diff --git a/src/content/publications/references.bib b/src/content/publications/references.bib index 048b05a..e8dcd80 100644 --- a/src/content/publications/references.bib +++ b/src/content/publications/references.bib @@ -1,6 +1,7 @@ % ============================================================================= % Martiniani Lab — Complete Publication List -% Sorted newest first +% Sorted newest first; auto-generated from Google Scholar profile +% Manual fields (note, localfile) are preserved across updates % ============================================================================= % --------------------------------------------------------------------------- @@ -8,86 +9,72 @@ % --------------------------------------------------------------------------- @unpublished{sharma2026crossview, - title = {Cross-View World Models}, + title = {Cross-view world models}, author = {Sharma, R. and Hogervorst, G. and Mackey, W.E. and Heeger, D.J. and Martiniani, S.}, year = {2026}, eprint = {2602.07277}, - url = {https://arxiv.org/abs/2602.07277} + url = {https://arxiv.org/abs/2602.07277}, } @unpublished{hoellmer2026omatgirl, - title = {Open Materials Generation with Inference-Time Reinforcement Learning}, - author = {Hoellmer, P. and Martiniani, S.}, + title = {Open materials generation with inference-time reinforcement learning}, + author = {Höllmer, P. and Martiniani, S.}, year = {2026}, eprint = {2602.00424}, - url = {https://arxiv.org/abs/2602.00424} + url = {https://arxiv.org/abs/2602.00424}, } -@unpublished{prakash2025superconductors, - title = {Guided Diffusion for the Discovery of New Superconductors}, - author = {Prakash, P. and Gibson, J.B. and Li, Z. and Di Gianluca, G. and Esquivel, J. and Fuemmeler, E. and Geisler, B. and Kim, J.S. and Roitberg, A. and Tadmor, E.B. and Liu, M. and Martiniani, S. and Stewart, G.R. and Hamlin, J.J. and Hirschfeld, P.J. and Hennig, R.G.}, - year = {2025}, - eprint = {2509.25186}, - url = {https://arxiv.org/abs/2509.25186} -} - -@unpublished{martirossyan2025structurematches, - title = {All that structure matches does not glitter}, - author = {Martirossyan, M.M. and Egg, T. and Hoellmer, P. and Karypis, G. and Transtrum, M. and Roitberg, A. and Liu, M. and Hennig, R.G. and Tadmor, E.B. and Martiniani, S.}, - year = {2025}, - eprint = {2509.12178}, - url = {https://arxiv.org/abs/2509.12178} +@unpublished{zeng2026molcrystalflow, + title = {MolCrystalFlow: Molecular Crystal Structure Prediction via Flow Matching}, + author = {Zeng, C. and Sullivan, H.W. and Egg, T. and Martirossyan, M.M. and Höllmer, P. and Jin, J. and Hennig, R.G. and Roitberg, A. and Martiniani, S. and Tadmor, E.B. and Liu, M.}, + year = {2026}, + url = {https://arxiv.org/abs/2602.16020}, } -@unpublished{luzzatto2025cluster, - title = {Spatial and Temporal Cluster Tomography of Active Matter}, - author = {Luzzatto, L.V. and Casiulis, M. and Martiniani, S. and Kovacs, I.}, - year = {2025}, - eprint = {2511.09444}, - url = {https://arxiv.org/abs/2511.09444} +@unpublished{anand2026spatial, + title = {Spatial self-organization driven by temporal noise}, + author = {Anand, S. and Zhang, G. and Martiniani, S.}, + year = {2026}, + url = {https://arxiv.org/abs/2601.23098}, } -@unpublished{han2025pkmzeta, - title = {Persistently increased expression of {PKM$\zeta$} and unbiased gene expression profiles identify hippocampal molecular traces of a long-term active place avoidance memory and ``shadow'' proteins}, - author = {Han, J. and Grau-Perales, A. and Harris, R.M. and Kao, H. and Pal, A. and Alarcon, J.M. and Sacktor, T. and Martiniani, S. and Hofmann, H.A. and Fenton, A.A.}, - year = {2025}, - eprint = {2025.04.28.651143}, - url = {https://doi.org/10.1101/2025.04.28.651143}, - note = {bioRxiv} +@unpublished{casiulis2026hyperuniform, + title = {Hyperuniform systems are maximally irreversible}, + author = {Casiulis, M. and Anand, S. and Martiniani, S.}, + year = {2026}, + url = {https://arxiv.org/abs/2607.07411}, } -@unpublished{barrows2025unifying, - title = {A unifying approach to self-organizing systems interacting via conservation laws}, - author = {Barrows, F. and Zhang, G. and Anand, S. and Chen, Z. and Lin, J. and Desai, A. and Martiniani, S. and Caravelli, F.}, - year = {2025}, - eprint = {2507.02575}, - url = {https://arxiv.org/abs/2507.02575} +@unpublished{rawat2026exact, + title = {Exact Variance and Fano Factor for Arbitrary Level Crossings in Stationary Gaussian Processes}, + author = {Rawat, S. and Morone, F. and Heeger, D.J. and Martiniani, S.}, + year = {2026}, + url = {https://arxiv.org/abs/2605.25278}, } -@unpublished{zhang2025clamp, - title = {Contrastive Self-Supervised Learning As Neural Manifold Packing}, - author = {Zhang, G. and Heeger, D.J. and Martiniani, S.}, +@unpublished{luzzatto2025cluster, + title = {Spatial and Temporal Cluster Tomography of Active Matter}, + author = {Luzzatto, L.V. and Casiulis, M. and Martiniani, S. and Kovacs, I.}, year = {2025}, - eprint = {2506.13717}, - url = {https://arxiv.org/abs/2506.13717} + eprint = {2511.09444}, + url = {https://arxiv.org/abs/2511.09444}, } @unpublished{pal2025circuit, title = {Hierarchical Neural Circuit Theory of Normalization and Inter-areal Communication}, - author = {Morone, F. and Pal, A. and Rawat, S. and Heeger, D.J. and Martiniani, S.