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  1. Article ; Online: Consistent Quantification of Complex Dynamics via a Novel Statistical Complexity Measure.

    Keul, Frank / Hamacher, Kay

    Entropy (Basel, Switzerland)

    2022  Volume 24, Issue 4

    Abstract: Natural systems often show complex dynamics. The quantification of such complex dynamics is an important step in, e.g., characterization and classification of different systems or to investigate the effect of an external perturbation on the dynamics. ... ...

    Abstract Natural systems often show complex dynamics. The quantification of such complex dynamics is an important step in, e.g., characterization and classification of different systems or to investigate the effect of an external perturbation on the dynamics. Promising routes were followed in the past using concepts based on (Shannon's) entropy. Here, we propose a new, conceptually sound measure that can be pragmatically computed, in contrast to pure theoretical concepts based on, e.g., Kolmogorov complexity. We illustrate the applicability using a toy example with a control parameter and go on to the molecular evolution of the HIV1 protease for which drug treatment can be regarded as an external perturbation that changes the complexity of its molecular evolutionary dynamics. In fact, our method identifies exactly those residues which are known to bind the drug molecules by their noticeable signal. We furthermore apply our method in a completely different domain, namely foreign exchange rates, and find convincing results as well.
    Language English
    Publishing date 2022-04-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2014734-X
    ISSN 1099-4300 ; 1099-4300
    ISSN (online) 1099-4300
    ISSN 1099-4300
    DOI 10.3390/e24040505
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  2. Book ; Thesis: Einfluß mütterlicher thrombogener Risikofaktoren auf das kindliche Geburtsgewicht

    Hamacher, Kerstin

    2001  

    Author's details vorgelegt von Kerstin Hamacher
    Language German
    Size 91 S. : graph. Darst.
    Publishing country Germany
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Köln, Univ., Diss., 2000
    HBZ-ID HT012994786
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2001 D 986 order for loan Magazin

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  3. Article ; Online: Dynamical regimes due to technological change in a microeconomical model of production.

    Hamacher, K

    Chaos (Woodbury, N.Y.)

    2012  Volume 22, Issue 3, Page(s) 33149

    Abstract: We develop a microeconomical model to investigate the impact of technological change onto production decisions of suppliers-modeling an effective feedback mechanism of the market. An important property-the time horizon of production planning-is related ... ...

    Abstract We develop a microeconomical model to investigate the impact of technological change onto production decisions of suppliers-modeling an effective feedback mechanism of the market. An important property-the time horizon of production planning-is related to the Kolmogorov entropy of the one-dimensional maps describing price dynamics. We simulate this price dynamics in an ensemble representing the whole macroeconomy. We show how this model can be used to support ongoing research in economic growth and incorporate the obtained microeconomic findings into the discussion about appropriate macroeconomic quantities such as the production function-thus effectively underpinning macroeconomics with microeconomical dynamics. From there we can show that the model exhibits different dynamical regimes (suggesting "phase transitions") with respect to an order parameter. The non-linear feedback under technological change was found to be the crucial mechanism. The implications of the obtained regimes are finally discussed.
    MeSH term(s) Commerce ; Economics ; Feedback ; Industry/economics ; Models, Economic ; Probability ; Technology ; Time Factors
    Language English
    Publishing date 2012-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1472677-4
    ISSN 1089-7682 ; 1054-1500
    ISSN (online) 1089-7682
    ISSN 1054-1500
    DOI 10.1063/1.4754876
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  4. Article ; Online: Erratum: Three-body interactions improve contact prediction within direct-coupling analysis [Phys. Rev. E 96, 052405 (2017)].

    Schmidt, Michael / Hamacher, Kay

    Physical review. E

    2021  Volume 104, Issue 1-2, Page(s) 19902

    Abstract: This corrects the article DOI: 10.1103/PhysRevE.96.052405. ...

    Abstract This corrects the article DOI: 10.1103/PhysRevE.96.052405.
    Language English
    Publishing date 2021-08-13
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.104.019902
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  5. Article ; Online: Identification of biophysical interaction patterns in direct coupling analysis.

    Schmidt, Michael / Hamacher, Kay

    Physical review. E

    2021  Volume 103, Issue 4-1, Page(s) 42418

    Abstract: Direct-coupling analysis is a statistical learning method for protein contact prediction based on sequence information alone. The maximum entropy principle leads to an effective inverse Potts model. Predictions on contacts are based on fitted local ... ...

