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The Aksimentiev Group
Theoretical and Computational Research at the Interface of Physics, Biology, and Nanotechnology
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Group
Aleksei Aksimentiev
Behzad Mehrafrooz
Christopher Maffeo
Hemani Chhabra
Jingqian Liu
Kumar Sarthak
Kush Coshic
Parth Chaturvedi
Pin-Yi Li
Siddharth Krishnan
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Research
DNA in biology
DNA–DNA interactions
Nanopores
Synthetic molecular systems
Models & Methodologies
DNA nanotechnology
CUFIX: Champaign-Urbana Non-bonded Fix (NBFIX)
Atomic Resolution Brownian Dynamics
Grid-steered molecular dynamics
Tutorials
Bionanotechnology Tutorial
Electrostatic Maps and Ion Conduction
Introduction to MD simulation of DNA-protein systems
Membrane Proteins Tutorial
Modeling Nanopores for Sequencing DNA
Modeling Synthetic Ion Channels with Coarse-Grained Molecular Dynamics
Rendering with Tachyon
User-Defined Forces in NAMD
VMD Images and Movies Tutorial
Visualizing MD Results: Stretching dsDNA Mini Tutorial
A Practical Guide to DNA Origami Simulations Using NAMD
Analyzing DNA Flexibility
A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems
Protocols in DNA Nanotechology
(2017)
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