Deep-WET: a deep learning-based approach for predicting DNA-binding proteins using word embedding techniques with weighted features.

DNA-binding proteins (DBPs) play a significant role in all phases of genetic processes, including DNA recombination, repair, and modification. They are often utilized in drug discovery as fundamental elements of steroids, antibiotics, and anticancer drugs. Predicting them poses the most challenging task in proteomics research. Conventional experimental methods for DBP identification are costly and sometimes biased toward prediction. Therefore, developing powerful computational methods that can accurately and rapidly identify DBPs from sequence information is an urgent need. In this study, we propose a novel deep learning-based method called Deep-WET to accurately identify DBPs from primary sequence information. In Deep-WET, we employed three powerful feature encoding schemes containing Global Vectors, Word2Vec, and fastText to encode the protein sequence. Subsequently, these three features were sequentially combined and weighted using the weights obtained from the elements learned through the differential evolution (DE) algorithm. To enhance the predictive performance of Deep-WET, we applied the SHapley Additive exPlanations approach to remove irrelevant features. Finally, the optimal feature subset was input into convolutional neural networks to construct the Deep-WET predictor. Both cross-validation and independent tests indicated that Deep-WET achieved superior predictive performance compared to conventional machine learning classifiers. In addition, in extensive independent test, Deep-WET was effective and outperformed than several state-of-the-art methods for DBP prediction, with accuracy of 78.08%, MCC of 0.559, and AUC of 0.805. This superior performance shows that Deep-WET has a tremendous predictive capacity to predict DBPs. The web server of Deep-WET and curated datasets in this study are available at https://deepwet-dna.monarcatechnical.com/ . The proposed Deep-WET is anticipated to serve the community-wide effort for large-scale identification of potential DBPs.

Atomic Layer Deposition-A Versatile Toolbox for Designing/Engineering Electrodes for Advanced Supercapacitors.

Atomic layer deposition (ALD) has become the most widely used thin-film deposition technique in various fields due to its unique advantages, such as self-terminating growth, precise thickness control, and excellent deposition quality. In the energy storage domain, ALD has shown great potential for supercapacitors (SCs) by enabling the construction and surface engineering of novel electrode materials. This review aims to present a comprehensive outlook on the development, achievements, and design of advanced electrodes involving the application of ALD for realizing high-performance SCs to date, as organized in several sections of this paper. Specifically, this review focuses on understanding the influence of ALD parameters on the electrochemical performance and discusses the ALD of nanostructured electrochemically active electrode materials on various templates for SCs. It examines the influence of ALD parameters on electrochemical performance and highlights ALD's role in passivating electrodes and creating 3D nanoarchitectures. The relationship between synthesis procedures and SC properties is analyzed to guide future research in preparing materials for various applications. Finally, it is concluded by suggesting the directions and scope of future research and development to further leverage the unique advantages of ALD for fabricating new materials and harness the unexplored opportunities in the fabrication of advanced-generation SCs.

A Novel Hybrid Approach for Classifying Osteosarcoma Using Deep Feature Extraction and Multilayer Perceptron.

Osteosarcoma is the most common type of bone cancer that tends to occur in teenagers and young adults. Due to crowded context, inter-class similarity, inter-class variation, and noise in H&E-stained (hematoxylin and eosin stain) histology tissue, pathologists frequently face difficulty in osteosarcoma tumor classification. In this paper, we introduced a hybrid framework for improving the efficiency of three types of osteosarcoma tumor (nontumor, necrosis, and viable tumor) classification by merging different types of CNN-based architectures with a multilayer perceptron (MLP) algorithm on the WSI (whole slide images) dataset. We performed various kinds of preprocessing on the WSI images. Then, five pre-trained CNN models were trained with multiple parameter settings to extract insightful features via transfer learning, where convolution combined with pooling was utilized as a feature extractor. For feature selection, a decision tree-based RFE was designed to recursively eliminate less significant features to improve the model generalization performance for accurate prediction. Here, a decision tree was used as an estimator to select the different features. Finally, a modified MLP classifier was employed to classify binary and multiclass types of osteosarcoma under the five-fold CV to assess the robustness of our proposed hybrid model. Moreover, the feature selection criteria were analyzed to select the optimal one based on their execution time and accuracy. The proposed model achieved an accuracy of 95.2% for multiclass classification and 99.4% for binary classification. Experimental findings indicate that our proposed model significantly outperforms existing methods; therefore, this model could be applicable to support doctors in osteosarcoma diagnosis in clinics. In addition, our proposed model is integrated into a web application using the FastAPI web framework to provide a real-time prediction.

