Analytical investigation of transient molecular-motor-assisted transport in elongated cells

This paper investigates analytically the molecular-motor-assisted transport between the cell nucleus and cell membrane in an elongated cell, which allows the formulation of governing equations in a cylindrical coordinate system. This problem is relevant to biomimetic transport systems as well as to many biological processes occurring in living cells, such as the viral infection of a cell. The obtained analytical solution is shown to agree well with a high-accuracy numerical solution of the same problem. The developed analytical technique extends the applicability of the generalized Fourier series method to a new type of problems involving intracellular transport of organelles.      

导线非共线的分子器件输运性质的第一性原理研究

分子器件是电子器件向小体积化发展的极限,分子器件中的电子在输运过程中体现出明显的量子效应,分子导线与分子接触的位置和导线间的角度等器件结构因素都会对分子器件的输运性质产生较大的影响.迄今为止,尚未见利用第一性原理量子输运计算方法研究导线非共线的分子器件输运性质的报道.本文以金-苯(硫醇)-金结构的分子器件为例,利用基于非平衡格林函数理论和密度泛函理论的第一性原理量子输运计算方法对其输运性质进行了系统研究,特别注重于研究随着非共线导线间导线夹角角度的变化及导线和苯(硫醇)分子接触位置的不同对器件输运性质的影响.计算表明,金导线与苯(硫醇)的接触位置及导线的夹角等器件结构细节不仅能够定量地影响金-苯(硫醇)-金分子器件的电流大小,还能够定性地改变器件的输运性质,使得部分器件结构出现负微分电阻效应.研究结果对全面理解分子器件的输运性质具有一定的指导意义.     

First-principle studies of I–V properties of a molecular wire

The elastic scattering Green function method has been developed to describe the I–V characteristics of molecular wires. The molecular electronic structure and the interaction between the molecule and the gold surface are two key factors for the charge transport properties of molecular wires in the formulas. Anab initio calculation at the hybrid density functional theory level is carried out to obtain the electronic structure of 4-4′-dimercaptodibenzene molecule. The frontier orbit theory and the perturbation theory are employed to determine the constant of the interaction energy between molecule and surface quantitatively. The numerical results show that the bonding between the sulfur atom and the gold atoms corresponds mainly to the covalent bond. Some molecular orbits are extended over molecule and gold cluster that certainly give channels for the charge transport, other molecular orbits are localized and the charge transport can take place by tunnel mechanism. At zero bias region, there exists a current gap. With the increasing bias, the conductance of the wire takes a shape of plateaus.     

In-Silico Study on the Interaction of Saffron Ligands and Beta-Lactoglobulin by Molecular Dynamics and Molecular Docking Approach

Safranal, crocetin, and dimethylcrocetin are secondary metabolites found in saffron and have a wide range of biological activities. An investigation of their interaction with a transport protein, such as β-lactoglobulin (β-lg), at the atomic level could be a valuable factor in controlling their transport to biological sites. The interaction of these ligands and β-lg as a transport protein was investigated using molecular docking and molecular dynamics (MD) simulation methods. The molecular docking results showed that safranal and crocetin bind on the surface of β-lg. However, dimethylcrocetin binds in the internal cavity of β-lg. The β-lg affinity for binding saffron ligands decreases in the following order: crocetin > dimethylcrocetin > safranal. The analysis of MD simulation trajectories showed that the β-lg and β-lg–ligand complexes became stable at approximately 3000 ps and that there was little conformational change in the β-lg–safranal and β-lg–dimethylcrocetin complexes over a 10-ns timescale. In addition, the profiles of atomic fluctuations showed the rigidity of the ligand binding site during the simulation time.     

