[{"date_updated":"2024-02-27T08:16:06Z","year":"2024","citation":{"ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503.","short":"P. Robin, Journal of Chemical Physics 160 (2024).","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>.","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>.","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” <i>Journal of Chemical Physics</i>, vol. 160, no. 6. AIP Publishing, 2024.","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>","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>"},"external_id":{"arxiv":["2311.11784"],"pmid":["38349632"]},"arxiv":1,"doi":"10.1063/5.0188215","day":"14","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."}],"volume":160,"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.","ddc":["540"],"pmid":1,"_id":"15024","scopus_import":"1","author":[{"last_name":"Robin","first_name":"Paul","full_name":"Robin, Paul","orcid":"0000-0002-5728-9189","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d"}],"issue":"6","publication_status":"published","department":[{"_id":"EdHa"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2024-02-25T23:00:55Z","title":"Correlation-induced viscous dissipation in concentrated electrolytes","intvolume":"       160","ec_funded":1,"quality_controlled":"1","file_date_updated":"2024-02-27T08:12:52Z","publisher":"AIP Publishing","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2024-02-14T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"oa":1,"file":[{"success":1,"access_level":"open_access","relation":"main_file","file_id":"15034","creator":"dernst","date_created":"2024-02-27T08:12:52Z","file_size":5452738,"checksum":"0a5e0ae70849bce674466fc054390ec0","date_updated":"2024-02-27T08:12:52Z","file_name":"2024_JourChemicalPhysics_Robin.pdf","content_type":"application/pdf"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Chemical Physics","has_accepted_license":"1","oa_version":"Published Version","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"month":"02","article_number":"064503","language":[{"iso":"eng"}]},{"ddc":["530"],"volume":159,"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.","abstract":[{"lang":"eng","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."}],"day":"11","doi":"10.1063/5.0165806","arxiv":1,"external_id":{"arxiv":["2306.17592"],"pmid":["37694742"]},"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>.","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023).","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.","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>","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.","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>."},"year":"2023","date_updated":"2023-09-20T09:48:12Z","article_type":"original","publisher":"AIP Publishing","file_date_updated":"2023-09-13T09:34:20Z","quality_controlled":"1","ec_funded":1,"intvolume":"       159","title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","date_created":"2023-09-13T09:25:09Z","department":[{"_id":"MiLe"}],"article_processing_charge":"Yes (in subscription journal)","publication_status":"published","issue":"10","author":[{"first_name":"Ragheed","last_name":"Al Hyder","full_name":"Al Hyder, Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e"},{"id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","first_name":"Alberto","full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"scopus_import":"1","pmid":1,"_id":"14321","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-09-13T09:34:20Z","file_name":"104103_1_5.0165806.pdf","content_type":"application/pdf","date_created":"2023-09-13T09:34:20Z","checksum":"507ab65ab29e2c987c94cabad7c5370b","file_size":5749653,"file_id":"14322","creator":"acappell","success":1,"access_level":"open_access","relation":"main_file"}],"oa":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"type":"journal_article","date_published":"2023-09-11T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"language":[{"iso":"eng"}],"article_number":"104103","month":"09","project":[{"grant_number":"101062862","name":"Non-equilibrium Field Theory of Molecular Rotations","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"The Journal of Chemical Physics"},{"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."}],"doi":"10.1063/5.0173341","arxiv":1,"day":"14","external_id":{"arxiv":["2308.10886"]},"date_updated":"2023-11-28T08:39:23Z","year":"2023","citation":{"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).","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.","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>","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>","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.","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>."},"ddc":["530","540"],"volume":159,"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.","title":"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals","intvolume":"       159","publication_status":"published","department":[{"_id":"BiCh"}],"date_created":"2023-11-26T23:00:54Z","article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Reinhardt","first_name":"Aleks","full_name":"Reinhardt, Aleks"},{"full_name":"Chew, Pin Yu","first_name":"Pin Yu","last_name":"Chew"},{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"issue":"18","_id":"14603","scopus_import":"1","article_type":"original","publisher":"AIP Publishing","file_date_updated":"2023-11-28T08:39:06Z","quality_controlled":"1","oa":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"date_published":"2023-11-14T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"status":"public","relation":"research_data","id":"14619"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2023_JourChemicalPhysics_Reinhardt.pdf","content_type":"application/pdf","date_updated":"2023-11-28T08:39:06Z","checksum":"f668ee0d07096eef81159d05bc27aabc","file_size":6276059,"date_created":"2023-11-28T08:39:06Z","creator":"dernst","file_id":"14620","relation":"main_file","success":1,"access_level":"open_access"}],"month":"11","article_number":"184110","oa_version":"Published Version","publication":"Journal of Chemical Physics","has_accepted_license":"1","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"oa_version":"Preprint","article_number":"074905","month":"02","publication":"Journal