A Proton Magnetic Resonance Study of the Association of Lysozyme with Monosaccharide Inhibitors

It has been shown that the acetamido methyl protons of N-acetyl-d-glucosamine undergo a chemical shift to higher fields in their proton magnetic resonance spectrum when the inhibitor is bound to lysozyme. The observed chemical shift in the presence of the enzyme is different for the agr- and ß-anomeric forms of 2-acetamido-2-deoxy-d-glucopyranose indicating either a difference in the affinity of the anomeric forms for lysozyme or different magnetic environments for the methyl protons in their enzyme-bound state. That the agr- and ß-anomeric forms of GlcAc bind to lysozyme in a competitive fashion was indicated by observing the proton magnetic resonance spectra in the presence of 2-acetamido-d3-2-deoxy-agr-d-glucopyranose. The methyl glycosides, methyl-agr-GlcAc and methyl-ß-GlcAc, were also shown to bind competitively with both anomers of GlcAc. Quantitative analysis of the chemical shift data observed for the association of GlcAc with lysozyme was complicated by the mutarotation of GlcAc between its agr- and ß-anomeric forms. However, in the case of the methyl glucosides, where the conformation of each anomer is frozen, it was possible to analyze the chemical shift data in a straightforward manner, and the dissociation constant as well as the chemical shift of the acetamido methyl protons of the enzyme-inhibitor complex was determined for both anomers. The results indicate that the two anomers of methyl-GlcAc bind to lysozyme with slightly different affinities but that the acetamido methyl groups of both anomers experience identical magnetic environments in the enzyme-inhibitor complex

A New Algorithm for Protein Design

We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach produces sequences that are likely to fold into desired structures. Our method is a significant improvement over previous attempts which used the energy function for designing sequences.Comment: 10 pages latex 2.09 no figures. Use uufiles to decod

Scalar Wave Falloff in Asymptotically Anti-de Sitter Backgrounds

Conformally invariant scalar waves in black hole spacetimes which are asymptotically anti-de Sitter are investigated. We consider both the $(2+1)$-dimensional black hole and $(3+1)$-dimensional Schwarzschild-anti-de Sitter spacetime as backgrounds. Analytical and numerical methods show that the waves decay exponentially in the $(2+1)$ dimensional black hole background. However the falloff pattern of the conformal scalar waves in the Schwarzschild-anti-de Sitter background is generally neither exponential nor an inverse power rate, although the approximate falloff of the maximal peak is weakly exponential. We discuss the implications of these results for mass inflation.Comment: 34 pages, Latex, 26 figures, uses psfi

Gravitational Collapse of a Massless Scalar Field and a Perfect Fluid with Self-Similarity of the First Kind in (2+1) Dimensions

Self-similar solutions of a collapsing perfect fluid and a massless scalar field with kinematic self-similarity of the first kind in 2+1 dimensions are obtained. Their local and global properties of the solutions are studied. It is found that some of them represent gravitational collapse, in which black holes are always formed, and some may be interpreted as representing cosmological models.Comment: 13 page

Geometrically Reduced Number of Protein Ground State Candidates

Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small: For the case of a two-parameter Hydrophobic-Polar lattice model for $L$-mers, the number of these candidates grows only as $L^2$. Moreover, the space of the interaction parameters of the model breaks up into well-defined domains, each corresponding to one ground state candidate, which are separated by sharp boundaries. In addition, by exact enumeration, we show there are some sequences which have one absolute unique native state. These absolute ground states have perfect stability against change of inter-monomer interaction potential.Comment: 9 page, 4 ps figures are include

