Atomistic insights into the selective therapeutic activity of 6-(2,4-difluorophenoxy)-5-((ethylmethyl)pyridine-3-yl)-8-methylpyrrolo[1,2-a]pyrazin-1(2H)-one towards bromodomain-containing proteins

Cross-target effect has been one of the major mechanisms of drug toxicity, this has necessitated the design of inhibitors that are specifically tailored to target particular biomolecules. 6-(2,4-difluorophenoxy)-5-((ethylmethyl)pyridine-3-yl)-8-methylpyrrolo[1,2-a] pyrazin-1(2H)-one (Cpd38) is an inhibitor possessing high inhibition rate and tailored specificity towards bromodomain-containing protein 4 (BRD4). In this research, we used an array of computational techniques to provide insight at the atomistic level the specific targeting of BRD4 by Cpd38 relative to the binding of Cpd38 with E1A binding protein P300 (EP300); another bromodomain-containing protein (BCP). Comparatively, binding of Cpd38 improved the conformational stability and compactness of BRD4 protein when compared to the Cpd38 bound EP300. Also, Cpd38 induced a conformational change in the active site of BRD4 that facilitated a complementary pose between Cpd38 and BRD4 suitable for effective atomistic interactions. Expectedly, thermodynamic calculations revealed that the Cpd38-BRD4 system had higher binding energy (−36.11 Kcal/mol) than the Cpd38-EP300 system with a free binding energy of −15.86 Kcal/mol. Noteworthy is the opposing role Trp81 (acting as hydrogen bond acceptor) and Pro1074 (acting as hydrogen bond donor) found on the WPF and LPF loops respectively play in maintaining Cpd38 stability. Furthermore, the hydrogen bond acceptor/donator ratio was approximately 4:1 in Cpd38-BRD4 system compared with 2:1 in Cpd38-EP300 system. Taken together, atomistic insights and structural perspectives detailed in this report supplements the experimental report supporting the improved selectivity of Cpd38 for BRD4 ahead of other BCPs while providing leeway for the future design of BET selective agents with better pharmacological profile.     

New insights into the anti-hepatoma mechanism of Alisol G-metal ions complexes based on c-myc DNA

This study investigated the anti-hepatoma molecular mechanism of Alisol G, which is an effective component of the Chinese medicine Alisma orientalis, in the presence of metal ions Cu²⁺ and Fe³⁺ based on c-myc DNA. Here, a combination of Alisol G and metal ions (Cu²⁺, Fe³⁺) to augment anti-hepatoma efficiencies of Alisol G has been identified by methyl thiazolyl tetrazolium (MTT) assay. Network pharmacology revealed that c-myc DNA was the potential target of Alisol G with respect to its anti-hepatoma effects. By performing multi-spectroscopic analyses, we showed that the interaction of Alisol G with c-myc DNA was a process of static quenching. The binding constants and thermodynamic constants indicated that a 1:1 complex was formed between Alisol G and c-myc DNA. Moreover, metal ions strengthened the interaction between Alisol G and c-myc DNA. Molecular docking and molecular dynamics simulation further unveiled that the higher binding affinity between Alisol G-Fe³⁺ complex and c-myc DNA as compared to Alisol G-Cu²⁺ complex. This probably resulted from the polarization of metal ions and the structural flexion of Alisol G. The C22-O31-H76 and C18-O32-H77 of Alisol G were key groups in the interaction with c-myc DNA. Addition of metal ion, had greatly changed the c-myc DNA-binding domain of Alisol G while didn’t affect the kinetic stability of the interaction, thus facilitating the insertion of Alisol G into c-myc DNA A-T base pair. Importantly, the DG113 of c-myc DNA was important for its binding to metal ions. Together, our findings suggested that Alisol G in combination with metal ions may be an efficient and promising option for the treatment of liver cancer.     

