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Biophysical simulations

Turing mechanism underlying a branching model for lung morphogenesis

Hui Xu, Mingzhu Sun, Xin Zhao

published 04 Apr 2017

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Automated numerical simulation of biological pattern formation based on visual feedback simulation framework

Mingzhu Sun, Hui Xu, Xingjuan Zeng, Xin Zhao

published 22 Feb 2017

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Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential

Katja Ostermeir, Martin Zacharias

published 16 Feb 2017

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Molecular modeling and molecular dynamic simulation of the effects of variants in the TGFBR2 kinase domain as a paradigm for interpretation of variants obtained by next generation sequencing

Michael T. Zimmermann, Raul Urrutia, Gavin R. Oliver, Patrick R. Blackburn, Margot A. Cousin, Nicole J. Bozeck, Eric W. Klee

published 09 Feb 2017

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Spheroid Formation of Hepatocarcinoma Cells in Microwells: Experiments and Monte Carlo Simulations

Yan Wang, Myung Hee Kim, Seyed R. Tabaei, Jae Hyeok Park, Kyuhwan Na, Seok Chung, Vladimir P. Zhdanov, Nam-Joon Cho

published 29 Aug 2016

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Multi-Scale Modelling of Deformation and Fracture in a Biomimetic Apatite-Protein Composite: Molecular-Scale Processes Lead to Resilience at the μm-Scale

Dirk Zahn, Patrick Duchstein

published 14 Jun 2016

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Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations

Kecheng Yang, Bartosz Różycki, Fengchao Cui, Ce Shi, Wenduo Chen, Yunqi Li

published 26 May 2016

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Spiral and Rotor Patterns Produced by Fairy Ring Fungi

Nathaniel Karst, David Dralle, Sally Thompson

published 02 Mar 2016

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Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters

Fei Liu, Monika Heiner, Ming Yang

published 24 Feb 2016

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CERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics

Atefeh Kazeroonian, Fabian Fröhlich, Andreas Raue, Fabian J. Theis, Jan Hasenauer

published 25 Jan 2016

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Nucleoporin's Like Charge Regions Are Major Regulators of FG Coverage and Dynamics Inside the Nuclear Pore Complex

Mohaddeseh Peyro, Mohammad Soheilypour, Ali Ghavami, Mohammad R. K. Mofrad

published 11 Dec 2015

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Glycosylation Effects on FSH-FSHR Interaction Dynamics: A Case Study of Different FSH Glycoforms by Molecular Dynamics Simulations

Biswa Ranjan Meher, Anshuman Dixit, George R. Bousfield, Gerald H. Lushington

published 24 Sep 2015

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Are Quasi-Steady-State Approximated Models Suitable for Quantifying Intrinsic Noise Accurately?

Dola Sengupta, Sandip Kar

published 01 Sep 2015

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