Dynamical Behaviors Of Molecules And Ions In Bio-and Nano-confined Spaces And Their Regulation

The dynamical behaviors including transport properties and conformation changes innanoconfined spaces involve a number of complex physical, chemical, and biological processes, andthus are a heat topic in the field of molecular physical mechanics. Although different confined spaceshave different specific topologies, but they can be generally divided into two types in terms of thedimensionality of the system: one-dimensional (1D) and two-dimensional (2D) confined spaces. In1D confined spaces, two translational degrees of freedom are restricted, while only one translationaldegree of freedom in2D confined spaces is restricted.As representative for the1D confined space, the1D nanometer-sized conduction pores of themembrane channel proteins widely exsiting in organisms allow fast transport of certain ions andsmall molecules across the cell membrane, thus playing fundamental roles in neural signaltransduction. With the fast development of nanoscience and nanotechnology, novel nanomaterialswith hollow structures are constantly emerging, including carbon and boron nitride nanotubes,providing us a simplified model for the research on the dynamical behaviors of confined moleculesand ions in1D nanochannels, as well as the possibility to reproduce the excellent properties ofbiological channels in artificial1D nanochannels such as high permeability. Researches based onsuch nanoconfined systems not only help to unveil the mechanism of structure-function correlationof biological channels, but also hold promise in the fields of designing novel nanodevices, efficientfiltration membranes and so on. In addition, when compressing a1D confined space along the freedirection to a thickness of single atom, one can obtain a novel type of nanoconfined space, such asthe nanometer-sized pores in a monolayer graphene or hexagonal boron nitride. Use of such confinedspace could greatly increase the resolution of single molecule characterization. The2D confinedspaces have two main types: solid surfaces that can adsorb liquid, and the confined area between twosolid surfaces separated by several nanometers. The dynamics such as fluidity and phase behavior ofconfined liquid in2D spaces are constantly the focus of the fields of nano-tribology and so on. Inthis thesis, using molecular dynamics simulations and first principle calculations, we investigate thenovel dynamical behaviors of molecules and ions in some typical biological and artificial1D and2Dconfined spaces as well as their regulation, and reveal the underlying physical mechanicalmechanism. The findings are briefly concluded as follows:(1) The solvation of ions confined in the1D conduction pore of a sodium ion channel and the structural stability of the channel protein. The sodium channel protein regulates the transportof sodium ions across cell membranes, playing a fundamental role in life activities. Compared tothose for potassium channels and NaK channels (a non-selective ion channels that can conduct bothpotassium and sodium ions), the selectivity filter of NavAb channel, a sodium channel fromArcobacter butzleri, is wider and shorter. Ions inside the selectivity filter present in a mostly hydratedstate. We determined by extensive molecular dynamics simulations the coordination states of sodiumions in the selectivity filter, and found that the coordination of ion in most regions of the selectivityfilter is nearly identical to that in bulk solution. When ion is located at the binding site, it canoccasionally coordinate with the channel protein, but the ligands are contributed only by residuesfrom one or two polypeptide chain(s) simultaneously. For instance, the sodium ion in the HFS sitecoordinates with the side chains of one or two Glu177, leading to the deflection of side chains andbreaking the symmetry of the four Glu177residues. Such change can be read from the RMSD profileof the selectivity filter. In addition, the RMSD results also suggest that the selectivity filter exhibitsrobust stability for various initial ion configurations even in the absence of ions, in sharp contrast tothe situations for the potassium and NaK channels, in which the selectivity filters can only be stablefor certain ion arrangements. Finally, the potential force mean profile shows that sodium ions candiffusion freely against slight energy barriers between different binding sites in the selectivity filter.(2) Directional transport of1D water chains confined in vibrating carbon nanotubes.Researches on fluid transport at the nanoscale hold great promise in the fields of designing novel fluidsensors and filration membranes. However, it is quite difficult to drive fluid transport at the nanoscalewith the principles involved in macroscopic pumps. We found by molecular dynamics simulations thata vibrating carbon nanotube can serve as an efficient nanopump for water transport. The water chaininside the nanotube is found to be always continuous when vibrating together with the tube. Theincrease in amplitude of vibration leads to the increase in the water flux, while increasing thefrequency beyond a critical value will reduce the water flux. Furthermore, the directional watertransport by a vibrating carbon nanotube holds good not only for a single-filed water chain in anarrow carbon nanotube, but also for bulk-like water columns inside wider nanotubes. As it has beensuggested that the vibration of nanotubes can be powered by the environmental energies such as wasteheat, noise and external fields, our present design provides a novel route to utilize such energies.(3) Detecting ssDNA at single-nucleotide resolution by nanopores in monoatomic graphene.The nanopores used in conventional nanopore DNA sequencing are several nanometers in length,which permit10~15nucleotides occupying them at a time. Thus it is very difficult to realizesingle-nucleotide resolution DNA detection using these nanopores. Graphene nanopores provide the possibility to significantly increase the resolution of nanopore DNA detection, due to itsone-atom-thick nature. We show by steered molecular dynamics simulations that a single-strandedDNA (ssDNA) transports in a ratchet-like fashion when pulled through a graphene nanopore with adiameter of~1nm. Different nucleotides can be readily distinguished at a resolution of a single base,by monitoring the strength of the peaks in the pulling force profile during the ssDNA passage. Forwider nanoproes, the ssDNA molecule can easily pass through, and one cannot obtain asingle-nucleotide resolution force signal. These findings indicate the critical role of the nanopore sizein fast nanopore DNA sequencing.(4) Electromelting of2D monolayer ice confined between two parallel plates. We investigateby molecular dynamics simulations the structure and dynamics of ice/water confined between twoplates, and found that the confined monolayer ice can melt into liquid water under perpendicularlyapplied electric field beyond3.8V/nm, which can be named as electromelting. This phase transition isin sharp contrast to the prevailing view that electric fields promote water freezing, and is caused bythe electric-field-induced breaking of the ordered network of hydrogen bond. The simulation resultsalso show that the melting temperature of the monolayer ice decreases with an increasing strength ofthe external field. When the field exceeds~30V/nm, the confined system transforms again into ahighly ordered crystal-like structure. These findings of phase transitions under electric fields shouldadd an important new ingredient to the physics of water.