Water Molecules In The Molecular Dynamics Simulation Of Carbon Nanotubes

Water confined in the nanoscale channel usually has new behaviors different from bulk water, and its micro dynamics properties and mechanism behind attract considerable attention. In the thesis, utilizing molecular dynamics simulations, we research some interesting topics of water and carbon nanotube system in nonuniform electric field, for example molecular water pump, molecular water probe, molecular flip-flop and molecular water gating.Achieving a fast, unidirectional flow of single-file water molecules (UFSWM) across nanochannels is important for membrane-based water purification or seawater desalination. For this purpose, electro-osmosis methods are recognized as a very promising approach and have been extensively discussed in the literature. Utilizing molecular dynamics simulations, here we propose a design for pumping water molecules in a single-walled carbon nanotube in the presence of a linearly gradient electric (GE) field. Such a GE field is inspired by GE fields generated from charged ions located adjacent to biological membrane water nanochannels that can conduct water in and out of cells and can be experimentally achieved by using the charged tip of an atomic force microscope. As a result, the maximum speed of the UFSWM can be1or2orders of magnitude larger than that in a uniform electric (UE) field. Also, inverse transportation of water molecules does not exist in case of the GE field but can appear for the UE field. Thus, the GE field yields a much more efficient UFSWM than the UE field. The giant pumping ability as revealed is attributed to the nonzero net electrostatic force acting on each water molecule confined in the nanotube. These observations have significance for the design of nanoscale devices for readily achieving controllable UFSWM at high speed.The detection of macromolecular conformation is particularly important in many physical and biological applications. Here we theoretically explore a method for achieving this detection, by probing electricity of sequential charged segments of macromolecules. Our analysis is based on molecular dynamics simulations, and we investigate a single file of water molecules confined in a half-capped single-walled carbon nanotube (SWCNT) with an external electric charge,+e or-e (e:the elementary charge). The charge is located in the vicinity of the cap of the SWCNT and along the centerline of the SWCNT. We reveal the picosecond timescale for the re-orientation (namely, from one unidirectional direction to the other) of the water molecules in response to a switch in the charge signal:-eâ†'+e or+eâ†'-e. Our results are well understood by taking into account the electrical interactions between water molecules or between water molecules and an external charge. Because such signals of re-orientations can be magnified and transported according to Tu et al.[2009Proc. Natl. Acad. Sci. USA10618120], it becomes possible to record "fingerprints" of electric signals arising from sequential charged segments of a macromolecule, which are expected to be useful for recognizing the conformation of some particular macromolecules.Based on molecular dynamics simulations, we exploit a class of charge-driven flip-flops that compose of several water molecules confined in a single-walled carbon nanotube. Such a flip-flop has two stable states and can be used to store state information. It can toggle between the two states within2.5-3.5ps (286GHz-400GHz). We reveal that the underlying mechanism is dominated by the interaction between the water molecules and nonuniform electric field generated by point charges. Namely, each water molecule tends to maintain its lowest electric energy by moving toward the location with the highest field strength. This kind of flip-flops may be of value for molecular computing.On the basis of molecular dynamics simulations, we investigate water permeation across a single-walled carbon nanotube (SWCNT) under the influence of four symmetrical half-rings, each having six LiF dipolar molecules. The flux remains almost fixed as the separation, R, between the rings and SWCNT is larger than1.562nm, but decreases significantly as0.944nm<R<1.562nm, and reaches zero as R<0.944nm. This nanochannel shows an excellent on-off gate that is both effectively resistant to dipole noises and sensitive to available signals. The finite element method reveals that the electrostatic field generated by LiF molecules plays a unique role in achieving the gating of the water SWCNT. Each water molecule tends to stay at the most stable state by moving to the location with the highest field strength in order to maintain its lowest electric energy. Our observations may have significance for the design of SWCNT-based nanoscale devices with dipolar molecules.