• DNA self-assembles into long end-to-end aggregates
  • MD provides structural model and mechanical properties of a complete microtubule
  • A coarse-grained model captures the atomic structure of single-stranded DNA

Trapping double-stranded DNA in a solid-state nanopore

The image of the double helix of DNA has become an icon of biotechnology and genetics. However, this double helix is more than just an aesthetically pleasing image: it gives double-stranded DNA peculiar mechanical properties that are pertinent to biology and biotechnology. We have previously shown that molecules of double-stranded DNA can be electrically driven through tiny pores smaller in diameter than the double helix.

Sequencing DNA using a nanopore capacitor

High-throughput technology for sequencing DNA has already provided invaluable information about the organization of the human genome and the common variations of the genome sequence among groups of individuals. To date, however, the high cost of whole genome-sequencing limits widespread use of this method in basic research and personal medicine. Using nanopores in synthetic silicon membranes for sequencing DNA can dramatic reduce the sequencing costs, as they enable, in principle, direct read out of the nucleotide sequence from the DNA strand via electric measurement.

Ion conductance properties of the phospholamban pentamer

Muscle cells respond to external nerve stimuli by releasing Ca2+ signaling ions from a storage organelle called the sarcoplasmic reticulum (SR). The Ca2+ exposes myosin binding sites on actin filaments, which allows myosin to ratchet along actin and causes the cell to contract. In order for muscle fibers to relax, Ca2+ must be transported from the cytoplasm back to the SR. The Ca2+-ATPase resides in the membrane of the SR and transports two Ca2+ ions against a concentration gradient by using energy of ATP hydrolysis.

Molecular dynamics reveals effective interaction between parallel DNA

DNA is so famously known as the carrier of genetic information that the structural and dynamical aspects of the molecule are often neglected. However, most cellular processes that involve DNA cannot be understood without consideration of its interactions with other DNA and proteins. Such interactions can give rise self-assembled structures, for example DNA supercoils, which we strive to understand using a bottom-up approach by examining the most basic constituents of a larger more complex system.

Electrostatic Tweezers

Understanding how protein machinery of a biological cell packages, copies, and transcribes the encyclopedic information encoded in the genome requires the capability of applying forces like those in nature in a laboratory dish. Although optical traps, magnetic beads and an atomic force microscope can be used to apply forces to individual biomolecules, these tools employ tethers to transmit force from micron-size objects to the biomolecules of interest and generally have low throughput.