Aligned Immobilization of Proteins Using AC Electric Fields

Protein molecules are aligned and immobilized from solution by AC electric fields. In a single‐step experiment, the enhanced green fluorescent proteins are immobilized on the surface as well as at the edges of planar nanoelectrodes. Alignment is found to follow the molecules' geometrical shape with their longitudinal axes parallel to the electric field. Simultaneous dielectrophoretic attraction and AC electroosmotic flow are identified as the dominant forces causing protein movement and alignment. Molecular orientation is determined by fluorescence microscopy based on polarized excitation of the proteins' chromophores. The chromophores' orientation with respect to the whole molecule supports X‐ray crystal data.     

A Bipedal DNA Motor that Travels Back and Forth between Two DNA Origami Tiles

In this work, the successful operation of a dynamic DNA device constructed from two DNA origami building blocks is reported. The device includes a bipedal walker that strides back and forth between the two origami tiles. Two different DNA origami tiles are first prepared separately; they are then joined together in a controlled manner by a set of DNA strands to form a stable track in high yield as confirmed by single‐molecule fluorescence (SMF). Second, a bipedal DNA motor, initially attached to one of the two origami units and operated by sequential interaction with “fuel” and “antifuel” DNA strands, moves from one origami tile to another and then back again. The operational yield, measured by SMF, was similar to that of a motor operating on a similar track embedded in a single origami tile, confirming that the transfer across the junction from one tile to the other does not result in dissociation that is any more than that of steps on a single tile. These results demonstrate that moving parts can reliably travel from one origami unit to another, and it demonstrates the feasibility of dynamic DNA molecular machines that are made of more than a single origami building block. This study is a step toward the development of motors that can stride over micrometer distances.     

Transient analysis of electro‐osmotic transport by a reduced‐order modelling approach

Transient behaviour of electro‐osmotic transport in typical electrokinetic channels is studied in this paper. The time needed for the electro‐osmotic flow to reach steady‐state exhibits multiple time scales depending on whether the flow is governed by either a viscous force, electrokinetic force or by a combination of both. When an intersection is present in the electrokinetic channel, such as in a cross or a T‐channel, the flow in the main channel and in the intersection gets to steady‐state at different times. A weighted Karhunen–Loève (KL) decomposition method is proposed in this paper to generate the global basis function for reduced‐order simulation. The key idea in a weighted KL approach is that, instead of minimizing a least‐squares measure of ‘error’ between the linear subspace spanned by the basis functions and the observation space, we minimize the weighted ‘error’ between the two spaces. The global basis functions in a weighted KL approach can be generated by computing the singular value decomposition (SVD) of the matrix containing the weighted snapshots. We show that the weighted KL decomposition based reduced‐order model is computationally more efficient and can capture the multiple time scales encountered in electro‐osmotic transport much more effectively compared to the classical KL decomposition based reduced‐order model. Copyright © 2003 John Wiley & Sons, Ltd.     

Modulation of Molecular Spatial Distribution and Chemisorption with Perforated Nanosheets for Ethanol Electro‐oxidation

Integrating thermodynamically favorable ethanol reforming reactions with hybrid water electrolysis will allow room‐temperature production of high‐value organic products and decoupled hydrogen evolution. However, electrochemical reforming of ethanol has not received adequate attention due to its low catalytic efficiency and poor selectivity, which are caused by the multiple groups and chemical bonds of ethanol. In addition to the thermodynamic properties affected by the electronic structure of the catalyst, the dynamics of molecule/ion dynamics in electrolytes also play a significant role in the efficiency of a catalyst. The relatively large size and viscosity of the ethanol molecule necessitates large channels for molecule/ion transport through catalysts. Perforated CoNi hydroxide nanosheets are proposed as a model catalyst to synergistically regulate the dynamics of molecules and electronic structures. Molecular dynamics simulations directly reveal that these nanosheets can act as a “dam” to enrich ethanol molecules and facilitate permeation through the nanopores. Additionally, the charge transfer behavior of heteroatoms modifies the local charge density to promote molecular chemisorption. As expected, the perforated nanosheets exhibit a small potential (1.39 V) and high Faradaic efficiency for the conversion of ethanol into acetic acid. Moreover, the concept in this work provides new perspectives for exploring other molecular catalysts.     

