Protein oligomers studied by solid-state NMR the case of the full-length nucleoid-associated protein histone-like nucleoid structuring protein

Members of the histone-like nucleoid structuring protein (H-NS) family play roles both as architectural proteins and as modulators of gene expression in Gram-negative bacteria. The H-NS protein participates in modulatory processes that respond to environmental changes in osmolarity, pH, or temperature. H-NS oligomerization is essential for its activity. Structural models of different truncated forms are available. However, high-resolution structural details of full-length H-NS and its DNA-bound state have largely remained elusive. We report on progress in characterizing the biologically active H-NS oligomers with solid-state NMR. We compared uniformly ((13)C,(15)N)-labeled ssNMR preparations of the isolated N-terminal region (H-NS 1-47) and full-length H-NS (H-NS 1-137). In both cases, we obtained ssNMR spectra of good quality and characteristic of well-folded proteins. Analysis of the results of 2D and 3D (13)C-(13)C and (15)N-(13)C correlation experiments conducted at high magnetic field led to assignments of residues located in different topological regions of the free full-length H-NS. These findings confirm that the structure of the N-terminal dimerization domain is conserved in the oligomeric full-length protein. Small changes in the dimerization interface suggested by localized chemical shift variations between solution and solid-state spectra may be relevant for DNA recoginition.

Resonant tunneling effects in semiconductor heterostructures

The thesis is devoted to a theoretical study of resonant tunneling phenomena in semiconductor heterostructures and nanostructures. It considers several problems relevant to modern solid state physics. Namely these are tunneling between 2D electron layers with spin-orbit interaction, tunnel injection into molecular solid material, resonant tunnel coupling of a bound state with continuum and resonant indirect exchange interaction mediated by a remote conducting channel. A manifestation of spin-orbit interaction in the tunneling between two 2D electron layers is considered. General expression is obtained for the tunneling current with account of Rashba and Dresselhaus types of spin-orbit interaction and elastic scattering. It is demonstrated that the tunneling conductance is very sensitive to relation between Rashba and Dresselhaus contributions and opens possibility to determine the spin-orbit interaction parameters and electron quantum lifetime in direct tunneling experiments with no external magnetic field applied. A microscopic mechanism of hole injection from metallic electrode into organic molecular solid (OMS) in high electric field is proposed for the case when the molecules ionization energy exceeds work function of the metal. It is shown that the main contribution to the injection current comes from direct isoenergetic transitions from localized states in OMS to empty states in the metal. Strong dependence of the injection current on applied voltage originates from variation of the number of empty states available in the metal rather than from distortion of the interface barrier. A theory of tunnel coupling between an impurity bound state and the 2D delocalized states in the quantum well (QW) is developed. The problem is formulated in terms of Anderson-Fano model as configuration interaction between the carrier bound state at the impurity and the continuum of delocalized states in the QW. An effect of this interaction on the interband optical transitions in the QW is analyzed. The results are discussed regarding the series of experiments on the GaAs structures with a -Mn layer. A new mechanism of ferromagnetism in diluted magnetic semiconductor heterosructures is considered, namely the resonant enhancement of indirect exchange interaction between paramagnetic centers via a spatially separated conducting channel. The underlying physical model is similar to the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction; however, an important difference relevant to the low-dimensional structures is a resonant hybridization of a bound state at the paramagnetic ion with the continuum of delocalized states in the conducting channel. An approach is developed, which unlike RKKY is not based on the perturbation theory and demonstrates that the resonant hybridization leads to a strong enhancement of the indirect exchange. This finding is discussed in the context of the known experimental data supporting the phenomenon.

Bound states by a pseudoscalar Coulomb potential in one-plus-one dimensions

The Dirac equation is solved for a pseudoscalar Coulomb potential in a two-dimensional world. An infinite sequence of bounded solutions are obtained. These results are in sharp contrast with those ones obtained in 3 + 1 dimensions where no bound-state solutions are found. Next the general two-dimensional problem for pseudoscalar power-law potentials is addressed consenting us to conclude that a nonsingular potential leads to bounded solutions. The behaviour of the upper and lower components of the Dirac spinor for a confining linear potential nonconserving- as well as conserving-parity, even if the potential is unbounded from below, is discussed in some detail. (C) 2003 Elsevier B.V. All rights reserved.

Relating pseudospin and spin symmetries through charge conjugation and chiral transformations: the case of the relativistic harmonic oscillator

We solve the generalized relativistic harmonic oscillator in 1+1 dimensions, i.e., including a linear pseudoscalar potential and quadratic scalar and vector potentials which have equal or opposite signs. We consider positive and negative quadratic potentials and discuss in detail their bound-state solutions for fermions and antifermions. The main features of these bound states are the same as the ones of the generalized three-dimensional relativistic harmonic oscillator bound states. The solutions found for zero pseudoscalar potential are related to the spin and pseudospin symmetry of the Dirac equation in 3+1 dimensions. We show how the charge conjugation and gamma(5) chiral transformations relate the several spectra obtained and find that for massless particles the spin and pseudospin symmetry-related problems have the same spectrum but different spinor solutions. Finally, we establish a relation of the solutions found with single-particle states of nuclei described by relativistic mean-field theories with scalar, vector, and isoscalar tensor interactions and discuss the conditions in which one may have both nucleon and antinucleon bound states.