}, + author = {Pal, A. and Rawat, S. and Heeger, D.J. and Martiniani, S.}, year = {2025}, eprint = {2025.07.15.664935}, - url = {https://doi.org/10.1101/2025.07.15.664935}, - note = {bioRxiv} + url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC12338607/}, + note = {bioRxiv}, } -@unpublished{morone2025rnn, - title = {Stabilization of recurrent neural networks through divisive normalization}, - author = {Morone, F. and Rawat, S. and Heeger, D.J. and Martiniani, S.}, - year = {2025}, - eprint = {2025.05.16.654567}, - url = {https://doi.org/10.1101/2025.05.16.654567}, - note = {bioRxiv} +@unpublished{suryadevara2024mirages, + title = {The Basins of Attraction of Soft Sphere Packings Are Not Fractal}, + author = {Suryadevara, P. and Casiulis, M. and Martiniani, S.}, + year = {2024}, + eprint = {2409.12113}, + url = {https://arxiv.org/abs/2409.12113}, } @unpublished{zhang2024absorbing, @@ -95,211 +82,325 @@ @unpublished{zhang2024absorbing author = {Zhang, G. and Martiniani, S.}, year = {2024}, eprint = {2411.11834}, - url = {https://arxiv.org/abs/2411.11834} -} - -@unpublished{suryadevara2024mirages, - title = {The Basins of Attraction of Soft Sphere Packings Are Not Fractal}, - author = {Suryadevara, P. and Casiulis, M. and Martiniani, S.}, - year = {2024}, - eprint = {2409.12113}, - url = {https://arxiv.org/abs/2409.12113} + url = {https://link.aps.org/doi/10.1103/sbv7-syp7}, } @unpublished{phan2024bacteria, - title = {Social Physics of Bacteria: Avoidance of an Information Black Hole}, + title = {Social physics of bacteria: Avoidance of an information black hole}, author = {Phan, T.V. and Li, S. and Ferreris, D. and Morris, R. and Bos, J. and Guo, B. and Martiniani, S. and Chaikin, P. and Kevrekidis, Y.G. and Austin, R.H.}, year = {2024}, eprint = {2401.16691}, - url = {https://arxiv.org/abs/2401.16691} + url = {https://arxiv.org/abs/2401.16691}, } % --------------------------------------------------------------------------- % Published % --------------------------------------------------------------------------- +@article{zeng2026propmolflow, + title = {PropMolFlow: property-guided molecule generation with geometry-complete flow matching}, + author = {Zeng, C. and Jin, J. and Ambrose, C. and Karypis, G. and Transtrum, M. and Tadmor, E.B. and Hennig, R.G. and Roitberg, A. and Martiniani, S. and Liu, M.}, + journal = {Nature Computational Science}, + volume = {6}, + number = {3}, + pages = {233-242}, + year = {2026}, + doi = {10.1038/s43588-025-00946-y}, + eprint = {2505.21469}, + url = {https://www.nature.com/articles/s43588-025-00946-y}, +} + @article{anand2026longrange, title = {Emergent universal long-range structure in random-organizing systems}, author = {Anand, S. and Zhang, G. and Martiniani, S.}, journal = {Nature Communications}, volume = {17}, + number = {1}, pages = {2346}, year = {2026}, doi = {10.1038/s41467-026-68601-2}, eprint = {2505.22933}, - url = {https://www.nature.com/articles/s41467-026-68601-2} + url = {https://www.nature.com/articles/s41467-026-68601-2}, } -@article{zeng2026propmolflow, - title = {PropMolFlow: Property-guided Molecule Generation with Geometry-Complete Flow Matching}, - author = {Zeng, C. and Jin, J. and Wang, W. and Banerjee, T. and Li, Z. and Martiniani, S. and Liu, M.}, - journal = {Nature Computational Science}, +@article{prakash2025superconductors, + title = {Guided diffusion for the discovery of new superconductors}, + author = {Prakash, P. and Gibson, J.B. and Li, Z. and Gianluca, G.D. and Esquivel, J. and Fuemmeler, E. and Geisler, B. and Kim, J.S. and Roitberg, A. and Tadmor, E.B. and Liu, M. and Martiniani, S. and Stewart, G.R. and Hamlin, J.J. and Hirschfeld, P.J. and Hennig, R.G.}, + journal = {npj Computational Materials}, year = {2026}, - doi = {10.1038/s43588-025-00946-y}, - eprint = {2505.21469}, - url = {https://arxiv.org/abs/2505.21469} + eprint = {2509.25186}, + url = {https://www.nature.com/articles/s41524-026-02117-7}, } -@article{casiulis2025gyromorphs, - title = {Gyromorphs: A New Class of Functional Disordered Materials}, - author = {Casiulis, M. and Shih, A. and Martiniani, S.}, - journal = {Phys. Rev. Lett.}, - volume = {135}, - pages = {196101}, - year = {2025}, - doi = {10.1103/gqrx-7mn2}, - eprint = {2410.09023}, - url = {https://arxiv.org/abs/2410.09023} +@article{han2025pkmzeta, + title = {Persistently increased expression of PKMzeta and unbiased gene expression profiles identify hippocampal molecular traces of a long‐term active place avoidance memory and “Shadow” proteins}, + author = {Han, J. and Grau‐Perales, A. and Harris, R.M. and Lesburguères, E. and Kao, H. and Pal, A. and Alarcon, J.M. and Sacktor, T.C. and Martiniani, S. and Hofmann, H.A. and Fenton, A.A.