    Abstract Direct-coupling analysis is a statistical learning method for protein contact prediction based on sequence information alone. The maximum entropy principle leads to an effective inverse Potts model. Predictions on contacts are based on fitted local fields and couplings from an empirical multiple sequence alignment. Typically, the l_{2} norm of the resulting two-body couplings is used for contact prediction. However, this procedure discards important information. In this paper we show that the usage of the full fields and coupling information improves prediction accuracy.
    Language English
    Publishing date 2021-05-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.103.042418
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  6. Article: Adding hydrogen atoms to molecular models via fragment superimposition.

    Kunzmann, Patrick / Anter, Jacob Marcel / Hamacher, Kay

    Algorithms for molecular biology : AMB

    2022  Volume 17, Issue 1, Page(s) 7

    Abstract: Background: Most experimentally determined structures of biomolecules lack annotated hydrogen positions due to their low electron density. However, thorough structure analysis and simulations require knowledge about the positions of hydrogen atoms. ... ...

    Abstract Background: Most experimentally determined structures of biomolecules lack annotated hydrogen positions due to their low electron density. However, thorough structure analysis and simulations require knowledge about the positions of hydrogen atoms. Existing methods for their prediction are either limited to a certain range of molecules or only work effectively on small compounds.
    Results: We present a novel algorithm that compiles fragments of molecules with known hydrogen atom positions into a library. Using this library the method is able to predict hydrogen positions for molecules with similar moieties. We show that the method is able to accurately assign hydrogen atoms to most organic compounds including biomacromolecules, if a sufficiently large library is used.
    Conclusions: We bundled the algorithm into the open-source Python package and command line program Hydride. Since usually no additional parametrization is necessary for the problem at hand, the software works out-of-box for a wide range of molecular systems usually within a few seconds of computation time. Hence, we believe that Hydride could be a valuable tool for structural biologists and biophysicists alike.
    Language English
    Publishing date 2022-03-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2224970-9
    ISSN 1748-7188
    ISSN 1748-7188
    DOI 10.1186/s13015-022-00215-x
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  7. Article: Relating sequence evolution of HIV1-protease to its underlying molecular mechanics.

    Hamacher, K

    Gene

    2008  Volume 422, Issue 1-2, Page(s) 30–36

    Abstract: We investigate the connection between sequence evolution of the human immunodeficiency virus (HIV) type 1 protease under neutral selection or selective pressure induced by protease inhibitors and the functional and molecular-stability characteristics of ... ...

    Abstract We investigate the connection between sequence evolution of the human immunodeficiency virus (HIV) type 1 protease under neutral selection or selective pressure induced by protease inhibitors and the functional and molecular-stability characteristics of the molecule in the physical domain. To this end we analyze sequence data on more than 45,000 patients with bioinformatical tools, namely mutual information between residue pairings. In addition we perform extensive computations on the molecular mechanics of the molecule subject to artificial mutations. The changes in the mechanics and dynamics of the molecule in three-dimensional space upon perturbation are then related to the sequence stability as described by the mutual information. We distinguish physical interactions by their evolutionary background and give hints for potential new drug targets. In addition we discuss how such targets can be efficiently chosen to give the HI virus less opportunity to develop resistance towards such drugs while maintaining the protease function at the same time. The interactions between residue no. 28 and 23' in different chains as well as the interaction between residue no. 92 and 94 within one chain were identified as particular crucial. In addition we find interactions in the beta-sheet-dimerization interface to be important for conserving the protein function and stability while these are at the same time evolutionary conserved - implications of and comparisons to experimental results are finally discussed.
    MeSH term(s) Dimerization ; Evolution, Molecular ; HIV Infections/diet therapy ; HIV Infections/enzymology ; HIV Infections/genetics ; HIV Protease/genetics ; HIV Protease Inhibitors/pharmacology ; HIV Protease Inhibitors/therapeutic use ; HIV-1/enzymology ; HIV-1/genetics ; Humans ; Protein Structure, Secondary/physiology ; Protein Structure, Tertiary/physiology ; Selection, Genetic ; Sequence Analysis, Protein/methods
    Chemical Substances HIV Protease Inhibitors ; HIV Protease (EC 3.4.23.-)
    Language English
    Publishing date 2008-10-01
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2008.06.007
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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  8. Article: Information theoretical measures to analyze trajectories in rational molecular design.

    Hamacher, K

    Journal of computational chemistry

    2007  Volume 28, Issue 16, Page(s) 2576–2580

    Abstract: We develop a new methodology to analyze molecular dynamics trajectories and other time series data from simulation runs. This methodology is based on an information measure of the difference between distributions of various data extract from such ... ...