MoS2/SnS异质结太阳能电池的模拟研究

硫化亚锡(SnS)是一种Ⅳ-Ⅵ族层状化合物半导体材料,其禁带宽度与太阳能电池最佳带隙1.5 eV非常接近,并且在可见光范围内光的吸收系数很大(α>10⁴ cm^-1),因此SnS是一种很有应用前景的材料。本文利用太阳能电池模拟软件wxAMPS模拟了MoS₂/SnS异质结太阳能电池,主要研究SnS吸收层的厚度、掺杂浓度和缺陷态等因素对太阳能电池性能的影响。研究发现:SnS吸收层最佳厚度为2 μm,最佳掺杂浓度为1.0×10¹⁵ cm^-3;同时高斯缺陷态浓度超过1.0×10¹⁵ cm^-3时,电池各项性能参数随着浓度的增加而减小,而带尾缺陷态超过1.0×10¹⁹ cm^-3·eV^-1时,电池性能才开始下降;其中界面缺陷态对太阳能电池影响比较严重,界面缺陷态浓度超过1.0×10¹² cm^-2时,开路电压、短路电流、填充因子和转换效率迅速下降。另外,通过模拟获得的转换效率高达24.87%,开路电压为0.88 V,短路电流为33.4 mA/cm²。由此可知,MoS₂/SnS异质结太阳能电池是一种很有发展潜力的光伏器件结构。     

基于NPP-VIIRS夜间灯光数据的山西省GDP空间化模拟

选取山西省为研究对象，以美国国家极轨合作仪件-可见红外成像辐射计套件（NPP-VIIRS）夜间灯光数据、GDP统计数据等为数据源，构建GDP空间化拟合模型，建立山西省GDP密度图，据此研究山西省经济的空间差异性。通过对NPP-VIIRS夜间灯光数据的空间化处理，提取灯光指数，并将其与GDP进行回归拟合，建立最佳回归模型，得到GDP密度拟合图；利用县级GDP数据进行线性纠正，从而提高GDP的模拟精度。结果表明：（1）NPP-VIIRS夜间灯光数据与GDP的相关性较高，可用于山西省GDP模拟；（2）与GDP分区建模相比，GDP整体建模的精度更高；（3）山西省GDP的空间分布整体呈由城市中心逐渐向周边辐射的特点，构成GDP过渡带。     

基于人体损伤的中低速正面碰撞气囊点火状态分析方法研究

为降低驾驶员在中低速碰撞下受到的损伤, 利用2010年版丰田Yaris整车模型建立100%正面刚性壁碰撞有限元模型, 并根据驾驶员舱布置及相关法规要求建立Madymo约束系统仿真模型, 以验证有限元模型的准确性. 利用建立的碰撞模型, 在中低速碰撞中对不同气囊点火状态下的驾驶员所受损伤进行仿真. 结果表明, 该车型在35 km●h^-1及以上车速时, 点爆气囊能有效减少驾驶员损伤; 30 km●h^-1及以下车速时, 气囊点火会对驾驶员造成额外伤害; 中低速碰撞下, 驾驶员的胸部损伤程度较头部更容易受气囊点火时间影响.     

水化硅酸钙纳米压痕分子动力学模拟方法优化

针对水化硅酸钙纳米压痕模型忽视了压头与基底之间相互作用的问题，由尺寸差异引起的金刚石压头难以计算的问题，以及Wittmann模型无法得到实际接触面积的问题，提出了新的模型与计算方法．结合分子动力学方法，采用金刚石压头-Wittmann模型基底的组合方式构建无定形态水化硅酸钙纳米压痕试验模型．在建模阶段，考虑到压头模型与基底模型粒子间尺寸差异，提出了等比例替换模型，通过公式推导并就不同尺寸模拟结果验证了等比例替换模型的可行性．在计算阶段，提出了局部前处理的弛豫方法进行模拟．确定最大荷载位置处的接触面积为546 nm2，进而求出水化硅酸钙模型硬度H为0.84 GPa、折合模量Er为30.52 GPa．并通过纳米压痕试验，验证了模拟结果的准确性，证明了模型的科学性，对今后水化硅酸钙(C-S-H)纳米层面的模拟具有重要借鉴意义．     

