Purification of RNA polymerase from mycobacteria for optimized promoter-polymerase interactions

In vitro transcription analysis is important to understand the mechanism of transcription. Various assays for the analysis of initiation, elongation and termination form the basis for better understanding of the process. Purified RNA polymerase (RNAP) with high specific activity is necessary to carry out variety of these specific reactions. The RNAP purified from Mycobacterium smegmatis from exponential phase showed low promoter specificity in promoter-polymerase interaction studies. This is due to the presence of a large number of sigma factors during exponential phase and under-representation of sigma(A) required for house-keeping transcription. We describe an in vivo reconstitution of RNAP holoenzyme with sigma(A) and its purification, which resulted in holoenzyme with stoichiometric sigma(A) content. The reconstituted holoenzyme showed enhanced promoter-specific binding and promoter-specific-transcription activity compared to the enzyme isolated using standard procedure. Such in vivo reconstitution of stoichiometric holoenzyme could facilitate promoter-specific transcription assays, especially in organisms which encode a large number of sigma factors.

Off-line signature verification using genetically optimized weighted features

This paper is concerned with off-line signature verification. Four different types of pattern representation schemes have been implemented, viz., geometric features, moment-based representations, envelope characteristics and tree-structured Wavelet features. The individual feature components in a representation are weighed by their pattern characterization capability using Genetic Algorithms. The conclusions of the four subsystems teach depending on a representation scheme) are combined to form a final decision on the validity of signature. Threshold-based classifiers (including the traditional confidence-interval classifier), neighbourhood classifiers and their combinations were studied. Benefits of using forged signatures for training purposes have been assessed. Experimental results show that combination of the Feature-based classifiers increases verification accuracy. (C) 1999 Pattern Recognition Society. Published by Elsevier Science Ltd. All rights reserved.

Intermittent Dynamics, Stochastic Resonance and Dynamical Heterogeneity in Supercooled Liquid Water

Here we find through computer simulations and theoretical analysis that the low temperature thermodynamic anomalies of liquid water arises from the intermittent fluctuation between its high density and low density forms, consisting largely of 5-coordinated and 4-coordinated water molecules, respectively. The fluctuations exhibit strong dynamic heterogeneity (defined by the four point time correlation function), accompanied by a divergence like growth of the dynamic correlation length, of the type encountered in fragile supercooled liquids. The intermittency has been explained by invoking a two state model often employed to understand stochastic resonance, with the relevant periodic perturbation provided here by the fluctuation of the total volume of the system.

Dynamical Transition of Water in the Grooves of DNA Duplex at Low Temperature

At low temperature (below its freezing/melting temperature), liquid water under confinement is known to exhibit anomalous dynamical features. Here we study structure and dynamics of water in the grooves of a long DNA duplex using molecular dynamics simulations with TIP5P potential at low temperature. We find signatures of a dynamical transition in both translational and orientational dynamics of water molecules in both the major and the minor grooves of a DNA duplex. The transition occurs at a slightly higher temperature (TGL ≈ 255 K) than the temperature at which the bulk water is found to undergo a dynamical transition, which for the TIP5P potential is at 247 K. Groove water, however, exhibits markedly different temperature dependence of its properties from the bulk. Entropy calculations reveal that the minor groove water is ordered even at room temperature, and the transition at T ≈ 255 K can be characterized as a strong-to-strong dynamical transition. Confinement of water in the grooves of DNA favors the formation of a low density four-coordinated state (as a consequence of enthalpy−entropy balance) that makes the liquid−liquid transition stronger. The low temperature water is characterized by pronounced tetrahedral order, as manifested in the sharp rise near 109° in the O−O−O angle distribution. We find that the Adams−Gibbs relation between configurational entropy and translational diffusion holds quite well when the two quantities are plotted together in a master plot for different region of aqueous DNA duplex (bulk, major, and minor grooves) at different temperatures. The activation energy for the transfer of water molecules between different regions of DNA is found to be weakly dependent on temperature.

