[{"intvolume":"       164","department":[{"_id":"BiCh"}],"publication_status":"published","arxiv":1,"publisher":"AIP Publishing","citation":{"mla":"Kim, Dongjin, and Bingqing Cheng. “Long-Range Electrostatics for Machine Learning Interatomic Potentials Is Easier than We Thought.” <i>The Journal of Chemical Physics</i>, vol. 164, no. 6, 060901, AIP Publishing, 2026, doi:<a href=\"https://doi.org/10.1063/5.0316886\">10.1063/5.0316886</a>.","ista":"Kim D, Cheng B. 2026. Long-range electrostatics for machine learning interatomic potentials is easier than we thought. The Journal of Chemical Physics. 164(6), 060901.","ieee":"D. Kim and B. Cheng, “Long-range electrostatics for machine learning interatomic potentials is easier than we thought,” <i>The Journal of Chemical Physics</i>, vol. 164, no. 6. AIP Publishing, 2026.","apa":"Kim, D., &#38; Cheng, B. (2026). Long-range electrostatics for machine learning interatomic potentials is easier than we thought. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0316886\">https://doi.org/10.1063/5.0316886</a>","chicago":"Kim, Dongjin, and Bingqing Cheng. “Long-Range Electrostatics for Machine Learning Interatomic Potentials Is Easier than We Thought.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2026. <a href=\"https://doi.org/10.1063/5.0316886\">https://doi.org/10.1063/5.0316886</a>.","short":"D. Kim, B. Cheng, The Journal of Chemical Physics 164 (2026).","ama":"Kim D, Cheng B. Long-range electrostatics for machine learning interatomic potentials is easier than we thought. <i>The Journal of Chemical Physics</i>. 2026;164(6). doi:<a href=\"https://doi.org/10.1063/5.0316886\">10.1063/5.0316886</a>"},"oa":1,"doi":"10.1063/5.0316886","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2512.18029"}],"day":"14","oa_version":"Preprint","volume":164,"scopus_import":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","title":"Long-range electrostatics for machine learning interatomic potentials is easier than we thought","month":"02","_id":"21381","date_updated":"2026-03-02T14:46:24Z","article_type":"original","external_id":{"arxiv":["2512.18029"]},"date_published":"2026-02-14T00:00:00Z","date_created":"2026-03-02T10:06:46Z","article_processing_charge":"No","OA_place":"repository","status":"public","OA_type":"free access","abstract":[{"lang":"eng","text":"The lack of long-range electrostatics is a key limitation of modern machine learning interatomic potentials (MLIPs), hindering reliable applications to interfaces, charge-transfer reactions, polar and ionic materials, and biomolecules. In this Perspective, we distill two design principles behind the Latent Ewald Summation framework, which can capture long-range interactions, charges, and electrical response just by learning from standard energy and force training data: (i) use a Coulomb functional form with environment-dependent charges to capture electrostatic interactions, and (ii) avoid explicit training on ambiguous density functional theory partial charges. When both principles are satisfied, substantial flexibility remains: essentially any short-range MLIP can be augmented; charge equilibration schemes can be added when desired; dipoles and Born effective charges can be inferred or fine-tuned; and charge/spin-state embeddings or tensorial targets can be further incorporated. We also discuss current limitations and open challenges. Together, these minimal, physics-guided design rules suggest that incorporating long-range electrostatics into MLIPs is simpler and perhaps more broadly applicable than is commonly assumed."}],"quality_controlled":"1","author":[{"first_name":"Dongjin","full_name":"Kim, Dongjin","last_name":"Kim"},{"last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"issue":"6","article_number":"060901","acknowledgement":"B.C. thanks Christoph Dellago for his mentorship and influence. In addition to his seminal contributions to statistical mechanics, Christoph Dellago is an early developer and adopter of machine learning interatomic potentials. B.C. did two exchanges in the groups of Christoph Dellago and Jörg Behler in 2018, with transformative impact on her research directions.\r\n\r\nWe thank Peichen Zhong and Daniel S. King for useful feedback on the manuscript and for the collaborations on the LES method.\r\n\r\nFunding acknowledgment: Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award No. R35GM159986. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","year":"2026"},{"oa":1,"citation":{"chicago":"Hübl, Maximilian, and Carl Peter Goodrich. “Simultaneous Optimization of Assembly Time and Yield in Programmable Self-Assembly.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2026. <a href=\"https://doi.org/10.1063/5.0304731\">https://doi.org/10.1063/5.0304731</a>.","ama":"Hübl M, Goodrich CP. Simultaneous optimization of assembly time and yield in programmable self-assembly. <i>Journal of Chemical Physics</i>. 2026;164(8). doi:<a href=\"https://doi.org/10.1063/5.0304731\">10.1063/5.0304731</a>","short":"M. Hübl, C.P. Goodrich, Journal of Chemical Physics 164 (2026).","mla":"Hübl, Maximilian, and Carl Peter Goodrich. “Simultaneous Optimization of Assembly Time and Yield in Programmable Self-Assembly.” <i>Journal of Chemical Physics</i>, vol. 164, no. 8, 084904, AIP Publishing, 2026, doi:<a href=\"https://doi.org/10.1063/5.0304731\">10.1063/5.0304731</a>.","apa":"Hübl, M., &#38; Goodrich, C. P. (2026). Simultaneous optimization of assembly time and yield in programmable self-assembly. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0304731\">https://doi.org/10.1063/5.0304731</a>","ista":"Hübl M, Goodrich CP. 2026. Simultaneous optimization of assembly time and yield in programmable self-assembly. Journal of Chemical Physics. 164(8), 084904.","ieee":"M. Hübl and C. P. Goodrich, “Simultaneous optimization of assembly time and yield in programmable self-assembly,” <i>Journal of Chemical Physics</i>, vol. 164, no. 8. AIP Publishing, 2026."},"publisher":"AIP Publishing","publication_status":"published","arxiv":1,"department":[{"_id":"CaGo"},{"_id":"GradSch"}],"intvolume":"       164","has_accepted_license":"1","volume":164,"scopus_import":"1","project":[{"name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks","grant_number":"FTI23-G-011","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5"}],"day":"28","oa_version":"Published Version","doi":"10.1063/5.0304731","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","date_updated":"2026-03-09T10:40:41Z","_id":"21408","month":"02","ddc":["540"],"title":"Simultaneous optimization of assembly time and yield in programmable self-assembly","corr_author":"1","OA_place":"publisher","status":"public","article_processing_charge":"Yes (via OA deal)","date_published":"2026-02-28T00:00:00Z","date_created":"2026-03-08T23:01:45Z","external_id":{"arxiv":["2510.07876"]},"article_type":"original","license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"lang":"eng","text":"Rational design strategies for self-assembly require a detailed understanding of both the equilibrium state and the assembly kinetics. While the former is starting to be well understood, the latter remains a major theoretical challenge, especially in programmable systems and the so-called semi-addressable regime, where binding is often nondeterministic and the formation of off-target structures negatively influences the assembly. Here, we show that it is possible to simultaneously sculpt the assembly outcome and the assembly kinetics through the underexplored design space of binding energies and particle concentrations. By formulating the assembly process as a complex reaction network, we calculate and optimize the tradeoff between assembly speed and quality and show that parameter optimization can speed up assembly by many orders of magnitude without lowering the yield of the target structure. Although the exact speedup varies from design to design, we find the largest speedups for nondeterministic systems where unoptimized assembly is the slowest, sometimes even making them assemble faster than optimized, fully addressable designs. Therefore, these results not only solve a key challenge in semi-addressable self-assembly but further emphasize the utility of semi-addressability, where designs have the potential to be faster as well as cheaper (fewer particle species) and better (higher yield). More broadly, our results highlight the importance of parameter optimization in programmable self-assembly and provide practical tools for simultaneous optimization of kinetics and yield in a wide range of systems."