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Optimizing the atom types of proteins through iterative knowledge-based potentials
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作者 汪心享 黄胜友 《Chinese Physics B》 SCIE EI CAS CSCD 2018年第2期43-50,共8页
Knowledge-based scoring functions have been widely used for protein structure prediction, protein-small molecule, and protein-nucleic acid interactions, in which one critical step is to find an appropriate representat... Knowledge-based scoring functions have been widely used for protein structure prediction, protein-small molecule, and protein-nucleic acid interactions, in which one critical step is to find an appropriate representation of protein structures. A key issue is to determine the minimal protein representations, which is important not only for developing of scoring func- tions but also for understanding the physics of protein folding. Despite significant progresses in simplifying residues into alphabets, few studies have been done to address the optimal number of atom types for proteins. Here, we have investigated the atom typing issue by classifying the 167 heavy atoms of proteins through 11 schemes with 1 to 20 atom types based on their physicochemical and functional environments. For each atom typing scheme, a statistical mechanics-based iterative method was used to extract atomic distance-dependent potentials from protein structures. The atomic distance-dependent pair potentials for different schemes were illustrated by several typical atom pairs with different physicochemical proper- ties. The derived potentials were also evaluated on a high-resolution test set of 148 diverse proteins for native structure recognition. It was found that there was a crossover around the scheme of four atom types in terms of the success rate as a function of the number of atom types, which means that four atom types may be used when investigating the basic folding mechanism of proteins. However, it was revealed by a close examination of typical potentials that 14 atom types were needed to describe the protein interactions at atomic level. The present study will be beneficial for the development of protein related scoring functions and the understanding of folding mechanisms. 展开更多
关键词 atom types knowledge-based potentials statistical mechanics ITERATION
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Effects of spontaneously induced coherence on absorption of a ladder-type atom 被引量:4
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作者 马红梅 龚尚庆 +2 位作者 孙真荣 李儒新 徐至展 《Chinese Physics B》 SCIE EI CAS CSCD 2006年第11期2588-2592,共5页
This paper investigates the effects of spontaneously induced coherence on absorption properties in a nearly equispaced three-level ladder-type system driven by two coherent fields. It find that the absorption properti... This paper investigates the effects of spontaneously induced coherence on absorption properties in a nearly equispaced three-level ladder-type system driven by two coherent fields. It find that the absorption properties of this system with the probe field applied on the lower transition can be significantly modified if this coherence is optimized. In the case of small spontaneous decay rate in the upper excited state, it finds that such coherence does not destroy the electromagnetically induced transparency (EIT). Nevertheless, the absorption peak on both sides of zero detuning and the linewidth of absorption line become larger and narrower than those in the case corresponding to the effects of spontaneously induced coherence; while in the case of large decay rate, it finds that, instead of EIT with low resonant absorption, a sharp absorption peak at resonance appears. That is, electromagnetically induced absorption in the nearly equispaced ladder-type system can occur due to such coherent effects. 展开更多
关键词 spontaneously induced coherence a ladder-type atom ABSORPTION
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Relative carrier-envelope phase dependence of resonant propagation of two-colour femtosecond pulses in V-type atomic medium 被引量:1
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作者 谭霞 王振东 +1 位作者 王蕾 樊锡君 《Chinese Physics B》 SCIE EI CAS CSCD 2010年第6期349-355,共7页
Using numerical solution of the full Maxwell-Bloch equations, which is obtained by the finite-difference time-domain method and the iterative predictor-orrector method, we investigate the modulation effect of relative... Using numerical solution of the full Maxwell-Bloch equations, which is obtained by the finite-difference time-domain method and the iterative predictor-orrector method, we investigate the modulation effect of relative carrierenvelope phase (hereinafter referred to as the relative phase) on resonant propagation of two-colour femtosecond ultrashort laser pulses in a V-type three-level atomic medium. It is found that the pulse splitting occurs for a smaller value of relative phase; when the value of relative phase increases to a certain value, only the variation of pulse shape is present and the pulse splitting does not occur any more; moreover, when the value of relative phase is smaller, the pulse group velocity is larger. The relative phase also has an obvious effect on population and spectral property. Different population transfers can be realized by adjusting the value of relative phase. Generally speaking, for the pulses with smaller areas their spectral strengths and frequency ranges decrease obviously with the value of relative phase increasing; for the pulses with larger areas, with value of the relative phase increasing, their spectral strengths decrease remarkably but the relative strengths of the higher frequency components increase significantly, while the spectral frequency range is not varied evidently. 展开更多
