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Improving performance of screening MM/PBSA in protein–ligand interactions via machine learning

Chinese Physics B 2025年第1期34卷 486-496页

作者： Yuan-Qiang Chen Yao Xu Yu-Qiang Ma Hong-Ming Ding Center for Soft Condensed Matter Physics and Interdisciplinary Research School of Physical Science and TechnologySoochow UniversitySuzhou 215006China National Laboratory of Solid State Microstructures and Department of Physics Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China

Accurately estimating protein–ligand binding free energy is crucial for drug design and biophysics, yet remains a challenging task. In this study, we applied the screening molecular mechanics/Poisson–Boltzmann surface area(MM/PBSA)method in combination with various machine learning techniques to compute the binding free energies of protein–ligand interactions. Our results demonstrate that machine learning outperforms direct screening MM/PBSA calculations in predicting protein–ligand binding free energies. Notably, the random forest(RF) method exhibited the best predictive performance,with a Pearson correlation coefficient(rp) of 0.702 and a mean absolute error(MAE) of 1.379 kcal/mol. Furthermore, we analyzed feature importance rankings in the gradient boosting(GB), adaptive boosting(Ada Boost), and RF methods, and found that feature selection significantly impacted predictive performance. In particular, molecular weight(MW) and van der Waals(VDW) energies played a decisive role in the prediction. Overall, this study highlights the potential of combining machine learning methods with screening MM/PBSA for accurately predicting binding free energies in biosystems.

关键词： molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) binding free energy machine learning protein-ligand interaction

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

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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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In-Memory Probabilistic Computing Using Gate-Tunable Layer Pseudospins in van der Waals Heterostructures

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Chinese Physics Letters 2025年第4期42卷 9-22页

作者： Jiao Xie Jun-Lin Xiong Bin Cheng Shi-Jun Liang Feng Miao Institute of Brain-Inspired Intelligence National Laboratory of Solid State MicrostructuresSchool of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China Institute of Interdisciplinary Physical Sciences School of ScienceNanjing University of Science and TechnologyNanjing 210094China Jiangsu Physical Science Research Center Nanjing 210093China

Layer pseudospins,exhibiting quantum coherence and precise multistate controllability,present significant potential for the advancement of future computing *** this work,we propose an in-memory probabilistic computing scheme based on the electrical manipulation of layer pseudospins in layered materials,by exploiting the interaction between real spins and layer pseudospins.

关键词： layer pseudospinsexhibiting layered materialsby real spins probabilistic computing advancement future computing technologiesin electrical manipulation layer pseudospins memory computing gate tunable layer pseudospins

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Andreev reflection in superconducting state of pressurized La_(3)Ni_(2)O_(7)

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science China(Physics,Mechanics & Astronomy) 2025年第4期68卷 180-188页

作者： Cong Liu Mengwu Huo Huan Yang Qing Li Yingjie Zhang Zhening Xiang Meng Wang Hai-Hu Wen National Laboratory of Solid State Microstructures and Department of Physics Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China Center for Neutron Science and Technology Guangdong Provincial Key Laboratory of Magnetoelectric Physics and DevicesSchool of PhysicsSun Yat-sen UniversityGuangzhou 510275China

The discovery of superconductivity with T_(c)above 77 K in pressurized La_(3)Ni_(2)O_(7)has stimulated enormous interest in the field of unconventional superconductivity.A recent experiment in La_(2)Pr Ni_(2)O_(7)has shown that the superconducting volume is close to100%.Because the superconductivity can only be achieved under high pressures,many intrinsic properties,such as the superconducting gaps,have not been measured *** report the Andreev reflection measurement of pressurized La_(3)Ni_(2)O_(7)with the onset superconducting transition temperature at about 77 *** data reveal a clear peak of differential conductivity near zero bias in the tunneling spectrum;and appear also are some temperature-dependent steps that may reflect other superconducting *** based on the Blonder-Tinkham-Klapwijk model with multiple components can roughly fit the data,and the central peak can be fitted with a d-wave gap with a magnitude of about 9 meV,and other two s-wave gaps at about 16 and 26 *** latter two large gaps are determined from the enhanced steps of the differential conductivity,which may have other *** results reveal possible evidence of a sign-reversal gap and multi-component features of the superconducting gaps in the nickelate 327 systems.