of Chemical Physics","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04810"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"oa":1,"type":"journal_article","date_published":"2023-02-21T00:00:00Z","publisher":"American Institute of Physics","article_type":"original","quality_controlled":"1","date_created":"2023-03-05T23:01:05Z","article_processing_charge":"No","department":[{"_id":"AnSa"}],"publication_status":"published","intvolume":"       158","title":"Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks","scopus_import":"1","_id":"12705","pmid":1,"issue":"7","author":[{"id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","orcid":"0000-0002-9645-6576","full_name":"Sorichetti, Valerio","first_name":"Valerio","last_name":"Sorichetti"},{"first_name":"Andrea","last_name":"Ninarello","full_name":"Ninarello, Andrea"},{"first_name":"José","last_name":"Ruiz-Franco","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"},{"first_name":"Cristian","last_name":"Micheletti","full_name":"Micheletti, Cristian"},{"first_name":"Walter","last_name":"Kob","full_name":"Kob, Walter"},{"first_name":"Lorenzo","last_name":"Rovigatti","full_name":"Rovigatti, Lorenzo"}],"volume":158,"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.","day":"21","arxiv":1,"doi":"10.1063/5.0134271","abstract":[{"lang":"eng","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."}],"citation":{"short":"V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).","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>.","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.","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>","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>","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.","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>."},"year":"2023","date_updated":"2023-10-03T11:31:51Z","external_id":{"isi":["000936943800002"],"pmid":["36813705"],"arxiv":["2211.04810"]},"isi":1},{"abstract":[{"text":"The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions.","lang":"eng"}],"arxiv":1,"doi":"10.1063/5.0135893","day":"07","isi":1,"external_id":{"arxiv":["2211.08070"],"isi":["000970038800001"]},"date_updated":"2023-08-01T14:08:47Z","citation":{"chicago":"Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2023. <a href=\"https://doi.org/10.1063/5.0135893\">https://doi.org/10.1063/5.0135893</a>.","ieee":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory of angulons and their rotational spectroscopy,” <i>The Journal of Chemical Physics</i>, vol. 158, no. 13. American Institute of Physics, 2023.","ama":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons and their rotational spectroscopy. <i>The Journal of Chemical Physics</i>. 2023;158(13). doi:<a href=\"https://doi.org/10.1063/5.0135893\">10.1063/5.0135893</a>","apa":"Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., &#38; Schmidt, R. (2023). Variational theory of angulons and their rotational spectroscopy. <i>The Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0135893\">https://doi.org/10.1063/5.0135893</a>","ista":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 158(13), 134301.","short":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical Physics 158 (2023).","mla":"Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational Spectroscopy.” <i>The Journal of Chemical Physics</i>, vol. 158, no. 13, 134301, American Institute of Physics, 2023, doi:<a href=\"https://doi.org/10.1063/5.0135893\">10.1063/5.0135893</a>."},"year":"2023","ddc":["530"],"volume":158,"acknowledgement":"We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt for their valuable discussions. We acknowledge support by the Max Planck Society and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.S. is supported by the National Key Research and Development Program of China (Grant No. 2017YFA0718304) and the National Natural Science Foundation of China (Grant Nos. 11974363, 12135018, and 12047503).","title":"Variational theory of angulons and their rotational spectroscopy","intvolume":"       158","publication_status":"published","department":[{"_id":"MiLe"}],"article_processing_charge":"No","date_created":"2023-04-16T22:01:07Z","author":[{"first_name":"Zhongda","last_name":"Zeng","full_name":"Zeng, Zhongda"},{"orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail"},{"full_name":"Shi, Tao","first_name":"Tao","last_name":"Shi"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"}],"issue":"13","_id":"12831","scopus_import":"1","article_type":"original","publisher":"American Institute of Physics","file_date_updated":"2023-04-17T07:28:38Z","ec_funded":1,"quality_controlled":"1","oa":1,"publication_identifier":{"eissn":["1089-7690"]},"date_published":"2023-04-07T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2023-04-17T07:28:38Z","file_name":"2023_JourChemicalPhysics_Zeng.pdf","content_type":"application/pdf","date_created":"2023-04-17T07:28:38Z","file_size":7388057,"checksum":"8d801babea4df48e08895c76571bb19e","file_id":"12841","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file"}],"month":"04","article_number":"134301","oa_version":"Published Version","project":[{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"publication":"The Journal of Chemical Physics","has_accepted_license":"1","language":[{"iso":"eng"}]},{"oa":1,"publication_identifier":{"eissn":["1089-7690"]},"date_published":"2023-04-24T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"link":[{"url":"https://github.com/BingqingCheng/mu-adsorption","relation":"software"},{"relation":"software","url":"https://github.com/BingqingCheng/S0"}]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2023-05-08T07:44:49Z","file_size":6499468,"checksum":"4ab8c965f2fa4e17920bfa846847f137","date_updated":"2023-05-08T07:44:49Z","content_type":"application/pdf","file_name":"2023_JourChemicalPhysics_Schmid.pdf","access_level":"open_access","relation":"main_file","success":1,"file_id":"12918","creator":"dernst"}],"month":"04","article_number":"161101 ","oa_version":"Published Version","publication":"The Journal of Chemical Physics","has_accepted_license":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes."