Simultaneous electrostatic trapping of merged cation & anion beams.

Simultaneous trapping of merged cation and anion beams in the hybrid electrostatic ion beam trap (HEIBT) opens new opportunities for the study of the interactions of isolated atomic molecular or cluster ions with oppositely charged ionic species. Application of the trapped merged beams requires a detailed understanding of the trapping dynamics and the effect of the Coulombic attractive and repulsive forces between the ions on their motion in the trap. The simultaneous trapping regime is explored experimentally for SF6- anion and SF5+ cation beams and compared to realistic ion trajectory simulations. The respective stability of the simultaneously trapped cation and anion beams is experimentally tracked by nondestructive and mass sensitive image charge monitoring. An approximate analytical potential model is presented for modeling the dynamics of trapped ions, providing insight into the role of ion-ion interactions, and suggesting a simplified mirror design.

Nonresonant Raman Effects on Femtosecond Pump-Probe with Chirped White Light: Challenges and Opportunities.

Impulsive Raman excitation in neat organic liquids far from resonance is followed using chirped broad-band supercontinuum probe pulses. Spectral modulations due to impulsively induced coherent vibrations vary in intensity 10-fold as a function of the probe's linear chirp. Simulations clarify why the vibrational signature is maximized for a group delay dispersion (GDD) in reduced units of νvib-2 = 0.5 while a probe GDD of twice that quenches the same spectral modulations. Accordingly, recent claims that chirped white-light probe pulses provide equivalent information on material response to their compressed analogues must be taken with caution. In particular, interactions that induce spectral shifts in the probe depend crucially on the arrival chronology of the continuum colors. On one hand, this presents limitations to application of chirped continuum radiation as-is in pump-probe experiments. It also presents the opportunity for using this dependence to control the relative amplitude of nonresonant interactions in pump-probe signals such as that of solvent vibrations.

Single-photon Coulomb explosion of methanol using broad bandwidth ultrafast EUV pulses.

Single-photon Coulomb explosion of methanol is instigated using the broad bandwidth pulse achieved through high-order harmonics generation. Using 3D coincidence fragment imaging of one molecule at a time, the kinetic energy release (KER) and angular distributions of the products are measured in different Coulomb explosion (CE) channels. Two-body CE channels breaking either the C-O or the C-H bonds are described as well as a proton migration channel forming H2O+, which is shown to exhibit higher KER. The results are compared to intense-field Coulomb explosion measurements in the literature. The interpretation of broad bandwidth single-photon CE data is discussed and supported by ab initio calculations of the predominant C-O bond breaking CE channel. We discuss the importance of these findings for achieving time resolved imaging of ultrafast dynamics.

Rewriting the Story of Excimer Formation in Liquid Benzene.

Formation of benzene excimer following UV excitation of the neat liquid is monitored with femtosecond spectroscopy. A prompt rise component in excimer transient absorption, which contradicts the classical scenario of gradual reorientation and pairing of the excited monomers, is observed. Three-pulse experiments in which the population of evolving excimers is depleted by a secondary dump pulse demonstrate that the excimer absorption band is polarized along the interfragment axis. The experiments furthermore prove that the subsequent 4-fold increase in excimer absorption over ∼50 ps is primarily due to an increase in the transition dipole of pairs which are formed early on, and not to excited monomers forming excimers in a delayed fashion due to unfavorable initial geometry. Results are analyzed in light of recent studies of local structure in the liquid benzene combined with advanced electronic structure calculations. The prompt absorption rise is ascribed to excited states delocalized over nearby benzene molecules, which are sufficiently close and nearly parallel in the pure liquid. Such low-symmetry structures, which differ considerably from the optimized structures of isolated benzene dimer and solid benzene, are sufficiently abundant in liquid benzene. Electronic structure calculations confirm the orientation of transition dipoles of the excimers along the interparticle axis and demonstrate how slow refinement of the intermolecular geometry leads to a significant increase in the excimer absorption strength.

Self-assembly of luminescent Ag nanocluster-functionalized nanowires.

Two different methods to self-assemble red- or yellow-luminescent nucleic acids-stabilized Ag nanoclusters (NCs) nanowires are presented. By one method, the autonomous hybridization-polymerization process between two nucleic acids leads to polymer chains consisting of sequence-specific loops for the stabilization of the red- or yellow-emitting Ag NCs. By the other method, the nucleic acid-triggered hybridization chain reaction (HCR) involving the cross-opening of two functional hairpins leads to sequence-specific DNA loops and a nucleic acid scaffold that stabilize the respective red- or yellow-emitting Ag NCs. The micrometer-long luminescent Ag NC-functionalized nanowires are imaged by AFM and confocal microscopy.

