Citations & Publications

How to cite the TSCC

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San Diego Supercomputer Center (2022): Triton Shared Computing Cluster. University of California, San Diego. Service.


Papers/Publications resulting from use of TSCC resources

  1. Francesco Paesani, Hydrogen bond dynamics in heavy water studied with quantum dynamical simulations, Chem. Chem. Phys., 2011,13, 19865-19875
  2. Kyoyeon Park, Wei Lin, and Francesco Paesani, A Refined MS-EVB Model for Proton Transport in Aqueous Environments, Phys. Chem. B 2012, 116, 1, 343–352
  3. Francesco Paesani, Hydrogen bond dynamics in heavy water studied with quantum dynamical simulations, Chem. Chem. Phys., 2011,13, 19865-19875
  4. Kyoyeon Park, Wei Lin, and Francesco Paesani, A Refined MS-EVB Model for Proton Transport in Aqueous Environments, Phys. Chem. B 2012, 116, 1, 343–352
  5. Jason S. Grosch and Francesco Paesani, Molecular-Level Characterization of the Breathing Behavior of the Jungle-Gym-type DMOF-1 Metal–Organic Framework, Am. Chem. Soc. 2012, 134, 9, 4207–4215
  6. Francesco Paesani, Water in metal-organic frameworks: structure and diffusion of H2O in MIL-53(Cr) from quantum simulations, Molecular Simulation, 2012, 38:8-9, 631-641
  7. Kyoyeon Park, Andreas W. Götz, Ross C. Walker, and Francesco Paesani, Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems, Chem. Theory Comput. 2012, 8, 8, 2868–2877
  8. Yimin Wang, Volodymyr Babin, Joel M. Bowman, and Francesco Paesani, The Water Hexamer: Cage, Prism, or Both. Full Dimensional Quantum Simulations Say Both, Am. Chem. Soc. 2012, 134, 27, 11116–11119
  9. Jordi Cirera and Francesco Paesani, Theoretical Prediction of Spin-Crossover Temperatures in Ligand-Driven Light-Induced Spin Change Systems, Chem. 2012, 51, 15, 8194–8201
  10. Jordi Cireraa, Jeffrey C. Sunga, Porter B. Howlanda, and Francesco Paesani, The effects of electronic polarization on water adsorption in metal-organic frameworks: H2O in MIL-53(Cr), Chem. Phys. 2012, 137, 054704
  11. Pushp Bajaj, Andreas W. Götz, and Francesco Paesani, Toward Chemical Accuracy in the Description of Ion–Water Interactions through Many-Body Representations. I. Halide–Water Dimer Potential Energy Surfaces, Chem. Theory Comput. 2016, 12, 6, 2698–2705
  12. Marc Riera, Narbe Mardirossian, Pushp Bajaj,  Andreas W. Götz, and Francesco Paesani, Toward chemical accuracy in the description of ion–water interactions through many-body representations. Alkali-water dimer potential energy surfaces, Chem. Phys. 2017, 147, 161715
  13. Pushp Bajaj, Xiao-Gang Wang, Tucker Carrington Jr., and Francesco Paesani, Vibrational spectra of halide-water dimers: Insights on ion hydration from full-dimensional quantum calculations on many-body potential energy surfaces, Chem. Phys. 2018, 148, 102321
  14. Brandon B. Bizzarro, Colin K. Egan, and Francesco Paesani, Nature of Halide–Water Interactions: Insights from Many-Body Representations and Density Functional Theory, Chem. Theory Comput. 2019, 15, 5, 2983–2995
  15. Pushp Bajaj, Jeremy O. Richardson and Francesco Paesani, Ion-mediated hydrogen-bond rearrangement through tunnelling in the iodide–dihydrate complex, Nature Chemistry, 2019, 11, 367-374
  16. Pushp Bajaj, Marc Riera, Jason K. Lin, Yaira E. Mendoza Montijo, Jessica Gazca, and Francesco Paesani, Halide Ion Microhydration: Structure, Energetics, and Spectroscopy of Small Halide–Water Clusters, Phys. Chem. A 2019, 123, 13, 2843–2852
  17. Pushp Bajaj, Debbie Zhuang, and Francesco Paesani, Specific Ion Effects on Hydrogen-Bond Rearrangements in the Halide–Dihydrate Complexes, Phys. Chem. Lett. 2019, 10, 11, 2823–2828
  18. Marc Riera, Eleftherios Lambros, Thuong T. Nguyen, Andreas W. Götz and Francesco Paesani, Low-order many-body interactions determine the local structure of liquid water, Sci., 2019,10, 8211-8218