}],"doi":"10.1063/5.0146711","arxiv":1,"day":"24","isi":1,"external_id":{"isi":["001010676000010"],"pmid":["37093149"],"arxiv":["2302.01297"]},"date_updated":"2023-08-01T14:34:49Z","year":"2023","citation":{"chicago":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0146711\">https://doi.org/10.1063/5.0146711</a>.","ieee":"R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined fluids,” <i>The Journal of Chemical Physics</i>, vol. 158, no. 16. AIP Publishing, 2023.","apa":"Schmid, R., &#38; Cheng, B. (2023). Computing chemical potentials of adsorbed or confined fluids. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0146711\">https://doi.org/10.1063/5.0146711</a>","ama":"Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids. <i>The Journal of Chemical Physics</i>. 2023;158(16). doi:<a href=\"https://doi.org/10.1063/5.0146711\">10.1063/5.0146711</a>","ista":"Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101.","mla":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” <i>The Journal of Chemical Physics</i>, vol. 158, no. 16, 161101, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0146711\">10.1063/5.0146711</a>.","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023)."},"ddc":["540"],"volume":158,"acknowledgement":"We thank Aleks Reinhardt and Daan Frenkel for their insightful comments and suggestions on the article. B.C. acknowledges 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.","title":"Computing chemical potentials of adsorbed or confined fluids","intvolume":"       158","publication_status":"published","article_processing_charge":"No","date_created":"2023-05-07T22:01:03Z","department":[{"_id":"BiCh"}],"author":[{"last_name":"Schmid","first_name":"Rochus","full_name":"Schmid, Rochus"},{"first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"issue":"16","_id":"12912","pmid":1,"scopus_import":"1","article_type":"original","publisher":"AIP Publishing","file_date_updated":"2023-05-08T07:44:49Z","quality_controlled":"1"},{"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).","volume":156,"ddc":["540"],"doi":"10.1063/5.0087769","day":"16","abstract":[{"lang":"eng","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."}],"date_updated":"2023-09-05T11:59:00Z","year":"2022","citation":{"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.","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>.","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>","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>","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.","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>.","short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022)."},"isi":1,"external_id":{"isi":["000797236000004"]},"publisher":"AIP Publishing","article_type":"original","quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-05-23T07:45:33Z","publication_status":"published","article_processing_charge":"No","department":[{"_id":"AnSa"}],"date_created":"2022-05-22T17:04:48Z","title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","intvolume":"       156","_id":"11400","author":[{"id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","last_name":"Palaia","first_name":"Ivan"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"}],"issue":"19","file":[{"date_created":"2022-05-23T07:45:33Z","checksum":"7fada58059676a4bb0944b82247af740","file_size":6387208,"date_updated":"2022-05-23T07:45:33Z","file_name":"2022_JourChemPhysics_Palaia.pdf","content_type":"application/pdf","success":1,"relation":"main_file","access_level":"open_access","file_id":"11405","creator":"dernst"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-05-16T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"oa_version":"Published Version","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"},{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"month":"05","article_number":"194902","publication":"The Journal of Chemical Physics","has_accepted_license":"1"},{"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.","volume":157,"ddc":["530","540"],"date_updated":"2023-08-04T09:43:11Z","citation":{"short":"B. Cheng, The Journal of Chemical Physics 157 (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>.","ista":"Cheng B. 2022. Computing chemical potentials of solutions from structure factors. The Journal of Chemical Physics. 157(12), 121101.","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>","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>","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.","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>."},"year":"2022","isi":1,"external_id":{"isi":["000862856000003"]},"doi":"10.1063/5.0107059","day":"30","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"}],"quality_controlled":"1","file_date_updated":"2023-01-30T09:07:00Z","publisher":"AIP Publishing","article_type":"original","_id":"12249","scopus_import":"1","author":[{"last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"issue":"12","publication_status":"published","department":[{"_id":"BiCh"}],"article_processing_charge":"No","date_created":"2023-01-16T09:56:20Z","title":"Computing chemical potentials of solutions from structure factors","intvolume":"       157","file":[{"relation":"main_file","access_level":"open_access","success":1,"creator":"dernst","file_id":"12441","checksum":"b0915b706568a663a9a372fca24adf35","file_size":4402384,"date_created":"2023-01-30T09:07:00Z","file_name":"2022_JourChemPhysics_Cheng.pdf","content_type":"application/pdf","date_updated":"2023-01-30T09:07:00Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"relation":"software","url":"https://github.com/ BingqingCheng/S0"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-09-30T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"oa":1,"language":[{"iso":"eng"}],"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"publication":"The Journal of Chemical Physics","has_accepted_license":"1","oa_version":"Published Version","month":"09","article_number":"121101"},{"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.","volume":152,"year":"2020","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>.","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>","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>","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.","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>."