染料敏化太阳能电池载流子传输的数值模拟

由于在染料敏化太阳能电池(dye-sensitized solar cell, DSSC)中存在染料弛豫、半导体薄膜中电子与氧化态染料分子发生反应和电子在电解质中与氧化态离子复合等不利反应,利用一个更完善的DSSC载流子传输模型对电池的光电性能进行模拟就显得非常重要。为此,本文基于由多重俘获理论建立的DSSC中的包括电子、染料阳离子、碘化物和三碘化物在内的载流子传输模型,数值模拟得到了不同TiO₂薄膜厚度、不同入射光强度与不同染料分子吸收系数下DSSC的J-V曲线。结果表明,随着TiO₂薄膜厚度的增加,太阳能电池的短路电流密度增大,开路电压减小,光电转换效率先增大后减小。当DSSC的TiO₂薄膜厚度为20 μm时,光电转换效率达到最大值7.41%,同时光电转换效率随入射光强度与染料分子吸收系数的增大均有一定程度提高,其中在吸收系数为4 500 cm^-1时,光电转换效率为6.73%。以上结果可以为改进DSSC的光电性能提供理论指导。     

Composition-dependent melting behaviour of NaxK55–x core–shell nanoalloys

Molecular dynamics simulations at constant temperature are performed to investigate melting-like transition in Na₁₃K₄₂, Na₁₉K₃₆ and Na₂₆K₂₉ nanoalloys using a second-moment-approximation tight-binding analytic potential to calculate the forces on the constituent atoms. A weighted histogram analysis method is employed to remove non-ergodicity issues due to the complex potential energy surface of these nanoalloys. The heat capacity shows three distinctive steps in melting for Na₁₃K₄₂, while Na₂₆K₂₉ and Na₁₉K₃₆ have two-step and one-step melting transition, respectively. The steepest descent method is used to quench the configurations in a given interval during the simulation and also study the isomerisation processes occurring at different temperatures. Analysing the configuration energies of quenched structures for the entire nanoalloy and the core atoms separately gives more details about the melting mechanism. The Lindemann parameter is also calculated at several temperatures during the simulation which shows a gradual increase for Na₁₃K₄₂ and Na₂₆K₂₉ while a sharp change is observed for Na₁₉K₃₆. These findings are in agreement with the multi-step nature of the phase transition in Na₁₃K₄₂ and Na₂₆K₂₉ and one-step melting of the Na₁₉K₃₆ magic composition.     

Molecular structure and properties of click hydrogels with controlled dangling end defect

In this study, controlled amount of dangling ends is introduced to the two series of poly(ethylene glycol)‐based hydrogel networks with three and four crosslinking functionality by using click chemistry. The structure of the gels with regulated defect percentage is confirmed by comparing the results of low‐field NMR characterization and Monte Carlo simulation. The mechanical properties of these gels were characterized by tensile stress–strain behaviors of the gels, and the results are analyzed by Gent model and Mooney–Rivlin model. The shear modulus of the swollen gels is found to be dependent on the functionality of the network, and decreases with the defect percentage. Furthermore, the value of shear modulus well obeys the Phantom model for all the gels with varied percentage of the defects. The maximum extension ratio, obtained from the fitting of Gent model, is also found to be dependent on the functionality of the network, and does not change with the defect percentage, except at very high defect percentage. The value of the maximum extension ratio is between that predicted from Phantom model and the Affine model. This indicates that at the large deformation, the fluctuation of the crosslinking points is suppressed for some extend but still exists. Polymer volume fractions at various defect percentages obtained from prediction of Flory–Rehner model are found to be in well agreement with the swelling experiment. All these results indicate that click chemistry is a powerful method to regulate the network structure and mechanical properties of the gels. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1227–1236     

Molecular dynamics simulation of poly(3‐hexylthiophene) helical structure In Vacuo and in amorphous polymer surrounding

The stability of poly(3‐hexylthiophene) (P3HT) helical structure has been investigated in vacuo and in amorphous polymer surrounding via molecular dynamics‐based simulations at temperatures below and above the P3HT melting point. The results show that the helical chain remains stable at room temperature both in vacuo and in amorphous surrounding, and promptly loses its structure at elevated temperatures. However, the amorphous surrounding inhibits the destruction of the helix at higher temperatures. In addition, it is shown that the electrostatic interactions do not significantly affect the stability of the helical structure. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2448–2456