TY - GEN A1 - Agarwal, Animesh A1 - Wang, Han A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - Chemical potential of liquids and mixtures via Adaptive Resolution Simulation N2 - We employ the adaptive resolution approach AdResS, in its recently developed Grand Canonicallike version (GC-AdResS) [Wang et al. Phys.Rev.X 3, 011018 (2013)], to calculate the excess chemical potential, $μ^{ex}$, of various liquids and mixtures. We compare our results with those obtained from full atomistic simulations using the technique of thermodynamic integration and show a satisfactory agreement. In GC-AdResS the procedure to calculate $μ^{ex}$ corresponds to the process of standard initial equilibration of the system; this implies that, independently of the specific aim of the study, $μ^{ex}$, for each molecular species, is automatically calculated every time a GC-AdResS simulation is performed. T3 - ZIB-Report - 14-25 KW - Coarse graining KW - adaptive resolution KW - molecular dynamics KW - chemical potential Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50972 SN - 1438-0064 ER - TY - JOUR A1 - Agarwal, Animesh A1 - Wang, Han A1 - Schütte, Christof A1 - Delle Site, Luigi T1 - Chemical potential of liquids and mixtures via Adaptive Resolution Simulation JF - The Journal of Chemical Physics Y1 - 2014 U6 - https://doi.org/10.1063/1.4886807 VL - 141 SP - 034102 ER - TY - JOUR A1 - Aiche, Stephan A1 - Reinert, Knut A1 - Schütte, Christof A1 - Hildebrand, Diana A1 - Schlüter, Hartmut A1 - Conrad, Tim T1 - Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs JF - PLoS ONE Y1 - 2012 UR - http://publications.imp.fu-berlin.de/1143/ U6 - https://doi.org/10.1371/journal.pone.0040656 VL - 7 IS - 7 SP - e40656 PB - Public Library of Science ER - TY - JOUR A1 - Antony, Jens A1 - Schmidt, Burkhard A1 - Schütte, Christof T1 - Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes JF - J. Chem. Phys. Y1 - 2005 UR - http://publications.imp.fu-berlin.de/57/ U6 - https://doi.org/10.1063/1.1829057 VL - 122 IS - 1 SP - 014309 ER - TY - JOUR A1 - Banisch, Ralf A1 - Djurdjevac Conrad, Natasa A1 - Schütte, Christof T1 - Reactive flows and unproductive cycles for random walks on complex networks JF - The European Physical Journal Special Topics, vol. 224, iss. 12 (2015) pp. 2369-2387 Y1 - 2015 U6 - https://doi.org/10.1140/epjst/e2015-02417-8 ER - TY - GEN A1 - Banisch, Ralf A1 - Djurdjevac Conrad, Natasa A1 - Schütte, Christof T1 - Reactive flows and unproductive cycles for random walks on complex networks N2 - We present a comprehensive theory for analysis and understanding of transition events between an initial set A and a target set B for general ergodic finite-state space Markov chains or jump processes, including random walks on networks as they occur, e.g., in Markov State Modelling in molecular dynamics. The theory allows us to decompose the probability flow generated by transition events between the sets A and B into the productive part that directly flows from A to B through reaction pathways and the unproductive part that runs in loops and is supported on cycles of the underlying network. It applies to random walks on directed networks and nonreversible Markov processes and can be seen as an extension of Transition Path Theory. Information on reaction pathways and unproductive cycles results from the stochastic cycle decomposition of the underlying network which also allows to compute their corresponding weight, thus characterizing completely which structure is used how often in transition events. The new theory is illustrated by an application to a Markov State Model resulting from weakly damped Langevin dynamics where the unproductive cycles are associated with periodic orbits of the underlying Hamiltonian dynamics. T3 - ZIB-Report - 15-19 KW - Complex networks KW - molecular transition networks KW - transition path theory KW - cycle decomposition KW - reactive trajectories KW - Markow State Methods Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54239 