  19. Colin K. Egan and Francesco Paesani, Assessing Many-Body Effects of Water Self-Ions. II: H3O+(H2O)n Clusters, Chem. Theory Comput. 2019, 15, 9, 4816–4833
  20. Marc Riera, Eric P. Yeh, and Francesco Paesani, Data-Driven Many-Body Models for Molecular Fluids: CO2/H2O Mixtures as a Case Study, Chem. Theory Comput. 2020, 16, 4, 2246–2257
  21. Yaoguang Zhai, Alessandro Caruso, Sicun Gao, and Francesco Paesani, Active learning of many-body configuration space: Application to the Cs+–water MB-nrg potential energy function as a case study, Chem. Phys. 2020, 152, 144103
  22. Colin K. Egan, Brandon B. Bizzarro, Marc Riera, and Francesco Paesani, Nature of Alkali Ion–Water Interactions: Insights from Many-Body Representations and Density Functional Theory. II, Chem. Theory Comput. 2020, 16, 5, 3055–3072
  23. Marc Riera, Justin J. Talbot, Ryan P. Steele, and Francesco Paesani, Infrared signatures of isomer selectivity and symmetry breaking in the Cs+(H2O)3 complex using many-body potential energy functions, Chem. Phys. 2020, 153, 044306
  24. Eleftherios Lambros and Francesco Paesani, How good are polarizable and flexible models for water: Insights from a many-body perspective, Chem. Phys. 2020, 153, 060901
  25. Eleftherios Lambros, Filippo Lipparini, Gerardo Andrés Cisneros, and Francesco Paesani, A Many-Body, Fully Polarizable Approach to QM/MM Simulations, Chem. Theory Comput. 2020, 16, 12, 7462–7472
  26. Marc Riera, Alan Hirales, Raja Ghosh, and Francesco Paesani, Data-Driven Many-Body Models with Chemical Accuracy for CH4/H2O Mixtures, Phys. Chem. B 2020, 124, 49, 11207–11221
  27. Vinícius Wilian D. Cruzeiro, Andrew Wildman, Xiaosong Li, and Francesco Paesani, Relationship between Hydrogen-Bonding Motifs and the 1b1 Splitting in the X-ray Emission Spectrum of Liquid Water, Phys. Chem. Lett. 2021, 12, 16, 3996–4002
  28. Vinícius Wilian D. Cruzeiro, Eleftherios Lambros, Marc Riera, Ronak Roy, Francesco Paesani, and Andreas W. Götz, Highly Accurate Many-Body Potentials for Simulations of N2O5 in Water: Benchmarks, Development, and Validation, Chem. Theory Comput. 2021, 17, 7, 3931–3945
  29. Eleftherios Lambros, Jie Hu, and Francesco Paesani, Assessing the Accuracy of the SCAN Functional for Water through a Many-Body Analysis of the Adiabatic Connection Formula, Chem. Theory Comput. 2021, 17, 6, 3739–3749
  30. Raja Ghosh and Francesco Paesani, Unraveling the effect of defects, domain size, and chemical doping on photophysics and charge transport in covalent organic frameworks, Sci., 2021,12, 8373-8384
  31. Kelly M. Hunter, Jackson C. Wagner, Mark Kalaj, Seth M. Cohen, Wei Xiong, and Francesco Paesani, Simulation Meets Experiment: Unraveling the Properties of Water in Metal–Organic Frameworks through Vibrational Spectroscopy, Phys. Chem. C 2021, 125, 22, 12451–12460
  32. Eleftherios Lambros, Saswata Dasgupta, Etienne Palos, Steven Swee, Jie Hu, and Francesco Paesani, General Many-Body Framework for Data-Driven Potentials with Arbitrary Quantum Mechanical Accuracy: Water as a Case Study, Chem. Theory Comput. 2021, 17, 9, 5635–5650
  33. Alessandro Caruso and Francesco Paesani, Data-driven many-body models enable a quantitative description of chloride hydration from clusters to bulk, Chem. Phys. 2021, 155, 064502
  34. Ethan F. Bull-Vulpe, Marc Riera, Andreas W. Götz, and Francesco Paesani, MB-Fit: Software infrastructure for data-driven many-body potential energy functions, Chem. Phys. 2021, 155, 124801
  35. Saswata Dasgupta, Eleftherios Lambros, John P. Perdew & Francesco Paesani, Elevating density functional theory to chemical accuracy for water simulations through a density-corrected many-body formalism, Nature Communications, 2021, 12, 6359
  36. Raja Ghosh and Francesco Paesani, Topology-Mediated Enhanced Polaron Coherence in Covalent Organic Frameworks, Phys. Chem. Lett. 2021, 12, 39, 9442–9448