关键词： nickelate superconductor La_(3)Ni_(2)O_(7) point contact spectrum sign-reversal gap multigap superconductor

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Gate-tunable high-responsivity photodiode based on 2D ambipolar semiconductor

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Chinese Physics B 2025年第1期34卷 189-193页

作者： Wentao Yu Long Zhao Yanfei Gao Shiping Gao Yuekun Yang Chen Pan Shi-Jun Liang Bin Cheng Institute of Interdisciplinary Physical Sciences School of PhysicsNanjing University of Science and TechnologyNanjing 210094China Institute of Brain-Inspired Intelligence National Laboratory of Solid State MicrostructuresSchool of PhysicsCollaborative Innovation Center of Advanced MicrostructuresJiangsu Physical Science Research CenterNanjing UniversityNanjing 210093China

Electrically tunable homojunctions based on ambipolar two-dimensional materials have attracted widespread attention in the field of intelligent *** devices exhibit inherent switchable positive and negative photovoltaic properties that effectively mimic the behavior of human retinal ***,the photovoltaic responsivity of most electrically tunable homojunctions remains significantly low due to the weak light absorption,making it challenging to meet the application requirements for high-sensitivity target detection in the field of intelligent ***,we propose a gate-tunable photodiode based on two-dimensional ambipolar WSe_(2)with an asymmetric gate electrode,achieving high photovoltaic *** adjusting the gate voltage and keeping bias voltage zero,we can dynamically realize reconfigurable n-–p and n-–n homojunction states,as well as gate-tunable photovoltaic response characteristics that range from positive to *** maximum photovoltaic responsivity of the electrically tunable WSe_(2)homojunction is approximately 0.4 A/W,which is significantly larger than the previously reported value~0.1 A/W in homojunction *** addition,the responsivity can be further enhanced to approximately 1.0 A/W when the n-–p photodiode operates in reverse bias mode,enabling highsensitivity detection of *** work paves the way for developing gate-tunable photodiodes with high photovoltaic responsivity and advancing high-performance intelligent vision technology.

关键词： reconfigurable homojunction in sensor computing ambipolar material

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Comprehensive optimization of piezoelectric coefficient and depolarization temperature in Mn-doped Bi_(0.5)Na_(0.5)TiO_(3)-Bi_(0.5)K_(0.5)TiO_(3)-BaTiO_(3)lead-free piezoceramics

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Journal of Materials science & technology 2024年第5期172卷 255-263页

作者： Huashan Zheng Enwei Sun Huajie Luo Xiaoyu Zhang Yixiao Yang Bin Yang Rui Zhang Shantao Zhang Wenwu Cao Condensed Matter Science and Technology Institute School of Instrumentation Science and EngineeringHarbin Institute of TechnologyHarbin150080China Advanced Innovation Center for Materials Genome Engineering University of Science and Technology BeijingBeijing100083China National Laboratory of Solid State Microstructures Department of Materials Science and EngineeringCollege of Engineering and Applied Science&Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210093China Department of Mathematics and Materials Research Institute The Pennsylvania State UniversityUniversity ParkPennsylvania16802United States of America

Lead-free Bi_(_(0.5))Na_(_(0.5))TiO_(3)(BNT)piezoelectric ceramics have the advantages of large coercive fields and high Curie *** the improvement of piezoelectric coefficient(d 33)is usually accompanied by a huge sacrifice of depolarization temperature(T d).In this work,a well-balanced performance of d 33 and T d is achieved in MnO_(2)-doped 0.79(Bi_(_(0.5))Na_(_(0.5))TiO_(3))-0.14(Bi_(0.5)K_(0.5)TiO_(3))-0.07BaTiO_(3)ternary *** in-corporation of 0.25 mol%MnO_(2)enhances the d 33 by more than 40%,while T d remains almost unchanged(i.e.,d 33=181 pC/N,T d=184℃).X-ray diffraction(XRD)shows that an appropriate fraction of the small axis-ratio ferroelectric phase(pseudo-cubic,P c)coexists with the long-range ferroelectric phase(tetrag-onal,T)under this MnO_(2)*** force microscopy(PFM)has revealed a special domain configuration,namely large striped and layered macro domains embedded with small *** study provides a distinctive avenue to design BNT-based piezoelectric ceramics with high piezoelectric performance and temperature stability.

