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Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free-Energy Simulation Methods

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CCS Chemistry 2021年第2期3卷 1026-1039页

作者： zhaoxi Sun john z.h.zhang State Key Laboratory of Precision Spectroscopy School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghai 200062 NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 Department of Chemistry New York UniversityNYNY 10003

Threofuranosyl nucleic acid(TNA)is an analogue of DNA with a shift in the internucleotide linkages from the wild-type 5’-to-3’direction to 3’-to-2.’This alteration leads to higher chemical stability,less reactive groups,and lower conformational *** observations indicate that these characteristic changes are attributable to a minimal perturbation of the interaction network,but the thermodynamic stability of the duplex remains unaltered in the TNA *** applied the equilibrium and nonequilibrium free-energy simulations employing three popular assisted model building with energy refinement(AMBER)force fields for nucleotides to investigate this mutation-dependent behavior in the base flipping from T(DNA)residue to the T-to-TFT mutation(TNA)*** force fields were performed similarly,as described in the base-paired ***,after exploring the high-energy regions with free-energy simulations,we observed that these three force fields behaved *** reports conclude that the net-neutral and excess-salt simulations provided similar ***,our free-energy simulation indicated that the presence of excess salt affected the thermodynamic *** free-energy barrier along the base-flipping pathway was generally elevated upon the addition of excess salts,but the relative height of the free-energy barriers in DNA and TNA duplexes did not change *** phenomenon emphasizes the importance of adding sufficient salts in the simulation scheme to reproduce the experimental condition.

关键词： free-energy simulation base flipping,TNA AMBER force fields salt concentration

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Three-dimensional quantum dynamics study of vibrational predissociation of heI_2 van der Waals molecule for low vibrational excitation using the time-dependent wave packet method

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Science China Chemistry 1997年第4期40卷 442-448页

作者：关大任赵显邓从豪 john z.h.zhang Institute of Theoretical Chemistry Shandong UniversityJinan 250100China Department of Chemistry New York UniversityNew YorkNY 10003USA

Three-dimensional quantum mechanical calculations for vibrational predissociation of heI2(B) van der Waals molecules are presented using the time-dependent wave packet technique within the golden rule approxima *** total and partial decay widths,lifetimes,rates and their dependence on initial vibrational states were obtained for heI2 at low initial vibrational excited *** calculations show that the calculated tota decay widths,lifetimes and rates agree well with those extrapolated from experimental data available The predicted total decay widths as a function of initial vibrational states exhibit highly nonlinear *** very short propagation time (*** 1 ps) required in the golden rule wave packet calculation is determined by the duration time of the final state inter-action between the fragments on the vibrationally deexcited adiabatic potential *** final state interaction between the fragments is shown to play an important role in determining the final rotational

关键词： time-dependent golden rule wave packet approach vibrational predissociation heI2 van der Waats molecule decay widths final rotational distribution

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Interaction Entropy and Quantitative Analysis of Protein-Protein Interaction

Interaction Entropy and Quantitative Analysis of Protein-Pro...

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第十三届全国量子化学会议

作者： john z.h.zhang School of Chemistry and Molecular Engineering East China Normal University NYU-ECNU Center for Computational Chemistry at New York University Shanghai Department of Chemistry New York University

＜正＞The theoretical calculation of protein-protein binding free energy is a grand challenge in computational biology. Accurate prediction of critical residues along with their specific and quantitative contributions to protein-protein binding free energy is extremely helpful to reveal binding mechanisms and identify druglike molecules that alter protein-protein interactions. In this talk we develop an efficient Interaction

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Force Field Development and Fragment based Ab Initio Molecular Dynamic Simulation for MetalloProteins

Force Field Development and Fragment based Ab Initio Molecul...

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第十五届全国化学动力学会议

作者：朱通 john z.h.zhang College of Chemistry and Molecular Engineering East China Normal University NYU-ECNU Center for Computational Chemistry at NYU Shanghai Department of Chemistry New York University

＜正＞A polarizable-charge transfer force field（QPCT）has been proposed to accurately describe the interaction dynamics of zinc–protein *** parameters of the QPCT force field were calibrated by quantum chemistry calculation and can capture the polarization and charge transfer *** are validated by molecular dynamic simulation of the hydration shell of the zinc ion,five proteins containing the most common zinc-binding sites,as

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Force Field Development and Quantum Fragment based Ab Initio Molecular Dynamics for MetalloProtein

Force Field Development and Quantum Fragment based Ab Initio...

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中国化学会第30届学术年会-第十九分会：化学中的量子与...

