2021Äê1ÔÂ
Fully coupled model for simulating highly nonlinear dynamic behaviors of a bubble near an elastic-plastic thin-walled plate
Wenbin Wu, Moubin Liu*, A-Man Zhang, and Yun-Long Liu
Abstract
Existing studies of bubble-structure interaction mainly focus on the interaction between a bubble and a movable rigid body or deformable linear elastic structure. The strong nonlinear interaction of a bubble with an elastic-plastic plate has rarely been studied while the inherent dynamic behavior is not clear. In this paper, we develop a three-dimensional fully coupled model to investigate the interaction between a bubble and an elastic-plastic thin-walled plate, which can consider the fluid disturbance on both sides of the thin-walled plate. In this developed model, the dynamic behaviors of the bubble are obtained by the boundary integral method based on the potential flow theory, and the nonlinear elasticplastic responses of the structure are resolved by the explicit finite element method on the basis of the Mindlin-Reissner plate theory. The structural nonlinear responses are incorporated into the fluid boundary integral equation (BIE), and the extra relation between the phi(t) (time derivative of velocity potential) jump across the two sides of the thin-walled plate and its normal derivative phi(tn) is derived, which can describe the hydrodynamic balance on both sides of the submerged plate. The derived relation is added to the BIE about phi(t), so that the bubble loading acting on the plate can be accurately calculated. The established coupled model is validated by comparing with experimental results. Using this numerical model, the influence of the standoff distance and plate thickness on the bubble-plate interaction is discussed. Subjected to the violent loading from the bubble, the oscillation characteristics and elastic-plastic deformation of the plate are analyzed. Due to the elastic-plastic effects of the plate, the bubble can display different interesting featured patterns, including attractive motion, repulsive motion, or splitting.
Source
PHYSICAL REVIEW FLUIDS
Volume6Issue1
DOI10.1103/PhysRevFluids.6.013605
2021Äê1ÔÂ
Modal decompositions of the kinematics of Crevalle jack and the fluid-caudal fin interaction
Muhammad Saif Ullah Khalid, Junshi Wang, Imran Akhtar, Haibo Dong, Moubin Liu
Abstract
To understand the governing mechanisms of bio-inspired swimming has always been challenging due to intense interactions between flexible bodies of natural aquatic species and water around them. Advanced modal decomposition techniques provide us with tools to develop more in-depth understating about these complex dynamical systems. In this paper, we employ proper orthogonal decomposition (POD) and dynamic mode decomposition (DMD) techniques 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 the structure in the remaining 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-order 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.
Source
BIOINSPIRATION & BIOMIMETICS
Volume16Issue1
DOI10.1088/1748-3190/abc294
2021Äê1ÔÂ
Artificial lateral line based relative state estimation between an upstream oscillating fin and a downstream robotic fish
Xingwen Zheng, Wei Wang, Liang Li and Guangming Xie
Abstract
The lateral line enables fish to efficiently sense the surrounding environment, thus assisting flow-related fish behaviors. Inspired by this phenomenon, varieties of artificial lateral line systems (ALLSs) have been developed and applied to underwater robots. This article focuses on using the pressure sensor arrays based ALLS-measured hydrodynamic pressure variations (HPVs) for estimating the relative states between an upstream oscillating fin and a downstream robotic fish. The HPVs and relative states are measured in flume experiments in which the oscillating fin and the robotic fish have been locate with upstream-downstream formation in a flume. The relative states include the relative oscillating frequency, amplitude, and offset of the upstream oscillating fin to the downstream robotic fish, the relative vertical distance, the relative yaw angle, the relative pitch angle, and the relative roll angle between the upstream oscillating fin and the downstream robotic fish. Regression models between the ALLS-measured and the mentioned relative states are investigated, and regression models-based relative state estimations are conducted. Specifically, two criteria are proposed firstly to investigate not only the sensitivity of each pressure sensor to the variations of relative state but also the insufficiency and redundancy of the pressure sensors. And thus the pressure sensors used for regression analysis are determined. Then four typical regression methods, including random forest (RF) algorithm, support vector regression, back propagation neural network, and multiple linear regression method are used for establishing regression models between the ALLS-measured HPVs and the relative states. Then regression effects of the four methods are compared and discussed. Finally, the RF-based method, which has the best regression effect, is used to estimate the relative yaw angle and oscillating amplitude using the ALLS-measured HPVs and exhibits excellent estimation performance.
Source
BIOINSPIRATION & BIOMIMETICS
Volume16Issue1
DOI10.1088/1748-3190/abb86c
2021Äê1ÔÂ
Higher-order algorithms for stable solutions of fractional time-dependent nonlinear telegraph equations in space
Usman, Muhammad; Hamid, Muhammad; Liu, Moubin
Abstract
In this article, three novel algorithms are developed and successfully applied to investigate the stable solutions of time-fractional nonlinear telegraph equations. Firstly, we presented the shifted Gegenbauer polynomials through appropriate transformations. The approximation of a function u(||x||, t) is defined via shifted Gegenbauer polynomials (SGPs) and then developed the operational matrices of a positive integer and non-integer derivatives assisted by multi-dimensional shifted Gegenbauer polynomials vectors. Linearized fully spectral method (LFSM) is proposed by means of function approximations and developed operational matrices whilst Picard iterative scheme is used to linearize the discussed problem. To introduce a semi-discrete method (SDM), the temporal derivative is approximated through a central difference scheme whereas spatial derivatives are approximated assisted by novel operational matrices. A fully numerical method (FNM) is proposed by introducing the central difference for temporal and spatial variables. Proposed computational methods transform the time-fractional nonlinear telegraph equation into a system of linear algebraic equations that are easier to tackle. An inclusive comparative study is witnesses that suggested schemes are effective, accurate and well-matched to investigate the approximate solutions of the problems udnerstudy. Convergence and error bound of the suggested methods are investigated theoretically whereas stability analysis is performed numerically. Moreover, the developed methods can be used conveniently to examine the numerical solution of other multi-dimensional highly nonlinear fractional or variable order problems of physical nature.
Source
NUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS
Volume38Issue5Page1293-1318
DOI10.1002/num.22744
2021Äê1ÔÂ
Decadal changes of seawater radiocarbon in the eastern tropical Indian Ocean and their oceanographic implications
Pan Gao, Na Qian, Liping Zhou, Kexin Liu
Abstract
Decadal changes of radiocarbon (C-14) of seawater in the eastern tropical Indian Ocean are evaluated by the reoccupation of three stations previously measured by the Geochemical Ocean Sections Study (GEOSECS) and the World Ocean Circulation Experiment (WOCE) expedition in the spring of 2014. The bomb-C-14 inventory in the whole water column increased by similar to 56% to a level of 7.7 x 10(9) atoms/cm(2) from 1978 to 2014, and the bomb-C-14 mean penetration depth reached similar to 550 m, which is more than triple of the depth in 1978. This is accompanied by a significant decrease of Delta C-14 in the upper layer, with an average decline rate of 2.5 parts per thousand per year for the surface water. The Delta C-14 in the range of similar to 100 m-similar to 750 m depth is found to increase with time, revealing an active downward transfer of bomb-C-14 signature from the upper water to the intermediate layer. The enhanced bomb-C-14 inventory through the water column in the region is attributed to the incursion of Pacific water into the Indian Ocean through the Indonesian Throughflow and the advection of C-14-enriched waters from the southern subtropical gyre. In addition, the Southwest Monsoon Current is inferred to have contributed to the observed small increase of C-14 at the site within the Bay of Bengal. This study therefore highlights the dynamic redistribution of anthropogenic bomb-C-14 through shallow-to-deep vertical mixing processes, as well as through the interand intrabasin circulations between the eastern tropical Indian Ocean and its adjacent areas.
