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Molecular dynamics simulations on the interactions between nucleic acids and a phospholipid bilayer

Chinese Physics B 2024年第2期33卷 512-521页

作者：徐耀黄舒伟丁泓铭马余强 National Laboratory of Solid State Microstructures and Department of Physics Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China Center for Soft Condensed Matter Physics and Interdisciplinary Research School of Physical Science and TechnologySoochow UniversitySuzhou 215006China

Recently,lipid nanoparticles(LNPs)have been extensively investigated as non-viral carriers of nucleic acid vaccines due to their high transport efficiency,safety,and straightforward production and ***,the molecular mechanism underlying the interactions between nucleic acids and phospholipid bilayers within LNPs remains *** this study,we employed the all-atom molecular dynamics simulation to investigate the interactions between single-stranded nucleic acids and a phospholipid *** findings revealed that hydrophilic bases,specifically G in single-stranded RNA(ssRNA)and single-stranded DNA(ssDNA),displayed a higher propensity to form hydrogen bonds with phospholipid head ***,ssRNA exhibited stronger binding energy than ***,divalent ions,particularly Ca2+,facilitated the binding of ssRNA to phospholipids due to their higher binding energy and lower dissociation rate from ***,our study provides valuable insights into the molecular mechanisms underlying nucleic acidphospholipid interactions,with potential implications for the nucleic acids in biotherapies,particularly in the context of lipid carriers.

关键词： RNA DNA lipid bilayer molecular dynamics interface interaction divalent cation

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Superconducting, plastic, and superionic states driven by four-membered lithium rings in a high-pressure lithium-lead compound

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Physical Review B 2024年第18期109卷 L180507-L180507页

作者： Qing Lu Chi Ding Qiuhan Jia Shuning Pan Jiuyang Shi Yu Han Junjie Wang Xiaomeng Wang Dingyu Xing Jian Sun National Laboratory of Solid State Microstructures School of Physics and Collaborative Innovation Center of Advanced Microstructures Nanjing University Nanjing 210093 China School of Physics and Electronic-Electrical Engineering Ningxia University Yinchuan 750021 China

Using a combination of crystal structure search methods, first-principles calculations, and machine learning potential based simulations, we explored the lithium-lead system and predicted five phases: I4/mcm LiPb2, Pnma LiPb, I4/mmm Li4Pb, C2/m Li5Pb, and Cmcm Li6Pb. Among them, I4/mmm Li4Pb displayed remarkable properties, including superconductivity, plasticity, and superionic behavior at varying temperature ranges. At lower temperatures, I4/mmm Li4Pb manifests superconductivity with a critical transition temperature of 4–5 K. Its superconducting behavior is attributed to the interplay between the B2 g vibration mode, which signifies the rotational motion of four-membered lithium rings within the stacking layer, and the participation of p-orbital electrons. As temperature rises, I4/mmm Li4Pb first transitions into a plastic phase, marked by continuous collective rotation of intralayer four-membered lithium rings, and then shows superionic behavior characterized by the emergence of interlayer lithium atom diffusion. These unique behaviors stem from stronger Li-Li bonds within four-membered lithium rings and a lower energy barrier for collective motion, distinct from interstitial localized electrons in electrides found in other lithium-based systems. This work provides an intriguing platform for exploring distinct states and establishes a correlation between various physical phenomena and the system's structure and bonding.

关键词： Crystal structure Liquid-solid phase transition Pressure effects Structural phase transition Superconductivity Ab initio molecular dynamics First-principles calculations Machine learning

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Electronic structures and Mott state of epitaxial TaS_(2) monolayers

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Science China(Physics,Mechanics & Astronomy) 2024年第5期67卷 91-97页

作者： Qichao Tian Chi Ding Xiaodong Qiu Qinghao Meng Kaili Wang Fan Yu Yuyang Mu Can Wang Jian Sun Yi Zhang National Laboratory of Solid State Microstructure School of PhysicsNanjing UniversityNanjing 20093China Collaborative Innovation Center of Advanced Microstructures Nanjing UniversityNanjing 210093China School of Physics and Electronic Sciences Changsha University of Science and TechnologyChangsha 410114China Hefei National Laboratory Hefei 230088China

