Ring-Shaped Plasmonic Logic Gates

Ring-shaped one-, two-, and three-bit plasmonic logic gate configurations and circuits have been proposed, which, besides being compact, are also versatile and can be easily cascaded, the output logic values being controlled by both the geometry of the multi-port rings and the phase of the incident beams. This latter degree of freedom, not fully exploited up to now in plasmonic circuits, offers a high degree of flexibility of logic gate configurations.

     

Effect of dielectric constant of medium on protonation equilibria of ethylenediamine

Abstract

The effect of dielectric constant of medium on protonation equilibria has been studied by determining protonation constants of ethylenediamine pH metrically in various concentrations (0–60%v/v) of acetoni-trile– and ethylene glycol–water mixtures, at an ionic strength of 0.16mol L^?1 and at 303.0 K. MINIQUAD75 computer program has been used for the calculation of protonation constants. Linear and non-linear variations of step-wise protonation constants with reciprocal of dielectric constant of the solvent mixtures have been attributed to the dominance of the electrostatic and non-electrostatic forces, respectively. The trend is explained on the basis of solute–solute and solute–solvent interactions, solvation, proton transfer processes and dielectric constants of the media.     

The Reactions of Hemoglobin in Various Media

The rate constants for the association of oxygen and of carbon monoxide with reduced hemoglobin and for the dissociation of oxygen from hemoglobin were studied in a variety of media. All three of these rates were essentially independent of diffusion rate and dielectric constant throughout a wide range. These results are very different from those found for other heme proteins whose rates are diffusion-controlled in very viscous solvents.

The interpretation of the average measured rates described herein in terms of the four rate constants discussed by Gibson and Roughton indicates that our measurements reflect most strongly the constants for the first reacting molecule in each case. For the purposes of these reactions, the reactants may be regarded as neutral molecules.

     

Effective Dielectric Constant of Plasmonic Nanofluid Containing Core-Shell Nanoparticles

This paper focuses on the effective dielectric constant of water-based plasmonic nanofluid containing SiO₂/Ag core/shell nanoparticles (NPs). Two effective models, based on S-parameter retrieval method and Maxwell-Garnett effective medium theory, are employed. The effective dielectric constants predicted by the two effective models are compared and the applicability is evaluated by comparing the reflectance and absorptance. Three influence factors, including volume fraction, core-shell ratio, and size of NPs, are considered. Results show both of the two effective models can predict reliable effective dielectric constants when the volume fraction, size, and core-shell ratio of nanoparticles are 5%, 25 nm, and 4:1 respectively. Only small deviations appear in the resonant region under this condition. With the increase of volume fraction, shell proportion, or size, deviations in the resonant region become larger for both of the two effective models. Therefore, the predicted effective dielectric constants are not suitable for the prediction of optical properties, because the resonant region is the key region of the solar conversion for plasmonic nanofluids. Hence, the parameters of NPs need to be changed to make the effective models applicable. Moreover, the effective model based on S-parameter retrieval can predict more reliable dielectric constant than the effective model based on Maxwell-Garnett theory.

     

Fluorescence for biological logic gates

Biological logic gates are smart probes able to respond to biological conditions in behaviors similar to computer logic gates, and they pose a promising challenge for modern medicine. Researchers are creating many kinds of smart nanostructures that can respond to various biological parameters such as pH, ion presence, and enzyme activity. Each of these conditions alone might be interesting in a biological sense, but their interactions are what define specific disease conditions. Researchers over the past few decades have developed a plethora of stimuli‐responsive nanodevices, from activatable fluorescent probes to DNA origami nanomachines, many explicitly defining logic operations. Whereas many smart configurations have been explored, in this review we focus on logic operations actuated through fluorescent signals. We discuss the applicability of fluorescence as a means of logic gate implementation, and consider the use of both fluorescence intensity as well as fluorescence lifetime.     

