Methods and Applications of In Silico Aptamer Design and Modeling

Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.     

平面结构冗余并联机构的误差敏感度分析

针对一种含闭环支链的平面结构冗余并联机构进行误差敏感度分析。分析了该机构的逆运动学和正运动学。基于矩阵法建立了机构的误差模型，并通过反解、正解结合的方法对该误差模型进行了验证。基于误差模型，得到了评价机构误差敏感度的指标，绘制了各指标在工作空间内的等值线图。基于误差敏感度指标，定义了低误差敏感性工作空间，绘制了低误差敏感性工作空间在工作空间中的分布图。与平面3-RRR并联机构进行了误差敏感度对比分析。结果表明，该机构的低误差敏感性工作空间占比较大，同时可以通过调节其冗余支链不断扩大低误差敏感性工作空间，使机构在大范围空间中保持低误差敏感性。     

Computational Analysis of the Solid-State and Solvation Properties of Carbamazepine in Relation to its Polymorphism

The solvent-dependent polymorphism of the active pharmaceutical ingredient (API) carbamazepine is interpreted from calculations of the solid-state and API-solvent intermolecular interactions. These simulations suggested that apolar solute-solute interactions could be disrupted by apolar solvents. In contrast, the polar solute-solute interactions were found to be easily disrupted by polar and protic solvents. This is consistent with experimental observations that the crystallization of the metastable form II is more dominant in apolar solvents. The Mercury program remains the gold standard in terms of usability; however, further expansion into more complex simulation techniques could make this package of even greater use in pharmaceutical manufacturing workflows.     

Static stress analysis of carbon nano-tube reinforced composite (CNTRC) cylinder under non-axisymmetric thermo-mechanical loads and uniform electro-magnetic fields

Static stresses analysis of carbon nano-tube reinforced composite (CNTRC) cylinder made of poly-vinylidene fluoride (PVDF) is investigated in this study. Non-axisymmetric thermo-mechanical loads are applied on cylinder in presence of uniform longitudinal magnetic field and radial electric field. The surrounded elastic medium is modeled by Pasternak foundation because of its advantages to the Winkler type. Distribution of radial, circumferential and effective stresses, temperature field and electric displacements in CNTRC cylinder are determined based on Mori–Tanaka theory. The detailed parametric study is conducted, focusing on the remarkable effects of magnetic field intensity, elastic medium, angle orientation and volume fraction of carbon nano-tubes (CNTs) on distribution of effective stress. Results demonstrated that fatigue life of CNTRC cylinder will be significantly dependent on magnetic intensity, angle orientation and volume fraction of CNTs. Results of this research can be used for optimum design of thick-walled cylinders under multi-physical fields.     

Hygrothermal deformation of orthotropic nanoplates based on the state-space concept

This paper deals with the investigation of the effect of hygrothermal conditions on the bending of nanoplates using Levy type solution model employing the state-space concept. The nanoplates are assumed to be subjected to a hygrothermal environment. The two-unknown function plate theory is used to derive the governing differential equations on the basis of Eringen's nonlocal elasticity theory. The governing equations contain the small scale effect as well as hygrothermal and mechanical effects. These equations are converted into a set of first-order linear ordinary differential equations with constant coefficients. Analytical solution of bending response for nanoplates under combinations of simply supported, clamped and free boundary conditions is obtained. Comparison of the results with those being in the open literature is made. The influences played by small scale parameter, temperature rise, the degree of moisture concentration, boundary conditions, plate aspect ratio and side-to-thickness ratio are studied.     

Enhanced ionic conductivity and thermal shock resistance of MgO stabilized ZrO2 doped with Y2O3

The present work focused on the effect of Y₂O₃ co-doping on the phase composition, microstructure, ionic conductivity and thermal shock resistance of 8 mol% MgO stabilized ZrO₂ (Mg-PSZ) electrolyte ceramics for high temperature applications. The addition of Y₂O₃ could promote the process of monoclinic-to-cubic/tetragonal phase transformation and became the metastable phase at room temperature. Meanwhile, the grain size of Mg-PSZ decreased. It was demonstrated that an appreciable increase in the ionic conductivity and compressive strength occurred on substituting MgO with Y₂O₃ in the Mg-PSZ electrolyte ceramics across the measured temperature range. Moreover, the Y₂O₃ addition could restrain the adverse effect of the cyclic thermal shock on the ionic conductivity and compressive strength of Mg-PSZ. The main reason was that the increase of the amount of monoclinic phase caused by cubic/tetragonal-to-monoclinic phase transformation by the cyclic thermal shock was restrained after the Y₂O₃ addition.     

番禺30-1砂岩强水驱气藏储层非均质性研究

针对垂向非均质性严重且边底水能量强的番禺30-1气田面临的潜在开发问题，通过岩心分析及测井二次解释，对其夹层特征及储层非均质性等进行了研究，划分出19个流动单元并定量描述了各流动单元的特征参数，建立了该气田的精细地质模型。综合评价表明，新建的地质模型具有较高的精度，为该气藏合理开发提供了坚实的地质基础。     

国有科研单位人才流失原因分析及对策

近年来,国有科研单位,尤其是地处经济不发达地区的国有科研单位,出现了较为严重的人才流失现象,一定程度上影响和制约了国有科研单位的发展。通过对国有科研单位人才流失原因的分析,提出了相应的对策。     

炼油厂全流程优化建模方法研究

为了克服使用线性规划和单处理单元非线性规划进行生产优化的内在缺点，在建立原油单元、催化裂化、催化重整和汽油调合等4个重要处理单元详细模型的基础上，将单处理单元非线性过程模型集成到一个全流程优化非线性模型中。优化的目标函数是使炼油厂全厂利润最大。决策变量是那些显著影响全厂效益的变量，约束条件是单个处理单元约束条件的集合。对某炼油厂进行实例研究，结果表明该全流程模型能有效处理全厂优化问题，所得利润在线性规划的基础上提高4．5％。     

波动方程数值模拟的隐式差分法

在有限差分波动方程数值模拟中,通常采用高阶差分方法来提高空间导数的数值逼近精度,以实现降低数值频散,提高数值模拟精度的目的。首先对差分频散进行了理论分析;然后讨论了估计一阶空间导数的隐式差分格式,并与通常采用的高阶精度显式差分格式进行了对比分析,结果表明,隐式差分格式能够在更宽的波数范围使差分频散控制在可接受的水平,如8阶精度的显式差分格式所适应的波数带宽约为O．55kmax,而隐式差分格式所适应的波数带宽约为0．7kmax;最后通过模型试算,对隐式差分格式的有效性进行了验证。模拟结果表明,用隐式差分格式在一定程度上降低了差分频散,提高了模拟精度。