}],"OA_type":"hybrid","file":[{"checksum":"9bdb8870930e83edb973408da3038559","file_name":"2026_JourChemPhysics_Huebl.pdf","date_created":"2026-03-09T10:38:55Z","relation":"main_file","date_updated":"2026-03-09T10:38:55Z","file_size":6903766,"file_id":"21415","success":1,"access_level":"open_access","creator":"dernst","content_type":"application/pdf"}],"article_number":"084904","issue":"8","author":[{"last_name":"Hübl","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","first_name":"Maximilian","full_name":"Hübl, Maximilian"},{"orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich"}],"quality_controlled":"1","year":"2026","language":[{"iso":"eng"}],"publication":"Journal of Chemical Physics","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"acknowledgement":"The research was supported by the Gesellschaft für Forschungsförderung Niederösterreich under Project No. FTI23-G-011.","file_date_updated":"2026-03-09T10:38:55Z"},{"acknowledgement":"The authors thank Nicolas Chapuis for fruitful discussions. L.B. acknowledges support from the ERC project n-AQUA under Grant Agreement No. 101071937. B.C. acknowledges support from the CFM Foundation and the NOMIS Foundation. N.K. acknowledges support from the Swiss National Science Foundation (SNSF) under Grant No. CRSK-2_237930.","file_date_updated":"2026-05-18T07:31:23Z","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"year":"2026","language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","PlanS_conform":"1","quality_controlled":"1","article_number":"134704","author":[{"last_name":"Coquinot","orcid":"0000-0001-5524-596X","full_name":"Coquinot, Baptiste","id":"f8417bd4-f599-11ee-a482-b927e3ed1e8e","first_name":"Baptiste"},{"last_name":"Lizée","first_name":"Mathieu","full_name":"Lizée, Mathieu"},{"last_name":"Bocquet","full_name":"Bocquet, Lydéric","first_name":"Lydéric"},{"full_name":"Kavokine, Nikita","first_name":"Nikita","last_name":"Kavokine"}],"issue":"13","file":[{"file_size":5497515,"date_updated":"2026-05-18T07:31:23Z","file_id":"21889","creator":"dernst","access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2026_JourChemPhysics_Coquinot.pdf","checksum":"a896969c829be2a79859bd277f87b44c","date_created":"2026-05-18T07:31:23Z","relation":"main_file"}],"abstract":[{"lang":"eng","text":"The transport properties of nanofluidic channels are usually studied under constant (DC) voltage or pressure driving. However, the frequency response under sinusoidal (AC) drivings offers rich insights into the time-dependent transport mechanisms. Inspired by recent electrochemical approaches, we investigate the couplings between ionic and electronic transport under AC driving. We show that conduction electrons of the channel walls participate in ionic current via capacitive electrochemical coupling, defining a critical frequency and length scale where electron-dominated conductivity emerges. We further analyze how electron–ion coupling modifies electro-osmotic flows and demonstrate that fluctuation-induced momentum transfer between the electrolyte and wall electrons produces distinct AC transport signatures, depending on the charge carrier polarity. Altogether, we establish a frequency-dependent transport matrix that couples ionic, electronic, and hydrodynamic flows. These findings establish AC nanofluidic transport as a powerful probe of interfacial phenomena under confinement and suggest new directions for engineering nanofluidic functionalities through electron–electrolyte coupling."}],"OA_type":"hybrid","external_id":{"arxiv":["2505.02478"]},"article_type":"original","article_processing_charge":"Yes (in subscription journal)","date_created":"2026-05-07T08:53:03Z","date_published":"2026-04-07T00:00:00Z","OA_place":"publisher","status":"public","ddc":["530"],"title":"Electron–electrolyte coupling in AC transport through nanofluidic channels","month":"04","date_updated":"2026-05-18T07:34:57Z","_id":"21840","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"07","oa_version":"Published Version","doi":"10.1063/5.0313352","volume":164,"scopus_import":"1","has_accepted_license":"1","intvolume":"       164","publication_status":"published","arxiv":1,"department":[{"_id":"MiLe"}],"publisher":"AIP Publishing","oa":1,"citation":{"ista":"Coquinot B, Lizée M, Bocquet L, Kavokine N. 2026. Electron–electrolyte coupling in AC transport through nanofluidic channels. The Journal of Chemical Physics. 164(13), 134704.","ieee":"B. Coquinot, M. Lizée, L. Bocquet, and N. Kavokine, “Electron–electrolyte coupling in AC transport through nanofluidic channels,” <i>The Journal of Chemical Physics</i>, vol. 164, no. 13. AIP Publishing, 2026.","apa":"Coquinot, B., Lizée, M., Bocquet, L., &#38; Kavokine, N. (2026). Electron–electrolyte coupling in AC transport through nanofluidic channels. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0313352\">https://doi.org/10.1063/5.0313352</a>","mla":"Coquinot, Baptiste, et al. “Electron–Electrolyte Coupling in AC Transport through Nanofluidic Channels.” <i>The Journal of Chemical Physics</i>, vol. 164, no. 13, 134704, AIP Publishing, 2026, doi:<a href=\"https://doi.org/10.1063/5.0313352\">10.1063/5.0313352</a>.","chicago":"Coquinot, Baptiste, Mathieu Lizée, Lydéric Bocquet, and Nikita Kavokine. “Electron–Electrolyte Coupling in AC Transport through Nanofluidic Channels.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2026. <a href=\"https://doi.org/10.1063/5.0313352\">https://doi.org/10.1063/5.0313352</a>.","short":"B. Coquinot, M. Lizée, L. Bocquet, N. Kavokine, The Journal of Chemical Physics 164 (2026).","ama":"Coquinot B, Lizée M, Bocquet L, Kavokine N. Electron–electrolyte coupling in AC transport through nanofluidic channels. <i>The Journal of Chemical Physics</i>. 2026;164(13). doi:<a href=\"https://doi.org/10.1063/5.0313352\">10.1063/5.0313352</a>"}},{"file":[{"relation":"main_file","file_name":"2025_JourChemicalPhysics_AlHyder.pdf","checksum":"e278631d949657baa9d5309dad5f4b77","date_created":"2025-06-23T14:03:30Z","success":1,"access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_updated":"2025-06-23T14:03:30Z","file_size":7202681,"file_id":"19881"}],"abstract":[{"text":"We investigate quantum transport in a two-dimensional electron system coupled to a chiral molecular potential, demonstrating how molecular chirality and orientation affect charge and spin transport properties. We propose a minimal model for realizing true chiral symmetry breaking on a magnetized surface, with a crucial role played by the tilt angle of the molecular dipole with respect to the surface. For non-zero tilting, we show that the Hall response exhibits clear signatures of chirality-induced effects, in both charge- and spin-resolved observables. Concerning the former, tilted enantiomers produce asymmetric Hall conductances and, even more remarkably, the persistence of this feature in the absence of spin–orbit coupling (SOC) signals how the enantiospecific charge response results from electron scattering off the molecular potential. Concerning spin-resolved observables where SOC plays a relevant role, we reveal that chiral symmetry breaking is crucial in enabling spin-flipping processes.","lang":"eng"}],"OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","date_published":"2025-06-21T00:00:00Z","date_created":"2025-06-23T13:55:28Z","OA_place":"publisher","status":"public","external_id":{"isi":["001512872900010"],"pmid":["40526561"],"arxiv":["2503.14124"]},"article_type":"original","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"year":"2025","isi":1,"publication":"The Journal of Chemical Physics","language":[{"iso":"eng"}],"file_date_updated":"2025-06-23T14:03:30Z","acknowledgement":"We thank Artem Volosniev, Narcis Avarvari, Georgios Koutentakis, Sandro Wimberger, and Binghai Yan for useful discussions. R.A. received funding from the Austrian Academy of Science ÖWA, Grant No. PR1029OEAW03. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A.C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862-NeqMolRot.","quality_controlled":"1","article_number":"234106","author":[{"last_name":"Al Hyder","first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","full_name":"Al Hyder, Ragheed"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cappellaro","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto"}],"issue":"23","project":[{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338","grant_number":"101062862","name":"Non-Equilibrium Field Theory of Molecular Rotations"},{"_id":"8fa7db46-16d5-11f0-9cad-917600954daf","name":"Polarons in Lead Halide Perovskites","grant_number":"12078"}],"scopus_import":"1","has_accepted_license":"1","volume":162,"oa_version":"Published Version","day":"21","doi":"10.1063/5.0271155","publisher":"AIP Publishing","oa":1,"citation":{"mla":"Al Hyder, Ragheed, et al. “Quantum Transport in the Presence of a Chiral Molecular Potential.” <i>The Journal of Chemical Physics</i>, vol. 162, no. 23, 234106, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0271155\">10.1063/5.0271155</a>.","ista":"Al Hyder R, Lemeshko M, Cappellaro A. 2025. Quantum transport in the presence of a chiral molecular potential. The Journal of Chemical Physics. 162(23), 234106.","apa":"Al Hyder, R., Lemeshko, M., &#38; Cappellaro, A. (2025). Quantum transport in the presence of a chiral molecular potential. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0271155\">https://doi.org/10.1063/5.0271155</a>","ieee":"R. Al Hyder, M. Lemeshko, and A. Cappellaro, “Quantum transport in the presence of a chiral molecular potential,” <i>The Journal of Chemical Physics</i>, vol. 162, no. 23. AIP Publishing, 2025.","chicago":"Al Hyder, Ragheed, Mikhail Lemeshko, and Alberto Cappellaro. “Quantum Transport in the Presence of a Chiral Molecular Potential.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0271155\">https://doi.org/10.1063/5.0271155</a>.","short":"R. Al Hyder, M. Lemeshko, A. Cappellaro, The Journal of Chemical Physics 162 (2025).","ama":"Al Hyder R, Lemeshko M, Cappellaro A. Quantum transport in the presence of a chiral molecular potential. <i>The Journal of Chemical Physics</i>. 