Atomic layer deposition of tungsten sulfide using a new metal-organic precursor and H2S: thin film catalyst for water splitting.

Transition metal dichalcogenides (TMDs) are extensively researched in the past few years due to their two-dimensional layered structure similar to graphite. This group of materials offers tunable optoelectronic properties depending on the number of layers and therefore have a wide range of applications. Tungsten disulfide (WS2) is one of such TMDs that has been studied relatively less compared to MoS2. Herein, WS x thin films are grown on several types of substrates by atomic layer deposition (ALD) using a new metal-organic precursor [tris(hexyne) tungsten monocarbonyl, W(CO)(CH3CH2C≡CCH2CH3)3] and H2S molecules at a relatively low temperature of 300 °C. The typical self-limiting film growth by varying both, precursor and reactant, is obtained with a relatively high growth per cycle value of ∼0.13 nm. Perfect growth linearity with negligible incubation period is also evident in this ALD process. While the as-grown films are amorphous with considerable S-deficiency, they can be crystallized as h-WS2 film by post-annealing in the H2S atmosphere above 700 °C as observed from x-ray diffractometry analysis. Several other analyses like Raman and x-ray photoelectron spectroscopy, transmission electron microscopy, UV-vis. spectroscopy are performed to find out the physical, optical, and microstructural properties of as-grown and annealed films. The post-annealing in H2S helps to promote the S content in the film significantly as confirmed by the Rutherford backscattering spectrometry. Extremely thin (∼4.5 nm), as-grown WS x films with excellent conformality (∼100% step coverage) are achieved on the dual trench substrate (minimum width: 15 nm, aspect ratio: 6.3). Finally, the thin films of WS x (as-grown and 600/700 °C annealed) on W/Si and carbon cloth substrate are investigated for electrochemical hydrogen evolution reaction (HER). The as-grown WS x shows poor performance towards HER and is attributed to the S-deficiency, amorphous character, and oxygen contamination of the WS x film. Annealing the WS x film at 700 °C results in the formation of a crystalline layered WS2 phase, which significantly improves the HER performance of the electrode. The study reveals the importance of sulfur content and crystallinity on the HER performance of W-based sulfides.

Hydrogen Evolution Reaction by Atomic Layer-Deposited MoNx on Porous Carbon Substrates: The Effects of Porosity and Annealing on Catalyst Activity and Stability.

Molybdenum-based compounds are considered as a potential replacement for expensive precious-metal electrocatalysts for the hydrogen evolution reaction (HER) in acid electrolytes. However, coating of thin films of molybdenum nitride or carbide on a large-area self-standing substrate with high precision is still challenging. Here, MoNx is uniformly coated on carbon cloth (CC) and nitrogen-doped carbon (NC)-modified CC (NCCC) substrates by atomic layer deposition (ALD). The as-deposited film has a nanocrystalline character close to amorphous and a composition of approximately Mo2 N with significant oxygen contamination, mainly at the surface. Among the as-prepared ALD-MoNx electrodes, the MoNx /NCCC has the highest HER activity (overpotential η≈236 mV to achieve 10 mA cm-2 ) owing to the high surface area and porosity of the NCCC substrate. However, the durability of the electrode is poor, owing to the poor adhesion of NC powder on CC. Annealing MoNx /NCCC in H2 atmosphere at 400 °C improves both the activity and durability of the electrode without significant change in the phase or porosity. Annealing at an elevated temperature of 600 °C results in formation of a Mo2 C phase that further enhances the activity (η≈196 mV to achieve 10 mA cm-2 ), although there is a huge reduction in the porosity of the electrode as a consequence of the annealing. The structure of the electrode is also systematically investigated by electrochemical impedance spectroscopy (EIS). A deviation in the conventional Warburg impedance is observed in EIS of the NCCC-based electrode and is ascribed to the change in the H+ ion diffusion characteristics, owing to the geometry of the pores. The change in porous nature with annealing and the loss in porosity are reflected in the EIS of H+ ion diffusion observed at high-frequency. The current work establishes a better understanding of the importance of various parameters for a highly active HER electrode and will help the development of a commercial electrode for HER using the ALD technique.

Low-Temperature Atomic Layer Deposition of Highly Conformal Tin Nitride Thin Films for Energy Storage Devices.

