TY - JOUR A1 - Durmaz, Vedat T1 - Markov model-based polymer assembly from force field-parameterized building blocks JF - Journal of Computer-Aided Molecular Design N2 - A conventional by hand construction and parameterization of a polymer model for the purpose of molecular simulations can quickly become very workintensive and time-consuming. Using the example of polyglycerol, I present a polymer decompostion strategy yielding a set of five monomeric residues that are convenient for an instantaneous assembly and subsequent force field simulation of a polyglycerol polymer model. Force field parameters have been developed in accordance with the classical Amber force field. Partial charges of each unit were fitted to the electrostatic potential using quantumchemical methods and slightly modified in order to guarantee a neutral total polymer charge. In contrast to similarly constructed models of amino acid and nucleotide sequences, the glycerol building blocks may yield an arbitrary degree of bifurcations depending on the underlying probabilistic model. The iterative development of the overall structure as well as the relation of linear to branching units is controlled by a simple Markov model which is presented with few algorithmic details. The resulting polymer is highly suitable for classical explicit water molecular dynamics simulations on the atomistic level after a structural relaxation step. Moreover, the decomposition strategy presented here can easily be adopted to many other (co)polymers. Y1 - 2015 U6 - https://doi.org/10.1007/s10822-014-9817-0 VL - 29 SP - 225 EP - 232 ER - TY - THES A1 - Nielsen, Adam T1 - Computation Schemes for Transfer Operators Y1 - 2016 ER - TY - JOUR A1 - Krebek, von, Larissa K. S. A1 - Achazi, Andreas J. A1 - Solleder, Marthe A1 - Weber, Marcus A1 - Paulus, Beate A1 - Schalley, Christoph A. T1 - Allosteric and Chelate Cooperativity in Divalent Crown Ether–Ammonium Complexes with Strong Binding Enhancements JF - Chem. Eur. J. Y1 - 2016 U6 - https://doi.org/10.1002/chem.201603098 N1 - Has been announced under the title: Cooperativity in Multivalent Binding: A Detailed Experimental and Theoretical Thermochemical Study of Divalent Crown Ether-Ammonium Complexes VL - 22 IS - 43 SP - 15475 EP - 15484 ER - TY - JOUR A1 - Igde, Sinaida A1 - Röblitz, Susanna A1 - Müller, Anne A1 - Kolbe, Katharina A1 - Boden, Sophia A1 - Fessele, Claudia A1 - Lindhorst, Thisbe A1 - Weber, Marcus A1 - Hartmann, Laura T1 - Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH JF - Marcomolecular Bioscience Y1 - 2017 U6 - https://doi.org/10.1002/mabi.201700198 VL - 17 IS - 12 SP - 1700198 ER - TY - JOUR A1 - Erlekam, Franziska A1 - Zumbansen, Maximilian A1 - Weber, Marcus T1 - Parameter estimation on multivalent ITC data sets JF - Scientific Reports N2 - The Wiseman fitting can be used to extract binding parameters from ITC data sets, such as heat of binding, number of binding sites, and the overall dissociation rate. The classical Wiseman fitting assumes a direct binding process and neglects the possibility of intermediate binding steps. In principle, it only provides thermodynamic information and not the kinetics of the process. In this article we show that a concentration dependent dissociation constant could possibly stem from intermediate binding steps. The mathematical form of this dependency can be exploited with the aid of the Robust Perron Cluster Cluster Analysis method. Our proposed extension of the Wiseman fitting rationalizes the concentration dependency, and can probably also be used to determine the kinetic parameters of intermediate binding steps of a multivalent binding process. The novelty of this paper is to assume that the binding rate varies per titration step due to the change of the ligand concentration and to use this information in the Wiseman fitting. We do not claim to produce the most accurate values of the binding parameters, we rather present a novel method of how to approach multivalent bindings from a different angle. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-17188-x VL - 12 SP - 13402 ER -