2025;162(23). doi:<a href=\"https://doi.org/10.1063/5.0271155\">10.1063/5.0271155</a>"},"intvolume":"       162","arxiv":1,"publication_status":"published","department":[{"_id":"MiLe"}],"month":"06","date_updated":"2025-09-30T13:40:55Z","_id":"19880","corr_author":"1","title":"Quantum transport in the presence of a chiral molecular potential","ddc":["530"],"type":"journal_article","pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1},{"abstract":[{"text":"Impurity motion in a many-body environment has been a central issue in the field of low-temperature physics for decades. In bosonic quantum fluids, the onset of a drag force experienced by point-like objects is due to collective environment excitations, driven by the exchange of linear momentum between the impurity and the many-body bath. In this work we consider a rotating impurity, with the aim of exploring how angular momentum is exchanged with the surrounding bosonic environment. In order to elucidate these issues, we employ a quasiparticle approach based on the angulon theory, which allows us to effectively deal with the non-trivial algebra of quantized angular momentum in the presence of a many-body environment. We uncover how impurity dressing by environmental excitations can establish an exchange channel, whose effectiveness crucially depends on the initial state of the impurity. Remarkably, we find that there is a critical value of initial angular momentum, above which this channel effectively freezes.","lang":"eng"}],"OA_type":"hybrid","file":[{"creator":"dernst","access_level":"open_access","success":1,"content_type":"application/pdf","file_size":6455134,"date_updated":"2025-03-04T10:48:03Z","file_id":"19292","relation":"main_file","checksum":"c67c37788a949af9f0f45b22a27f8087","file_name":"2025_JourChemicalPhysics_Cappellaro.pdf","date_created":"2025-03-04T10:48:03Z"}],"external_id":{"arxiv":["2501.16066"],"pmid":["39964008"],"isi":["001427233100008"]},"article_type":"original","status":"public","OA_place":"publisher","article_processing_charge":"Yes (via OA deal)","date_published":"2025-02-21T00:00:00Z","date_created":"2025-03-02T23:01:51Z","file_date_updated":"2025-03-04T10:48:03Z","acknowledgement":"We acknowledge Henrik Stapelfeldt for enlightening discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A.C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862—NeqMolRot.","isi":1,"year":"2025","publication":"Journal of Chemical Physics","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"PlanS_conform":"1","article_number":"074104","issue":"7","author":[{"last_name":"Cappellaro","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto"},{"full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","last_name":"Bighin"},{"last_name":"Cherepanov","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","first_name":"Igor","full_name":"Cherepanov, Igor"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"}],"quality_controlled":"1","day":"21","oa_version":"Published Version","doi":"10.1063/5.0253451","scopus_import":"1","volume":162,"has_accepted_license":"1","project":[{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"101062862","name":"Non-Equilibrium Field Theory of Molecular Rotations","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338"}],"arxiv":1,"publication_status":"published","department":[{"_id":"MiLe"}],"intvolume":"       162","oa":1,"citation":{"mla":"Cappellaro, Alberto, et al. “Environment-Limited Transfer of Angular Momentum in Bose Liquids.” <i>Journal of Chemical Physics</i>, vol. 162, no. 7, 074104, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0253451\">10.1063/5.0253451</a>.","apa":"Cappellaro, A., Bighin, G., Cherepanov, I., &#38; Lemeshko, M. (2025). Environment-limited transfer of angular momentum in Bose liquids. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0253451\">https://doi.org/10.1063/5.0253451</a>","ieee":"A. Cappellaro, G. Bighin, I. Cherepanov, and M. Lemeshko, “Environment-limited transfer of angular momentum in Bose liquids,” <i>Journal of Chemical Physics</i>, vol. 162, no. 7. AIP Publishing, 2025.","ista":"Cappellaro A, Bighin G, Cherepanov I, Lemeshko M. 2025. Environment-limited transfer of angular momentum in Bose liquids. Journal of Chemical Physics. 162(7), 074104.","ama":"Cappellaro A, Bighin G, Cherepanov I, Lemeshko M. Environment-limited transfer of angular momentum in Bose liquids. <i>Journal of Chemical Physics</i>. 2025;162(7). doi:<a href=\"https://doi.org/10.1063/5.0253451\">10.1063/5.0253451</a>","short":"A. Cappellaro, G. Bighin, I. Cherepanov, M. Lemeshko, Journal of Chemical Physics 162 (2025).","chicago":"Cappellaro, Alberto, Giacomo Bighin, Igor Cherepanov, and Mikhail Lemeshko. “Environment-Limited Transfer of Angular Momentum in Bose Liquids.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0253451\">https://doi.org/10.1063/5.0253451</a>."},"publisher":"AIP Publishing","ddc":["530"],"title":"Environment-limited transfer of angular momentum in Bose liquids","corr_author":"1","date_updated":"2026-01-20T10:11:27Z","_id":"19276","month":"02","ec_funded":1,"pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article"},{"type":"journal_article","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"month":"02","_id":"19279","date_updated":"2025-09-30T10:44:48Z","corr_author":"1","ddc":["540"],"title":"Ionic association and Wien effect in 2D confined electrolytes","publisher":"AIP Publishing","citation":{"mla":"Toquer, Damien, et al. “Ionic Association and Wien Effect in 2D Confined Electrolytes.” <i>Journal of Chemical Physics</i>, vol. 162, no. 6, 064703, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0241949\">10.1063/5.0241949</a>.","apa":"Toquer, D., Bocquet, L., &#38; Robin, P. (2025). Ionic association and Wien effect in 2D confined electrolytes. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0241949\">https://doi.org/10.1063/5.0241949</a>","ista":"Toquer D, Bocquet L, Robin P. 2025. Ionic association and Wien effect in 2D confined electrolytes. Journal of Chemical Physics. 162(6), 064703.","ieee":"D. Toquer, L. Bocquet, and P. Robin, “Ionic association and Wien effect in 2D confined electrolytes,” <i>Journal of Chemical Physics</i>, vol. 162, no. 6. AIP Publishing, 2025.","ama":"Toquer D, Bocquet L, Robin P. Ionic association and Wien effect in 2D confined electrolytes. <i>Journal of Chemical Physics</i>. 2025;162(6). doi:<a href=\"https://doi.org/10.1063/5.0241949\">10.1063/5.0241949</a>","short":"D. Toquer, L. Bocquet, P. Robin, Journal of Chemical Physics 162 (2025).","chicago":"Toquer, Damien, Lydéric Bocquet, and Paul Robin. “Ionic Association and Wien Effect in 2D Confined Electrolytes.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0241949\">https://doi.org/10.1063/5.0241949</a>."},"oa":1,"intvolume":"       162","department":[{"_id":"EdHa"}],"arxiv":1,"publication_status":"published","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"has_accepted_license":"1","volume":162,"scopus_import":"1","doi":"10.1063/5.0241949","oa_version":"Published Version","day":"14","quality_controlled":"1","author":[{"first_name":"Damien","full_name":"Toquer, Damien","last_name":"Toquer"},{"last_name":"Bocquet","first_name":"Lydéric","full_name":"Bocquet, Lydéric"},{"first_name":"Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","orcid":"0000-0002-5728-9189","full_name":"Robin, Paul","last_name":"Robin"}],"issue":"6","article_number":"064703","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"year":"2025","isi":1,"publication":"Journal of Chemical Physics","language":[{"iso":"eng"}],"acknowledgement":"The authors thank B. Coquinot and G. Monet for fruitful discussions. L.B. acknowledges support from ERC-Synergy Grant Agreement No. 101071937, n-AQUA. P.R. acknowledges support from the European Union’s Horizon 2020 research and innovation program under Marie Sklodowska-Curie Grant Agreement No. 101034413.","file_date_updated":"2025-03-04T10:29:36Z","date_created":"2025-03-02T23:01:52Z","date_published":"2025-02-14T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","status":"public","OA_place":"publisher","article_type":"original","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"isi":["001421300300001"],"pmid":["39932241"],"arxiv":["2410.03316"]},"file":[{"file_name":"2025_JourChemicalPhysics_Toquer.pdf","checksum":"c9008c2c50c917673aa588f75acbcb40","date_created":"2025-03-04T10:29:36Z","relation":"main_file","date_updated":"2025-03-04T10:29:36Z","file_size":5807062,"file_id":"19290","success":1,"access_level":"open_access","creator":"dernst","content_type":"application/pdf"}],"OA_type":"hybrid","abstract":[{"text":"Recent experimental advances in nanofluidics have allowed to explore ion transport across molecular-scale pores, in particular, for iontronic applications. Two-dimensional nanochannels—in which a single molecular layer of electrolyte is confined between solid walls—constitute a unique platform to investigate fluid and ion transport in extreme confinement, highlighting unconventional transport properties. In this work, we study ionic association in 2D nanochannels, and its consequences on non-linear ionic transport, using both molecular dynamics simulations and analytical theory. We show that under sufficient confinement, ions assemble into pairs or larger clusters in a process analogous to a Kosterlitz–Thouless transition, here modified by the dielectric confinement. We further show that the breaking of pairs results in an electric-field dependent conduction, a mechanism usually known as the second Wien effect. However the 2D nature of the system results in non-universal, temperature-dependent, scaling of the conductivity with electric field, leading to ionic coulomb blockade in some regimes. A 2D generalization of the Onsager theory fully accounts for the non-linear transport. These results suggest ways to exploit electrostatic interactions between ions to build new nanofluidic devices.","lang":"eng"}]},{"pmid":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","ddc":["000"],"title":"How local is “local”? Deep learning reveals locality of the induced magnetic field of polycyclic aromatic hydrocarbons","corr_author":"1","_id":"19595","date_updated":"2025-09-30T12:06:51Z","month":"04","department":[{"_id":"AlBr"}],"publication_status":"published","intvolume":"       162","citation":{"chicago":"Davidson, Yair, Aviad Philipp, Sabyasachi Chakraborty, Alex M. Bronstein, and Renana Gershoni-Poranne. “How Local Is ‘Local’? Deep Learning Reveals Locality of the Induced Magnetic Field of Polycyclic Aromatic Hydrocarbons.