In Silico Study on the Interaction of Thiazolidinediones and β-Lactoglobulin by Molecular Dynamics and Docking Approach

Thiazolidinediones are widely used in the treatment of diabetes mellitus type 2. An investigation of their interaction with a transport protein, such as β-lactoglobulin (BLG), at the atomic level could be a valuable factor in controlling their transport to biological sites. The interaction of troglitazone, pioglitazone, and rosiglitazone, as representative thiazolidinediones, and BLG, as a transport protein, was investigated using molecular docking and molecular dynamics (MD) simulation methods. The molecular docking results showed that these thiazolidinediones bind to the internal cavity of BLG and the BLG affinity for binding the thiazolidinediones decreases in the following order: troglitazone > pioglitazone > rosiglitazone. The analysis of MD simulation trajectories showed that the BLG and BLG-thiazolidinedione complexes became stable at approximately 2500 ps and that there was little conformational change in the BLG-thiazolidinedione complexes over a 10 ns timescale. In addition, the profiles of atomic fluctuations showed the rigidity of the ligand-binding site during the simulation time.     

以石墨烯为电极的有机噻吩分子整流器的设计及电输运特性研究

传统硅基半导体器件受到了量子尺寸效应的限制,发展分子电子学器件有可能解决这一难题.本文提出了由石墨烯电极和有机噻吩分子相结合构造分子器件的思想,建构了"石墨烯-噻吩分子-石墨烯"结构的分子器件,并运用非平衡态格林函数结合密度泛函理论的方法研究了其电输运特性.系统地分析了电子给体"氨基"和电子受体"硝基"两种取代基的位置对有机噻吩分子电输运的影响.计算表明,有机噻吩二聚物被"氨基"和"硝基"取代后会产生明显的负微分电阻效应和整流效应.进一步对产生这些效应的物理机制进行分析,发现氨基的位置可以调整负微分电阻的强弱,硝基的位置可以改变整流的方向.     

棱形石墨烯纳米孔道内离子传输性能的分子动力学模拟

纳米通道的尺寸、结构和表面化学对其内部溶液的分布结构和输运性质有着重大影响.本文研究了一种全新的菱形石墨烯纳米通道.这种理想的通道与最近被广泛研究的金属有机框架材料(MOF)的内部结构类似,有着与传统的碳纳米管截然不同的内部结构.本文使用分子动力学模拟的方法研究在不同尺寸的菱形石墨烯纳米通道内的KCl溶液的性质,并将其与同尺寸的单壁碳纳米管进行了比较.研究结果表明在小孔道内(<20?)其内部的溶液结构呈现若干个密度极高的聚集区域,即出现了结晶化的趋势．这一研究结果,将为MOF的结构设计提供思路,从而有望实现类似于生物离子通道的高选择性和高传输能力.     

Effect of crystallographic orientations on transport properties of methylthiol-terminated permethyloligosilane molecular junction

The understanding of the influence of electrode characteristics on charge transport is essential in the field of molecular electronics. In this work, we investigate the electronic transport properties of molecular junctions comprising methylthiol-terminated permethyloligosilanes and face-centered crystal Au/Ag electrodes with crystallographic orientations of (111) and (100), based on the ab initio quantum transport simulations. The calculations reveal that the molecular junction conductance is dominated by the electronic coupling between two interfacial metal-S bonding states, which can be tuned by varying the molecular length, metal material of the electrodes, and crystallographic orientation. As the permethyloligosilane backbone elongates, although the σ conjugation increases, the decreasing of coupling induced by the increasing number of central Si atoms reduces the junction conductance. The molecular junction conductance of methylthiol-terminated permethyloligosilanes with Au electrodes is higher than that with Ag electrodes with a crystallographic orientation of (111). However, the conductance trend is reversed when the electrode crystallographic orientation varies from (111) to (100), which can be ascribed to the reversal of interfacial coupling between two metal-S interfacial states. These findings are conducive to elucidating the mechanism of molecular junctions and improving the transport properties of molecular devices by adjusting the electrode characteristics.     

On the viscosity and thermal conductivity of dense gases

The modified Enskog theory (MET) of transport in dense gases can be used to predict the density dependence of transport coefficients provided the function y, which is a product of a dimensionless density and a pair correlation function, is known as a function of density. In this communication we consider the inverse problem, extracting information on the y function from measured transport property data, both to resolve some peculiarities found by others, and to provide the basis for improved MET predictions.     