关键词 two-colour ultrashort pulses relative carrier envelope phase resonant propagation V- type three-level atomic medium
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Noticeable positive Doppler effect on optical bistability in an N-type active Raman gain atomic system 被引量:2
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作者 常增光 钮月萍 +1 位作者 张敬涛 龚尚庆 《Chinese Physics B》 SCIE EI CAS CSCD 2012年第11期280-284,共5页
We theoretically investigate the Doppler effect on optical bistability in an N-type active Raman gain atomic system inside an optical ring cavity. It is shown that the Doppler effect can greatly enhance the dispersion... We theoretically investigate the Doppler effect on optical bistability in an N-type active Raman gain atomic system inside an optical ring cavity. It is shown that the Doppler effect can greatly enhance the dispersion and thus create the bistable behaviour or greatly increase the bistable region, which has been known as the positive Doppler effect on optical bistability. In addition, we find that a positive Doppler effect can change optical bistability from the hybrid dispersion-gain type to a dispersive type. 展开更多
关键词 positive Doppler effect optical bistability N-type atomic system active Raman gain
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Growth of nitrogen-doped p-type ZnO thin films prepared by atomic layer epitaxy 被引量:2
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作者 LEE Chongmu LIM Jongmin +1 位作者 PARK Suyoung KIM Hyounwoo 《Rare Metals》 SCIE EI CAS CSCD 2006年第z1期110-114,共5页
Nitrogen-doped, p-type ZnO thin films were grown successfully on sapphire (0001) substrates by using atomic layer epitaxy (ALE). Zn(C2H5)2 [Diethylzinc, DEZn], H2O and NH3 were used as a zinc precursor, an oxidant and... Nitrogen-doped, p-type ZnO thin films were grown successfully on sapphire (0001) substrates by using atomic layer epitaxy (ALE). Zn(C2H5)2 [Diethylzinc, DEZn], H2O and NH3 were used as a zinc precursor, an oxidant and a doping source gas, respectively. The lowest electrical resistivity of the p-type ZnO films grown by ALE and annealed at 1000 ℃ in an oxygen atmosphere for 1 h was 18.3 Ω·cm with a hole concentration of 3.71×1017 cm-3. Low temperature-photoluminescence analysis and time-dependent Hall measurement results support that the nitrogen-doped ZnO after annealing is a p-type semiconductor. 展开更多
关键词 p-type ZnO atomic layer deposition electrical resistivity carrier concentration PHOTOLUMINESCENCE
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A scheme for conditional quantum phase gate via bimodal cavity and a∧-type three-level atom 被引量:3
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作者 蔡建武 方卯发 +1 位作者 廖湘平 郑小娟 《Chinese Physics B》 SCIE EI CAS CSCD 2006年第11期2518-2522,共5页
We propose a scheme to implement a two-qubit conditional quantum phase gate for the intracavity field via a single three-level ∧-type atom driven by two modes in a high-Q cavity. The quantum inforraation is encoded o... We propose a scheme to implement a two-qubit conditional quantum phase gate for the intracavity field via a single three-level ∧-type atom driven by two modes in a high-Q cavity. The quantum inforraation is encoded on the Fock states of the bimodal cavity. The gate's averaged fidelity is expected to reach 99.8%. 展开更多
关键词 quantum phase gate ∧-type three-level atom bimodal cavity FIDELITY
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Emission spectrum of a harmonically trapped Λ-type three-level atom
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作者 郭红 汤佩 《Chinese Physics B》 SCIE EI CAS CSCD 2013年第5期310-314,共5页
We theoretically investigate the emission spectrum for a A-type three-level atom trapped in the node of a standing wave. We show that the atomic center-of-mass motion not only directly affects the peak number, peak po... We theoretically investigate the emission spectrum for a A-type three-level atom trapped in the node of a standing wave. We show that the atomic center-of-mass motion not only directly affects the peak number, peak position, and peak height in the atomic emission spectrum, but also influences the effects of the cavity field and the atomic initial state on atomic emission spectrum. 展开更多
关键词 emission spectrum the atomic center-of-mass motion A-type three-level atom
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Entanglement swapping without joint measurement via a ∧-type atom interacting with bimodal cavity field