}, + journal = {Advanced Science}, + volume = {13}, + number = {28}, + pages = {e21254}, + year = {2026}, + eprint = {2025.04.28.651143}, + url = {https://advanced.onlinelibrary.wiley.com/doi/abs/10.1002/advs.202521254}, + note = {bioRxiv}, } -@article{casiulis2025swarm, - title = {A geometric condition for robot-swarm cohesion and cluster-flock transition}, - author = {Casiulis, M. and Arbel, E. and van Waes, C. and Lahini, Y. and Martiniani, S. and Oppenheimer, N. and Ben Zion, M.Y.}, - journal = {Proc. Natl. Acad. Sci.}, - volume = {122}, - number = {37}, - pages = {e2502211122}, +@article{morone2025rnn, + title = {Stabilization of recurrent neural networks through divisive normalization}, + author = {Morone, F. and Rawat, S. and Heeger, D.J. and Martiniani, S.}, + journal = {Proceedings of the National Academy of Sciences}, + volume = {123}, + number = {30}, + pages = {e2601841123}, + year = {2026}, + eprint = {2025.05.16.654567}, + url = {https://www.pnas.org/doi/abs/10.1073/pnas.2601841123}, + note = {bioRxiv}, +} + +@article{martirossyan2026frameworkconstrained, + title = {Framework-Constrained Materials Generation}, + author = {Martirossyan, M.M. and Pan, H. and Höllmer, P. and Martiniani, S.}, + journal = {ICLR 2026 Workshop AI4Mat, 2026}, + year = {2026}, +} + +@article{aaron2026system, + title = {System, method and computer-accessible medium for accelerated generation of statistically correlated point structures}, + author = {Aaron, S. and CASIULIS, M. and MARTINIANI, S.}, + journal = {US Patent App. 19/219,966, 2026}, + year = {2026}, + url = {https://patents.google.com/patent/US20260050647A1/en}, +} + +@article{jacobs2025mlips, + title = {A Practical Guide to Machine Learning Interatomic Potentials–Status and Future}, + author = {Jacobs, R. and Morgan, D. and Attarian, S. and Meng, J. and Shen, C. and Wu, Z. and Xie, C. and Yang, J.H. and Artrith, N. and Blaiszik, B. and Ceder, G. and Choudhary, K. and Csanyi, G. and Deng, B. and Drautz, R. and Godwin, J. and Honavar, V. and Isayev, O. and Johansson, A. and Martiniani, S. and Ong, S.P. and Poltavsky, I. and Schmidt, K. and Takamoto, S. and Thompson, A. and Westermayr, J.}, + journal = {Current opinion in solid state materials science, 2025}, + volume = {35}, + pages = {101214}, year = {2025}, - doi = {10.1073/pnas.2502211122} + doi = {10.1016/j.cossms.2025.101214}, + url = {https://www.sciencedirect.com/science/article/pii/S1359028625000014}, } @article{wang2025designspace, title = {On the design space between molecular mechanics and machine learning force fields}, - author = {Wang, Y. and Takaba, K. and Chen, M.S. and Wieder, M. and Xu, Y. and Zhu, T. and Zhang, J.Z.H. and Nagle, A. and Yu, K. and Wang, X. and Cole, D.J. and Rackers, J.A. and Cho, K. and Greener, J.G. and Eastman, P. and Martiniani, S. and Tuckerman, M.E.}, - journal = {Appl. Phys. Rev.}, + author = {Wang, Y. and Takaba, K. and Chen, M.S. and Wieder, M. and Xu, Y. and Zhu, T. and Zhang, J.Z. and Nagle, A. and Yu, K. and Wang, X. and Cole, D.J. and Rackers, J.A. and Cho, K. and Greener, J.G. and Eastman, P. and Martiniani, S. and Tuckerman, M.E.}, + journal = {Applied Physics Reviews 12 (2), 2025}, volume = {12}, + number = {2}, pages = {021304}, year = {2025}, - doi = {10.1063/5.0237876} + doi = {10.1063/5.0237876}, + url = {https://pubs.aip.org/aip/apr/article/12/2/021304/3342041}, } @article{hoellmer2025omatg, title = {Open Materials Generation with Stochastic Interpolants}, - author = {Hoellmer, P. and Egg, T. and Martirossyan, M.M. and Fuemmeler, E. and Gupta, A. and Shui, Z. and Prakash, P. and Roitberg, A. and Liu, M. and Karypis, G. and Transtrum, M. and Hennig, R.G. and Tadmor, E.B. and Martiniani, S.}, - journal = {Proc. 42nd Int. Conf. Mach. Learn. (ICML), PMLR 267}, + author = {Höllmer, P. and Egg, T. and Martirossyan, M.M. and Fuemmeler, E. and Shui, Z. and Gupta, A. and Prakash, P. and Roitberg, A. and Liu, M. and Karypis, G. and Transtrum, M. and Hennig, R.G. and Tadmor, E.B. and Martiniani, S.}, + journal = {Proceedings of the 42nd International Conference on Machine Learning, Vancouver, Canada. PMLR 267, 2025}, year = {2025}, eprint = {2502.02582}, - url = {https://arxiv.org/abs/2502.02582} + url = {https://arxiv.org/abs/2502.02582}, } -@article{jacobs2025mlips, - title = {A practical guide to machine learning interatomic potentials -- Status and future}, - author = {Jacobs, R. and Morgan, D. and Attarian, S. and Meng, J. and Shen, C. and Wu, Z. and Xie, C.Y. and Yang, J.H. and Artrith, N. and Blaiszik, B. and Ceder, G. and Choudhary, K. and Csanyi, G. and Cubuk, E.D. and Deng, B. and Drautz, R. and Fu, X. and Godwin, J. and Honavar, V. and Isayev, O. and Johansson, A. and Kozinsky, B. and Martiniani, S. and Ong, S.P. and Poltavsky, I. and Schmidt, K.J. and Takamoto, S. and Thompson, A. and Westermayr, J. and Wood, B.M.}, - journal = {Curr. Opin. Solid State Mater. Sci.}, - volume = {35}, - pages = {101214}, +@article{casiulis2025swarm, + title = {A geometric condition for robot-swarm cohesion and cluster–flock transition}, + author = {Casiulis, M. and Arbel, E. and Waes, C.V. and Lahini, Y. and Martiniani, S. and Oppenheimer, N. and Zion, M.Y.B.