2020-01
Numerical analysis of MHD flow and nanoparticle migration within a permeable space containing Non-equilibrium model
Truong Khang Nguyen; Muhammad Usman; M. Sheikholeslami; Rizwan Ul Haq; Ahmad Shafee; Abdul Khader Jilani; I. Tlili;
Abstract:
This article deals with the numerical simulation to examine the significant effects of MHD flow and nanoparticle migration inside a permeable space including two temperature model. For more physical situation, thermal radiation influence is considered. Viable transformation is assumed to alter the governing set of PDEs into dimensionless form. CVFEM was adopted to model this article. Impacts of radiation parameter, Rayleigh number (10 3 < Ra < 10 4 ), nanofluid–solid interface factor (10 < Nhs <1000), Hartmann number (0 < Ha < 20) and nanoparticles’ shape (3 < m < 5.7) on nanofluid behavior were demonstrated. Outcomes depict that stronger convection can be obtained with augmenting in shape factor. Average Nusselt number increases as enhancing the buoyancy and radiation effect whereas decreases as enhancing nanofluid–solid interface factor and Hartmann number. Comparison of the numerical outputs achieved by means of CVFEM with published data was also deliberated. It is evident that the applied approach is very accurate to investigate solution of the discussed problem.
Reference:
Truong Khang Nguyen; Muhammad Usman; M. Sheikholeslami; Rizwan Ul Haq; Ahmad Shafee; Abdul Khader Jilani; I. Tlili.Numerical analysis of MHD flow and nanoparticle migration within a permeable space containing Non-equilibrium model, Physica A: Statistical Mechanics and its Applications, Volume 537,10.1016/j.physa.2019.122459.
2020-01
Interaction between shock wave and a movable sphere with cavitation effects in shallow water
Wu, WB; Zhang, AM; Liu, YL; Liu, MB；
Abstract:
In this paper, we establish a fluid-structure interaction (FSI) model to investigate the dynamic interactions between the underwater explosion (UNDEX) shock wave and a movable sphere near the free surface. We utilize the local discontinuous Galerkin (LDG) method to capture the propagation of the shock wave in the fluid domain and employ the pressure cutoff model to calculate cavitation effects. The fluid elements at the fluid-structure interface are directly coupled to the structural dynamic model, and the structural transient dynamic responses are coupled with fluid acoustic pressure at the fluid-structure interface in the governing equation. The validity of the present FSI model is verified by comparing with the continuous Galerkin method. Due to the advantage of the LDG method in capturing the discontinuous wave, the present model shows better properties than the traditional coupled acoustic-structural model. With the present FSI model, we investigate the interaction between the UNDEX shock wave and a submerged and floated sphere. Under the combined effects of the free surface and structure, the UNDEX shock and cavitation loading characteristics are analyzed, and the influences of complicated cavitation effects on dynamic responses of the sphere are discussed. Published under license by AlP Publishing.
Reference:
Wu, WB; Zhang, AM; Liu, YL; Liu, MB. Interaction between shock wave and a movable sphere with cavitation effects in shallow water, PHYSICS OF FLUIDS, Volume 32, DOI:
Performance improvement of dual-pulse heterodyne distributed acoustic sensor for sound detection
He, XG; Zhang, M; Gu, LJ; Xie, SR; Liu, F; Lu, HL;
Abstract:
Phase fading is fatal to the performance of distributed acoustic sensors (DASs) influencing its capability of distributed measurement as well as its noise level. Here, we report the experimental observation of a strong negative correlation between the relative power spectrum density (PSD) at the heterodyne frequency and the noise floor of the detected phase for the heterodyne demodulated distributed acoustic sensor (HD-DAS) system. We further propose a weighted-channel stack algorithm (WCSA) to alleviate the phase fading noise via an enhancement of the relative PSD at the heterodyne frequency. Experimental results show that the phase noise of the demodulated signal can be suppressed by 13.7 dB under optimal condition. As a potential application, we exploited the improved HD-DAS system to retrieve a piece of music lasted for 205 s, demonstrating the reliability of detecting wideband sound signal without distortion.