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作者 林秀 李洪才 +1 位作者 杨榕灿 黄志平 《Chinese Physics B》 SCIE EI CAS CSCD 2007年第4期919-922,共4页
This paper proposes a scheme for realizing entanglement swapping in cavity QED. The scheme is based on the resonant interaction of a two-mode cavity field with a ∧-type three-level atom. In contrast with the previous... This paper proposes a scheme for realizing entanglement swapping in cavity QED. The scheme is based on the resonant interaction of a two-mode cavity field with a ∧-type three-level atom. In contrast with the previously proposed schemes, the present scheme is ascendant, since the fidelity is 1.0 and the joint measurement isn't needed. And the scheme is experimentally feasible based on the current cavity QED technique. 展开更多
关键词 entanglement swapping ∧-type atom two-mode cavity field joint measurement
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Output three-mode entanglement via coherently prepared inverted Y-type atoms
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作者 王飞 邱晶 《Chinese Physics B》 SCIE EI CAS CSCD 2014年第4期262-267,共6页
In this paper, the output quantum correlations of three fields interacting with inverted Y-type atoms inside a three-mode cavity are investigated. By numerically calculating the stationary noise spectra of the fields,... In this paper, the output quantum correlations of three fields interacting with inverted Y-type atoms inside a three-mode cavity are investigated. By numerically calculating the stationary noise spectra of the fields, we show that it is possible to generate the genuine tripartite continuous variable entanglement outside the cavity by coherently preparing the atoms in a superposition of the upper excited state and two ground states initially. Our numerical results demonstrate that both zero frequency entanglement and sideband frequency entanglement can be obtained under different initial coherent conditions. In addition, we investigate the thermal fluctuation effects on the quantum entanglement. It is found out that the entanglement occurring in a high frequency regime is more robust against thermal noise than the zero frequency entanglement, which may be useful for quantum communication. 展开更多
关键词 tripartite entanglement correlated spontaneous emission laser inverted Y-type atom
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Interaction of a pair coherent state with a three-level Λ-type atom and generation of a modified Bessel-Gaussian state with a vortex structure
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作者 唐慧琴 李绍新 +2 位作者 唐英 郑小娟 朱开成 《Chinese Physics B》 SCIE EI CAS CSCD 2013年第2期115-119,共5页
The evolution of a system state is derived based on the nonresonant interaction of a three-level "Λ" type atom with two cavity modes at a pair coherent state and two classic fields,and a cavity field state is analy... The evolution of a system state is derived based on the nonresonant interaction of a three-level "Λ" type atom with two cavity modes at a pair coherent state and two classic fields,and a cavity field state is analyzed in detail under conditional detecting.It is found that the quantized modified Bessel-Gaussian states as well as the superposition states consisting of the quantized vortex states with different weighted coefficients may be prepared through carefully preparing an initial atomic state and appropriately adjusting the interaction time.The scheme provides an additional choice to realize the two-mode quantized vortex state within the context of cavity quantum electrodynamics(QED). 展开更多
关键词 quantized vortex state three-level Λ-type atom cavity quantum electrodynamics(QED)
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AlO_x prepared by atomic layer deposition for high efficiency-type crystalline silicon solar cell
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作者 仇洪波 李惠琪 +2 位作者 刘邦武 张祥 沈泽南 《Chinese Physics B》 SCIE EI CAS CSCD 2014年第2期448-451,共4页
The influence of atomic layer deposition parameters on the negative charge density in AlOx film is investigated by the corona-charge measurement. Results show that the charge density can reach up to -1.56×10^12 c... The influence of atomic layer deposition parameters on the negative charge density in AlOx film is investigated by the corona-charge measurement. Results show that the charge density can reach up to -1.56×10^12 cm%-2 when the thickness of the film is 2.4 nm. The influence of charge density on cell conversion efficiency is further simulated using solar cell analyzing software (PC1D). With AlOx passivating the rear surface of the silicon, the cell efficiency of 20.66% can be obtained. 展开更多
关键词 AlOx atomic layer deposition P-type negative charge density solar cell analyzing software
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Generation of entangled coherent states for two cavity modes via resonant interaction with a V-type three-level atom
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作者 郑仕标 《Chinese Physics B》 SCIE EI CAS CSCD 2008年第6期2143-2146,共4页