Source
JOURNAL OF MARINE SYSTEMS
Volume213
DOI10.1016/j.jmarsys.2020.103453
2021Äê1ÔÂ
Realizing the ultimate scaling of the convection turbulence by spatially decoupling the thermal and viscous boundary layers
Shufan Zou and Yantao Yang
Abstract
Turbulent convection plays a crucial role in many natural environments, ranging from Earth ocean, mantle and outer core, to various astrophysical systems. For such flows with extremely strong thermal driving, an ultimate scaling was proposed for the heat flux and velocity. Despite numerous experimental and numerical studies, a conclusive observation of the ultimate regime has not been reached yet. Here we show that the ultimate scaling can be perfectly realized once the thermal boundary layer is fully decoupled from the viscous boundary layer and locates inside the turbulent bulk. The heat flux can be greatly enhanced by one order of magnitude. Our results provide concrete evidences for the appearance of the ultimate state when the entire thermal boundary layer is embedded in the turbulent region, which is probably the case in many natural convection systems.
Source
arXiv, January 17, 2021
2021Äê2ÔÂ
Isolation and characterization of the novel Pseudomonas stutzeri bacteriophage 8P
Xinwu Liu, Zhou Feng, Xiangyu Fan, Yong Nie & Xiao-Lei Wu
Abstract
Bacteriophage 8P was isolated with a Pseudomonas stutzeri strain isolated from an oil reservoir as its host bacterium. The phage genome comprises 63,753 base pairs with a G+C content of 64.35. The phage encodes 63 predicted proteins, and 27 of them were functionally assigned. No tRNA genes were found. Comparative genomics analysis showed that 8P displayed some relatedness to F116-like phages (78% identity, 20% query coverage). The genome has very low sequence similarity to the other phage genomes in the GenBank database and Viral Sequence Database. Based on whole-genome analysis and transmission electron microscopy imaging, 8P is proposed to be a member of a new species in the genus Hollowayvirus, family Podoviridae.
Source
ARCHIVES OF VIROLOGY
Volume166Issue2Page601-606
DOI10.1007/s00705-020-04912-z
2021Äê2ÔÂ
Higher dimensional semi-relativistic time-fractional Vlasov-Maxwell code for numerical simulation based on linear polarization and 2D Landau damping instability
Zubair, Tamour; Lu, Tiao; Usman, Muhammad
Abstract
The "Vlasov-Maxwell system" is a groundbreaking algorithm to model, simulate and further analyze the vigorous performance of the collisionless plasma in the presence of the electromagnetic fields. In this frame of reference, the inquiry of this system with the deep conceptions of the time-fractional derivative is a novel benchmark and also the key intentions of this study. For this purpose, higher dimensional semi-relativistic time-fractional Vlasov-Maxwell system is formulated with the physical significances of the geometry. Furthermore, to fabricate the numerical consequences, we suggest an innovative algorithm which based on spectral and finite-difference approximations. The spatial and temporal variables are handled by using shifted Gegenbauer polynomials and finite-difference approximations respectively. Numerous simulations are carried out to validate the reliability and accuracy of the anticipated method. Error bound convergence and stability of the method is inspected numerically. Furthermore, the established technique can be used conveniently to observe the numerical result of other multi-dimensional time-fraction with variable-order problems of physical nature.
Source
APPLIED MATHEMATICS AND COMPUTATION
Volume401
DOI10.1016/j.amc.2021.126100
2021Äê3ÔÂ
A third-order weighted variational reconstructed discontinuous Galerkin method for solving incompressible flows
Zhang, Fan; Liu, Tiegang; Liu, Moubin
Abstract
In this paper, a third-order reconstructed discontinuous Galerkin (DG) method based on a weighted variational minimization principle, which is denoted as P1P2(WVr) method, is presented for solving the incompressible flows on unstructured grids. In this method, the first-order degrees of freedom (DoFs) are obtained directly from the underlying secondorder DG method, while the second-order DoFs are reconstructed through the weighted variational reconstruction. Specifically, we first introduce a weighted interfacial jump integration (WIJI) function which represents a measure of the jump between the reconstructed polynomial solutions from two neighboring cells. Then, we build the constitutive relations by minimizing this WIJI function using the variational method. A number of incompressible flow problems in both steady and unsteady forms are presented to assess the performance of the proposed P1P2(WVr) method. The numerical results demonstrate that the P1P2(WVr) method is able to achieve the designed optimal third-order accuracy at a significantly reduced computational costs. Moreover, when a suitable value of the weight parameter is chosen to be used, the P1P2(WVr) method outperforms the reconstructed DG methods based on either least-squares or Green-Gauss reconstruction for the simulations of incompressible flows. (C) 2020 Elsevier Inc. All rights reserved.
Source
APPLIED MATHEMATICAL MODELLING
Volume91Page1037-1060
DOI10.1016/j.apm.2020.10.011
2021Äê3ÔÂ
Why do anguilliform swimmers perform undulation with wavelengths shorter than their bodylengths?
Muhammad Saif Ullah Khalid; Junshi Wang; Imran Akhtar; Haibo Dong; Moubin Liu; Arman Hemmati
Abstract
Understanding the connection between physiology and kinematics of natural swimmers is of great importance to design efficient bio-inspired underwater vehicles. This study looks at high-fidelity three-dimensional numerical simulations for flows over an undulating American eel with prescribed anguilliform kinematics. Particularly, our work focuses on why natural anguilliform swimmers employ wavelengths shorter than their bodylengths while performing wavy kinematics. For this purpose, we vary the undulatory wavelength for a range of values generally observed in different aquatic animals at Strouhal numbers 0.30 and 0.40. We observe that our anguilliform swimmer is able to demonstrate more suitable hydrodynamic performance for wavelengths of 0.65 and 0.80. For longer wavelengths, the swimmer experiences large frictional drag, which deteriorates its performance. The wake topology was dominated by hairpin-like structures, which are closely linked with the underlying physics of anguilliform swimming found in nature.
Source
PHYSICS OF FLUIDS
Volume33Issue3
DOI10.1063/5.0040473
2021Äê3ÔÂ
Novel operational matrices-based finite difference/spectral algorithm for a class of time-fractional Burger equation in multidimensions
Usman, Muhammad; Hamid, Muhammad; Liu, Moubin
Abstract
In this work, an innovative computational scheme is developed to compute stable solutions of time fractional coupled viscous Burger's equation in multi-dimensions. To discretize the problem, the temporal derivative is approximated through a forward difference scheme whereas the spatial derivatives are approximated assisted by novel operational matrices that have been constructed via shifted Gegenbauer wavelets (SGWs). The piecewise functions are utilized to construct the operational matrices of multidimensional SGWs vectors although related theorems are offered to authenticate the scheme mathematically. The proposed computational algorithm converts the model understudy to a system of linear algebraic equations that are easier to tackle. To validate the accuracy, credibility, and reliability of the present method, the time-fractional viscous Burger's models are considered in one, two, and three dimensions. An inclusive comparative study is reported which demonstrates that the proposed computational scheme is effective, accurate, and well-matched to find the numerical solutions of the aforementioned problems. Convergence, error bound, and stability of the suggested method is investigated theoretically and numerically.
