MoS2 Nanopores Research Articles

A molecular dynamics study on water desalination using single-layer MoSe2 nanopore

Development of low-cost and high-efficiency seawater desalination technologies is critical for solving the global water crisis. In this study, we proposed a fast water filtering method, with a high salt rejection rate, that uses MoSe2 nanopore via molecular dynamics (MD) simulation. These simulation results suggest that fast water filtering and high salt rejection rates can be achieved using MoSe2 nanopore with a pore size of 66.54 Å2. Water permeation through the MoSe2 nanopore is larger than that through the MoS2 nanopore of various size, and the water flux through both MoSe2 and MoS2 nanopores is much larger than that through the graphene nanopore of similar nanopore size. The underlying mechanism of water transportation through both MoSe2 and MoS2 nanopores are discussed after analysis of the water permeation potential of mean force (PMF), the 2D density of the water molecule inside the nanopores, the dipole of water molecules during transportation, etc. Our results suggest that a 1-cm2 MoSe2 nanopore (66.54 Å2) membrane can produce freshwater with a flow rate of 10.1 L per day per MPa under 150 MPa, which it is about 2 orders of magnitude higher than the currently used commercial reverse osmosis (RO) membrane.

Study on the adsorption orientation of DNA on two-dimensional MoS2 surface via molecular dynamics simulation: A vertical orientation phenomenon

The development of two-dimensional materials rise new options on the promising application of biosensors and DNA sequencing. In particular, molybdenum disulfide (MoS2) material has become the focus of current research due to its unique properties and advantages. An in-depth understanding of the interfacial interaction between materials and biomolecules is critical in biomedical field. Therefore, the directional selection of double-stranded DNA (ds-DNA) on the MoS2 surface was studied by molecular dynamics (MD) simulation in this work. The simulation results showed that double-strand DNA (ds-DNA) was vertically adsorbed on the MoS2 surface through terminal bases, and the main driving forces is Van der Waals force. In addition, our results indicate that the length and base sequence of ds-DNA are independent of its selection of vertically adsorbed orientation, which may be beneficial for improving the development of fast DNA sequencing technology through MoS2 nanopore in the future. Moreover, the ds-DNA structure is still stable after adsorption on the surface of MoS2. These simulation results greatly enhanced our understanding on the interaction between ds-DNA and MoS2 and may promote the promising application of MoS2 in the field of biosensor and DNA sequencing.

Water transport through graphene and MoS2 nanopores

In this work, pressure-driven water transport through graphene and molybdenum disulfide (MoS2) nanopores is investigated through molecular dynamics simulations. The dependence of water flow rate on the pore area and pressure drop is studied for various pore structures. Power-law relationships, Q∝Aα, with α ranging from 1.6 to 1.9 between the flow rate (Q) and the pore area (A), are found, while the flow rate increases linearly with increasing pressure drop. The transport results are explained by the diffusion coefficient and friction coefficient of water molecules through the nanopores, as well as the free energy barriers at the pores.

Nanopores in 2D MoS2: Defect-Mediated Formation and Density Modulation

Oxidation is a scalable process for introducing nanopores in two-dimensional transitional metal dichalcogenides (TMDs) for membrane applications. The nanopore density is determined by the areal density of their nucleation sites; understanding the nature of the defects and their control would enable tailoring of TMD membranes for targeted applications. In this work, we show that the nanopore distribution is dramatically different in strained and unstrained MoS2 crystals. We correlate this spatial distribution to the underlying arrangement of dislocations in MoS2 crystals, in contrast to previously suggested sulfur vacancies. To control the nucleation density of MoS2 nanopores, we demonstrate that the pore density can be modulated by electron beam exposure prior to the nanopore formation. Raman analysis of electron beam-exposed samples indicates that hydrocarbon adsorption activates defect species other than dislocations, which significantly enhances the nanopore density in MoS2.

Light-Enhanced Blue Energy Generation Using MoS2 Nanopores

Summary Blue energy relies on the chemical potential difference between solutions of high and low ionic concentrations, potentially providing an independent energy source at estuaries around the world. The energy conversion relies on reverse electrodialysis via ion-selective membranes. A novel generation of these membranes is based on nanopores in atomically thin material. Single nanopores in molybdenum disulfide (MoS2)-based membranes have shown record-high power outputs in alkaline conditions. By increasing the surface charge of MoS2 membranes by light, we can double the osmotic power generated by a single nanopore at a neutral pH. The increased surface charge at the pore rim enhances the ion selectivity and leads to a larger osmotic voltage (dominating in small pores), while the increased surface charge of the membrane enhances the surface conductance, leading to a larger osmotic current (dominating in larger pores). The combination of these effects could efficiently boost the energy generation using membranes containing arrays of nanopores of varying sizes.

