Single Nucleotides Moving through Nanoslits Composed of Self-Assembled Monolayers via Equilibrium and Nonequilibrium Molecular Dynamics

Abstract

Nonequilibrium molecular dynamics (MD) simulations were used to study the effect of three chemical surface groups on the separation of DNA mononucleotide velocity (or time-of-flight) distributions as they pass through nanoslits. We used nanoslits functionalize with self-assembled monolayers (SAMs) since they have relatively smooth surfaces. The SAM molecules were terminated with either a methyl, methylformyl, or phenoxy group, and the nucleotides were driven electrophoretically with an electric field intensity of 0.1 V/nm in slits about 3 nm wide. Although these large driving forces are physically difficult to achieve experimentally, the simulations are still of great value as they provide molecular level insight into nucleotide translocation events and allow comparison of different surfaces. Nucleotides adsorbed and desorbed from the slit surface multiple times during the simulations. The required slit length for 99% accuracy in identifying the deoxynucleotide monophosphates (dNMPs), based on the separation of the distributions of time of flight, was used to compare the surfaces with shorter lengths indicating more efficient separation. The lengths were 6.5 μm for phenoxy-terminated SAMs, 270 μm for methylformyl-terminated SAMs, and 2400 μm for methyl-terminated SAMs. Our study showed that a slit with a section with methyl termination and the second section with methylformyl termination lead to a required length of 120 μm, which was significantly lower than for only a methylformyl- or methyl-terminated surface.

Electrokinetic transport properties of deoxynucleotide monophosphates (dNMPs) through α-phase phosphorene carbide nanochannel for electrophoretic detection

“…However, nanostructures are usually rich in surface defects 49,50 and surface charges, 51,52 which can significantly influence the adsorption and diffusion of biomolecules on the surface. Furthermore, surface roughness 29 and chemical modification 28 can also affect the interactions of biomolecules with nanostructures. The effects of these factors on the sensing accuracy of the nanodevice certainly deserve further study.…”

“…26 From the theoretical perspective, Moldovanh et al simulated the migration of nucleotides in nanochannels driven by electric fields or water flow and further explored nanochannels modified by chemical surface groups to improve the identification accuracy. [27][28][29] The significance of molecular movements in nanofluid is a unique phenomenon associated with this length scale that is distinct from the microscale. When the dimensions are reduced to the nanoscale, the confinement of liquid can cause significant differences in the molecule's apparent mobility that cannot be achieved at the micro-and macroscale.…”

“…26 From the theoretical perspective, Moldovanh et al simulated the migration of nucleotides in nanochannels driven by electric fields or water flow and further explored nanochannels modified by chemical surface groups to improve the identification accuracy. 27–29…”

Human gait modelling and tracking based on motion functionalisation

“…To eliminate the measurement error caused by irregular gait, we obtain the standard limb movement trajectory and various characteristic parameters, and analyse the same using secondary offline data processing. In the process, a high-order polynomial fitting method is first used to fit the actual measurement data to obtain the error curve and the error data at each sampling point [5]. This curve reflects the macroscopic position of the limbs during walking.…”