Unusual dynamical arrest in polymer grafted nanoparticles

We present results of temperature dependent measurements of dynamics of polymer grafted nanoparticles with high grafting density with star polymerlike morphology. We observed for the low grafting density and hence low functionality sample, a dynamically arrested state with lowering of temperature, similar to what was conjectured earlier. However the high grafting density sample shows liquidlike relaxation at all measured temperatures. Possible origin of dynamical arrest in the two grafting density sample is discussed.

A pseudo-dynamical systems approach to a class of inverse problems in engineering

A pseudo-dynamical approach for a class of inverse problems involving static measurements is proposed and explored. Following linearization of the minimizing functional associated with the underlying optimization problem, the new strategy results in a system of linearized ordinary differential equations (ODEs) whose steady-state solutions yield the desired reconstruction. We consider some explicit and implicit schemes for integrating the ODEs and thus establish a deterministic reconstruction strategy without an explicit use of regularization. A stochastic reconstruction strategy is then developed making use of an ensemble Kalman filter wherein these ODEs serve as the measurement model. Finally, we assess the numerical efficacy of the developed tools against a few linear and nonlinear inverse problems of engineering interest.

Space and time efficiency of the forest-of-quadtrees representation

A forest of quadtrees is a refinement of a quadtree data structure that is used to represent planar regions. A forest of quadtrees provides space savings over regular quadtrees by concentrating vital information. The paper presents some of the properties of a forest of quadtrees and studies the storage requirements for the case in which a single 2m × 2m region is equally likely to occur in any position within a 2n × 2n image. Space and time efficiency are investigated for the forest-of-quadtrees representation as compared with the quadtree representation for various cases.

Representation of functional dependencies in relational databases using linear graphs

Functional dependencies in relational databases are investigated. Eight binary relations, viz., (1) dependency relation, (2) equipotence relation, (3) dissidence relation, (4) completion relation, and dual relations of each of them are described. Any one of these eight relations can be used to represent the functional dependencies in a database. Results from linear graph theory are found helpful in obtaining these representations. The dependency relation directly gives the functional dependencies. The equipotence relation specifies the dependencies in terms of attribute sets which functionally determine each other. The dissidence relation specifies the dependencies in terms of saturated sets in a very indirect way. Completion relation represents the functional dependencies as a function, the range of which turns out to be a lattice. Depletion relation which is the dual of the completion relation can also represent functional dependencies and similarly can the duals of dependency, equipotence, and dissidence relations. The class of depleted sets, which is the dual of saturated sets, is defined and used in the study of depletion relations.

Linear time geometrical design rule checker based on quadtree representation of VLSI mask layouts

An efficient geometrical design rule checker is proposed, based on operations on quadtrees, which represent VLSI mask layouts. The time complexity of the design rule checker is O(N), where N is the number of polygons in the mask. A pseudoPascal description is provided of all the important algorithms for geometrical design rule verification.

Identification of dynamical systems with fractional derivative damping models using inverse sensitivity analysis

The problem of identifying parameters of time invariant linear dynamical systems with fractional derivative damping models, based on a spatially incomplete set of measured frequency response functions and experimentally determined eigensolutions, is considered. Methods based on inverse sensitivity analysis of damped eigensolutions and frequency response functions are developed. It is shown that the eigensensitivity method requires the development of derivatives of solutions of an asymmetric generalized eigenvalue problem. Both the first and second order inverse sensitivity analyses are considered. The study demonstrates the successful performance of the identification algorithms developed based on synthetic data on one, two and a 33 degrees of freedom vibrating systems with fractional dampers. Limited studies have also been conducted by combining finite element modeling with experimental data on accelerances measured in laboratory conditions on a system consisting of two steel beams rigidly joined together by a rubber hose. The method based on sensitivity of frequency response functions is shown to be more efficient than the eigensensitivity based method in identifying system parameters, especially for large scale systems.