A potential sensing mechanism for DNA nucleobases by optical properties of GO and MoS2 Nanopores

We propose a new DNA sensing mechanism based on optical properties of graphene oxide (GO) and molybdenum disulphide (MoS2) nanopores. In this method, GO and MoS2 is utilized as quantum dot (QD) nanopore and DNA molecule translocate through the nanopore. A recently-developed hybrid quantum/classical method (HQCM) is employed which uses time-dependent density functional theory and quasi-static finite difference time domain approach. Due to good biocompatibility, stability and excitation wavelength dependent emission behavior of GO and MoS2 we use them as nanopore materials. The absorption and emission peaks wavelengths of GO and MoS2 nanopores are investigated in the presence of DNA nucleobases. The maximum sensitivity of the proposed method to DNA is achieved for the 2-nm GO nanopore. Results show that insertion of DNA nucleobases in the nanopore shifts the wavelength of the emitted light from GO or MoS2 nanopore up to 130 nm. The maximum value of the relative shift between two different nucleobases is achieved by the shift between cytosine (C) and thymine (T) nucleobases, ~111 nm for 2-nm GO nanopore. Results show that the proposed mechanism has a superior capability to be used in future DNA sequencers.

Fabrication and practical applications of molybdenum disulfide nanopores.

Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS2) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin membranes have the advantage of providing relatively high ionic currents at very small pore sizes. This increases the signal generated during translocation of biomolecules and improves the nanopores' efficiency when used for desalination or reverse electrodialysis applications. The atomic thickness of MoS2 nanopores approaches the inter-base distance of DNA, creating a potential candidate for DNA sequencing. In terms of geometry, MoS2 nanopores have a well-defined vertical profile due to their atomic thickness, which eliminates any unwanted effects associated with uneven pore profiles observed in other materials. This protocol details all the necessary procedures for the fabrication of solid-state devices. We discuss different methods for transfer of monolayer MoS2, different approaches for the creation of nanopores, their applicability in detecting DNA translocations and the analysis of translocation data through open-source programming packages. We present anticipated results through the application of our nanopores in DNA translocations and osmotic power generation. The procedure comprises four parts: fabrication of devices (2-3 d), transfer of MoS2 and cleaning procedure (24 h), the creation of nanopores within MoS2 (30 min) and performing DNA translocations (2-3 h). We anticipate that our protocol will enable large-scale manufacturing of single-molecule-analysis devices as well as next-generation DNA sequencing.

Molecular Dynamics Investigation of Polylysine Peptide Translocation through MoS2 Nanopores.

Solid-state nanopores (SSN) made of two-dimensional materials such as molybdenum disulfide (MoS2) have emerged as candidate devices for biomolecules sequencing. SSN sequencing is based on measuring the variations in ionic conductance as charged biomolecules translocate through nanometer-sized channels, in response to an external voltage applied across the membrane. Although several experiments on DNA translocation through SSNs have been performed in the past decade, translocation of proteins has been less studied, partly due to small protein size and detection limits. Moreover, the threading of proteins through nanopore channels is challenging, because proteins can exhibit neutral global charge and not be sensitive to the electric field. In this paper, we investigate the translocation of lysine residues and a model protein with polylysine tags through MoS2 nanoporous membranes using molecular dynamics simulations. Adding lysine tags to biological peptides is the method proposed here to promote the entrance of proteins through SSN. Specifically, we study the relationship existing between the translocation events and the ionic conductance signal drops. We show that individual lysine residues translocate easily through MoS2 nanopores, but the translocation speed is extremely fast, which leads to indiscernible ionic conductance drops. To reduce the translocation speed, we demonstrate that increasing the thickness of the membrane from single-layer to bilayer MoS2 reveals a stepwise process of translocation with discernible conductance drops that could be measured experimentally. Finally, a study of the threading of proteins with polylysine tags through MoS2 nanopores is presented. The addition of the positively charged tag to the neutral protein allows the threading and full translocation of the protein through the pore (at least two lysine residues are necessary in this case to observe translocation) and a similar sequence of translocation events is detected, independently of the tag length.

