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In this paper, terahertz (THz) spectra of four DNA nucleosides (Adenosine, Thymidine, Cytidine and Guanosine) and two nucleoside derivatives (Ribavirin and Entecavir, first time reported) in the solid phase were studied experimentally by Fourier Transform Infrared Spectroscopy (FTIR) in the frequency of 1-10 THz. The lattice energy, geometric structure, vibration spectrum of them were analyzed theoretically by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF) and the density functional theory (DFT). The intra- and inter-molecular weak interactions corresponding to the vibrational modes of the crystal, polymer and monomer were obtained, with the help of the potential energy distribution (PED) and reduced density gradient (RDG) methods. It was found that the sum of electronic and thermal free energies increased from the monomer to polymer, and from the polymer to crystal. For example, the inter-molecular interaction energy from the monomer to dimer of adenosine increased 6.969 kcal/mol, and that from the dimer to crystal (the periodic boundary conditions were considered) increased 666.792 kcal/mol. Therefore, only the crystal structure constrained the periodic boundary conditions could well describe the experimental results, although the former scholars chose the monomer or polymer as the initial configuration due to the limitation of computing resources and methods. In THz band, the vibrational modes were generally originated from the collective vibration (more than 99% of them were vibration, only less than 1% of them were rotation and translation) of all molecules involved, which could reflect the molecular structure and spatial distribution of different substances. In order to accurately identify the spectra, we studied the location, type and contribution of all weak interactions, and found that the strong characteristic peaks corresponding to the strong hydrogen bonds came from inter-molecular, while the weak hydrogen bonds mainly originated from intra- and inter-molecular, the out-of-plane bending made the largest contribution, accounting for more than 90%. Furthermore, taking guanine, guanosine and two guanosine derivatives (Ribavirin and Entecavir) as examples, the differences of weak interaction among them caused by different molecular configuration, arrangement and substituent position were studied, and the fundamental reason of THz spectrum change was found. This research can lay a foundation for crystal engineering, supramolecular chemistry, molecular recognition and self-assembly, protein-ligand interaction, etc.
Fang Wang; Xiaolin Sun; Jianan Zan; Mingshi Li; Yunfei Liu; Jingyi Chen. Terahertz spectra and weak intermolecular interactions of nucleosides or nucleoside drugs. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2021, 120344 .
AMA StyleFang Wang, Xiaolin Sun, Jianan Zan, Mingshi Li, Yunfei Liu, Jingyi Chen. Terahertz spectra and weak intermolecular interactions of nucleosides or nucleoside drugs. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2021; ():120344.
Chicago/Turabian StyleFang Wang; Xiaolin Sun; Jianan Zan; Mingshi Li; Yunfei Liu; Jingyi Chen. 2021. "Terahertz spectra and weak intermolecular interactions of nucleosides or nucleoside drugs." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy , no. : 120344.
Both CrB and FeB monolayers are FM metals with a moderate magnetic anisotropy energy by saturation with functional groups, which indicates that the 2D transition metal borides have great potential application in information storage devices.
Min Dou; Huan Li; Qingnian Yao; Jiabao Wang; Yunfei Liu; Fang Wu. Room-temperature ferromagnetism in two-dimensional transition metal borides: a first-principles investigation. Physical Chemistry Chemical Physics 2021, 23, 10615 -10620.
AMA StyleMin Dou, Huan Li, Qingnian Yao, Jiabao Wang, Yunfei Liu, Fang Wu. Room-temperature ferromagnetism in two-dimensional transition metal borides: a first-principles investigation. Physical Chemistry Chemical Physics. 2021; 23 (17):10615-10620.
Chicago/Turabian StyleMin Dou; Huan Li; Qingnian Yao; Jiabao Wang; Yunfei Liu; Fang Wu. 2021. "Room-temperature ferromagnetism in two-dimensional transition metal borides: a first-principles investigation." Physical Chemistry Chemical Physics 23, no. 17: 10615-10620.
Due to the various shapes, textures, and colors of fires, forest fire detection is a challenging task. The traditional image processing method relies heavily on manmade features, which is not universally applicable to all forest scenarios. In order to solve this problem, the deep learning technology is applied to learn and extract features of forest fires adaptively. However, the limited learning and perception ability of individual learners is not sufficient to make them perform well in complex tasks. Furthermore, learners tend to focus too much on local information, namely ground truth, but ignore global information, which may lead to false positives. In this paper, a novel ensemble learning method is proposed to detect forest fires in different scenarios. Firstly, two individual learners Yolov5 and EfficientDet are integrated to accomplish fire detection process. Secondly, another individual learner EfficientNet is responsible for learning global information to avoid false positives. Finally, detection results are made based on the decisions of three learners. Experiments on our dataset show that the proposed method improves detection performance by 2.5% to 10.9%, and decreases false positives by 51.3%, without any extra latency.