SN - 1438-0064 ER - TY - GEN A1 - Banisch, Ralf A1 - Schütte, Christof A1 - Djurdjevac Conrad, Natasa T1 - Module Detection in Directed Real-World Networks N2 - We investigate the problem of finding modules (or clusters, communities) in directed networks. Until now, most articles on this topic have been oriented towards finding complete network partitions despite the fact that this often is unwanted. We present a novel random walk based approach for non-complete partitions of the directed network into modules in which some nodes do not belong to only one of the modules but to several or to none at all. The new random walk process is reversible even for directed networks but inherits all necessary information about directions and structure of the original network. We demonstrate the performance of the new method in application to a real-world earthquake network. T3 - ZIB-Report - 14-13 KW - Module identification and classification KW - cycle decomposition KW - communication KW - directed networks Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-49849 SN - 1438-0064 ER - TY - JOUR A1 - Becker, Fabian A1 - Djurdjevac Conrad, Natasa A1 - Eser, Raphael A. A1 - Helfmann, Luzie A1 - Schütt, Brigitta A1 - Schütte, Christof A1 - Zonker, Johannes T1 - The Furnace and the Goat—A spatio-temporal model of the fuelwood requirement for iron metallurgy on Elba Island, 4th century BCE to 2nd century CE JF - PLOS ONE Y1 - 2020 UR - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241133 U6 - https://doi.org/10.1371/journal.pone.0241133 VL - 15 SP - 1 EP - 37 PB - Public Library of Science ER - TY - JOUR A1 - Benn, Andreas A1 - Hiepen, Christian A1 - Osterland, Marc A1 - Schütte, Christof A1 - Zwijsen, An A1 - Knaus, Petra T1 - Role of bone morphogenetic proteins in sprouting angiogenesis: differential BMP receptor-dependent signaling pathways balance stalk vs. tip cell competence JF - FASEB Journal N2 - Before the onset of sprouting angiogenesis, the endothelium is prepatterned for the positioning of tip and stalk cells. Both cell identities are not static, as endothelial cells (ECs) constantly compete for the tip cell position in a dynamic fashion. Here, we show that both bone morphogenetic protein (BMP) 2 and BMP6 are proangiogenic in vitro and ex vivo and that the BMP type I receptors, activin receptor-like kinase (ALK)3 and ALK2, play crucial and distinct roles in this process. BMP2 activates the expression of tip cell–associated genes, such as DLL4 (delta-like ligand 4) and KDR (kinase insert domain receptor), and p38-heat shock protein 27 (HSP27)–dependent cell migration, thereby generating tip cell competence. Whereas BMP6 also triggers collective cell migration via the p38-HSP27 signaling axis, BMP6 induces in addition SMAD1/5 signaling, thereby promoting the expression of stalk cell–associated genes, such as HES1 (hairy and enhancer of split 1) and FLT1 (fms-like tyrosine kinase 1). Specifically, ALK3 is required for sprouting from HUVEC spheroids, whereas ALK2 represses sprout formation. We demonstrate that expression levels and respective complex formation of BMP type I receptors in ECs determine stalk vs. tip cell identity, thus contributing to endothelial plasticity during sprouting angiogenesis. As antiangiogenic monotherapies that target the VEGF or ALK1 pathways have not fulfilled efficacy objectives in clinical trials, the selective targeting of the ALK2/3 pathways may be an attractive new approach. Y1 - 2017 U6 - https://doi.org/10.1096/fj.201700193RR VL - 31 IS - 11 SP - 4720 EP - 4733 ER - TY - CHAP A1 - Bernhard, Stefan A1 - Zoukra, Kristine Al A1 - Schütte, Christof ED - Daskalaki, A. ED - Lazakidou, A. T1 - From non-invasive hemodynamic measurements towards patient-specific cardiovascular diagnosis T2 - Quality Assurance in Healthcare Service Delivery, Nursing and Personalized Medicine Y1 - 2010 UR - http://publications.imp.fu-berlin.de/945/ PB - Hershey, PA: Medical Information Science Reference ER -