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Biophysical simulations

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

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

Dola Sengupta, Sandip Kar

In Silico Adoption of an Orphan Nuclear Receptor NR4A1

Harald Lanig, Felix Reisen, [ ... ], Timothy Clark

The Mechanism by which 146-N-Glycan Affects the Active Site of Neuraminidase

Pi Liu, Zhonghua Wang, [ ... ], Jianping Lin

Weak Interactions between Salmonella enterica FlhB and Other Flagellar Export Apparatus Proteins Govern Type III Secretion Dynamics

Jonathan L. McMurry, Tohru Minamino, [ ... ], Keiichi Namba

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions

Stephen A. Wells, Marc W. van der Kamp, John D. McGeagh, Adrian J. Mulholland

Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter

Hyun Deok Song, Fangqiang Zhu

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations

Federico Fogolari, Alessandra Corazza, [ ... ], Gennaro Esposito

Experimental and Theoretical Investigation of Crystallographic Orientation Dependence of Nanoscratching of Single Crystalline Copper

Yanquan Geng, Junjie Zhang, [ ... ], Tao Sun

An Atlas of Network Topologies Reveals Design Principles for Caenorhabditis elegans Vulval Precursor Cell Fate Patterning

Xianfeng Ping, Chao Tang

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