},"date_updated":"2024-08-07T07:16:53Z","external_id":{"isi":["000530448300001"],"arxiv":["1912.02658"]},"isi":1,"day":"27","arxiv":1,"doi":"10.1063/1.5144759","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"quality_controlled":"1","publisher":"AIP Publishing","article_type":"original","_id":"8587","issue":"16","author":[{"id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Xiang","first_name":"Xiang","last_name":"Li"},{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","last_name":"Yakaboylu"},{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","first_name":"Giacomo","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"last_name":"Deuchert","first_name":"Andreas","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","date_created":"2020-09-30T10:33:17Z","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"publication_status":"published","intvolume":"       152","title":"Intermolecular forces and correlations mediated by a phonon bath","main_file_link":[{"url":"https://arxiv.org/abs/1912.02658","open_access":"1"}],"related_material":{"record":[{"id":"8958","relation":"dissertation_contains","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","type":"journal_article","date_published":"2020-04-27T00:00:00Z","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"oa":1,"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"name":"A path-integral approach to composite impurities","grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"oa_version":"Preprint","article_number":"164302","month":"04"},{"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"oa":1,"type":"journal_article","date_published":"2020-01-31T00:00:00Z","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"}],"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Submitted Version","article_number":"044103","month":"01","publication":"The Journal of Chemical Physics","language":[{"iso":"eng"}],"day":"31","arxiv":1,"doi":"10.1063/1.5134461","abstract":[{"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.","lang":"eng"}],"citation":{"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>","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>","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>.","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.","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>.","short":"B. Cheng, M. Ceriotti, G.A. Tribello, The Journal of Chemical Physics 152 (2020).","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."},"year":"2020","date_updated":"2023-02-23T14:03:55Z","external_id":{"arxiv":["1910.13481"],"pmid":["32007057"]},"volume":152,"extern":"1","date_created":"2021-07-15T07:22:24Z","article_processing_charge":"No","publication_status":"published","intvolume":"       152","title":"Classical nucleation theory predicts the shape of the nucleus in homogeneous solidification","scopus_import":"1","_id":"9658","pmid":1,"issue":"4","author":[{"last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"},{"full_name":"Tribello, Gareth A.","first_name":"Gareth A.","last_name":"Tribello"}],"publisher":"AIP Publishing","article_type":"original","quality_controlled":"1"},{"language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","article_number":"054108","month":"02","oa_version":"Preprint","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.09364"}],"type":"journal_article","date_published":"2019-02-07T00:00:00Z","oa":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"quality_controlled":"1","article_type":"original","publisher":"AIP Publishing","issue":"5","author":[{"last_name":"Sokolowski","first_name":"Thomas R","full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paijmans","first_name":"Joris","full_name":"Paijmans, Joris"},{"full_name":"Bossen, Laurens","first_name":"Laurens","last_name":"Bossen"},{"first_name":"Thomas","last_name":"Miedema","full_name":"Miedema, Thomas"},{"full_name":"Wehrens, Martijn","last_name":"Wehrens","first_name":"Martijn"},{"full_name":"Becker, Nils B.","first_name":"Nils B.","last_name":"Becker"},{"full_name":"Kaizu, Kazunari","first_name":"Kazunari","last_name":"Kaizu"},{"first_name":"Koichi","last_name":"Takahashi","full_name":"Takahashi, Koichi"},{"full_name":"Dogterom, Marileen","last_name":"Dogterom","first_name":"Marileen"},{"first_name":"Pieter Rein","last_name":"ten Wolde","full_name":"ten Wolde, Pieter Rein"}],"_id":"7422","intvolume":"       150","title":"eGFRD in all dimensions","date_created":"2020-01-30T10:34:36Z","department":[{"_id":"GaTk"}],"article_processing_charge":"No","publication_status":"published","volume":150,"external_id":{"isi":["000458109300009"],"arxiv":["1708.09364"]},"isi":1,"year":"2019","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>","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.","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>.","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).","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>.","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."},"date_updated":"2023-09-06T14:59:28Z","abstract":[{"lang":"eng","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."}],"day":"07","doi":"10.1063/1.5064867","arxiv":1},{"scopus_import":"1","pmid":1,"_id":"9659","issue":"23","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"}],"article_processing_charge":"No","date_created":"2021-07-15T07:51:42Z","publication_status":"published","intvolume":"       148","title":"Communication: Computing the Tolman length for solid-liquid interfaces","quality_controlled":"1","publisher":"AIP Publishing","article_type":"original","year":"2018","citation":{"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>.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 148 (2018).","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>","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>","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.","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>."},"date_updated":"2023-02-23T14:03:57Z","external_id":{"pmid":["29935495"],"arxiv":["1803.09140"]},"day":"21","doi":"10.1063/1.5038396","arxiv":1,"abstract":[{"lang":"eng","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."