}, + journal = {Proceedings of the National Academy of Sciences}, + volume = {122}, + number = {37}, + pages = {e2502211122}, + year = {2025}, + doi = {10.1073/pnas.2502211122}, + url = {https://www.pnas.org/doi/abs/10.1073/pnas.2502211122}, +} + +@article{casiulis2025gyromorphs, + title = {Gyromorphs: a new class of functional disordered materials}, + author = {Casiulis, M. and Shih, A. and Martiniani, S.}, + journal = {Physical Review Letters}, + volume = {135}, + number = {19}, + pages = {196101}, + year = {2025}, + doi = {10.1103/gqrx-7mn2}, + eprint = {2410.09023}, + url = {https://link.aps.org/doi/10.1103/gqrx-7mn2}, +} + +@article{martirossyan2025structurematches, + title = {All that structure matches does not glitter}, + author = {Martirossyan, M.M. and Egg, T. and Hoellmer, P. and Karypis, G. and Transtrum, M. and Roitberg, A. and Liu, M. and Hennig, R.G. and Tadmor, E.B. and Martiniani, S.}, + journal = {Advances in Neural Information Processing Systems (NeurIPS 2025)}, + year = {2025}, + eprint = {2509.12178}, + url = {https://proceedings.neurips.cc/paper_files/paper/2025/hash/390a00871e5593fcf8717f83b2c1395f-Abstract-Datasets_and_Benchmarks_Track.html}, +} + +@article{zhang2025clamp, + title = {Contrastive Self-Supervised Learning As Neural Manifold Packing}, + author = {Zhang, G. and Heeger, D.J. and Martiniani, S.}, + journal = {Advances in Neural Information Processing Systems (NeurIPS 2025)}, + year = {2025}, + eprint = {2506.13717}, + url = {https://proceedings.neurips.cc/paper_files/paper/2025/hash/c3fabe2972510ffdb31223508bcd02e4-Abstract-Conference.html}, +} + +@article{jin2025molguidance, + title = {MolGuidance: Advanced Guidance Strategies for Conditional Molecular Generation with Flow Matching}, + author = {Jin, J. and Zeng, C. and Prakash, P. and Tadmor, E.B. and Roitberg, A. and Hennig, R.G. and Martiniani, S. and Liu, M.}, + journal = {Journal of Chemical Information and Modeling}, + year = {2025}, + url = {https://pubs.acs.org/jcisd8/article/doi/10.1021/acs.jcim.6c00964/5224534}, +} + +@article{barrows2025unifying, + title = {A Unifying Approach to Self‐Organizing Systems Interacting via Conservation Laws}, + author = {Barrows, F. and Zhang, G. and Anand, S. and Chen, Z. and Lin, J. and Desai, A. and Martiniani, S. and Caravelli, F.}, + journal = {Advanced Intelligent Discovery}, + pages = {e202500190}, year = {2025}, - doi = {10.1016/j.cossms.2025.101214} + eprint = {2507.02575}, + url = {https://advanced.onlinelibrary.wiley.com/doi/abs/10.1002/aidi.202500190}, } @article{miret2025ai4mat, - title = {Perspective on Artificial Intelligence for Accelerated Materials Design ({AI4Mat}) Workshops in 2024}, - author = {Miret, S. and Skreta, M. and Wellawatte, G. and Martiniani, S. and Krishnan, N.M.A. and Karypis, G. and Jablonka, K.M.}, - journal = {Mach. Learn.: Sci. Technol.}, + title = {Perspective on artificial intelligence for accelerated materials design (AI4Mat) workshops in 2024}, + author = {Miret, S. and Skreta, M. and Wellawatte, G. and Martiniani, S. and Krishnan, N.A. and Karypis, G. and Jablonka, K.M.}, + journal = {Machine Learning: Science and Technology 6 (4), 040201, 2025}, volume = {6}, number = {4}, pages = {040201}, year = {2025}, - doi = {10.1088/2632-2153/adc786} + doi = {10.1088/2632-2153/adc786}, + url = {https://iopscience.iop.org/article/10.1088/2632-2153/ae0d5d/meta}, +} + +@article{shih2024disorder, + title = {Fast generation of spectrally shaped disorder}, + author = {Shih, A. and Casiulis, M. and Martiniani, S.}, + journal = {Physical Review E}, + volume = {110}, + number = {3}, + pages = {034122}, + year = {2024}, + doi = {10.1103/PhysRevE.110.034122}, + url = {https://journals.aps.org/pre/abstract/10.1103/PhysRevE.110.034122}, + note = {Editor's Suggestion. Highlighted in [Old Movie Demos New Tech](https://physics.aps.org/articles/v17/134), Physics 17, 134 (2024)}, } @article{anand2024rectification, - title = {Transport and Energetics of Bacterial Rectification}, + title = {Transport and energetics of bacterial rectification}, author = {Anand, S. and Ma, X. and Guo, S. and Martiniani, S. and Cheng, X.}, - journal = {Proc. Natl. Acad. Sci.}, + journal = {Proceedings of the National Academy of Sciences}, volume = {121}, number = {52}, pages = {e2411608121}, year = {2024}, doi = {10.1073/pnas.2411608121}, - url = {https://www.pnas.org/doi/10.1073/pnas.2411608121} + url = {https://www.pnas.org/doi/abs/10.1073/pnas.2411608121}, } -@article{rawat2024neurips, - title = {Unconditional stability of a recurrent neural circuit implementing divisive normalization}, - author = {Rawat, S. and Martiniani, S.}, - journal = {Adv. Neural. Inf. Process. Syst. 38 (NeurIPS 2024)}, - year = {2024}, - url = {https://openreview.net/forum?id=5lLb7aXRN9&referrer=%5Bthe%20profile%20of%20Stefano%20Martiniani%5D(%2Fprofile%3Fid%3D~Stefano_Martiniani1)} -} - -@article{fuemmeler2024colabfit, - title = {Advancing the ColabFit Exchange towards a Web-scale Data Source for Machine Learning Interatomic Potentials}, - author = {Fuemmeler, E. and Wolfe, G. and Gupta, A. and Vita, J.A. and Tadmor, E.B. and Martiniani, S.}, - journal = {AI for Accelerated Materials Design - NeurIPS 2024}, +@article{gonzales2024benchmarking, + title = {Benchmarking of Universal Machine Learning Interatomic Potentials for Structural Relaxation}, + author = {Gonzales, C. and Fuemmeler, E. and Tadmor, E.B. and Martiniani, S. and Miret, S.