Simple method for the stretching and alignment of single adsorbed synthetic polycations

Spin-coating of isolated positively charged macromolecules onto mica in the presence of octylamine was found to be a simple and general method of stretching and aligning the macromolecular chains. The contour length and molar mass for the stretched macromolecules can be directly measured by atomic force microscopy, which makes this method a very useful analytical tool. Moreover, the molecular height is increased by co-deposition with octylamine, which drastically improves the molecular resolution and allows even ultrathin polycations to be visualized. The reason for the key role of the octylamine is found in the formation of an ultrathin liquidlike alkylamine film, which reduces the surface energy of mica and weakens the interactions between the surface and the charged macromolecules.     

An implicit–explicit solution method for electro‐osmotic flow through three‐dimensional micro‐channels

This paper presents a comprehensive finite‐element modelling approach to electro‐osmotic flows on unstructured meshes. The non‐linear equation governing the electric potential is solved using an iterative algorithm. The employed algorithm is based on a preconditioned GMRES scheme. The linear Laplace equation governing the external electric potential is solved using a standard pre‐conditioned conjugate gradient solver. The coupled fluid dynamics equations are solved using a fractional step‐based, fully explicit, artificial compressibility scheme. This combination of an implicit approach to the electric potential equations and an explicit discretization to the Navier–Stokes equations is one of the best ways of solving the coupled equations in a memory‐efficient manner. The local time‐stepping approach used in the solution of the fluid flow equations accelerates the solution to a steady state faster than by using a global time‐stepping approach. The fully explicit form and the fractional stages of the fluid dynamics equations make the system memory efficient and free of pressure instability. In addition to these advantages, the proposed method is suitable for use on both structured and unstructured meshes with a highly non‐uniform distribution of element sizes. The accuracy of the proposed procedure is demonstrated by solving a basic micro‐channel flow problem and comparing the results against an analytical solution. The comparisons show excellent agreement between the numerical and analytical data. In addition to the benchmark solution, we have also presented results for flow through a fully three‐dimensional rectangular channel to further demonstrate the application of the presented method. Copyright © 2007 John Wiley & Sons, Ltd.     

Numerical modelling of electromechanical coupling using fictitious domain and level set methods

We present a finite element formulation for simulation of electromechanical coupling using a combination of fictitious domain and level set methods. The electric field is treated with a fixed (Eulerian‐like) mesh, whereas the structure (taken as a perfect conductor) is modelled with a conventional Lagrangian approach. The compatibility between the potential of the conductor and of the electric domain is obtained by introducing a Lagrange multiplier function, defined on the boundary of the conductor. The electromechanical forces are obtained using a variational formulation for the coupled electromechanical domain. We use a Heaviside function on the level set to remove the electric energy in the conductor domain. Results are presented for an radio frequency switch and an element of a comb drive. Copyright © 2009 John Wiley & Sons, Ltd.     

The Brownian and Flow‐Driven Rotational Dynamics of a Multicomponent DNA Origami‐Based Rotor

Nanomechanical devices are becoming increasingly popular due to the very diverse field of potential applications, including nanocomputing, robotics, and drug delivery. DNA is one of the most promising building materials to realize complex 3D structures at the nanoscale level. Several mechanical DNA origami structures have already been designed capable of simple operations such as a DNA box with a controllable lid, bipedal walkers, and cargo sorting robots. However, the nanomechanical properties of mechanically interlinked DNA nanostructures that are in general highly deformable have yet to be extensively experimentally evaluated. In this work, a multicomponent DNA origami‐based rotor is created and fully characterized by electron microscopy under negative stain and cryo preparations. The nanodevice is further immobilized on a microfluidic chamber and its Brownian and flow‐driven rotational behaviors are analyzed in real time by single‐molecule fluorescence microscopy. The rotation in previous DNA rotors based either on strand displacement, electric field or Brownian motion. This study is the first to attempt to manipulate the dynamics of an artificial nanodevice with fluidic flow as a natural force.     

