Investigating conformational changes of Prefoldin β1 as result of applying external mechanical force without any position constraint

Manipulating molecular scale bio‐nanorobots and influencing their behaviour is one of the major challenges of new researches. Many coiled coil type proteins are involved in important biological functions due to physical properties that make them ideal for both nanoscale manipulation and sensing. The Prefoldin beta subunit from Thermococcus strain KS‐1(Prefoldin β1) is one of the possible proteins that can serve as a new bio‐nano‐actuator. Besides having a balanced architecture, Prefoldin β1 can exhibit a wide range of exclusive authorities. In this study, steered molecular dynamics simulation is applied along with the centre of mass pulling and analyses of Prefoldin β1 conformational changes to characterise some of those abilities. Thus, applying external mechanical force without any position constraint shows that it has no movement throughout simulations. This proposes a novel method to capture different sizes and shapes of cargoes. During simulations, each arm was found to be very flexible, allowing it to enlarge its central cavity and capture different cargoes. For a more accurate analysis, the variations in the cavity of nano‐actuator are investigated qualitatively and quantitatively with different parameters. Also, the force analysis of the arms can provide us with decent information about the performance of this nano‐actuator.Inspec keywords: nanobiotechnology, proteins, molecular biophysics, microrobots, molecular dynamics method, biological techniquesOther keywords: external mechanical force, coiled coil type proteins, nanoscale manipulation, Thermococcus strain KS‐1, steered molecular dynamics simulation, prefoldin beta subunit, bionanoactuator, prefoldin β1 conformational changes, molecular scale bionanorobots, centre‐of‐mass pulling     

Tunable Two‐Dimensional Binary Molecular Networks

A novel approach to constructing tunable and robust 2D binary molecular nanostructures on an inert graphite surface is presented. The guest molecules are embedded into a host molecular matrix and constrained via the formation of multiple intermolecular hydrogen bonds. By varying the binary molecular ratio and the molecular geometry, various molecular arrays with tunable intermolecular distances are fabricated. The results suggest a promising route for the fabrication of ordered and stable molecular nanostructure arrays for molecular sensors, molecular spintronic devices, and molecular p–n nanojunctions.     

Semi-artificial Fluorescent Molecular Machine for DNA Damage Detection

The design of artificial molecular machines is complicated because the mechanics used in macromachines is not readily adaptable for nano environments. We constructed a semi-artificial molecular device, which contains a naturally occurring molecular machine-a vaccinia virus encoded protein-linked with an artificial part. The self-assembled construct makes two fluorescently labeled detector units. It is the first sensor capable of selectively detecting different types of DNA breaks, exemplifying a practical approach to the design of molecular devices.     

Design and assembly of rotaxane-based molecular switches and machines

Mechanically interlocked molecules, such as catenanes and rotaxanes, are at the heart of the development of molecular machines chemistry. They are able to self-organize, self-assemble, and self-control themselves into new materials with potential application as molecular devices. In this review, an overview of some recent progress on molecular machines is given, including new methodologies for their synthesis and self-assembly and their recent applications as dual or multilevel fluorescent molecular switches, as potential sensors, and even as a molecular-level transporter. In one development, a molecular machine containing a charge-transfer chromophore was designed to generate controllable aggregate structures through the reversible movement of a macrocycle over a thread; this was done in order to better understand the application of a molecular shuttle in solid state. Light is shed on how the novel properties and functions of molecular machines are extended, and examples of the ways in which molecular machines have been applied to the design and process of intelligentized systems are provided.     

Monitoring the Dynamic Process of Formation of Plasmonic Molecular Junctions during Single Nanoparticle Collisions

The capability to study the dynamic formation of plasmonic molecular junction is of fundamental importance, and it will provide new insights into molecular electronics/plasmonics, single‐entity electrochemistry, and nanooptoelectronics. Here, a facile method to form plasmonic molecular junctions is reported by utilizing single gold nanoparticle (NP) collision events at a highly curved gold nanoelectrode modified with a self‐assembled monolayer. By using time‐resolved electrochemical current measurement and surface‐enhanced Raman scattering spectroscopy, the current changes and the evolution of interfacial chemical bonding are successfully observed in the newly formed molecular tunnel junctions during and after the gold NP “hit‐n‐stay” and “hit‐n‐run” collision events. The results lead to an in‐depth understanding of the single NP motion and the associated molecular level changes during the formation of the plasmonic molecular junctions in a single NP collision event. This method also provides a new platform to study molecular changes at the single molecule level during electron transport in a dynamic molecular tunnel junction.     

