Complete all-atom hydrodynamics of protein unfolding in uniform flow.

The unfolding dynamics of a protein, ubiquitin, pinned in several uniform flows, was studied at low and high flow rates in an all-atom style through a non-equilibrium molecular dynamics approach with explicit water molecules included. Atomic hydrodynamic force components on individual amino acids, as a function of time, due to the collisional interactions with the flowing water molecules were calculated explicitly. The protein conformational change in response to those time-varying forces was computed completely at the high flow rate up to nanosecond until the fully stretched state was reached.

Atomic hydrodynamics of DNA: coil-uncoil-coil transitions in a wall-bounded shear flow.

Extensive experimental work on the response of DNA molecules to externally applied forces and on the dynamics of DNA molecules flowing in microchannels and nanochannels has been carried out over the past two decades, however, there has not been available, until now, any atomic-scale means of analyzing nonequilibrium DNA response dynamics. There has not therefore been any way to investigate how the backbone and side-chain atoms along the length of a DNA molecule interact with the molecules and ions of the flowing solvent and with the atoms of passing boundary surfaces. We report here on the application of the nonequilibrium biomolecular dynamics simulation method that we developed [G.

Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows.

In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels.

A computational investigation of the three-dimensional unsteady aerodynamics of Drosophila hovering and maneuvering.

Three-dimensional unsteady computations of the flow past a fruit fly Drosophila under hovering and free flight conditions are computed. The kinematics of the wings and the body of the fruit fly are prescribed from experimental observations. The computed unsteady lift and thrust forces are validated with experimental results and are in excellent agreement.

Fluid dynamics of flapping aquatic flight in the bird wrasse: three-dimensional unsteady computations with fin deformation.

Many fishes that swim with the paired pectoral fins use fin-stroke parameters that produce thrust force from lift in a mechanism of underwater flight. These locomotor mechanisms are of interest to behavioral biologists, biomechanics researchers and engineers. In the present study, we performed the first three-dimensional unsteady computations of fish swimming with oscillating and deforming fins.

A three-dimensional computational study of the aerodynamic mechanisms of insect flight.

A finite element flow solver was employed to compute unsteady flow past a three-dimensional Drosophila wing undergoing flapping motion. The computed thrust and drag forces agreed well with results from a previous experimental study. A grid-refinement study was performed to validate the computational results, and a grid-independent solution was achieved.