Reference:
He, XG; Zhang, M; Gu, LJ; Xie, SR; Liu, F; Lu, HL. Performance Improvement of Dual-Pulse Heterodyne Distributed Acoustic Sensor for Sound Detection, SENSORS, Volume
2020-03
CFD based parameter tuning for motion control of robotic fish
Tian, RY; Li, L; Wang, W; Chang, XH; Ravi, S; Xie, GM;
Abstract:
After millions of years of evolution, fishes have been endowed with agile swimming ability to accomplish various behaviourally relevant tasks. In comparison, robotic fish are still quite poor swimmers. One of the unique challenges facing robotic fish is the difficulty in tuning the motion control parameters on the robot directly. This is mainly due to the complex fluid environment robotic fish need to contend with and endurance limitations (i.e. battery capacity limitations). To overcome these limitations, we propose a computational fluid dynamics (CFD) simulation platform to first tune the motion control parameters for the computational robotic fish and then refine the parameters by experiments on robotic fish. Within the simulation platform, the body morphology and gait control of the computational robotic fish are designed according to a robotic fish. The gait control is implemented by a central pattern generator (CPG); The CFD model is solved by using a hydrodynamic-kinematics strong-coupling method. We tested our simulation platform with three basic tasks under active disturbance rejection control (ADRC) and try-and-error-based parameter tuning. Trajectory comparisons between the computational robotic fish and robotic fish verify the effectiveness of our simulation platform. Moreover, power costs and swimming efficiency under the motion control are also analyzed based on the outputs from the simulation platform. Our results indicate that the CFD based simulation platform is powerful and robust, and shed new light on the efficient design and parameter optimization of the motion control of robotic fish.
Reference:
Tian R , Li L , Wang W , et al. CFD based parameter tuning for motion control of robotic fish, Bioinspiration & Biomimetics, Volume
2020-03
Observer-based event-triggered circle formation control for first- and second-order multiagent systems
Xu, P; Xie, GM; Tao, J; Xu, MY; Zhou, Q;
Abstract:
This paper proposes an observer-based event-triggered algorithm to solve circle formation control problems for both first- and second-order multiagent systems, where the communication topology is modeled by a spanning tree-based directed graph with limited resources. In particular, the observation-based event-triggering mechanism is used to reduce the update frequency of the controller, and the triggering time depends on the norm of the state function and the trigger threshold of measurement errors. The analysis shows that sufficient conditions are established for achieving the desired circle formation, while there exists at least one agent for which the next interevent interval is strictly positive. Numerical simulations of both first- and second-order multiagent systems are also given to demonstrate the effectiveness of the proposed control laws.
Reference:
Xu, P; Xie, GM; Tao, J; Xu, MY; Zhou, Q. Observer-Based Event-Triggered Circle Formation Control for First- and Second-Order Multiagent Systems, COMPLEXITY, Volume 2020, 10.1155/2020/4715315.
2020-03
Comprehensive study and comparison of equilibrium and kinetic models in simulation of hydratereaction in porous media
Teng, YH; Zhang, DX;
Abstract:
Coupling hydrate reaction in fluid transport in porous media is essential for simulation of gas hydrate production, as well as carbon sequestration in deep-sea sediments. It can be conceptualized as multiphase, multicomponent, and non-isothermal reactive transport. Two types of models have been developed for the description of hydrate reaction in numerical models. The equilibrium model (EM) assumes instantaneous chemical equilibrium among species, and thus ignores reaction kinetics. The kinetic model (KM) incorporates reaction kinetics by introducing a term of reaction rate dependent on fugacity difference. Although KM achieves a more accurate description of the reaction, it is potentially more computationally intensive due to the increased degree of freedom in the nonlinear equation system. Although several previous studies have investigated the similarities and differences between these two models, inconsistencies exist in their studies, and the mechanisms to distinguish these two models are still not well understood. In our study, in order to identify the reasons for these inconsistencies and elucidate the mechanisms that control the differences between the two reaction models, we provide a comprehensive investigation and comparison of these two models via theoretical analysis and numerical experiments. Through comparing the basic assumptions, mathematical model and the equation systems, we pointed out the basic difference of these two models, which results from the different calculations of physical parameters. Dimensionless analysis of the governing equations of KM yields several characteristic numbers, representing the relative strength of different physical processes. We performed numerical experiments to investigate the effect of characteristic numbers on the difference between the two models, and the results indicate that there exist critical values for these characteristic numbers, lower than which lead to an obvious gap between the results of EM and KM. It turns out that the relative strength of the hydrate reaction and other physical processes controls the magnitude of difference between these two models. EM is essentially a special case of KM when the time scale of the hydrate reaction is sufficiently smaller than other physical processes, such as convective and diffusive transport of mass and heat. Comparison between the time and iteration steps in the two reaction models provides insights into the computational efficiency of the two models. (C) 2019 Elsevier Inc. All rights reserved.
Reference:
Teng, YH; Zhang, DX. Comprehensive study and comparison of equilibrium and kinetic models in simulation of hydratereaction in porous media, JOURNAL OF COMPUTATIONAL PHYSICS, Volume 404, 10.1016/j.jcp.2019.109094.