Reflexive Incidence Matrx (RIM) Representation of Petr Nets

Although incidence matrix representation has been used to analyze the Petri net based models of a system, it has the limitation that it does not preserve reflexive properties (i.e., the presence of selfloops) of Petri nets. But in many practical applications self-loops play very important roles. This paper proposes a new representation scheme for general Petri nets. This scheme defines a matrix called "reflexive incidence matrix (RIM) c which is a combination of two matrices, a "base matrix Cb,,, and a "power matrix CP." This scheme preserves the reflexive and other properties of the Petri nets. Through a detailed analysis it is shown that the proposed scheme requires less memory space and less processing time for answering commonly encountered net queries compared to other schemes. Algorithms to generate the RIM from the given net description and to decompose RIM into input and output function matrices are also given. The proposed Petri net representation scheme is very useful to model and analyze the systems having shared resources, chemical processes, network protocols, etc., and to evaluate the performance of asynchronous concurrent systems.

Representation of functional dependencies in relational databases using linear graphs

Functional dependencies in relational databases are investigated. Eight binary relations, viz., (1) dependency relation, (2) equipotence relation, (3) dissidence relation, (4) completion relation, and dual relations of each of them are described. Any one of these eight relations can be used to represent the functional dependencies in a database. Results from linear graph theory are found helpful in obtaining these representations. The dependency relation directly gives the functional dependencies. The equipotence relation specifies the dependencies in terms of attribute sets which functionally determine each other. The dissidence relation specifies the dependencies in terms of saturated sets in a very indirect way. Completion relation represents the functional dependencies as a function, the range of which turns out to be a lattice. Depletion relation which is the dual of the completion relation can also represent functional dependencies and similarly can the duals of dependency, equipotence, and dissidence relations. The class of depleted sets, which is the dual of saturated sets, is defined and used in the study of depletion relations.

A new formalism for representation of binary thermodynamic data

The applicability of a formalism involving an exponential function of composition x1 in interpreting the thermodynamic properties of alloys has been studied. The excess integral and partial molar free energies of mixing are expressed as: $$\begin{gathered} \Delta F^{xs} = a_o x_1 (1 - x_1 )e^{bx_1 } \hfill \\ RTln\gamma _1 = a_o (1 - x_1 )^2 (1 + bx_1 )e^{bx_1 } \hfill \\ RTln\gamma _2 = a_o x_1^2 (1 - b + bx_1 )e^{bx_1 } \hfill \\ \end{gathered} $$ The equations are used in interpreting experimental data for several relatively weakly interacting binary systems. For the purpose of comparison, activity coefficients obtained by the subregular model and Krupkowski’s formalism have also been computed. The present equations may be considered to be convenient in describing the thermodynamic behavior of metallic solutions.

Representation and properties of para-Bose oscillator operators. II. Coherent states and the minimum uncertainty states

The energy, position, and momentum eigenstates of a para-Bose oscillator system were considered in paper I. Here we consider the Bargmann or the analytic function description of the para-Bose system. This brings in, in a natural way, the coherent states ||z;alpha> defined as the eigenstates of the annihilation operator ?. The transformation functions relating this description to the energy, position, and momentum eigenstates are explicitly obtained. Possible resolution of the identity operator using coherent states is examined. A particular resolution contains two integrals, one containing the diagonal basis ||z;alpha><−z;alpha||. We briefly consider the normal and antinormal ordering of the operators and their diagonal and discrete diagonal coherent state approximations. The problem of constructing states with a minimum value of the product of the position and momentum uncertainties and the possible alpha dependence of this minimum value is considered. Journal of Mathematical Physics is copyrighted by The American Institute of Physics.

Stabilization of linear and nonlinear dynamical systems using an observer-controller configuration

In this paper the problem of stabilization of systems by means of stable compensations is considered, and results are derived for systems using observer�controller structures, for systems using a cascade structure, and for nonlinear systems