}],"volume":148,"extern":"1","publication":"The Journal of Chemical Physics","oa_version":"Submitted Version","article_number":"231102","month":"06","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2018-06-21T00:00:00Z","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/1.5038396"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public"},{"month":"03","article_number":"124306","oa_version":"None","publication":"The Journal of Chemical Physics","language":[{"iso":"eng"}],"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"date_published":"2017-03-28T00:00:00Z","type":"journal_article","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Theory of attosecond delays in molecular photoionization","intvolume":"       146","publication_status":"published","date_created":"2023-08-10T06:36:19Z","article_processing_charge":"No","author":[{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Wörner, Hans Jakob","last_name":"Wörner","first_name":"Hans Jakob"}],"issue":"12","_id":"14006","pmid":1,"scopus_import":"1","article_type":"original","publisher":"AIP Publishing","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"doi":"10.1063/1.4977933","day":"28","external_id":{"pmid":["28388142"]},"date_updated":"2023-08-22T08:30:59Z","citation":{"short":"D.R. Baykusheva, H.J. Wörner, The Journal of Chemical Physics 146 (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>.","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>","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>","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.","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>."},"year":"2017","extern":"1","volume":146},{"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"oa":1,"type":"journal_article","date_published":"2017-09-14T00:00:00Z","main_file_link":[{"url":"https://pure.qub.ac.uk/en/publications/the-gibbs-free-energy-of-homogeneous-nucleation-from-atomistic-nuclei-to-the-planar-limit(4599cdb4-dcc4-4522-8763-7b2a165ebf12).html","open_access":"1"}],"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Submitted Version","article_number":"104707","month":"09","publication":"The Journal of Chemical Physics","language":[{"iso":"eng"}],"day":"14","arxiv":1,"doi":"10.1063/1.4997180","abstract":[{"text":"In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.","lang":"eng"}],"citation":{"mla":"Cheng, Bingqing, et al. “The Gibbs Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.” <i>The Journal of Chemical Physics</i>, vol. 147, no. 10, 104707, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4997180\">10.1063/1.4997180</a>.","short":"B. Cheng, G.A. Tribello, M. Ceriotti, The Journal of Chemical Physics 147 (2017).","ista":"Cheng B, Tribello GA, Ceriotti M. 2017. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. 147(10), 104707.","apa":"Cheng, B., Tribello, G. A., &#38; Ceriotti, M. (2017). The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4997180\">https://doi.org/10.1063/1.4997180</a>","ama":"Cheng B, Tribello GA, Ceriotti M. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. <i>The Journal of Chemical Physics</i>. 2017;147(10). doi:<a href=\"https://doi.org/10.1063/1.4997180\">10.1063/1.4997180</a>","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit,” <i>The Journal of Chemical Physics</i>, vol. 147, no. 10. AIP Publishing, 2017.","chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “The Gibbs Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4997180\">https://doi.org/10.1063/1.4997180</a>."},"year":"2017","date_updated":"2023-02-23T14:04:02Z","external_id":{"arxiv":["1703.06062"],"pmid":["28915742"]},"volume":147,"extern":"1","date_created":"2021-07-15T08:13:29Z","article_processing_charge":"No","publication_status":"published","intvolume":"       147","title":"The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit","scopus_import":"1","_id":"9660","pmid":1,"issue":"10","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing"},{"full_name":"Tribello, Gareth A.","last_name":"Tribello","first_name":"Gareth A."},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"publisher":"AIP Publishing","article_type":"original","quality_controlled":"1"},{"publication":"The Journal of Chemical Physics","oa_version":"Preprint","article_number":"034106","month":"01","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2017-01-21T00:00:00Z","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1610.01322","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","scopus_import":"1","_id":"9661","pmid":1,"issue":"3","author":[{"last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"article_processing_charge":"No","date_created":"2021-07-15T08:27:31Z","publication_status":"published","intvolume":"       146","title":"Bridging the gap between atomistic and macroscopic models of homogeneous nucleation","quality_controlled":"1","publisher":"AIP Publishing","article_type":"original","year":"2017","citation":{"mla":"Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation.” <i>The Journal of Chemical Physics</i>, vol. 146, no. 3, 034106, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4973883\">10.1063/1.4973883</a>.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 146 (2017).","ista":"Cheng B, Ceriotti M. 2017. Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. The Journal of Chemical Physics. 146(3), 034106.","ama":"Cheng B, Ceriotti M. Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. <i>The Journal of Chemical Physics</i>. 2017;146(3). doi:<a href=\"https://doi.org/10.1063/1.4973883\">10.1063/1.4973883</a>","apa":"Cheng, B., &#38; Ceriotti, M. (2017). Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4973883\">https://doi.org/10.1063/1.4973883</a>","ieee":"B. Cheng and M. Ceriotti, “Bridging the gap between atomistic and macroscopic models of homogeneous nucleation,” <i>The Journal of Chemical Physics</i>, vol. 146, no. 3. AIP Publishing, 2017.","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4973883\">https://doi.org/10.1063/1.4973883</a>."},"date_updated":"2021-08-09T12:31:57Z","external_id":{"arxiv":["1610.01322"],"pmid":["28109231"]},"day":"21","doi":"10.1063/1.4973883","arxiv":1,"abstract":[{"text":"Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms, by capturing the microscopic configurations of all the atoms. In this paper, we introduce a thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework for testing the limits of classical nucleation theory.","lang":"eng"}],"volume":146,"extern":"1"},{"extern":"1","acknowledgement":"We acknowledge support from the Human Frontier Science Program and Emmanuel College (A.