2020-04
Investigations on sloshing mitigation using elastic baffles by coupling smoothed finite elementmethod and decoupled finite particle method
Zhang, ZL; Khalid, MSU; Long, T; Chang, JZ; Liu, MB;
Abstract:
Liquid sloshing in partially filled containers is widely observed in various engineering systems where the forces exerted by the liquid on tank walls may result in the instability of tank or even a structural failure. To enhance the hydrodynamic damping ratio and consequently decrease the sloshing forces, baffles have been designed as effective internal components inside containers in most of the practical engineering problems. In this work, we numerically investigate the sloshing mitigation using elastic baffles through our recently developed methodology based on the coupling strategy of smoothed finite element method (SFEM) and an improved version of smoothed particle hydrodynamics (SPH) offering better accuracy. First, we simulate a benchmark problem of sloshing flow interacting with an elastic baffle installed in a container, and the numerical results agree well with the experimental data. Further, various cases are conducted to study the sloshing mitigation by using deformable baffles with different configurations and elasticities. Our current observations and findings based on the simulation results demonstrate that the impact pressure on the tank wall is significantly influenced by the geometric orientations and complex configurations of elastic baffles. The timing of sloshing flow impacting on the container wall can be passively controlled by adequately choosing the baffle elasticity. The damping performances of different elastic baffles are quantified by the numerically obtained Pressure-E-baffle lines. The relevant analysis in this paper can greatly help explore the effective solutions to mitigate the liquid sloshing in engineering systems. (C) 2020 Elsevier Ltd. All rights reserved.
Reference:
Zhang, ZL; Khalid, MSU; Long, T; Chang, JZ; Liu, MB. Investigations on sloshing mitigation using elastic baffles by coupling smoothed finite elementmethod and decoupled finite particle method, JOURNAL OF FLUIDS AND STRUCTURES, Volume
2020-04
Online state estimation of a fin-actuated underwater robot using artificial lateral line system
Zheng, XW; Wang, W; Xiong, ML; Xie, GM；
Abstract:
A lateral line system is a flow-responsive organ system, with which fish can effectively sense the surrounding flow field, thus serving functions in flow-aided fish behaviors. Inspired by such a biological characteristic, artificial lateral line systems (ALLSs) have been developed for promoting technological innovations of underwater robots. In this article, we focus on investigating state estimation of a freely swimming robotic fish in multiple motions, including rectilinear motion, turning motion, gliding motion, and spiral motion. The state refers to motion parameters, including linear velocity, angular velocity, motion radius, etc., and trajectory of the robotic fish. Specifically, for each motion, a pressure variation (PV) model that links motion parameters to PVs surrounding the robotic fish is first built; then, a linear regression analysis method is used for determining the model parameters. Based on the acquired PV model, motion parameters can be estimated by solving the PV model inversely using the PVs measured by the ALLS. Finally, a trajectory estimation method is proposed for estimating trajectory of the robotic fish based on the ALLS-estimated motion parameters. The experimental results show that the robotic fish is able to estimate its trajectory in the aforementioned multiple motions with the aid of ALLS, with small estimation errors.
Reference:
Zheng, XW; Wang, W; Xiong, ML; Xie, GM. Online State Estimation of a Fin-Actuated Underwater Robot Using Artificial Lateral Line System, IEEE TRANSACTIONS ON ROBOTICS, Volume 36, 10.1109/TRO.2019.2956343.
2020-04
基于Processing实现多智能体环形围捕仿真
海金涛；谢广明；文家燕；罗文广；
Abstract:
在以往多智能体编队研究的仿真分析中,相关物理量和运动轨迹常采用静态曲线描述,较少关注系统运动过程的实时动态刻画。针对上述问题,提出了一种基于Processing的动态仿真方法,首先,利用三阶贝塞尔曲线构造了一种新型软体仿生鱼模型。其次,综合虚拟结构法和人工势场法设计了能解决个体避碰问题的多智能体环形围捕控制律。最后,应用仿生鱼模型对多智能体环形围捕控制算法进行动态仿真。仿真结果表明,新型仿真方法直观增强了智能体位姿信息的动态可视化,验证了二阶积分器多智能体系统环形围捕算法的可行性。
Reference:
海金涛, 谢广明, 文家燕, et al. 基于Processing实现多智能体环形围捕仿真[J]. 计算机仿真, 2020, v.37(04):345-351.
2020-05
Novel operational matrices-based method for solving fractional-order delay differential equationsvia shifted gegenbauer polynomials
Usman, M; Hamid, M; Zubair, T; Haq, RU; Wang, W; Liu, MB;
Abstract:
Accurate solutions of nonlinear multi-dimensional delay problems of fractional-order arising in mathematical physics and engineering recently have been found to be a challenging task for the research community. This paper witnesses that an efficient fully spectral operational matrices-based scheme is developed and successfully applied for stable solutions of time-fractional delay differential equations (DDEs). Monomials are introduced in order to proposed the novel operational matrices for fractional-order integration I-nu and derivative D-nu by means of shifted Gegenbauer polynomials. Some ordinary and partial delay differential equations of fractional-order are considered to show reliability, efficiency and appropriateness of the proposed method. In order to approximate the delay term in DDEs a novel delay operational matrix Theta(a)(b) is introduced with the help of shifted Gegenbauer polynomials. The proposed algorithm transform the problem understudy into a system of algebraic equations which are easier to tackle. Analytical solutions of the mentioned problem are effectively obtained, and an inclusive comparative study is reported which reveals that the proposed computational scheme is effective, accurate and well-matched to investigate the solutions of aforementioned problems. Error bound analysis is enclosed in our investigation to reveal the consistency and support the mathematical formulation of the algorithm. This proposed scheme can be extended to explore the solution of more dervisfy problem of physical nature in complex geometry. (C) 2019 Elsevier Inc. All rights reserved.