Influence of dielectric constant on protonation equilibria of maleic acid and L-asparagine in acetonitrile water-mixtures

Abstract

The protonation constants of maleic acid and L-asparagine have been studied pH-metrically in various concentrations (0–50% v/v) of acetonitrile–water mixtures maintaining an ionic strength of 0.16 mol L^-1 at 30⁰C. The protonation constants have been calculated using the computer program MINIQUAD75 and are selected based on statistical parameters. Linear variation of step-wise protonation constants (log K) with the reciprocal of the dielectric constant of the solvent mixture has been attributed to the dominance of the electrostatic forces.     

Speciation of ternary complexes of lead(II), cadmium(II) and mercury(II) with L-dopa and phenanthroline in propanediol-water mixtures

Abstract

The formation constants of ternary complexes of title systems have been determined pH-metrically in biologically relevant conditions at an ionic strength of 0.16 mol dm^-3 and 303 K. The overall stability constants have been evaluated using MINIQUAD75 computer program. The complexation equilibria have been derived on the basis of species distribution diagram. In the present study L-Dopa and 1, 10-phenanthroline are found to be compatible ligands, proving greater stability of ternary complexes as compared to binary ones. The trend in variation of stability constants with change in dielectric constant of medium is explained on the basis of electrostatic and non-electrostatic forces. Distributions of the species with pH at different compositions of propanediol-water mixtures are also presented. The factors responsible for the compatibility of both the ligands have also been discussed.     

Statistical Description of Nucleic Acid Secondary Structure Folding

Abstract

A simple statistical model describing the folding of nucleic acids is proposed. For long sequences the real configuration of the secondary structure is a quasi equilibrium state that cannot be characterised by minimal free energy. This is because the time required to achieve complete thermal equilibrium considerably exceeds the life-time of the molecule. The formation of the secondary structure is represented as a random walk process in the space of all possible molecular configurations. TTie quasi equilibrium structure is obtained by successive linking and disruptions of helix segments with probabilities determined by the rate constants of corresponding unimolecular reactions. The probabilities of configurations consisting of all possible compatible helices are calculated. Structures of some t - RNAs and ribosomal RNAs are analysed.     

Effects of Oil Type on Sterol-Based Organogels and Emulsions

The present study investigates the effect of oil type on the formation, morphology and mechanical properties of phytosterol-based organogels. The formation of organogels can be satisfactorily predicted with a criterion based on Hansen Solubility Parameters (HSPs), provided that the sterol and sterol ester in these systems assemble as tubules. When structures other than tubules are formed, the predictability of the HSP-based criterion becomes void. In cases where organogelling occurred, the morphology and mechanical properties of the tubular network of the gels and water-in-oil emulsions were investigated. The findings revealed that the structure of the tubular network formed in oils with different compositions, could be grouped based on the dielectric constants of the oils. Curly and bundled tubules which formed networks, were observed in gels prepared with low dielectric constant oils (i.e. decane and limonene). For oils with a moderate dielectric constant (i.e. castor oil and sunflower oil), the tubules became less curly and straighter. Upon increasing the dielectric constant of the oil (eugenol), individual tubules were observed next to the bundled tubules. The results showed that straighter, bundled tubules are associated with firmer gels, whereas less straight (i.e. curly) tubules rendered weaker gels. The tubular network of the water-in-oil emulsions obtained for oils with a low dielectric constant appeared more open with straighter tubules. For oils with relatively high dielectric constant, the water-in-oil emulsions lost most of their tubular structure and only a few tubules could be observed. In the presence of emulsion droplets fewer tubules are formed, resulting in weaker networks.

     

The Application of the Reaction-Field Method to the Calculation of Dielectric Constants

Abstract

The behaviour of the popular TIP3P water model has been investigated using both molecular dynamics and Monte Carlo simulation procedures. Long-range electrostatic interactions were included through a reaction-field treatment, and the nonbonded interactions were either truncated at the cutoff distance, or smoothly scaled to zero using a switching function. The thermodynamic observables, and in particular the dipole-dipole correlation functions, are found to differ between the two simulation techniques if a rigid nonbonded cutoff is applied. However, use of a switching function gives exact agreement between the simulation methodologies. This difference is ascribed to the effect of energy pumping in the molecular dynamics simulations, and suggests that dielectric constants calculated using this simulation method with the fluctuation procedure in conjunction with a reaction field should be reappraised. Thus the Monte Carlo simulation procedure offers a number of intrinsic advantages over molecular dynamics for the calculation of dielectric constants with a reaction field. The most precise value for the dielectric constant of TIP3P is calculated to be 102 ± 3 at 298 K.     

