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The Aksimentiev Group
Theoretical and Computational Research at the Interface of Physics, Biology, and Nanotechnology
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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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Review Articles
Cover Gallery
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
Tutorials
A Practical Guide to DNA Origami Simulations Using NAMD
Introduction to Molecular Dynamics Showcase
Analyzing the Changes in DNA Flexibility due to Base Modifications Using NAMD
Introduction to MD simulations of Plasmonic Nanotweezers
Multi-resolution simulations of self-assembled DNA nanostructures
Images and animations of DNA nanostructures with VMD
All-atom simulation membrane-spanning DNA nanopores
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