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.     

Bilayer-mediated assembly of cationic nanoparticles adsorbed to lipid bilayers: Insights from molecular simulations

Understanding interactions between functionalized gold nanoparticles (NPs) and lipid bilayers is essential for biomedical applications. Experiments have shown that NPs that are stable in solution can assemble into clusters when adsorbed to a lipid bilayer, suggesting that bilayer-mediated interactions facilitate assembly. In this work, we use coarse-grained molecular dynamics simulations to study bilayer-mediated interactions between NPs adsorbed to single- and multicomponent lipid bilayers. We perform unbiased simulations and umbrella sampling calculations using an implicit solvent force field to determine the thermodynamic contributions to assembly. We show that bilayer-mediated interactions drive the assembly of NPs into linear aggregates on liquid-disordered bilayers, which we attribute to a reduction in bilayer curvature. Similar bilayer-mediated interactions induce the alignment of NP clusters with phase boundaries in phase-separated bilayers. Together, these simulation results provide new physical insight into the balance of forces that dictate the assembly of charged NPs at multicomponent lipid bilayer interfaces.     

Volatile organic compound profiles of yoghurt produced from cow's milk with different somatic cell counts

The present study aimed to investigate the effect of somatic cell count (SCC) of raw cow's milk on the volatile organic compound (VOC) profiles of yoghurt. Test yoghurt samples were produced from three batches of cow's milk with low, medium and high SCC, respectively. The VOCs were determined by gas chromatography–mass spectrometry (GC–MS) analysis. A lower diacetyl and acetoin content and a higher content of 2‐heptanone, and butanoic and hexanoic acids were established in the yoghurt samples from batches with high SCC of above 1 000 000 cells/cm³. The increased SCC of cow's milk had a negative effect on the volatile organic compound profiles of yoghurt.     

1,5-己二烯交联烯烃聚合物的合成及其抗剪切稳定性

以金属配合物为催化剂、1,5-己二烯为交联剂,采用本体聚合法合成了交联超高相对分子质量烯烃类聚合物(简称交联聚合物)。用傅里叶变换红外光谱、核磁共振、凝胶渗透色潜表征交联聚合物的结构和相对分子质量。用旋转黏度计和超声波仪研究了1,5-己二烯用量对交联聚合物溶液表观黏度的影响及交联聚合物的相对分子质量对交联聚合物溶液抗剪切稳定性的影响。实验结果表明,在最佳聚合条件(单体80mL、助催化剂0．4mL、CS-1催化剂0．090g、1,5-己二烯0．40mL、0℃、24 b)下所合成的交联聚合物的重均相对分子质量为7．7×106,数均相对分子质量3．6×106。加入少量1,5-己二烯能提高交联聚合物的抗剪切能力,同时也能提高交联聚合物的相对分子质量。交联聚合物的相对分子质量越大,抗剪切稳定性越好。1,5-己二烯用量约为0．1 mL时(单体40 mL),交联聚合物溶液的表观黏度达到最大值(16．8 mPa·s)。     

高浓度聚合物驱提高采收率方法实验研究

为探索一种新的提高原油采收率的方法,在外形尺寸为4.5 cm×4.5 cm×30 cm、气测渗透率0.9~1.0μm2、变异系数为0.72的二维纵向非均质人造岩心上,模拟大庆油田油藏流体性质及温度条件,研究了高浓度聚合物(HPAM)驱注入时机、聚合物相对分子质量、聚合物段塞体积及段塞组合对驱油效果的影响。通过注入大分子量、高浓度聚合物,结合合理的注入方式,在化学剂成本与三元复合驱相当的情况下,采收率比水驱提高20个百分点以上,接近或超过三元复合驱的水平。实验表明,采用高浓度聚合物驱油是一种较好的提高原油采收率的方法。     

凝胶渗透色谱法测定基础油PAO的相对分子质量及分布

聚α-烯烃是一种性能优良的润滑油基础油，其相对分子质量及分布直接影响宏观性能。本研究建立了一种用于表征1-癸烯齐聚物相对分子质量及分布的方法。采用带示差折光检测器的凝胶渗透色谱系统，综合考虑分离效果和测试可操作性，优化了流动相流速和凝胶色谱柱的组合方式。以四氢呋喃为流动相，流速为0.8 mL/min，色谱柱组合方式为Styragel HR 0.5,Styragel HR 1,PLGEL 3μm MIXED-E三柱串联，以聚苯乙烯作为标准样品，采用普适校正方法处理色谱流出曲线。此方法测得样品的质均相对分子质量与凝胶渗透色谱-光散射法所测定结果相比较，相对误差相对偏差在3%以内。     

MD膜驱剂的粘土稳定性研究Ⅰ.静态试验

粘土的膨胀和分散是引起地层伤害的两个重要因素。通过测定Zeta电位、XRD、悬浮液透光率、FT-IR考察了MD膜驱剂（MDFFA）对粘土稳定性的作用。结果表明，MDFFA的浓度低于0．3 mmol／g（以蒙脱土质量计）时，蒙脱土悬浮液Zeta电位的提高是由于膜驱剂分子的吸附改变了蒙脱土的层电荷；高于此浓度时，Zeta电位进一步提高是由于双电层的压缩。随着MDFFA浓度的增大，蒙脱土的完全膨胀层向部分膨胀层转化，并且经水冲洗、浸泡后，其XRD谱峰位置变化不大。较高浓度的MDFFA，能有效地抑制蒙脱土的分散，且不会形成对地层有害的絮凝体。MDFFA使蒙脱土层间水的含量明显降低。     

RI/VI联用测定聚乙烯相对分子质量及其分布

150℃测试温度下，以1，2，4-三氯苯为溶剂，采用示差折光指数器，毛细管黏度计双检测器联用凝胶渗透色谱技术测定了聚乙烯的相对分子质量及其分布。与常规凝胶渗透色谱法对比，该方法不仅能直接得到聚乙烯较精确的相对分子质量和分布形态，同时可以得到聚乙烯的特性黏数分布。     

聚合物驱偏心分质注入技术

大庆油田主力油层聚驱结束后，聚驱驱替对象已转向渗透率更低、层间差异更大的二、三类油层，分注技术面临着新的矛盾。高渗透率油层需要控制注入量，同时要降低粘损率；低渗透油层要适当降低相对分子质量和粘度，以保证不堵塞油层又有足够的注入速度。为此，研究了聚合物驱偏心分质注入技术，可实现对分层相对分子质量、注入量的双重调节，并在注聚区块开展了现场试验，见到了明显效果。     

无油分子泵机组的组装

介绍了将ALCATEL公司生产的一台ATPl00涡轮分子泵、一台MDP50ll牵引分子泵及一台VRC公司生产的lBy6型干泵组装成无油分子泵机组的过程。文中给出了泵间配合的计算、机组方案的设计、连接管路、仪器支架的设计及选择。本机组所采取的设计方案使三个泵都最大限度地发挥了优点避免了缺陷，较好地满足了使用要求，为今后选购单泵和组装无油分子泵机组提供了可靠的理论和实验依据。