Tuning structural and mechanical properties of two-dimensional molecular crystals: the roles of carbon side chains

A key requirement for the future applicability of molecular electronics devices is a resilience of their properties to mechanical deformation. At present, however, there is no fundamental understanding of the origins of mechanical properties of molecular films. Here we use quinacridone, which possesses flexible carbon side chains, as a model molecular system to address this issue. Eight molecular configurations with different molecular coverage are identified by scanning tunneling microscopy. Theoretical calculations reveal quantitatively the roles of different molecule-molecule and molecule-substrate interactions and predict the observed sequence of configurations. Remarkably, we find that a single Young's modulus applies for all configurations, the magnitude of which is controlled by side chain length, suggesting a versatile avenue for tuning not only the physical and chemical properties of molecular films but also their elastic properties.     

Coupled surface-enhanced Raman spectroscopy and electrical conductivity measurements of 1,4-phenylene diisocyanide in molecular electronic junctions

Probing the structure of molecules in a metal-molecule-metal junction under an applied voltage is critical for understanding molecular electron transport properties. We present an approach that allows recording surface-enhanced Raman spectra simultaneously with electrical measurements of a monolayer of molecules in molecular electronic junctions. 1,4-Phenylene diisocyanide in two different types of junctions was used to illustrate the approach. The results show that the molecular integrity was intact in the molecular junctions and under the applied bias. The monolayer sensitivity of the approach provides a new powerful tool for characterizing molecular structure in a molecular electronic junction.     

Molecular imaging perspectives.

Molecular imaging is an emerging technology at the life science/physical science interface which is set to revolutionize our understanding and treatment of disease. The tools of molecular imaging are the imaging modalities and their corresponding contrast agents. These facilitate interaction with a biological target at a molecular level in a number of ways. The diverse nature of molecular imaging requires knowledge from both the life and physical sciences for its successful development and implementation. The aim of this review is to introduce the subject of molecular imaging from both life science and physical science perspectives. However, we will restrict our coverage to the prominent in vivo molecular imaging modalities of magnetic resonance imaging, optical imaging and nuclear imaging. The physical basis of these imaging modalities, the use of contrast agents and the imaging parameters of sensitivity, temporal resolution and spatial resolution are described. Then, the specificity of contrast agents for targeting and sensing molecular events, and some applications of molecular imaging in biology and medicine are given. Finally, the diverse nature of molecular imaging and its reliance on interdisciplinary collaboration is discussed.     

线型高分子无规交联和裂解的一个动力学模型

建立了线型高分子无规交联和裂解的一个动力学模型。通过模型,推导了一级反应的数均分子量的计算公式,探讨了交联和裂解速率对最终产物数均分子量的影响,以及在纯交联过程中,起始分子量分布对凝胶化时间的影响。文中指出,无规裂解的Simha模型仅仅是本模型中的一个特例。     

Nanocell logic gates for molecular computing

Molecular electronics seeks to build electrical devices to implement computation - logic and memory - using individual or small collections of molecules. These devices have the potential to reduce device size and fabrication costs, by several orders of magnitude, relative to conventional CMOS. However, the construction of a practical molecular computer will require the molecular switches and their related interconnect technologies to behave as large-scale diverse logic, with input/output wires scaled to molecular dimensions. It is unclear whether it is necessary or even. possible to control the precise regular placement and interconnection of these diminutive molecular systems. This paper describes genetic algorithm-based simulations of molecular device structures in a nanocell where placement and connectivity of the internal molecular switches are not specifically directed and the internal topology is generally disordered. With some simplifying assumptions, these results show that it is possible to use easily fabricated nanocells as logic devices by setting the internal molecular switch states after the topological molecular assembly is complete. Simulated logic devices include an inverter, a NAND gate, an XOR gate and a 1-bit adder. Issues of defect and fault tolerance are addressed.     