作者： Tong zhu john z.h.zhang Department of Physics East China Normal University NYU-ECNU Center for Computational Chemistry at NYU Shanghai Department of Chemistry New York University

＜正＞A polarizable-charge transfer force field（QPCT） has been proposed to accurately describe the interaction dynamics of zinc–protein *** parameters of the QPCT force field were calibrated by quantum chemistry calculation and can capture the polarization and charge transfer *** are validated by molecular

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The QM/MM Simulations of Specific Vibrations of GTP in Ras Protein

The QM/MM Simulations of Specific Vibrations of GTP in Ras P...

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中国化学会第十二届全国量子化学会议

作者： Fei Xia john z.h.zhang Department of Chemistry East China Normal University (ECNU) State Key Laboratory of Precision Spectroscopy and Department of Physics ECNU

The guanine nucleotide-binding proteins are responsible for various cellular processes in eukaryotic cells,including heterotrimeric G-proteins and members of Ras-related *** Ras protein has the catalytic activity of hydrolyzing the guanosine triphosphate（GTP）to guanosine diphosphate（GDP）,which is called the *** cycling of hydrolysis of GTP and GDP in Ras plays an important role in the signal processes involved in cell.A malfunction of Ras protein can lead to uncontrolled cell proliferation,which eventually causes *** take insight in the function of Ras family in controlling signal processes,an elaborate investigation of the hydrolysis mechanism of GTP in Ras protein needs to be performed at the atomic level with a combination of experimental and theoretical ***,a big amount of experimental data associated with the specific vibrations of P-O bonds in GTP measured from Fourier-transformed infrared spectroscopy（FTIR）is available,which provide the experimental implications of hydrolysis mechanism of *** therefore used QM/MM simulations to calculate the spectra and the normal vibrational modes GTP in various environments such as the aqueous solution,Ras and Ras GAP *** simulation results show the GTPs adopt distinctive structural conformations and coordination patterns with Mg2+cations in different *** calculated specific vibrational frequencies of bonds in GTP are in good agreement with the experimentally measured difference spectra,providing a very good validation of conformations obtained by the *** the first time,we suggest band assignments of the vibrational modes of GTP in Ras below800cm-1 by comparison of calculated and experimental spectra.

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Rational design of AgGaS/znS/znS quantum dots with a near-unity photoluminescence quantum yield via double shelling scheme

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Journal of Materials Science & Technology 2024年第2期169卷 235-242页

作者： h.X.Lu h.Liu z.z.Fu Y.Y.Chen h.Q.Dai z.hu W.L.zhang R.Q.Guo Institute for Electric Light Sources School of Information Science and TechnologyFudan UniversityShanghai 200433China Institute of Future Lighting Academy for Engineering and TechnologyFudan UniversityShanghai 200433China Yiwu Research Institute of Fudan University YiwuZhejiang 322000China zhongshan-Fudan Joint Innovation Center Zhongshan 528437China

In this study,a two-step method was used to synthesize highly luminescent AgGaS/znS/znS quantum dots(QDs).In the first step,an inner znS shell was formed via a one-pot method,which resulted in a smaller lattice mismatch between the AgGaS core and the outer znS shell,thereby facilitating the formation of a thick outer *** the two-step shelling process,the synthesized AgGaS/znS/znS QDs showed an excellent photoluminescence quantum yield(PLQY)of 96.4%with a peak wavelength of 508 nm,repre-senting the highest PLQY reported thus far for AgGaS ***,the effect of halogen ions in zn precursors on the shelling process was *** was proposed that the capacity of halogen ions to coordinate with the QDs influenced the balance between zn cation diffusion and znS shelling ***,the znS shelling reaction was dominant when znCl_(2)was employed,while zn cation diffusion was the dominant process under the I^(−)-rich *** work provides insights into the interfacial restructuring during the znS shelling and offers a clear map for the tailored synthesis of core/shell QDs.

关键词： AgGaS Quantum dots Photoluminescence Core/shell Alloyed core/shell interface

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Functional Loop dynamics of S-component in ECF transporter

Functional Loop dynamics of S-component in ECF transporter

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第十三届全国量子化学会议

作者： Linqiong Qiu Jianing Song john z.h.zhang School of Chemistry and Molecular Engineering East China Normal University State Key Laboratory of Precision Spectroscopy East China Normal University NYU-ECNU Center for Computational Chemistry at NYU Shanghai Department of Chemistry New York University Collaborative Innovation Center of Extreme Optics Shanxi University

ECF transporters are responsible for many micronutrients uptake in organisms. S component FolT of ECF transporter is recently crystallized and provides solid basis to study the micronutrients binding mechanism. In this work, Molecular Dynamics(MD) simulations are applied to study the dynamic difference of loops in floate-bound and floate-free state of FolT. Further, MD-RAMD(Random accelerate molecular dynamics) simulations and SMD simulations are used to enhance the sampling of conformational transitions of loops. The results show that loops play important role and are cooperated with each other in ligand binding process(Loop1, Loop3 and Loop5). Although the three loops are quite important in folate binding, Loop1 is supposed to be the gate controlling the folate binding, based on our dynamics analysis and static state analysis of open/closed XRD structures of FloT, which agrees well with the experimental data.

