Development of a structured program for conversion to prenex normal form

The method of structured programming or program development using a top-down, stepwise refinement technique provides a systematic approach for the development of programs of considerable complexity. The aim of this paper is to present the philosophy of structured programming through a case study of a nonnumeric programming task. The problem of converting a well-formed formula in first-order logic into prenex normal form is considered. The program has been coded in the programming language PASCAL and implemented on a DEC-10 system. The program has about 500 lines of code and comprises 11 procedures.

A Parallel Progressive Refinement Image Rendering Algorithm on a Scalable Multithreaded VLSI Processor Array

In this paper we develop a multithreaded VLSI processor linear array architecture to render complex environments based on the radiosity approach. The processing elements are identical and multithreaded. They work in Single Program Multiple Data (SPMD) mode. A new algorithm to do the radiosity computations based on the progressive refinement approach[2] is proposed. Simulation results indicate that the architecture is latency tolerant and scalable. It is shown that a linear array of 128 uni-threaded processing elements sustains a throughput close to 0.4 million patches/sec.

High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2

The X-ray structure of recombinant bovine pancreatic phospholipase A(2) (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 Angstrom resolution. The crystal belongs to the space group P2(1)2(1)2(1) with unit-cell parameters a = 47.12, b = 64.59 and c = 38.14 Angstrom similar to the native enzyme reported previously by Dijkstra et nl. [J. Mel. Biol. (1981), 147, 97-123]. The refinement converged to an R value of 18.4% (R-free = 22.8%) for 16 374 reflections between 10.0 and 1.5 Angstrom resolution. The surface-loop residues (60-70) art: ordered in the present orthorhombic recombinant enzyme, but disordered in the trigonal recombinant enzyme. The active-site residues, His48, Asp99, and the catalytic water superimpose well with the trigonal form. Besides the catalytic water which is hydrogen bonded to His48, it is often seen that there is a second water attached to the same N atom of His48 and simultaneously hydrogen bonded to the O atom of Asp49. It is thought that the second water facilitates the tautomerism of His48 for enzyme catalysis, The catalytic water is also hydrogen bonded to the equatorial water coordinated to the calcium ion, In addition to the equatorial water, there is also an axial calcium water and the additional structural water. These five common water molecules are hydrogen bonded to the additional 16 water molecules in the present orthorhombic structure which may further enhance the structural integrity of the active site. Besides the protein and one calcium ion, a total of 134 water molecules were located in the present high-resolution refinement.

Refinement of defection strategies stabilizes cooperation

Cooperation among unrelated individuals is an enduring evolutionary riddle and a number of possible solutions have been suggested. Most of these suggestions attempt to refine cooperative strategies, while little attention is given to the fact that novel defection strategies can also evolve in the population. Especially in the presence of punishment to the defectors and public knowledge of strategies employed by the players, a defecting strategy that avoids getting punished by selectively cooperating only with the punishers can get a selective benefit over non-conditional defectors. Furthermore, if punishment ensures cooperation from such discriminating defectors, defectors who punish other defectors can evolve as well. We show that such discriminating and punishing defectors can evolve in the population by natural selection in a Prisoner’s Dilemma game scenario, even if discrimination is a costly act. These refined defection strategies destabilize unconditional defectors. They themselves are, however, unstable in the population. Discriminating defectors give selective benefit to the punishers in the presence of non-punishers by cooperating with them and defecting with others. However, since these players also defect with other discriminators they suffer fitness loss in the pure population. Among the punishers, punishing cooperators always benefit in contrast to the punishing defectors, as the latter not only defect with other punishing defectors but also punish them and get punished. As a consequence of both these scenarios, punishing cooperators get stabilized in the population. We thus show ironically that refined defection strategies stabilize cooperation. Furthermore, cooperation stabilized by such defectors can work under a wide range of initial conditions and is robust to mistakes.

A computational algorithm for the verification of tautologies in propositional calculus

A computational algorithm (based on Smullyan's analytic tableau method) that varifies whether a given well-formed formula in propositional calculus is a tautology or not has been implemented on a DEC system 10. The stepwise refinement approch of program development used for this implementation forms the subject matter of this paper. The top-down design has resulted in a modular and reliable program package. This computational algoritlhm compares favourably with the algorithm based on the well-known resolution principle used in theorem provers.

