Biomedical subjects

M E Tuckerman

Publications and source records attributed to M E Tuckerman.

2 recordsLinked to original sources

PubMed2004

Long time molecular dynamics for enhanced conformational sampling in biomolecular systems.

Although molecular dynamics methods are commonly used to drive biomolecular simulations, the technique provides insufficient sampling to impact studies of the 200-300 residue proteins of greatest interest. One severe limitation of molecular dynamics is that the integrators are restricted by resonance phenomena to small time steps (Delta t<8 fs) much slower then the time scales of important structural and solvent rearrangements. Here, a novel set of equations of motion and a reversible, resonance-free, integrator are designed which permit step sizes on the order of 100 fs to be used.

Algorithms↗

PubMed2001

Heavy-atom skeleton quantization and proton tunneling in "intermediate-barrier" hydrogen bonds.

Quantum effects on proton transfer through barriers of several kcal/mol in hydrogen bonds are investigated theoretically in malonaldehyde. Such "intermediate-barrier" proton transfer processes play a key role in the catalytic activity of some enzymes. Tunneling is shown to be significant in this reaction even at room temperature. More importantly, the quantum nature of the heavy molecular frame atoms is found to substantially enhance proton tunneling. These findings have far-reaching implications for common modeling strategies of proton transfer in complex systems such as biomolecules.

Journal Article↗