B. Scott Day

The dynamics of gas-surface energy exchange in collisions of Ar atoms with ω-functionalized self-assembled monolayers

Atomic-beam scattering experiments using n-alkanethiol and ω-functionalized alkanethiol self-assembled monolayers (SAMs) on gold are employed to explore the dynamics of gas-surface energy exchange in collisions with model organic surfaces. The studies are performed by directing a nearly monoenergetic beam of 80 kJ/mol Ar atoms onto a particular SAM at an incident angle of 30° with respect to the surface normal and recording the time-of-flight distributions for the atoms as they scatter from the surface at a final angle of 30°. Among the monolayers studied, long-chain CH3-terminated SAMs are found to be the most effective at dissipating the translational energy of impinging atoms. For alkanethiols with greater than seven total carbon atoms (HS(CH2)n>6CH3), we find that, for specular scattering conditions, over 80% of the incident energy is transferred to the surface and that over 60% of the impinging atoms approach thermal equilibrium with the surface before scattering back into the gas phase. In contrast ...

Packing density and structure effects on energy-transfer dynamics in argon collisions with organic monolayers

A combined experimental and molecular-dynamics simulation study has been used to investigate energy-transfer dynamics of argon atoms when they collide with n-alkanethiols adsorbed to gold and silver substrates. These surfaces provide the opportunity to explore how surface structure and packing density of alkane chains affect energy transfer in gas-surface collisions while maintaining the chemical nature of the surface. The chains pack standing up with 12 degrees and 30 degrees tilt angles relative to the surface normal and number densities of 18.9 and 21.5 A(2)molecule on the silver and gold substrates, respectively. For 7-kJmol argon scattering, the two surfaces behave equivalently, fully thermalizing all impinging argon atoms. In contrast, these self-assembled monolayers (SAMs) are not equally efficient at absorbing the excess translational energy from high-energy, 35 and 80 kJmol, argon collisions. When high-energy argon atoms are scattered from a SAM on silver, the fraction of atoms that reach thermal equilibrium with the surface and the average energy transferred to the surface are lower than for analogous SAMs on gold. In the case of argon atoms with 80 kJmol of translational energy scattering from long-chain SAMs, 60% and 45% of the atoms detected have reached thermal equilibrium with the monolayers on gold and silver surfaces, respectively. The differences in the scattering characteristics are attributed to excitation efficiencies of different types of surface modes. The high packing density of alkyl chains on silver restricts certain low-energy degrees of freedom from absorbing energy as efficiently as the lower-density monolayers. In addition, molecular-dynamics simulations reveal that the extent to which argon penetrates into the monolayer is related to packing density. For argon atoms with 80-kJmol incident energy, we find 16% and 7% of the atoms penetrate below the terminal methyl groups of C(10) SAMs on gold and silver, respectively.

Classical trajectory study of collisions of Ar with alkanethiolate self-assembled monolayers: potential-energy surface effects on dynamics.

We have investigated collisions between Ar and alkanethiolate self-assembled monolayers (SAMs) using classical trajectory calculations with several potential-energy surfaces. The legitimacy of the potential-energy surfaces is established through comparison with molecular-beam data and ab initio calculations. Potential-energy surfaces used in previous work overestimate the binding of Ar to the SAM, leading to larger energy transfer than found in the experiments. New calculations, based on empirical force fields that better reproduce ab initio calculations, exhibit improved agreement with the experiments. In particular, polar-angle-dependent average energies calculated with explicit-atom potential-energy surfaces are in excellent agreement with the experiments. Polar- and azimuthal-angle-dependent product translational energies are examined to gain deeper insight into the dynamics of Ar+SAM collisions.

Utilization of myosin and actin bundles for the transport of molecular cargo.

The utilization of motor proteins for the movement and assembly of synthetic components is currently a goal of nanoengineering research. Application of the myosin actin motor system for nanotechnological uses has been hampered due to the low flexural rigidity of individual F-actin filaments. Here it is demonstrated how actin bundling can be used to affect the translational behavior of myosin-propelled filaments, transport molecules across a motor-patterned surface, and that the movement of bundled actin can be regulated photonically. These data suggest that actin bundling may significantly improve the applicability of the myosin motor for future nanotechnological applications.

