@misc{WeberQuer2015, author = {Weber, Marcus and Quer, Jannes}, title = {Estimating exit rates in rare event dynamical systems via extrapolation}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-56622}, year = {2015}, abstract = {In this article we present a new idea for approximating exit rates for diffusion processes living in a craggy landscape. We are especially interested in the exit rates of a process living in a metastable regions. Due to the fact that Monte Carlo simulations perform quite poor and are very computational expensive in this setting we create several similar situations with a smoothed potential. For this we introduce a new parameter \$\lambda \in [0,1]\$ (\$\lambda = 1\$ very smoothed potential, \$\lambda=0\$ original potential) into the potential which controls the influence the smoothing. We then sample the exit rate for different parameters \$\lambda\$ the exit rate from a given region. Due to the fact that \$\lambda\$ is connected to the exit rate we can use this dependency to approximate the real exit rate. The method can be seen as something between hyperdynamics and temperature accelerated MC.}, language = {en} } @article{BujotzekSchuettNielsenetal.2014, author = {Bujotzek, Alexander and Sch{\"u}tt, Ole and Nielsen, Adam and Fackeldey, Konstantin and Weber, Marcus}, title = {ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling}, volume = {52}, journal = {Journal of Mathematical Chemistry}, number = {3}, doi = {10.1007/s10910-013-0265-1}, pages = {781 -- 804}, year = {2014}, language = {de} } @article{TyagiMalhotraThuenemannetal.2013, author = {Tyagi, Rahul and Malhotra, Shashwat and Th{\"u}nemann, Andreas F. and Sedighi, Amir and Weber, Marcus and Sch{\"a}fer, Andreas and Haag, Rainer}, title = {Investigations of Host-Guest Interactions with Shape-persistent Nonionic Dendritic Micelles}, volume = {117}, journal = {J. Phys. Chem. C}, number = {23}, pages = {12307 -- 12317}, year = {2013}, language = {de} } @article{Durmaz2015, author = {Durmaz, Vedat}, title = {Markov model-based polymer assembly from force field-parameterized building blocks}, volume = {29}, journal = {Journal of Computer-Aided Molecular Design}, doi = {10.1007/s10822-014-9817-0}, pages = {225 -- 232}, year = {2015}, abstract = {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.}, language = {en} } @phdthesis{Nielsen2016, author = {Nielsen, Adam}, title = {Computation Schemes for Transfer Operators}, year = {2016}, language = {en} } @article{KrebekvonAchaziSollederetal.2016, author = {Krebek, von, Larissa K. S. and Achazi, Andreas J. and Solleder, Marthe and Weber, Marcus and Paulus, Beate and Schalley, Christoph A.}, title = {Allosteric and Chelate Cooperativity in Divalent Crown Ether-Ammonium Complexes with Strong Binding Enhancements}, volume = {22}, journal = {Chem. Eur. J.}, number = {43}, doi = {10.1002/chem.201603098}, pages = {15475 -- 15484}, year = {2016}, language = {en} } @article{IgdeRoeblitzMuelleretal.2017, author = {Igde, Sinaida and R{\"o}blitz, Susanna and M{\"u}ller, Anne and Kolbe, Katharina and Boden, Sophia and Fessele, Claudia and Lindhorst, Thisbe and Weber, Marcus and Hartmann, Laura}, title = {Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH}, volume = {17}, journal = {Marcomolecular Bioscience}, number = {12}, doi = {10.1002/mabi.201700198}, pages = {1700198}, year = {2017}, language = {en} } @article{ErlekamZumbansenWeber2022, author = {Erlekam, Franziska and Zumbansen, Maximilian and Weber, Marcus}, title = {Parameter estimation on multivalent ITC data sets}, volume = {12}, journal = {Scientific Reports}, doi = {10.1038/s41598-022-17188-x}, pages = {13402}, year = {2022}, abstract = {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.}, language = {en} }