Steady and unsteady incompressible flow in a double driven cavity using the artificial compressibility (AC)‐based characteristic‐based split (CBS) scheme

In this paper, the explicit characteristic‐based split (CBS) scheme has been employed to solve both steady and unsteady flows inside a non‐rectangular double driven cavity. This problem is recently suggested as a benchmark problem for incompressible flows. Both unstructured and structured meshes have been employed in the present study to make sure that the predicted results are as close to reality as possible. The results obtained show the existence of steady state at lower Reynolds numbers (?1000) and transient states at higher Reynolds numbers. The flow approaches a turbulent state as the Reynolds number is increased to 10 000. Copyright © 2005 John Wiley & Sons, Ltd.     

Scale effect on flow and thermal boundaries in micro‐/nano‐channel flow using molecular dynamics–continuum hybrid simulation method

The molecular dynamics (MD)–continuum hybrid simulation method has been developed in two aspects in the present work: (1) The energy equation has been combined into the coupling method in order to obtain the hybrid temperature profile and (2) the coupling method has been improved by the local linearization to obtain a smoother parametric profile. The developed method is primarily validated by analytical solutions and full MD results. Then, it is employed to study the scale effect on the flow and thermal boundaries in micro‐/nano‐channel flow. The hybrid velocity and temperature profiles are obtained with the channel height (H) ranging from 60σ to 2014σ and the solid–liquid coupling (β) ranging from 0.1 to 50. Scale effect has shown strong influence on the boundaries. Obvious slip characteristics can be found in the profiles, i.e. velocity slip and temperature jump, when H is small and β is large. However, the results also show that the profiles can be well predicted to converge to the macroscale non‐slip/non‐jump analytical solutions when H is large enough, where the effect of β can be omitted and the slip characteristics disappear. Correlations of relative slip length, relative temperature jump and pressure gradient with H are fitted from the simulation results. Copyright © 2009 John Wiley & Sons, Ltd.     

A new method for Stokes problems with circular boundaries using degenerate kernel and Fourier series

This study is concerned with the Stokes flow of an incompressible fluid of constant density and viscosity with circular boundaries. To fully capture the circular boundary, the boundary densities in the direct and indirect boundary integral equations (BIEs) are expanded in terms of Fourier series. The kernel functions in either the direct BIE or the indirect BIE are expanded to degenerate kernels by using the separation of field and source points. Consequently, the improper integrals are transformed to series sum and are easily calculated. The linear algebraic system can be established by matching the boundary conditions at the collocation points. Then, the unknown Fourier coefficients can be easily determined. Finally, several examples including circular and eccentric domains are presented to demonstrate the validity of the present method. Five gains were obtained: (1) meshless approach; (2) free of boundary‐layer effect; (3) singularity free; (4) exponential convergence; and (5) well‐posed model. Copyright © 2007 John Wiley & Sons, Ltd.     

Investigation of fluid–structure interactions using a velocity‐linked P2/P1 finite element method and the generalized‐ α method

A velocity‐linked algorithm for solving unsteady fluid–structure interaction (FSI) problems in a fully coupled manner is developed using the arbitrary Lagrangian–Eulerian method. The P2/P1 finite element is used to spatially discretize the incompressible Navier–Stokes equations and structural equations, and the generalized‐ α method is adopted for temporal discretization. Common velocity variables are employed at the fluid–structure interface for the strong coupling of both equations. Because of the velocity‐linked formulation, kinematic compatibility is automatically satisfied and forcing terms do not need to be calculated explicitly. Both the numerical stability and the convergence characteristics of an iterative solver for the coupled algorithm are investigated by solving the FSI problem of flexible tube flows. It is noteworthy that the generalized‐ α method with small damping is free from unstable velocity fields. However, the convergence characteristics of the coupled system deteriorate greatly for certain Poisson's ratios so that direct solvers are essential for these cases. Furthermore, the proposed method is shown to clearly display the advantage of considering FSI in the simulation of flexible tube flows, while enabling much larger time‐steps than those adopted in some previous studies. This is possible through the strong coupling of the fluid and structural equations by employing common primitive variables. Copyright © 2012 John Wiley & Sons, Ltd.