Single-molecule chiral recognition on a surface by chiral molecular tips

Chiral surfaces attract increasing interest due to their vital role in a variety of scientific fields, such as chiral separation and heterogeneous enantioselective catalysis. The most urgent issue in research on such two-dimensional chirality is a lack of methodologies that recognize molecular chirality on a surface. Here we show that the chiral molecular tips enable for the first time discrimination of enantiomers on a single-molecule basis. The chiral selectivity is attributed to favorable chemical interactions that the molecular tips form with only one of two enantiomers. The stereoselective observation reveals spatial distribution of the enantiomers on a surface at the molecular level. The chiral molecular tips open a way for control of organization of enantiomers toward the advanced functionality of these chiral surfaces through knowledge on pivotal roles of chirality on molecular assemblies as shown here.     

Advances in Molecular Electronics: A Brief Review

The field of molecular electronics, also known as moletronics, deals with the assembly of molecular electronic components using molecules as the building blocks. It is an interdisciplinary field that includes physics, chemistry, materials science, and engineering. Moletronics mainly deals with the reduction of size of silicon components. Novel research has been performed in developing electrical-equivalent molecular components. Moletronics has established its influence in electronic and photonic applications, such as conducting polymers, photochromics, organic superconductors, electrochromics, and many more. Since there is a need to reduce the size of the silicon chip, attaining such technology at the molecular level is essential. Although the experimental verification and modeling of molecular devices present a daunting task, vital breakthroughs have been achieved in this field. This article combines an overview of various molecular components, such as molecular transistors, diodes, capacitors, wires, and insulators, with a discussion of the potential applications of different molecules suitable for such components. We emphasize future developments and provide a brief review of different achievements that have been made regarding graphene-based molecular devices.     

Coherent collective precession of molecular rotors with chiral propellers

Successful attempts to manufacture synthetic molecular motors have recently been reported. However, compared with natural systems such as motor proteins, synthetic motors are smaller molecules and are therefore subject to thermal fluctuations that prevent them from performing any useful function. A mechanism is needed to amplify the single molecular motion to such a level that it becomes distinguishable from the thermal background. Condensation of molecular motors into soft ordered phases (such as liquid crystals) will be a feasible approach, because there is evidence that they support molecularly driven non-equilibrium motions. Here we show that a chiral liquid-crystalline monolayer spread on a glycerol surface acts as a condensed layer of molecular rotors, which undergo a coherent molecular precession driven by the transmembrane transfer of water molecules. Composed of simple rod-like molecules with chiral propellers, the monolayer exhibits a spatiotemporal pattern in molecular orientations that closely resembles 'target patterns' in Belousov-Zhabotinsky reactions. Inversion of either the molecular chirality or the transfer direction of water molecules reverses the rotation direction associated with switching from expanding to converging target patterns. Endowed only with the soft directional order, the liquid crystal is an optimal medium that helps molecular motors to manifest their individual motions collectively.     

Shrinkage as a measure of the deformation efficiency of ultra-oriented high density polyethylene

A simple test is described that allows the evaluation of the molecular extension in solid state extruded high density polyethylene at maximum extrusion draw ratio 36. The samples, which were prepared by shaving the extrudates to films of average thickness 0.4 mm, were melted very rapidly and shrunk at 160° C. Experimental evidence shows that at high heating rates (800° C min⁻¹) all the molecular extension is recovered elastically. The variation of shrinkage with molecular weight indicates a difference in the molecular extension produced during the extrusion, and a simple relationship between molecular draw ratio and modulus is considered.     

Detection of High Molecular Weight Narrow Polydisperse Polymers up to 1.5 Million Daltons by MALDI Mass Spectrometry

The detection of very high molecular weight narrow polydisperse poly(styrene) samples by MALDI time-of-flight mass spectrometry is reported. It is shown that accurate molecular weight determinations of samples up to 1 million can be achieved very rapidly from the singly charged polymeric species. For a poly(styrene) with a molecular weight of approximately 1.5 million, signals corresponding to the multiply charged ions of the principal distribution are observed. The molecular weights obtained by MALDI are in good agreement with classical molecular weight determination techniques. all-trans-Retinoic acid was used as the organic matrix for the laser desorption procedure, and the samples were analyzed as their silver cation adducts. This work demonstrates that, with proper matrix selection and sample preparation, MALDI can be a very useful tool for high molecular weight polymer sample analysis.     