This paper proposes a scheme for the generation of entangled coherent states for two cavity modes. In the scheme a V-type three-level atom is sent through a two-mode cavity filled with a coherent field. After the atom... This paper proposes a scheme for the generation of entangled coherent states for two cavity modes. In the scheme a V-type three-level atom is sent through a two-mode cavity filled with a coherent field. After the atom cavity interaction and detection of the atomic state the cavity modes may evolve to a superposition of two-mode coherent states. As the scheme is based on resonant atom-cavity interaction, the required interaction time is short, which is important in view of the decoherence. Moreover, additional classical pulses are unnecessary before and after the atom-cavlty interaction. 展开更多
关键词 entangled coherent state resonant interaction V-type three-level atom
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Three-Level Λ-Type Atomic System Localized by the Parameters of the Two Orthogonal Standing-Wave Fields
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作者 Shuncai Zhao Qixuan Wu 《Journal of Applied Mathematics and Physics》 2016年第8期1546-1553,共8页
Localization of the three-level Λ-type atomic system interacting with two orthogonal standing-wave fields is proposed. Two equal and tunable peaks in the 2D plane are obtained by the detunings corresponding to the tw... Localization of the three-level Λ-type atomic system interacting with two orthogonal standing-wave fields is proposed. Two equal and tunable peaks in the 2D plane are obtained by the detunings corresponding to the two orthogonal standing-wave fields when the decreasing intensities of spontaneously generated coherence (SGC) arise in the three-level Λ-type atomic system, while one circular ring with shrinking radii in the 2D plane is obtained by the adjusted phases and wave vectors of the standing-wave fields when the increasing intensities of SGC occur in the three-level Λ-type atomic system. 2D atom localization with the single ring with shrinking radii realized by the multiple parametric manipulations demonstrated the flexibility for our scheme. 展开更多
关键词 Three-Level Λ-type atomic System atom Localization Spontaneously Generated Coherence (SGC)
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Electromagnetically induced transparency of single Λ-type three-level atoms in a high-finesse optical cavity
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作者 孙燕芬 谭磊 徐岩 《Chinese Physics B》 SCIE EI CAS CSCD 2013年第3期158-162,共5页
We study the features of electromagnetically induced transparency(EIT) in a single Λ-type three-level atom placed in a high-finesse cavity under the action of a coupling laser and a probe laser.Our calculations sho... We study the features of electromagnetically induced transparency(EIT) in a single Λ-type three-level atom placed in a high-finesse cavity under the action of a coupling laser and a probe laser.Our calculations show that three transparency windows appear when the pump strength is large enough.This can be explained by the residual pump in the cavity mostly resulting in energy splitting.The level |3 is split into four slightly different energy levels,and interference takes place between the excitation pathways.Furthermore,it is also shown that the frequencies of the EIT windows can be tuned by changing the coupling field detuning 2,and that the reflection profile is very sensitive to the cavity field detuning △c. 展开更多
关键词 Λ-type three-level atom high-finesse optical cavity electromagnetically induced transparency
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The First Hybrid Wells-Dawson-type Polytungstate Monosupported by Cd-coordination Complex via Di-bridging O-atom 被引量:2
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作者 陈武华 张著森 +1 位作者 胡志彪 宓锦校 《Chinese Journal of Structural Chemistry》 SCIE CAS CSCD 2014年第10期1550-1559,共10页
Polyoxometalates(POMs) with Cd-coordination complexes acting as supporting units are rarely reported. The linkage of the supporting units with inorganic building block(polyanion) is generally established on termin... Polyoxometalates(POMs) with Cd-coordination complexes acting as supporting units are rarely reported. The linkage of the supporting units with inorganic building block(polyanion) is generally established on terminal O-atoms, but scarcely via bridging O-atoms. By introducing liquid small organic molecule(pyridine, C5NH5) as assistant "structure-directing agent", we obtained a novel organic-inorganic hybrid polytungstate,(Hpy)4[Cd(phen)2(P2W18O62)]·nH2O(1, n ≈ 3, py = pyridine, phen = 1,10-phenanthroline), under hydrothermal conditions. The single-crystal X-ray diffraction analysis shows that 1 is the first compound containing an asymmetric heteropolyanion, [Cd(phen)2(P2W18O62)]4–, a Wells-Dawson-type polyanion monosupported by Cd-coordination complex via di-bridging O-atoms. 展开更多
关键词 hybrid compound Wells-Dawson-type Cd-coordination complex monosupported structure bi-bridging O-atom
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基于原子系综系统实现控制Hadamard门和制备多量子比特的W-type态
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作者 魏海红 徐琳琳 +1 位作者 王发强 梁瑞生 《华南师范大学学报(自然科学版)》 CAS 北大核心 2011年第1期58-61,共4页
利用Rydberg阻滞机制,提出了实现基于原子系综系统的控制Hadamard门和制备n个量子比特W-type态的方案.该方案可以得到高保真度的n个量子比特W-type态,在量子信息处理方面具有可扩展性.