Source
CHAOS SOLITONS & FRACTALS
Volume144
DOI10.1016/j.chaos.2021.110701
2021Äê3ÔÂ
Thermodynamically favorable reactions shape the archaeal community affecting bacterial community assembly in oil reservoirs
Jie-Yu Zhao, Bing Hu, Jan Dolfing, Yan Li, Yue-Qin Tang, Yiming Jiang, Chang-Qiao Chi, Jianmin Xing, Yong Nie, Xiao-Lei Wu
Abstract
Microbial community assembly mechanisms are pivotal for understanding the ecological functions of microorganisms in biogeochemical cycling in Earth's ecosystems, yet rarely investigated in the context of deep terrestrial ecology. Here, the microbial communities in the production waters collected from water injection wells and oil production wells across eight oil reservoirs throughout northern China were determined and analyzed by proportional distribution analysis and null model analysis. A 'core' microbiota consisting of three bacterial genera, including Arcobacter, Pseudomonas and Acinetobacter, and eight archaeal genera, including Archaeoglobus, Methanobacterium, Methanothermobacter, unclassified Methanobacteriaceae, Methanomethylovorans, Methanoculleus, Methanosaeta and Methanolinea, was found to be present in all production water samples. Canonical correlation analysis reflected that the core archaea were significantly influenced by temperature and reservoir depth, while the core bacteria were affected by the combined impact of the core archaea and environmental factors. Thermodynamic calculations indicate that bioenergetic constraints are the driving force that governs the enrichment of two core archaeal guilds, aceticlastic methanogens versus hydrogenotrophic methanogens, in low-and high-temperature oil reservoirs, respectively. Collectively, our study indicates that microbial community structures in wells of oil reservoirs are structured by the thermodynamic window of opportunity, through which the core archaeal communities are accommodated directly followed by the deterministic recruiting of core bacterial genera, and then the stochastic selection of some other microbial members from local environments. Our study enhances the understanding of the microbial assembly mechanism in deep terrestrial habitats. Meanwhile, our findings will support the development of functional microbiota used for bioremediation and bioaugmentation in microbial enhanced oil recovery.
Source
SCIENCE OF THE TOTAL ENVIRONMENT
Volume781
DOI10.1016/j.scitotenv.2021.146506
2021Äê3ÔÂ
Coupling edge-based smoothed finite element method with smoothed particle hydrodynamics for fluid structure interaction problems
Long, Ting; Huang, Can; Hu, Dean; Liu, Moubin
Abstract
Numerical simulation of fluid structure interaction (FSI) problems is one of the most challenging topics in computational fluid dynamics. In this paper, coupling edge-based smoothed finite element method (ES-FEM) and smoothed particle hydrodynamics (SPH) method (ES-FEM-SPH) is proposed for solving FSI problems, where the edge-based smoothed finite element method is used to model the movement and deformation of structures, and the smoothed particle hydrodynamics is used to model the fluid flow. In ES-FEM, the gradient smoothing technique is applied over the smoothing domain and it can effectively overcome the ``overly-stiff'' effect in conventional FEM model. Some correction algorithms including density correction, kernel gradient correction and particle shift technique are integrated into the SPH method to improve computational stability and accuracy. A virtual particle coupling scheme is used to implement the coupling of ES-FEM and SPH with complex geometry interface. As ES-FEM is more accurate than conventional FEM, and it is expected that this ES-FEM-SPH coupling approach should be superior than existing FEM-SPH coupling approaches. A number of test examples with FSI are investigated with the presented ES-FEM-SPH, and compared with results from other approaches including FEM-SPH. From the obtained numerical results, we can conclude that the ES-FEM-SPH coupling approach is effective to simulate FSI problems.
Source
OCEAN ENGINEERING
Volume225
DOI10.1016/j.oceaneng.2021.108772
2021Äê3ÔÂ
Fish Lateral Line Inspired Flow Sensors and Flow-aided Control: A Review
Yufan Zhai, Xingwen Zheng & Guangming Xie
Abstract
Any phenomenon in nature is potential to be an inspiration for us to propose new ideas. Lateral line is a typical example which has attracted more interest in recent years. With the aid of lateral line, fish is capable of acquiring fluid information around, which is of great significance for them to survive, communicate and hunt underwater. In this paper, we briefly introduce the morphology and mechanism of the lateral line first. Then we focus on the development of artificial lateral line which typically consists of an array of sensors and can be installed on underwater robots. A series of sensors inspired by the lateral line with different sensing principles have been summarized. And then the applications of artificial lateral line systems in hydrodynamic environment sensing and vortices detection, dipole oscillation source detection, and autonomous control of underwater robots have been reviewed. In addition, the existing problems and future foci in this field have been further discussed in detail. The current works and future foci have demonstrated that artificial lateral line has great potentials of applications and contributes to the development of underwater robots.
Source
Journal of Bionic Engineering, Volume 18, Issue 2, Pages 264-291, March 2021
2021Äê3ÔÂ
Hybrid fully spectral linearized scheme for time-fractional evolutionary equations
Muhammad Hamid, Muhammad Usman, Wei Wang, Zhenfu Tian
Abstract
In the current study, we proposed an operational matrix-based spectral computational method coupled with the Picard technique and successfully employed to seek the solutions to a family of nonlinear evolution differential equations. However, the operational matrices are constructed assisted by monomials, and relevant theorems are available to authenticate the approach mathematically. The iterative form of residual vector for the problems understudy has been presented to seek some new results of a nonlinear family of evolutionary fractional problems. The coupling of spectral technique with the Picard method can easily tackle the high nonlinearities including quadratic, cubic, exponential, and hyperbolic, while it brings more accurate and efficient results than the published results. A worthy comparative study with exact solutions and existing techniques including numerical and analytical is being made, which shows an excellent level of accuracy for the problems under study. The authenticity of the proposed method is validated via convergence, error-bound, and norms, while the set of graphs is illustrated for integer and noninteger orders. Hence, this unlocks the opportunities to deal with solutions of the weakly singular integral and lattice Toda equations and other complex nonlinear problems arising in applied sciences and may provide a better observation of physical mechanism.