Reference:
Usman, M; Hamid, M; Zubair, T; Haq, RU; Wang, W; Liu, MB. Novel operational matrices-based method for solving fractional-order delay differential equationsvia shifted gegenbauer polynomials, APPLIED MATHEMATICS AND COMPUTATION, Volume
2020-05
Modal decompositions of the kinematics of crevalle jack and the fluid-caudal fin interaction
Khalid, M.S.U.; Junshi Wang; Akhtar, I.; Haibo Dong; Moubin Liu；
Abstract:
To understand the governing mechanisms of bio-inspired swimming has always been challenging due to intense interactions between the flexible bodies of natural aquatic species and water around them. In this paper, we employ advanced modal decomposition techniques; proper orthogonal decomposition and dynamic mode decomposition, to extract energetically strongest spatio-temporal orthonormal components of complex kinematics of a Crevalle Jack (Caranx hippos) fish. Then, we present a computational framework for handling fluid-structure interaction related problems in order to investigate their contributions towards the overall dynamics of highly nonlinear systems. We find that the undulating motion of this fish can be described by only two standing-wave like spatially orthonormal modes. Constructing the data set from our numerical simulations for flows over the membranous caudal fin of the Jack fish, our modal analyses reveal that only the first few modes receive energy from both the fluid and structure, but the contribution of fluid in the higher modes is minimal. For the viscous and transitional flow conditions considered here, both spatially and temporally orthonormal modes show strikingly similar coherent flow structures. Our investigations are expected to assist in developing data-driven reduced-dimensional mathematical models to examine the dynamics of bio-inspired swimming robots and develop new and effective control strategies to bring their performance closer to real fish species.
2020-06
Multiple states and transport properties of double-diffusive convection turbulence
Yang, YT; Chen, WY; Verzicco, R; Lohse, D；
Abstract:
When fluid stratification is induced by the vertical gradients of two scalars with different diffusivities, double-diffusive convection (DDC) may occur and play a crucial role in mixing. Such a process exists in many natural and engineering environments. Especially in the ocean, DDC is omnipresent since the seawater density is affected by temperature and salinity. The most intriguing phenomenon caused by DDC is the thermohaline staircase, i.e., a stack of alternating well-mixed convection layers and sharp interfaces with very large gradients in both temperature and salinity. Here we investigate DDC and thermohaline staircases in the salt finger regime, which happens when warm saltier water lies above cold fresher water and is commonly observed in the (sub)tropic regions. By conducting direct numerical simulations over a large range of parameters, we reveal that multiple equilibrium states exist in fingering DDC and staircases even for the same control parameters. Different states can be established from different initial scalar distributions or different evolution histories of the flow parameters. Hysteresis appears during the transition from a staircase to a single salt finger interface. For the same local density ratio, salt finger interfaces in the single-layer state generate very different fluxes compared to those within staircases. However, the salinity flux for all salt finger interfaces follows the same dependence on the salinity Rayleigh number of the layer and can be described by an effective power law scaling. Our findings have direct applications to oceanic thermohaline staircases.
Reference:
Yang, YT; Chen, WY; Verzicco, R; Lohse, D. Multiple states and transport properties of double-diffusive convection turbulence, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Volume 117 ,10.1073/pnas.2005669117.
2020-06
A robust scheme based on novel-operational matrices for some classes of time-fractional nonlinear problems arising in mechanics and mathematical physics
Usman, M; Hamid, M; Khalid, MSU; Ul Haq, R; Liu, MB;
Abstract:
In this paper, we present a novel approach based on shifted Gegenbauer wavelets to attain approximate solutions of some classed of time-fractional nonlinear problems. First, we present the approximation of a function of two variablesu(x,t) with help of shifted Gegenbauer wavelets and then some novel operational matrices are proposed with the help of piecewise functions to investigate the positive integer derivative (D(x)andD(t)), fractional-order derivative (Px alpha andPt beta), fractional-order integration (Jx alpha andJt beta) and delay terms (DbaandDdc) of approximated functionu(x,t). In order to transform the discussed nonlinear problem into linear problem Picard iterative scheme has been adopt. The current scheme converts the discussed highly nonlinear time-fractional problem into system of linear algebraic equation the help of developed operational matrices and Picard idea. Analysis on the error bound and convergence to authenticate the mathematical formulation of the computational algorithm. We solve various test problems, such as the van der Pol oscillator model, generalized Burger-Huxley, neutral delay parabolic differential equations, sine-Gordon, parabolic integro-differential equation and nonlinear Schrodinger equations to show the efficiency and accuracy of linearized shifted Gegenbauer wavelets method. A comprehensive comparative examination shows the credibility, accuracy, and reliability of the presently proposed computational approach. Also, this scheme can be extended conveniently to other multi-dimensional physical problems of highly nonlinear fractional or variable order of complex nature.