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0257558\">https://doi.org/10.1063/5.0257558</a>.","short":"Y. Davidson, A. Philipp, S. Chakraborty, A.M. Bronstein, R. Gershoni-Poranne, Journal of Chemical Physics 162 (2025).","ama":"Davidson Y, Philipp A, Chakraborty S, Bronstein AM, Gershoni-Poranne R. How local is “local”? Deep learning reveals locality of the induced magnetic field of polycyclic aromatic hydrocarbons. <i>Journal of Chemical Physics</i>. 2025;162(14). doi:<a href=\"https://doi.org/10.1063/5.0257558\">10.1063/5.0257558</a>","mla":"Davidson, Yair, et al. “How Local Is ‘Local’? Deep Learning Reveals Locality of the Induced Magnetic Field of Polycyclic Aromatic Hydrocarbons.” <i>Journal of Chemical Physics</i>, vol. 162, no. 14, 144101, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0257558\">10.1063/5.0257558</a>.","ieee":"Y. Davidson, A. Philipp, S. Chakraborty, A. M. Bronstein, and R. Gershoni-Poranne, “How local is ‘local’? Deep learning reveals locality of the induced magnetic field of polycyclic aromatic hydrocarbons,” <i>Journal of Chemical Physics</i>, vol. 162, no. 14. AIP Publishing, 2025.","ista":"Davidson Y, Philipp A, Chakraborty S, Bronstein AM, Gershoni-Poranne R. 2025. How local is “local”? Deep learning reveals locality of the induced magnetic field of polycyclic aromatic hydrocarbons. Journal of Chemical Physics. 162(14), 144101.","apa":"Davidson, Y., Philipp, A., Chakraborty, S., Bronstein, A. M., &#38; Gershoni-Poranne, R. (2025). How local is “local”? Deep learning reveals locality of the induced magnetic field of polycyclic aromatic hydrocarbons. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0257558\">https://doi.org/10.1063/5.0257558</a>"},"oa":1,"publisher":"AIP Publishing","doi":"10.1063/5.0257558","oa_version":"Published Version","day":"14","scopus_import":"1","volume":162,"has_accepted_license":"1","project":[{"grant_number":"863839","name":"Acoustics-based drone navigation and interaction","_id":"92f4a086-16d5-11f0-9cad-c929f5c58b0c"}],"author":[{"full_name":"Davidson, Yair","first_name":"Yair","last_name":"Davidson"},{"last_name":"Philipp","full_name":"Philipp, Aviad","first_name":"Aviad"},{"first_name":"Sabyasachi","full_name":"Chakraborty, Sabyasachi","last_name":"Chakraborty"},{"orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein"},{"full_name":"Gershoni-Poranne, Renana","first_name":"Renana","last_name":"Gershoni-Poranne"}],"issue":"14","article_number":"144101","quality_controlled":"1","file_date_updated":"2025-04-22T09:27:43Z","acknowledgement":"The authors express their gratitude to Professor Dr. Peter Chen for his continued support. The authors acknowledge the Branco Weiss Fellowship for supporting this research as part of a Society in Science grant and the Israel Science Foundation for financial support (Grant No. 1745/23 to R.G.-P.). R.G.-P. is a Branco Weiss Fellow, a Horev Fellow, and an Alon Scholarship recipient. A.M.B. was supported by the ERC StG EARS and the Israeli Science Foundation.","year":"2025","isi":1,"language":[{"iso":"eng"}],"publication":"Journal of Chemical Physics","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"article_type":"original","license":"https://creativecommons.org/licenses/by-nc/4.0/","external_id":{"pmid":["40197568"],"isi":["001466311300030"]},"related_material":{"link":[{"url":"https://gitlab.com/porannegroup/magnetic_locality","relation":"software"}]},"OA_place":"publisher","status":"public","date_created":"2025-04-20T22:01:28Z","date_published":"2025-04-14T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","OA_type":"hybrid","abstract":[{"lang":"eng","text":"We investigate the locality of magnetic response in polycyclic aromatic molecules using a novel deep-learning approach. Our method employs graph neural networks (GNNs) with a graph-of-rings representation to predict nucleus independent chemical shifts (NICS) in the space around the molecule. We train a series of models, each time reducing the size of the largest molecules used in training. The accuracy of prediction remains high (MAE < 0.5 ppm), even when training the model only on molecules with up to four rings, thus providing strong evidence for the locality of magnetic response. To overcome the known problem of generalization of GNNs, we implement a k-hop expansion strategy and succeed in achieving accurate predictions for molecules with up to 15 rings (almost 4 times the size of the largest training example). Our findings have implications for understanding the magnetic response in complex molecules and demonstrate a promising approach to overcoming GNN scalability limitations. Furthermore, the trained models enable rapid characterization, without the need for more expensive DFT calculations."}],"file":[{"date_created":"2025-04-22T09:27:43Z","checksum":"20a31a4c506b52de863bab7d3ff989ef","file_name":"2025_JourChemicalPhysics_Davidson.pdf","relation":"main_file","file_id":"19606","file_size":7812182,"date_updated":"2025-04-22T09:27:43Z","content_type":"application/pdf","access_level":"open_access","creator":"dernst","success":1}]},{"doi":"10.1063/5.0188215","oa_version":"Published Version","day":"14","volume":160,"has_accepted_license":"1","scopus_import":"1","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"department":[{"_id":"EdHa"}],"publication_status":"published","arxiv":1,"intvolume":"       160","citation":{"short":"P. Robin, Journal of Chemical Physics 160 (2024).","ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. <i>Journal of Chemical Physics</i>. 2024;160(6). doi:<a href=\"https://doi.org/10.1063/5.0188215\">10.1063/5.0188215</a>","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0188215\">https://doi.org/10.1063/5.0188215</a>.","mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” <i>Journal of Chemical Physics</i>, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0188215\">10.1063/5.0188215</a>.","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” <i>Journal of Chemical Physics</i>, vol. 160, no. 6. AIP Publishing, 2024.","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503.","apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0188215\">https://doi.org/10.1063/5.0188215</a>"},"oa":1,"publisher":"AIP Publishing","ddc":["540"],"title":"Correlation-induced viscous dissipation in concentrated electrolytes","corr_author":"1","_id":"15024","date_updated":"2025-09-04T12:07:33Z","month":"02","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"type":"journal_article","abstract":[{"lang":"eng","text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions."}],"file":[{"relation":"main_file","date_created":"2024-02-27T08:12:52Z","file_name":"2024_JourChemicalPhysics_Robin.pdf","checksum":"0a5e0ae70849bce674466fc054390ec0","content_type":"application/pdf","success":1,"creator":"dernst","access_level":"open_access","file_id":"15034","date_updated":"2024-02-27T08:12:52Z","file_size":5452738}],"article_type":"original","external_id":{"arxiv":["2311.11784"],"pmid":["38349632"],"isi":["001161104900003"]},"status":"public","date_created":"2024-02-25T23:00:55Z","date_published":"2024-02-14T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-02-27T08:12:52Z","acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","language":[{"iso":"eng"}],"publication":"Journal of Chemical Physics","isi":1,"year":"2024","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"author":[{"last_name":"Robin","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","first_name":"Paul","orcid":"0000-0002-5728-9189","full_name":"Robin, Paul"}],"issue":"6","article_number":"064503","quality_controlled":"1"},{"related_material":{"link":[{"url":"https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0","relation":"software"}]},"external_id":{"isi":["001281819100016"],"pmid":["39007379"],"arxiv":["2405.02216"]},"article_type":"original","article_processing_charge":"No","date_created":"2024-07-21T22:01:00Z","date_published":"2024-07-14T00:00:00Z","status":"public","abstract":[{"text":"An azeotrope is a constant boiling point mixture, and its behavior is important for fluid separation processes. Predicting azeotropes from atomistic simulations is difficult due to the complexities and convergence problems of Monte Carlo and free-energy perturbation techniques. Here, we present a methodology for predicting the azeotropes of binary mixtures, which computes the compositional dependence of chemical potentials from molecular dynamics simulations using the S0 method and employs experimental boiling point and vaporization enthalpy data. Using this methodology, we reproduce the azeotropes, or lack thereof, in five case studies, including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and acetone/chloroform mixtures. We find that it is crucial to use the experimental boiling point and vaporization enthalpy for reliable azeotrope predictions, as empirical force fields are not accurate enough for these quantities. Finally, we use regular solution models to rationalize the azeotropes and reveal that they tend to form when the mixture components have similar boiling points and strong interactions.","lang":"eng"}],"quality_controlled":"1","article_number":"034111","author":[{"id":"8dff9c62-32b0-11ee-9fa8-fc73025e10f3","first_name":"Xiaoyu","full_name":"Wang, Xiaoyu","last_name":"Wang"},{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng"}],"issue":"3","acknowledgement":"B.C. thanks Alessandro Laio, who introduced the phenomenon of azeotrope and suggested using the S0 method to compute it. B.C. and X.W. thank Felix Wodaczek for the insightful comments and suggestions on the manuscript. B.C. and X.W. