Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Experimental and theoretical studies of Mn(II) and Co(II) metal complexes of a tridentate Schiff's base ligand and their biological activities

We have used the condensation method to synthesize 2-acetyl-5-methylsemicarbazone ligand. Manganese(II) and Cobalt(II) complexes having formula [ML₂]X₂ were synthesized where M = Mn(II) and Co(II), L = ligand, X = Cl⁻, CH₃COO⁻, NO₃⁻, ½SO₄²⁻. The characterization data suggests the octahedral geometry for all the synthesized complexes. Tridentate nature of the 2-acetyl-5-methylsemicarbazone ligand was revealed by IR studies. Molar conductance analysis suggested the electrolytic nature of the complexes. The theoretical study includes geometrical optimization, HOMO-LUMO energy gap, energetic parameters and dipole moment. These results also confirmed the tridentate nature of the ligand and the octahedral geometry of complexes. The molecular electrostatic potential (MEP) study suggested the reactive sites for an electrophilic or nucleophilic attack in the ligand. We tested the synthesized compounds for their antifungal and antibacterial action via well diffusion method and found that parent ligand after the coordination with the metal ion showed more effective inhibition against bacteria and fungi.     

Enhanced electronic and nonlinear optical responses of C24N24 cavernous nitride fullerene by decoration with first row transition metals; A computational investigation

The electronic (energy gap and work function) as well as electrical properties (dipole moment, polarizability, and first hyperpolarizabilities) of the first-row transition metals decorated C₂₄N₂₄ cavernous nitride fullerene were explored using DFT calculations. The transition metals are decorated at N4 cavity of C₂₄N₂₄ fullerene. According to our spin polarized computations, the most stable spin state monotonically increases to sextet for Mn@C₂₄N₂₄ and thereafter dropped off gradually to singlet state for Zn@C₂₄N₂₄ system. The findings demonstrate that transition metals can remarkably decrease the HOMO-LUMO energy gap and work function values up to 63% and 21% of bare C₂₄N₂₄, respectively. As can be seen, when the Sc and Ti metals are located above the N4 cavity of fullerene, systems of enhanced static hyperpolarizabilities (β₀) are delivered. These findings might provide an effective strategy to design high performance eletcro-optical materials based on carbon- nitride fullerene.     

介质材料二次电子发射特性对微波击穿的影响

以介质填充的平行板放电结构为例,本文主要研究了介质填充后微波低气压放电和微放电的物理过程.为了探究介质材料特性对微波低气压放电和微放电阈值的影响,本文采用自主研发的二次电子发射特性测量装置,测量了7种常见介质材料的二次电子发射系数和二次电子能谱.依据二次电子发射过程中介质表面正带电的稳定条件,计算了介质材料稳态表面电位与二次电子发射系数以及能谱参数的关系.在放电结构中引入与表面电位相应的等效直流电场后,依据电子扩散模型和微放电中电子谐振条件,分别探讨了介质表面稳态表面电位的大小对微波低气压放电和微放电阈值的影响.结果表明,介质材料的二次电子发射系数以及能谱参数越大,介质材料的稳态表面电位也越大,对应的微波低气压放电和微放电阈值也越大.所得结论对于填充介质的选择有一定的理论指导价值.     

Nucleon effective mass splitting and density-dependent symmetry energy effects on elliptic flow in heavy ion collisions at E_(lab)= 0.09 ～ 1.5 GeV/nucleon

By incorporating an iso spin-dependent form of the momentum-dependent potential in the ultra-relativistic quantum molecular dynamics(UrQMD) model,we systematically investigate effects of the neutron-proton effective mass splitting m*_(n-p)=m*_n-m*_p/m and the density-dependent nuclear symmetry energy E_(sym)(ρ) on the elliptic flow v_2 in~(197)Au+~(197) Au collisions at beam energies from 0.09 to 1.5 GeV/nucleon.It is found that at higher beam energies(≥0.25 GeV/nucleon) with the approximately 75 MeV difference in slopes of the two different E_(sym)(ρ),and the variation of m*_(n-p) ranging from-0.03 to 0.03 at saturation density with isospin asymmetry δ=(ρ_n-ρ_p)/ρ-0.2,the E_(sym)(ρ) has a stronger influence on the difference in v_2 between neutrons and protons,i.e.,v_2~n-v_2~p,than m*_(n-p) has.Meanwhile,at lower beam energies(≤0.25 GeV/nucleon),v_2~n-v_2~p is sensitive to both the E_(sym)(ρ) and the m*_(n-p).Moreover,the influence of m*_(n-p) on v_2~n-v_2~p is more evident with the parameters of this study when using the soft,rather than stiff,symmetry energy.     

