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Highlight: DNA Nanosensors Designed Computationally

DNA graphene

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DNA sequencing is achieved by following a strand of DNA at a speed that permits recognition of the DNA bases in their actual order, thousands of bases or more for each pass. Nanotechnology can assist in the task, in principle, by furnishing sensors that can resolve single DNA bases and nano-mechanical actuators that pull the DNA in a controlled fashion passing through the sensor. Instead of building and testing actual sensors and actuators it is cheaper and faster to simulate them. Nanoengineers have indeed succeeded with such simulations over the last decade focussing on silicon technology (see October 2004 highlight: Transistor Meets DNA). Now the engineers have moved with their simulations to graphene technology that promises much better resolving power as sensors are thinner and as signals can be detected electronically in graphene (December 2013 and November 2014 highlights). The main unsolved problem is the mechanical actuator: how can one control movement of DNA through a graphene sensor such that measured signals become less noisy and bases can be recognized? A recent study, based on molecular dynamics simulations with NAMD and quantum electronics calculations of graphene, suggests use of an actuator that simultaneously stretches the DNA and pulls it through the sensor. This manipulation leads to a stepwise translocation of DNA through the graphene nanosensor, slowing down DNA translocation and stabilizing DNA bases inside the sensor. Read more on our graphene nanopore website.
Editorials

The Future of Biomolecular Modeling

A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee. Read more

Computational Biology of Membrane Proteins

Since 1988 Illinois researchers have consistently honed their skills in parallel computing, which enabled them to elucidate dynamic processes occurring in many membrane proteins and produce exciting discoveries. By Lisa Pollack Read more

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