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service, funded by EPSRC Tier-2 capital (Grant No. EP/P020259/1).","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"language":[{"iso":"eng"}],"isi":1,"year":"2024","publication":"Journal of Chemical Physics","intvolume":"       161","arxiv":1,"publication_status":"published","department":[{"_id":"BiCh"},{"_id":"GradSch"}],"publisher":"AIP Publishing","oa":1,"citation":{"ama":"Wang X, Cheng B. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. <i>Journal of Chemical Physics</i>. 2024;161(3). doi:<a href=\"https://doi.org/10.1063/5.0217232\">10.1063/5.0217232</a>","short":"X. Wang, B. Cheng, Journal of Chemical Physics 161 (2024).","chicago":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0217232\">https://doi.org/10.1063/5.0217232</a>.","mla":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” <i>Journal of Chemical Physics</i>, vol. 161, no. 3, 034111, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0217232\">10.1063/5.0217232</a>.","apa":"Wang, X., &#38; Cheng, B. (2024). Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0217232\">https://doi.org/10.1063/5.0217232</a>","ieee":"X. Wang and B. Cheng, “Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures,” <i>Journal of Chemical Physics</i>, vol. 161, no. 3. AIP Publishing, 2024.","ista":"Wang X, Cheng B. 2024. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. 161(3), 034111."},"oa_version":"Preprint","day":"14","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.02216","open_access":"1"}],"doi":"10.1063/5.0217232","scopus_import":"1","volume":161,"type":"journal_article","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","title":"Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures","month":"07","date_updated":"2025-09-08T08:26:09Z","_id":"17278"},{"external_id":{"isi":["001133333600011"],"pmid":["37694742"],"arxiv":["2306.17592"]},"article_type":"original","status":"public","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-09-11T00:00:00Z","date_created":"2023-09-13T09:25:09Z","abstract":[{"text":"We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.","lang":"eng"}],"file":[{"relation":"main_file","date_created":"2023-09-13T09:34:20Z","file_name":"104103_1_5.0165806.pdf","checksum":"507ab65ab29e2c987c94cabad7c5370b","content_type":"application/pdf","success":1,"access_level":"open_access","creator":"acappell","file_id":"14322","date_updated":"2023-09-13T09:34:20Z","file_size":5749653}],"article_number":"104103","issue":"10","author":[{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed","full_name":"Al Hyder, Ragheed","last_name":"Al Hyder"},{"first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359","last_name":"Cappellaro"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev"}],"quality_controlled":"1","file_date_updated":"2023-09-13T09:34:20Z","acknowledgement":"We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot.","language":[{"iso":"eng"}],"year":"2023","publication":"The Journal of Chemical Physics","isi":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publication_status":"published","arxiv":1,"department":[{"_id":"MiLe"}],"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"intvolume":"       159","oa":1,"citation":{"mla":"Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>.","ista":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103.","apa":"Al Hyder, R., Cappellaro, A., Lemeshko, M., &#38; Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>","ieee":"R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10. AIP Publishing, 2023.","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023).","ama":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. 2023;159(10). doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>","chicago":"Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>."},"publisher":"AIP Publishing","oa_version":"Published Version","day":"11","doi":"10.1063/5.0165806","has_accepted_license":"1","volume":159,"scopus_import":"1","project":[{"grant_number":"101062862","name":"Non-Equilibrium Field Theory of Molecular Rotations","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"type":"journal_article","ddc":["530"],"title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","corr_author":"1","date_updated":"2025-09-09T12:57:42Z","_id":"14321","month":"09"},{"citation":{"ieee":"A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals,” <i>Journal of Chemical Physics</i>, vol. 159, no. 18. AIP Publishing, 2023.","ista":"Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 159(18), 184110.","apa":"Reinhardt, A., Chew, P. Y., &#38; Cheng, B. (2023). A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>","mla":"Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>, vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>.","short":"A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).","ama":"Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. 2023;159(18). doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>","chicago":"Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>."},"oa":1,"publisher":"AIP Publishing","department":[{"_id":"BiCh"}],"publication_status":"published","arxiv":1,"intvolume":"       159","volume":159,"has_accepted_license":"1","scopus_import":"1","doi":"10.1063/5.0173341","oa_version":"Published Version","day":"14","pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","_id":"14603","date_updated":"2025-09-09T13:32:46Z","month":"11","title":"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals","ddc":["530","540"],"corr_author":"1","status":"public","date_created":"2023-11-26T23:00:54Z","date_published":"2023-11-14T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","article_type":"original","external_id":{"arxiv":["2308.10886"],"pmid":["37962445"],"isi":["001137066700001"]},"related_material":{"record":[{"relation":"research_data","id":"14619","status":"public"}]},"abstract":[{"lang":"eng","text":"Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances."}],"file":[{"file_id":"14620","date_updated":"2023-11-28T08:39:06Z","file_size":6276059,"content_type":"application/pdf","success":1,"creator":"dernst","access_level":"open_access","date_created":"2023-11-28T08:39:06Z","file_name":"2023_JourChemicalPhysics_Reinhardt.pdf","checksum":"f668ee0d07096eef81159d05bc27aabc","relation":"main_file"}],"author":[{"last_name":"Reinhardt","full_name":"Reinhardt, Aleks","first_name":"Aleks"},{"last_name":"Chew","first_name":"Pin Yu","full_name":"Chew, Pin Yu"},{"last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"issue":"18","article_number":"184110","quality_controlled":"1","language":[{"iso":"eng"}],"year":"2023","publication":"Journal of Chemical Physics","isi":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"acknowledgement":"A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.","file_date_updated":"2023-11-28T08:39:06Z"},{"intvolume":"       158","department":[{"_id":"AnSa"}],"publication_status":"published","arxiv":1,"publisher":"American Institute of Physics","citation":{"ama":"Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. <i>Journal of Chemical Physics</i>. 2023;158(7). doi:<a href=\"https://doi.org/10.1063/5.0134271\">10.1063/5.0134271</a>","short":"V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).","chicago":"Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” <i>Journal of Chemical Physics</i>. American Institute of Physics, 2023. <a href=\"https://doi.org/10.1063/5.0134271\">https://doi.org/10.1063/5.0134271</a>.","ista":"Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.","ieee":"V. Sorichetti <i>et al.</i>, “Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks,” <i>Journal of Chemical Physics</i>, vol. 158, no. 7. American Institute of Physics, 2023.","apa":"Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli, E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. <i>Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0134271\">https://doi.org/10.1063/5.0134271</a>","mla":"Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” <i>Journal of Chemical Physics</i>, vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:<a href=\"https://doi.org/10.1063/5.0134271\">10.1063/5.0134271</a>."