Reference:
Usman, M; Hamid, M; Khalid, MSU; Ul Haq, R; Liu, MB. A robust scheme based on novel-operational matrices for some classes of time-fractional nonlinear problems arising in mechanics and mathematical physics, NUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS, 10.1002/num.22492.
2020-06
Chartarlactams Q-T, dimeric phenylspirodrimanes with antibacterial and antiviral activities
Liu, D; Li, Y; Guo, XC; Ji, W; Lin, WH；
Abstract:
Four new phenylspirodrimane-type dimers, namely chartarlactams Q-T, along with stachyin B were isolated from the fermentation broth of a sponge-derived fungus Stachybotrys chartarum WGC-25 C-6. Chartarlactams Q-T were structurally featured by the dimerization of two units of phenylspirodrimane linked by a C-N bond. Their structures were determined on the basis of extensive spectroscopic analysis, while quantum ECD calculation and modified Mosher's method were used for the assignment of absolute configurations. Chartarlactams Q-S and stachyin B showed moderate inhibition against bacterial pathogen Staphylococcus aureus with MIC values ranging from 4 mu g/mL to 16 mu g/mL, and chartarlactam T exhibited significant inhibition toward ZIKV virus.
Reference:
Liu, D; Li, Y; Guo, XC; Ji, W; Lin, WH. Chartarlactams Q-T, Dimeric Phenylspirodrimanes with Antibacterial and Antiviral Activities, CHEMISTRY & BIODIVERSITY, 10.1002/cbdv.202000170.
2020-07
Piperazine ring formation by a single-module NRPS and cleavage by an alpha-KG-dependent nonheme iron dioxygenase in brasiliamide biosynthesis
Yuan, BC; Liu, D; Guan, X; Yan, YC; Zhang, JP; Zhang, YP; Yang, DH; Ma, M; Lin, WH；
Abstract:
Brasiliamides are a class of piperazine-containing alkaloids produced by Penicillium brasilianum with a range of pharmaceutical activities. The mechanism of brasiliamide biosynthesis, including piperazine ring formation and multiple tailoring modifications, still remains unclear. In this study, the biosynthetic gene cluster of brasiliamides, brs, was identified from the marine-derived fungal strain Penicillium brasilianum WZXY-M122-9. Deletion of a histone deacetylase-encoding gene using a CRISPR/Cas9 gene editing system led to the production of a new compound, namely brasiliamide I (1). The brs-encoded single-module nonribosomal peptide synthetase (NRPS) BrsA is involved in the formation of the piperazine skeleton of brasiliamides. Full-length BrsA protein (113.6 kDa) was purified, and reconstitution of enzymatic activity in vitro confirmed that BrsA stereoselectively accepts l-phenylalanine as the substrate. Multiple deletion of tailoring genes and analysis of purified proteins in vitro enabled us to propose a brasiliamide biosynthetic pathway. In the tailoring steps, an alpha-ketoglutarate (KG)-dependent nonheme iron dioxygenase, BrsJ, was identified to catalyze piperazine ring cleavage during biosynthesis of brasiliamide A (2).
Reference:
Yuan, BC; Liu, D; Guan, X; Yan, YC; Zhang, JP; Zhang, YP; Yang, DH; Ma, M; Lin, WH. Piperazine ring formation by a single-module NRPS and cleavage by an alpha-KG-dependent nonheme iron dioxygenase in brasiliamide biosynthesis, APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 10.1007/s00253-020-10678-w.