Renjie Xu; Haifeng Lin; Kangjie Lu; Lin Cao; Yunfei Liu. A Forest Fire Detection System Based on Ensemble Learning. Forests 2021, 12, 217 .
AMA StyleRenjie Xu, Haifeng Lin, Kangjie Lu, Lin Cao, Yunfei Liu. A Forest Fire Detection System Based on Ensemble Learning. Forests. 2021; 12 (2):217.
Chicago/Turabian StyleRenjie Xu; Haifeng Lin; Kangjie Lu; Lin Cao; Yunfei Liu. 2021. "A Forest Fire Detection System Based on Ensemble Learning." Forests 12, no. 2: 217.
The terrestrial laser scanner (TLS) has been widely used in forest inventories. However, with increasing precision of TLS, storing and transmitting tree point clouds become more challenging. In this paper, a novel compressed sensing (CS) scheme for broad-leaved tree point clouds is proposed by analyzing and comparing different sparse bases, observation matrices, and reconstruction algorithms. Our scheme starts by eliminating outliers and simplifying point clouds with statistical filtering and voxel filtering. The scheme then applies Haar sparse basis to thin the coordinate data based on the characteristics of the broad-leaved tree point clouds. An observation procedure down-samples the point clouds with the partial Fourier matrix. The regularized orthogonal matching pursuit algorithm (ROMP) finally reconstructs the original point clouds. The experimental results illustrate that the proposed scheme can preserve morphological attributes of the broad-leaved tree within a range of relative error: 0.0010%–3.3937%, and robustly extend to plot-level within a range of mean square error (MSE): 0.0063–0.2245.
Renjie Xu; Ting Yun; Lin Cao; Yunfei Liu. Compression and Recovery of 3D Broad-Leaved Tree Point Clouds Based on Compressed Sensing. Forests 2020, 11, 257 .
AMA StyleRenjie Xu, Ting Yun, Lin Cao, Yunfei Liu. Compression and Recovery of 3D Broad-Leaved Tree Point Clouds Based on Compressed Sensing. Forests. 2020; 11 (3):257.
Chicago/Turabian StyleRenjie Xu; Ting Yun; Lin Cao; Yunfei Liu. 2020. "Compression and Recovery of 3D Broad-Leaved Tree Point Clouds Based on Compressed Sensing." Forests 11, no. 3: 257.
This paper, we introduced Sub-terahertz (Sub-THz) technology to identify nematode DNA sequence. First, data mining technology and restriction enzyme digestion were used to cut out two corresponding sequences, each containing about 100 base pairs that could represent the characteristic fragments of Bursaphelenchus xylophilus (Bx) and Bursaphelenchus mucronatus (Bm) rDNA in internal transcribed spacer 1 (ITS1) region. Then, vibration spectra of the two enzyme-cut sequences were measured by Fourier transform infrared spectroscopy (FTIR). Meanwhile, the spectrum was analyzed by molecular dynamics method. It was found that the calculated and experimental spectra of the two enzyme-cut sequences were consistent, although the differences of the sequences could not be well reflected in the spectra. The vibration modes corresponding to diverse absorption peaks in the spectra were quite different, which were closely related to the internal bases sequencing. This can be used as an indicator for identifying Bx and Bm DNA. Moreover, the normal mode analysis (NMA) method was first adopted for spectral attribution analysis of DNA long sequences. Finally, the vibration spectra of shorter sequences predicted by second-order Markov chains and Monte Carlo method were studied. To some extent, the predicted short sequences can represent the complete sequence as the initial calculation structure.
Fang Wang; Ling Jiang; Jun Song; Lin Huang; Yunwei Ju; Yunfei Liu. Sub-THz spectroscopic characterization identification for pine wood nematode ribosomal DNA. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2020, 232, 118152 .
AMA StyleFang Wang, Ling Jiang, Jun Song, Lin Huang, Yunwei Ju, Yunfei Liu. Sub-THz spectroscopic characterization identification for pine wood nematode ribosomal DNA. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2020; 232 ():118152.
Chicago/Turabian StyleFang Wang; Ling Jiang; Jun Song; Lin Huang; Yunwei Ju; Yunfei Liu. 2020. "Sub-THz spectroscopic characterization identification for pine wood nematode ribosomal DNA." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 232, no. : 118152.
