Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations

Through the use of the one-step perturbation approach, 130 free energies of base stacking and 1024 free energies of base pairing in DNA have been calculated from only five simulations of a nonphysical reference state. From analysis of a diverse set of 23 natural and unnatural bases, it appears that stacking free energies and stacking conformations play an important role in pairing of DNA nucleotides. On the one hand, favourable pairing free energies were found for bases that do not have the possibility to form canonical hydrogen bonds, while on the other hand, good hydrogen-bonding possibilities do not guarantee a favourable pairing free energy if the stacking of the bases dictates an unfavourable conformation. In this application, the one-step perturbation approach yields a wealth of both energetic and structural information at minimal computational cost.     

Site‐Specifically Arraying Small Molecules or Proteins on DNA Using An Expanded Genetic Alphabet

A class of replicable unnatural DNA base pairs formed between d 5SICS and either d MMO2 , d DMO , or d NaM were developed. To explore the use of these pairs to produce site‐specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase‐mediated replication, and subsequent site‐specific modification of the amplified DNA by Click chemistry is reported. With the d 5SICS scaffold a propynyl ether linker is accommodated better than its aliphatic analogue, but not as well as the protected propargyl amine linker explored previously. It was also found that with the d MMO2 and d DMO analogues, the d MMO2 position para to the glycosidic linkage is best suited for linker attachment and that although aliphatic and ether‐based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogues, a variety of them were used to site‐selectively attach a biotin tag to the amplified DNA. Finally, we use d 5SICS^CO –d NaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps “evolution” of nanomaterials.     

A soft lithography method to generate arrays of microstructures onto hydrogel surfaces

Materials bearing microscale patterns on the surface have important biomedical applications such as scaffolds in tissue engineering, drug delivery systems, sensors, and actuators. Hydrogels are an attractive class of materials that has excellent biocompatibility, biodegradability, and tunable mechanical properties that meet the requirements of the aforementioned applications. Generating patterns of intricate microstructures onto the hydrogel surfaces, however, is challenging due to properties such as the crosslinking density, low mechanical strength, adhesion, or chemical incompatibility of hydrogels with various molds. Here, we report the use of a soft lithography technique to successfully transfer arrays of micropillars onto a poly(2‐hydroxyethyl methacrylate)‐based hydrogel. The swelling of the hydrogel in solvents, such as phosphate‐buffered saline, deionized water, 60% ethanol, and absolute ethanol, facilitates the reproducible replication of the pattern. Furthermore, the micropillar pattern promotes the attachment of HeLa cells onto this hydrogel which is not inherently adhesive when unpatterned. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 1144–1157     

Solid‐state NMR and EPR Spectroscopy of Mn2+‐Substituted ATP‐Fueled Protein Engines

Paramagnetic metal ions deliver structural information both in EPR and solid‐state NMR experiments, offering a profitable synergetic approach to study bio‐macromolecules. We demonstrate the spectral consequences of Mg²⁺/ Mn²⁺ substitution and the resulting information contents for two different ATP:Mg²⁺‐fueled protein engines, a DnaB helicase from Helicobacter pylori active in the bacterial replisome, and the ABC transporter BmrA, a bacterial efflux pump. We show that, while EPR spectra report on metal binding and provide information on the geometry of the metal centers in the proteins, paramagnetic relaxation enhancements identified in the NMR spectra can be used to localize residues at the binding site. Protein engines are ubiquitous and the methods described herein should be applicable in a broad context.     

带比例交易成本的投资组合选择

介绍了在完备市场下用鞅方法解决最优投资组合的问题．存在交易成本和交易约束的情况下，提出了用条件Delta对冲模型进行期权复制，最小化复制误差，得到最优对冲下的波动率，即调整后的波动率，再将调整后的波动率代替鞅方法下的投资组合波动率，就得到了存在交易成本和交易约束下的最优投资组合．通过Monte Carlo模拟的方法来计算最优投资组合．数值结果显示了交易成本和其他参数对最优投资组合策略的影响，并将其与完备市场下的投资组合进行了比较．     

Option Replication in Discrete Time with Illiquidity

Abstract

This article studies a replication of a contingent claim in an illiquid market. We represent the liquidity as a supply curve in a discrete time model. Because the trade price of the illiquid asset is a function of the trade size in this model, it is important whether the contingent claim is physically settled or settled in cash. In both cases, we give a condition where a replication strategy exists uniquely and show some properties of the replication strategy. Further we analyse the liquidity cost numerically.     

Systems Chemistry: Logic Gates,Arithmetic Units,and Network Motifs in Small Networks

How much “systems chemistry” really exists within small networks? To answer this question, the authors study tertiary networks that facilitate molecular replication through all Boolean logic operations and show how such gates can be wired together to perform computational and feed‐forward based network motifs (see graphic).

     

用复制法制作的轻质金属反射镜

本文简单介绍复制轻质金属反射镜的方法,从应用角度着重分析了用复制方法制作的轻质金属反射镜的主要优缺点,并提出了改进方法。     

Statistical mechanics of Eigen's evolution model

The correspondence between Eigen's model of macromolecular evolution and the equilibrium statistical mechanics of an inhomogeneous Ising system is developed. The free energy landscape of random Ising systems with the Hopfield Hamiltonian as a special example is applied to the replication rate coefficient landscape. The coupling constants are scaled with 1/l, since the maxima of any landscape must not increase with the length of the macromolecules. The calculated error threshold relation then agrees with Eigen's expression, which was derived in a different way. It gives an explicit expression for the superiority parameter in terms of the parameters of the landscape. The dynamics of selection and evolution is discussed.