Layered material TaS2hosts multiple structural phases and exotic correlated quantum states,including charge density wave(CDW),superconductivity,quantum spin liquid,and Mott insulating ***,we synthesized TaS_(2)monolayers in H and T phases using the molecular beam epitaxial(MBE)method and studied their electronic structures via angle-resolved photoemission spectroscopy(ARPES).We found that the H phase TaS_(2)(H-TaS_(2))monolayer is metallic,with an energy band crossing the Fermi *** contrast,the T phase TaS_(2)(T-TaS_(2))monolayer shows an insulated energy gap at the Fermi level,while the normal calculated band structure implies it should be metallic without any band ***,by considering Hubbard interaction potential U,further density functional theory(DFT)calculation suggests that monolayer T-TaS_(2)could be a CDW Mott insulator,and the DFT+U calculation matches well with the ARPES *** significantly,the temperature-dependent ARPES result indicates that the CDW Mott state in the T-TaS_(2)monolayer is more robust than its bulk counterpart and can persist at room *** results reveal that the dimensional effect can enhance the CDW Mott state and provide valuable insights for further exploring the exotic properties of monolayer TaS2.

关键词： temperature monolayer state

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High Energy Density Polymeric Nitrogen Nanotubes inside Carbon Nanotubes

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Chinese Physics Letters 2022年第3期39卷 28-35页

作者： Chi Ding Junjie Wang Yu Han Jianan Yuan Hao Gao Jian Sun National Laboratory of Solid State Microstructures School of Physics and Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China

Polymeric nitrogen as a new class of high energy density materials has promising *** develop a new scheme of crystal structure searching in a confined space using external confining potentials fitted from firstprinciples *** a showcase,this method is employed to systematically explore novel polymeric nitrogen structures confined in single-walled carbon *** quasi-one-dimensional single-bonded polymeric nitrogen structures are realized,two of them are composed of nanotubes instead of *** new polymeric nitrogen phases are mechanically stable at ambient pressure and temperature according to phonon calculations and ab initio molecular dynamics *** is revealed that the stabilization of zigzag and armchair chains confined in carbon nanotubes are mostly attributed to the charge transfer from carbon to ***,for the novel nitrogen nanotube systems,electrons overlapping in the middle space provide strong Coulomb repulsive forces,which not only induce charge transfer from the middle to the sides but also stabilize the polymeric *** work provides a new strategy for designing novel high-energy-density polymeric nitrogen materials,as well as other new materials with the help of confined space inside porous systems,such as nanotubes,covalent organic frameworks,and zeolites.

关键词： polymeric chains stabilization

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Pressure-induced ferroelectric and anti-ferroelectric phase transitions in LaN

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Science China(Physics,Mechanics & Astronomy) 2023年第2期66卷 122-130页

作者： Chi Ding Jianan Yuan Beatriz H.Cogollo-Olivo Yunlong Wang Xiaomeng Wang Jian Sun National Laboratory of Solid State Microstructures School of Physics and Collaborative Innovation Center of Advanced MicrostructuresNanjingUniversityNanjing 210093China Applied Math Institute University of CartagenaCartagena de Indias 130001Colombia

In this work,we focus on the structural and electronic properties of lanthanum mono-nitride s under high *** on firstprinciples calculations and crystal structure predictions,we identified an anti-ferroelectric orthogonal phase with space group *** is predicted to be thermodynamically stable from 20 to 60 GPa,above which the tetragonal phase without the antiferroelectric distortion will substitute ***,the anti-ferroelectric distortion can be enhancedby reducing the pressure,and a phase transition to a NiAs-type(B8,P63/mmc) structure occurs at about 20 *** calculated double-well potential for La atoms along the c direction in the B8 phase reveals that it should exhibit ferroelectric properties at low *** calculations well confirm their phase transition sequences under high *** properties calculations suggest that all the newly identified phases are semiconductors and the corresponding structural distortions can increase their *** increasing the pressure to 50 GPa,the tetragonal phase undergoes a semiconductor-to-semimetal *** the spin-orbit coupling into account,the semimetal phase becomes a topological insulator with a small ***,given the similarities between the ionic compounds LaN and BaO,we predict that the most stable phase for BaO at about 25 GPa should also be the anti-ferroelectric orthogonal phase instead of the tetragonal phase.