Organic field effect transistor composed by fullerene C60 and heterojunctions

We present a study of the complex electronic behavior of a fullerene (C₆₀) molecule attached to six leads (heterojunctions), which works as a three-dimension rectifier. In addition, we confirmed that the fullerene works not only as an electron donor, but also as barrier and transport channel to electrons through the molecule. Moreover, when the phenylpropanodinilla (PPP) lead is orthogonally subjected to bias voltage, the charge distribution and the current displays regions of saturation and resonance similar to semiconductor devices. In order to understand the electronic transport in the molecule, we applied non-equilibrium green function (NEGF) method and performed Fowler-Nordheim (FN) and Millikan-Lauritsen (ML) analyses. The ML curves proved to be sufficient to describe the FN characteristics. In this work, we report the theoretical design for electronic transport of a 3D device (6-terminal).     

Computational transport methodology based on decomposition of a problem domain into transport and diffusive subdomains

A large class of radiative transfer and particle transport problems contain highly diffusive regions. It is possible to reduce computational costs by solving a diffusion problem in diffusive subdomains instead of the transport equation. This enables one to decrease the dimensionality of the transport problem. In this paper we present a methodology for decomposition of a spatial domain of a transport problem into transport and diffusion subregions. We develop methods for solving one-group problems in 1D slab geometry. To identify and locate diffusive regions, we develop metrics for measuring transport effects that are based on the quasidiffusion (Eddington) factor. We present the results of test problems that demonstrate the accuracy of the proposed methodology.     

Modeling transport through single-molecule junctions

Non-equilibrium Green's functions (NEGF) formalism combined with extended Hückel (EHT) and charging model are used to study electrical conduction through single-molecule junctions. The analyzed molecular complex is composed of the asymmetric 1,4-Bis((2′-para-mercaptophenyl)-ethinyl)-2-acetyl-amino-5-nitrobenzene molecule symmetrically coupled to two gold electrodes. Owing to this model, the accurate values of the current flowing through such junctions can be obtained by utilizing basic fundamentals and coherently deriving model parameters. Furthermore, the influence of the charging effect on the transport characteristics is emphasized. In particular, charging-induced reduction of conductance gap, charging-induced rectification effect and charging-generated negative value of the second derivative of the current with respect to voltage are observed and examined for the molecular complex.     

Computational Studies on the Interaction of Arctiin and Liquiritin With β-lactoglobulin

The study of the interaction of drugs purified from natural sources and a transport protein, such as β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to study the interaction of arctiin and liquiritin as natural drugs and BLG as the transport protein. The molecular docking results indicated that these drugs bind in the internal cavity of BLG and the BLG affinity for binding the liquiritin is greater than arctiin. The docking results also indicated that the hydrogen bond interactions have a dominant role in the BLG-drug complex stability. The analysis of MD simulation trajectories showed that the root mean square deviation (RMSD) of BLG-liquiritin, unliganded BLG, and BLG-arctiin reached equilibrium and fluctuated around the mean value at about 1000, 3500, and 4000 ps, respectively. The time evolution of the radius of gyration and total solvent accessible surface of the protein showed that BLG-arctiin and BLG-liquiritin complexes became stable around 2500 and 5000 ps, respectively. Also, the profiles of atomic fluctuations during the simulation showed the rigidity of the ligand binding sites.     

A simplified tether model for molecular motor transporting cargo

Molecular motors are proteins or protein complexes which function as transporting engines in biological cells. This paper models the tether between motor and its cargo as a symmetric linear potential. Different from Elston and Peskin's work for which performance of the system was discussed only in some limiting cases, this study produces analytic solutions of the problem for general cases by simplifying the transport system into two physical states, which makes it possible to discuss the dynamics of the motor--cargo system in detail. It turns out that the tether strength between motor and cargo should be greater than a threshold or the motor will fail to transport the cargo, which was not discussed by former researchers yet. Value of the threshold depends on the diffusion coefficients of cargo and motor and also on the strength of the Brownian ratchets dragging the system. The threshold approaches a finite constant when the strength of the ratchet tends to infinity.     