关键词 原子系综 Rydberg阻滞 控制Hadamard门 W-type
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General calculation formulas and recurrence relations of radial matrix elements for relativistic n-dimensional hydrogen atom of spin S=0 被引量:1
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作者 CHENChang-yuan LUFa-lin SUNDong-sheng 《原子与分子物理学报》 CAS CSCD 北大核心 2004年第3期432-440,共9页
In this paper, the general calculation formulas of radial matrix elements for relativistic n-dimensional hydrogen atom of spin S=0 are obtained, and the recurrence relation of different power order radial matrix eleme... In this paper, the general calculation formulas of radial matrix elements for relativistic n-dimensional hydrogen atom of spin S=0 are obtained, and the recurrence relation of different power order radial matrix elements are also derived. 展开更多
关键词 n-dimensional hydrogen atom-type potential Klein-Cordon equation Radial matrix dements GENERAL calculation FORMULAS RECURRENCE relations
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Effects of atomization parameters of dust removal nozzles on the de-dusting results for different dust sources 被引量:7
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作者 Cheng Weimin Ma Youying +1 位作者 Yang Junlei Sun Biao 《International Journal of Mining Science and Technology》 SCIE EI CSCD 2016年第6期1025-1032,共8页
In order to obtain appropriate spray pressure and enhance the spraying and dust removal efficiency, various factors including the dust characteristics, nozzle spraying angle, effective spraying range, water consumptio... In order to obtain appropriate spray pressure and enhance the spraying and dust removal efficiency, various factors including the dust characteristics, nozzle spraying angle, effective spraying range, water consumption and droplet size are taken into account. The dust characteristics from different mines and atomization parameters of different pressure nozzles were measured. It was found that the internal pressure of coal cutters and roadheaders should be kept at 2 MPa, which could ensure large droplet size, large spraying angle and low water consumption and hence realizing a large-area covering and capture for large particle dusts. However, the external spray pressure should be kept at 4 MPa for smaller droplet size and longer effective spraying range, leading to effective dust removal in the operator zone. The spray pressure of support moving, drawing opening, and stage loader on a fully mechanized caving face and stage loader on a fully mechanized driving face should be kept at 8 MPa, under which the nozzles have long effective spraying range, high water flow and small droplet size for the rapid capture of instantaneous, high-concentration and small size dust groups. From the applications on the caving and driving faces in the coal mines, it is indicated that the optimization of spray pressure in different spraying positions could effectively enhance dust removal efficiency. Selecting appropriate nozzles according to the dust characteristics at different positions is also favorable for dust removal efficiency. With the selected nozzles under optimal pressures, the removal rates of both total dust and respirable dust could reach over70%, showing a significant de-dusting effect. 展开更多
关键词 Dust sources Dust size types of spraying nozzle Spray pressure atomization parameters
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BOUNDEDNESS OF COMMUTATORS OF GENERALIZED FRACTIONAL INTEGRAL OPERATORS ON WEIGHTED HERZ-TYPE HARDY SPACES 被引量:1
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作者 Aiwen Sun Lisheng Shu 《Analysis in Theory and Applications》 2010年第2期101-109,共9页
In this paper, we study the boundedness of higher order commutators of gen- eralized fractional integral operators on weighted Lp spaces and Herz-type Hardy spaces.
关键词 generalized fractional integral COMMUTATOR weighted Herz-type Hardy space atom
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Estimates of commutators for multilinear operators on Herz-type spaces 被引量:1
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作者 ZHOU Jiang CAO Yong-hui LI Liang 《Applied Mathematics(A Journal of Chinese Universities)》 SCIE CSCD 2010年第2期177-184,共8页
In this paper, the boundedness of mulitilinear commutator [-b,T] on Herz-type space is considered, where T is a standard Calderon-Zygmund singular operator and -b ∈ (BMO(Rn))m.
关键词 Multilinear Calderdn-Zygmund singular integral COMMUTATOR Herz-type space central atom.
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