  37. Thomas E. Gartner III, Kelly M. Hunter, Eleftherios Lambros, Alessandro Caruso, Marc Riera, Gregory R. Medders, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti, and Francesco Paesani, Anomalies and Local Structure of Liquid Water from Boiling to the Supercooled Regime as Predicted by the Many-Body MB-pol Model, Phys. Chem. Lett. 2022, 13, 16, 3652–3658
  38. Shuwen Yue, Marc Riera,  Raja Ghosh,  Athanassios Z. Panagiotopoulos, and Francesco Paesani, Transferability of data-driven, many-body models for CO2 simulations in the vapor and liquid phases, Chem. Phys. 2022, 156, 104503
  39. Etienne Palos, Eleftherios Lambros, Steven Swee, Jie Hu, Saswata Dasgupta, and Francesco Paesani, Assessing the Interplay between Functional-Driven and Density-Driven Errors in DFT Models of Water, Chem. Theory Comput. 2022, 18, 6, 3410–3426
  40. Victor Naden Robinson, Raja Ghosh, Colin K. Egan, Marc Riera,  Christopher Knight,  Francesco Paesani, and Ali Hassanali, The behavior of methane–water mixtures under elevated pressures from simulations using many-body potentials, Chem. Phys. 2022, 156, 194504
  41. Etienne Palos, Eleftherios Lambros, Saswata Dasgupta, and Francesco Paesani, Density functional theory of water with the machine-learned DM21 functional, Chem. Phys. 2022, 156, 161103
  42. Saswata Dasgupta, Chandra Shahi, Pradeep Bhetwal, John P. Perdew, and Francesco Paesani, How Good Is the Density-Corrected SCAN Functional for Neutral and Ionic Aqueous Systems, and What Is So Right about the Hartree–Fock Density? J. Chem. Theory Comput. 2022, 18, 4745
  43. S.L. Bore, P.M. Piaggi, R. Car, F. Paesani, Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations, J. Chem. Phys. 2022, 157, 054504
  44. A. Caruso, X. Zhu, J.L. Fulton, F. Paesani, Accurate modeling of bromide and iodide hydration with data-driven many-body potentials, J. Phys. Chem. B. 2022, 126, 8266
  45. D. Zhuang, M. Riera, R. Zhou, A. Deary, F. Paesani, Hydration structure of Na+ and K+ ions in solution predicted by data-driven many-body potentials, J. Phys. Chem. 2022, 126, 9349
  46. E.F. Bull-Vulpe, M. Riera, S.L. Bore, F. Paesani, Data-driven many-body potential energy functions for generic molecules: Linear alkanes as a proof-of-concept application, J. Chem. Theory Comput. In press.
  47. R. Ghosh, F. Paesani, Connecting the dots for fundamental understanding of structure-photophysics-property relationships o fCOFs, MOFs, and perovskites using a multiparticle Holstein formalism, Chem. Sci. In press.
  48. Chung, C., Yang, X., Bae, T. et al., Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development, Nat Genet 2023,
  49. Yang, X., Xu, X., Breuss, M.W. et al., Control-independent mosaic single nucleotide variant detection with DeepMosaic, Nat Biotechnol 2023,
  50. Chan, T. K., et al., The impact of cosmic rays on dynamical balance and disc–halo interaction in L⋆ disc galaxies, Monthly Notices of the Royal Astronomical Society 517.1 (2022): 597-615
  51. Saak, Christina C., et al., Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities, Msystems (2023): e00701-22
  52. Petljak M, Alexandrov LB, Brammeld JS, Price S, Wedge DC, Grossmann S, Dawson KJ, Ju YS, Iorio F, Tubio JMC, Koh CC, Georgakopoulos-Soares I, Rodríguez–Martín B, Otlu B, O’Meara S, Butler AP, Menzies A, Bhosle SG, Raine K, Jones DR, Teague JW, Beal Km Latimer C, O’Neill L, Zamora J, Anderson E, Patel N, Maddison M, Ng BL, Graham J, Garnett MJ, McDermott U, Nik-Zainal S, Campbell PJ, and Stratton MR, Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis, Cell (2019): 176 (6), 1282-1294
