Asymmetric spin-1/2 two-leg ladders

We consider asymmetric spin-1/2 two-leg ladders with non-equal antiferromagnetic (AF) couplings J_|| and \kappa J_|| along legs (\kappa <= 1) and ferromagnetic rung coupling, J_\perp. This model is characterized by a gap \Delta in the spectrum of spin excitations. We show that in the large J_\perp limit this gap is equivalent to the Haldane gap for the AF spin-1 chain, irrespective of the asymmetry of the ladder. The behavior of the gap at small rung coupling falls in two different universality classes. The first class, which is best understood from the case of the conventional symmetric ladder at \kappa=1, admits a linear scaling for the spin gap \Delta ~ J_\perp. The second class appears for a strong asymmetry of the coupling along legs, \kappa J_|| << J_\perp << J_|| and is characterized by two energy scales: the exponentially small spin gap \Delta ~ J_\perp \exp(-J_|| / J_\perp), and the bandwidth of the low-lying excitations induced by a Suhl-Nakamura indirect exchange ~ J_\perp^2 /J_|| . We report numerical results obtained by exact diagonalization, density matrix renormalization group and quantum Monte Carlo simulations for the spin gap and various spin correlation functions. Our data indicate that the behavior of the string order parameter, characterizing the hidden AF order in Haldane phase, is different in the limiting cases of weak and strong asymmetry. On the basis of the numerical data, we propose a low-energy theory of effective spin-1 variables, pertaining to large blocks on a decimated lattice.Comment: 18 pages, 11 figure

Spin gap and string order parameter in the ferromagnetic Spiral Staircase Heisenberg Ladder: a quantum Monte Carlo study

We consider a spin-1/2 ladder with a ferromagnetic rung coupling J_\perp and inequivalent chains. This model is obtained by a twist (\theta) deformation of the ladder and interpolates between the isotropic ladder (\theta=0) and the SU(2) ferromagnetic Kondo necklace model (\theta=\pi). We show that the ground state in the (\theta,J_\perp) plane has a finite string order parameter characterising the Haldane phase. Twisting the chain introduces a new energy scale, which we interpret in terms of a Suhl-Nakamura interaction. As a consequence we observe a crossover in the scaling of the spin gap at weak coupling from \Delta/J_\| \propto J_\perp/J_\| for \theta < \theta_c \simeq 8\pi/9 to \Delta/J_\| \propto (J_\perp/J_\|)^2 for \theta > \theta_c. Those results are obtained on the basis of large scale Quantum Monte Carlo calculations.Comment: 4 page

Equilibrium Sampling From Nonequilibrium Dynamics

We present some applications of an Interacting Particle System (IPS) methodology to the field of Molecular Dynamics. This IPS method allows several simulations of a switched random process to keep closer to equilibrium at each time, thanks to a selection mechanism based on the relative virtual work induced on the system. It is therefore an efficient improvement of usual non-equilibrium simulations, which can be used to compute canonical averages, free energy differences, and typical transitions paths

To B or not to B: a question of resolution?

A simple rule of thumb based on resolution is not adequate to identify the best treatment of atomic displacements in macromolecular structural models. The choice to use isotropic B factors, anisotropic B factors, TLS models or some combination of the three should be validated through statistical analysis of the model refinement

QMCube (QM3): An all‐purpose suite for multiscale QM/MM calculations

QMCube (QM3) is a suite written in the Python programming language, initially focused on multiscale QM/MM simulations of biological systems, but open enough to address other kinds of problems. It allows the user to combine highly efficient QM and MM programs, providing unified access to a wide range of computational methods. The suite also supplies additional modules with extra functionalities. These modules facilitate common tasks such as performing the setup of the models or process the data generated during the simulations. The design of QM3 has been carried out considering the least number of external dependencies (only an algebra library, already included in the distribution), which makes it extremely portable. Also, the modular structure of the suite should help to expand and develop new computational methods

Protein folding using contact maps

We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three dimensional conformation from a contact map and the Monte Carlo dynamics in contact map space. We then discuss two approximations to the free energy of the contact maps and a method to derive energy parameters based on perceptron learning. Finally we present results, first for predictions based on threading and then for energy minimization of crambin and of a set of 6 immunoglobulins. The main result is that we proved that the two simple approximations we studied for the free energy are not suitable for protein folding. Perspectives are discussed in the last section.Comment: 29 pages, 10 figure

High-resolution NMR studies of structure and dynamics of human ERp27 indicate extensive interdomain flexibility

ERp27 (endoplasmic reticulum protein 27.7 kDa) is a homologue of PDI (protein disulfide-isomerase) localized to the endoplasmic reticulum. ERp27 is predicted to consist of two thioredoxinfold domains homologous with the non-catalytic b and b domains of PDI. The structure in solution of the N-terminal blike domain of ERp27 was solved using high-resolution NMR data. The structure confirms that it has the thioredoxin fold and that ERp27 is a member of the PDI family. 15N-NMR relaxation data were obtained and ModelFree analysis highlighted limited exchange contributions and slow internal motions, and indicated that the domain has an average order parameter S 2 of 0.79. Comparison of the single-domain structure determined in the present study with the equivalent domain within fulllength ERp27, determined independently by X-ray diffraction, indicated very close agreement. The domain interface inferred from NMR data in solution was much more extensive than that observed in the X-ray structure, suggesting that the domains flex independently and that crystallization selects one specific interdomain orientation. This led us to apply a new rapid method to simulate the flexibility of the full-length protein, establishing that the domains show considerable freedom to flex (tilt and twist) about the interdomain linker, consistent with the NMR data

Structure of Tagatose-1,6-bisphosphate Aldolase. Insight into chiral discrimination, mechanism, and specificity of class II aldolases

Tagatose-1,6-bisphosphate aldolase (TBPA) is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate. The high resolution (1.45 Å) crystal structure of the Escherichia coli enzyme, encoded by the agaY gene, complexed with phosphoglycolohydroxamate (PGH) has been determined. Two subunits comprise the asymmetric unit, and a crystallographic 2-fold axis generates the functional tetramer. A complex network of hydrogen bonds position side chains in the active site that is occupied by two cations. An unusual Na(+) binding site is created using a interaction with Tyr(183) in addition to five oxygen ligands. The catalytic Zn(2+) is five-coordinate using three histidine nitrogens and two PGH oxygens. Comparisons of TBPA with the related fructose-1,6-bisphosphate aldolase (FBPA) identifies common features with implications for the mechanism. Because the major product of the condensation catalyzed by the enzymes differs in the chirality at a single position, models of FBPA and TBPA with their cognate bisphosphate products provide insight into chiral discrimination by these aldolases. The TBPA active site is more open on one side than FBPA, and this contributes to a less specific enzyme. The availability of more space and a wider range of aldehyde partners used by TBPA together with the highly specific nature of FBPA suggest that TBPA might be a preferred enzyme to modify for use in biotransformation chemistry

Thermal conductivity of the Toda lattice with conservative noise

We study the thermal conductivity of the one dimensional Toda lattice perturbed by a stochastic dynamics preserving energy and momentum. The strength of the stochastic noise is controlled by a parameter $\gamma$. We show that heat transport is anomalous, and that the thermal conductivity diverges with the length $n$ of the chain according to $\kappa(n) \sim n^\alpha$, with $0 < \alpha \leq 1/2$. In particular, the ballistic heat conduction of the unperturbed Toda chain is destroyed. Besides, the exponent $\alpha$ of the divergence depends on $\gamma$