On the Fourier refinement of protein structures

The situation normally encountered in the high-resolution refinement of protein structures is one in which the inaccurate positions of P out of a total of N atoms are known whereas those of the remaining atoms are unknown. Fourier maps with coefficients (FN -- F'P) × exp (i[alpha]'P) and (mFN -- nF'P) exp (i[alpha]'P), where FN is the observed structure factor and F'P and [alpha]'P are the magnitude and the phase angle of the calculated structure factor corresponding to the inaccurate atomic positions, are often used to correct the positions of the P atoms and to determine those of the Q unknown atoms. A general theoretical approach is presented to elucidate the effect of errors in the positions of the known atoms on the corrected positions of the known atoms and the positions of the unknown atoms derived from such maps. The theory also leads to the optimal choice of parameters used in the different syntheses. When the errors in the positions of the input atoms are systematic, their effects are not taken care of automatically by the syntheses.

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of mn K-edge XANES data

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K-edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3. The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K-edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

Confirmation of linkage and refinement of the RP28 locus for autosomal recessive retinitis pigmentosa on chromosome 2p14-p15 in an Indian family

PURPOSE: To report the linkage analysis of retinitis pigmentosa (RP) in an Indian family. METHODS: Individuals were examined for symptoms of retinitis pigmentosa and their blood samples were withdrawn for genetic analysis. The disorder was tested for linkage to known 14 adRP and 22 arRP loci using microsatellite markers. RESULTS: Seventeen individuals including seven affecteds participated in the study. All affected individuals had typical RP. The age of onset of the disease ranged from 8-18 years. The disorder in this family segregated either as an autosomal recessive trait with pseudodominance or an autosomal dominant trait. Linkage to an autosomal recessive locus RP28 on chromosome 2p14-p15 was positive with a maximum two-point lod score of 3.96 at theta=0 for D2S380. All affected individuals were homozygous for alleles at D2S2320, D2S2397, D2S380, and D2S136. Recombination events placed the minimum critical region (MCR) for the RP28 gene in a 1.06 cM region between D2S2225 and D2S296. CONCLUSIONS : The present data confirmed linkage of arRP to the RP28 locus in a second Indian family. The RP28 locus was previously mapped to a 16 cM region between D2S1337 and D2S286 in a single Indian family. Haplotype analysis in this family has further narrowed the MCR for the RP28 locus to a 1.06 cM region between D2S2225 and D2S296. Of 15 genes reported in the MCR, 14 genes (KIAA0903, OTX1, MDH1, UGP2, VPS54, PELI1, HSPC159, FLJ20080, TRIP-Br2, SLC1A4, KIAA0582, RAB1A, ACTR2, and SPRED2) are either expressed in the eye or retina. Further study needs to be done to test which of these genes is mutated in patients with RP linked to the RP28 locus.

Refinement of the thermodynamic properties of ruthenium dioxide and osmium dioxide

The standard Gibbs energies of formation of RuO2 and OsO2 at high temperature have been determined with high precision, using a novel apparatus that incorporates a buffer electrode between the reference and working electrodes, The buffer electrode absorbs the electrochemical flux of oxygen through the solid electrolyte from the electrode with higher oxygen chemical potential to the electrode with lower oxygen potential, The buffer electrode prevents polarization of the measuring electrode and ensures accurate data, The standard Gibbs energies of formation (Delta(f)G degrees) of RuO2, in the temperature range of 900-1500 K, and OsO2, in the range of 900-1200 K, can be represented by the equations Delta(f)G degrees(RuO2)(J/mol) = -324 720 + 354.21T - 23.490T In T Delta(f)G degrees(OsO2)(J/mol) = -304 740 + 318.80T - 18.444T In T where the temperature T is given in Kelvin and the deviation of the measurement is +/- 80 J/mol, The high-temperature heat ;capacities of RuO2 and OsO2 are measured using differential scanning calorimetry. The information for both the low- and high-temperature heat rapacity of RuO2 is coupled with the Delta(f)G degrees data obtained in this study to evaluate the standard enthalpy of formation of RuO2 at 298.15 K (Delta(f)H degrees(298.15K)). The low-temperature heat capacity of OsO2 has not been measured: therefore, the standard enthalpy and entropy of formation of OsO2 at 298.15 K (Delta(f)H degrees(298.15K) and S degrees(298.15K), respectively) are derived simultaneously through an optimization procedure from the high-temperature heat capacity and the Gibbs energy of formation. Both Delta fH degrees(298.15K) and S degrees(298.15K) are treated as variables in the optimization routine, For RuO2, the standard enthalpy of formation at 298.15 K is Delta fH degrees(298.15K) (RuO2) -313.52 +/- 0.08 kJ/mol, and that for OsO2 is Delta(f)H degrees(298.15K) (OSO2) = -295.96 +/- 0.08 kJ/mol. The standard entropy of OsO2 at 298.15 K that has been obtained from the optimization is given as S degrees(298.15K) (OsO2) = 49.8 +/- 0.2 J (mol K)(-1).