Š.), St John’s and Peterhouse Colleges (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council (T.C.T.M., T.P.J.K., and D.F.), and the Engineering and Physical Sciences Research Council (D.F.).","volume":145,"external_id":{"arxiv":["1610.02320"],"pmid":["28799382"]},"date_updated":"2021-11-29T10:33:11Z","citation":{"chicago":"Šarić, Anđela, Thomas C. T. Michaels, Alessio Zaccone, Tuomas P. J. Knowles, and Daan Frenkel. “Kinetics of Spontaneous Filament Nucleation via Oligomers: Insights from Theory and Simulation.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4965040\">https://doi.org/10.1063/1.4965040</a>.","ieee":"A. Šarić, T. C. T. Michaels, A. Zaccone, T. P. J. Knowles, and D. Frenkel, “Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation,” <i>The Journal of Chemical Physics</i>, vol. 145, no. 21. American Institute of Physics, 2016.","ama":"Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. <i>The Journal of Chemical Physics</i>. 2016;145(21). doi:<a href=\"https://doi.org/10.1063/1.4965040\">10.1063/1.4965040</a>","apa":"Šarić, A., Michaels, T. C. T., Zaccone, A., Knowles, T. P. J., &#38; Frenkel, D. (2016). Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. <i>The Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4965040\">https://doi.org/10.1063/1.4965040</a>","ista":"Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. 2016. Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. The Journal of Chemical Physics. 145(21), 211926.","mla":"Šarić, Anđela, et al. “Kinetics of Spontaneous Filament Nucleation via Oligomers: Insights from Theory and Simulation.” <i>The Journal of Chemical Physics</i>, vol. 145, no. 21, 211926, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4965040\">10.1063/1.4965040</a>.","short":"A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal of Chemical Physics 145 (2016)."},"year":"2016","abstract":[{"text":"Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a process that has broad implications in many research areas ranging from medicine to nanotechnology. As such, spontaneous nucleation of protein fibrils has received much attention in recent years with many theoretical and experimental studies focusing on the underlying physical principles. In this paper we make a step forward in this direction and explore the early time behaviour of filamentous protein growth in the context of nucleation theory. We first provide an overview of the thermodynamics and kinetics of spontaneous nucleation of protein filaments in the presence of one relevant degree of freedom, namely the cluster size. In this case, we review how key kinetic observables, such as the reaction order of spontaneous nucleation, are directly related to the physical size of the critical nucleus. We then focus on the increasingly prominent case of filament nucleation that includes a conformational conversion of the nucleating building-block as an additional slow step in the nucleation process. Using computer simulations, we study the concentration dependence of the nucleation rate. We find that, under these circumstances, the reaction order of spontaneous nucleation with respect to the free monomer does no longer relate to the overall physical size of the nucleating aggregate but rather to the portion of the aggregate that actively participates in the conformational conversion. Our results thus provide a novel interpretation of the common kinetic descriptors of protein filament formation, including the reaction order of the nucleation step or the scaling exponent of lag times, and put into perspective current theoretical descriptions of protein aggregation.","lang":"eng"}],"doi":"10.1063/1.4965040","arxiv":1,"day":"01","quality_controlled":"1","article_type":"original","publisher":"American Institute of Physics","author":[{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"full_name":"Zaccone, Alessio","first_name":"Alessio","last_name":"Zaccone"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."},{"first_name":"Daan","last_name":"Frenkel","full_name":"Frenkel, Daan"}],"issue":"21","_id":"10376","pmid":1,"scopus_import":"1","title":"Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation","intvolume":"       145","publication_status":"published","article_processing_charge":"No","date_created":"2021-11-29T10:01:57Z","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02320"}],"date_published":"2016-12-01T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"language":[{"iso":"eng"}],"keyword":["physical and theoretical chemistry","general physics and astronomy"],"publication":"The Journal of Chemical Physics","month":"12","article_number":"211926","oa_version":"Preprint"},{"abstract":[{"lang":"eng","text":"Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally induced fields depend on the underlying treatment of long-ranged interactions. For the short-ranged Wolf method and Ewald summation, we find the peak strength of the field to range between 2 × 107 and 5 × 107 V/m for a temperature gradient of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139, 014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show that this discrepancy can be traced back to the use of an incorrect kernel in the calculation of the electrostatic field. More seriously, we find that the Wolf method fails to predict correct molecular orientations, resulting in dipole densities with opposite sign to those computed using Ewald summation. By considering two different multipole expansions, we show that, for inhomogeneous polarisations, the quadrupole contribution can be significant and even outweigh the dipole contribution to the field. Finally, we propose a more accurate way of calculating the electrostatic potential and the field. In particular, we show that averaging the microscopic field analytically to obtain the macroscopic Maxwell field reduces the error bars by up to an order of magnitude. As a consequence, the simulation times required to reach a given statistical accuracy decrease by up to two orders of magnitude."