We present an atomic layer deposition (ALD) process for the synthesis of tin nitride (SnNx) thin films using tetrakis(dimethylamino) tin (TDMASn, Sn(NMe2)4) and ammonia (NH3) as the precursors at low deposition temperatures (70-200 °C). This newly developed ALD scheme exhibits ideal ALD features such as self-limited film growth at 150 °C. The growth per cycle (GPC) was found to be ∼0.21 nm/cycle at 70 °C, which decreased with increasing deposition temperature. Interestingly, when the deposition temperature was between 125 and 180 °C, the GPC remained almost constant at ∼0.10 nm/cycle, which suggests an ALD temperature window, whereas upon further increasing the temperature to 200 °C, the GPC considerably decreased to ∼0.04 nm/cycle. Thermodynamic analysis via density functional theory calculations showed that the self-saturation of TDMASn would occur on an NH2-terminated surface. Moreover, it also suggests that the condensation of a molecular precursor and the desorption of surface *NH2 moieties would occur at lower and higher temperatures outside the ALD window, respectively. Thanks to the characteristics of ALD, this process could be used to conformally and uniformly deposit SnNx onto an ultranarrow dual-trench Si structure (minimum width: 15 nm; aspect ratio: ∼6.3) with ∼100% step coverage. Several analysis tools such as transmission electron microscopy, X-ray diffraction (XRD), X-ray photoelectron spectroscopy, Rutherford backscattering spectrometry, and secondary-ion mass spectrometry were used to characterize the film properties under different deposition conditions. XRD showed that a hexagonal SnN phase was obtained at a relatively low deposition temperature (100-150 °C), whereas cubic Sn3N4 was formed at a higher deposition temperature (175-200 °C). The stoichiometry of these thermally grown ALD-SnNx films (Sn-to-N ratio) deposited at 150 °C was determined to be ∼1:0.93 with negligible impurities. The optoelectronic properties of the SnNx films, such as the band gap, wavelength-dependent refractive index, extinction coefficient, carrier concentration, and mobility, were further evaluated via spectroscopic ellipsometry analysis. Finally, ALD-SnNx-coated Ni-foam (NF) and hollow carbon nanofibers were successfully used as free-standing electrodes in electrochemical supercapacitors and in Li-ion batteries, which showed a higher charge-storage time (about eight times greater than that of the uncoated NF) and a specific capacity of ∼520 mAh/g after 100 cycles at 0.1 A/g, respectively. This enhanced performance might be due to the uniform coverage of these substrates by ALD-SnNx, which ensures good electric contact and mechanical stability during electrochemical reactions.

Atomic Layer Deposition of Nickel Using a Heteroleptic Ni Precursor with NH3 and Selective Deposition on Defects of Graphene.

Atomic layer deposition (ALD) of Ni was demonstrated by introducing a novel oxygen-free heteroleptic Ni precursor, (η3-cyclohexenyl)(η5-cyclopentadienyl)nickel(II) [Ni(Chex)(Cp)]. For this process, non-oxygen-containing reactants (NH3 and H2 molecules) were used within a deposition temperature range of 320-340 °C. Typical ALD growth behavior was confirmed at 340 °C with a self-limiting growth rate of 1.1 Å/cycle. Furthermore, a postannealing process was carried out in a H2 ambient environment to improve the quality of the as-deposited Ni film. As a result, a high-quality Ni film with a substantially low resistivity (44.9 µΩcm) was obtained, owing to the high purity and excellent crystallinity. Finally, this Ni ALD process was also performed on a graphene surface. Selective deposition of Ni on defects of graphene was confirmed by transmission electron microscopy and atomic force microscopy analyses with a low growth rate (∼0.27 Å/cycle). This unique method can be further used to fabricate two-dimensional functional materials for several potential applications.

Revealing the Simultaneous Effects of Conductivity and Amorphous Nature of Atomic-Layer-Deposited Double-Anion-Based Zinc Oxysulfide as Superior Anodes in Na-Ion Batteries.

Although sodium-ion batteries (SIBs) are considered promising alternatives to their Li counterparts, they still suffer from challenges like slow kinetics of the sodiation process, large volume change, and inferior cycling stability. On the other hand, the presence of additional reversible conversion reactions makes the metal compounds the preferred anode materials over carbon. However, conductivity and crystallinity of such materials often play the pivotal role in this regard. To address these issues, atomic layer deposited double-anion-based ternary zinc oxysulfide (ZnOS) thin films as an anode material in SIBs are reported. Electrochemical studies are carried out with different O/(O+S) ratios, including O-rich and S-rich crystalline ZnOS along with the amorphous phase. Amorphous ZnOS with the O/(O+S) ratio of ≈0.4 delivers the most stable and considerably high specific (and volumetric) capacities of 271.9 (≈1315.6 mAh cm-3 ) and 173.1 mAh g-1 (≈837.7 mAh cm-3 ) at the current densities of 500 and 1000 mA g-1 , respectively. A dominant capacitive-controlled contribution of the amorphous ZnOS anode indicates faster electrochemical reaction kinetics. An electrochemical reaction mechanism is also proposed via X-ray photoelectron spectroscopy analyses. A comparison of the cycling stability further establishes the advantage of this double-anion-based material over pristine ZnO and ZnS anodes.