Source
Mathematical Methods in the Applied Sciences, Volume 44, Issue 5, Pages 3890-3912, March 30, 2021
2021Äê4ÔÂ
Linearized novel operational matrices-based scheme for classes of nonlinear time-space fractional unsteady problems in 2D
Muhammad Usman, Muhammad Hamid, Rizwan Ul Haq, Moubin Liu
Abstract
Finding analytical and semi-analytical solutions of two-dimensional nonlinear fractional order problems arising in mathematical physics is a challenging task for research community. In this work, an innovative scheme is proposed based on the shifted Gegenbauer wavelets. For this purpose first, we introduce shifted Gegenbauer polynomials via suitable transformation. Then, we present three-dimensional shifted Gegenbauer wavelets using shifted Gegenbauer polynomials. We illustrate function approximation of three variables, for example, u(x, y, t) through shifted Gegenbauer wavelets. To compute the novel operational matrices of positive integer and non-integer order derivative of shifted Gegenbauer wavelets vector in one, two and three dimensionals piecewise functions are utilized. Moreover, we describe associated theorems to validate our newly proposed scheme mathematically. The proposed algorithm is innovative because of the incorporation of Picard iterative scheme to tackle highly nonlinear problems of fractional-order. The current computational scheme coverts a mathematical model to a system of linear algebraic equations that are easier to solve. To validate the accuracy, credibility, and reliability of the present method, we analyze various fractional-order problems, including Bloch-Torrey, Burgers, Schrodinger, Rayleigh-Stokes and sine-Gordon. We also conduct a detailed comparative study, which demonstrates that the proposed computational scheme is effective to find the analytical and semi-analytical solutions of the aforementioned problems. Moreover, the proposed computational method can be utilized to analyze the solutions of other higher dimensional nonlinear fractional or variable order problems of physical nature. (C) 2020 IMACS. Published by Elsevier B.V. All rights reserved.
Source
APPLIED NUMERICAL MATHEMATICS
Volume162Page351-373
DOI10.1016/j.apnum.2020.12.021
2021Äê4ÔÂ
Energy Saving of Schooling Robotic Fish in Three-Dimensional Formations
Li, Liang; Zheng, Xingwen; Mao, Rui; Xie, Guanming
Abstract
It has long been proposed that animals flying in the air and swimming in the water could extract energy from neighbour-induced flows. A large number of mechanisms have been proposed to explain whether, and if so how, animals can save energy by moving in two-dimensional (2D) formations-individuals swim in the horizontal plane. Seldom studies explore the mechanisms in three-dimensional (3D) formations-individuals swim in both horizontal and vertical planes, even though most animals perform 3D behaviour. In this letter, taking a pair of bio-inspired robotic fish as experimental physical models, we explore the energy cost of the follower when swimming close to a neighbour in 3D formations (mainly in the vertical plane). We found the cost of the follower is mainly affected by how it spatiotemporally interacts with the 3D vortices shed by the neighbour in 3D formations. A simple linear correlation was found between the spatial factor (the height difference) and temporal factor (the body phase difference) when the follower saves most energy compared to swimming alone. Preliminary flow visualisations and 3D computational fluid dynamic simulations show this is due to the structure of vortices along the span of the caudal fin's trailing edge. Our studies shed new light on the energy saving control of multiple artificial underwater robots in 3D formations.
Source
IEEE ROBOTICS AND AUTOMATION LETTERS
Volume6Issue2Page1694-1699
DOI10.1109/LRA.2021.3059629
2021Äê5ÔÂ
Isolation Chip Increases Culturable Bacterial Diversity and Reduces Cultivation Bias
Xinwu Liu, Miaoxiao Wang, Yong Nie, Xiao-Lei Wu
Abstract
Conventional cultivation methods, including petri dish plating, are selective and biased to enrich specific microorganisms, such as big population and fast-growing bacteria. In this study, we evaluated the ability of isolation chip (ichip) to reduce cultivation bias. We used the ichip and petri dish plating methods to cultivate bacteria from soil contaminated with (contaminated soil) or without (natural soil) crude oil. Ichip improved the richness and evenness of bacterial isolates in both the natural and contaminated soil samples. Using the petri dish plating method, Pseudomonas and Lysinibacillus isolates were found to be the most abundant, with over 50% of the relative abundance in the natural and oil-polluted soil-cultured communities, respectively. In comparison, using the ichip method, the isolates with the highest relative abundances were from Bacillus and Aeromonas in natural and contaminated soil-cultured communities, which only accounted for 20% and 28% of the total isolates, respectively. Interestingly, the evenness and richness of the bacteria varied slightly between the natural and oil-polluted soil samples, indicating that ichip had the ability to reduce the cultivation bias. In addition, oil selective pressure enriched the functional bacteria isolated using the petri dish plating method. In summary, ichip allows bacteria to grow evenly, as well as allowing for substance exchange between the environment and single cells. As such, it is a very good method for increasing culturable bacterial diversity and reducing cultivation bias.
Source
CURRENT MICROBIOLOGY
Volume78Issue5Page2025-2032
DOI10.1007/s00284-021-02474-0
2021Äê5ÔÂ
Using a robotic platform to study the influence of relative tailbeat phase on the energetic costs of side-by-side swimming in fish
Liang Li; Sridhar Ravi; Guangming Xie; Iain D. Couzin
Abstract
A potential benefit of swimming together in coordinated schools is to allow fish to extract energy from vortices shed by their neighbours, thus reducing the costs of locomotion. This hypothesis has been very hard to test in real fish schools, and it has proven very difficult to replicate the complex hydrodynamics at relevant Reynolds numbers using computational simulations. A complementary approach, and the one we adopt here, is to develop and analyse the performance of biomimetic autonomous robotic models that capture the salient kinematics of fish-like swimming, and also interact via hydrodynamic forces. We developed bio-inspired robotic fish which perform sub-carangiform locomotion, and measured the speed and power consumption of robots when swimming in isolation and when swimming side-by-side in pairs. We found that swimming side-by-side confers a substantial increase in both the speed and efficiency of locomotion of both fish regardless of the relative phase relationship of their body undulations. However, we also find that each individual can slightly increase their own power efficiency if they change relative tailbeat phase by approximately 0.25 pi with respect to, and at the energetic expense of, their neighbour. This suggests the possibility of a competitive game-theoretic dynamic between individuals in swimming groups. Our results also demonstrate the potential applicability of our platform, and provide a natural connection between the biology and robotics of collective motion.
Source
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
Volume477Issue2249
DOI10.1098/rspa.2020.0810
2021Äê5ÔÂ
A spectral approach to analyze the nonlinear oscillatory fractional-order differential equations
Muhammad Hamid, Muhammad Usman, Rizwan Ul Haq, Zhenfu Tian
Abstract
The study of complex nonlinear mathematical models of fractional-order needs more attention in recent decades due to its enormous contribution to science and technology. Herein, a combined algorithm is proposed using the Chelyshkov polynomial method (CPM) and Picard iterative (PI) scheme. The proposed Picard Chelyshkov polynomial method (PCPM) is used to attain nonlinear oscillatory problems of arbitrary orders that do not have the exact solutions in the literature. The PCPM covert the highly nonlinear fractional-order oscillatory Problems into a linear algebraic equations system. However, the Picard scheme is to tackle the nonlinearity factor that appears in the differential equations. The proposed method's performance is examined through some test problems of fractional order while authenticated via some numerical methods. A comprehensive comparative study discussed with published work to show that the presented PCPM. To summarize, a more efficient and accurate tool is found to inspect the solution of fractional-order highly nonlinear models.
