Investigation of a scale-up manufacturing approach for nanostructures by using a nanoscale multi-tip diamond tool

Increasing interest in commercializing functional nanostructured devices heightens the need for cost-effective manufacturing approaches for nanostructures. This paper presents an investigation of a scale-up manufacturing approach for nanostructures through diamond turning using a nanoscale multi-tip diamond tool (four tip tool with tip width of 150 nm) fabricated by focused ion beam (FIB). The manufacturing capacity of this new technique is evaluated through a series of cutting trials on copper substrates under different cutting conditions (depth of cut 100–500 nm, spindle speed 12–120 rpm). The machined surface roughness and nanostructure patterns are measured by using a white light interferometer and a scanning electron microscope, respectively. Results show that the form accuracy and integrity of the machined nanostructures were degraded with the increase of the depth of cut and the cutting speed. The burr and the structure damage are two major machining defects. High precision nano-grooves (form error of bottom width < 6.7 %) was achieved when a small depth of cut of 100 nm was used (spindle speed = 12 rpm). Initial tool wear was found at both the clearance cutting edge and the side edges of tool tips after a cutting distance of 2.5 km. Moreover, the nanometric cutting process was emulated by molecular dynamic (MD) simulations. The research findings obtained from MD simulation reveal the underlying mechanism for machining defects and the initialization of tool wear observed in experiments

Quantifying Spatiotemporal Dynamics of Solar Radiation over the Northeast China Based on ACO-BPNN Model and Intensity Analysis

Reliable information on the spatiotemporal dynamics of solar radiation plays a crucial role in studies relating to global climate change. In this study, a new backpropagation neural network (BPNN) model optimized with an Ant Colony Optimization (ACO) algorithm was developed to generate the ACO-BPNN model, which had demonstrated superior performance for simulating solar radiation compared to traditional BPNN modelling, for Northeast China. On this basis, we applied an intensity analysis to investigate the spatiotemporal variation of solar radiation from 1982 to 2010 over the study region at three levels: interval, category, and conversion. Research findings revealed that (1) the solar radiation resource in the study region increased from the 1980s to the 2000s and the average annual rate of variation from the 1980s to the 1990s was lower than that from the 1990s to the 2000s and (2) the gains and losses of solar radiation at each level were in different conditions. The poor, normal, and comparatively abundant levels were transferred to higher levels, whereas the abundant level was transferred to lower levels. We believe our findings contribute to implementing ad hoc energy management strategies to optimize the use of solar radiation resources and provide scientific suggestions for policy planning

Review on FIB-induced damage in diamond materials

Background: Although various advanced FIB processing methods for the fabrication of 3D nanostructures have been successfully developed by many researchers, the FIB milling has an unavoidable result in terms of the implantation of ion source materials and the formation of damaged layer at the near surface. Understanding the ion-solid interactions physics provides a unique way to control the FIB produced defects in terms of their shape and location. Methods: We have carefully selected peer-reviewed papers which mainly focusing on the review questions of this paper. A deductive content analysis method was used to analyse the methods, findings and conclusions of these papers. Based on their research methods, we classify their works in different groups. The theory of ion-matter interaction and the previous investigation on ion-induced damage in diamond were reviewed and discussed. Results: The previous research work has provided a systematic analysis of ion-induced damage in diamond. Both experimental and simulation methods have been developed to understand the damage process. The damaged layers created in FIB processing process can significantly degrade/alter the device performance and limit the applications of FIB nanofabrication technique. There are still challenges involved in fabricating large, flat, and uniform TEM samples in undoped non-conductive diamond. Conclusions: The post-facto-observation leaves a gap in understanding the formation process of ioninduced damage, forcing the use of assumptions. In contrast, MD simulations of ion bombardment have shed much light on ion beam mixing for decades. These activities make it an interesting and important task to understand what the fundamental effects of energetic particles on matter are

Bound States and Critical Behavior of the Yukawa Potential

We investigate the bound states of the Yukawa potential $V(r)=-\lambda \exp(-\alpha r)/ r$, using different algorithms: solving the Schr\"odinger equation numerically and our Monte Carlo Hamiltonian approach. There is a critical $\alpha=\alpha_C$, above which no bound state exists. We study the relation between $\alpha_C$ and $\lambda$ for various angular momentum quantum number $l$, and find in atomic units, $\alpha_{C}(l)= \lambda [A_{1} \exp(-l/ B_{1})+ A_{2} \exp(-l/ B_{2})]$, with $A_1=1.020(18)$, $B_1=0.443(14)$, $A_2=0.170(17)$, and $B_2=2.490(180)$.Comment: 15 pages, 12 figures, 5 tables. Version to appear in Sciences in China

PlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information

We have designed and implemented a web-based database system, called PlantQTL-GE, to facilitate quantitatine traits locus (QTL) based candidate gene identification and gene function analysis. We collected a large number of genes, gene expression information in microarray data and expressed sequence tags (ESTs) and genetic markers from multiple sources of Oryza sativa and Arabidopsis thaliana. The system integrates these diverse data sources and has a uniform web interface for easy access. It supports QTL queries specifying QTL marker intervals or genomic loci, and displays, on rice or Arabidopsis genome, known genes, microarray data, ESTs and candidate genes and similar putative genes in the other plant. Candidate genes in QTL intervals are further annotated based on matching ESTs, microarray gene expression data and cis-elements in regulatory sequences. The system is freely available at