Bound states of the Duffin-Kemmer-Petiau equation with a mixed minimal-nonminimal vector cusp potential

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Scattering and bound states of spin-0 particles in a nonminimal vector double-step potential

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Insights into metal ion binding in phospholipases A(2): ultra high-resolution crystal structures of an acidic phospholipase A(2) in the Ca2+ free and bound states

The electrophile Ca2+ is an essential multifunctional co-factor in the phospholipase A(2) mediated hydrolysis of phospholipids. Crystal structures of an acidic phospholipase A(2) from the venom of Bothrops jararacussu have been determined both in the Ca2+ free and bound states at 0.97 and 1.60 angstrom resolutions, respectively. In the Ca2+ bound state, the Ca2+ ion is penta-coordinated by a distorted pyramidal cage of oxygen and nitrogen atoms that is significantly different to that observed in structures of other Group I/II phospholipases A(2). In the absence of Ca2+, a water molecule occupies the position of the Ca2+ ion and the side chain of Asp49 and the calcium-binding loop adopts a different conformation. (c) 2005 Elsevier SAS. All rights reserved.

Bound states of attractive Bose-Einstein condensates in shallow traps in two and three dimensions

Using variational and numerical solutions of the mean-field Gross-Pitaevskii equation for attractive interaction (with cubic or Kerr nonlinearity), we show that a stable bound state can appear in a Bose-Einstein condensate (BEC) in a localized exponentially screened radially symmetric harmonic potential well in two and three dimensions. We also consider an axially symmetric configuration with zero axial trap and a exponentially screened radial trap so that the resulting bound state can freely move along the axial direction like a soliton. The binding of the present states in shallow wells is mostly due to the nonlinear interaction with the trap playing a minor role. Hence, these BEC states are more suitable to study the effect of the nonlinear force on the dynamics. We illustrate the highly nonlinear nature of breathing oscillations of these states. Such bound states could be created in BECs and studied in the laboratory with present knowhow.

Positronium-hydrogen-atom scattering in a five-state model

The scattering of orthopositronium (Ps) by hydrogen atoms has been investigated in a five-state coupled-channel model allowing for Ps(1s)H(2s,2p) and Ps(2s,2p)H(1s) excitations using a recently proposed electron-exchange model potential. The higher (n greater than or equal to 3) excitations and ionization of the Ps atom are calculated using the first Born approximation. Calculations are reported of scattering lengths, phase shifts. elastic, Ps and H excitation, and total cross sections. Remarkable correlations are observed between the S-wave Ps-H binding energy and the singlet scattering length, effective range, and resonance energy obtained in various model calculations. These correlations suggest that if a Ps-H dynamical model yields the correct result for one of these four observables, it is expected to lead to the correct result for the other three. The present model, which is constructed so as to reproduce the Ps-H resonance at 4.01 eV, automatically yields a Ps-H bound state at - 1.05 eV that compares well with the accurate value of - 1.067 eV. The model leads to a singlet scattering length of 3.72a(0) and effective range of 1.67a(0), whereas the correlations suggest the precise values of 3.50a(0) and 1.65a(0) for these observables, respectively. [S1050-2947(99)07703-3].

Three- and Four-Nucleon Bound States in Three Dimensions, Without PW Decomposition

A brief review of a three-dimensional (3D) numerical method to solve few-nucleon bound and scattering states, without the standard partial-wave (PW) decomposition, is presented. The approach is applied to three-and four-nucleon bound states, by considering the solutions of the corresponding Faddeev-Yakubovsky (FY) integral equations in momentum space. Realistic spin-isospin dependent 3D and PW formalism are presented for the alpha particle and the triton binding energies, with numerical results given in both schemes for comparison.

Trajectory of virtual, bound and resonant Efimov states

The pole trajectory of Efimov states for a three-body alpha alpha beta system with alpha alpha unbound and alpha beta bound is calculated using a zero-range Dirac-delta potential. It is shown that a three-body bound state turns into a virtual one by increasing the alpha beta binding energy. This result is consistent with previous results for three equal mass particles. The present approach considers the n-n-(18)C halo nucleus. However, the results have good perspective to be tested and applied in ultracold atomic systems, where one can realize such three-body configuration with tunable two-body interaction.

Scaling and universality in two dimensions: three-body bound states with short-ranged interactions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Universality and Scaling Limit of Weakly-Bound Tetramers

The occurrence of a new limit cycle in few-body physics, expressing a universal scaling function relating the binding energies of two successive tetramer states, is revealed by considering a renormalized zero-range two-body interaction in bound state of four identical bosons. The tetramer energy spectrum is obtained by adding a boson to an Efimov bound state with energy B-3 in the unitary limit (for zero two-body binding energy or infinite two-body scattering length). Each excited N-th tetramer energy B-4((N)) is shown to slide along a scaling function as a short-range four-body scale is changed, emerging from the 3+1 threshold for a universal ratio B-4((N))/B-3 = 4.6, which does not depend on N. The new scale can also be revealed by a resonance in the atom-trimer recombination process.

J/Psi-nuclear bound states

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Renormalization in non-relativistic quantum mechanics

The importance and usefulness of renormalization are emphasized in non-relativistic quantum mechanics. The momentum space treatment of both two-body bound state and scattering problems involving some potentials singular at the origin exhibits ultraviolet divergence. The use of renormalization techniques in these problems leads to finite converged results for both the exact and perturbative solutions. The renormalization procedure is carried out for the quantum two-body problem in different partial waves for a minimal potential possessing only the threshold behaviour and no form factors. The renormalized perturbative and exact solutions for this problem are found to be consistent with each other. The useful role of the renormalization group equations for this problem is also pointed out.