DNA computing circuits using libraries of DNAzyme subunits.

Biological systems that are capable of performing computational operations could be of use in bioengineering and nanomedicine, and DNA and other biomolecules have already been used as active components in biocomputational circuits. There have also been demonstrations of DNA/RNA-enzyme-based automatons, logic control of gene expression, and RNA systems for processing of intracellular information. However, for biocomputational circuits to be useful for applications it will be necessary to develop a library of computing elements, to demonstrate the modular coupling of these elements, and to demonstrate that this approach is scalable. Here, we report the construction of a DNA-based computational platform that uses a library of catalytic nucleic acids (DNAzymes), and their substrates, for the input-guided dynamic assembly of a universal set of logic gates and a half-adder/half-subtractor system. We demonstrate multilayered gate cascades, fan-out gates and parallel logic gate operations. In response to input markers, the system can regulate the controlled expression of anti-sense molecules, or aptamers, that act as inhibitors for enzymes.

Logic gates and antisense DNA devices operating on a translator nucleic Acid scaffold.

A series of logic gates, "AND", "OR", and "XOR", are designed using a DNA scaffold that includes four "footholds" on which the logic operations are activated. Two of the footholds represent input-recognition strands, and these are blocked by complementary nucleic acids, whereas the other two footholds are blocked by nucleic acids that include the horseradish peroxidase (HRP)-mimicking DNAzyme sequence. The logic gates are activated by either nucleic acid inputs that hybridize to the respective "footholds", or by low-molecular-weight inputs (adenosine monophosphate or cocaine) that yield the respective aptamer-substrate complexes. This results in the respective translocation of the blocking nucleic acids to the footholds carrying the HRP-mimicking DNAzyme sequence, and the concomitant release of the respective DNAzyme. The released product-strands then self-assemble into the hemin/G-quadruplex-HRP-mimicking DNAzyme that biocatalyzes the formation of a colored product and provides an output signal for the different logic gates. The principle of the logic operation is, then, implemented as a possible paradigm for future nanomedicine. The nucleic acid inputs that bind to the blocked footholds result in the translocation of the blocking nucleic acids to the respective footholds carrying the antithrombin aptamer. The released aptamer inhibits, then, the hydrolytic activity of thrombin. The system demonstrates the regulation of a biocatalytic reaction by a translator system activated on a DNA scaffold.

Ultrasensitive surface plasmon resonance detection of trinitrotoluene by a bis-aniline-cross-linked Au nanoparticles composite.

A bis-aniline-cross-linked Au nanoparticles (NPs) composite is electropolymerized on Au surfaces. The association of trinitrotoluene, TNT, to the bis-aniline bridging units via pi-donor-acceptor interactions allows the amplified detection of TNT by following the surface plasmon resonance (SPR) reflectance changes as a result of the coupling between the localized plasmon of the AuNPs and the surface plasmon wave associated with the gold surface. The detection limit for analyzing TNT by this method is approximately 10 pM. The electropolymerization of the bis-aniline-cross-linked AuNPs composite in the presence of picric acid results in a molecular-imprinted matrix for the enhanced binding of TNT. The imprinted AuNPs composite enabled the sensing of TNT with a detection limit that corresponded to 10 fM. Analysis of the SPR reflectance changes in the presence of different concentrations of TNT revealed a two-step calibration curve that included the ultrasensitive detection of TNT by the imprinted sites in the composite, KassI. for the association of TNT to the imprinted sites, 6.4 x 10(12) M-1, followed by a less sensitive detection of TNT by the nonimprinted pi-donor bis-aniline sites (KNIass. = 3.9 x 10(9) M-1). The imprinted AuNPs composite reveals impressive selectivity. The structural and functional features of the bis-aniline-cross-linked AuNPs composites were characterized by different methods including ellipsometry, AFM, and electrochemical means. The dielectric properties of the AuNPs composite in the presence of different concentrations of TNT were evaluated by the theoretical fitting of the respective experimental SPR curves. The ultrasensitive detection of the TNT by the AuNPs composite was attributed to the changes of the dielectric properties of the composite, as a result of the formation of the pi-donor-acceptor complexes between TNT and the bis-aniline units. These changes in the dielectric properties lead to a change in the conductivity of the AuNPs matrix.

