Structural DNA profiles: single sequence queries

Structural DNA profiles use the structural properties of the constituent octamers either to observe any characteristics of a single sequence that are unusual (a single sequence query) or to visualize a pattern common to a set of sequences (a multiple sequence query). They are an aid in understanding structural reasons for functional DNA activity. Profiles that answer single sequence queries are introduced and Profile Manager (a software application developed to automate profile generation) is presented. Two sequences that are similar by their nucleotide composition but are known to be very different by structure are analyzed, resulting in useful illustrations that agree with the experimental nuclear magnetic resonance structures.     

Test of an integral approximation scheme based on semiorthogonalized orbitals in LCAO SCF MO CI calculations of naphthalene

Ab initio LCAO SCF MO CI calculations of naphthalene are carried out with a minimal basis set to test an integral approximation scheme proposed in a previous paper. When 71.3 and 53.0% of the two-electron integrals are neglected, the errors in the SCF total energy are only ?0.0534 and ?0.0006 a.u., respectively. In the latter case, the maximum absolute errors of the orbital energy and the gross AO population are 0.007 a.u. and 0.001, respectively. Even in the former case the errors of the excitation energies are less than 0.0004 a.u. Errors of oscillator strengths are also examined and are found to be tolerably small.     

Detecting Reaction Pathways and Computing Reaction Rates in Condensed Phase

Methods for the computation of rate constants that characterize classical reactions occurring in the condensed phase are discussed. While microscopic expressions for these transport properties are well known, their computation presents challenges for simulation since reactive events often occur rarely, and the long time scales that are typical for reactive processes are not accessible using simple molecular dynamics methods. Furthermore, the underlying free energy surface is very complex with many saddle points that prevent sampling of possible reaction pathways. As a result, the reaction coordinate may be a complex many-body function of the system’s degrees of freedom. Since there is not an a priori way to define a “good” reaction coordinate, methods are being developed to assist in a systematic construction of a reaction coordinate. These methods are reviewed and examples of non-trivial reaction coordinates are presented.     

Application of power expansion in the thermodynamics of compressible Markovian copolymers

The problem of constructing phase diagrams for a compressible melt of a binary Markovian copolymer is reduced to a set of nonlinear differential equations in partial derivatives with transcendental relationships. Using power expansions, the closed set of nonlinear differential equations is derived. This set allows its further analytical study. Eigenvalues of a linearized system are analyzed, and the boundaries of the thermodynamic stability of melts are defined. Nonlinear equations in normal coordinates are obtained; for symmetric melts, these equations are reduced to a single equation by adiabatic elimination of small-scale variables. Binodal curves are calculated for such solutions of this equation, which correspond to the free energy minimum of melts. Corrections reflecting the effect of melt nonsymmetry are found. The results are applied for copolymers, whose composition is similar to that of homopolymers, diblock copolymers, and random and regularly alternating copolymers. Spinodals and binodals corresponding to microphase separation are constructed.     

Does Marcus theory apply to redox processes in ionic liquids? A simulation study

Simulation studies on a model system of a spherical ion with various charges in two imidazolium ionic liquids and in acetonitrile are compared. The average vertical ionisation potentials as a function of the charge on the ion are similar for all three systems. The Landau free energies of each system as a function of the vertical ionisation potential are computed and are close to being parabolic. Results are shown for the solvent reorganisation energies and for the activation free energies. The similarities of all these quantities are interpreted in terms of continuum models. However, the dynamics are likely to be very different in a polar liquid and in an ionic liquid as in the former case screening occurs by reorientation of molecules and in the latter case it occurs by translation of ions.     

Sequences of ultrafast non-resonant multiphoton transitions in a three-electronic level molecule

Non-resonant multiphoton transitions between three electronic states of a molecular system are studied. Based on a projection operator formalism which is formulated in the framework of the so-called time-local as well as the time-nonlocal approach, time-dependent Schrödinger equations are obtained, which include effective couplings to the laser field. For both procedures a slowly varying amplitude approximation can be invoked. The resulting time-local equations are solved in a much more efficient way than the original effective Schrödinger equations. The validity of these approximations is verified numerically for a two-photon process. Furthermore, the effective Schrödinger equations are specified to sequences of two-photon and three-photon transitions. The derived equations are applied to a molecular system consisting of three electronic states with Morse-type potential energy curves. Using different laser pulse scenarios the conditions are discussed under which a sequence of two-photon and three-photon transitions can take place.     

Characteristics of atomic vibrational motion in a one-component defective crystal

Vibrations of atoms in a defective argon crystal are considered. Frequencies are calculated in the harmonic approximation and Mie and Einstein approximations. The vibrations are calculated for a set of local clusters differing in the position of a vacancy at different distances from a selected atom. Probabilities for these clusters are calculated within a quasichemical approximation of the lattice gas model. It is shown that when combined contributions from lateral interactions and vibrational motions are allowed for in the free crystal energy, there is an increase in the lattice constant upon a rise in temperature in all approximations. It is found that the frequencies calculated using the Mie model become closer to the frequency distribution in the harmonic approximation as the degree of crystal defectiveness increases.     