}, + journal = {AI for Accelerated Materials Design-NeurIPS 2024, 2024}, year = {2024}, - url = {https://openreview.net/forum?id=b8qZpGJIkw} + url = {https://openreview.net/forum?id=fNyXCCZ0g6}, } -@article{gonzales2024benchmarking, - title = {Benchmarking of Universal Machine Learning Interatomic Potentials for Structural Relaxation}, - author = {Gonzales, A.C. and Fuemmeler, E. and Tadmor, E.B. and Martiniani, S. and Miret, S.}, - journal = {AI for Accelerated Materials Design - NeurIPS 2024}, +@article{rawat2024neurips, + title = {Unconditional stability of a recurrent neural circuit implementing divisive normalization}, + author = {Rawat, S. and Heeger, D.J. and Martiniani, S.}, + journal = {Advances in Neural Information Processing Systems (NeurIPS 2024)}, year = {2024}, - url = {https://openreview.net/forum?id=fNyXCCZ0g6&referrer=%5Bthe%20profile%20of%20Eric%20Fuemmeler%5D(/profile?id=~Eric_Fuemmeler1)} + url = {https://proceedings.neurips.cc/paper_files/paper/2024/hash/1abed6ee581b9ceb4e2ddf37822c7fcb-Abstract-Conference.html}, } @article{rawat2024psd, - title = {Element-wise and Recursive Solutions for the Power Spectral Density of Biological Stochastic Dynamical Systems at Fixed Points}, + title = {Element-wise and recursive solutions for the power spectral density of biological stochastic dynamical systems at fixed points}, author = {Rawat, S. and Martiniani, S.}, - journal = {Phys. Rev. Research}, + journal = {Physical Review Research}, volume = {6}, + number = {4}, pages = {043179}, year = {2024}, doi = {10.1103/PhysRevResearch.6.043179}, - eprint = {2305.19890} + eprint = {2305.19890}, + url = {https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.6.043179}, } -@article{shih2024disorder, - title = {Fast Generation of Spectrally-Shaped Disorder}, - author = {Shih, A. and Casiulis, M. and Martiniani, S.}, - journal = {Phys. Rev. E}, - volume = {110}, - pages = {034122}, +@article{fuemmeler2024colabfit, + title = {Advancing the ColabFit Exchange towards a Web-scale Data Source for Machine Learning Interatomic Potentials}, + author = {Fuemmeler, E. and Wolfe, G. and Gupta, A. and Vita, J.A. and Tadmor, E.B. and Martiniani, S.}, + journal = {AI for Accelerated Materials Design-NeurIPS 2024, 2024}, year = {2024}, - doi = {10.1103/PhysRevE.110.034122}, - url = {https://journals.aps.org/pre/abstract/10.1103/PhysRevE.110.034122}, - note = {Editor's Suggestion. Highlighted in [Old Movie Demos New Tech](https://physics.aps.org/articles/v17/134), Physics 17, 134 (2024)} + url = {https://openreview.net/pdf?id=b8qZpGJIkw}, +} + +@article{rawat2024comprehensive, + title = {A Comprehensive Large-Scale Model of the Primary Visual Cortex (V1)}, + author = {Rawat, S. and Heeger, D. and Martiniani, S.}, + journal = {Bulletin of the American Physical Society}, + year = {2024}, + url = {https://2024.ccneuro.org/pdf/579_Paper_authored_CCN_abstract.pdf}, } @article{gupta2024kusp, title = {KUSP: Python server for deploying ML interatomic potentials}, author = {Gupta, A. and Tadmor, E.B. and Martiniani, S.}, - journal = {AI for Accelerated Materials Design - Vienna 2024}, + journal = {AI for Accelerated Materials Design-Vienna 2024, 2024}, year = {2024}, - url = {https://openreview.net/forum?id=lQAnpCF7nq} + url = {https://openreview.net/forum?id=lQAnpCF7nq}, +} + +@article{anzivino2023rcp, + title = {Estimating random close packing in polydisperse and bidisperse hard spheres via an equilibrium model of crowding}, + author = {Anzivino, C. and Casiulis, M. and Zhang, T. and Moussa, A.S. and Martiniani, S. and Zaccone, A.}, + journal = {The Journal of Chemical Physics}, + volume = {158}, + number = {4}, + pages = {044901}, + year = {2023}, + url = {https://pubs.aip.org/aip/jcp/article/158/4/044901/2876768}, + localfile = {pdf/jcp2023.pdf}, } @article{vita2023colabfit, title = {ColabFit Exchange: open-access datasets for data-driven interatomic potentials}, - author = {Vita, A. and Fuemmeler, E.G. and Gupta, A. and Wolfe, G.P. and Tao, A.Q. and Elliott, R.S. and Martiniani, S. and Tadmor, E.B.}, - journal = {J. Chem. Phys.}, + author = {Vita, J.A. and Fuemmeler, E.G. and Gupta, A. and Wolfe, G.P. and Tao, A.Q. and Elliott, R.S. and Martiniani, S. and Tadmor, E.B.}, + journal = {The Journal of Chemical Physics 159, 154802}, volume = {159}, pages = {154802}, year = {2023}, - url = {papers/jcp2023b.pdf}, - localfile = {pdf/jcp2023b.pdf} + url = {https://pubs.aip.org/aip/jcp/article/159/15/154802/2917782}, + localfile = {pdf/jcp2023b.pdf}, +} + +@article{casiulis2023entropy, + title = {When you can’t count, sample! Computable entropies beyond equilibrium from basin volumes}, + author = {Martiniani, S. and Casiulis, M.