Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase.The role of conserved residues and complementary mutations

The active site of triosephosphate isomerase (TIM, EC: 5.3.1.1), a dimeric enzyme, lies very close to the subunit interface. Attempts to engineer monomeric enzymes have yielded well-folded proteins with dramatically reduced activity. The role of dimer interface residues in the stability and activity of the Plasmodium falciparum enzyme, PfTIM, has been probed by analysis of mutational effects at residue 74. The PfTIM triple mutant W11F/W168F/Y74W (Y74W*) has been shown to dissociate at low protein concentrations, and exhibits considerably reduced stability in the presence of denaturants, urea and guanidinium chloride. The Y74W* mutant exhibits concentration-dependent activity, with an approximately 22-fold enhancement of kcat over a concentration range of 2.5–40 μm, suggesting that dimerization is obligatory for enzyme activity. The Y74W* mutant shows an approximately 20-fold reduction in activity compared to the control enzyme (PfTIM WT*, W11F/W168F). Careful inspection of the available crystal structures of the enzyme, together with 412 unique protein sequences, revealed the importance of conserved residues in the vicinity of the active site that serve to position the functional K12 residue. The network of key interactions spans the interacting subunits. The Y74W* mutation can perturb orientations of the active site residues, due to steric clashes with proximal aromatic residues in PfTIM. The available crystal structures of the enzyme from Giardia lamblia, which contains a Trp residue at the structurally equivalent position, establishes the need for complementary mutations and maintenance of weak interactions in order to accommodate the bulky side chain and preserve active site integrity.

A world of Bose particles

Editor's Note: Satyendranath Bose, known primarily as one of the co–founders of quantum statistics, died on 4 February 1974, a few weeks after a symposium in honor of his 80th birthday was held at the Saha Institute for Nuclear Physics in Calcutta. The following paper, originally prepared in that connection, reviews some of the more important developments in particle physics which followed from the fundamental insight contained in a four–page paper published by Bose exactly fifty years ago. At the request of the editors of the AJP, Professor Sudarshan has kindly consented to adapt his paper for reproduction here. We would like to thank William Blanpied for bringing this paper to our attention.

Boson-fermion duality in SU(m vertical bar n) supersymmetric Haldane-Shastry spin chain

By using the Y(gl(m|n)) super Yangian symmetry of the SU(m|n) supersymmetric Haldane-Shastry spin chain, we show that the partition function of this model satisfies a duality relation under the exchange of bosonic and fermionic spin degrees of freedom. As a byproduct of this study of the duality relation, we find a novel combinatorial formula for the super Schur polynomials associated with some irreducible representations of the Y(gl(m|n)) Yangian algebra. Finally, we reveal an intimate connection between the global SU(m|n) symmetry of a spin chain and the boson-fermion duality relation. (C) 2007 Elsevier B.V. All rights reserved.

Low energy properties of the SU(m|n) supersymmetric Haldane–Shastry spin chain

The ground state and low energy excitations of the SU(m|n) supersymmetric Haldane–Shastry spin chain are analyzed. In the thermodynamic limit, it is found that the ground state degeneracy is finite only for the SU(m|0) and SU(m|1) spin chains, while the dispersion relation for the low energy and low momentum excitations is linear for all values of m and n. We show that the low energy excitations of the SU(m|1) spin chain are described by a conformal field theory of m non-interacting Dirac fermions which have only positive energies; the central charge of this theory is m/2. Finally, for ngreater-or-equal, slanted1, the partition functions of the SU(m|n) Haldane–Shastry spin chain and the SU(m|n) Polychronakos spin chain are shown to be related in a simple way in the thermodynamic limit at low temperatures.

Geant4 Hadronic Cascade Models and CMS Data Analysis : Computational Challenges in the LHC era

This work belongs to the field of computational high-energy physics (HEP). The key methods used in this thesis work to meet the challenges raised by the Large Hadron Collider (LHC) era experiments are object-orientation with software engineering, Monte Carlo simulation, the computer technology of clusters, and artificial neural networks. The first aspect discussed is the development of hadronic cascade models, used for the accurate simulation of medium-energy hadron-nucleus reactions, up to 10 GeV. These models are typically needed in hadronic calorimeter studies and in the estimation of radiation backgrounds. Various applications outside HEP include the medical field (such as hadron treatment simulations), space science (satellite shielding), and nuclear physics (spallation studies). Validation results are presented for several significant improvements released in Geant4 simulation tool, and the significance of the new models for computing in the Large Hadron Collider era is estimated. In particular, we estimate the ability of the Bertini cascade to simulate Compact Muon Solenoid (CMS) hadron calorimeter HCAL. LHC test beam activity has a tightly coupled cycle of simulation-to-data analysis. Typically, a Geant4 computer experiment is used to understand test beam measurements. Thus an another aspect of this thesis is a description of studies related to developing new CMS H2 test beam data analysis tools and performing data analysis on the basis of CMS Monte Carlo events. These events have been simulated in detail using Geant4 physics models, full CMS detector description, and event reconstruction. Using the ROOT data analysis framework we have developed an offline ANN-based approach to tag b-jets associated with heavy neutral Higgs particles, and we show that this kind of NN methodology can be successfully used to separate the Higgs signal from the background in the CMS experiment.

