Recent Publications from the Theory Research Interest Group

Encoding molecular structures in quantum machine learning

C Boy, E Altamura, D Manawadu, DJ Wales, S Mensa, I Tavernelli

Machine Learning: Science and Technology

(2025)

045076

Compositional Control of Aging Kinetics in TDP-43 Condensates

NH Espejo, A Feito, I Sanchez-Burgos, A Garaizar, MM Conde, A Rey, E Pedraza, A Castro, R Collepardo-Guevara, AR Tejedor, JR Espinosa

PRX Life

(2025)

043018

(doi: 10.1103/w7g3-6rsd)

How accurate are DFT forces? Unexpectedly large uncertainties in molecular datasets.

D Kuryla, F Berger, G Csányi, A Michaelides

Journal of Chemical Physics

(2025)

163

224313

(doi: 10.1063/5.0296997)

Inhibition of IRAK4 by microbial trimethylamine blunts metabolic inflammation and ameliorates glycemic control

J Chilloux, F Brial, A Everard, D Smyth, P Andrikopoulos, L Zhang, H Plovier, A Myridakis, L Hoyles, JM Moreno-Navarrete, JL Luque, V Casagrande, R Menghini, B Ahmetaj-Shala, C Blancher, L Martinez-Gili, S Gencer, JF Fearnside, RH Barton, AL Neves, AR Rothwell, C Gérard, S Calderari, MJ Williamson, JE Fuchs, L Govada, CL Boulangé, S Patel, J Scott, M Thursz, N Chayen, RC Glen, NJ Gooderham, JK Nicholson, M Federici, JM Fernández-Real, D Gauguier, PP Liu, PD Cani, M-E Dumas

Nature Metabolism

(2025)

2531

(doi: 10.1038/s42255-025-01413-8)

Comparison of protein-glycosaminoglycan interactions in ff14sb/GLYCAM06j and CHARMM36m force fields

K Bojarski, P Wesołowski, D Dewan, Ł Dziadek, V Neuman, B Brooks, J Czub, M Zacharias, A Sieradzan, D Wales

(2025)

(doi: 10.26434/chemrxiv-2025-fl9pf)

Multiscale structure of chromatin condensates explains phase separation and material properties.

H Zhou, J Huertas, MJ Maristany, K Russell, JH Hwang, R-W Yao, N Samanta, J Hutchings, R Billur, M Shiozaki, X Zhao, LK Doolittle, BA Gibson, A Soranno, M Riggi, JR Espinosa, Z Yu, E Villa, R Collepardo-Guevara, MK Rosen

Science

(2025)

390

eadv6588

(doi: 10.1126/science.adv6588)

Monte Carlo methods, 70 years after "Equation of state calculations by fast computing machines" by Nicholas Metropolis, Arianna Rosenbluth, Marshall Rosenbluth, Augusta Teller, and Edward Teller (1953).

EJ Maginn, JI Siepmann, KA Fichthorn, D Frenkel, Y Okamoto, W Krauth, C Filippi

The Journal of chemical physics

(2025)

163

210402

(doi: 10.1063/5.0309018)

Author Correction: The first-principles phase diagram of monolayer nanoconfined water

V Kapil, C Schran, A Zen, J Chen, CJ Pickard, A Michaelides

Nature

(2025)

648

E15

(doi: 10.1038/s41586-025-09872-5)

A note on the minimal pairwise distance in optimal Lennard-Jones N-body clusters

MK-H Kiessling, DJ Wales

Molecular Physics

(2025)

ahead-of-print

e2590148

(doi: 10.1080/00268976.2025.2590148)

Unveiling the scaling laws behind spin-phonon enhanced decorrelation in spin chains

I Srpak, MJ Willatt, SC Althorpe, A Alavi

Physical Review B

(2025)

112

205132

(doi: 10.1103/11dp-8sm4)

Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organization

L Tamon, Z Fahmi, J Ashford, R Collepardo-Guevara, AB Sahakyan

NAR Genomics and Bioinformatics

(2025)

lqaf146

(doi: 10.1093/nargab/lqaf146)

A foundation model for atomistic materials chemistry.