}, + journal = {Papers in Physics}, + volume = {15}, + pages = {150001}, + year = {2023}, + url = {https://www.papersinphysics.org/papersinphysics/article/view/837}, + localfile = {pdf/pip2023.pdf}, + note = {Invited perspective in ``Focus Series on Challenges in Granular Matter''}, } @article{golinski2023protein, - title = {Predicting and Interpreting Protein Developability via Transfer of Convolutional Sequence Representation}, + title = {Predicting and interpreting protein developability via transfer of convolutional sequence representation}, author = {Golinski, A.W. and Schmitz, Z.D. and Nielsen, G.H. and Johnson, B. and Saha, D. and Appiah, S. and Hackel, B.J. and Martiniani, S.}, - journal = {ACS Synthetic Biology}, + journal = {ACS synthetic biology}, volume = {12}, number = {9}, - pages = {2600--2615}, + pages = {2600-2615}, year = {2023}, - url = {papers/synbio2023.pdf}, - localfile = {pdf/synbio2023.pdf} -} - -@article{rawat2023coherence, - title = {Coherence influences the dimensionality of communication subspaces}, - author = {Rawat, S. and Heeger, D. and Martiniani, S.}, - journal = {Cosyne Abstracts}, - year = {2023}, - url = {papers/cosyne2023.pdf}, - localfile = {pdf/cosyne2023.pdf} + url = {https://pubs.acs.org/asbcd6/article/12/9/2600/333115}, + localfile = {pdf/synbio2023.pdf}, } @article{martiniani2023bitpropelled, @@ -308,220 +409,212 @@ @article{martiniani2023bitpropelled journal = {Journal Club for Condensed Matter Physics}, year = {2023}, url = {papers/jccm2023.pdf}, - localfile = {pdf/jccm2023.pdf} -} - -@article{casiulis2023entropy, - title = {When you can't count sample! Computable entropies beyond equilibrium from basin volumes}, - author = {Casiulis, M. and Martiniani, S.}, - journal = {Papers in Physics}, - volume = {15}, - pages = {150001}, - year = {2023}, - url = {papers/pip2023.pdf}, - localfile = {pdf/pip2023.pdf}, - note = {Invited perspective in ``Focus Series on Challenges in Granular Matter''} + localfile = {pdf/jccm2023.pdf}, } -@article{anzivino2023rcp, - title = {Estimating random close packing in polydisperse and bidisperse hard spheres via an equilibrium model of crowding}, - author = {Anzivino, C. and Casiulis, M. and Zhang, T. and Moussa, A.S. and Martiniani, S. and Zaccone, A.}, - journal = {J. Chem. Phys.}, - volume = {158}, - pages = {044901}, +@article{rawat2023coherence, + title = {Coherence influences the dimensionality of communication subspaces}, + author = {Rawat, S. and Heeger, D. and Martiniani, S.}, + journal = {Cosyne Abstracts 2023, 2023}, year = {2023}, - url = {papers/jcp2023.pdf}, - localfile = {pdf/jcp2023.pdf} + url = {papers/cosyne2023.pdf}, + localfile = {pdf/cosyne2023.pdf}, } @article{ro2022entropy, - title = {Model-Free Measurement of Local Entropy Production and Extractable Work in Active Matter}, + title = {Model-free measurement of local entropy production and extractable work in active matter}, author = {Ro, S. and Guo, B. and Shih, A. and Phan, T.V. and Austin, R.H. and Levine, D. and Chaikin, P.M. and Martiniani, S.}, - journal = {Phys. Rev. Lett.}, + journal = {Physical Review Letters}, volume = {129}, + number = {22}, pages = {220601}, year = {2022}, - url = {papers/prl2022.pdf}, + url = {https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.129.220601}, localfile = {pdf/prl2022.pdf}, - note = {Cover article. Editor's Suggestion. Highlighted in [Viewpoint: Measuring Entropy in Active-Matter Systems](https://physics.aps.org/articles/v15/179), Physics 15, 179 (2022)} + note = {Cover article. Editor's Suggestion. Highlighted in [Viewpoint: Measuring Entropy in Active-Matter Systems](https://physics.aps.org/articles/v15/179), Physics 15, 179 (2022)}, } @article{golinski2021highthroughput, - title = {High-Throughput Developability Assays Enable Library-Scale Identification of Producible Protein Scaffold Variants}, - author = {Golinski, A.W. and Mischler, K.M. and Laxminarayan, S. and Neurock, N. and Fossing, M. and Pichman, H. and Martiniani, S. and Hackel, B.J.}, - journal = {Proc. Natl. Acad. Sci.}, + title = {High-throughput developability assays enable library-scale identification of producible protein scaffold variants}, + author = {Golinski, A.W. and Mischler, K.M. and Laxminarayan, S. and Neurock, N.L. and Fossing, M. and Pichman, H. and Martiniani, S. and Hackel, B.J.}, + journal = {Proceedings of the National Academy of Sciences}, volume = {118}, number = {23}, year = {2021}, - url = {papers/pnas2021.pdf}, - localfile = {pdf/pnas2021.pdf} + url = {https://www.pnas.org/doi/abs/10.1073/pnas.2026658118}, + localfile = {pdf/pnas2021.pdf}, } @article{cavagna2021vicsek, - title = {Vicsek Model by Time-Interlaced Compression: a Dynamical Computable Information Density}, + title = {Vicsek model by time-interlaced compression: A dynamical computable information density}, author = {Cavagna, A. and Chaikin, P.M. and Levine, D. and Martiniani, S. and Puglisi, A. and Viale, M.}, - journal = {Phys. Rev. E}, + journal = {Physical Review E}, volume = {103}, + number = {6}, pages = {062141}, year = {2021}, - url = {papers/pre2021.pdf}, - localfile = {pdf/pre2021.pdf} + url = {https://journals.aps.org/pre/abstract/10.1103/PhysRevE.103.062141}, + localfile = {pdf/pre2021.pdf}, } @article{martiniani2020correlation, title = {Correlation lengths in the language of computable information}, author = {Martiniani, S. and Lemberg, Y. and Chaikin, P.M. and Levine, D.}, - journal = {Phys. Rev. Lett.