关键词： ferroelectric phase distortion

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Pressure-induced color change arising from transformation between intra-and inter-band transitions in LuH_(2±x)N_(y)

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Science China(Physics,Mechanics & Astronomy) 2024年第2期67卷 161-166页

作者： Zhe Liu Yingjie Zhang Shenyang Huang Xue Ming Qing Li Chenghao Pan Yaomin Dai Xiaoxiang Zhou Xiyu Zhu Hugen Yan Hai-Hu Wen Center for Superconducting Physics and Materials National Laboratory of Solid State Microstructures and Department of PhysicsNational Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China State Key Laboratory of Surface Physics Key Laboratory of Micro and Nano-Photonic Structures of the Ministry of EducationDepartment of PhysicsFudan UniversityShanghai 200433China

The pressure-induced color change in the nitrogen-doped lutetium hydride has triggered extensive discussions about the underlying physics and potential ***,we study the optical response of LuH_(2±x)N_(y)in a broad frequency range at ambient pressure and its evolution with pressure in the visible spectral *** broad-band optical spectra at ambient pressure reveal a Drude component associated with intra-band electronic transitions and two Lorentz components(L1 and L2)arising from inter-band electronic *** application of pressure causes a spectral weight transfer from L1 to the Drude component,leading to a blue shift of the plasma edge in the reflectivity spectrum alongside a reduction of the high-frequency *** results suggest that the pressure-induced color change in LuH_(2±x)N_(y)is closely related to the transformation between intra-and inter-band electronic transitions,providing new insights into the mechanism of the pressure-induced color change in LuH_(2±x)N_(y).

关键词： nitrogen-doped lutetium hydride optical spectroscopy high-pressure technique color change

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Interface-induced topological phase and doping-modulated bandgap of two-dimensioanl graphene-like networks

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Chinese Physics B 2023年第1期32卷 434-439页

作者：杨柠境杨海金国钧 School of Physics Science and Technology Kunming UniversityKunming 650214China National Laboratory of Solid State Microstructures Department of Physicsand Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China

Biphenylene is a new topological material that has attracted much attention *** amplifying its size of unit cell,we construct a series of planar structures as homogeneous carbon allotropes in the form of polyphenylene *** first use the low-energy effective model to prove the topological three periodicity for these ***,through first-principles calculations,we show that the topological phase has the Dirac *** the size of per unit cell increases,the influence of the quaternary rings decreases,leading to a reduction in the anisotropy of the system,and the Dirac cone undergoes a transition from type II to type *** confirm that there are two kinds of non-trivial topological phases with gapless and gapped bulk ***,we add a built-in electric field to the gapless system by doping with B and N atoms,which opens a gap for the bulk ***,by manipulating the built-in electric field,the dispersion relations of the edge modes will be transformed into a linear *** findings provide a hopeful approach for designing the topological carbon-based materials with controllable properties of edge states.