Protonation equilibria of glycine, 1,10-phenanthroline and 2,2-bipyridyl in ethylene glycol–water mixtures

Abstract

The solute–solvent interactions of glycine, 1,10-phenanthroline and 2,2-bipyridyl have been studied in 0–60% v/v ethylene glycol–water media by a pH metric method. The protonation constants were estimated with the computer program MINIQUAD75. Selection of the best fit chemical model of the protonation equilibria is based on the standard deviation in protonation constants and residual analysis using a sum of squares of residuals in all mass-balance equations. The observed linear variation of protonation constants with the inverse of dielectric constant of the solvent mixture can be attributed to the dominance of the electrostatic forces. The distribution of species, protonation equilibria and effects of influential parameters on the protonation constants are also presented.     

Effect of dielectric constant on protonation equilibria of 2, 3-dihydroxybenzoic acid and malonic acid in 1, 2-propanediol-water mixtures

Abstract

The protonation constants of 2,3-diydroxybenzoic acid (2, 3-DHBA) and malonic acid (MA) at 303.0 ± 0.1 K and 0.16 mol L^-1 ionic strength in various concentrations (0–60% v/v) of 1,2-propanediol–water-mixtures were determined by pH-metric method. The protonation constants were calculated with MINIQUAD75 computer program. Selection of the best fit chemical models of the acid–base equilibria was based on statistical parameters. The log K values were found to increase with the increase in percentage of 1,2-propanediol and vary linearly with the reciprocal of the dielectric constant of the medium. This has been attributed to the dominance of electrostatic forces. Distributions of species and effect of influential parameters on the protonation constants are also presented.     

Deoxyribozyme-based three-input logic gates and construction of a molecular full adder

We have developed an array of seven deoxyribozyme-based molecular logic gates that behaves as a full adder in a single solution, with three oligonucleotides as inputs and two independent fluorogenic cleavage reactions as carry and sum outputs. The sum output consisted of four new deoxyribozyme-based logic gates: an ANDAND gate and three ANDNOTANDNOT gates. These gates required the design of a generic three-input deoxyribozyme-based logic gate that can use any three-way combination of activating or inactivating inputs. This generic gate design utilizes an additional inverting element that hybridizes to convert YES logic into NOT logic and vice versa. The system represents the first solution-phase, single test tube, enzymatic full adder and shows the complexity of control over molecular scale events that can be achieved with deoxyribozyme-based logic gates. Similar systems could be applied to control autonomous therapeutic and diagnostic devices.     

Chemical speciation of L-proline complexes of Ca(II), Zn(II) and Mn(II) in acetonitrile-water mixtures

Abstract

Chemical speciation of binary complexes of Ca(II), Zn(II) and Mn(II) with L-proline is investigated pH-metrically in acetonitrile-water mixtures. The stability constants are calculated using the computer program MINIQUAD75. The best-fit chemical models are selected based on statistical parameters and residual analysis. The models for the binary species contained ML⁺, MLH²⁺and ML₂H⁺ for Ca(II), Zn(II) and Mn(II). The trend in variation of stability constants with change in the dielectric constant of the medium is explained on the basis of structure forming nature of acetonitrile. Distribution of the species with pH at different variations (0.0-60.0% v/v) in acetonitrile-water mixtures is also presented.     

