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made with VMD
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.
made with VMD
For centuries, millions of people around the globe have been troubled with a movement disorder that usually starts with a tremor in one hand. The disorder, later known as Parkinson's disease, affects commonly older individuals and disrupts patient's movement, sleep and speech from the brain. There is currently no cure for the disease. Key to the disease, progressively occurring in patient's brain, is the loss of neuron cells due to aggregation of a small protein named α-synuclein. Extensive studies have been carried out, yet the function of the protein remains a mystery. It is amazing that aggregation of such small proteins eventually leads to neuronal cell death and generates tremendous difficulties in peoples' life. In a recent report, a team of computational scientists attributed the cause of α-synuclein aggregation to a hairpin structure involving just a small region (amino acids 38-53) in the middle of the protein. With extensive simulations (over 180 μs in total), the researchers revealed that a short fragment encompassing region 38-53, exhibiting a high probability of forming a β-hairpin structure, is a key region during α-synuclein aggregation. Moreover, the researchers predicted a mutation that impedes β-hairpin formation, thereby retarding α-synuclein aggregation. The discoveries, made possible through the software NAMD and VMD, are expected to shed light on the mechanism underlying Parkinson's disease and to inspire the design of drugs. More on our α-synuclein website.