2020-07
Dual-sensor fusion based attitude holding of a fin-actuated robotic fish
Zheng, JZ; Zheng, XW; Zhang, TH; Xiong, ML; Xie, GM；
Abstract:
In nature, the lateral line system (LLS) is a critical sensor organ of fish for rheotaxis in complex environments. Inspired by the LLS, numbers of artificial lateral line systems (ALLSs) have been designed to the fish-like robots for flow field perception, assisting the robots to be stable in the face of flow disturbances. However, almost all pressure sensor based ALLSs face the challenge of the low signal to noise ratio (SNR), resulting in inaccurate perception information. To solve this problem, this paper describes a dual-sensor fusion method by integrating the ALLSs with the inertial measurement unit (IMU), and shows the excellent performance by a higher precision and lower latency attitude holding of robotic fish. First, low-pass filtering is performed on ALLS data with low-SNR. Second, the ALLS data is mapped to the angle of attack based on an artificial neural network. Finally, a fusion perception method is established based on the time correlation between ALLS and IMU. To demonstrate the efficacy of our proposed method, we compare the result of attitude holding by three methods (dual-sensor fusion method, IMU based method, and ALLS based method). Furthermore, dual-sensor fusion method is tested at varied flow velocities and varied desired angles of attack, indicating that the algorithm can enable the robotic fish to perform dynamic movements in the incoming flow. This work provides a method for the attitude control of autonomous underwater vehicles (AUVs) by fusing the sensory data of ALLS and IMU, which is also applicable to other flow sensors and IMU.
Reference:
Zheng, JZ; Zheng, XW; Zhang, TH; Xiong, ML; Xie, GM. Dual-sensor fusion based attitude holding of a fin-actuated robotic fish, BIOINSPIRATION & BIOMIMETICS, 10.1088/1748-3190/ab810a.
2020-08
Junceellolide B, a novel inhibitor of Hepatitis B virus
Li, XD; Liu, H; Cheng, W; Wang, J; Zhang, H; Lu, FM; Chen, XM; Lin, WH；
Abstract:
HBV infection is a common cause of liver disease with a high burden worldwide. Current therapeutic strategy relies on interferon and nucleos(t)ide-type drugs with the limitation of functional cure. In this study, a structurebased screening of marine natural products from an in-house library was performed to hit HBV inhibitors, and the gorgonian-derived briarane-type diterpenoids showed inhibitory effects against HBV DNA replication in HepAD38 cells. Preliminary analyses of structure-activity relationship demonstrated that a briarane-based scaffold with an 3E,5(16)-diene and a chlorine-substitution at C-6 is required for the anti-HBV activity. Junceellolide B is one of the potent HBV inhibitors exhibiting efficient reduction of HBsAg and HBeAg production in HBV infected HepG2-NTCP cells with a dose-dependent manner (p < 0.001). It also significantly reduced the secreted HBV DNA, HBV RNA, and HBeAg in HepAD38 cells with the EC50 values of 0.83, 2.87 and 7.75 mu M, respectively. Mechanistically, junceellolide B potently inhibited HBV RNA transcription without promoting HBV RNA degradation. RNA-seq analysis indicated that junceellolide B significantly decreased HBV cccDNA-transcripted products accompanying stable down-regulation of the expression of RNA polymerase II related host transcription factors (ZBED6 and ZBTB7B). These findings suggest junceellolide B to be a transcription inhibitor of cccDNA and a promising lead for the development of new anti-HBV agent.
Reference:
Li, XD; Liu, H; Cheng, W; Wang, J; Zhang, H; Lu, FM; Chen, XM; Lin, WH. Junceellolide B, a novel inhibitor of Hepatitis B virus, BIOORGANIC & MEDICINAL CHEMISTRY, Volume 28 ,10.1016/j.bmc.2020.115603.
2020-08
Pan-genomic analysis reveals that the evolution ofDietziaspecies depends on their living habitats
Fang, H; Xu, JB; Nie, Y; Wu, XL;
Abstract:
The bacterial genusDietziais widely distributed in various environments. The genomes of 26 diverse strains ofDietzia, including almost all the type strains, were analysed in this study. This analysis revealed a lipid metabolism gene richness, which could explain the ability ofDietziato live in oil related environments. The pan-genome consists of 83,976 genes assigned into 10,327 gene families, 792 of which are shared by all the genomes ofDietzia. Mathematical extrapolation of the data suggests that theDietziapan-genome is open. Both gene duplication and gene loss contributed to the open pan-genome, while horizontal gene transfer was limited.Dietziastrains primarily gained their diverse metabolic capacity through more ancient gene duplications. Phylogenetic analysis ofDietziaisolated from aquatic and terrestrial environments showed two distinct clades from the same ancestor. The genome sizes ofDietziastrains from aquatic environments were significantly larger than those from terrestrial environments, which was mainly due to the occurrence of more gene loss events during the evolutionary progress of the strains from terrestrial environments. The evolutionary history ofDietziawas tightly coupled to environmental conditions, and iron concentrations should be one of the key factors shaping the genomes of theDietzialineages.
Reference:
Fang, H; Xu, JB; Nie, Y; Wu, XL. Pan-genomic analysis reveals that the evolution ofDietziaspecies depends on their living habitats, ENVIRONMENTAL MICROBIOLOGY, 10.1111/1462-2920.15176.