Speciation of binary complexes of Co(II), Ni(II) and Cu(II) with L-aspartic acid in propylene glycol–water mixtures

Abstract

Speciation of binary complexes of Co(II), Ni(II) and Cu(II) with L-aspartic acid in (0-60% v/v) propylene glycol-water mixtures was studied pH metrically at 303.0±0.1 K and at an ionic strength of 0.16 mol L^-1. The binary species refined were ML, ML₂, ML₂H₂, ML₂H₃ and ML₂H₄. The stabilities of the complexes followed the Irving-Williams order i.e.Co(II) <Ni(II) < Cu(II). The linear variation of stability constants as a function of dielectric constant of the medium indicated the dominance of electrostatic forces over non-electrostatic forces. Some species were stabilised due to electrostatic interactions and some were destabilised due to the decreased dielectric constant. The order of ingredients influencing the magnitudes of stability constants due to incorporation of errors in their concentrations was alkali > acid > ligand > metal. Equilibria for the formation of binary complexes were proposed based on the forms of the ligand and their existence at different pH values.     

Monte-Carlo Simulation of Molten CsCl Using a ‘Deformation Dipole’ Polarisable Ion Potential

Abstract

We have simulated the structure of molten CsCl at 943 K using a form of interionic potential, based on the deformation dipole model of Hardy and Karo, where ions have both point charges and dipoles. The magnitude of the dipole on an ion is determined by two factors, one being the local electric field and the other the repulsive potential due to overlap with neighbouring ions. Parameters are determined directly from the crystal lattice constant, compressibility and dielectric constants. Good agreement with experimental results is obtained. The potential is compared to the shell model of ionic polarisability which does not produce good agreement with experiment.     

A Visual Dual-Aptamer Logic Gate for Sensitive Discrimination of Prion Diseases-Associated Isoform with Reusable Magnetic Microparticles and Fluorescence Quantum Dots

Molecular logic gates, which have attracted increasing research interest and are crucial for the development of molecular-scale computers, simplify the results of measurements and detections, leaving the diagnosis of disease either “yes” or “no”. Prion diseases are a group of fatal neurodegenerative disorders that happen in human and animals. The main problem with a diagnosis of prion diseases is how to sensitively and selectively discriminate and detection of the minute amount of PrP^Res in biological samples. Our previous work had demonstrated that dual-aptamer strategy could achieve highly sensitive and selective discrimination and detection of prion protein (cellular prion protein, PrP^C, and the diseases associated isoform, PrP^Res) in serum and brain. Inspired by the advantages of molecular logic gate, we further conceived a new concept for dual-aptamer logic gate that responds to two chemical input signals (PrP^C or PrP^Res and Gdn-HCl) and generates a change in fluorescence intensity as the output signal. It was found that PrP^Res performs the “OR” logic operation while PrP^C performs “XOR” logic operation when they get through the gate consisted of aptamer modified reusable magnetic microparticles (MMPs-Apt1) and quantum dots (QDs-Apt2). The dual-aptamer logic gate simplifies the discrimination results of PrP^Res, leaving the detection of PrP^Res either “yes” or “no”. The development of OR logic gate based on dual-aptamer strategy and two chemical input signals (PrP^Res and Gdn-HCl) is an important step toward the design of prion diseases diagnosis and therapy systems.     

Probing protein electrostatic interactions through temperature/reduction potential profiles

 The change in the equilibrium reduction potentials of the iron-sulfur proteins, Pyrococcus furiosus rubredoxin and P. furiosus ferredoxin, and heme protein, horse cytochrome c, has been calculated as a function of temperature using a numerical solution to the Poisson-Boltzman equation. Working curves for different internal dielectric constants were generated to best reproduce experimental observation. Based on a comparison of the experimental and simulated change in reduction potential with temperature, it is concluded that the dielectric constant of proteins is temperature-dependent and varies from protein to protein. For example, the temperature-dependent reduction potential of cytochrome c can only be simulated using a different temperature-dependent dielectric constant for each oxidation state, but this was not the case for rubredoxin or ferredoxin. The role of changes in ionization states of cytochrome c at alkaline pHs, where the reduction potential is known to be pH-dependent at room temperature, is also discussed in terms of electrostatic interaction energies as a function of temperature. It appears that temperature/reduction potential profiles may provide a direct method for measuring relative changes in internal protein dielectric constants. Received: 29 April 1996 / Accepted: 1 August 1996