An Enzyme‐Based Half‐Adder and Half‐Subtractor with a Modular Design

A half‐adder and a half‐subtractor have been realized using enzymatic reaction cascades performed in a flow cell device. The individual cells were modified with different enzymes and assembled in complex networks to perform logic operations and arithmetic functions. The modular design of the logic devices allowed for easy re‐configuration, enabling them to perform various functions. The final output signals, represented by redox species [Fe(CN)₆]^3?/4? or NADH/NAD⁺, were analyzed optically to derive the calculation results. These output signals might be applicable in the future for actuation processes, for example, substance release activated by logically processed signals.     

Pathogen detection using engineered bacteriophages

Bacteriophages, or phages, are bacterial viruses that can infect a broad or narrow range of host organisms. Knowing the host range of a phage allows it to be exploited in targeting various pathogens. Applying phages for the identification of microorganisms related to food and waterborne pathogens and pathogens of clinical significance to humans and animals has a long history, and there has to some extent been a recent revival in these applications as phages have become more extensively integrated into novel detection, identification, and monitoring technologies. Biotechnological and genetic engineering strategies applied to phages are responsible for some of these new methods, but even natural unmodified phages are widely applicable when paired with appropriate innovative detector platforms. This review highlights the use of phages as pathogen detector interfaces to provide the reader with an up-to-date inventory of phage-based biodetection strategies.     

Interfacial energy exchange and reaction dynamics in collisions of gases on model organic surfaces

Molecular beam scattering experiments and molecular dynamics simulations have been combined to develop an atomic-level understanding of energy transfer, accommodation, and reactions during collisions between gases and model organic surfaces. The work highlighted in this progress report has been motivated by the scientific importance of understanding fundamental interfacial chemical reactions and the relevance of reactions on organic surfaces to many areas of environmental chemistry. The experimental investigations have been accomplished by molecular beam scattering from ω-functionalized self-assembled monolayers (SAMs) on gold. Molecular beams provide a source of reactant molecules with precisely characterized collision energy and flux; SAMs afford control over the order, structure, and chemical nature of the surface. The details of molecular motion that affect energy exchange and scattering have been elucidated through classical-trajectory simulations of the experimental data using potential energy surfaces derived from ab initio calculations. Our investigations began by employing rare-gas scattering to explore how alkanethiol chain length and packing density, terminal group relative mass, orientation, and chemical functionality influence energy transfer and accommodation at organic surfaces. Subsequent studies of small molecule scattering dynamics provided insight into the influence of internal energy, molecular orientation, and gas–surface attractive forces in interfacial energy exchange. Building on the understanding of scattering dynamics in non-reactive systems, our work has recently explored the reaction probabilities and mechanisms for O₃ and atomic fluorine in collisions with a variety of functionalized SAM surfaces. Together, this body of work has helped construct a more comprehensive understanding of reaction dynamics at organic surfaces.     

Tailored pump-probe transient spectroscopy with time-dependent density-functional theory: controlling absorption spectra

Recent advances in laser technology allow us to follow electronic motion at its natural time-scale with ultra-fast time resolution, leading the way towards attosecond physics experiments of extreme precision. In this work, we assess the use of tailored pumps in order to enhance (or reduce) some given features of the probe absorption (for example, absorption in the visible range of otherwise transparent samples). This type of manipulation of the system response could be helpful for its full characterization, since it would allow us to visualize transitions that are dark when using unshaped pulses. In order to investigate these possibilities, we perform first a theoretical analysis of the non-equilibrium response function in this context, aided by one simple numerical model of the hydrogen atom. Then, we proceed to investigate the feasibility of using time-dependent density-functional theory as a means to implement, theoretically, this absorption-optimization idea, for more complex atoms or molecules. We conclude that the proposed idea could in principle be brought to the laboratory: tailored pump pulses can excite systems into light-absorbing states. However, we also highlight the severe numerical and theoretical difficulties posed by the problem: large-scale non-equilibrium quantum dynamics are cumbersome, even with TDDFT, and the shortcomings of state-of-the-art TDDFT functionals may still be serious for these out-of-equilibrium situations.     

