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Biophysical simulations

Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state

Becka M. Warfield, Peter C. Anderson

Turing mechanism underlying a branching model for lung morphogenesis

Hui Xu, Mingzhu Sun, Xin Zhao

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

Mingzhu Sun, Hui Xu, Xingjuan Zeng, Xin Zhao

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

Katja Ostermeir, Martin Zacharias

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, [ ... ], Eric W. Klee

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

Yan Wang, Myung Hee Kim, [ ... ], Nam-Joon Cho

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

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

Kecheng Yang, Bartosz Różycki, [ ... ], Yunqi Li

Spiral and Rotor Patterns Produced by Fairy Ring Fungi

Nathaniel Karst, David Dralle, Sally Thompson

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

Fei Liu, Monika Heiner, Ming Yang

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

Atefeh Kazeroonian, Fabian Fröhlich, [ ... ], Jan Hasenauer

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

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

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