},"oa":1,"doi":"10.1063/5.0134271","day":"21","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04810","open_access":"1"}],"oa_version":"Preprint","volume":158,"scopus_import":"1","type":"journal_article","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks","month":"02","_id":"12705","date_updated":"2023-10-03T11:31:51Z","article_type":"original","external_id":{"arxiv":["2211.04810"],"isi":["000936943800002"],"pmid":["36813705"]},"date_created":"2023-03-05T23:01:05Z","date_published":"2023-02-21T00:00:00Z","article_processing_charge":"No","status":"public","abstract":[{"text":"The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.","lang":"eng"}],"quality_controlled":"1","issue":"7","author":[{"last_name":"Sorichetti","orcid":"0000-0002-9645-6576","full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","first_name":"Valerio"},{"full_name":"Ninarello, Andrea","first_name":"Andrea","last_name":"Ninarello"},{"last_name":"Ruiz-Franco","first_name":"José","full_name":"Ruiz-Franco, José"},{"last_name":"Hugouvieux","first_name":"Virginie","full_name":"Hugouvieux, Virginie"},{"last_name":"Zaccarelli","first_name":"Emanuela","full_name":"Zaccarelli, Emanuela"},{"full_name":"Micheletti, Cristian","first_name":"Cristian","last_name":"Micheletti"},{"last_name":"Kob","first_name":"Walter","full_name":"Kob, Walter"},{"last_name":"Rovigatti","full_name":"Rovigatti, Lorenzo","first_name":"Lorenzo"}],"article_number":"074905","acknowledgement":"We thank Michael Lang for helpful discussions. We acknowledge financial support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC) and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir” French Government program, managed by the French National Research Agency (ANR). W.K. is a senior member of the Institut Universitaire de France.","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"language":[{"iso":"eng"}],"year":"2023","publication":"Journal of Chemical Physics","isi":1},{"file":[{"relation":"main_file","date_created":"2023-01-30T09:07:00Z","file_name":"2022_JourChemPhysics_Cheng.pdf","checksum":"b0915b706568a663a9a372fca24adf35","content_type":"application/pdf","success":1,"access_level":"open_access","creator":"dernst","file_id":"12441","date_updated":"2023-01-30T09:07:00Z","file_size":4402384}],"abstract":[{"text":"The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures, a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. ","lang":"eng"}],"related_material":{"link":[{"url":"https://github.com/ BingqingCheng/S0","relation":"software"}]},"article_type":"original","external_id":{"isi":["000862856000003"],"pmid":["36182422"]},"date_created":"2023-01-16T09:56:20Z","date_published":"2022-09-30T00:00:00Z","article_processing_charge":"No","status":"public","acknowledgement":"I thank Daan Frenkel for providing feedback on an early draft and for stimulating discussions, Debashish Mukherji and Robinson Cortes-Huerto for sharing the trajectories for urea–water mixtures, and Aleks Reinhardt for useful suggestions on the manuscript.","file_date_updated":"2023-01-30T09:07:00Z","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publication":"The Journal of Chemical Physics","year":"2022","language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","issue":"12","author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng"}],"article_number":"121101","doi":"10.1063/5.0107059","day":"30","oa_version":"Published Version","has_accepted_license":"1","volume":157,"scopus_import":"1","intvolume":"       157","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"department":[{"_id":"BiCh"}],"publication_status":"published","publisher":"AIP Publishing","citation":{"chicago":"Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure Factors.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0107059\">https://doi.org/10.1063/5.0107059</a>.","ama":"Cheng B. Computing chemical potentials of solutions from structure factors. <i>The Journal of Chemical Physics</i>. 2022;157(12). doi:<a href=\"https://doi.org/10.1063/5.0107059\">10.1063/5.0107059</a>","short":"B. Cheng, The Journal of Chemical Physics 157 (2022).","apa":"Cheng, B. (2022). Computing chemical potentials of solutions from structure factors. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0107059\">https://doi.org/10.1063/5.0107059</a>","ista":"Cheng B. 2022. Computing chemical potentials of solutions from structure factors. The Journal of Chemical Physics. 157(12), 121101.","ieee":"B. Cheng, “Computing chemical potentials of solutions from structure factors,” <i>The Journal of Chemical Physics</i>, vol. 157, no. 12. AIP Publishing, 2022.","mla":"Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure Factors.” <i>The Journal of Chemical Physics</i>, vol. 157, no. 12, 121101, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0107059\">10.1063/5.0107059</a>."},"oa":1,"corr_author":"1","ddc":["530","540"],"title":"Computing chemical potentials of solutions from structure factors","month":"09","_id":"12249","date_updated":"2025-06-11T13:41:59Z","type":"journal_article","pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"acknowledgement":"The authors thank Longhui Zeng and Xiaolei Su (Yale University) for bringing the topic to their attention and for useful comments. This work has received funding from the European Research Council under the European Union’s Horizon\r\n2020 research and innovation program (ERC Grant No. 802960 and Marie Skłodowska-Curie Grant No. 101034413). The authors are grateful to the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by EPSRC (Grant Nos. EP/P020194/1 and EP/T022213/1). The authors acknowledge support from ISTA and from the Royal Society (Grant No. UF160266).","file_date_updated":"2022-05-23T07:45:33Z","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","year":"2022","isi":1,"quality_controlled":"1","article_number":"194902","author":[{"first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","last_name":"Palaia"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"}],"issue":"19","file":[{"file_id":"11405","date_updated":"2022-05-23T07:45:33Z","file_size":6387208,"content_type":"application/pdf","success":1,"access_level":"open_access","creator":"dernst","date_created":"2022-05-23T07:45:33Z","checksum":"7fada58059676a4bb0944b82247af740","file_name":"2022_JourChemPhysics_Palaia.pdf","relation":"main_file"}],"abstract":[{"text":"By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.","lang":"eng"}],"external_id":{"isi":["000797236000004"],"pmid":["35597653"]},"article_type":"original","article_processing_charge":"No","date_published":"2022-05-16T00:00:00Z","date_created":"2022-05-22T17:04:48Z","status":"public","corr_author":"1","title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","ddc":["540"],"month":"05","date_updated":"2025-06-11T14:00:32Z","_id":"11400","ec_funded":1,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"pmid":1,"day":"16","oa_version":"Published Version","doi":"10.1063/5.0087769","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"has_accepted_license":"1","scopus_import":"1","volume":156,"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"intvolume":"       156","publication_status":"published","department":[{"_id":"AnSa"}],"publisher":"AIP Publishing","oa":1,"citation":{"short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022).","ama":"Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. 2022;156(19). doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>","chicago":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>.","mla":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>.","apa":"Palaia, I., &#38; Šarić, A. (2022). Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>","ieee":"I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary mixtures with specific interactions,” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19. AIP Publishing, 2022.","ista":"Palaia I, Šarić A. 2022. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. 156(19), 194902."}},{"month":"09","_id":"17907","date_updated":"2024-12-10T10:46:25Z","title":"Tight-binding analysis of helical states in carbyne","type":"journal_article","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","volume":153,"doi":"10.1063/5.0021146","oa_version":"None","day":"28","publisher":"AIP Publishing","citation":{"chicago":"Gunasekaran, Suman, and Latha Venkataraman. “Tight-Binding Analysis of Helical States in Carbyne.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/5.0021146\">https://doi.org/10.1063/5.0021146</a>.","ama":"Gunasekaran S, Venkataraman L. Tight-binding analysis of helical states in carbyne. <i>The Journal of Chemical Physics</i>. 2020;153(12). doi:<a href=\"https://doi.org/10.1063/5.0021146\">10.1063/5.0021146</a>","short":"S. Gunasekaran, L. Venkataraman, The Journal of Chemical Physics 153 (2020).","ista":"Gunasekaran S, Venkataraman L. 2020. Tight-binding analysis of helical states in carbyne. The Journal of Chemical Physics. 153(12), 124304.","apa":"Gunasekaran, S., &#38; Venkataraman, L. (2020). Tight-binding analysis of helical states in carbyne. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0021146\">https://doi.org/10.1063/5.0021146</a>","ieee":"S. Gunasekaran and L. Venkataraman, “Tight-binding analysis of helical states in carbyne,” <i>The Journal of Chemical Physics</i>, vol. 153, no. 12. AIP Publishing, 2020.","mla":"Gunasekaran, Suman, and Latha Venkataraman. “Tight-Binding Analysis of Helical States in Carbyne.” <i>The Journal of Chemical Physics</i>, vol. 153, no. 12, 124304, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/5.0021146\">10.1063/5.0021146</a>."},"intvolume":"       153","publication_status":"published","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"extern":"1","year":"2020","language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","quality_controlled":"1","issue":"12","author":[{"full_name":"Gunasekaran, Suman","first_name":"Suman","last_name":"Gunasekaran"},{"last_name":"Venkataraman","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089"}],"article_number":"124304 ","OA_type":"closed access","abstract":[{"lang":"eng","text":"Carbyne is a linear allotrope of carbon that is composed of a chain of sp-hybridized carbon atoms. Through appropriate engineering of the chain termination, carbyne can harbor helical states where the π-electron delocalization twists along the axis of the chain. Herein, we present a comprehensive analysis of these helical states at the tight-binding level. We demonstrate that, in general, the molecular orbital coefficients of the helical states trace out an ellipse, in analogy to elliptically polarized light. Helical states can be realized in a model, inspired by the structure of cumulene, which considers a chain terminated by sp2-hybridized atoms oriented at a nontrivial dihedral angle. We provide a complete analytic solution for this model. Additionally, we present a variation of the model that yields perfect helical states that trace out a circle as opposed to an ellipse. Our results provide a deeper understanding of helical states and lay a foundation for more advanced levels of theory."