Catalytic Mechanism Investigation of Lysine-Specific Demethylase 1 (LSD1): A Computational Study

Lysine-specific demethylase 1 (LSD1), the first identified histone demethylase, is a flavin-dependent amine oxidase which specifically demethylates mono- or dimethylated H3K4 and H3K9 via a redox process. It participates in a broad spectrum of biological processes and is of high importance in cell proliferation, adipogenesis, spermatogenesis, chromosome segregation and embryonic development. To date, as a potential drug target for discovering anti-tumor drugs, the medical significance of LSD1 has been greatly appreciated. However, the catalytic mechanism for the rate-limiting reductive half-reaction in demethylation remains controversial. By employing a combined computational approach including molecular modeling, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, the catalytic mechanism of dimethylated H3K4 demethylation by LSD1 was characterized in details. The three-dimensional (3D) model of the complex was composed of LSD1, CoREST, and histone substrate. A 30-ns MD simulation of the model highlights the pivotal role of the conserved Tyr761 and lysine-water-flavin motif in properly orienting flavin adenine dinucleotide (FAD) with respect to substrate. The synergy of the two factors effectively stabilizes the catalytic environment and facilitated the demethylation reaction. On the basis of the reasonable consistence between simulation results and available mutagenesis data, QM/MM strategy was further employed to probe the catalytic mechanism of the reductive half-reaction in demethylation. The characteristics of the demethylation pathway determined by the potential energy surface and charge distribution analysis indicates that this reaction belongs to the direct hydride transfer mechanism. Our study provides insights into the LSD1 mechanism of reductive half-reaction in demethylation and has important implications for the discovery of regulators against LSD1 enzymes

Molecular Basis of NDM-1, a New Antibiotic Resistance Determinant

The New Delhi Metallo-β-lactamase (NDM-1) was first reported in 2009 in a Swedish patient. A recent study reported that Klebsiella pneumonia NDM-1 positive strain or Escherichia coli NDM-1 positive strain was highly resistant to all antibiotics tested except tigecycline and colistin. These can no longer be relied on to treat infections and therefore, NDM-1 now becomes potentially a major global health threat

Investigation of the Acetylation Mechanism by GCN5 Histone Acetyltransferase

The histone acetylation of post-translational modification can be highly dynamic and play a crucial role in regulating cellular proliferation, survival, differentiation and motility. Of the enzymes that mediate post-translation modifications, the GCN5 of the histone acetyltransferase (HAT) proteins family that add acetyl groups to target lysine residues within histones, has been most extensively studied. According to the mechanism studies of GCN5 related proteins, two key processes, deprotonation and acetylation, must be involved. However, as a fundamental issue, the structure of hGCN5/AcCoA/pH3 remains elusive. Although biological experiments have proved that GCN5 mediates the acetylation process through the sequential mechanism pathway, a dynamic view of the catalytic process and the molecular basis for hGCN5/AcCoA/pH3 are still not available and none of theoretical studies has been reported to other related enzymes in HAT family. To explore the molecular basis for the catalytic mechanism, computational approaches including molecular modeling, molecular dynamic (MD) simulation and quantum mechanics/molecular mechanics (QM/MM) simulation were carried out. The initial hGCN5/AcCoA/pH3 complex structure was modeled and a reasonable snapshot was extracted from the trajectory of a 20 ns MD simulation, with considering post-MD analysis and reported experimental results. Those residues playing crucial roles in binding affinity and acetylation reaction were comprehensively investigated. It demonstrated Glu80 acted as the general base for deprotonation of Lys171 from H3. Furthermore, the two-dimensional QM/MM potential energy surface was employed to study the sequential pathway acetylation mechanism. Energy barriers of addition-elimination reaction in acetylation obtained from QM/MM calculation indicated the point of the intermediate ternary complex. Our study may provide insights into the detailed mechanism for acetylation reaction of GCN5, and has important implications for the discovery of regulators against GCN5 enzymes and related HAT family enzymes

The Long-Term Mechanical Properties of BS Perpendicular to the Grain

As a modern bamboo composite with good mechanical properties, bamboo scrimber (BS) has achieved prominence in the sustainable architecture field. When used as a structural material, it is inevitably under continual tension perpendicular to the grain, therefore its mechanical response under long-term loading is significant for structural design. In this study, tensile tests were conducted on BS under short-term and long-term loads perpendicular to the grain. The duration of load (DOL) effect on BS perpendicular to grain and its creep effect were analyzed. Compared with BS parallel to the grain, the DOL effect on BS perpendicular to the grain was less severe, and the capacity for creep resistance was weaker. The threshold stress ratio and relative creep strain of BS perpendicular to the grain were 0.40 and 0.87, respectively. It was found that the DOL models and the viscoelastic model accurately predicted the DOL factor and creep strain. This study provides a scientific reference for the safe lifetime service of BS in practical engineering