I Batatia, P Benner, Y Chiang, AM Elena, DP Kovács, J Riebesell, XR Advincula, M Asta, M Avaylon, WJ Baldwin, F Berger, N Bernstein, A Bhowmik, F Bigi, SM Blau, V Cărare, M Ceriotti, S Chong, JP Darby, S De, F Della Pia, VL Deringer, R Elijošius, Z El-Machachi, E Fako, F Falcioni, AC Ferrari, JLA Gardner, MJ Gawkowski, A Genreith-Schriever, J George, REA Goodall, J Grandel, CP Grey, P Grigorev, S Han, W Handley, HH Heenen, K Hermansson, CH Ho, S Hofmann, C Holm, J Jaafar, KS Jakob, H Jung, V Kapil, AD Kaplan, N Karimitari, JR Kermode, P Kourtis, N Kroupa, J Kullgren, MC Kuner, D Kuryla, G Liepuoniute, C Lin, JT Margraf, I-B Magdău, A Michaelides, JH Moore, AA Naik, SP Niblett, SW Norwood, N O'Neill, C Ortner, KA Persson, K Reuter, AS Rosen, LAM Rosset, LL Schaaf, C Schran, BX Shi, E Sivonxay, TK Stenczel, C Sutton, V Svahn, TD Swinburne, J Tilly, C van der Oord, S Vargas, E Varga-Umbrich, T Vegge, M Vondrák, Y Wang, WC Witt, T Wolf, F Zills, G Csányi

J Chem Phys

(2025)

163

184110

(doi: 10.1063/5.0297006)

Cyclically sheared colloidal gels: structural change and delayed failure time

H Bhaumik, JE Hallett, TB Liverpool, RL Jack, CP Royall

Soft matter

(2025)

8555

(doi: 10.1039/d5sm00647c)

Towards Routine Condensed Phase Simulations with Delta-Learned Coupled Cluster Accuracy: Application to Liquid Water.

N O'Neill, BX Shi, WJ Baldwin, WC Witt, G Csányi, JD Gale, A Michaelides, C Schran

Journal of chemical theory and computation

(2025)

11710

(doi: 10.1021/acs.jctc.5c01377)

Visualising the Energy Landscape for a Molecular Dynamics Trajectory

V Neuman, P Wesołowski, K Bojarski, D Dewan, M Schäffler, P Smardz, D Wales

(2025)

(doi: 10.26434/chemrxiv-2025-6f4zq)

Vibrational energy landscapes and energy flow in GPCRs: comparison between class A and class B GPCRs using all atom and coarse-grained models.

H Poudel, PH Shaon, DJ Wales, DM Leitner

Physical Chemistry Chemical Physics Pccp

(2025)

22394

(doi: 10.1039/d5cp02918j)

Determination of nucleotide-nucleotide and nucleotide-amino acid binding interactions from all-atom potential-of-mean-force calculations

A Feito, E Pedraza, E Cuesta, A Castro, I Sanchez-Burgos, A Rey, R Collepardo-Guevara, AR Tejedor, JR Espinosa

(2025)

(doi: 10.1101/2025.10.27.684844)

Energy Landscape and Kinetic Analysis of Molecular Dynamics Simulations for Intrinsically Disordered Proteins

M Schäffler, DJ Wales, B Strodel

J Phys Chem B

(2025)

129

11430

(doi: 10.1021/acs.jpcb.5c05390)

Differential stability and dynamics of DNA-based and RNA-based coacervates affect non-enzymatic RNA chemistry

KK Nakashima, FZ Mihoubi, JS Saraya, KO Russell, F Rahmatova, JD Robinson, MJ Maristany, J Huertas, R Rubio-Sánchez, R Collepardo-Guevara, DK O’Flaherty, C Bonfio

Nature Communications

(2025)

9296

(doi: 10.1038/s41467-025-64335-9)