Thiolated Dendrimers as Multi-Point Binding Headgroups for DNA Immobilization on Gold

The synthesis of multithiolated DNA molecules that can be used to produce self-assembled monolayers of single-stranded DNA oligonucleotides on gold substrates is described. Generation 3 polyamidoamine (PAMAM) dendrimers were conjugated to DNA oligomers and functionalized with ~30 protected thiol groups. The protected thiol groups-thioacetate groups-allowed the dendrimer-DNA constructs to be stored in a buffer solution for at least 2 months before deprotection without any observable decrease in their ability to assemble into functional layers. The monolayers formed using these multithiolated DNA probe strands demonstrate target capture efficiencies comparable to those of analogous monolayers assembled with DNA functionalized with single thiol groups. A functional advantage of using dendrimer headgroups is the resistance to probe strand loss in prolonged exposure to buffer solutions at a high temperature (95 °C).

Impedance measurements on a DNA junction

1 microm double-stranded DNA molecules are immobilized between pairs of gold and pairs of platinum microelectrodes with gaps of 0.4 and 1 microm, respectively, and their electrical characteristics are determined under the application of constant and sinusoidal bias voltages. Due to their extremely high impedance for constant voltage bias, the samples of DNA are excellent insulators; however, their impedances show strong frequency dependence in the range of 10 Hz-7.5 MHz. Favorable response in the gold electrodes is attributed to the higher ability of DNA molecules to bridge the narrower gold electrode gaps in contrast to that in the wider platinum junctions.

Application of Poly(amidoamine) Dendrimers for Use in Bionanomotor Systems

The study and utilization of bionanomotors represents a rapid and progressing field of nanobiotechnology. Here, we demonstrate that poly(amidoamine) (PAMAM) dendrimers are capable of supporting heavy meromyosin dependent actin motility of similar quality to that observed using nitrocellulose, and that microcontact printing of PAMAM dendrimers can be exploited to produce tracks of active myosin motors leading to the restricted motion of actin filaments across a patterned surface. These data suggest that the use of dendrimer surfaces will increase the applicability of using protein biomolecular motors for nanotechnological applications.

Homologous, long-chain alkyl dendrons form homologous thin films on silver oxide surfaces.

As suggested by X-ray crystal structures, homologous, long-chain alkyl dendrons with three carboxyl groups form thin films on silver oxide surfaces, which give reflection-absorption infrared spectra that show a linear increase in intensities of methylene C-H stretching absorptions.

Plasma treatment of PDMS for applications of in vitro motility assays

In vitro motility assays are readily used to simplify the complex environments within the cell and in muscle tissue. These assays have afforded considerable insight into the fundamentals of their underlying biophysics, interactions with cargo, intracellular regulation, and motor cooperation/competition. Extension of the standard in vitro motility assay into a more automated and cost-effective fluidic design while providing availability to the scientific community without expertise in lithographic fabrication is critical for the continued advancement of the field. In this work, we utilized a standard plasma cleaner to oxidize the widely prevalent material polydimethylsiloxane (PDMS) to create flow cells that could be used for in vitro motility assays. Our analysis indicated that a 40 min pre-treatment of the PDMS with plasma exposure resulted in optimal bundle motility. This finding was attributed to the condition at which the least amount of oxygen permeates the PDMS slab, enters the motility buffer, and oxidizes the motor proteins. Based on these findings, we developed a method for constructing microfluidic devices from glass and plasma-treated PDMS molds in which motility could be observed.

Origami Arrays as Substrates for the Determination of Reaction Kinetics Using High-Speed Atomic Force Microscopy

DNA nanostructures (DN) are powerful platforms for the programmable assembly of nanomaterials. As applications for DN both as a structural material and as a support for functional biomolecular sensing systems develop, methods enabling the determination of reaction kinetics in real time become increasingly important. In this report, we present a study of the kinetics of streptavidin binding onto biotinylated DN constructs enabled by these planar structures. High-speed AFM was employed at a 2.5 frame/s rate to evaluate the kinetics and indicates that the binding fully saturates in less than 60 s. When the the data was fitted with an adsorption-limited kinetic model, a forward rate constant of 5.03 × 105 s-1 was found.