关键词： BNT-BKT-BT ceramics Mn doping Piezoelectric Depolarization temperature Phase structure

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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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Improving the electrical performances of InSe transistors by interface engineering

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Chinese Physics B 2024年第4期33卷 153-158页

作者：曹天俊郝松吴晨晨潘晨戴玉頔程斌梁世军缪峰 Institute of Brain-Inspired Intelligence National Laboratory of Solid State MicrostructuresSchool of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China Institute of Interdisciplinary Physical Sciences School of PhysicsNanjing University of Science and TechnologyNanjing 210014China

InSe has emerged as a promising candidate for next-generation electronics due to its predicted ultrahigh electrical ***,the efficacy of the InSe transistor in meeting application requirements is hindered due to its sensitivity to *** this study,we have achieved notable enhancement in the electrical performance of InSe transistors through interface *** engineered an InSe/h-BN heterostructure,effectively suppressing dielectric layer-induced ***,we successfully established excellent metal-semiconductor contacts using graphene ribbons as a buffer *** a methodical approach to interface engineering,our graphene/InSe/h-BN transistor demonstrates impressive on-state current,field-effect mobility,and on/off ratio at room temperature,reaching values as high as 1.1 mA/μm,904 cm^(2)·V^(-1)·s^(-1),and>10~6,*** computations corroborate that the graphene/InSe heterostructure shows significant interlayer charge transfer and weak interlayer interaction,contributing to the enhanced performance of InSe *** research offers a comprehensive strategy to elevate the electrical performance of InSe transistors,paving the way for their utilization in future electronic applications.

关键词： two-dimensional materials InSe van der Waals heterostructure electrical performances charge density difference

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Effects of Thickness and Anisotropic Strain on Polarization Switching Properties of Sub-10nm Epitaxial Hf_(0.5)Zr_(0.5)O_(2)Thin Films

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Chinese Physics Letters 2024年第11期41卷 221-232页

作者： Kuan Liu Kai Liu Xingchang Zhang Jie Fang Feng Jin Wenbin Wu Chao Ma Lingfei Wang Hefei National Research Center for Physical Sciences at the Microscale University of Science and Technology of ChinaHefei 230026China College of Materials Science and Engineering Hunan UniversityChangsha 410082China Collaborative Innovation Center of Advanced Microstructures Nanjing UniversityNanjing 210093China

Doped HfO_(2)-based ferroelectric(FE)films are emerging as leading contenders for next-generation FE nonvolatile memories due to their excellent compatibility with complementary metal oxide semiconductor processes and robust ferroelectricity at nanoscale *** the considerable attention paid to the FE properties of HfO_(2)-based films in recent years,enhancing their polarization switching speed remains a critical research *** demonstrate the strong ferroelectricity of sub-10nm Hf_(0.5)Zr_(0.5)O_(2)(HZO)thin films and show that the polarization switching speed of these thin films can be significantly affected by HZO thickness and anisotropically strained La_(0.67)Sr_(0.33)MO_(3)-buffered *** observations indicate that the HZO thin film thickness and anisotropically strained La_(0.67)Sr_(0.33)MO_(3)layer influence the nucleation of reverse domains by altering the phase composition of the HZO thin film,thereby reducing the polarization switching *** the increase in HZO thickness and anisotropic compressive strain hinder the formation of the FE phase,they can enable faster *** findings suggest that FE HZO ultrathin films with polar orthorhombic structures have broad application prospects in microelectronic *** insights into novel methods for increasing polarization switching speed are poised to advance the development of high-performance FE devices.

关键词： ferroelectric anisotropic film

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Temperature-Dependent Anisotropy and Two-Band Superconductivity Revealed by Lower Critical Field in Organic Superconductorκ-(BEDT-TTF)_(2)Cu[N(CN)_(2)]Br

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Chinese Physics Letters 2023年第6期40卷 56-62页

作者：睦惠景司进杨琴珪相英杨海朋闻海虎 National Laboratory of Solid State Microstructures and Department of Physics Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China College of Materials Science and Engineering Shenzhen Key Laboratory of Polymer Science and TechnologyShenzhen UniversityShenzhen 518060China

Resistivity and magnetization have been measured at different temperatures and magnetic fields in organic superconductorsκ-(BEDT-TTF)_(2)Cu[N(CN)_(2)]*** lower critical field and upper critical field are determined,which allow to depict a complete phase *** the comparison between the upper critical fields with magnetic field perpendicular and parallel to the conducting ac-planes,and the scaling of the in-plane resistivity with field along different directions,we find that the anisotropyΓis strongly dependent on *** is realized thatΓis quite large(above 20)near Tc,which satisfies the 2D model,but approaches a small value in the low-temperature *** 2D-Tinkham model can also be used to fit the data at high *** is explained as a crossover from the orbital depairing mechanism in high-temperature and low-field region to the paramagnetic depairing mechanism in the high-field and low-temperature *** temperature dependence of lower critical field,Hc1(T),shows a concave shape in wide temperature *** is found that neither a single d-wave nor a single s-wave gap can fit the Hc1(T),however a two-gap model containing an s-wave and a d-wave can fit the data rather well,suggesting two-band superconductivity and an unconventional pairing mechanism in this organic superconductor.

关键词： temperature satis directions

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