Source
CHAOS SOLITONS & FRACTALS
Volume146
DOI10.1016/j.chaos.2021.110921
2021Äê5ÔÂ
Neuronal dynamics and electrophysiology fractional model: A modified wavelet approach
Muhammad Usman, Muhammad Hamid, Zafar Hayat Khan, Rizwan Ul Haq
Abstract
The modeling and numerical simulations of fractional-order cable type problems can provide a proper structure of anomalous-diffusion in the measure of ions in complex neuronal dynamics and electrophysiology. In the present work, a novel approach of Gegenbauer wavelets (GWM) based on the operational matrices with their derivatives is proposed. New operational matrices are established for fractional-order derivative and variable-order derivative with the help of piecewise functions. The given problem is converted into a system of nonlinear equations via Gegenbauer wavelets in the suggested method. The fractional cable equation of variable-order is taken to account and successfully solved using a new algorithm. The present study also contains the convergence and error bound analysis of the proposed approach. Solutions obtained via operational matrix-based algorithm are validating the accuracy, efficiency and reliability of the suggested method. The comparative study in tabular form, as well as graphical plots (2D and 3D) for solutions and absolute error, has been reported. Hence, outcomes are validating the suggested method as an accurate and efficient tool and could be adopted for other types of fractional-order nonlinear complex dynamical problems.
Source
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
Volume570
DOI10.1016/j.physa.2021.125805
2021Äê5ÔÂ
A Galerkin approach to analyze MHD flow of nanofluid along converging/diverging channels
Muhammad Hamid, Muhammad Usman, Rizwan Ul Haq & Zhenfu Tian
Abstract
In this article, we numerically analyzed the MHD flow of a nanofluid in converging/diverging channels through the Galerkin approach. The walls are assumed to be stretchable. The governing equations of flow are reduced to nonlinear ODE system by using the appropriate nondimensionalized technique. The results are simulated numerically by means of Galerkin method. A detailed evaluation of outcomes obtained by Galerkin scheme with the fourth-order Runge¨CKutta technique (RK-4) is available to support our numerical results. The significant effects of the various physical parameters are presented graphically. Prandtl numbers cause an increase in the temperature profile, while they cause a decrease in the concentration profile. The shrinking decreases the fluid velocity nearby the channel walls, while the stretching of diverging channel provides an enhancement in flow nearby the channel walls. An identical behavior is found for the convergent channel. The influence of Grashof numbers is negligible but effect of opposing flow forces is a little dominant than assisting flow forces. The comparative study with existing literature and RK-4 as well as convergence analysis indicates that the proposed method is an efficient mathematical tool to analyze the problems arising in mechanics.
Source
Archive of Applied Mechanics, Volume 91, Issue 5, Pages 1907-1924, May 2021
2021Äê7ÔÂ
Tracing Water Masses and Assessing Boundary Scavenging Intensity With Beryllium Isotopes in the Northern South China Sea
Kong, W. Y.; Zhou, L. P.
Abstract
The cosmogenic radionuclide Be-10 and its stable isotope Be-9 can be used as a tracer for water mass mixing, but such applications are rare in both open oceans and marginal seas. Here we report distributions of dissolved Be-9 and Be-10 concentrations of the seawater in the surface and water columns along a section from shelf to deep basin in the northern South China Sea (SCS). The concentrations of Be-9 and Be-10 in surface waters range between 8.8-43.6 pmol/kg and 118-576 atoms/g, respectively. The Be-9 in the northern SCS is dominantly sourced from river waters, while Be-10 has a prominent input from the western Pacific, resulting in the highest Be-10/Be-9 ratio of 10.9 x 10(-8) closest to the Luzon Strait. Along the depth section, the Be-9 concentrations decrease southward while Be-10 concentrations increase with the maximum value of 1,237 atoms/g occurring at 2,843 m depth of Station A10. The Be-10/Be-9 ratios are interpreted with consideration of water mixing and boundary scavenging, which reveal evidence of a branch of the intruding Kuroshio Current (>7.7 x 10(-8)) in subsurface water and a deep cyclonic current (>8.9 x 10(-8)). A box model yields a sedimentation flux of Be-10 around 1,167 atoms/m(2)/s, that is, 4.6 times of the atmospheric deposition flux, pointing to active boundary scavenging of Be-10. The residence time of Be-10 in the deep water is estimated to be longer than 79 years in the northern SCS. The beryllium isotopes as a water mass tracer will find wide applications in basins where the endmembers are sufficiently differentiated.
Source
JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS
Volume126Issue7
DOI10.1029/2021JC017236
2021Äê7ÔÂ
Discovery of cyclohexadepsipeptides with anti-Zika virus activities and biosynthesis of the nonproteinogenic building block (3S)-methyl-L-proline
Yuan, Bochuan; Wu, Ziwei; Ji, Wei; Liu, Dong; Guo, Xiang; Yang, Donghui; Fan, Aili; Jia, Hongli; Ma, Ming; Lin, Wenhan
Abstract
The fungal cyclohexadepsipeptides destruxins (DTXs), isaridins (ISDs), and isariins (ISRs) are nonribosomal peptides whose structures include a 19-membered ring composed of five amino acid residues and one alpha- or beta-hydroxy acid residue. These cyclohexadepsipeptides contain unusual nonproteinogenic amino acid-building blocks and possess a range of antiviral, antibacterial, and other activities. The biosynthetic gene clusters for ISDs and ISRs have not been identified, and the biosynthesis of the nonproteinogenic (3S)-methyl-L-proline residue, which is found in DTXs, ISDs, and many other natural products, lacks full characterization. In an ongoing effort to identify compounds that can inhibit the Zika virus (ZIKV), we examined the extract of marine-derived fungus Beauveria felina SX-6-22 and discovered 30 DTXs, ISDs, and ISRs (1-30) including seven new compounds (1-7). The anti-ZIKV assays showed that 9-12 and 16-18 possess inhibitory activities against ZIKV RNA replication and NS5 (nonstructural protein 5) production in ZIKV-infected A549 cells. We sequenced the genome of B. felina SX-6-22 and identified three biosynthetic gene clusters detx, isd and isr, which are responsible for the biosynthesis of DTXs, ISDs, and ISRs, respectively. Comparative analyses of the three gene clusters clarified the biosynthetic relationships among these cyclohexadepsipeptides. Finally, we characterized the entire biosynthesis of nonproteinogenic building block (3S)-methyl-L-proline. The.1-pyrroline-5-carboxylate reductases (P5CRs), also used in the biosynthesis of L-proline, were demonstrated to catalyze the final reduction step in (3S)-methyl-L-proline formation, suggesting potential cross talk between primary and secondary metabolisms. These results provide opportunities for biosynthetic pathway engineering to generate new anti-ZIKV cyclohexadepsipeptides.