2020-08
Complete genome sequence of a novelBacillusphage, P59, that infectsBacillus oceanisediminis
Feng, Z; Liu, XW; Liu, W; Nie, Y; Wu, XL；
Abstract:
P59, a virulent phage ofBacillus oceanisediminis, was isolated from the sediment of Weiming Lake at Peking University (Beijing, China). P59 showed the typical morphology of myovirids. The complete genome sequence of P59 is 159,363 bp in length with a G+C content of 42.34%. The genome sequence has very low similarity to the other phage genome sequences in the GenBank database, suggesting that P59 is a new phage. A total of 261 open reading frames and 15 tRNA genes were predicted. Based on its morphological and genetic traits, we propose phage P59 to be a new member of the familyHerelleviridae.
Reference:
Feng, Z; Liu, XW; Liu, W; Nie, Y; Wu, XL. Complete genome sequence of a novelBacillusphage, P59, that infectsBacillus oceanisediminis, ARCHIVES OF VIROLOGY, 10.1007/s00705-020-04761-w.
2020-08
Novel modification in wavelets method to analyze unsteady flow of nanofluid between two infinitely parallel plates
Usman, M; Zubair, T; Hamid, M; Haq, RU；
Abstract:
The present article devoted to analyze the unsteady incompressible flow of nanofluid between the two infinite parallel plates. The nonlinear system of governing equations reduced to set of or-dinary differential equations by means of the suitable transformations. A new modification is introduced in well-known Legendre wavelets method (LWM) to investigate the solutions of the attained set of ODEs. Analysis of square residual error shows an excellent agreement. The modified version of LWM reduces the number of unknowns which leads less computational cost but the trial solution must satisfy the given problem. Moreover, graphical description of the velocity, temperature and concentrations profiles are plotted by varying the emerging para-meters. Effect of physical parameters on local skin friction and Nusselt number also presented. It is noticed that squeeze and permeable velocity parameters are providing a decreasing coefficient of skin-friction and an opposite behavior is found for Hartmann number while the Nusselt numbers found at minimum for these parameters. The thermophoretic and Prandtl number are respectively causing an enhanced and dropped concentration. The obtained outcomes are wit-nesses that the proposed modification is highly effective and can be extended to other nonlinear problems.
Reference:
Usman, M; Zubair, T; Hamid, M; Haq, RU. Novel modification in wavelets method to analyze unsteady flow of nanofluid between two infinitely parallel plates, CHINESE JOURNAL OF PHYSICS, Volume 66 , 10.1016/j.cjph.2020.03.031.
2020-08
A chelyshkov polynomial based algorithm to analyze the transport dynamics and anomalous diffusion in fractional model
Hamid, M; Usman, M; Haq, RU; Wang, W；
Abstract:
The evolution equations with fractional or variable order derivatives can deliver a proper mathematical modeling to define the transport dynamics and anomalous diffusion in complex dynamical structures. Herein, a hybrid method based on operational matrices of derivative is proposed and successfully applied to explore the solution of mobile-immobile advection-dispersion problem of variable order. The variable order of the model is considered as function of space and time. The operational matrices of derivative named exact and approximate are constructed with the aid of two different approaches and related theorems are available to support the mathematical justification. The error bound and convergence analysis is presented to validate the mathematical formulation of the computational algorithm. A comparative study is enclosed in our investigation which endorses the credibility of the exact operational matrix of derivative. The numerical simulations for various problems are encountered and set of graphs are presented. The numerical examples are endorsing that the proposed mathematical algorithm is computationally effective and efficient tool and one can extend it to other physical problems of fractional or variable order. (C) 2020 Elsevier B.V. All rights reserved.
Reference:
Hamid, M; Usman, M; Haq, RU; Wang, W. A Chelyshkov polynomial based algorithm to analyze the transport dynamics and anomalous diffusion in fractional model, PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, Volume 551 , 10.1016/j.physa.2020.124227.
2020-08
Double diffusive convection in the finger regime for different Prandtl and Schmidt numbers
Yang, YT；
Abstract:
In this work fingering double diffusive convection, i.e. the buoyancy-driven flow with fluid density being affected by two different scalar components, is investigated numerically with special efforts on the influences of the physical properties of two scalar components. We show that different scalar properties can affect the global transport behaviors. The concentration flux exhibits different exponents in their power-law scalings for different combinations of scalar components. The scaling exponents of heat flux, however, depend mainly on the ratio of the diffusivities of two scalars. If one uses the local parameters of the finger layer in the bulk, the behaviors are very similar to those found in the fully periodic simulations. The horizontal width of the fingers is consistent with the wavelength of the fast growing mode. For one case we observe evidences of the thermohaline staircase, namely, the typical width of the flow structures changes significantly in different layers within the flow domain.
