{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T03:27:20Z","timestamp":1787282840046,"version":"build-2736575974"},"reference-count":24,"publisher":"Society for Industrial & Applied Mathematics (SIAM)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Multiscale Model. Simul."],"published-print":{"date-parts":[[2014,1]]},"abstract":"<jats:p>In this paper we show that the binding kinetics of a molecular system can be identified by a projection of a continuous process onto a finite number of macro states. We thus interpret binding kinetics as a projection. When projecting onto nonoverlapping macro states the Markovianity is spoiled. As a consequence, the description of, e.g., a receptor-ligand system by a two state kinetics, is not accurate. By assigning a degree of membership to each state, we abandon the nonoverlapping approach. This overlap is crucial for a correct mapping of binding effects by Markov state models with regard to their long time behavior. It enables us to describe the highly discussed rebinding effect, where the spatial arrangement of the system has the be included. By introducing a \u201cdegree of fuzziness,\u201d we have an indicator for the strength of the rebinding effect such that the minimal rebinding effect can be derived from an optimization problem. The fuzziness also includes some new paradigms for molecular kinetics. These new model paradigms show good agreement with experimental data.<\/jats:p>","DOI":"10.1137\/13091124x","type":"journal-article","created":{"date-parts":[[2014,3,18]],"date-time":"2014-03-18T13:51:43Z","timestamp":1395150703000},"page":"318-334","source":"Crossref","is-referenced-by-count":7,"title":["Computing the Minimal Rebinding Effect Included in a Given Kinetics"],"prefix":"10.1137","volume":"12","author":[{"given":"M.","family":"Weber","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K.","family":"Fackeldey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"351","published-online":{"date-parts":[[2014,3,18]]},"reference":[{"key":"atypb1","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-5-48"},{"key":"atypb2","doi-asserted-by":"crossref","unstructured":"P. Deuflhard, M. Dellnitz, O. Junge, and Ch. Schu\u0308tte,\n                      Computation of essential molecular dynamics by subdivision techniques\n                      , in Computational Molecular Dynamics: Challenges, Methods, Ideas, P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, and R. D. Skeel, eds., Lecture Notes in Comput. Sci. Eng. 4, Springer, Berlin, 1999, pp. 98-115.","DOI":"10.1007\/978-3-642-58360-5_5"},{"key":"atypb3","doi-asserted-by":"publisher","DOI":"10.1016\/S0024-3795(00)00095-1"},{"key":"atypb4","doi-asserted-by":"publisher","DOI":"10.1016\/j.laa.2004.10.026"},{"key":"atypb5","first-page":"391","volume":"361","author":"W. E","year":"2010","journal-title":"Ann. Rev. Phys. Chem."},{"key":"atypb6","first-page":"899","author":"Fackeldey K.","year":"2011","journal-title":"Spain"},{"key":"atypb7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0049770"},{"key":"atypb8","unstructured":"D. Prada Gracia and F. Rao,\n                      Rethinking Hydrogen-Bond Kinetics\n                      , preprint, arXiv:1308. 1030, 2013."},{"key":"atypb9","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemosphere.2007.11.009"},{"key":"atypb10","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.37.1.115"},{"key":"atypb11","doi-asserted-by":"publisher","DOI":"10.1021\/jp208585r"},{"key":"atypb12","doi-asserted-by":"publisher","DOI":"10.1063\/1.2404953"},{"key":"atypb13","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.105.065300"},{"key":"atypb14","doi-asserted-by":"publisher","DOI":"10.1021\/ja992648l"},{"key":"atypb15","doi-asserted-by":"publisher","DOI":"10.1137\/090764049"},{"key":"atypb16","unstructured":"Ch. Schu\u0308tte,\n                      Conformational Dynamics: Modelling, Theory, Algorithm and Application to Biomolecules\n                      , Habilitation thesis, Freie Universita\u0308t, Berlin, 1999."},{"key":"atypb17","doi-asserted-by":"publisher","DOI":"10.1063\/1.2102898"},{"key":"atypb18","doi-asserted-by":"publisher","DOI":"10.1517\/17460441.2010.512037"},{"key":"atypb19","doi-asserted-by":"publisher","DOI":"10.1517\/17460441.2012.687720"},{"key":"atypb20","unstructured":"M. Weber,\n                      Meshless Methods in Conformation Dynamics\n                      , Ph.D. thesis, Freie Universita\u0308t, Berlin, 2006."},{"key":"atypb21","unstructured":"M. Weber,\n                      A Subspace Approach to Molecular Markov State Models via a New Infinitesimal Generator\n                      , Habilitation thesis, Freie Universita\u0308t, Berlin, 2011."},{"key":"atypb22","first-page":"147","author":"Weber M.","year":"2013","journal-title":"Berlin"},{"key":"atypb23","doi-asserted-by":"publisher","DOI":"10.1063\/1.4739501"},{"key":"atypb24","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio0808-435"}],"container-title":["Multiscale Modeling &amp; Simulation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/epubs.siam.org\/doi\/pdf\/10.1137\/13091124X","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T13:41:37Z","timestamp":1787233297000},"score":1,"resource":{"primary":{"URL":"https:\/\/epubs.siam.org\/doi\/10.1137\/13091124X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1]]},"references-count":24,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,1]]}},"alternative-id":["10.1137\/13091124X"],"URL":"https:\/\/doi.org\/10.1137\/13091124x","relation":{},"ISSN":["1540-3459","1540-3467"],"issn-type":[{"value":"1540-3459","type":"print"},{"value":"1540-3467","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1]]}}}