}, + journal = {Physical Review Letters 125, 170601}, volume = {125}, pages = {170601}, year = {2020}, - url = {papers/prl2020.pdf}, - localfile = {pdf/prl2020.pdf} + url = {https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.125.170601}, + localfile = {pdf/prl2020.pdf}, } @article{martiniani2019hidden, - title = {Quantifying hidden order out of equilibrium}, + title = {Quantifying Hidden Order out of Equilibrium}, author = {Martiniani, S. and Chaikin, P.M. and Levine, D.}, - journal = {Phys. Rev. X}, + journal = {Physical Review X 9, 011031}, volume = {9}, pages = {011031}, year = {2019}, - url = {papers/prx2019.pdf}, + url = {https://journals.aps.org/prx/abstract/10.1103/PhysRevX.9.011031}, localfile = {pdf/prx2019.pdf}, - note = {Highlighted in [File compression uncovers hidden order](https://pubs.aip.org/physicstoday/online/4666/File-compression-uncovers-hidden-order), Physics Today (2019)} + note = {Highlighted in [File compression uncovers hidden order](https://pubs.aip.org/physicstoday/online/4666/File-compression-uncovers-hidden-order), Physics Today (2019)}, +} + +@article{ballard2017landscapes, + title = {Energy landscapes for machine learning}, + author = {Ballard, A.J. and Das, R. and Martiniani, S. and Mehta, D. and Sagun, L. and Stevenson, J.D. and Wales, D.J.}, + journal = {Physical Chemistry Chemical Physics}, + volume = {19}, + number = {20}, + pages = {12585-12603}, + year = {2017}, + url = {https://pubs.rsc.org/cp/article-abstract/19/20/12585/559033}, + localfile = {pdf/jccp2017.pdf}, + note = {Cover article for Phys. Chem. Chem. Phys.}, } @article{martiniani2017edwards, - title = {Numerical test of the Edwards conjecture shows that all packings become equally probable at jamming}, + title = {Numerical test of the Edwards conjecture shows that all packings are equally probable at jamming}, author = {Martiniani, S. and Schrenk, K.J. and Ramola, K. and Chakraborty, B. and Frenkel, D.}, - journal = {Nature Physics}, + journal = {Nature Physics, 13, 848–851}, volume = {13}, pages = {848--851}, year = {2017}, - url = {papers/nphys2017.pdf}, + url = {https://www.nature.com/articles/nphys4168}, localfile = {pdf/nphys2017.pdf}, - note = {Highlighted in [Intuition harnessed in the name of particle packing](https://www.nature.com/articles/546575b), Nature 546, 575 (2017); [A thermodynamic theory of granular material endures](https://pubs.aip.org/physicstoday/article/70/9/20/908192), Physics Today 70, 9 (2017); [A jammy guess?](https://www.nature.com/articles/nmat4817), Nature Materials 15, 1227 (2016)} + note = {Highlighted in [Intuition harnessed in the name of particle packing](https://www.nature.com/articles/546575b), Nature 546, 575 (2017); [A thermodynamic theory of granular material endures](https://pubs.aip.org/physicstoday/article/70/9/20/908192), Physics Today 70, 9 (2017); [A jammy guess?](https://www.nature.com/articles/nmat4817), Nature Materials 15, 1227 (2016)}, } @article{frenkel2017montecarlo, title = {Monte Carlo sampling for stochastic weight functions}, author = {Frenkel, D. and Schrenk, K.J. and Martiniani, S.}, - journal = {Proc. Natl. Acad. Sci.}, + journal = {Proceedings of the National Academy of Sciences}, volume = {114}, number = {27}, + pages = {6924-6929}, year = {2017}, - url = {papers/pnas2017.pdf}, - localfile = {pdf/pnas2017.pdf} + url = {https://www.pnas.org/doi/abs/10.1073/pnas.1620497114}, + localfile = {pdf/pnas2017.pdf}, } -@article{ballard2017landscapes, - title = {Energy Landscapes for Machine Learning}, - author = {Ballard, A.J. and Das, R. and Martiniani, S. and Mehta, D. and Sagun, L. and Stevenson, J.D. and Wales, D.J.}, - journal = {Phys. Chem. Chem. Phys.}, - volume = {19}, - pages = {12585}, +@article{martiniani2017thesis, + title = {On the complexity of energy landscapes: algorithms and a direct test of the Edwards conjecture}, + author = {Martiniani, S.}, + journal = {University of Cambridge, 2017}, year = {2017}, - url = {papers/jccp2017.pdf}, - localfile = {pdf/jccp2017.pdf}, - note = {Cover article for Phys. Chem. Chem. Phys.} -} - -@article{martiniani2016structural, - title = {Structural analysis of high dimensional basins of attraction}, - author = {Martiniani, S. and Schrenk, K.J. and Stevenson, J.D. and Wales, D.J. and Frenkel, D.}, - journal = {Phys. Rev. E}, - volume = {94}, - pages = {031301}, - year = {2016}, - url = {papers/pre2016r.pdf}, - localfile = {pdf/pre2016r.pdf} + url = {https://www.repository.cam.ac.uk/items/c19fd3db-c779-4b38-91f3-8fc79de899ae}, + localfile = {pdf/thesis_sm.pdf}, } @article{martiniani2016counting, title = {Turning intractable counting into sampling: computing the configurational entropy of three-dimensional jammed packings}, author = {Martiniani, S. and Schrenk, K.J. and Stevenson, J.D. and Wales, D.J. and Frenkel, D.