Enhanced activity of highly conformal and layered tin sulfide (SnSx) prepared by atomic layer deposition (ALD) on 3D metal scaffold towards high performance supercapacitor electrode.

Layered Sn-based chalcogenides and heterostructures are widely used in batteries and photocatalysis, but its utilizations in a supercapacitor is limited by its structural instability and low conductivity. Here, SnSx thin films are directly and conformally deposited on a three-dimensional (3D) Ni-foam (NF) substrate by atomic layer deposition (ALD), using tetrakis(dimethylamino)tin [TDMASn, ((CH3)2N)4Sn] and H2S that serves as an electrode for supercapacitor without any additional treatment. Two kinds of ALD-SnSx films grown at 160 °C and 180 °C are investigated systematically by X-ray diffractometry, Raman spectroscopy, X-ray photoelectron spectroscopy, and transmission electron microscopy (TEM). All of the characterization results indicate that the films deposited at 160 °C and 180 °C predominantly consist of hexagonal structured-SnS2 and orthorhombic-SnS phases, respectively. Moreover, the high-resolution TEM analyses (HRTEM) reveals the (001) oriented polycrystalline hexagonal-SnS2 layered structure for the films grown at 160 °C. The double layer capacitance with the composite electrode of SnSx@NF grown at 160 °C is higher than that of SnSx@NF at 180 °C, while pseudocapacitive Faradaic reactions are evident for both SnSx@NF electrodes. The superior performance as an electrode is directly linked to the layered structure of SnS2. Further, the optimal thickness of ALD-SnSx thin film is found to be 60 nm for the composite electrode of SnSx@NF grown at 160 °C by controlling the number of ALD cycles. The optimized SnSx@NF electrode delivers an areal capacitance of 805.5 mF/cm2 at a current density of 0.5 mA/cm2 and excellent cyclic stability over 5000 charge/discharge cycles.

Atomic-Layer-Deposited MoN x Thin Films on Three-Dimensional Ni Foam as Efficient Catalysts for the Electrochemical Hydrogen Evolution Reaction.

Future realization of a hydrogen-based economy requires a high-surface-area, low-cost, and robust electrocatalyst for the hydrogen evolution reaction (HER). In this study, the MoN x thin layer is synthesized on to a high-surface-area three-dimensional (3D) nickel foam (NF) substrate using atomic layer deposition (ALD) for HER catalysis. MoN x is grown on NF by the sequential exposure of Mo(CO)6 and NH3 at 225 °C. The thickness of the thin film is controlled by varying the number of ALD cycles to maximize the HER performance of the MoN x/NF composite catalyst. The scanning electron microscopy and transmission electron microscopy (TEM) images of MoN x/NF highlight that ALD facilitates uniform and conformal coating. TEM analysis highlights that the MoN x film is predominantly amorphous with the nanocrystalline MoN grains (4 nm) dispersed throughout it. Moreover, the high-resolution (HR)-TEM analysis shows a rough surface of the MoN x film with an overall composition of Mo0.59N0.41. X-ray photoelectron spectroscopy depth-profile analysis reveals that oxygen contamination is concentrated at the surface because of surface oxidation of the MoN x film under ambient conditions. The HER activity of MoN x is evaluated under acidic (0.5 M H2SO4) and alkaline (0.1 M KOH) conditions. In an acidic electrolyte, the sample prepared with 700 ALD cycles exhibits significant HER activity and a low overpotential (η) of 148 mV at 10 mA cm-2. Under an alkaline condition, it achieves 10 mA cm-2 with η of 125 mV for MoN x/NF (700 cycles). In both electrolytes, the MoN x thin film exhibits enhanced activity and stability because of the uniform and conformal coating on NF. Thus, this study facilitates the development of a large-area 3D freestanding catalyst for efficient electrochemical water-splitting, which may have commercial applicability.