}],"arxiv":1,"doi":"10.1063/1.4953036","day":"10","external_id":{"arxiv":["1602.02734"],"pmid":["27305991"]},"date_updated":"2021-11-29T13:09:08Z","citation":{"short":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The Journal of Chemical Physics 144 (2016).","mla":"Wirnsberger, P., et al. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” <i>The Journal of Chemical Physics</i>, vol. 144, no. 22, 224102, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4953036\">10.1063/1.4953036</a>.","ista":"Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. 2016. Non-equilibrium simulations of thermally induced electric fields in water. The Journal of Chemical Physics. 144(22), 224102.","apa":"Wirnsberger, P., Fijan, D., Šarić, A., Neumann, M., Dellago, C., &#38; Frenkel, D. (2016). Non-equilibrium simulations of thermally induced electric fields in water. <i>The Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4953036\">https://doi.org/10.1063/1.4953036</a>","ama":"Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium simulations of thermally induced electric fields in water. <i>The Journal of Chemical Physics</i>. 2016;144(22). doi:<a href=\"https://doi.org/10.1063/1.4953036\">10.1063/1.4953036</a>","chicago":"Wirnsberger, P., D. Fijan, Anđela Šarić, M. Neumann, C. Dellago, and D. Frenkel. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4953036\">https://doi.org/10.1063/1.4953036</a>.","ieee":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, and D. Frenkel, “Non-equilibrium simulations of thermally induced electric fields in water,” <i>The Journal of Chemical Physics</i>, vol. 144, no. 22. American Institute of Physics, 2016."},"year":"2016","extern":"1","acknowledgement":"The authors should like to dedicate this paper to the memory of Simon de Leeuw, who was a pioneer in the calculation of Coulomb effects in simulations. P.W. would like to thank the Austrian Academy of Sciences for financial support through a DOC Fellowship, and for covering the travel expenses for the CECAM workshop in Zaragoza in May 2015, where these results were first presented. P.W. would also like to thank Chao Zhang for pointing out the equivalence of the two expressions for the electric field discussed in Sec. VI D, Michiel Sprik for emphasising the importance of the quadrupole contribution in experimental studies of interfacial systems, as well as Aleks Reinhardt and other members of the Frenkel and Dellago groups for their advice. We further acknowledge support from the Federation of Austrian Industry (IV) Carinthia (P.W.), the University of Zagreb and Erasmus SMP (D. Fijan), the Human Frontier Science Program and Emmanuel College (A.Š.), the Austrian Science Fund FWF within the SFB Vicom project F41 (C.D.), and the Engineering and Physical Sciences Research Council Programme Grant No. EP/I001352/1 (D.F.). Additional data related to this publication are available at the University of Cambridge data repository (http://dx.doi.org/10.17863/CAM.118).","volume":144,"title":"Non-equilibrium simulations of thermally induced electric fields in water","intvolume":"       144","publication_status":"published","date_created":"2021-11-29T11:08:52Z","article_processing_charge":"No","author":[{"full_name":"Wirnsberger, P.","last_name":"Wirnsberger","first_name":"P."},{"last_name":"Fijan","first_name":"D.","full_name":"Fijan, D."},{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Neumann, M.","first_name":"M.","last_name":"Neumann"},{"first_name":"C.","last_name":"Dellago","full_name":"Dellago, C."},{"full_name":"Frenkel, D.","last_name":"Frenkel","first_name":"D."}],"issue":"22","pmid":1,"_id":"10380","scopus_import":"1","article_type":"original","publisher":"American Institute of Physics","quality_controlled":"1","oa":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"date_published":"2016-06-10T00:00:00Z","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1602.02734","open_access":"1"}],"month":"06","article_number":"224102","oa_version":"Preprint","publication":"The Journal of Chemical Physics","language":[{"iso":"eng"}],"keyword":["physical and theoretical chemistry","general physics and astronomy"]},{"abstract":[{"text":"The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra of deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺) to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2 rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.","lang":"eng"}],"doi":"10.1063/1.4890744","day":"14","external_id":{"pmid":["25134581"]},"date_updated":"2023-08-22T09:01:31Z","citation":{"ieee":"K. Vasilatou, J. M. Michaud, D. R. Baykusheva, G. Grassi, and F. Merkt, “The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra,” <i>The Journal of Chemical Physics</i>, vol. 141, no. 6. AIP Publishing, 2014.","chicago":"Vasilatou, K., J. M. Michaud, Denitsa Rangelova Baykusheva, G. Grassi, and F. Merkt. “The Cyclopropene Radical Cation: Rovibrational Level Structure at Low Energies from High-Resolution Photoelectron Spectra.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2014. <a href=\"https://doi.org/10.1063/1.4890744\">https://doi.org/10.1063/1.4890744</a>.","ama":"Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. <i>The Journal of Chemical Physics</i>. 2014;141(6). doi:<a href=\"https://doi.org/10.1063/1.4890744\">10.1063/1.4890744</a>","apa":"Vasilatou, K., Michaud, J. M., Baykusheva, D. R., Grassi, G., &#38; Merkt, F. (2014). The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4890744\">https://doi.org/10.1063/1.4890744</a>","ista":"Vasilatou K, Michaud JM, Baykusheva DR, Grassi G, Merkt F. 2014. The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra. The Journal of Chemical Physics. 141(6), 064317.","mla":"Vasilatou, K., et al. “The Cyclopropene Radical Cation: Rovibrational Level Structure at Low Energies from High-Resolution Photoelectron Spectra.” <i>The Journal of Chemical Physics</i>, vol. 141, no. 6, 064317, AIP Publishing, 2014, doi:<a href=\"https://doi.org/10.1063/1.4890744\">10.1063/1.4890744</a>.","short":"K. Vasilatou, J.M. Michaud, D.R. Baykusheva, G. Grassi, F. Merkt, The Journal of Chemical Physics 141 (2014)."