Thermodynamic Comparison and the Ideal Glass Transition of A Monatomic Systems Modeled as an Antiferromagnetic Ising Model on Husimi and Cubic Recursive Lattices of the Same Coordination Number

Two kinds of recursive lattices with the same coordination number but different unit cells (2-D square and 3-D cube) are constructed and the antiferromagnetic Ising model is solved exactly on them to study the stable and metastable states. The Ising model with multi-particle interactions is designed to represent a monatomic system or an alloy. Two solutions of the model exhibit the crystallization of liquid, and the ideal glass transition of supercooled liquid respectively. Based on the solutions, the thermodynamics on both lattices was examined. In particular, the free energy, energy, and entropy of the ideal glass, supercooled liquid, crystal, and liquid state of the model on each lattice were calculated and compared with each other. Interactions between particles farther away than the nearest neighbor distance are taken into consideration. The two lattices show comparable properties on the transition temperatures and the thermodynamic behaviors, which proves that both of them are practical to describe the regular 3-D case, while the different effects of the unit types are still obvious.Comment: 27 pages, 13 figure

Properties of layer-by-layer vector stochastic models of force fluctuations in granular materials

We attempt to describe the stress distributions of granular packings using lattice-based layer-by-layer stochastic models that satisfy the constraints of force and torque balance and non-tensile forces at each site. The inherent asymmetry in the layer-by-layer approach appears to lead to an asymmetric force distribution, in disagreement with both experiments and general symmetry considerations. The vertical force component probability distribution is robust and in agreement with predictions of the scalar q model while the distribution of horizontal force components is qualitatively different and depends on the details of implementation.Comment: 18 pages, 12 figures (with subfigures), 1 table. Uses revtex, epsfig,subfigure, and cite. Submitted to PRE. Plots have been bitmapped. High-resolution version is available. Email [email protected] or download from http://rainbow.uchicago.edu/~mbnguyen/research/vm.htm

Regional Conformational Flexibility Couples Substrate Specificity and Scissile Phosphate Diester Selectivity in Human Flap Endonuclease 1

Human flap endonuclease-1 (hFEN1) catalyzes the divalent metal ion-dependent removal of single-stranded DNA protrusions known as flaps during DNA replication and repair. Substrate selectivity involves passage of the 5′-terminus/flap through the arch and recognition of a single nucleotide 3′-flap by the α2–α3 loop. Using NMR spectroscopy, we show that the solution conformation of free and DNA-bound hFEN1 are consistent with crystal structures; however, parts of the arch region and α2–α3 loop are disordered without substrate. Disorder within the arch explains how 5′-flaps can pass under it. NMR and single-molecule FRET data show a shift in the conformational ensemble in the arch and loop region upon addition of DNA. Furthermore, the addition of divalent metal ions to the active site of the hFEN1–DNA substrate complex demonstrates that active site changes are propagated via DNA-mediated allostery to regions key to substrate differentiation. The hFEN1–DNA complex also shows evidence of millisecond timescale motions in the arch region that may be required for DNA to enter the active site. Thus, hFEN1 regional conformational flexibility spanning a range of dynamic timescales is crucial to reach the catalytically relevant ensemble

Topological geon black holes in Einstein-Yang-Mills theory

We construct topological geon quotients of two families of Einstein-Yang-Mills black holes. For Kuenzle's static, spherically symmetric SU(n) black holes with n>2, a geon quotient exists but generically requires promoting charge conjugation into a gauge symmetry. For Kleihaus and Kunz's static, axially symmetric SU(2) black holes a geon quotient exists without gauging charge conjugation, and the parity of the gauge field winding number determines whether the geon gauge bundle is trivial. The geon's gauge bundle structure is expected to have an imprint in the Hawking-Unruh effect for quantum fields that couple to the background gauge field.Comment: 27 pages. v3: Presentation expanded. Minor corrections and addition

Enzymatic production of β-glucose 1,6-bisphosphate through manipulation of catalytic magnesium coordination

Manipulation of enzyme behaviour represents a sustainable technology that can be harnessed to enhance the production of valuable metabolites and chemical precursors. β-Glucose 1,6-bisphosphate (βG16BP) is a native reaction intermediate in the catalytic cycle of β-phosphoglucomutase (βPGM) that has been proposed as a treatment for human congenital disorder of glycosylation involving phosphomannomutase 2. Strategies to date for the synthesis of βG16BP suffer from low yields or use chemicals and procedures with significant environmental impacts. Herein, we report the efficient enzymatic synthesis of anomer-specific βG16BP using the D170N variant of βPGM (βPGMD170N), where the aspartate to asparagine substitution at residue 170 perturbs the coordination of a catalytic magnesium ion. Through combined use of NMR spectroscopy and kinetic assays, it is shown that the weakened affinity and reactivity of βPGMD170N towards βG16BP contributes to the pronounced retardation of the second step in the two-step catalytic cycle, which causes a marked accumulation of βG16BP, especially at elevated MgCl2 concentrations. Purification, employing a simple environmentally considerate precipitation procedure requiring only a standard biochemical toolset, results in a βG16BP product with high purity and yield. Overall, this synthesis strategy illustrates how manipulation of the catalytic magnesium coordination of an enzyme can be utilised to generate large quantities of a valuable metabolite