Improved model of ionic transport in 2-D MoS2 membranes with sub-5 nm pores

Solid-state nanopores made of two-dimensional materials such as molybdenum disulfide are of great interest thanks in part to promising applications such as ion filtration and biomolecule translocation. Controlled fabrication and tunability of nanoporous membranes require a better understanding of their ionic conductivity capabilities at the nanoscale. Here, we developed a model of ionic conductivity for a KCl electrolyte through sub 5-nm single-layer MoS2 nanopores using equilibrium all-atom molecular dynamics simulations. We investigate the dynamics of K+ and Cl− ions inside the pores in terms of concentration and mobility. We report that, for pore dimensions below 2.0 nm, which are of particular interest for biomolecule translocation applications, the behaviors of the concentration and mobility of ions strongly deviate from bulk properties. Specifically, we show that the free-energy difference for insertion of an ion within the pore is proportional to the inverse surface area of the pore and that the inverse mobility scales linearly as the inverse diameter. Finally, we provide an improved analytical model taking into account the deviation of ion dynamics from bulk properties, suitable for direct comparison with experiments.

Generating Sub-nanometer Pores in Single-Layer MoS2 by Heavy-Ion Bombardment for Gas Separation: A Theoretical Perspective.

Single-layer molybdenum disulfide (MoS2) filters with nanometer-size pores have attracted great attention recently due to their promising performance for membrane separation. Generating nanopores in MoS2 controllably, however, is still a challenging task, which greatly limits the real application of MoS2 filters. In this work, the pore forming process in single-layer MoS2 by heavy-ion bombardment was investigated in detail using molecular dynamics simulations. We found that pores with sub-nanometer size (0.6-1.2 nm) can be created in the MoS2 sheet by single-ion bombardment, with a probability as high as 0.8 pores per incident ion. The size and shape of the nanopore can be tuned controllably by adjusting bombardment parameters. Furthermore, the performance of the MoS2 filter with these sub-nanometer-size pores for separation of He, Ne, H2, Ar, and Kr gases was evaluated by density functional theory-based first-principles calculations. The MoS2 filter was found to show much higher selectivity for separating H2/He and He/Ne than that reported for graphene and other membranes. Such high selectivity was attributed to the interaction between gases and the charged edge of pores in MoS2. Our results suggest the potential application of ion beam technology in single-layer MoS2 for membrane separation.

In Situ Repair of 2D Chalcogenides under Electron Beam Irradiation.

Molybdenum disulfide (MoS2 ) and bismuth telluride (Bi2 Te3 ) are the two most common types of structures adopted by 2D chalcogenides. In view of their unique physical properties and structure, 2D chalcogenides have potential applications in various fields. However, the excellent properties of these 2D crystals depend critically on their crystal structures, where defects, cracks, holes, or even greater damage can be inevitably introduced during the preparation and transferring processes. Such defects adversely impact the performance of devices made from 2D chalcogenides and, hence, it is important to develop ways to intuitively and precisely repair these 2D crystals on the atomic scale, so as to realize high-reliability devices from these structures. Here, an in situ study of the repair of the nanopores in MoS2 and Bi2 Te3 is carried out under electron beam irradiation by transmission electron microscopy. The experimental conditions allow visualization of the structural dynamics of MoS2 and Bi2 Te3 crystals with unprecedented resolution. Real-time observation of the healing of defects at atomic resolution can potentially help to reproducibly fabricate and simultaneously image single-crystalline free-standing 2D chalcogenides. Thus, these findings demonstrate the viability of using an electron beam as an effective tool to precisely engineer materials to suit desired applications in the future.

Transverse Detection of DNA in a MoS2 Nanopore

Solid-state nanopores can be used for single-molecule detection and potentially provide a platform for rapid DNA sequencing. DNA molecules along with water and ions are electrophoretically driven through a small orifice in a membrane. The ionic current blockade is measured and provides information about the size and the length of the molecule. Typically, solid-state nanopores are fabricated in relatively thick material (20nm), thus not providing single-base resolution. Recently, monolayer materials such as MoS2 have proven very useful in detecting and differentiating single nucleotides. Compared to e.g. graphene, monolayer MoS2 is an intrinsic semiconductor with a bandgap of 1.8eV and can thus be used to fabricate a field effect transistor. Here we show that a nanopore in monolayer MoS2 can be integrated with a two-dimensional field-effect transistor. We report simultaneous and correlated detection of the ionic current trace and the transverse sheet current through suspended MoS2 during DNA translocation. Signal-to-noise ratios in the sheet current are superior to ionic current and seem to follow a different sensing principle. During translocation through the nanopore, the negative charge of DNA decreases the drain-source conductance of the n-type semiconductor, effectively gating the semiconductor. Such a device configuration might overcome resolution limitations due to the dominating access-resistance in ionic current through ultra-thin membranes. Furthermore, this technology provides a simple way of parallelization: An array of nanopores can be created on the same membrane without the need of fabricating individually addressable microfluidic chambers. The ionic voltage would then just act as the driving force of bringing the molecules to the field-effect transistor and all detection is done on the transistors. Further work is required in order to better understand the sensing principle and establish the resolution of these new devices.