}, - journal = {Phys. Rev. E}, + journal = {Physical Review E 93, 012906}, volume = {93}, pages = {012906}, year = {2016}, - url = {papers/pre2016.pdf}, + url = {https://journals.aps.org/pre/abstract/10.1103/PhysRevE.93.012906}, localfile = {pdf/pre2016.pdf}, - note = {Highlighted in NewScientist and [other news sources](https://www.cam.ac.uk/research/news/how-many-ways-can-you-arrange-128-tennis-balls-researchers-solve-an-apparently-impossible-problem)} + note = {Highlighted in NewScientist and [other news sources](https://www.cam.ac.uk/research/news/how-many-ways-can-you-arrange-128-tennis-balls-researchers-solve-an-apparently-impossible-problem)}, +} + +@article{martiniani2016structural, + title = {Structural analysis of high-dimensional basins of attraction}, + author = {Martiniani, S. and Schrenk, K.J. and Stevenson, J.D. and Wales, D.J. and Frenkel, D.}, + journal = {Physical Review E}, + volume = {93}, + number = {3}, + pages = {031301}, + year = {2016}, + url = {https://journals.aps.org/pre/abstract/10.1103/PhysRevE.94.031301}, + localfile = {pdf/pre2016r.pdf}, } @article{ballard2015exploiting, title = {Exploiting the potential energy landscape to sample free energy}, - author = {Ballard, A.J. and Martiniani, S. and Stevenson, J.D. and Somani, S. and Wales, D.J.}, - journal = {WIREs Comput. Mol. Sci.}, + author = {Ballard, A. and Martiniani, S. and Stevenson, J.D. and Somani, S. and Wales, D.J.}, + journal = {WIREs computational molecular science}, volume = {5}, pages = {273}, year = {2015}, - url = {papers/wires2015.pdf}, - localfile = {pdf/wires2015.pdf} + url = {https://wires.onlinelibrary.wiley.com/doi/abs/10.1002/wcms.1217}, + localfile = {pdf/wires2015.pdf}, } @article{martiniani2014sens, title = {Superposition Enhanced Nested Sampling}, author = {Martiniani, S. and Stevenson, J.D. and Wales, D.J. and Frenkel, D.}, - journal = {Phys. Rev. X}, + journal = {Physical Review X}, volume = {4}, + number = {3}, pages = {031034}, year = {2014}, - url = {papers/prx2014.pdf}, - localfile = {pdf/prx2014.pdf} + url = {https://journals.aps.org/prx/abstract/10.1103/PhysRevX.4.031034}, + localfile = {pdf/prx2014.pdf}, } @article{magistris2013squaraine, - title = {Near-infrared absorbing squaraine dye with extended $\pi$ conjugation for dye-sensitized solar cells}, - author = {Magistris, C. and Martiniani, S. and Barbero, N. and Park, J. and Benzi, C. and Anderson, A. and Law, C.H. and Barolo, C. and O'Regan, B.C.}, + title = {Near-infrared absorbing squaraine dye with extended π conjugation for dye-sensitized solar cells}, + author = {Magistris, C. and Martiniani, S. and Barbero, N. and Park, J. and Benzi, C. and Anderson, A. and Law, C. and Barolo, C. and O'Regan, B.}, journal = {Renewable Energy}, volume = {60}, - pages = {672}, + pages = {672-678}, year = {2013}, - url = {papers/renen2013.pdf}, - localfile = {pdf/renen2013.pdf} + url = {https://www.sciencedirect.com/science/article/pii/S096014811300311X}, + localfile = {pdf/renen2013.pdf}, } @article{richards2012mechanism, - title = {The Mechanism of Iodine Reduction by TiO2 Electrons and the Kinetics of Recombination in Dye-Sensitized Solar Cells}, - author = {Richards, C.E. and Anderson, A.Y. and Martiniani, S. and Law, C. and O'Regan, B.C.}, - journal = {J. Phys. Chem. Lett.}, + title = {The Mechanism of Iodine Reduction by TiO2 Electrons and the Kinetics of Recombination in Dye Sensitized Solar Cells}, + author = {Richards, C.E. and Anderson, A.Y. and Martinani, S. and Law, C. and O'Regan, B.C.}, + journal = {The Journal of Physical Chemistry Letters}, volume = {3}, pages = {1980}, year = {2012}, - url = {papers/jpcl2012.pdf}, - localfile = {pdf/jpcl2012.pdf} + url = {https://pubs.acs.org/doi/abs/10.1021/jz3006755}, + localfile = {pdf/jpcl2012.pdf}, } @article{martiniani2012regeneration, - title = {New insight into the regeneration kinetics of dye sensitised solar cells}, + title = {New insight into the regeneration kinetics of organic dye sensitised solar cells}, author = {Martiniani, S. and Anderson, A.Y. and Law, C. and O'Regan, B.C. and Barolo, C.}, - journal = {Chem. Commun.}, + journal = {Chemical Communications}, volume = {48}, - pages = {2406}, + number = {18}, + pages = {2406-2408}, year = {2012}, - url = {papers/chemcomm2012.pdf}, - localfile = {pdf/chemcomm2012.pdf} + url = {https://pubs.rsc.org/cc/article-abstract/48/18/2406/360305}, + localfile = {pdf/chemcomm2012.pdf}, } % --------------------------------------------------------------------------- % Ph.D. Theses % --------------------------------------------------------------------------- -@phdthesis{golinski2021thesis, - title = {Data-driven approach to engineering protein evolvability and developability}, - author = {Golinski, A.}, - school = {University of Minnesota}, - year = {2021}, - url = {papers/thesis_ag.pdf}, - localfile = {pdf/thesis_ag.pdf} -} - -@phdthesis{martiniani2017thesis, - title = {On the complexity of energy landscapes: algorithms and a direct test of the Edwards conjecture}, - author = {Martiniani, S.}, - school = {University of Cambridge}, - year = {2017}, - url = {papers/thesis_sm.pdf}, - localfile = {pdf/thesis_sm.pdf} +@phdthesis{yan2026askchem, + title = {AskChem: Claim-Centered Infrastructure for Chemistry Literature Synthesis}, + author = {Yan, B. and Wolfe, G. and Martiniani, S. and Cho, K.}, + school = {arXiv preprint arXiv:2607.28618}, + year = {2026}, + url = {https://arxiv.org/abs/2607.28618}, }