Quantitative structural refinement of mn K edge XANES in LaMnO3 and CaMnO3 perovskites

The special magnetotransport properties of hole doped manganese perovskites originate from a complex interplay among structural, magnetic and electronic degree of freedom. In this picture the local atomic structure around Mn ions plays a special role and this is the reason why short range order techniques like X-ray absorption spectroscopy (XAS) have been deeply exploited for studying these compounds. The analysis of near edge region features (XANES) of XAS spectra can provide very fine details of the local structure around Mn, complementary to the EXAFS, so contributing to the full understanding of the peculiar physical properties of these materials. Nevertheless the XANES analysis is complicated by the large amount of structural and electronic details involved making difficult the quantitative interpretation.This work exploits the recently developed MXAN code to achieve a full structural refinement of the Mn K edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3, in which the Mn ions are present only in one charge state as Mn3+ and Mn4+ respectively. The good agreement between the results derived from the analysis of near edge and extended region of the XAS spectra demonstrates that a quantitative picture of the local structure call be obtained from structural refinement of Mn K edge XANES data in these crystalline compounds. The XANES analysis offers, in addition.. the possibility to directly achieve information on the topology of local atomic structure around the absorber not directly achievable from EXAFS.

New a posteriori error estimator and adaptive mesh refinement strategy for 2-D crack problems

A posteriori error estimation and adaptive refinement technique for fracture analysis of 2-D/3-D crack problems is the state-of-the-art. The objective of the present paper is to propose a new a posteriori error estimator based on strain energy release rate (SERR) or stress intensity factor (SIF) at the crack tip region and to use this along with the stress based error estimator available in the literature for the region away from the crack tip. The proposed a posteriori error estimator is called the K-S error estimator. Further, an adaptive mesh refinement (h-) strategy which can be used with K-S error estimator has been proposed for fracture analysis of 2-D crack problems. The performance of the proposed a posteriori error estimator and the h-adaptive refinement strategy have been demonstrated by employing the 4-noded, 8-noded and 9-noded plane stress finite elements. The proposed error estimator together with the h-adaptive refinement strategy will facilitate automation of fracture analysis process to provide reliable solutions.

Successive refinement of structures with data of increasing resolution: a theoretical study for triclinic space groups

The method of least squares could be used to refine an imperfectly related trial structure by adoption of one of the following two procedures: (i) using all the observed at one time or (ii) successive refinement in stages with data of increasing resolution. While the former procedure is successful in the case of trial structures which are sufficiently accurate, only the latter has been found to be successful when the mean positional error (i.e.<|[Delta]r|>) for the atoms in the trial structure is large. This paper makes a theoretical study of the variation of the R index, mean phase-angle error, etc. as a function of <|[Delta]r|> for data corresponding to different esolutions in order to find the best refinement procedure [i.e. (i) or (ii)] which could be successfully employed for refining trial structures in which <|[Delta]r|> has large, medium and low values. It is found that a trial structure for which the mean positional error is large could be refined only by the method of successive refinement with data of increasing resolution.

A microcomputer program to analyze the CD spectrum of proteins and nucleic acids—Use of LOTUS 1-2-3 spread sheet

A user friendly interactive computer program, CIRDIC, is developed which calculates the molar ellipticity and molar circular dichroic absorption coefficients from the CD spectrum. This, in combination with LOTUS 1-2-3 spread sheet, will give the spectra of above parameters vs wavelength. The code is implemented in MicroSoft FORTRAN 77 which runs on any IBM compatible PC under MSDOS environment.

Structure of bovine prothrombin fragment 1 refined at 2.25 Å resolution

The structure of bovine prothrombin fragment 1 has been refined at 2.25 Å resolution using high resolution measurements made with the synchrotron beam at CHESS. The synchrotron data were collected photographically by oscillation methods (R-merge = 0.08). These were combined with lower order diffractometer data for refinement purposes. The structure was refined using restrained least-squares methods with the program PROLSQ to a crystallographic R-value of 0.175. The structure includes 105 water molecules with occupancies of >0·6. The first 35 residues (Ala1-Leu35) of the N-terminal ?-carboxy glutamic acid-domain (Ala1-Cys48) of fragment 1 are disordered as are two carbohydrate chains of Mr ? 5000; the latter two combine to render 40% of the structure disordered. The folding of the kringle of fragment 1 is related to the close intramolecular contact between the inner loop disulfide groups. Half of the conserved sequence of the kringle forms an inner core surrounding these disulfide groups. The remainder of the sequence conservation is associated with the many turns of the main chain. The Pro95 residue of the kringle has a cis conformation and Tyr74 is ordered in fragment 1, although nuclear magnetic resonance studies indicate that the comparable residue of plasminogen kringle 4 has two positions. Surface accessibility calculations indicate that none of the disulfide groups of fragment 1 is accessible to solvent.

HELANAL: A program to characterise helix geometry in proteins,

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.