关键词： ECF transporter MD folate transporter functional loop gate loop

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Molecular dynamics simulation of protein crystal with polarized protein-specific force field

Molecular dynamics simulation of protein crystal with polari...

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中国化学会第十二届全国量子化学会议

作者： Yongxiu Li john z.h.zhang Ye Mei State Key Laboratory of Precision Spectroscopy Department of Physics and Institute of Theoretical and Computational ScienceEast China Normal University NYU-ECNU Center for Computational Chemistry at NYU Shanghai

The explicitly polarized force field model is indispensable in the simulation of protein crystal due to its particular electrostatic environment which is different from that in water *** polarized protein-specific charge（PPC）has shown important priorities for the study of protein-ligand binding and protein ***,the applicability of PPC in the simulation of protein crystal is yet to be *** 250 ns molecular simulations were carried out to study the structure and dynamics of crystal toxin protein Ⅱ from the scorpion Androctonus australis hector employing PPC as well as the standard AMBER99SB force field to investigate the effect of electrostatic polarization on the crystal *** simulation results showed that under PPC,the monomer in the subunit cell and the lattice in the supercell were more stable with much smaller RMSDs and the lattice atomic fluctuations were also better in line with the crystallographic *** of the interactions at interfaces in the X-ray structure were well preserved,underscoring the important effect of polarization on maintaining the crystal ***,our results also showed that the hydrogen bond between Asp53 and Gln37 and the cation-лinteraction between Arg56 and his64 were not as stable,indicating that further optimization of force field with van der Waals interaction parameters is desired.

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Microstructure evolution and shape memory behaviors of Ni_(47)Ti_(44)Nb_(9)alloy subjected to multistep thermomechanical loading with different prestrain levels

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Journal of Materials Science & Technology 2024年第4期171卷 80-93页

作者： Y.h.zhang h.Li z.W.Yang X.Liu Q.F.Gu State Key Laboratory of Solidification Processing School of Materials Science and EngineeringNorthwestern Polytechnical UniversityXi’an 710072China Shaanxi Key Laboratory of high-Performance Precision Forming Technology and Equipment Northwestern Polytechnical UniversityXi’an 710072China

Ni_(47)Ti_(44)Nb_(9)shape memory alloy(SMA)is a promising material in the aerospace field due to its wide transformation *** application of shape memory effect depends on multistep thermomechan-ical loading,viz.,low-temperature deformation and subsequent heating to ***-temperature deformation prestrain plays a pivotal role in shape memory properties tailoring of SMA ***,microstructure evolution and deformation mechanisms of Ni_(47)Ti_(44)Nb_(9)SMA subjected to vari-ous prestrain levels are still *** this end,microstructure evolution and shape memory behaviors of Ni_(47)Ti_(44)Nb_(9)alloy subjected to multistep thermomechanical loading with prestrain levels of 8%-16%at-28℃(M_(s)+30℃)were *** results demonstrate that the stress-strain curve of the specimen exhibits four distinct stages at a maximal prestrain of 16%.Whereas stageⅡand stageⅢend at prestrains of∼8%and∼12%,*** stageⅡ,the stress-induced martensitic transformation is accompanied by the dislocation slip of the NiTi matrix andβ-Nb *** stageⅢ,in addition to the higher density of dislocations and further growth of stress-induced martensite variants(SIMVs),(001)compound twins are introduced as a result of the(001)deformation twinning in stress-induced ***{20-1}martensite twins are gradually introduced in stageⅣ.Correspondingly,after subsequent unloading and heating,a higher density of{114}austenite twins form in the specimen with a larger prestrain of 16%.With increasing prestrain from 8%to 16%,the recoverable strainε_(re)^(T)upon heating increases first and then ***ε_(re)^(T)obtains a maximum of 7.03%at 10%prestrain and de-creases to 6.17%at 16%*** increase ofε_(re)^(T)can be attributed to the formation of new SIMVs,the further growth of existing SIMVs,and the recoverable(001)compound *** the decrease ofε_(re)^(T)is mainly associated with the irrecoverable strain by{20−1}martensite *** effe

关键词： Ni_(47)Ti_(44)Nb_(9)shape memory alloy Wide transformation hysteresis Thermomechanical loading Microstructure evolution Shape memory behaviors Stress-induced martensitic transformation Deformation twinning

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