Protein Translocation through a MoS2 Nanopore:A Molecular Dynamics Study

Single-molecule protein sequencing is essential for a wide range of research and application fields, where the recently emerging 2D nanopores have open unprecedented possibilities. The protein translocating through a 2D nanopore plays vital roles in the nanopore-based analysis, where various detection or sequencing method could be employed. It is critically important to study the protein translocating through various 2D nanopores, which may help design efficient nanopore devices. However, few 2D materials other than graphene have been studied in this context yet. In this work, molecular dynamics (MD) simulations were employed to investigate the feasibility of single-molecule protein sequencing with a MoS2 nanopore. Both phenylalanine–glycine repeat peptides and a peptide with the sequence taken from the thioredoxin protein were studied in their extended unfolded state, which adsorbed onto the MoS2 membrane spontaneously. These peptides kept adsorbing onto MoS2 and permeated unidirectionally through the Mo...

Theoretical studies on key factors in DNA sequencing using atomically thin molybdenum disulfide nanopores.

Nanopore-based DNA sequencing is considered to be a low-cost, high resolution and superfast method. Solid state nanopores, especially MoS2 nanopores, have been considered to be a promising choice for DNA sequencing. However, researchers still have a very limited understanding of the effects of multiple factors on MoS2-based DNA sequencing. In this study, the effects of the applied voltage and the diameter of the MoS2 nanopore on the resolution of DNA sequencing were investigated. Our results demonstrate that the translocation time of DNA can increase with a decrease in the applied voltage. DNA can be stretched significantly to translocate a 2 nm nanopore under a high applied voltage (>400 mV nm-1). To achieve a 1 base per μs translocation speed (1 GHz bandwidth), we suggest that three methods could be applied, including a decrease in the applied voltage, a decrease in the diameter of the MoS2 nanopore or modification of the MoS2 nanopore. In addition, the size of the nanopore can severely affect the possibility of DNA entering the nanopore, and the translocation time of DNA could be significantly increased with a smaller MoS2 nanopore. These findings may help to design MoS2 nanopores with higher resolution for use in DNA sequencing.

The impact of membrane surface charges on the ion transport in MoS2 nanopore power generators

Recent experiments demonstrated giant osmotic effects induced in a single-atomic-layer MoS2 nanopore by imposing a KCl concentration bias, thereby highlighting the prospect of ultrathin nanopores as power generators. In this work, we report on an electrokinetic analysis of the ionic transport in the MoS2 nanopore system. By taking membrane surface chemistry into account, we found profound roles of surface charges in and out of the nanopore on the cross-pore ion transport, which shed light on the intriguing experimental observations of a high pore conductance with a large open-circuit voltage in the MoS2 system. The present work establishes a theoretical model capable of dealing with ultrathin membrane surface charges for evaluating the energy conversion performance of nanopore power generators constructed with two-dimensional materials.

Physical Model for Rapid and Accurate Determination of Nanopore Size via Conductance Measurement.

Nanopores have been explored for various biochemical and nanoparticle analyses, primarily via characterizing the ionic current through the pores. At present, however, size determination for solid-state nanopores is experimentally tedious and theoretically unaccountable. Here, we establish a physical model by introducing an effective transport length, Leff, that measures, for a symmetric nanopore, twice the distance from the center of the nanopore where the electric field is the highest to the point along the nanopore axis where the electric field falls to e-1 of this maximum. By [Formula: see text], a simple expression S0 = f (G, σ, h, β) is derived to algebraically correlate minimum nanopore cross-section area S0 to nanopore conductance G, electrolyte conductivity σ, and membrane thickness h with β to denote pore shape that is determined by the pore fabrication technique. The model agrees excellently with experimental results for nanopores in graphene, single-layer MoS2, and ultrathin SiNx films. The generality of the model is verified by applying it to micrometer-size pores.