Online induction heating for determination of isotope composition of woody stem water with laser spectrometry: a methods assessment

Application of stable isotopes of water to studies of plant–soil interactions often requires a substantial preparatory step of extracting water from samples without fractionating isotopes. Online heating is an emerging approach for this need, but is relatively untested and major questions of how to best deliver standards and assess interference by organics have not been evaluated. We examined these issues in our application of measuring woody stem xylem of sagebrush using a Picarro laser spectrometer with online induction heating. We determined (1) effects of cryogenic compared to induction-heating extraction, (2) effects of delivery of standards on filter media compared to on woody stem sections, and (3) spectral interference from organic compounds for these approaches (and developed a technique to do so). Our results suggest that matching sample and standard media improves accuracy, but that isotopic values differ with the extraction method in ways that are not due to spectral interference from organics.     

Halophilic reactions of a stable silylene with chloro and bromocarbons

A number of disilanes have been synthesized from a stable silylene, 1 (N,N'-di-tert-butyl-1,3-diaza-2-silacyclopent-4-en-2-ylidene), and a variety of halocarbons. It is proposed that disilane formation is a result of an initial halophilic interaction between the silylene and halocarbon. Formation of disilanes from 1 and CCl4, 2a, CHCl3, 2b, CH2Cl2, 2c, benzyl chloride, 2d, and bromobenzene, 5, are described here. An X-ray crystal structure of 2b was determined.     

Limitations of atom-centered dielectric functions in implicit solvent models

Many recent advances in Poisson-Boltzmann and generalized Born implicit solvent models have used atom-centered polynomial or Gaussian functions to define the boundary separating low and high dielectric regions. In contrast to the Lee and Richards molecular surface, atom-centered surfaces result in interatomic crevices and buried pockets of high dielectric which are too small for a solvent molecule to occupy. We show that these interstitial high dielectric regions are of significant magnitude in globular proteins, that they artificially increase solvation energies, and that they distort the free energy surface of nonbonded interactions. These results suggest that implicit solvent dielectric functions must exclude interstitial high dielectric regions in order to yield physically meaningful results.     

Effects of adsorption-induced microstructural changes on separation of xylene isomers through MFI-type zeolite membranes

Various factors were found to affect the performance of MFI-type zeolite membranes in separating xylene isomers (p-xylene, PX; o-xylene, OX) by pervaporation. In this work the effect of membrane microstructure, membrane quality, and pervaporation operating conditions were investigated using three membrane microstructures: random, c-oriented, and h,0,h-oriented. Operation under pervaporation conditions means that high loadings of PX will be present in the framework; therefore, the role of PX–framework and PX–OX interactions needs to be taken into consideration. Single component experiments demonstrated that the order of experimentation with OX and PX will affect the ideal selectivity. Multi-component studies showed that membrane performance is highly dependent on the relative concentration of the isomers in the feed; the higher the PX concentration the lower the selectivity observed. However, although high selectivity (18) was observed at low PX concentrations in the feed, it was not stable over time. Similar trends were observed for all membrane microstructures but differences in the selectivity values occurred. The structural deformation caused by high loadings of PX into the silicalite crystal affects each microstructure differently, ultimately leading to differences in performance.     

Diffusiophoresis in suspensions of highly charged soft particles

Diffusiophoresis phenomenon of aoft particles suspended in binary electrolyte solutions is explored theoretically in this study based on the spherical cell model, focusing on the chemiphoresis component in absence of diffusion potential. Both the electrostatic and hydrodynamic aspects of the boundary confinement, or steric effect, due to the presence of neighboring particles are examined extensively under various electrokinetic conditions. Significant local extrema are found in mobility profiles expressed as functions of the Debye length in general, synchronized with the strength of the motion-inducing double layer polarization. Moreover, a seemingly peculiar phenomenon is observed that the soft particles may move faster in more concentrated suspensions. The competition between the simultaneous enhancement of the motion-inducing electric driving force and the motion-retarding hydrodynamic drag force from the boundary confinement effect of the neighboring particles is found to be responsible for it. The above findings are also demonstrated experimentally in a very recent study on the diffusiophoretic motion of soft particles through porous collagen hydrogels. The results presented here are useful in various practical applications of soft particles like drug delivery.