Items where Subject is "Mathematical and Computer Sciences > Mathematics > Mathematical Modelling"

A

Aiche, S. and Reinert, K. and Schütte, Ch. and Hildebrand, D. and Schlüter, H. and Conrad, T. O. F. (2012) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs. PLoS ONE, 7 (7). e40656. ISSN 1932-6203

Albrecht, D. and Winterflood, C. M. and Sadeghi, M. and Tschager, T. and Noé, F. and Ewers, H. (2016) Nanoscopic compartmentalization of membrane protein motion at the axon initial segment. J. Cell Biol., 215 (1). pp. 37-46.

Alchikh, Maren and Conrad, T. O. F. and Obermeier, Patrick E. and Ma, Xiaolin and Schweiger, Brunhilde and Opota, Onya and Rath, Barbara A. (2024) Disease Burden and Inpatient Management of Children with Acute Respiratory Viral Infections during the Pre-COVID Era in Germany: A Cost-of-Illness Study. Viruses, 16 (4).

B

Benner, P. and Breiten, T. and Hartmann, C. and Schmidt, B. (2020) Model reduction of controlled Fokker-Planck and Liouville-von Neumann equations. J. Comp. Dyn., 7 (1). pp. 1-33.

Bernhard, S. (2005) Oscillatory flow in a tube with time-dependent wall deformation and its application to Myocardial Bridges. ESAIM: Proc., 14 . pp. 25-40.

Bernhard, S. (2006) Transient integral boundary layer method to calculate the translesional pressure drop and the fractional flow reserve in myocardial bridges. BioMedical Engineering OnLine, 5 (42).

Bittracher, Andreas and Hartmann, C. and Junge, O. and Koltai, Péter (2015) Pseudo generators for under-resolved molecular dynamics. The European Physical Journal Special Topics, 224 (12). pp. 2463-2490. ISSN 1951-6355

Blaskovic, Filip and Conrad, T. O. F. and Klus, Stefan and Djurdjevac Conrad, Natasa (2024) Clustering Time-Snapshots of Temporal Networks: From Synthetic Data to Real-World Applications. arXiv . (Submitted)

Bostanci, Inan and Conrad, T. O. F. (2024) Integrating Agent-Based and Compartmental Models for Infectious Disease Modeling: A Novel Hybrid Approach. Journal of Artificial Societies and Social Simulation . (Submitted)

D

Delle Site, L. and Praprotnik, M. (2017) Molecular systems with open boundaries: Theory and Simulation. Physics Reports, 693 . pp. 1-56. ISSN 0370-1573

Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2010) On Markov State Models for Metastable Processes. In: ICM 2010.

Duwal, S. and Schütte, Ch. and von Kleist, M. (2012) Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir & Prophylactic Efficacy against HIV-1 Infection. PLoS One, 7 (7). e40382.

Duwal, S. and Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2015) Optimal treatment strategies in the context of 'treatment for prevention' against HIV-1 in resource-poor settings. PLOS Computational Biology, 11 . e1004200.

Duwal, S. and von Kleist, M. (2016) Top-down and bottom-up modelling in system pharmacology to understand clinical efficacy : An example with NRTIs of HIV-1. European Journal of Pharmaceutical Sciences, 94 . pp. 72-83. ISSN 0928-0987

F

Frank, M. and von Kleist, M. and Kunz, A. and Harms, G. and Schütte, Ch. and Kloft, Ch. (2011) Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1: A combined pharmacokinetic, pharmaco- and viral dynamic analysis to predict clinical outcomes. Antimicrob. Agents Chemother., 55 (12). pp. 5529-5540.

G

Gaskin, Thomas and Conrad, T. O. F. and Pavliotis, Grigorios A. and Schütte, Ch. (2024) Neural parameter calibration and uncertainty quantification for epidemic forecasting. PLoS ONE, 19 (10). ISSN 1932-6203

Gupta, Pooja and Reinsch , Norbert and Spötter, Andreas and Conrad, T. O. F. and Bienefeld, Kaspar (2013) Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera). BMC Genetics, 14 (36).

Gupta, Pooja and Gramatke, A and Einspanier, R and Schütte, Ch. and von Kleist, M. and Sharbati, J (2017) In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements. Toxicology in Vitro, 41 . pp. 179-188. ISSN 08872333

H

Hartmann, C. and Latorre, J.C. and Ciccotti, G. (2011) On two possible definitions of the free energy for collective variables. Eur. Phys. J. Special Topics, 200 (1). pp. 73-89.

Helfmann, Luzie and Heitzig, Jobst and Koltai, Péter and Kurths, Jürgen and Schütte, Ch. (2021) Statistical analysis of tipping pathways in agent-based models. The European Physical Journal Special Topics . ISSN 1951-6355

J

Jayrannejad, Fahrnaz and Conrad, T. O. F. (2017) Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining. Springer Lecture Notes in Artificial Intelligence .

K

Kenfack, A. and Marquardt, F. and Paramonov, G. K. and Barth, I. and Lasser, C. and Paulus, B. (2010) Initial-state dependence of coupled electronic and nuclear fluxes in molecules. Phys. Rev. A, 81 (5). 052502.