Dominance of Dispersion Interactions and Entropy over Electrostatics in Determining the Wettability and Friction of Two-Dimensional MoS2 Surfaces.

The existence of partially ionic bonds in molybdenum disulfide (MoS2), as opposed to covalent bonds in graphene, suggests that polar (electrostatic) interactions should influence the interfacial behavior of two-dimensional MoS2 surfaces. In this work, using molecular dynamics simulations, we show that electrostatic interactions play a negligible role in determining not only the equilibrium contact angle on the MoS2 basal plane, which depends solely on the total interaction energy between the surface and the liquid, but also the friction coefficient and the slip length, which depend on the spatial variations in the interaction energy. While the former is found to result from the exponential decay of the electric potential above the MoS2 surface, the latter results from the trilayered sandwich structure of the MoS2 monolayer, which causes the spatial variations in dispersion interactions in the lateral direction to dominate over those in electrostatic interactions in the lateral direction. Further, we show that the nonpolarity of MoS2 is specific to the two-dimensional basal plane of MoS2 and that other planes (e.g., the zigzag plane) in MoS2 are polar with respect to interactions with water, thereby illustrating the role of edge effects, which could be important in systems involving vacancies or nanopores in MoS2. Finally, we simulate the temperature dependence of the water contact angle on MoS2 to show that the inclusion of entropy, which has been neglected in recent mean-field theories, is essential in determining the wettability of MoS2. Our findings reveal that the basal planes in graphene and MoS2 are unexpectedly similar in terms of their interfacial behavior.

Single-layer MoS2 nanopores as nanopower generators.

Making use of the osmotic pressure difference between fresh water and seawater is an attractive, renewable and clean way to generate power and is known as 'blue energy'. Another electrokinetic phenomenon, called the streaming potential, occurs when an electrolyte is driven through narrow pores either by a pressure gradient or by an osmotic potential resulting from a salt concentration gradient. For this task, membranes made of two-dimensional materials are expected to be the most efficient, because water transport through a membrane scales inversely with membrane thickness. Here we demonstrate the use of single-layer molybdenum disulfide (MoS2) nanopores as osmotic nanopower generators. We observe a large, osmotically induced current produced from a salt gradient with an estimated power density of up to 10(6) watts per square metre--a current that can be attributed mainly to the atomically thin membrane of MoS2. Low power requirements for nanoelectronic and optoelectric devices can be provided by a neighbouring nanogenerator that harvests energy from the local environment--for example, a piezoelectric zinc oxide nanowire array or single-layer MoS2 (ref. 12). We use our MoS2 nanopore generator to power a MoS2 transistor, thus demonstrating a self-powered nanosystem.

Water desalination with a single-layer MoS2 nanopore.

Efficient desalination of water continues to be a problem facing the society. Advances in nanotechnology have led to the development of a variety of nanoporous membranes for water purification. Here we show, by performing molecular dynamics simulations, that a nanopore in a single-layer molybdenum disulfide can effectively reject ions and allow transport of water at a high rate. More than 88% of ions are rejected by membranes having pore areas ranging from 20 to 60 Å2. Water flux is found to be two to five orders of magnitude greater than that of other known nanoporous membranes. Pore chemistry is shown to play a significant role in modulating the water flux. Pores with only molybdenum atoms on their edges lead to higher fluxes, which are ∼70% greater than that of graphene nanopores. These observations are explained by permeation coefficients, energy barriers, water density and velocity distributions in the pores.

Identification of single nucleotides in MoS2 nanopores.

The size of the sensing region in solid-state nanopores is determined by the size of the pore and the thickness of the pore membrane, so ultrathin membranes such as graphene and single-layer molybdenum disulphide could potentially offer the necessary spatial resolution for nanopore DNA sequencing. However, the fast translocation speeds (3,000-50,000 nt ms(-1)) of DNA molecules moving across such membranes limit their usability. Here, we show that a viscosity gradient system based on room-temperature ionic liquids can be used to control the dynamics of DNA translocation through MoS2 nanopores. The approach can be used to statistically detect all four types of nucleotide, which are identified according to current signatures recorded during their transient residence in the narrow orifice of the atomically thin MoS2 nanopore. Our technique, which exploits the high viscosity of room-temperature ionic liquids, provides optimal single nucleotide translocation speeds for DNA sequencing, while maintaining a signal-to-noise ratio higher than 10.