Kokonaisvaltainen fysiikanopetus peruskoulussa fysiikan valinnaiskurssilla

Holistic physics education in upper secondary level based on the optional course of physics Keywords: physics education, education, holistic, curriculum, world view, values A physics teacher s task is to put into practice all goals of the curriculum. Holistic physics education means in this research teaching, in which the school s common educational goals and the goals particular to the physics curriculum are taken into account. These involve knowledge, skills and personal value and attitude goals. Research task was to clarify how the educational goals involving student s values and attitudes can be carried out through the subject content of physics. How does the physics teacher communicate the modern world view through the content of the physics class? The goal of this research was to improve teaching, to find new points of view and to widen the perspective on how physics is taught. The teacher, who acted also as a researcher, planned and delivered an optional course where she could study the possibilities of holistic physics education. In 2001-2002 ten girls and two boys of the grade 9th class participated in that elective course. According to principles of action research the teacher-researcher reflected also on her own teaching action. Research method was content analysis that involved both analyzing student feedback, and relevant features of the teacher s knowledge, which are needed for planning and giving the physics lessons. In this research that means taking into account the subject matter knowledge, curriculum, didactic and the pedagogical content knowledge of the teacher. The didactic includes the knowledge of the learning process, students motivation, specific features of the physics didactics and the research of physics education. Among other things, the researcher constructed the contents of the curriculum and abstracted sentences as keywords, from which she drew a concept map. The concept maps, for instance, the map of educational goals and the mapping of the physics essence, were tools for studying contents which are included in the holistic physics education. Moreover, conclusions were reached concerning the contents of physics domains by which these can be achieved. According to this research, the contents employing the holistic physics education is as follows: perception, the essence of science, the development of science, new research topics and interactions in physics. The starting point of teaching should be connected with the student s life experiences and the approach to teaching should be broadly relevant to those experiences. The teacher-researcher observed and analyzed the effects of the experimental physics course, through the lens of a holistic physics education. The students reported that the goals of holistic physics education were achieved in the course. The discourses of the students indicated that in the experimental course they could express their opinions and feelings and make proposals and evaluations. The students had experiences about chances to affect the content of the course, and they considered the philosophical physics course interesting, it awakened questions, increased their self-esteem and helped them to become more aware of their world views. The students analytic skills developed in the interactive learning environment. The physics teacher needs broad knowledge for planning his or her teaching, which is evaluated in this research from contents maps made for the tools of the teaching. In the holistic physics education the teacher needs an open and curious mind and skills for interaction in teaching. This research indicates the importance of teaching physics in developing attitudes and values beside substance of the physics in class environment. The different points of view concerning human beings life make it possible to construct the modern world view of the students and to develop analytic skills and the self-esteem and thus help them in learning. Overall and wide points of view also help to transfer knowledge to practice. Since such contents is not employed by teaching the physics included in the standard curriculum, supplement relevant teaching material that includes such topics are needed.

Geometries of the antiproton-nucleus optical potentials at 180 MeV

The moments of the real and the absorptive parts of the antiproton optical potentials are evaluated for the first time to study the geometries of the potentials at 180 MeV. Interesting features are revealed which are found to be comparable to the proton case in general despite the presence of strong annihilation. A few interesting deviations, however, are also found compared to the proton case.

Elliptic flow of thermal photons in heavy-ion collisions at Relativistic Heavy Ion Collider and Large Hadron Collider

We calculate the thermal photon transverse momentum spectra and elliptic flow in $\sqrt{s_{NN}} = 200$ GeV Au+Au collisions at RHIC and in $\sqrt{s_{NN}} = 2.76$ TeV Pb+Pb collisions at the LHC, using an ideal-hydrodynamical framework which is constrained by the measured hadron spectra at RHIC and LHC. The sensitivity of the results to the QCD-matter equation of state and to the photon emission rates is studied, and the photon $v_2$ is discussed in the light of the photonic $p_T$ spectrum measured by the PHENIX Collaboration. In particular, we make a prediction for the thermal photon $p_T$ spectra and elliptic flow for the current LHC Pb+Pb collisions.