Source
JOURNAL OF BIOLOGICAL CHEMISTRY
Volume297Issue1
DOI10.1016/j.jbc.2021.100822
2021Äê7ÔÂ
Epigenetic Manipulation to Trigger Production of Guaiane-Type Sesquiterpenes from a Marine-Derived Spiromastix sp. Fungus with Antineuroinflammatory Effects
Xiang Guo, Qinyu Meng, Siwen Niu, Jie Liu, Xingchen Guo, Zhaolun Sun, Dong Liu, Yucheng Gu, Jian Huang, Aili Fan*, Wenhan Lin*
Abstract
Epigenetic manipulation of a deep-sea sediment-derived Spiromastix sp. fungus using suberoylanilide hydroxamic acid (SAHA) induction resulted in the activation of a terpenerelated biosynthetic gene cluster, and nine new guaiane-type sesquiterpenes, spiromaterpenes A-I (1-9), were isolated. Their structures were determined using various spectroscopic techniques, in association with the modified Mosher's method, computed electronic circular dichroism (ECD) spectra, and chemical conversion for configurational assignments. Compounds 4-6 exhibited significant effects against the NO production on lipopolysaccharide (LPS)-induced microglia cells BV2, and the preliminary SAR analyses demonstrated that a 2(R),11-diol unit is favorable. The most active 5 abolished LPS-induced NF-kappa B translocation from the cytosol to the nucleus in BV-2 microglial cells, accompanied by the marked reduction of the transcription levels of pro-inflammatory cytokines, including IL-1 beta, IL-6, and TNF-alpha dose-dependently in both LPS-induced BV-2 and BV-2 cells, as well as the protein and mRNA levels of iNOS and COX-2. This study complements the gap in knowledge regarding the antineuroinflammatory activity of guaiane-type sesquiterpenoids at the cellular level and suggests that 5 is promising for further optimization as a multifunctional agent for antineuroinflammation.
Source
JOURNAL OF NATURAL PRODUCTS
Volume84Issue7Page1993-2003
DOI10.1021/acs.jnatprod.1c00293
2021Äê7ÔÂ
A triboelectric-based artificial whisker for reactive obstacle avoidance and local mapping
Peng Xu, Xinyu Wang, Siyuan Wang, Tianyu Chen, Jianhua Liu, Jiaxi Zheng, Wenxiang Li , Minyi Xu, Jin Tao and Guangming Xie
Abstract
Since designing efficient tactile sensors for autonomous robots is still a challenge, this paper proposes a perceptual system based on a bioinspired triboelectric whisker sensor (TWS) that is aimed at reactive obstacle avoidance and local mapping in unknown environments. The proposed TWS is based on a triboelectric nanogenerator (TENG) and mimics the structure of rat whisker follicles. It operates to generate an output voltage via triboelectrification and electrostatic induction between the PTFE pellet and copper films (0.3mm thickness), where a forced whisker shaft displaces a PTFE pellet (10mm diameter). With the help of a biologically inspired structural design, the artificial whisker sensor can sense the contact position and approximate the external stimulation area, particularly in a dark environment. To highlight this sensor's applicability and scalability, we demonstrate different functions, such as controlling LED lights, reactive obstacle avoidance, and local mapping of autonomous surface vehicles. The results show that the proposed TWS can be used as a tactile sensor for reactive obstacle avoidance and local mapping in robotics.
Source
AAAS Research
Volume 2021, Article ID 9864967, 10 pages
https://doi.org/10.34133/2021/9864967
2021Äê7ÔÂ
Larger wavelengths suit hydrodynamics of carangiform swimmers
Muhammad Saif Ullah Khalid, Junshi Wang, Imran Akhtar, Haibo Dong, Moubin Liu*, and Arman Hemmati
Abstract
The wavelength of undulatory kinematics of fish is an important parameter to determine their hydrodynamic performance. This study focuses on numerical examination of this feature by reconstructing the real physiological model and kinematics of steadily swimming Jack Fish. We perform three-dimensional numerical simulations for flows over these models composed of the trunk, and dorsal, anal, and caudal fins. Moreover, we prescribe the carangiform-like motion for its undulation for a range of wavelengths. Undulation with larger wavelengths improves the hydrodynamic performance of the carangiform swimmer in terms of better thrust production by the caudal fin, lower drag production on the trunk, and reduced power consumption by the trunk. This coincides with the formation of stronger posterior body vortices and leading-edge vortices with more circulation on the caudal fin. The real kinematics of Jack Fish surpasses the performance of those with prescribed motion owing to the flexibility of the caudal fin.
Source
Physical Review Fluids, Volume 6, Issue 7, July 2021
2021Äê8ÔÂ
A novel temperate phage, vB_PstS-pAN, induced from the naphthalene-degrading bacterium Pseudomonas stutzeri AN10
Zhou Feng, Xinwu Liu, Miaoxiao Wang, Yong Nie & Xiao-Lei Wu
Abstract
A novel temperate phage named vB_PstS-pAN was induced by mitomycin C treatment from the naphthalene-degrading bacterium Pseudomonas stutzeri AN10. The phage particles have icosahedral heads and long non-contractile tails, and vB_PstS-pAN can therefore be morphologically classified as a member of the family Siphoviridae. The whole genome of vB_PstS-pAN is 39,466 bp in length, with an 11-nt 3' overhang cohesive end. There are 53 genes in the vB_PstS-pAN genome, including genes responsible for phage integration, replication, morphogenesis, and bacterial lysis. The vB_PstS-pAN genome has low similarity to other phage genomes in the GenBank database, suggesting that vB_PstS-pAN is a novel member of the family Siphoviridae.
Source
ARCHIVES OF VIROLOGY
Volume166Issue8Page2267-2272
DOI10.1007/s00705-021-05098-8
2021Äê8ÔÂ
Anti-HIV Effects of Baculiferins Are Regulated by the Potential Target Protein DARS
Jianrong LiuLing MaChang SongHui XingShan Cen*Wenhan Lin*
Abstract
Baculiferins are a group of marine sponge-derived polycyclic alkaloids with anti-HIV (human immunodeficiency virus) activities. To identify additional baculiferin-based congeners for SAR analysis and to investigate the mode of action, a total of 18 new baculiferin-type derivatives were synthesized. The inhibitory activities of the congeners against the HIV-1 virus were evaluated in vitro, and the relevant SAR was discussed. Compound 18 exerted the most potent activity toward VSV-G-pseudotyped HIV-1 (IC50 of 3.44 ¦ÌM) and HIV-1 strain SF33 (IC50 of 2.80 ¦ÌM) in vitro. To identify the cellular targets, three photoaffinity baculiferin probes were simultaneously synthesized. Photoaffinity labeling experiments together with LC-MS/MS data identified aspartate-tRNA ligase (DARS) as a putative target protein of 18. The overexpression and knockdown of DARS in HEK293T cells provided additional data to demonstrate that DARS is a potential target protein in the regulation of HIV virus infection. The modes of antiviral baculiferins 13 and 18 binding to DARS were determined by a molecular docking simulation. Thus, baculiferin 18 is considered a promising lead as a new molecular target for the development of anti-HIV agents.