Review of chemical methods for the determination of penicillin

The published methods for the analysis of penicillin are classified according to whether they are intended a) to differentiate between types of penicillin, or b) to determine the total penicillins present in a given sample.The limitations of many of these methods are indicated, and those which are attractive for possible routine application are discussed in detail.     

Integration of multiple-ion-sensing on a capillary-assembled microchip

Multiple-ion-sensing functions are integrated on a capillary-assembled microchip (CAs-CHIP). Since the CAs-CHIPs are fabricated by embedding various chemically functionalized square capillaries onto a lattice PDMS channel plate having same channel dimensions as outer dimensions of square capillaries, integration of parallel multiple-ion-sensing is easily realized. Here, three ion-sensing capillaries are prepared and used for integrating these functions onto a single microchip. Ion-sensing square capillaries (sodium, potassium, calcium) are prepared by attaching ion-selective optode membranes to inner wall of capillaries, and are characterized in terms of response time, response range, and ion selectivity. Finally, fully characterized ion-sensing capillaries are embedded into PDMS channel plate in parallel to fabricate a multiple-ion-sensing chip. The CAs-CHIP-based strategy is promising for integrating multiple chemical sensing functions onto a single microchip.     

Interactions between a polystyrene particle and hydrophilic and hydrophobic surfaces in aqueous solutions

The interaction between a colloidal polystyrene particle mounted on an AFM cantilever and a hydrophilic and a hydrophobic surface in aqueous solution is investigated. Despite the apparent simplicity of these two types of systems a variety of different types of interactions are observed. The system containing the polystyrene particle and a hydrophilic surface shows DLVO-like interactions characteristic of forces between charged surfaces. However, when the surface is hydrophobized the interaction changes dramatically and shows evidence of a bridging air bubble being formed between the particle and the surface. For both sets of systems, plateaus of constant force in the force curves are obtained when the particle is retracted from the surface after being in contact. These events are interpreted as a number of individual polystyrene molecules that are bridging the polystyrene particle and the surface. The plateaus of constant force are expected for pulling a hydrophobic polymer in a bad (hydrophilic) solvent. The plateau heights are found to be of uniform spacing and independent of the type of surface, which suggests a model by which collapsed polymers are extended into the aqueous medium. This model is supported by a full stretching curve showing also the backbone elasticity and a stretching curve obtained in pentanol, where the plateau changes to a nonlinear force response, which is typical for a polymer in a good or neutral solvent. We suggest that these polymer bridges are important in particular for the interaction between polystyrene and the hydrophilic surface, where they to some extent counteract the long-range electrostatic repulsion.     

Living with multiple standards – QA in a multidisciplinary laboratory

 The paper describes the experiences of a medium-sized analytical laboratory in implementing and developing a quality system compliant with several standards. The effect of the laboratory's changing role and work pattern on the quality system are considered. The laboratory costs are explored. The laboratory's particular experiences are shown to be consistent with recent market research in the United Kingdom. Some of the factors a laboratory needs to consider in formulating a quality strategy are described, including the possibility of joint assessments. Also, possible courses of development of the standards themselves are suggested. These developments could simplify the existing situation where laboratories are forced into a quality approach based on multiple standards and assessment. Received: 1 October 1998 · Accepted: 26 January 1999     

Energy levels of paramagnetic ions: Algebra. II

The correspondence rules between the algebra of coupling coefficients of the special unitary group SU(2) and the associated algebra of a subgroup G of SU(2) are presented. The matrix elements of the irreducible representations of G are written in a convenient quantization scheme and different relations between these matrix elements and the Clebsch-Gordan coefficients of G are derived. Such a formalism is appropriate for numerous spectroscopic problems. As an example, it is applied to crystal field theory and electron paramagnetic resonance. General formulas from which a large number of results are rederived and generalized in a straightforward fashion are given. Numerical values of coupling coefficients for the tetragonal and cubic groups are listed in the Appendix.     

Gold ultra-microelectrode arrays: application to the steady-state voltammetry of hydroxide ion in aqueous solution.

Gold ultra-microelectrode arrays are used to explore the electrochemical oxidation of hydroxide ions and are shown to be analytical useful. Two types of ultra-microelectrode arrays are used; the first consist of 256 individual electrodes of 5 microm in radius, 170 of which are electrochemically active in a cubic arrangement which are separated from their nearest neighbour by a distance of 100 microm. The second array compromises 2597 electrodes of 2.5 microm in radius and of which 1550 of which are electrochemically active in a hexagonal arrangement separated by the nearest neighbour by 55 microm. Well defined voltammetric waves are found with peak currents proportional to the concentration of hydroxide ions in the range 50 microM to 1 mM. Detection limits of 20 microM using the 170 ultra-microelectrode and 10 microM with the 1550 ultra-microelectrode array are shown to be possible but with a higher sensitivity of 4 mA M(-1) observed using the 1550 ultra-microelectrode array compared to 1.2 mA M(-1) with the 170 ultra-microelectrode array.     