Highly Uniform Atomic Layer-Deposited MoS2@3D-Ni-Foam: A Novel Approach To Prepare an Electrode for Supercapacitors.

This article takes an effort to establish the potential of atomic layer deposition (ALD) technique toward the field of supercapacitors by preparing molybdenum disulfide (MoS2) as its electrode. While molybdenum hexacarbonyl [Mo(CO)6] serves as a novel precursor toward the low-temperature synthesis of ALD-grown MoS2, H2S plasma helps to deposit its polycrystalline phase at 200 °C. Several ex situ characterizations such as X-ray diffractometry (XRD), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and so forth are performed in detail to study the as-grown MoS2 film on a Si/SiO2 substrate. While stoichiometric MoS2 with very negligible amount of C and O impurities was evident from XPS, the XRD and high-resolution transmission electron microscopy analyses confirmed the (002)-oriented polycrystalline h-MoS2 phase of the as-grown film. A comparative study of ALD-grown MoS2 as a supercapacitor electrode on 2-dimensional stainless steel and on 3-dimensional (3D) Ni-foam substrates clearly reflects the advantage and the potential of ALD for growing a uniform and conformal electrode material on a 3D-scaffold layer. Cyclic voltammetry measurements showed both double-layer capacitance and capacitance contributed by the faradic reaction at the MoS2 electrode surface. The optimum number of ALD cycles was also found out for achieving maximum capacitance for such a MoS2@3D-Ni-foam electrode. A record high areal capacitance of 3400 mF/cm2 was achieved for MoS2@3D-Ni-foam grown by 400 ALD cycles at a current density of 3 mA/cm2. Moreover, the ALD-grown MoS2@3D-Ni-foam composite also retains high areal capacitance, even up to a high current density of 50 mA/cm2. Finally, this directly grown MoS2 electrode on 3D-Ni-foam by ALD shows high cyclic stability (>80%) over 4500 charge-discharge cycles which must invoke the research community to further explore the potential of ALD for such applications.

Atomic layer deposited tungsten nitride thin films as a new lithium-ion battery anode.

This article demonstrates the atomic layer deposition (ALD) of tungsten nitride using tungsten hexacarbonyl [W(CO)6] and ammonia [NH3] and its use as a lithium-ion battery anode. In situ quartz crystal microbalance (QCM), ellipsometry and X-ray reflectivity (XRR) measurements are carried out to confirm the self-limiting behaviour of the deposition. A saturated growth rate of ca. 0.35 Å per ALD cycle is found within a narrow temperature window of 180-195 °C. In situ Fourier transform infrared (FTIR) vibrational spectroscopy is used to determine the reaction pathways of the surface bound species after each ALD half cycle. The elemental presence and chemical composition is determined by XPS. The as-deposited material is found to be amorphous and crystallized to h-W2N upon annealing at an elevated temperature under an ammonia atmosphere. The as-deposited materials are found to be n-type, conducting with an average carrier concentration of ca. 10(20) at room temperature. Electrochemical studies of the as-deposited films open up the possibility of this material to be used as an anode material in Li-ion batteries. The incorporation of MWCNTs as a scaffold layer further enhances the electrochemical storage capacity of the ALD grown tungsten nitride (WNx). Ex situ XRD analysis confirms the conversion based reaction mechanism of the as-grown material with Li under operation.

Atomic layer deposited molybdenum nitride thin film: a promising anode material for Li ion batteries.

Molybdenum nitride (MoNx) thin films are deposited by atomic layer deposition (ALD) using molybdenum hexacarbonyl [Mo(CO)6] and ammonia [NH3] at varied temperatures. A relatively narrow ALD temperature window is observed. In situ quartz crystal microbalance (QCM) measurements reveal the self-limiting growth nature of the deposition that is further verified with ex situ spectroscopic ellipsometry and X-ray reflectivity (XRR) measurements. A saturated growth rate of 2 Å/cycle at 170 °C is obtained. The deposition chemistry is studied by the in situ Fourier transform infrared spectroscopy (FTIR) that investigates the surface bound reactions during each half cycle. As deposited films are amorphous as observed from X-ray diffraction (XRD) and transmission electron microscopy electron diffraction (TEM ED) studies, which get converted to hexagonal-MoN upon annealing at 400 °C under NH3 atmosphere. As grown thin films are found to have notable potential as a carbon and binder free anode material in a Li ion battery. Under half-cell configuration, a stable discharge capacity of 700 mAh g(-1) was achieved after 100 charge-discharge cycles, at a current density of 100 µA cm(-2).