Source
ACS CHEMICAL BIOLOGY
Volume16Issue8Page1377-1389
DOI10.1021/acschembio.1c00148
2021Äê8ÔÂ
A cell-centered indirect Arbitrary-Lagrangian-Eulerian discontinuous Galerkin scheme on moving unstructured triangular meshes with topological adaptability
Wu, Wenbin; Zhang, A-Man; Liu, Moubin
Abstract
In this paper, we present a novel cell-centered indirect Arbitrary-Lagrangian-Eulerian (ALE) discontinuous Galerkin (DG) scheme on moving unstructured triangular meshes with mesh topological adaptability, aiming to deal with the strong distortions and large deformation flow problems. The scheme combines the explicit time marching Lagrangian DG methodology with the adaptive mesh topology optimization technique. The scheme consists of the following three steps. Firstly, we utilize the Runge-Kutta DG method to solve the compressible Euler equation in Lagrangian framework, and employ a nodal solver to obtain the nodal velocity and numerical fluxes across element boundaries. The physical variable and nodal position are updated in this step. Secondly, the adaptive mesh topology optimization technique, which includes the mesh refinement, edge collapse operation and mesh regularization, is implemented to eliminate the highly distorted elements and improve the mesh quality. Thirdly, the conservative remapping algorithm is employed, which can maintain the conservative interpolation of the Lagrangian solution onto the remeshed grid. The present indirect ALE DG scheme can ensure the high quality of the mesh by optimizing the topology connectivity, so that the present scheme can successfully simulate complex vortical flow problems for a sufficient simulation time. Due to the inherent Lagrangian nature, the present scheme can naturally track the multimaterial flow interface, rather than using algorithms with interface reconstruction or diffuse interfaces. The scheme is validated with several benchmark flow problems. It is demonstrated that the present indirect ALE DG scheme with topological adaptability can accurately simulate flow problems with large fluid deformations and distortions. It can achieve remarkable improvements compared with the conventional Lagrangian DG method with fixed topological connectivity. (C) 2021 Elsevier Inc. All rights reserved.
Source
JOURNAL OF COMPUTATIONAL PHYSICS
Volume438
DOI10.1016/j.jcp.2021.110368
2021Äê8ÔÂ
Multi-resolution technique integrated with smoothed particle element method (SPEM) for modeling fluid-structure interaction problems with free surfaces
Long, Ting; Zhang, Zhilang; Liu, Moubin
Abstract
Free-surface flows, especially those associated with fluid-structure interactions (FSIs), pose challenging problems in numerical simulations. The authors of this work recently developed a smoothed particle element method (SPEM) to simulate FSIs. In this method, both the fluid and solid regions are initially modeled using a smoothed finite element method (S-FEM) in a Lagrangian frame, whereas the fluid regions undergoing large deformations are adaptively converted into particles and modeled with an improved smoothed particle hydrodynamics (SPH) method. This approach greatly improves computational accuracy and efficiency because of the advantages of the S-FEM in efficiently treating solid/fluid regions showing small deformations and the SPH method in effectively modeling moving interfaces. In this work, we further enhance the efficiency of the SPEM while effectively capturing local fluid information by introducing a multi-resolution technique to the SPEM and developing an effective approach to treat multi-resolution element-particle interfaces. Various numerical examples demonstrate that the multiresolution SPEM can significantly reduce the computational cost relative to the original version with a constant resolution. Moreover, the novel approach is effective in modeling various incompressible flow problems involving FSIs.
Source
SCIENCE CHINA-PHYSICS MECHANICS & ASTRONOMY
Volume64Issue8
DOI10.1007/s11433-021-1694-8
2021Äê8ÔÂ
Learning for Attitude Holding of a Robotic Fish: An End-to-End Approach With Sim-to-Real Transfer
Junzheng Zheng; Tianhao Zhang; Chen Wang; Minglei Xiong; Guangming Xie
Abstract
Controlling biomimetic underwater robots in unknown flow fields remains a challenge due to the strong nonlinearity of the fluid. This article investigates the attitude holding task of a robotic fish swimming in reality. Such a typical sensing-based control task requires the fish to keep a desired angle of attack in an unknown and even varied incoming flow. To this end, we propose a learning-based approach by using a deep neural network directly maps the raw data of sensors equipped on the robot to the continuous control signals in an end-to-end manner. First, based on experimental data of the physical robot, we construct a data-driven simulation environment including three modules of dynamic, sensor, and control. The dynamic and sensor modules are established to model the dynamics of the fish and to generate its sensors' data, based on which a deep reinforcement learning (DRL) algorithm in the control module is trained to get a control policy. Then, we directly deploy the trained policy to a physical robotic fish for attitude holding task. Experimental results demonstrate the robustness and effectiveness of the DRL policy and, thus, verify the success of our approach to achieving sim-to-real transfer.
Source
IEEE TRANSACTIONS ON ROBOTICS
Volume38Issue2Page1287-1303
DOI10.1109/TRO.2021.3098239
2021Äê8ÔÂ
Computational analysis of radiative Williamson hybrid nanofluid comprising variable thermal conductivity
Tamour Zubair, Muhammad Usman, Muhammad Hamid, Muhammad Sohail, Umar Nazir, Kottakkaran Sooppy Nisar and Velusamy Vijayakumar
Abstract
This article demonstrates the study of thermal energy with the rheology of Williamson liquid over a rotating surface. The correlations between nanoparticles and hybrid nanoparticles in the base fluid are considered to determine the comparative analysis in nanoparticles and hybrid nanostructures. The variable terms are thermal conductivity and thermal radiation, which are also inserted in the energy equation with the associations of nano and hybrid nanoparticles. The ordinary differential equations (ODEs) are generated from the modeled problem using transformation. In contrast, the least square method is used to simulate analytic solutions of required ODEs, and further results are compared with a numerical scheme. The simulations of temperature and motion of fluid particles are performed in graphs and tables. The reduction in motion of fluid particles is captured versus the variation of Williamson number and magnetic number. At the same time, Williamson's number and magnetic parameter also reduce momentum boundary layer thickness. The hybrid nanoparticles play a vital impact on producing a high rate of acceleration in flow, and hybrid nanoparticles are useful to produce maximum energy compared to nanostructures.
Source
JAPANESE JOURNAL OF APPLIED PHYSICS
Volume60Issue8
DOI10.35848/1347-4065/ac1388
2021Äê9ÔÂ
Chlorinated metabolites with antibacterial activities from a deep-sea-derived Spiromastix fungus
Siwen Niu, Dong Liu, Zongze Shao, Jiang Huang, Aili Fana and Wenhan Lin
Abstract
Chromatographic separation of the solid cultures of a deep-sea-derived Spiromastix fungus (MCCC 3A00308) resulted in the isolation of eight compounds. Their structures were identified on the basis of the spectroscopic data. Compounds 1-8 are classified as depsidone-type (1-4), isocoumarin-type (5 and 6), and benzothiazole-type (7 and 8), of which 1-7 are new compounds and 1-3 along with 5 and 6 are chlorinated. Compound 3 is characterized by trichlorination and shows potent activities against Gram-positive pathogenic bacteria including Staphylococcus aureus ATCC 25923, Bacillus thuringiensis ATCC 10792, and Bacillus subtilis CMCC 63501, with minimum inhibitory concentration (MIC) values ranging from 0.5 to 1.0 mu g mL(-1). This study extends the chemical diversity of chlorinated natural products from marine-derived fungi and provides a promising lead for the development of antibacterial agents.