First-principle studies of I-V properties of a molecular wire

The elastic scattering Green function method has been developed to describe the I-V characteristics of molecular wires. The molecular electronic structure and the interaction between the molecule and the gold surface are two key factors for the charge transport properties of molecular wires in the formulas. An ab initio calculation at the hybrid density functional theory level is carried out to obtain the electronic structure of 4-4′-dimercaptodibenzene molecule. The frontier orbit theory and the perturbation theory are employed to determine the constant of the interaction energy between molecule and surface quantitatively. The numerical results show that the bonding between the sulfur atom and the gold atoms corresponds mainly to the covalent bond. Some molecular orbits are extended over molecule and gold cluster that certainly give channels for the charge transport, other molecular orbits are localized and the charge transport can take place by tunnel mechanism. At zero bias region, there exists a current gap. With the increasing bias, the conductance of the wire takes a shape of plateaus.     

Role of mesoscopic morphology in charge transport of doped polyaniline

In doped polyaniline (PANI), the charge transport properties are determined by mesoscopic morphology, which in turn is controlled by the molecular recognition interactions among polymer chain, dopant and solvent, Molecular recognition plays a significant role in chain conformation and charge delocalization. The resistivity of PANI doped by camphor sulfonic acid (CSA)/2-acrylo-amido-1-propane sulfonic acid (AMPSA)/dodecyl benzene sulfonic acid (DBSA) is around 0.02 Ω cm. PANI-CSA and PANI-AMPSA show a metallic positive temperature coefficient of resistivity above 150 K. with a finite value of conductivity at 1.4 K; whereas, PANI-DBSA shows hopping transport at low temperatures. The magnetoresistance is positive (negative) for PANI-CSA (PANI-AMPSA); and PANI-DBSA has a large positive MR. The behavior of MR suggests subtle variations in mesoscopic morphology between PANI-CSA and PANI-AMPSA.     

分子结电学特性的理论研究

在第一性原理的基础上，对共扼分子2-氨基-5-硝基-1，4-二乙炔基-4’，-苯硫醇基苯(2-amino-5-nitro-1,4-diethyny-4’-benzenethiol-benzene)与金表面形成的分子结的电学特性进行了理论研究.利用密度泛函理论计算了该分子及扩展分子的电子结构；讨论了分子与金表面的相互作用，定量地确定了耦合常数，求出了电子的迁移强度；利用弹性散射格林函数法研究了该分子结的伏—安特性.计算结果表明，当外加偏压小于0.9V时分子结存在电流禁区，随着偏压升高，分子结的电导出现平台特 关键词： 化学吸附 分子结 分子电子学     

分子聚集溶液理论及其应用

本文应用经典热力学和分子热力学方法建立了分子聚集溶液理论。该理论具有通用性；它不仅适用于非电解质溶液，而且也可应用于电解质溶液。另外，溶液的分子聚集度参数与组分浓度的相关性规律还可用来描述电解质溶液的传递性质。     

液体水银在碳纳米管中传输的压力控制模型

碳纳米管在纳米技术中有一个很重要的应用,就是它可以作为纳米管道传输液体. 本文用分子动力学模拟方法,结合一个液体压力控制模型,对液体水银由于外部压力作用在碳纳米管中传输的现象进行研究. 研究结果表明,当液体水银的内部压强超过一个临界值时,液体水银能够浸入到碳纳米管内部;不断增大液体内部的压强,碳纳米管可以连续地传输液体;而当对液体水银进行循环加压时,碳纳米管可以间断地传输液体水银. 关键词： 碳纳米管 流体传输 分子动力学     

液体水银在碳纳米管中传输的压力控制模型

碳纳米管在纳米技术中有一个很重要的应用，就是它可以作为纳米管道传输液体. 本文用分子动力学模拟方法，结合一个液体压力控制模型，对液体水银由于外部压力作用在碳纳米管中传输的现象进行研究. 研究结果表明，当液体水银的内部压强超过一个临界值时，液体水银能够浸入到碳纳米管内部；不断增大液体内部的压强，碳纳米管可以连续地传输液体；而当对液体水银进行循环加压时，碳纳米管可以间断地传输液体水银.