The objective of this study was to explore the potential of an acoustic impact test as a nondestructive evaluation procedure to assess the soundness of hardwood logs in terms of internal decay, void, and defect ratio. Fifteen logs of four hardwood species (black cherry, white oak, red oak, and cottonwood) were obtained and subjected to acoustic impact testing. The logs were subsequently dissected for visual examination and physical mapping of the internal defects. The acoustic response signals were analyzed to derive acoustic velocity (through FFT), time centroid (through moment analysis), and the first- and second-order damping ratio (through continuous wavelet transform). The longitudinal acoustic velocity was found to have a negative, nonlinear relationship with defect ratio (R2 = 0.72), but it lacked sensitivity to small defects and was affected by species. Time centroid proved to be a better predictor than acoustic velocity with an improved correlation with log defect ratio (R2 = 0.87). Wavelet-based damping ratio was found to have a close linear relationship with log defect ratio. Comparing with the first-order damping ratio, the second-order damping ratio had a better predicting power (R2 = 0.92) and was not affected by type and location of defects. The results further indicated that a combination of acoustic velocity, time centroid, and the first- and second-order damping ratios could yield the optimal prediction of log defect ratio. However, considering the sensitivity and simplicity of the waveform analysis, the second-order damping ratio of the response signals could be the best single predicting parameter for assessing the internal soundness of hardwood logs.
Feng Xu; Yunfei Liu; Xiping Wang; Brian K. Brashaw; Lon A. Yeary; Robert J. Ross. Assessing internal soundness of hardwood logs through acoustic impact test and waveform analysis. Wood Science and Technology 2019, 53, 1111 -1134.
AMA StyleFeng Xu, Yunfei Liu, Xiping Wang, Brian K. Brashaw, Lon A. Yeary, Robert J. Ross. Assessing internal soundness of hardwood logs through acoustic impact test and waveform analysis. Wood Science and Technology. 2019; 53 (5):1111-1134.
Chicago/Turabian StyleFeng Xu; Yunfei Liu; Xiping Wang; Brian K. Brashaw; Lon A. Yeary; Robert J. Ross. 2019. "Assessing internal soundness of hardwood logs through acoustic impact test and waveform analysis." Wood Science and Technology 53, no. 5: 1111-1134.
Fourier infrared spectrometer and X-ray diffractometer were used to detect the spectra of lab-made U:A (uracil and adenine hydrate dried at room temperature), lab-made C:G (cytosine and guanine hydrate dried at room temperature), U + A (mixture of uracil and adenine), and C + G (mixture of cytosine and guanine). The results of our testing showed that U:A did not form a eutectic, but C:G did. In order to further characterize the vibrational modes of RNA base pair crystals, the absorption spectra of 1‑methyl‑5‑bromouracil‑9‑methyladenine (abbreviated as 1M5BU:9MA) and 1‑methylcytosine‑9‑ethylguanine (abbreviated as 1MC:9EG) were calculated based on the PBC-GEBF (generalized energy-based fragmentation approach under periodic boundary conditions) method. To further study the effect of substituents on the vibrational mode of the crystal structure, the substituents of 1M5BU:9MA and 1MC:9EG were artificially removed. The results of calculation brought out that methyl and ethyl as substituents have little effect on the vibrational spectrum, but halogen atoms such as Br atom in 1M5BU:9MA has a certain influence on the spectrum. Furthermore, THz (terahertz) spectra of the RNA nucleotide sequence 5′-AUCG-3′ was analyzed. In the perspective of the spectra with DNA signatures, their spectra show a great deal of similarity regardless of RNA or DNA, or the base sequence difference. This study will provide a very important information for revealing the role of RNA in the formation of biological macromolecules and its mechanism.
Fang Wang; Dongbo Zhao; Ling Jiang; Jun Song; Yunfei Liu. THz vibrational spectroscopy for RNA basepair cocrystals and oligonucleotide sequences. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2018, 209, 49 -54.
AMA StyleFang Wang, Dongbo Zhao, Ling Jiang, Jun Song, Yunfei Liu. THz vibrational spectroscopy for RNA basepair cocrystals and oligonucleotide sequences. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2018; 209 ():49-54.
Chicago/Turabian StyleFang Wang; Dongbo Zhao; Ling Jiang; Jun Song; Yunfei Liu. 2018. "THz vibrational spectroscopy for RNA basepair cocrystals and oligonucleotide sequences." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 209, no. : 49-54.