    Abstract We develop a new methodology to analyze molecular dynamics trajectories and other time series data from simulation runs. This methodology is based on an information measure of the difference between distributions of various data extract from such simulations. The method is fast as it only involves the numerical integration/summation of the distributions in one dimension while avoiding sampling issues at the same time. The method is most suitable for applications in which different scenarios are to be compared, e.g. to guide rational molecular design. We show the power of the proposed method in an application of rational drug design by reduced model computations on the BH3 motif in the apoptosis inducing BCL(2) protein family.
    MeSH term(s) Computer Simulation ; Drug Design ; Information Theory ; Models, Molecular ; Peptide Fragments/chemistry ; Proto-Oncogene Proteins/chemistry
    Chemical Substances Bax protein (53-86) ; Peptide Fragments ; Proto-Oncogene Proteins
    Language English
    Publishing date 2007-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1479181-x
    ISSN 1096-987X ; 0192-8651
    ISSN (online) 1096-987X
    ISSN 0192-8651
    DOI 10.1002/jcc.20759
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  9. Article ; Online: Weak Cation Selectivity in HCN Channels Results From K

    Bauer, Daniel / Wissmann, Jan / Moroni, Anna / Thiel, Gerhard / Hamacher, Kay

    Function (Oxford, England)

    2022  Volume 3, Issue 3, Page(s) zqac019

    Abstract: Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels generate the pacemaker current which plays an important role in the timing of various biological processes like the heart beat. We used umbrella sampling to explore the potential of mean ... ...

    Abstract Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels generate the pacemaker current which plays an important role in the timing of various biological processes like the heart beat. We used umbrella sampling to explore the potential of mean force for the conduction of potassium and sodium through the open HCN4 pore. Our data explain distinct functional features like low unitary conductance and weak selectivity as a result of high energetic barriers inside the selectivity filter of this channel. They exceed the 3-5 kJ/mol threshold which is presumed as maximal barrier for diffusion-limited conductance. Furthermore, simulations provide a thermodynamic explanation for the weak cation selectivity of HCN channels that contain only two ion binding sites in the selectivity filter (SF). We find that sodium ions bind more strongly to the SF than potassium and are easier released by binding of potassium than of another sodium. Hence ion transport and selectivity in HCN channels is not determined by the same mechanism as in potassium-selective channels; it rather relies on sodium as a weak blocker that can only be released by potassium.
    Language English
    Publishing date 2022-04-22
    Publishing country England
    Document type Journal Article
    ISSN 2633-8823
    ISSN (online) 2633-8823
    DOI 10.1093/function/zqac019
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  10. Article ; Online: SPIKE: secure and private investigation of the kidney exchange problem.

    Birka, Timm / Hamacher, Kay / Kussel, Tobias / Möllering, Helen / Schneider, Thomas

    BMC medical informatics and decision making

    2022  Volume 22, Issue 1, Page(s) 253

    Abstract: Background: The kidney exchange problem (KEP) addresses the matching of patients in need for a replacement organ with compatible living donors. Ideally many medical institutions should participate in a matching program to increase the chance for ... ...

    Abstract Background: The kidney exchange problem (KEP) addresses the matching of patients in need for a replacement organ with compatible living donors. Ideally many medical institutions should participate in a matching program to increase the chance for successful matches. However, to fulfill legal requirements current systems use complicated policy-based data protection mechanisms that effectively exclude smaller medical facilities to participate. Employing secure multi-party computation (MPC) techniques provides a technical way to satisfy data protection requirements for highly sensitive personal health information while simultaneously reducing the regulatory burdens.
    Results: We have designed, implemented, and benchmarked SPIKE, a secure MPC-based privacy-preserving KEP protocol which computes a locally optimal solution by finding matching donor-recipient pairs in a graph structure. SPIKE matches 40 pairs in cycles of length 2 in less than 4 min and outperforms the previous state-of-the-art protocol by a factor of [Formula: see text] in runtime while providing medically more robust solutions.
    Conclusions: We show how to solve the KEP in a robust and privacy-preserving manner achieving significantly more practical performance than the current state-of-the-art (Breuer et al., WPES'20 and CODASPY'22). The usage of MPC techniques fulfills many data protection requirements on a technical level, allowing smaller health care providers to directly participate in a kidney exchange with reduced legal processes. As sensitive data are not leaving the institutions' network boundaries, the patient data underlie a higher level of protection than in the currently employed (centralized) systems. Furthermore, due to reduced legal barriers, the proposed decentralized system might be simpler to implement in a transnational, intereuropean setting with mixed (national) data protecion laws.
    MeSH term(s) Computer Security ; Humans ; Kidney ; Privacy
    Language English
    Publishing date 2022-09-22
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2046490-3
    ISSN 1472-6947 ; 1472-6947
    ISSN (online) 1472-6947
    ISSN 1472-6947
    DOI 10.1186/s12911-022-01994-4
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