Optimization of Enzymatic Biochemical Logic for Noise Reduction and Scalability: How Many Biocomputing Gates Can Be Interconnected in a Circuit?

We report an experimental evaluation of the "input-output surface" for a biochemical AND gate. The obtained data are modeled within the rate-equation approach, with the aim to map out the gate function and cast it in the language of logic variables appropriate for analysis of Boolean logic for scalability. In order to minimize "analog" noise, we consider a theoretical approach for determining an optimal set for the process parameters to minimize "analog" noise amplification for gate concatenation. We establish that under optimized conditions, presently studied biochemical gates can be concatenated for up to order 10 processing steps. Beyond that, new paradigms for avoiding noise build-up will have to be developed. We offer a general discussion of the ideas and possible future challenges for both experimental and theoretical research for advancing scalable biochemical computing

Two-dimensional Arrays of Amphiphilic Zn2+ -cyclens for Guided Molecular Recognition at Interfaces

The sterically guided molecular recognition of nucleobases, phosphates, adenosine, and uridine nucleotides on Langmuir monolayers and Langmuir-Blodgett monolayers of amphiphilic mono- or bis(Zn2+-cyclen)s assembled on thiolated surfaces was investigated. The stepwise selective binding of metal ions, uracil, or phosphate by dicetyl cyclen monolayers with variously tuned structures at the air/water interface was corroborated by the measurements of the corresponding LB films deposited onto quartz crystals. Two types of recognition surfaces were fabricated from Zn2+-dicetyl cyclen. The surface covered with a complex preformed in the Langmuir monolayer was capable both of imide and of phosphate binding. The similar complex formed directly in an LB film on thiolated gold was inactive with respect to imide. The surface plasmon resonance measurements evidenced the stepwise assembly of complementary nucleotides on SAM/LB templates through consecutive phosphate-Zn2+-cyclen coordination. Base pairing between nucleotides resulted in a formation of A-U bilayers comprising two complementary monolayers. Finally, we report on SAM/LB patterns designed for divalent molecular recognition of uridine phosphate by amphiphilic bis(Zn2+-cyclen)

Control of Photochemical Properties of Monolayers and Langmuir-Blodgett Films of Amphiphilic Chromoionophores

Control of the structure of ultrathin films that determine the steric conditions of the passing of intermolecular interactions is one of the most promising methods of implementing the advantages of planar supramolecular systems as basic elements of nanosize information devices. This work studies the behavior of Langmuir monolayers of a new amphiphilic crown-substituted chromoionophore I on a water subphase. It is found that dithiaazacrown ether in molecule I selectively binds Hg2+ cations both in organic solvents and from aqueous subphase. The electronic absorption spectra of the monolayer showed that H-aggregation occurs actively in the course of two-dimensional compression on deionized water, which hinders the complexation process, while the presence of Na+ and Ba2+ cations in the subphase results in the effective inhibition of this aggregation. This conclusion is confirmed by spectral fluorimetric studies of monolayers of a dye with a similar structure that contains a chromophoric group with a much higher fluorescence quantum yield. Monolayer aggregation on deionized water at the surface pressure values of just 4-6 mN/m leads to the three to fourfold fluorescence quenching, while in the case of subphases containing inert (noncomplementary to the dye ionophoric fragment) cations, the compression of the monolayer to pressures of 25-30 mN/m reduces the fluorescence intensity by no more than 25-35%. It was thus found that variations in the subphase composition allows one to monitor the degree of aggregation of the monolayer and the efficiency of cation recognition

Rational Design of Hemicyanine Langmuir Monolayers by Cation-Induced Preorganization of Their Structure for Sensory Response Enhancement

This study takes a novel approach to the enhancement of receptor properties of thin-film sensors based on hemicyanine dyes with dithia-aza-crown-ionophoric moiety. By means of in situ UV–vis and X-ray reflectivity (XRR) measurements, it was revealed that the introduction of up to 0.25 mmol of Hg²⁺ under a preliminarily compressed monolayer, formed on pure water, does not lead to cation binding. This is due to the formation of “head-to-tail” aggregates (H-type), in which ionophoric group is blocked by the neighboring molecule. However, the presence of barium cations in the subphase under the forming Langmuir monolayer of the mentioned compound causes codirectional (head-to-head) orientation of chromoionophore fragments. This provides preorganization of a monolayer structure that facilitates the binding of complementary mercury cations, even in a compressed state: asymmetric sandwich complexes containing two dye molecules coordinate a Hg²⁺ cation between them. This complex structure was confirmed by molecular modeling based on the electron density distribution calculated from XRR measurement data. Such preorganization of supramolecular ensembles induced by cations, which do not participate in the complex formation with macroheterocyclic receptors, may have applications in fields where strict control of molecular orientation at the interface is required, such as nanoelectronics, sensorics, catalysis, etc