Fang Hai-Ping

Protein Folding under Mediation of Ordering Water: an Off-Lattice Gō-Like Model Study

Water plays an important role in the sturcture and function of bimolecules. Water confined at the nanascale usually exhibits phenomena not seen in bulk water, including the ice-like ordering structure on the surfaces of many substrates. We investigate the behaviour of protein folding in which the proteins are assumed in an environment with ordering water by using of an off-lattice G (o) over bar -like model. It is found that in the physiological temperature, both the folding rate and the thermodynamic stability of the protein are greatly promoted by the existence of ordering of water.

Test of the Possible Application of the Half-Way Bounce-Back Boundary Condition for Lattice Boltzmann Methods in Complex Geometry*

The way of handling boundary conditions with simple bounce-back rule in the lattice gas and lattice Boltzmann method had been considered as one of the advantage compared with other numerical schemes. The half-way bounce-back rule inherits the advantage of the bounce-back rule and improves the accuracy to the second-order on flat boundaries. In this paper, we test the possible application of the half-way bounce-back rule to the system with complex geometry. Our simulation results show that the half-way bounce-back rule is a good boundary condition in the problems without emphasis on accuracy.

Lattice Boltzmann simulation of transverse wave travelling in Maxwell viscoelastic fluid

A nine-velocity lattice Boltzmann method for Maxwell viscoelastic fluid is proposed. Travelling of transverse wave in Maxwell viscoelastic fluid is simulated. The instantaneous oscillating velocity, transverse shear speed and decay rate agree with theoretical results very well.

LATTICE BOLTZMANN METHOD SIMULATION ON THE FLOW OF TWO IMMISCIBLE FLUIDS IN COMPLEX GEOMETRY

The multicomponent nonideal gas lattice Boltzmann model by Shan and Chen (S-C) can be used to simulate the immiscible fluid flow. In this paper, we show that the relaxation constant τ ≤ 1 is a necessary condition for the immiscible fluid flow in the S-C model. In a system with very complex boundary geometry, for 0.8 ≤ τ ≤ 1, the S-C model describes the immiscible flow quite well, and τ=1 is the best.

A Lattice Boltzmann Boundary Condition at Impermeable Boundaries

A hydrodynamic boundary condition for the lattice Boltzmann model at impermeable boundaries is developed. This boundary condition satisfies both the no-slip condition and the fluid conservation at boundary nodes. Poiseuille flow and Couette flow are calculated with this technique to demonstrate the accuracy of the present boundary condition.

Local Compression Properties of Double-Stranded DNA Based on a Dynamic Simulation

The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA are systematically studied by changing the tip size. The compression simulation results for the 16 nm diameter sphere tip are well consistent with the experimental results. With the diameter of the tip decreasing, the radial compressive elastic properties under external loads become sensitive to the tip size and the local DNA conformation. There appears a suddenly force break in the compression-force curve when the sphere size is less than or equal to 12 nm diameter. The analysis of the hydrogen bonds and base stacking interaction shows there is a local unwinding process occurs. During the local unwinding process, first the hydrogen bonds between complement base pairs are broken. With the compression aggregating, the local backbones in the compression center are unwound from the double helix conformation to a kind of parallel conformation. This local unwinding behavior deducing by external loads is helpful to understand the biological process, and important to DNA-based nanomechanical devices.

Understanding symmetric and asymmetric DNA patterns by water flow on a solid surface

In order to use DNA for making molecular device, specific DNA patterns on a solid surface should be constructed. In this paper, we will show that the random interactions between the DNA segments and the solid surface play an important role in the final. symmetric and asymmetric DNA patterns obtained by water flow.

A Scaling Property in the Non-stationary Dissipative Dynamical Systems*

A scaling property about the parameter shifts for the critical points of the period-doubling bifurcation is exploited for the non-stationary dynamical systems.