}],"date_published":"2020-09-28T00:00:00Z","date_created":"2024-09-09T07:17:20Z","article_processing_charge":"No","status":"public","article_type":"original","external_id":{"pmid":["33003709"]}},{"article_number":"044103","issue":"4","author":[{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng"},{"last_name":"Ceriotti","first_name":"Michele","full_name":"Ceriotti, Michele"},{"last_name":"Tribello","full_name":"Tribello, Gareth A.","first_name":"Gareth A."}],"quality_controlled":"1","publication":"The Journal of Chemical Physics","year":"2020","language":[{"iso":"eng"}],"extern":"1","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"external_id":{"pmid":["32007057"],"arxiv":["1910.13481"]},"article_type":"original","status":"public","article_processing_charge":"No","date_created":"2021-07-15T07:22:24Z","date_published":"2020-01-31T00:00:00Z","abstract":[{"lang":"eng","text":"Macroscopic models of nucleation provide powerful tools for understanding activated phase transition processes. These models do not provide atomistic insights and can thus sometimes lack material-specific descriptions. Here, we provide a comprehensive framework for constructing a continuum picture from an atomistic simulation of homogeneous nucleation. We use this framework to determine the equilibrium shape of the solid nucleus that forms inside bulk liquid for a Lennard-Jones potential. From this shape, we then extract the anisotropy of the solid-liquid interfacial free energy, by performing a reverse Wulff construction in the space of spherical harmonic expansions. We find that the shape of the nucleus is nearly spherical and that its anisotropy can be perfectly described using classical models."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","pmid":1,"type":"journal_article","title":"Classical nucleation theory predicts the shape of the nucleus in homogeneous solidification","date_updated":"2023-02-23T14:03:55Z","_id":"9658","month":"01","publication_status":"published","arxiv":1,"intvolume":"       152","oa":1,"citation":{"chicago":"Cheng, Bingqing, Michele Ceriotti, and Gareth A. Tribello. “Classical Nucleation Theory Predicts the Shape of the Nucleus in Homogeneous Solidification.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/1.5134461\">https://doi.org/10.1063/1.5134461</a>.","short":"B. Cheng, M. Ceriotti, G.A. Tribello, The Journal of Chemical Physics 152 (2020).","ama":"Cheng B, Ceriotti M, Tribello GA. Classical nucleation theory predicts the shape of the nucleus in homogeneous solidification. <i>The Journal of Chemical Physics</i>. 2020;152(4). doi:<a href=\"https://doi.org/10.1063/1.5134461\">10.1063/1.5134461</a>","mla":"Cheng, Bingqing, et al. “Classical Nucleation Theory Predicts the Shape of the Nucleus in Homogeneous Solidification.” <i>The Journal of Chemical Physics</i>, vol. 152, no. 4, 044103, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/1.5134461\">10.1063/1.5134461</a>.","ista":"Cheng B, Ceriotti M, Tribello GA. 2020. Classical nucleation theory predicts the shape of the nucleus in homogeneous solidification. The Journal of Chemical Physics. 152(4), 044103.","apa":"Cheng, B., Ceriotti, M., &#38; Tribello, G. A. (2020). Classical nucleation theory predicts the shape of the nucleus in homogeneous solidification. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5134461\">https://doi.org/10.1063/1.5134461</a>","ieee":"B. Cheng, M. Ceriotti, and G. A. Tribello, “Classical nucleation theory predicts the shape of the nucleus in homogeneous solidification,” <i>The Journal of Chemical Physics</i>, vol. 152, no. 4. AIP Publishing, 2020."},"publisher":"AIP Publishing","day":"31","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://pure.qub.ac.uk/en/publications/classical-nucleation-theory-predicts-the-shape-of-the-nucleus-in-homogeneous-solidification(56af848b-eee8-4e9b-93cf-667373e4a49b).html"}],"doi":"10.1063/1.5134461","scopus_import":"1","volume":152},{"oa":1,"citation":{"chicago":"Li, Xiang, Enderalp Yakaboylu, Giacomo Bighin, Richard Schmidt, Mikhail Lemeshko, and Andreas Deuchert. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/1.5144759\">https://doi.org/10.1063/1.5144759</a>.","ama":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. Intermolecular forces and correlations mediated by a phonon bath. <i>The Journal of Chemical Physics</i>. 2020;152(16). doi:<a href=\"https://doi.org/10.1063/1.5144759\">10.1063/1.5144759</a>","short":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The Journal of Chemical Physics 152 (2020).","mla":"Li, Xiang, et al. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” <i>The Journal of Chemical Physics</i>, vol. 152, no. 16, 164302, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/1.5144759\">10.1063/1.5144759</a>.","ista":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. 2020. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 152(16), 164302.","ieee":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, and A. Deuchert, “Intermolecular forces and correlations mediated by a phonon bath,” <i>The Journal of Chemical Physics</i>, vol. 152, no. 16. AIP Publishing, 2020.","apa":"Li, X., Yakaboylu, E., Bighin, G., Schmidt, R., Lemeshko, M., &#38; Deuchert, A. (2020). Intermolecular forces and correlations mediated by a phonon bath. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5144759\">https://doi.org/10.1063/1.5144759</a>"},"publisher":"AIP Publishing","arxiv":1,"publication_status":"published","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"intvolume":"       152","volume":152,"project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02641","name":"A path-integral approach to composite impurities"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.02658"}],"oa_version":"Preprint","day":"27","doi":"10.1063/1.5144759","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"type":"journal_article","ec_funded":1,"date_updated":"2026-04-08T07:26:09Z","_id":"8587","month":"04","title":"Intermolecular forces and correlations mediated by a phonon bath","corr_author":"1","status":"public","article_processing_charge":"No","date_created":"2020-09-30T10:33:17Z","date_published":"2020-04-27T00:00:00Z","external_id":{"arxiv":["1912.02658"],"isi":["000530448300001"],"pmid":["32357791"]},"article_type":"original","related_material":{"record":[{"status":"public","id":"8958","relation":"dissertation_contains"}]},"abstract":[{"lang":"eng","text":"Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the effective interaction and the resulting correlations between two diatomic molecules immersed in a bath of bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system in different parameter regimes and apply several theoretical approaches to describe its properties. Using a Born–Oppenheimer approximation, we investigate the dependence of the effective intermolecular interaction on the rotational state of the two molecules. In the strong-coupling regime, a product-state ansatz shows that the molecules tend to have a strong alignment in the ground state. To investigate the system in the weak-coupling regime, we apply a one-phonon excitation variational ansatz, which allows us to access the energy spectrum. In comparison to the angulon quasiparticle, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. These features are proposed as an experimentally observable signature for the formation of the biangulon quasiparticle. Finally, by using products of single angulon and bare impurity wave functions as basis states, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"article_number":"164302","author":[{"id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","first_name":"Xiang","full_name":"Li, Xiang","last_name":"Li"},{"last_name":"Yakaboylu","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"},{"last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"},{"last_name":"Schmidt","first_name":"Richard","full_name":"Schmidt, Richard"},{"last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","last_name":"Deuchert"}],"issue":"16","quality_controlled":"1","year":"2020","isi":1,"language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"acknowledgement":"We are grateful to Areg Ghazaryan for valuable discussions. M.L. acknowledges support from the Austrian Science Fund (FWF) under Project No. P29902-N27 and from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No. M2461-N27. A.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the European Research Council (ERC) Grant Agreement No. 694227 and under the Marie Sklodowska-Curie Grant Agreement No. 836146. R.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2111 – 390814868."},{"title":"eGFRD in all dimensions","_id":"7422","date_updated":"2023-09-06T14:59:28Z","month":"02","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","doi":"10.1063/1.5064867","main_file_link":[{"url":"https://arxiv.org/abs/1708.09364","open_access":"1"}],"day":"07","oa_version":"Preprint","volume":150,"department":[{"_id":"GaTk"}],"arxiv":1,"publication_status":"published","intvolume":"       150","citation":{"ama":"Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. <i>The Journal of Chemical Physics</i>. 