Statistical structure of the velocity field in cavitating flow around a 2D hydrofoil

Transformation of flow turbulence structure with cavitation occurrence, determination of the flow conditions favorable for nucleation of cavitation bubbles, influence of the statistical structure of turbulence on this process and the inverse effect of cavitation on the flow dynamics are challenging problems in modern fluid mechanics. The paper reports on the results of statistical processing of the velocity fields measured by a PIV technique in cavitating flow over a 2D symmetric hydrofoil for four flow conditions, starting from a cavitation-free regime and finishing by unsteady cloud cavitation. We analyze basic information on the statistical structure of velocity fluctuations in the form of histograms and Q-Q diagrams along with profiles of the mean velocity and turbulent kinetic energy. The research reveals that the flow turbulence pattern and distributions of turbulent fluctuations change significantly with the cavitation development. Under unsteady cloud cavitation conditions, the probability density function of the fluctuating velocity has a two-mode distribution, which indicates switching of two alternating flow conditions in a region above the hydrofoil aft part due to periodic passing of cavitation clouds. Behaviors of the mean and most probable velocities unexpectedly appear to be different with a monotonous increase of the incoming flow velocity. This finding must be caused by modification of the skewness coefficient of the fluctuating velocity.     

大脑血液动力学现象中的能量编码

神经信息的编码与解码是神经科学中的核心研究内容,同时又极具挑战性.传统的编码理论都具有各自的局限性,很难从脑的全局运行方式上给出有效的理论.而由于能量是一个标量具有可叠加性,因此能量编码理论可以从神经元活动的能量特征出发来研究脑功能的全局神经编码问题,取得了一系列的研究成果.本研究以王-张神经元能量计算模型为基础,构建了一个多层次结构的神经网络,通过计算机数值模拟得到了神经网络的能量消耗和血液中葡萄糖供能的变化情况.计算结果显示,和网络的神经活动达到峰值的时间相比,血液中葡萄糖的供能达到峰值的时间延迟了约5.6s.从定量的角度再现了功能性核磁共振(fMRI)中的血液动力学现象:大脑某个脑区的神经元集群被激活以后经过5~7 s的延迟,脑血流的变化才会大幅增加.模拟结果表明先前发表的由王-张神经元模型所揭示的负能量机制在控制大脑的血液动力学现象中起着核心的作用,预测了刺激条件下大脑的能量代谢与血流之间变化的本质是由神经元在发放动作电位过程中正、负能量之间的非平衡、不匹配性质所决定的.本文的研究结果为今后进一步探究血液动力学现象的生理学机制提供了新的研究方向,在神经网络的建模与计算方面给出了一个新的视角和研究方法.      

A STUDY OF LOW CYCLE FATIGUE PROPERTIES OF MATERIALS BASED ON THE FUNNEL-SHEET SPECIMENS1)

根据能量等效方法,针对漏斗薄片试样,提出了关联Ramberg-Osgood 幂律参数、试样几何参数的载荷-位移半解析统一模型。采用有限元数值模拟,正、反向验证了该模型的有效性。在此基础上,提出了通过漏斗薄片试样低循环试验实现材料低周疲劳性能的预测方法。基于薄片试样低循环试验数据,完成了SS316L, N18及SAPH440 三种材料的低周疲劳性能预测,预测结果与标准试样试验结果具有良好的一致性。并利用该方法完成了N18与SAPH在不同温度条件下的低周疲劳性能预测。     

EXPERIMENTAL RESEARCH ON FAILURE AND ENERGY DISSIPATION CHRACTERISTICS OF THE SANDSTONE1)

通过三轴卸荷试验,探究了不同路径下卸荷速率对砂岩力学特性及破坏过程中的能量耗散的影响。试验结果表明在全过程应力-应变曲线的弹性阶段,轴向变形起主导作用,弹塑性阶段,环向应变的增加值大于轴向应变增加值。在围压卸荷阶段,卸荷速率越小,卸荷阶段的应变折合柔度越大,此时岩样的变形不充分,呈现明显的脆性破坏。恒主应力差路径下的耗散能大于恒轴压路径下的耗散能的35%,卸荷速率越大,岩样的弹性应变能越小。