The absence of magnetic moments in pristine two-dimensional (2D) semiconducting materials has attracted many research interests. Transition-metal (TM) decoration has been found to be an effective strategy to introduce magnetic moments in non-magnetic 2D semiconductors. However, the stability of TM atoms modified 2D semiconductors has not been well explored. Here, taking 2D Tin (II) sulfide (SnS) monolayer as a prototype, we explored the stability of magnetic semiconductors through this method. In our studies, all possible configurations of TM decoration have been considered, namely, adsorption on the intact surface, S vacancy, and Sn vacancy. Based on the energy gain and electronic analysis, our results revealed that most of the TM atoms will form a cluster, and only several TM atoms can be effectively doped into the SnS monolayer. Furthermore, the band calculations showed that only Mn substitution will give rise to a magnetic semiconductor. Thus, the reported results here provide some hidden information for further realization of the magnetic semiconductors and serve as a paradigm to prepare 2D magnetic semiconductors.
Fangfang Wang; Liyu Zhou; Zhen Ma; Mingxue He; Fang Wu; Yunfei Liu. First-principles Investigations of Magnetic Semiconductors: An example of Transition Metal Decorated Two-dimensional SnS Monolayer. Nanomaterials 2018, 8, 789 .
AMA StyleFangfang Wang, Liyu Zhou, Zhen Ma, Mingxue He, Fang Wu, Yunfei Liu. First-principles Investigations of Magnetic Semiconductors: An example of Transition Metal Decorated Two-dimensional SnS Monolayer. Nanomaterials. 2018; 8 (10):789.
Chicago/Turabian StyleFangfang Wang; Liyu Zhou; Zhen Ma; Mingxue He; Fang Wu; Yunfei Liu. 2018. "First-principles Investigations of Magnetic Semiconductors: An example of Transition Metal Decorated Two-dimensional SnS Monolayer." Nanomaterials 8, no. 10: 789.
The generalized energy-based fragmentation (GEBF) approach has been applied to study the THz spectra and vibrational modes of base pair cocrystals under periodic boundary conditions (denoted as PBC-GEBF). Results of vibrational mode reveal that hydrogen bonds play a pivotal role in the pairing process of base crystals, where most NH and CH bonds stretch to some extent. We also found that hydrogen bonds of a self-made A:T cocrystal completely break in a transition from liquid to the solid state, while self-made C:G cocrystal is different and easier to form a cocrystal, as confirmed by X-ray diffraction (XRD) and terahertz (THz) spectra. Furthermore, we have studied DNA polynucleotides (in both A and B forms) found that the vibrational modes changed a lot during the process of their forming double strand. Despite the key role played by hydrogen bonds, the key contribution originates from collective motions of the main skeleton. A comparative study of the spectra of some stranded fragments suggests that different sequences or forms have similar spectra in THz band. They distinguish from each other mainly in the low-frequency regions, especially below 1 THz. This study would make great contributions to the molecular dynamics model based DNA long-chain structure simulation in the future study.
Fang Wang; Dongbo Zhao; Hao Dong; Ling Jiang; Lin Huang; Yunfei Liu; Shuhua Li. THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2018, 200, 195 -201.
AMA StyleFang Wang, Dongbo Zhao, Hao Dong, Ling Jiang, Lin Huang, Yunfei Liu, Shuhua Li. THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2018; 200 ():195-201.
Chicago/Turabian StyleFang Wang; Dongbo Zhao; Hao Dong; Ling Jiang; Lin Huang; Yunfei Liu; Shuhua Li. 2018. "THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 200, no. : 195-201.
Terahertz (THz) spectra of DNA nucleobase crystals were experimentally studied by terahertz time domain spectroscopy (THz-TDS), Fourier transform infrared spectroscopy (FTIR), and computationally studied by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). We analyzed the vibrational spectra of solid-state DNA nucleobases and assigned the corresponding vibrational modes to the main peaks in the experimental spectra with the PBC-GEBF results. The computational results were verified to be in good accordance with the experimental data. Harmonic vibrational frequency results revealed that all the vibrational modes belong to collective vibrational modes, which involve complicated mixtures of inter- and intramolecular displacements, somewhere in the vicinity of 0.5-9THz.
Fang Wang; Dongbo Zhao; Hao Dong; Ling Jiang; Yunfei Liu; Shuhua Li. Terahertz spectra of DNA nucleobase crystals: A joint experimental and computational study. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2017, 179, 255 -260.
AMA StyleFang Wang, Dongbo Zhao, Hao Dong, Ling Jiang, Yunfei Liu, Shuhua Li. Terahertz spectra of DNA nucleobase crystals: A joint experimental and computational study. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2017; 179 ():255-260.
Chicago/Turabian StyleFang Wang; Dongbo Zhao; Hao Dong; Ling Jiang; Yunfei Liu; Shuhua Li. 2017. "Terahertz spectra of DNA nucleobase crystals: A joint experimental and computational study." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 179, no. : 255-260.