Source
RSC ADVANCES
Volume11Issue47Page29661-29667
DOI10.1039/d1ra05736g
2021Äê9ÔÂ
Fish can save energy via proprioceptive sensing
Liang Li, Danshi Liu, Jian Deng, Matthew J Lutz and Guangming Xie
Abstract
Fish have evolved diverse and robust locomotive strategies to swim efficiently in complex fluid environments. However, we know little, if anything, about how these strategies can be achieved. Although most studies suggest that fish rely on the lateral line system to sense local flow and optimise body undulation, recent work has shown that fish are still able to gain benefits from the local flow even with the lateral line impaired. In this paper, we hypothesise that fish can save energy by extracting vortices shed from their neighbours using only simple proprioceptive sensing with the caudal fin. We tested this hypothesis on both computational and robotic fish by synthesising a central pattern generator (CPG) with feedback, proprioceptive sensing, and reinforcement learning. The CPG controller adjusts the body undulation after receiving feedback from the proprioceptive sensing signal, decoded via reinforcement learning. In our study, we consider potential proprioceptive sensing inputs to consist of low-dimensional signals (e.g. perceived forces) detected from the flow. With simulations on a computational robot and experiments on a robotic fish swimming in unknown dynamic flows, we show that the simple proprioceptive sensing is sufficient to optimise the body undulation to save energy, without any input from the lateral line. Our results reveal a new sensory-motor mechanism in schooling fish and shed new light on the strategy of control for robotic fish swimming in complex flows with high efficiency.
Source
BIOINSPIRATION & BIOMIMETICS
Volume16Issue5
DOI10.1088/1748-3190/ac165e
2021Äê12ÔÂ
E-DSDV routing protocol for mobile ad hoc network for underwater electrocommunication
Ruijun Liu, Qinghao Wang, Chen Wang, Guangming Xie & Wenguang Luo
Abstract
We realized the dynamic networking of underwater electrocommunication for the first time through experiments.The E-DSDV routing protocol based on underwater electrocommunication also belongs to the proactive routing protocol.In the E-DSDV protocol,each node needs to establish and maintain a routing table,which contains the source node,destination node,next-hop node,the total number of hops to the destination node,and node sequence number.The E-DSDV protocol can transform the voltage signal detected at the receiver and transmitter into the distance information between neighbors on time and the distance information between neighbors into the sequence number required in the protocol.After topology transformation of nodes in the network,they can update their sequence numbers in time and give the updated information to neighbors,so as to change the routing information of the network and timely change the routing table to maintain accurate routing information.The principle of the E-DSDV protocol is as follows.
Source
SCIENCE CHINA-INFORMATION SCIENCES
Volume64Issue12
DOI10.1007/s11432-019-2966-0
2021Äê12ÔÂ
On the determination of grid size/smoothing distance in un-/semi-resolved CFD-DEM simulation of particulate flows
Wang, Zekun; Liu, Moubin
Abstract
Unresolved and semi-resolved CFD-DEM coupling are frequently used for modeling particulate flows due to their high efficiency and satisfying accuracy. The grid size (in unresolved CFD-DEM) and smoothing distance (in semi resolved CFD-DEM) are usually around three times of the particle diameter so as to properly reproduce the background flow field. An over-estimation of the grid size or smoothing distance can lead to low-fidelity flow fields, while under-estimations of these parameters can produce an inaccurate drag force. Therefore in practices, the size ratio is usually empirical, and how does it vary with cases remains unclear. In this paper, we provide an approach to identify the most suitable grid size or smoothing distance in coupled CFD-DEM. Firstly, resolved simulations based on immersed boundary method (IBM) are conducted to compute particles' drag forces. The obtained forces are then compared with those calculated by force models with certain smoothing lengths to identify an optimal smoothing length or effective grid size. During this process, integral scale of each case is also computed. Finally, linearity between integral length and the optimal smoothing distance or grid size is found. This correlation can offer guidance to CFD-DEM modeling in future and provide insights for novel drag force models. (c) 2021 Elsevier B.V. All rights reserved.
Source
POWDER TECHNOLOGY
Volume394Page73-82
DOI10.1016/j.powtec.2021.08.044
2021Äê12ÔÂ
Chemical epigenetic manipulation triggers the production of sesquiterpenes from the deep-sea derived Eutypella fungus
Siwen Niu, Dong Liu, Zongze Shao, Jianrong Liu, Aili Fan, Wenhan Lin
Abstract
Chemical epigenetic manipulation of a deep-sea-derived Eutypella sp. fungus by the co-treatment with a histonedeacetylase inhibitor (suberohydroxamic acid, SBHA) and a DNA methyltransferase inhibitor (5-azacytidine, 5-Aza), resulted in the activation of a sesquiterpene-related biosynthetic gene cluster. Chromatographic separation of the elicitor-treated cultures led the isolation of 21 sesquiterpenes, including 17 undescribed compounds, eutypeterpenes A-Q. Their structures were identified by the extensive analysis of the spectroscopic data, including the single-crystal X-ray diffraction, chemical conversion, and the calculated NMR and ECD data for configurational assignments. Eutypeterpene A is a first bergamotene-type sesquiterpene incorporated with a dioxolanone unit, and eutypeterpenes O-Q with a cyclopentane ring represent an undescribed subtype of sesquiterpenes. The bioassay results showed that most compounds exert inhibitory effects against the lipopolysaccharide (LPS)-induced NO production in RAW 264.7 macrophages, and eutypeterpene N is the most active. This study demonstrates that the epigenetic manipulation is an effective approach to trigger the production of cryptic metabolites from deep-sea derived fungus. The significant inhibition against LPS-induced NO production in vitro suggests eutypeterpenes to be potential for the development as anti-inflammatory agents.
Source
PHYTOCHEMISTRY
Volume192
DOI10.1016/j.phytochem.2021.112978
2021Äê12ÔÂ
Toward Coordination Control of Multiple Fish-Like Robots: Real-Time Vision-Based Pose Estimation and Tracking via Deep Neural Networks
Tianhao Zhang; Jiuhong Xiao; Liang Li; Chen Wang; Guangming Xie
Abstract
Controlling multiple multi-joint fish-like robots has long captivated the attention of engineers and biologists, for which a fundamental but challenging topic is to robustly track the postures of the individuals in real time. This requires detecting multiple robots, estimating multi-joint postures, and tracking identities, as well as processing fast in real time. To the best of our knowledge, this challenge has not been tackled in the previous studies. In this paper, to precisely track the planar postures of multiple swimming multi-joint fish-like robots in real time, we propose a novel deep neural network-based method, named TAB-IOL. Its TAB part fuses the top-down and bottom-up approaches for vision-based pose estimation, while the IOL part with long short-term memory considers the motion constraints among joints for precise pose tracking. The satisfying performance of our TAB-IOL is verified by testing on a group of freely swimming fish-like robots in various scenarios with strong disturbances and by a deed comparison of accuracy, speed, and robustness with most state-of-the-art algorithms. Further, based on the precise pose estimation and tracking realized by our TAB-IOL, several formation control experiments are conducted for the group of fish-like robots. The results clearly demonstrate that our TAB-IOL lays a solid foundation for the coordination control of multiple fish-like robots in a real working environment. We believe our proposed method will facilitate the growth and development of related fields.
Source
IEEE/CAA Journal of Automatica Sinica, Volume 8, Issue 12, Pages 1964-1976, December 2021