},"year":"2014","extern":"1","volume":141,"title":"The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra","intvolume":"       141","publication_status":"published","article_processing_charge":"No","date_created":"2023-08-10T06:38:30Z","author":[{"full_name":"Vasilatou, K.","last_name":"Vasilatou","first_name":"K."},{"full_name":"Michaud, J. M.","last_name":"Michaud","first_name":"J. M."},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"full_name":"Grassi, G.","last_name":"Grassi","first_name":"G."},{"first_name":"F.","last_name":"Merkt","full_name":"Merkt, F."}],"issue":"6","pmid":1,"_id":"14019","scopus_import":"1","article_type":"original","publisher":"AIP Publishing","quality_controlled":"1","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"date_published":"2014-08-14T00:00:00Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","month":"08","article_number":"064317","oa_version":"None","publication":"The Journal of Chemical Physics","language":[{"iso":"eng"}],"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"]},{"language":[{"iso":"eng"}],"oa_version":"Preprint","article_number":"244112","month":"12","publication":"The Journal of Chemical Physics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.1308"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"oa":1,"type":"journal_article","date_published":"2014-12-28T00:00:00Z","publisher":"AIP Publishing","article_type":"original","quality_controlled":"1","date_created":"2021-07-15T09:22:49Z","article_processing_charge":"No","publication_status":"published","intvolume":"       141","title":"Direct path integral estimators for isotope fractionation ratios","scopus_import":"1","pmid":1,"_id":"9662","issue":"24","author":[{"last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"last_name":"Ceriotti","first_name":"Michele","full_name":"Ceriotti, Michele"}],"volume":141,"extern":"1","day":"28","arxiv":1,"doi":"10.1063/1.4904293","abstract":[{"text":"Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons.","lang":"eng"}],"year":"2014","citation":{"ista":"Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 141(24), 244112.","mla":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” <i>The Journal of Chemical Physics</i>, vol. 141, no. 24, 244112, AIP Publishing, 2014, doi:<a href=\"https://doi.org/10.1063/1.4904293\">10.1063/1.4904293</a>.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).","ieee":"B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation ratios,” <i>The Journal of Chemical Physics</i>, vol. 141, no. 24. AIP Publishing, 2014.","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2014. <a href=\"https://doi.org/10.1063/1.4904293\">https://doi.org/10.1063/1.4904293</a>.","ama":"Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation ratios. <i>The Journal of Chemical Physics</i>. 2014;141(24). doi:<a href=\"https://doi.org/10.1063/1.4904293\">10.1063/1.4904293</a>","apa":"Cheng, B., &#38; Ceriotti, M. (2014). Direct path integral estimators for isotope fractionation ratios. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4904293\">https://doi.org/10.1063/1.4904293</a>"},"date_updated":"2021-08-09T12:32:24Z","external_id":{"arxiv":["1412.1308"],"pmid":["25554138"]}},{"oa_version":"Submitted Version","month":"04","article_number":"164314","publication":"The Journal of Chemical Physics","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"oa":1,"date_published":"2013-04-28T00:00:00Z","type":"journal_article","main_file_link":[{"url":"https://pubmed.ncbi.nlm.nih.gov/23635145/","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publication_status":"published","date_created":"2021-07-15T09:27:58Z","article_processing_charge":"No","title":"Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion","intvolume":"       138","_id":"9663","pmid":1,"scopus_import":"1","author":[{"first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Ngan, Alfonso H. W.","first_name":"Alfonso H. W.","last_name":"Ngan"}],"issue":"16","publisher":"AIP Publishing","article_type":"original","quality_controlled":"1","doi":"10.1063/1.4802025","day":"28","abstract":[{"text":"Molecular dynamics simulations of small Cu nanoparticles using three different interatomic potentials at rising temperature indicate that small nanoparticles can undergo solid-solid structural transitions through a direct geometrical conversion route. The direct geometrical conversion can happen for cuboctahedral nanoparticles, which turn into an icosahedra shape: one diagonal of the square faces contracts, and the faces are folded along the diagonal to give rise to two equilateral triangles. The transition is a kinetic process that cannot be fully explained through an energetic point of view. It has low activation energy and fast reaction time in the simulations. The transition mechanism is via the transmission of shear waves initiated from the particle surface and does not involve dislocation activity.","lang":"eng"}],"date_updated":"2021-08-09T12:35:34Z","citation":{"short":"B. Cheng, A.H.W. Ngan, The Journal of Chemical Physics 138 (2013).","mla":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” <i>The Journal of Chemical Physics</i>, vol. 138, no. 16, 164314, AIP Publishing, 2013, doi:<a href=\"https://doi.org/10.1063/1.4802025\">10.1063/1.4802025</a>.","ista":"Cheng B, Ngan AHW. 2013. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. The Journal of Chemical Physics. 138(16), 164314.","apa":"Cheng, B., &#38; Ngan, A. H. W. (2013). Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4802025\">https://doi.org/10.1063/1.4802025</a>","ama":"Cheng B, Ngan AHW. Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion. <i>The Journal of Chemical Physics</i>. 2013;138(16). doi:<a href=\"https://doi.org/10.1063/1.4802025\">10.1063/1.4802025</a>","chicago":"Cheng, Bingqing, and Alfonso H. W. Ngan. “Thermally Induced Solid-Solid Structural Transition of Copper Nanoparticles through Direct Geometrical Conversion.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2013. <a href=\"https://doi.org/10.1063/1.4802025\">https://doi.org/10.1063/1.4802025</a>.","ieee":"B. Cheng and A. H. W. Ngan, “Thermally induced solid-solid structural transition of copper nanoparticles through direct geometrical conversion,” <i>The Journal of Chemical Physics</i>, vol. 138, no. 16. AIP Publishing, 2013."},"year":"2013","external_id":{"pmid":["23635145"]},"volume":138,"extern":"1"}]