Perturbative corrections for staggered four-fermion operators

We present results for one-loop matching coefficients between continuum four-fermion operators, defined in the Naive Dimensional Regularization scheme, and staggered fermion operators of various types. We calculate diagrams involving gluon exchange between quark fines, and ''penguin'' diagrams containing quark loops. For the former we use Landau-gauge operators, with and without O(a) improvement, and including the tadpole improvement suggested by Lepage and Mackenzie. For the latter we use gauge-invariant operators. Combined with existing results for two-loop anomalous dimension matrices and one-loop matching coefficients, our results allow a lattice calculation of the amplitudes for KKBAR mixing and K --> pipi decays with all corrections of O(g2) included. We also discuss the mixing of DELTAS = 1 operators with lower dimension operators, and show that, with staggered fermions, only a single lower dimension operator need be removed by non-perturbative subtraction.

Bloch-Nordsieck thermometers: One-loop exponentiation in finite temperature QED

We study the scattering of hard external particles in a heat bath in a real-time formalism for finite temperature QED. We investigate the distribution of the 4-momentum difference of initial and final hard particles in a fully covariant manner when the scale of the process, Q, is much larger than the temperature, T. Our computations are valid for all T subject to this constraint. We exponentiate the leading infra-red term at one-loop order through a resummation of soft (thermal) photon emissions and absorptions. For T > 0, we find that tensor structures arise which are not present at T = 0. These carry thermal signatures. As a result, external particles can serve as thermometers introduced into the heat bath. We investigate the phase space origin of log (Q/M) and log (Q/T) terms.

Photon-photon total cross-section

We study the total inelastic gamma gamma cross-section and discuss predictions from different models, with a special attention to their dependence on the input parameters. In particular we examine the results from a simple extension of the Regge Pomeron exchange model and those from the eikonalized mini-jet model. We then compare both of them with recent LEP data.

Phenylboronic acids in crystal engineering: Utility of the energetically unfavorable syn,syn-conformation in co-crystal design

Phenylboronic acids can exist, in principle, in three different conformers (syn,syn; syn,anti and anti,anti) with distinct energy profiles. In their native state, these compounds prefer the energetically favored syn, anti-conformation. In molecular complexes, however, the functionality exhibits conformational diversity. In this paper we report a series of co-crystals, with N-donor compounds, prepared by a design strategy involving the synthons based on the syn, syn-conformation of the boronic acid functionality. For this purpose, we employed compounds with the 1,2-diazo fragment (alprazolam, 1H-tetrazole, acetazolamide and benzotriazole), 1,10-phenanthroline and 2,2'-bipyridine for the co-crystallization experiments. However, our study shows that the mere presence of the 1,2-diazo fragment in the coformer does not guarantee the successful formation of co-crystals with a syn, syn-conformation of the boronic acid. [GRAPHICS] The -B(OH)(2) fragment makes unsymmetrical O-H center dot center dot center dot N heterosynthons with alprazolam (ALP) and 1,10-phenanthroline (PHEN). In the co-crystals of phenylboronic acids with 1H-tetrazole (TETR) and 2,2'-bipyridine (BPY), the symmetrical boronic acid dimer is the major synthon. In the BPY complex, boronic acid forms linear chains and the pyridine compound interacts with the lateral OH of boronic acid dimers that acts as a connector, thus forming a ladder structure. In the TETR complex, each heterocycle interacts with three boronic acids. While two boronic acids interact using the phenolic group, the third molecule generates O-H center dot center dot center dot N hydrogen bonds using the extra OH group, of -B(OH)(2) fragment, left after the dimer formation. Thus, although molecules were selected retrosynthetically with the 1,2-diazo fragment or with nearby hetero-atoms to induce co-crystal formation using the syn,syn-orientation of the -B(OH)(2) functionality, co-crystal formation is in fact selective and is probably driven by energy factors. Acetazolamide (ACET) contains self-complementary functional groups and hence creates stable homosynthons. Phenylboronic acids being weak competitors fail to perturb the homosynthons and hence the components crystallize separately. Therefore, besides the availability of possible hydrogen bond acceptors in the required position and orientation, the ability of the phenyl-boronic acid to perturb the existing interactions is also a prerequisite to form co-crystals. This is illustrated in the table below. In the case of ALP, PHEN and BPY, the native structures are stabilized by weak interactions and may be influenced by the boronic acid fragment. Thus phenylboronic acids can attain co-crystals with those compounds, wherein the cyclic O-H center dot center dot center dot N hydrogen bonds are stronger than the individual homo-interactions. This can lower the lattice energy of the molecular complex as compared with the individual crystals. [GRAPHICS] Phenylboronic acids show some selectivity in the formation of co-crystals with N-heterocycles. The differences in solubility of the components fall short to provide a possible reason for the selective formation of co-crystals only with certain compounds. These compounds, being weak acids, do not follow the Delta pK(a) analysis and hence fail to provide any conclusive observation. Theoretical results show that of the three conformers possible, the syn,anti conformer is the most stable. The relative stabilities of the three conformers syn,anti,syn,syn and anti,anti are 0.0, 2.18 and 3.14 kcal/mol, respectively. The theoretical calculations corroborate the fact that only energetically favorable synthons can induce the formation of heterosynthons, as in ALP and PHEN complexes. From a theoretical and structural analysis it is seen that phenylboronic acids will form interactions with those molecules wherein the heterocyclic and acidic fragments can interrupt the homosynthons. However, the energy profile is shallow and can be perturbed easily by the presence of competing functional groups (such as OH and COOH) in the vicinity. [GRAPHICS] .