Reference:
Yang, YT.Double diffusive convection in the finger regime for different Prandtl and Schmidt numbers, ACTA MECHANICA SINICA, Volume 36 , 10.1007/s10409-020-00973-0.
2020-09
基于我国受威胁海洋鱼类分布与捕捞压力的保护空缺分析
陈航通；姚锦仙；卜思涵；朱争光；
Abstract:
从专业物种数据库(IUCN, OBIS 和 GBIF)、文献数据库和专著中提取并整合分布在我国海域的86种受威胁海洋鱼类的基础信息数据, 利用GIS技术得到热点分布区域和捕捞压力格局, 通过比较物种丰度图层和脆弱度指数加权丰度图层, 探讨我国受威胁海洋鱼类的分布与受威胁状况, 并结合现有保护区信息与渔业捕捞热点区域进行保护空缺分析。结果表明: 1) 我国受威胁海洋鱼类分布热点区域包括台湾海峡海域、闽南海域、台湾以东海域、粤东海域和珠江口海域, 面积达到 23.1 万 km2, 占我国海域总面积的 7.7%; 2) 我国海洋保护区面积仅占受威胁海洋鱼类分布热点区域的 2.3%, 覆盖度需要加强; 3) 浙中南部分海域既是捕捞“热点”区域, 也是客观上受捕捞威胁严重的区域, 需加强管理; 4) 结合 Global Fishing Watch 的捕捞数据分析显示,我国的禁渔政策对鱼类多样性保护效果显著, 在休渔期捕捞强度降低80%以上, 但整体捕捞压力仍巨大。
Reference:
陈航通, 姚锦仙, 卜思涵, 朱争光. 基于我国受威胁海洋鱼类分布与捕捞压力的保护空缺分析[J].北京大学学报(自然科学版),2020.
2020-10
Modeling hydrate-bearing sediment with a mixed smoothed particle hydrodynamics
Huang, C; Liu, MB;
Abstract:
Marine gas hydrate is an important energy source while its extraction may induce environmental problems such as subsea landslide, which is usually challengeable for numerical simulation due to the marine environment with high pressure and the existence of gas hydrate. Smoothed particle hydrodynamics (SPH) is a Lagrangian particle method which is attractive in modeling problems with large deformations and fluid-solid interactions (FSI) for continuum and granular materials. However, the conventional SPH suffers from numerical instability when modeling the soil mechanics with the high confining stress. A mixed SPH is developed in this study to simulate hydrate-bearing sediment with the characteristics of high confining stress. In the mixed SPH model, the conventional SPH is used to discretize the momentum equations, and the kernel gradient correction (KGC) SPH is used to discretize strain and spin rate tensors. In order to consider the effect of hydrate saturation on the strength of soil-hydrate material, an existing linear model is applied into the mixed SPH to define the mechanic parameters of soil-hydrate material. The mixed SPH method is validated by several examples and the obtained numerical results are in close agreement with experimental observations. Finally, the mixed SPH method is used to model landslide of hydrate bearing sediments. The results show that the saturation of hydrate has important impact on the stability of hydrate bearing sediments.
Reference:
Huang, C; Liu, MB. Modeling hydrate-bearing sediment with a mixed smoothed particle hydrodynamics, COMPUTATIONAL MECHANICS, Volume 66 ,10.1007/s00466-020-01895-1.
2020-10
Extracellular heme recycling and sharing across species by novel mycomembrane vesicles of a Gram-positive bacterium
Wang, Meng; Nie, Yong; Wu, Xiao-Lei;
Abstract:
Microbes spontaneously release membrane vesicles (MVs), which play roles in nutrient acquisition and microbial interactions. Iron is indispensable for microbes, but is a difficult nutrient to acquire. However, whether MVs are also responsible for efficient iron uptake and therefore involved in microbial interaction remains to be elucidated. Here, we used a Gram-positive strain, Dietzia sp. DQ12-45-1b, to analyze the function of its MVs in heme-iron recycling and sharing between species. We determined the structure and constituent of MVs and showed that DQ12-45-1b releases MVs originating from the mycomembrane. When comparing proteomes of MVs between iron-limiting and iron-rich conditions, we found that under iron-limiting conditions, heme-binding proteins are enriched. Next, we proved that MVs participate in extracellular heme capture and transport, especially in heme recycling from environmental hemoproteins. Finally, we found that the heme carried in MVs is utilized by multiple species, and we further verified that membrane fusion efficiency and species evolutionary distance determine heme delivery. Together, our findings strongly suggest that MVs act as a newly identified pathway for heme recycling, and represent a public good shared between phylogenetically closely related species.
Reference:
Wang, Meng; Nie, Yong; Wu, Xiao-Lei. Extracellular heme recycling and sharing across species by novel mycomembrane vesicles of a Gram-positive bacterium, The ISME journal, DOI:10.1038/s41396-020-00800-1.