  53. Baez-Ortega A, Gori K, Strakova A, Domracheva C, Keenan D, Huerta E, Manrique H, Kwon YM, Quintana L, Castañeda M, Leathlobhair MN, Gutierrez R, Stammnitz M, Martínez T, Ngoka T, Wang J, Stratton MR, Alexandrov LB, Martincorena I, and Murchison EP (2019), Somatic evolution and global expansion of an ancient transmissible cancer lineage, Science365 (6452):eaau9923
  54. Wang Z, Wu VH, Allevato MM, Gilardi M, He Y, Callejas-Valera JL, Vitale-Cross L, Martin D, Amornphimoltham P, Mcdermott J, Yung BS, Goto Y, Molinolo AA, Sharabi AN, Cohen EEW, Chen Q, Lyons JG, Alexandrov LB, and Gutkin JS (2019), Syngeneic animal models of tobacco-associated oral cancer reveal the activity of in situ anti-CTLA-4 Nature Communications 10 (1), 5546
  55. Li YR, Halliwill KD, Adams CJ, Iyer V, Riva L, Mamunur R, Jen KY, del Rosario R, Fredlund E, Hirst G, Alexandrov LB, Adams DJ, and Balmain A (2020), Mutational signatures in tumours induced by high and low energy radiation in Trp53 deficient mice Nature Communications 11 (1), 394
  56. Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Ng AWT, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V, PCAWG Mutational Signatures Working Group, Getz G, Rozen SG, Stratton MR, and PCAWG Consortium (2020), The repertoire of mutational signatures in human cancer, Nature (578), 94–101
  57. Riva L, Pandiri AR, Li YR, Droop A, Hewinson J, Quail MA, Iyer V, Shepherd R, Herbert RA, Campbell PJ, Sills RC, Alexandrov LB, Balmain A, and Adams DJ (2020), The mutational signature profile of known and suspected human carcinogens in mice, Nature Genetics, 52 (11), 1189-1197
  58. Jiang Q, Isquith J, Ladel L, Mark A, Holm F, Mason C, He Y, Mondala P, Oliver I, Pham J, Ma W, Reynoso E, Ali S, Morris IJ, Diep R, Nasamran C, Xu G, Sasik R, Rosenthal SB, Birmingham A, Coso S, Pineda G, Crews L, Donohoe ME, Venter JC, Whisenant T, Mesa RA, Alexandrov LB, Fisch KM, and Jamieson C (2021), Inflammation-driven deaminase deregulation fuels human pre-leukemia stem cell evolution, Cell Reports 34 (4), 108670
  59. Moody S, Senkin S, Ashiqul ISM, Wang J, Nasrollahzadeh D, Penha RCC, Fitzgerald S, Bergstrom EN, Atkins J, He Y, Khandekar A, Smith-Byrne K, Carreira C, Gaborieau V, Latimer C, Thomas E, Abnizova I, Bucciarelli PE, Jones D, Teague JW, Abedi-Ardekani B, Serra S, Scoazec JY, Saffar H, Azmoudeh-Ardalan F, Sotoudeh M, Nikmanesh A, Poustchi H, Niavarani A, Gharavi S, Eden M, Richman P, Campos LS, Fitzgerald RC, Ribeiro LF, Soares-Lima SC, Dzamalala C, Mmbaga BT, Shibata T, Menya D, Goldstein AM, Hu N, Malekzadeh R, Fazel A, McCormack V, McKay J, Perdomo S, Scelo G, Chanudet E, Humphreys L, Alexandrov LB, Brennan P, and Stratton MR (2021), Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence, Nature Genetics 53 (10), 1553-1563
  60. Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, and Alexandrov LB (2022), Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA, Nature (602), 510–517
  61. Steele CD, Abbasi A, Islam SMA, Bowes A, Khandekar A, Haase K, Hames-Fathi S, Ajayi D, Verfaillie A, Dhami P, McLatchie A, Lechner M, Light N, Shlien A, Malkin D, Feber A, Proszek P, Lesluyes T, Mertens F, Flanagan AM, Tarabichi M, Van Loo P, Alexandrov LB, and Pillay N (2022), Signatures of copy number alterations in human cancer, Nature, (606), 984–991
  62. Petljak M, Dananberg A, Chu K, Bergstrom EN, Striepen J, von Morgen P, Chen Y, Shah H, Sale JE, Alexandrov LB, Stratton MR, and Maciejowski J (2022), Mechanisms of APOBEC3 mutagenesis in human cancer cells, Nature, (607), 799–807
  63. Islam SMA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, and Alexandrov LB (2022), Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor, Cell Genomics 2 (11), 100179
  64. Zhivagui M, Hoda A, Valenzuela N, Yeh Y, Dai J, He Y, Nandi SP, Otlu B, Van Houten B, and Alexandrov LB (2023), DNA damage and somatic mutations in mammalian cells after irradiation with a nail polish dryer, Nature Communications (14), Article number: 276