI: 10.1063/1.5089541)
Solubilities of pyrene in organic solvents: Comparison between chemical potential calculations using a cavity-based method and direct coexistence simulations
CR Wand, M Fayaz-Torshizi, G Jiménez-Serratos, EA Müller, D Frenkel
– Journal of Chemical Thermodynamics
(2019)
131,
620
(DOI: 10.1016/j.jct.2018.11.029)
Dynamics of an adenine-adenine RNA conformational switch from discrete path sampling
D Chakraborty, DJ Wales
– Journal of Chemical Physics
(2019)
150,
125101
(DOI: 10.1063/1.5070152)
Apelin peptides linked to anti-serum albumin domain antibodies retain affinity in vitro and are efficacious receptor agonists in vivo
C Read, P Yang, RE Kuc, D Nyimanu, TL Williams, RC Glen, LJ Holt, H Arulanantham, A Smart, AP Davenport, JJ Maguire
– Basic & clinical pharmacology & toxicology
(2019)
bcpt.13227
(DOI: 10.1111/bcpt.13227)
Are smooth pseudopotentials a good choice for representing short-range interactions?
P Jeszenszki, A Alavi, J Brand
– Physical Review A
(2019)
99,
033608
(DOI: 10.1103/PhysRevA.99.033608)
Diagrammatic Coupled Cluster Monte Carlo
CJC Scott, R Di Remigio, TD Crawford, AJW Thom
– The Journal of Physical Chemistry Letters
(2019)
10,
925
(DOI: 10.1021/acs.jpclett.9b00067)
Signalling and transcriptional network propagation uncovers novel ulcerative colitis pathogenetic pathways from single-nucleotide polymorphisms
D Modos, J Brooks, P Sudhakar, B Verstockt, B Alexander-Dann, A Zoufir, D Fazekas, S Vermeire, T Korcsmaros, A Bender
– Journal of Crohn's and Colitis
(2019)
13,
S091
(DOI: 10.1093/ecco-jcc/jjy222.135)
OP10 Systems genomics of ulcerative colitis: combining GWAS and signalling networks for patient stratification and individualised drug targeting in ulcerative colitis
J Brooks, D Modos, P Sudhakar, D Fazekas, A Zoufir, A Watson, M Tremelling, B Verstockt, S Vermeire, A Bender, S Carding, T Korcsmaros
– Journal of Crohn's and Colitis
(2019)
13,
S006
(DOI: 10.1093/ecco-jcc/jjy222.009)
RNA Structure and Kinetics Including Pseudoknots through Complete Landscape Enumeration
O Kimchi, T Cragnolini, R Garmann, VN Manoharan, MP Brenner, LJ Colwell
– Biophysical Journal
(2019)
116,
353A
(DOI: 10.1016/j.bpj.2018.11.1922)
Multivalent Recognition at Fluid Surfaces: The Interplay of Receptor Clustering and Superselectivity
GV Dubacheva, T Curk, D Frenkel, RP Richter
– Journal of the American Chemical Society
(2019)
141,
2577
(DOI: 10.1021/jacs.8b12553)

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