2019;150(5). doi:<a href=\"https://doi.org/10.1063/1.5064867\">10.1063/1.5064867</a>","short":"T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019).","chicago":"Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2019. <a href=\"https://doi.org/10.1063/1.5064867\">https://doi.org/10.1063/1.5064867</a>.","ista":"Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108.","apa":"Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5064867\">https://doi.org/10.1063/1.5064867</a>","ieee":"T. R. Sokolowski <i>et al.</i>, “eGFRD in all dimensions,” <i>The Journal of Chemical Physics</i>, vol. 150, no. 5. AIP Publishing, 2019.","mla":"Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” <i>The Journal of Chemical Physics</i>, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:<a href=\"https://doi.org/10.1063/1.5064867\">10.1063/1.5064867</a>."},"oa":1,"publisher":"AIP Publishing","isi":1,"year":"2019","publication":"The Journal of Chemical Physics","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"author":[{"full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski"},{"full_name":"Paijmans, Joris","first_name":"Joris","last_name":"Paijmans"},{"first_name":"Laurens","full_name":"Bossen, Laurens","last_name":"Bossen"},{"last_name":"Miedema","first_name":"Thomas","full_name":"Miedema, Thomas"},{"first_name":"Martijn","full_name":"Wehrens, Martijn","last_name":"Wehrens"},{"first_name":"Nils B.","full_name":"Becker, Nils B.","last_name":"Becker"},{"full_name":"Kaizu, Kazunari","first_name":"Kazunari","last_name":"Kaizu"},{"last_name":"Takahashi","first_name":"Koichi","full_name":"Takahashi, Koichi"},{"last_name":"Dogterom","first_name":"Marileen","full_name":"Dogterom, Marileen"},{"last_name":"ten Wolde","first_name":"Pieter Rein","full_name":"ten Wolde, Pieter Rein"}],"issue":"5","article_number":"054108","quality_controlled":"1","abstract":[{"text":"Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions.","lang":"eng"}],"article_type":"original","external_id":{"isi":["000458109300009"],"arxiv":["1708.09364"]},"status":"public","date_published":"2019-02-07T00:00:00Z","date_created":"2020-01-30T10:34:36Z","article_processing_charge":"No"},{"date_created":"2021-07-15T07:51:42Z","date_published":"2018-06-21T00:00:00Z","article_processing_charge":"No","status":"public","article_type":"original","external_id":{"arxiv":["1803.09140"],"pmid":["29935495"]},"abstract":[{"text":"The curvature dependence of interfacial free energy, which is crucial in quantitatively predicting nucleation kinetics and the stability of bubbles and droplets, is quantified by the Tolman length δ. For solid-liquid interfaces, however, δ has never been computed directly due to various theoretical and practical challenges. Here we perform a direct evaluation of the Tolman length from atomistic simulations of a solid-liquid planar interface in out-of-equilibrium conditions, by first computing the surface tension from the amplitude of thermal capillary fluctuations of a localized version of the Gibbs dividing surface and by then calculating how much the surface energy changes when it is defined relative to the equimolar dividing surface. We computed δ for a model potential, and found a good agreement with the values indirectly inferred from nucleation simulations. The agreement not only validates our approach but also suggests that the nucleation free energy of the system can be perfectly described using classical nucleation theory if the Tolman length is taken into account.","lang":"eng"}],"quality_controlled":"1","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng"},{"last_name":"Ceriotti","full_name":"Ceriotti, Michele","first_name":"Michele"}],"issue":"23","article_number":"231102","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"extern":"1","year":"2018","language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","publisher":"AIP Publishing","citation":{"ama":"Cheng B, Ceriotti M. Communication: Computing the Tolman length for solid-liquid interfaces. <i>The Journal of Chemical Physics</i>. 2018;148(23). doi:<a href=\"https://doi.org/10.1063/1.5038396\">10.1063/1.5038396</a>","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 148 (2018).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Communication: Computing the Tolman Length for Solid-Liquid Interfaces.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2018. <a href=\"https://doi.org/10.1063/1.5038396\">https://doi.org/10.1063/1.5038396</a>.","mla":"Cheng, Bingqing, and Michele Ceriotti. “Communication: Computing the Tolman Length for Solid-Liquid Interfaces.” <i>The Journal of Chemical Physics</i>, vol. 148, no. 23, 231102, AIP Publishing, 2018, doi:<a href=\"https://doi.org/10.1063/1.5038396\">10.1063/1.5038396</a>.","ista":"Cheng B, Ceriotti M. 2018. Communication: Computing the Tolman length for solid-liquid interfaces. The Journal of Chemical Physics. 148(23), 231102.","apa":"Cheng, B., &#38; Ceriotti, M. (2018). Communication: Computing the Tolman length for solid-liquid interfaces. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5038396\">https://doi.org/10.1063/1.5038396</a>","ieee":"B. Cheng and M. Ceriotti, “Communication: Computing the Tolman length for solid-liquid interfaces,” <i>The Journal of Chemical Physics</i>, vol. 148, no. 23. AIP Publishing, 2018."},"oa":1,"intvolume":"       148","publication_status":"published","arxiv":1,"volume":148,"scopus_import":"1","doi":"10.1063/1.5038396","day":"21","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/1.5038396"}],"oa_version":"Submitted Version","type":"journal_article","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","pmid":1,"month":"06","_id":"9659","date_updated":"2023-02-23T14:03:57Z","title":"Communication: Computing the Tolman length for solid-liquid interfaces"},{"intvolume":"       146","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"publication_status":"published","publisher":"AIP Publishing","citation":{"ama":"Baykusheva DR, Wörner HJ. Theory of attosecond delays in molecular photoionization. <i>The Journal of Chemical Physics</i>. 2017;146(12). doi:<a href=\"https://doi.org/10.1063/1.4977933\">10.1063/1.4977933</a>","short":"D.R. Baykusheva, H.J. Wörner, The Journal of Chemical Physics 146 (2017).","chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Theory of Attosecond Delays in Molecular Photoionization.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4977933\">https://doi.org/10.1063/1.4977933</a>.","ista":"Baykusheva DR, Wörner HJ. 2017. Theory of attosecond delays in molecular photoionization. The Journal of Chemical Physics. 146(12), 124306.","apa":"Baykusheva, D. R., &#38; Wörner, H. J. (2017). Theory of attosecond delays in molecular photoionization. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4977933\">https://doi.org/10.1063/1.4977933</a>","ieee":"D. R. Baykusheva and H. J. Wörner, “Theory of attosecond delays in molecular photoionization,” <i>The Journal of Chemical Physics</i>, vol. 146, no. 12. AIP Publishing, 2017.","mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Theory of Attosecond Delays in Molecular Photoionization.” <i>The Journal of Chemical Physics</i>, vol. 146, no. 12, 124306, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4977933\">10.1063/1.4977933</a>."},"doi":"10.1063/1.4977933","oa_version":"None","day":"28","scopus_import":"1","volume":146,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"title":"Theory of attosecond delays in molecular photoionization","month":"03","_id":"14006","date_updated":"2023-08-22T08:30:59Z","article_type":"original","external_id":{"pmid":["28388142"]},"date_created":"2023-08-10T06:36:19Z","date_published":"2017-03-28T00:00:00Z","article_processing_charge":"No","status":"public","abstract":[{"text":"We present a theoretical formalism for the calculation of attosecond delays in molecular photoionization. It is shown how delays relevant to one-photon-ionization, also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole matrix elements provided by molecular quantum scattering theory. These results are used to derive formulae for the delays measured by two-photon attosecond interferometry based on an attosecond pulse train and a dressing femtosecond infrared pulse. These effective delays are first expressed in the molecular frame where maximal information about the molecular photoionization dynamics is available. The effects of averaging over the emission direction of the electron and the molecular orientation are introduced analytically. We illustrate this general formalism for the case of two polyatomic molecules. N2O serves as an example of a polar linear molecule characterized by complex photoionization dynamics resulting from the presence of molecular shape resonances. H2O illustrates the case of a non-linear molecule with comparably simple photoionization dynamics resulting from a flat continuum. Our theory establishes the foundation for interpreting measurements of the photoionization dynamics of all molecules by attosecond metrology.","lang":"eng"}],"quality_controlled":"1","author":[{"last_name":"Baykusheva","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova"},{"last_name":"Wörner","first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob"}],"issue":"12","article_number":"124306","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"extern":"1","year":"2017","language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics"}]