液氮温度下分子筛的真空吸附特性试验研究

为探究低温容器夹层所用分子筛吸附剂的吸附特性,采用静态膨胀法进行试验,获得了平衡压力为10-3Pa～103Pa范围内4A、5A和13X分子筛对N2、O2单一组分以及空气的吸附等温线,比较了不同分子筛对气体的吸附能力差异,探究了分子筛的吸附机理.研究结果表明:液氮温度下,5A和13X分子筛在真空条件下对N2及O2的吸附性...     

A liftoff technique for molecular nanopatterning

For quantum-dot cellular automata molecular electronic devices, one of the fundamental tasks is to arrange the molecules on a surface in a controlled manner. In this report, we discuss a molecular lift off technique to form nanopatterns toward the development of molecular circuits. In our molecular lift off technique, we use electron beam lithography to form nano-trenches on a polymethylmethacrylate (PMMA) film on a SiO2 wafer. This wafer is soaked in a Creutz-Taube ion [(NH3)5Ru(pyrazine)Ru(NH3)5](o-toluenesulfonate)5 (CT5) aqueous solution. After residual PMMA removal, atomic force microscopy is used to investigate the resulting surface. Thirty-five nanometer CT5 lines are demonstrated on a SiO2 surface. Compared with other molecular nanopatterning techniques, ours is both economical and capable of high-resolution.     

High-fidelity formation of a molecular-junction device using a thickness-controlled bilayer architecture

The device yield of molecular junctions has become a major issue for the practical application of molecular electronics based on a crossbar system of a metal-molecule-metal (MMM) junction. As the thickness of self-assembled monolayers (SAMs) is typically 1-2 nm, it is difficult to avoid electrical shorts due to the penetration of top metal particles into the SAMs. A simple and effective strategy for the creation of a reliable molecular junction using a thickness-controlled bilayer with a bifunctional heterostructure is presented. In the MMM device, the Au adlayer on the molecular layer is spontaneously formed with deposition of the top Au metals and the sandwiched molecular layer maintains the quality of the SAMs. This method greatly reduces electrical shorts by preventing the diffusion of the top metal electrode and offsetting the surface roughness of the bottom metal electrode, resulting in a device yield of more than 90%.     

Spin-polarized current of a transistor in single Mn12 molecular magnets

Focusing on the framework of how to realize the molecular spintronics in a single molecular magnet, we present theoretical studies on the spin-polarized quantum transport behavior through a single Mn12 molecular magnet. Our theoretical results were obtained by carrying out density functional theoretical calculation within the Keldysh nonequilibrium Green function formalism. The ultimate goal of the molecular spintronics is to develop single molecule transistors which generate spin-polarized currents through the molecular magnet. We obtained the density of states, the transmission coefficients and the characteristic features of the current-voltage (I-V) on the spin-polarized transport properties of Mn12 by the theoretical calculation. These results show the possibility for the realization of molecular spintroinics using single molecular magnets.     

乙烯在不同结构PE/分子筛膜中的吸附蒙特卡洛模拟

目的利用蒙特卡洛法模拟分析基体PE的结构变化对其吸附乙烯的影响,从微观角度展现新型活性包装材料PE/分子筛膜对乙烯的吸收过程,揭示微观吸收机理。方法通过MaterialsStudio软件分别构建不同聚合度和分子链数目的 PE/分子筛高分子模型,采用蒙特卡洛法模拟PE/分子筛体系对乙烯的吸附过程,并绘制吸附等温线来分析吸附效果。结果 PE/分子筛体系对乙烯的吸附量随聚合度的增加而减小,随分子链数目的增加而增加;达到吸附平衡后,吸附量在一定范围内存在明显的波动。结论基体结构对活性包装材料PE/分子筛膜的吸收效果有较大的影响。在相同条件下,以低聚合度和多分子链数目结构形成的PE/分子筛包装体系更有利于对乙烯的吸附,且该吸附平衡是一个吸附与脱吸同时发生的动态平衡。