Controlled-Rate Thermal Desorptton

A new way of conducting thermal desorption experiments is described. The method consists in maintaining the desorption rate constant by a rigorous control of temperature. The equations for two models of constant rate desorption are described: from a surface with only one type of adsorption site, and with two different types. The technique is applied to two real systems and the kinetic parameters are determined. The results are compared with those obtained by using TPD. The main advantages are discussed and the methodology and modifications required for a TPD set-up to work at a constant desorption rate are described.     

Inorganic electrides

Inorganic electrides are a novel kind of ionic compounds in which the anions are electrons confined in a complex array of cavities or channels and the cations are nanoscale arrays of alkali metal ions that provide charge balance. In electrides the donated electron behaves like a low-density correlated electron gas, whereby the dimensionality of the electron gas and its electronic and magnetic properties are determined by the topology of the cavities in the host matrix. Unlike traditional electrides, in which alkali cations are encapsulated within an organic cage, inorganic electrides are thermally stable. The current inorganic electrides based on alkali metal loaded zeolites can be designed as useful reduced-dimensionality materials. Inorganic electrides are powerful reducing agents, and they are able to reduce small aromatic molecules to the radical anions within the channels of the zeolite.     

New indices for analysing partial ranking diagrams

Interest is growing in decision making strategies and several techniques are now available. The assessment of priorities is a typical premise before final decisions are taken. Total and partial order ranking (POR) strategies, which from a mathematical point of view are based on elementary methods of discrete mathematics, appear as an attractive and simple tool to asses priorities. Despite the well-known total ranking strategies, which are scalar methods combining the different criteria values into a global index which always ranks elements in an ordered sequence, the partial order ranking is a vectorial approach which recognises that not all the elements can be directly compared with all the others. In fact when many criteria are considered, contradictions in the ranking are bound to exist and the higher the number of criteria, the higher the probability that contradictions in the ranking occur. The Hasse diagram technique (HDT) is a very useful tool to perform partial order ranking. The results of the partial order ranking are visualised in a diagram, called Hasse diagram. Incomparable elements are located at the same geometrical height and as high as possible in the diagram, thus incomparable elements are arranged in levels. The quality of a ranking procedure has to be evaluated by a deep analysis and by several indices, i.e. scalar functions that describe features of an ordered set and allow comparison among different rankings. For this purpose, new indices for ranking analysis are proposed here, compared with the ones found in literature and tested on theoretical examples and on real data.     

Analysis of kinetic isotope effects for nonadiabatic reactions

Factors influencing the rates of quantum mechanical particle transfer reactions in many-body systems are discussed. The investigations are carried out on a simple model for a proton transfer reaction that captures generic features seen in more realistic models of condensed phase systems. The model involves a bistable quantum oscillator coupled to a one-dimensional double-well reaction coordinate, which is in turn coupled to a bath of harmonic oscillators. Reactive-flux correlation functions that involve quantum-classical Liouville dynamics for chemical species operators and quantum equilibrium sampling are used to estimate the reaction rates. Approximate analytical expressions for the quantum equilibrium structure are derived. Reaction rates are shown to be influenced significantly by both the quantum equilibrium structure and nonadiabatic dynamics. Nonadiabatic dynamical effects are found to play the major role in determining the magnitude of the kinetic isotope effect for the model transfer reaction.     

Expert system for precision testing in validation of liquid chromatographic methods

After a liquid chromatographic method has been developed, it must be validated to establish its limitations in daily use. Method validation is becoming increasingly important as stricter rules are applied by regulatory authorities. Precision testing is a vital step in this validation; both intralaboratory testing and interlaboratory testing are needed. In an intralaboratory test, repeatability and ruggedness tests are usually done. Expert systems are available for both tests. Here they are integrated to form an intralaboratory precision-testing expert system; special integration architecture is described. Important features of the integrated system are a supervisor containing planning knowledge about the tests and a common data structure containing all the objects necessary for an expert system in this area.     

Shape and buckling transitions in solid-stabilized drops

We study shape and buckling transitions of particle-laden sessile and pendant droplets that are forced to shrink in size. Monodisperse polystyrene particles were placed at the interface between water and decane at conditions that are known to produce hexagonal, crystalline arrangements on flat interfaces. As the volumes of the drops are reduced, the surface areas are likewise diminished. This effectively compresses the particle monolayer coating and induces a transition from a fluid film to a solid film. Since the particles are firmly attached to the interface by capillary forces, the shape transitions are reversible and shape/volume curves are the same for drainage and inflation. Measurements of the internal pressure of the drops reveal a strong transition in this variable as the buckling transition is approached.