Enzyme cascades activated on topologically programmed DNA scaffolds.

The ability of DNA to self-assemble into one-, two- and three-dimensional nanostructures, combined with the precision that is now possible when positioning nanoparticles or proteins on DNA scaffolds, provide a promising approach for the self-organization of composite nanostructures. Predicting and controlling the functions that emerge in self-organized biomolecular nanostructures is a major challenge in systems biology, and although a number of innovative examples have been reported, the emergent properties of systems in which enzymes are coupled together have not been fully explored. Here, we report the self-assembly of a DNA scaffold made of DNA strips that include 'hinges' to which biomolecules can be tethered. We attach either two enzymes or a cofactor-enzyme pair to the scaffold, and show that enzyme cascades or cofactor-mediated biocatalysis can proceed effectively; similar processes are not observed in diffusion-controlled homogeneous mixtures of the same components. Furthermore, because the relative position of the two enzymes or the cofactor-enzyme pair is determined by the topology of the DNA scaffold, it is possible to control the reactivity of the system through the design of the individual DNA strips. This method could lead to the self-organization of complex multi-enzyme cascades.

Characterization of nanostructured surfaces generated by reconstitution of the porin MspA from Mycobacterium smegmatis.

Nanostructures with long-term stability at the surface of gold electrodes are generated by reconstituting the porin MspA from Mycobacterium smegmatis into a specially designed monolayer of long-chain lipid surfactant on gold. Tailored surface coverage of gold electrodes with long-chain surfactants is achieved by electrochemically assisted deposition of organic thiosulfates (Bunte salts). The subsequent reconstitution of the octameric-pore MspA is guided by its extraordinary self-assembling properties. Importantly, electrochemical reduction of copper(II) yields copper nanoparticles within the MspA nanopores. Electrochemical impedance spectroscopy, reflection electron microscopy, and atomic force microscopy (AFM) show that: 1) the MspA pores within the self-assembled monolayer (SAM) are monodisperse and electrochemically active, 2) MspA reconstitutes in SAMs and with a 10-nm thickness, 3) AFM is a suitable method to detect pores within SAMs, and 4) the electrochemical reduction of Cu2+ to Cu0 under overpotential conditions starts within the MspA pores.

Concatenated logic gates using four coupled biocatalysts operating in series.

The assembly of three concatenated enzyme-based logic gates consisting of OR, AND, XOR is described. Four biocatalysts, acetylcholine esterase, choline oxidase, microperoxidase-11, and the NAD+-dependent glucose dehydrogenase, are used to assemble the gates. Four inputs that include acetylcholine, butyrylcholine, O2, and glucose are used to drive the concatenated-gates system. The cofactor NAD+, and its reduced 1,4-dihydro form, NADH, are used as a reporter couple, and these provide an optical output for the gates. The modulus of the absorbance changes of NADH is used as a readout signal.

Logic gates and elementary computing by enzymes.

Different selected enzymes, glucose oxidase (GOx), catalase (Cat), glucose dehydrogenase (GDH), horseradish peroxidase (HRP), and formaldehyde dehydrogenase (FDH), are used alone or coupled to construct eight different logic gates. The added substrates for the respective enzymes, glucose and H(2)O(2), act as the gate inputs, while the biocatalytically generated gluconic acid or NADH are the output signals that follow the operation of the gates. Different enzyme-based gates are XOR, INHIBIT A, INHIBIT B, AND, OR, NOR, Identity and Inverter gates. By combining the AND and XOR or the XOR and INHIBIT A gates, the half-adder and half-subtractor are constructed, respectively, opening the way to elementary computing by the use of enzymes.

An electrochemical/photochemical information processing system using a monolayer-functionalized electrode.

An electroactive and photoisomerizable monolayer associated with a Au electrode acts as a Write-Read-Erase information processing system and as a flip-flop Set/Reset memory element.

Two coupled enzymes perform in parallel the 'AND' and 'InhibAND' logic gate operations.

The coupled activation of two enzymes: glucose dehydrogenase (GDH) and horseradish peroxidase (HRP), is used to construct the parallel-operating AND and InhibAND logic gates. The added substrates for the respective enzymes, glucose and H(2)O(2), act as the gate inputs, while the biocatalytically generated NADH and gluconic acid provide the output signals that follow the operations of the gates. The two gates are generated in the same vial, thus allowing the logic operations to take place in parallel, and the simultaneous readout of the functions of the gates.