Koltai, Péter and Weiss, Stephan (2020) Diffusion maps embedding and transition matrix analysis of the large-scale flow structure in turbulent Rayleigh-Bénard convection. Nonlinearity, 33 (4). p. 1723. ISSN 0951-7715

L

Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus (2013) A Square Root Approximation of Transition Rates for a Markov State Model. SIAM Journal on Matrix Analysis and Applications, 34 (2). p. 738. ISSN 0895-4798

M

Maier, Kristina and Weiser, Martin and Conrad, T. O. F. (2024) Hybrid PDE-ODE Models for Efficient Simulation of Infection Spread in Epidemiology. Proceedings of the Royal Society A . (In Press)

Melnyk, Kateryna and Klus, S. and Montavon, Grègoire and Conrad, T. O. F. (2020) Graph Kernel Koopman Embedding for Human Microbiome Analysis. Applied Network Science, 5 (96). ISSN 2364-8228

Menz, St. and Matthiesen, R. and Dehmel, Ch. and Barembruch, C. and Hengge, R. and Huisinga, W. (2010) Precise Switching of Flagellar Gene Expression in Escherichia Coli by the FlgM–FliA Regulatory Network. PLoS Computational Biology . (Submitted)

Mollenhauer, Mattes and Koltai, Péter (2021) Nonparametric approximation of conditional expectation operators. arXiv . (Unpublished)

Müller, Sebastian and Paltra, Sydney and Rehmann, Jakob and Nagel, Kai and Conrad, T. O. F. (2023) Explicit Modelling of Antibody Levels for Infectious Disease Simulations in the Context of SARS-CoV-2. iScience, 26 (9). ISSN 2589-0042

O

Obermeier, P. and Muehlhans, S. and Hoppe, Ch. and Karsch, K. and Tief, F. and Seeber, L. and Chen, X. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2016) Enabling Precision Medicine With Digital Case Classification at the Point-of-Care. EBioMedicine, 4 . pp. 191-196.

R

Rath, B. A. and Yousef, K. P. and Katzenstein, D. K. and Shafer, R. W. and Schütte, Ch. and von Kleist, M. and Merigan, T. C. (2013) In vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis. PLoS ONE, 8 (4). e61102. ISSN 1932-6203

S

Sarich, M. and Schütte, Ch. (2012) Approximating Selected Non-dominant Timescales by Markov State Models. Comm. Math. Sci., 10 (3). pp. 1001-1013.

Schmidt, B. and Hartmann, C. (2018) WavePacket: A Matlab package for numerical quantum dynamics. II: Open quantum systems, optimal control, and model reduction. Comp. Phys. Comm., 228 . pp. 229-244.

Smyth, R.P. and Despons, L. and Huili, G. and Bernacchi, S. and Hijnen, M. and Mak, J. and Jossinet, F. and Weixi, L. and Paillart, J.-C. and von Kleist, M. and Marquet, R. (2015) Mutational Interference Mapping Experiment (MIME) for studying the relationship between RNA structure and function. Nature Methods, 12 . pp. 866-872. ISSN 1548-7091

V

von Kleist, M. and Huisinga, W. (2009) Pharmacokinetic–pharmacodynamic relationship of NRTIs and its connection to viral escape: An example based on zidovudine. European Journal of Pharmaceutical Sciences, 36 . pp. 532-543.

von Kleist, M. and Menz, S. and Huisinga, W. (2010) Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV. Plos Computational Biology, 6 (3). e1000720.

von Kleist, M. and Menz, S. and Stocker, H. and Arasteh, K. and Huisinga, W. and Schütte, Ch. (2011) HIV Quasispecies Dynamics during Pro-active Treatment Switching: Impact on Multi-Drug Resistance and Resistance Archiving in Latent Reservoirs. Plos One, 6 (3). e18204.

von Kleist, M. and Metzner, Ph. and Marquet, R. and Schütte, Ch. (2012) Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection. Plos Computational Biology, 8 (1). e1002359.

W

Wang, H. and Hartmann, C. and Schütte, Ch. and Delle Site, L. (2013) Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique. Phys. Rev. X, 3 . 011018.

Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2013) Markov Control Processes with Rare State Observation: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1. International Journal of Biomathematics and Biostatistics, 2 (1). ISSN 0973-7340

Wulkow, Hanna and Conrad, T. O. F. and Djurdjevac Conrad, Natasa and Mueller, Sebastian Alexander and Nagel, Kai and Schütte, Ch. (2021) Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts. PLoS ONE, 16 (4). ISSN 1932-6203

Wulkow, Niklas and Koltai, Péter and Schütte, Ch. (2021) Memory-Based Reduced Modelling and Data-Based Estimation of Opinion Spreading. Journal of Nonlinear Science, 31 . ISSN 1432-1467 (online)

Y

Yousef, K. P. and Meixenberger, K. and Smith, M. and Jansen, K. and Bartmeyer, B. and Hamouda, O. and Kücherer, C. and von Kleist, M. (2016) Inferring HIV-1 transmission dynamics in Germany from recently transmitted viruses. Journal of Acquired Immunodeficiency Virus, 73 (3). pp. 356-363. ISSN 1525-4135

Yousef, K. P. and Streck, A. and Schütte, Ch. and Siebert, H. and Hengge, R. and von Kleist, M. (2015) Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. BMC Systems Biology, 9 . p. 39. ISSN 1752-0509

Z

Zhang, W. and Hartmann, C. and von Kleist, M. (2018) Optimal control of Markov jump processes: Asymptotic analysis, algorithms, and application to modelling of chemical reaction systems. Communications in Mathematical Sciences, 16 (2). pp. 293-331. ISSN 1539-6746

Zhang, W. and Klus, S. and Conrad, T. O. F. and Schütte, Ch. (2019) Learning chemical reaction networks from trajectory data. SIAM Journal on Applied Dynamical Systems, 18 (4). ISSN 1536-0040