In Rechargeable Wireless Sensor Networks (R-WSNs), in order to achieve the maximum data collection rate it is critical that sensors operate in very low duty cycles because of the sporadic availability of energy. A sensor has to stay in a dormant state in most of the time in order to recharge the battery and use the energy prudently. In addition, a sensor cannot always conserve energy if a network is able to harvest excessive energy from the environment due to its limited storage capacity. Therefore, energy exploitation and energy saving have to be traded off depending on distinct application scenarios. Since higher data collection rate or maximum data collection rate is the ultimate objective for sensor deployment, surplus energy of a node can be utilized for strengthening packet delivery efficiency and improving the data generating rate in R-WSNs. In this work, we propose an algorithm based on data aggregation to compute an upper data generation rate by maximizing it as an optimization problem for a network, which is formulated as a linear programming problem. Subsequently, a dual problem by introducing Lagrange multipliers is constructed, and subgradient algorithms are used to solve it in a distributed manner. At the same time, a topology controlling scheme is adopted for improving the network’s performance. Through extensive simulation and experiments, we demonstrate that our algorithm is efficient at maximizing the data collection rate in rechargeable wireless sensor networks.
Haifeng Lin; Di Bai; Demin Gao; Yunfei Liu. Maximum Data Collection Rate Routing Protocol Based on Topology Control for Rechargeable Wireless Sensor Networks. Sensors 2016, 16, 1201 .
AMA StyleHaifeng Lin, Di Bai, Demin Gao, Yunfei Liu. Maximum Data Collection Rate Routing Protocol Based on Topology Control for Rechargeable Wireless Sensor Networks. Sensors. 2016; 16 (8):1201.
Chicago/Turabian StyleHaifeng Lin; Di Bai; Demin Gao; Yunfei Liu. 2016. "Maximum Data Collection Rate Routing Protocol Based on Topology Control for Rechargeable Wireless Sensor Networks." Sensors 16, no. 8: 1201.
We have investigated the terahertz spectra of L-ascorbic acid and thiamine hydrochloride measured by terahertz time-domain spectroscopy (THz-TDS) and Fourier transform infrared spectroscopy (FTIR). The measured absorption spectra were demonstrated to be in good agreement with the results simulated by Density Functional Theory (DFT) using hybrid functional B3LYP with basis set of 6-31G (d), except with slight frequency shift and few peaks missing. We presented the comparison of measured spectra by the FTIR spectroscopy employing low temperature silicon bolometer as detector and the TDS system. The measured spectra of the L-ascorbic acid showed shoulder bands at 0.25, 1.1, 1.5, 1.82, 2.03, 2.30, 2.44, 2.67, 2.97, 3.12, and 3.40 THz, respectively. The spectra of the thiamine hydrochloride show shoulder bands at 0.48, 1.11, 1.57, 1.75, 1.92, 2.08, 2.31, 2.53, 2.69, 2.85, 3.12, 3.22, and 3.31 THz. Most absorption peaks of the two samples agree with the results simulated by Density Function Theory (DFT) method of Gaussian 09 software. In our work, more spectral peaks based on experimental and theoretical results were found in comparison to that of other groups, since we employed higher sensitive FTIR measurement system and considered the effect of number of molecule unit in simulation. The study suggests that the effect of intermolecular vibration is stronger than intramolecular interaction on the absorption bands in THz region.
Ling Jiang; Miao Li; Chun Li; Haijun Sun; Li Xu; Biaobin Jin; Yunfei Liu. Terahertz Spectra of L-Ascorbic Acid and Thiamine Hydrochloride Studied by Terahertz Spectroscopy and Density Functional Theory. Journal of Infrared, Millimeter, and Terahertz Waves 2014, 35, 871 -880.
AMA StyleLing Jiang, Miao Li, Chun Li, Haijun Sun, Li Xu, Biaobin Jin, Yunfei Liu. Terahertz Spectra of L-Ascorbic Acid and Thiamine Hydrochloride Studied by Terahertz Spectroscopy and Density Functional Theory. Journal of Infrared, Millimeter, and Terahertz Waves. 2014; 35 (10):871-880.
Chicago/Turabian StyleLing Jiang; Miao Li; Chun Li; Haijun Sun; Li Xu; Biaobin Jin; Yunfei Liu. 2014. "Terahertz Spectra of L-Ascorbic Acid and Thiamine Hydrochloride Studied by Terahertz Spectroscopy and Density Functional Theory." Journal of Infrared, Millimeter, and Terahertz Waves 35, no. 10: 871-880.