Magneto-switchable single-electron charging of Au-nanoparticles using hydrophobic magnetic nanoparticles.

Reversible magneto-switchable quantum charging of a Au nanoparticle array associated with a Au electrode is observed in the presence of hydrophobic magnetic nanoparticles attracted to the functionalized electrode surface.

Endonuclease-based logic gates and sensors using magnetic force-amplified readout of DNA scission on cantilevers.

The endonuclease scission of magnetic particles functionalized with sequence-specific DNAs, which are associated on cantilevers, is followed by the magnetic force-amplified readout of the reactions by the nano-mechanical deflection/retraction of the cantilevers. The systems are employed to develop AND or OR logic gates and to detect single base mismatch specificity of the endonucleases. The two endonucleases EcoRI (E(A)) and AscI (E(B)) are used as inputs. The removal of magnetic particles linked to the cantilever by the duplexes 1/1a and 2/2a via the simultaneous cleavage of the DNAs by E(A) and E(B) leads to the retraction of the magnetically deflected cantilever and to the establishment of the "AND" gate. The removal of the magnetic particles linked to the cantilevers by the duplex 3/3a by either E(A) or E(B) leads to the retraction of the magnetically deflected cantilever and to the establishment of the "OR" gate. The magnetic force-amplified readout of endonuclease activities is also employed to reveal single base mismatch specificity of the biocatalysts.

Magnetomechanical detection of the specific activities of endonucleases by cantilevers.

Thiolated nucleic acids 1 or 2 are immobilized on Au-coated cantilevers and hybridized with the complementary nucleic acids 1a or 2a associated with magnetic particles. The duplexes 1/1a or 2/2a include specific sequences for the scission by Apa I or Mse I, respectively. The cantilevers positioned in a flow cell are subjected to an external magnetic field, leading to the deflection of the cantilevers. Upon the specific scission of the DNA duplexes by Apa I or Mse I, the magnetic particles are disconnected from the cantilevers leading to their retraction to the rest position. The deflection/retraction of the cantilevers are followed by a conventional atomic force microscope optical detection system.

Magnetic field effects on bioelectrocatalytic reactions of surface-confined enzyme systems: enhanced performance of biofuel cells.

The effect of a constant magnetic field on bioelectrocatalytic transformations of three different enzyme assemblies linked to electrodes is examined and correlated with a theoretical magnetohydrodynamic model. The systems consist of surface-reconstituted glucose oxidase (GOx), an integrated lactate dehydrogenase/nicotinamide/pyrroloquinoline quinone assembly (LDH/NAD+ -PQQ), and a cytochrome c/cytochrome oxidase system (Cyt c/COx) linked to the electrodes. Pronounced effects of a constant magnetic field applied parallel to the electrode surface are observed for the bioelectrocatalyzed oxidation of glucose and lactate by the GOx-electrode and LDH/NAD+ -PQQ-electrode, respectively. The enhancement of the bioelectrocatalytic processes correlates nicely with the magnetohydrodynamic model, and the limiting current densities (iL) relate to B1/3 (B = magnetic flux density) and to C4/3 (C* = bulk concentration of the substrate). A small magnetic field effect is observed for the Cyt c/COx-electrode, and its origin is still questionable. The effect of the constant magnetic field on the performance of biofuel cells with different configurations is examined. For the biofuel cell consisting of LDH/NAD+ -PQQ anode and Cyt c/COx cathode, a 3-fold increase in the power output was observed at an applied magnetic field of B = 0.92 T and external load of 1.2 kOhms.

Magnetic field effects on cytochrome c-mediated bioelectrocatalytic transformations.

Constant magnetic fields affect many biological transformations, but we lack mechanistic understanding of the processes. The magnetohydrodynamic effect may account for the enhancement of bioelectrocatalytic transformations at interfaces. This is exemplified by the bioelectrocatalyzed cytochrome c-mediated reduction of oxygen and oxidation of lactate in the presence of cytochrome oxidase and lactate dehydrogenase, respectively. We observe significant magnetic field effects on the rates of bioelectrochemical transformations (ca. 3-fold increase) at the functionalized interfaces at field strengths, B, up to 1 T. We show that the limiting current is proportional to the B(1/3)C*(4/3), where C is the concentration of electroactive species. The results may have important implications on the understanding of the magnetic field effects on natural biocatalytic processes at membranes and on the enhancement of biotransformations in biotechnology.