Ising Spins on Thin Graphs

The Ising model on ``thin'' graphs (standard Feynman diagrams) displays several interesting properties. For ferromagnetic couplings there is a mean field phase transition at the corresponding Bethe lattice transition point. For antiferromagnetic couplings the replica trick gives some evidence for a spin glass phase. In this paper we investigate both the ferromagnetic and antiferromagnetic models with the aid of simulations. We confirm the Bethe lattice values of the critical points for the ferromagnetic model on $\phi^3$ and $\phi^4$ graphs and examine the putative spin glass phase in the antiferromagnetic model by looking at the overlap between replicas in a quenched ensemble of graphs. We also compare the Ising results with those for higher state Potts models and Ising models on ``fat'' graphs, such as those used in 2D gravity simulations.Comment: LaTeX 13 pages + 9 postscript figures, COLO-HEP-340, LPTHE-Orsay-94-6

Nonequivalence of second sphere "noncatalytic" residues in pentaerythritol tetranitrate reductase in relation to local dynamics linked to H-transfer in reactions with NADH and NADPH coenzymes

Many enzymes that catalyze hydride transfer reactions work via a mechanism dominated by quantum mechanical tunneling. The involvement of fast vibrational modes of the reactive complex is often inferred in these reactions, as in the case of the NAD(P)H-dependent pentaerythritol tetranitrate reductase (PETNR). Herein, we interrogated the H-transfer mechanism in PETNR by designing conservative (L25I and I107L) and side chain shortening (L25A and I107A) PETNR variants and using a combination of experimental approaches (stopped-flow rapid kinetics, X-ray crystallography, isotope/temperature dependence studies of H-transfer and NMR spectroscopy). X-ray data show subtle changes in the local environment of the targeted side chains but no major structural perturbation caused by mutagenesis of these two second sphere active site residues. However, temperature dependence studies of H-transfer revealed a coenzyme-specific and complex thermodynamic equilibrium between different reactive configurations in PETNR–coenzyme complexes. We find that mutagenesis of these second sphere “noncatalytic” residues affects differently the reactivity of PETNR with NADPH and NADH coenzymes. We attribute this to subtle, dynamic structural changes in the PETNR active site, the effects of which impact differently in the nonequivalent reactive geometries of PETNR−NADH and PETNR−NADPH complexes. This inference is confirmed through changes observed in the NMR chemical shift data for PETNR complexes with unreactive 1,4,5,6-tetrahydro-NAD(P) analogues. We show that H-transfer rates can (to some extent) be buffered through entropy–enthalpy compensation, but that use of integrated experimental tools reveals hidden complexities that implicate a role for dynamics in this relatively simple H-transfer reaction. Similar approaches are likely to be informative in other enzymes to understand the relative importance of (distal) hydrophobic side chains and dynamics in controlling the rates of enzymatic H-transfer

Decoupling of the S=1/2 antiferromagnetic zig-zag ladder with anisotropy

The spin-1/2 antiferromagnetic zig-zag ladder is studied by exact diagonalization of small systems in the regime of weak inter-chain coupling. A gapless phase with quasi long-range spiral correlations has been predicted to occur in this regime if easy-plane (XY) anisotropy is present. We find in general that the finite zig-zag ladder shows three phases: a gapless collinear phase, a dimer phase and a spiral phase. We study the level crossings of the spectrum,the dimer correlation function, the structure factor and the spin stiffness within these phases, as well as at the transition points. As the inter-chain coupling decreases we observe a transition in the anisotropic XY case from a phase with a gap to a gapless phase that is best described by two decoupled antiferromagnetic chains. The isotropic and the anisotropic XY cases are found to be qualitatively the same, however, in the regime of weak inter-chain coupling for the small systems studied here. We attribute this to a finite-size effect in the isotropic zig-zag case that results from exponentially diverging antiferromagnetic correlations in the weak-coupling limit.Comment: to appear in Physical Review

Dispersive Approach to Semileptonic Form-Factors in Heavy-to-Light Meson Decays

We study the semileptonic decays of heavy mesons into light pseudoscalars by making use of dispersion relations. Constraints from heavy quark symmetry, chiral symmetry and perturbative QCD are implemented into a dispersive model for the form-factors. Large deviations from $B^*$-pole dominance are observed in $B\to\pi\ell\nu$. We discuss the model prediction for this mode and its possible impact on the extraction of $|V_{ub}|$.Comment: 30 pages, including 5 Postcript figure

Scroll waves in isotropic excitable media : linear instabilities, bifurcations and restabilized states

Scroll waves are three-dimensional analogs of spiral waves. The linear stability spectrum of untwisted and twisted scroll waves is computed for a two-variable reaction-diffusion model of an excitable medium. Different bands of modes are seen to be unstable in different regions of parameter space. The corresponding bifurcations and bifurcated states are characterized by performing direct numerical simulations. In addition, computations of the adjoint linear stability operator eigenmodes are also performed and serve to obtain a number of matrix elements characterizing the long-wavelength deformations of scroll waves.Comment: 30 pages 16 figures, submitted to Phys. Rev.