关键词： polyphenylene interface band structure Zak phase edge state

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Transient logic operations in acoustics through dynamic modulation

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Physical Review Applied 2024年第1期21卷 L011001-L011001页

作者： Zhao-xian Chen Ling-ling Ma Shi-jun Ge Ze-Guo Chen Ming-hui Lu Yan-feng Chen Yan-qing Lu College of Engineering and Applied Sciences Collaborative Innovation Center of Advanced Microstructures and National Laboratory of Solid State Microstructures Nanjing University Nanjing 210023 China School of Materials Science and Intelligent Engineering Nanjing University Suzhou 215163 China

In quantum logic operations, information is carried by the wave function rather than the energy distribution. Therefore, the relative phase is essential. Abelian and non-Abelian phases can be emulated in classical waves using passive coupled waveguides with geometric modulation. However, the dynamic phase interference induced by waveguide structure variation is inevitable. To overcome the challenges, we introduce an electroacoustic coupled system that enables the precise control of phase distribution through dynamic modulation of hopping. Such effective hopping is electronically controlled and is utilized to construct various paths in parameter space. These paths lead to state evolution with matrix-valued geometric phases, which correspond to logic operations. We report experimental realizations of several logic operations, including the Y gate, Z gate, Hadamard gate, and non-Abelian braiding. Our work introduces a temporal process to manipulate transient modes in a compact structure, providing a versatile experimental testbed for exploring other logic gates and exotic topological phenomena.

关键词： Acoustic metamaterials Acoustic wave phenomena Geometric & topological phases Transport phenomena Devices for digital logic, storage & processing Waveguide arrays Cavity resonators Sound wave techniques

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Tailoring OAM spectrum of high-order harmonic generation driven by two mixed Laguerre–Gaussian beams with nonzero radial nodes

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Chinese Physics B 2023年第12期32卷 80-89页

作者：汪倍羽韩嘉鑫金成 Institute for Advanced Materials and Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials South China Academy of Advanced OptoelectronicsSouth China Normal UniversityGuangzhou 510006China Laboratory of Solid State Microstructures and Innovation Center of Advanced Microstructures Nanjing UniversityNanjing 210093China

The extreme ultraviolet(XUV)light beam carrying orbital angular momentum(OAM)can be produced via high-order harmonic generation(HHG)due to the interaction of an intense vortex infrared laser and a gas *** we show that the OAM spectrum of vortex HHG can be readily tailored by varying the radial node(from 0 to 2)in the driving laser consisting of two mixed Laguerre-Gaussian(LG)*** find that due to the change in spatial profile of HHG,the distribution range of the OAM spectrum can be broadened and its shape can be modified by increasing the radial *** also show that the OAM mode range becomes much wider and its distribution shape becomes more symmetric when the harmonic order is increased from the plateau to the cutoff when the driving laser has the nonzero radial *** the map of coherence length and the evolution of harmonic field in the medium,we reveal that the favorable off-axis phase-matching conditions are greatly modified due to the change of intensity and phase distributions of driving laser with the radial *** anticipate this work to stimulate some interests in generating the XUV vortex beam with tunable OAM spectrum through the gaseous HHG process achieved by manipulating the mode properties of the driving laser beam.

关键词： orbital angular momentum(OAM)spectrum high-order harmonic generation Laguerre–Gaussian beam radial nodes phase-matching

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Coexistence of All-Order Topological states in a Three-Dimensional Phononic Topological Crystalline Insulator

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Research 2024年第2期2023卷 511-518页

作者： Hua-Shan Lai Hao Chen Chu-Hao Xia Si-Yuan Yu Cheng He Yan-Feng Chen National Laboratory of Solid State Microstructures&Department of Materials Science and Engineering Nanjing UniversityNanjng 210093China Collaborative Innovation Center of Advanced Microstructures Nanjing University Nanjng 210093China Jiangsu Key Laboratory of Artificial Functional Materials Nanjing University Nanjing 210093China

Classical-wave topological materials lacking intrinsic half-integer spins are less robust while more ***,we explore a single 3-dimensional phononic topological crystalline insulator that simultaneously exhibits a whole family of first-order quadratic surface,second-order hinge,and third-order corner states within the same *** a topological crystalline insulator hosting all-order phases originates from the different topological nature when hierarchically projected onto different facets and lower dimensions,thus free from trivial cladding *** work offers an ideal platform for either robust wave propagation or localization in on-demand dimensions and may facilitate dimension division multiplexing technology.

关键词： topological dimensions crystalline

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