The Nature of Bond Critical Points in Dinuclear Copper(I) Complexes

Closed-shell contacts between two copper(I) ions are expected to be repulsive. However, such contacts are quite frequent and are well documented. Crystallographic characterization of such contacts in unsupported and bridged multinuclear copper(I) complexes has repeatedly invited debates on the existence of cuprophilicity. Recent developments in the application of Baders theory of atoms-in-molecules (AIM) to systems in which weak hydrogen bonds are involved suggests that the copper(I)copper(I) contacts would benefit from a similar analysis. Thus the nature of electron-density distributions in copper(I) dimers that are unsupported, and those that are bridged, have been examined. A comparison of complexes that are dimers of symmetrical monomers and those that are dimers of two copper(I) monomers with different coordination spheres has also been made. AIM analysis shows that a bond critical point (BCP) between two Cu atoms is present in most cases. The nature of the BCP in terms of the electron density, ?, and its Laplacian is quite similar to the nature of critical points observed in hydrogen bonds in the same systems. The ? is inversely correlated to Cu?Cu distance. It is higher in asymmetrical systems than what is observed in corresponding symmetrical systems. By examining the ratio of the local electron potential-energy density (Vc) to the kinetic energy density (Gc), |Vc|/Gc at the critical point suggests that these interactions are not perfectly ionic but have some shared nature. Thus an analysis of critical points by using AIM theory points to the presence of an attractive metallophilic interaction similar to other well-documented weak interactions like hydrogen bonding.

Hypernuclear matter in strong magnetic field

Compact stars with strong magnetic fields (magnetars) have been observationally determined to have surface magnetic fields of order of 10(14)-10(15) G, the implied internal field strength being several orders larger. We study the equation of state and composition of dense hypernuclear matter in strong magnetic fields in a range expected in the interiors of magnetars. Within the non-linear Boguta-Bodmer-Walecka model we find that the magnetic field has sizable influence on the properties of matter for central magnetic field B >= 10(17) G, in particular the matter properties become anisotropic. Moreover, for the central fields B >= 10(18) G, the magnetized hypernuclear matter shows instability, which is signalled by the negative sign of the derivative of the pressure parallel to the field with respect to the density, and leads to vanishing parallel pressure at the critical value B-cr congruent to 10(19) G. This limits the range of admissible homogeneously distributed fields in magnetars to fields below the critical value B-cr. (c) 2012 Elsevier B.V. All rights reserved.

Clusters of bound particles in the derivative delta-function Bose gas

In this paper we discuss a novel procedure for constructing clusters of bound particles in the case of a quantum integrable derivative delta-function Bose gas in one dimension. It is shown that clusters of bound particles can be constructed for this Bose gas for some special values of the coupling constant, by taking the quasi-momenta associated with the corresponding Bethe state to be equidistant points on a single circle in the complex momentum plane. We also establish a connection between these special values of the coupling constant and some fractions belonging to the Farey sequences in number theory. This connection leads to a classification of the clusters of bound particles associated with the derivative delta-function Bose gas and allows us to study various properties of these clusters like their size and their stability under the variation of the coupling constant. (C) 2013 Elsevier B.V. All rights reserved.