CONCENTRIC TUBE-FOULING RIG FOR INVESTIGATION OF FOULING DEPOSIT FORMATION FROM PASTEURISER OF VISCOUS FOOD LIQUID

This paper reports the work on developing concentric tube-fouling rig, a new fouling deposit monitoring device. This device can detect and quantify the level of fouling deposit formation. It can also functioning as sampler for fouling deposit study, which can be attached at any food processing equipment. The design is initiated with conceptual design. The rig is designed with inner diameter of 7 cm and with tube length of 37 cm. A spiral insert with 34.5 cm length and with 5.4 cm diameter is fitted inside the tube to ensure the fluid flows around the tube. In this work, the rig is attached to the lab-scale concentric tube-pasteurizer to test its effectiveness and to collect a fouling sample after pasteurization of pink guava puree. Temperature changes are recorded during the pasteurization and the data is used to plot the heat transfer profile. Thickness of the fouling deposit is also measured. The trends for thickness, heat resistance profile and heat transfer profile for concentric tube-fouling rig matched the trends obtained from lab-scale concentric tube-pasteurizer very well. The findings from this work have shown a good potential of this rig however there is a limitation with spiral insert, which is discussed in this paper

New Charged Dilaton Solutions in 2+1 Dimensions and Solutions with Cylindrical Symmetry in 3+1 Dimensions

We report a new family of solutions to Einstein-Maxwell-dilaton gravity in 2+1 dimensions and Einstein-Maxwell gravity with cylindrical symmetry in 3+1 dimensions. A set of static charged solutions in 2+1 dimensions are obtained by a compactification of charged solutions in 3+1 dimensions with cylindrical symmetry. These solutions contain naked singularities for certain values of the parameters considered. New rotating charged solutions in 2+1 dimensions and 3+1 dimensions are generated treating the static charged solutions as seed metrics and performing $SL(2;R)$ transformations.Comment: Latex. No figure

Exact Black Hole and Cosmological Solutions in a Two-Dimensional Dilaton-Spectator Theory of Gravity

Exact black hole and cosmological solutions are obtained for a special two-dimensional dilaton-spectator ($\phi-\psi$) theory of gravity. We show how in this context any desired spacetime behaviour can be determined by an appropriate choice of a dilaton potential function $V(\phi)$ and a ``coupling function'' $l(\phi)$ in the action. We illustrate several black hole solutions as examples. In particular, asymptotically flat double- and multiple- horizon black hole solutions are obtained. One solution bears an interesting resemblance to the $2D$ string-theoretic black hole and contains the same thermodynamic properties; another resembles the $4D$ Reissner-Nordstrom solution. We find two characteristic features of all the black hole solutions. First the coupling constants in $l(\phi)$ must be set equal to constants of integration (typically the mass). Second, the spectator field $\psi$ and its derivative $\psi^{'}$ both diverge at any event horizon. A test particle with ``spectator charge" ({\it i.e.} one coupled either to $\psi$ or $\psi^{'}$), will therefore encounter an infinite tidal force at the horizon or an ``infinite potential barrier'' located outside the horizon respectively. We also compute the Hawking temperature and entropy for our solutions. In $2D$ $FRW$ cosmology, two non-singular solutions which resemble two exact solutions in $4D$ string-motivated cosmology are obtained. In addition, we construct a singular model which describes the $4D$ standard non-inflationary big bang cosmology ($big-bang\rightarrow radiation\rightarrow dust$). Motivated by the similaritiesbetween $2D$ and $4D$ gravitational field equations in $FRW$ cosmology, we briefly discuss a special $4D$ dilaton-spectator action constructed from the bosonic part of the low energy heterotic string action andComment: 34 pgs. Plain Tex, revised version contains some clarifying comments concerning the relationship between the constants of integration and the coupling constants

Statistical Properties of Contact Maps

A contact map is a simple representation of the structure of proteins and other chain-like macromolecules. This representation is quite amenable to numerical studies of folding. We show that the number of contact maps corresponding to the possible configurations of a polypeptide chain of N amino acids, represented by (N-1)-step self avoiding walks on a lattice, grows exponentially with N for all dimensions D>1. We carry out exact enumerations in D=2 on the square and triangular lattices for walks of up to 20 steps and investigate various statistical properties of contact maps corresponding to such walks. We also study the exact statistics of contact maps generated by walks on a ladder.Comment: Latex file, 15 pages, 12 eps figures. To appear on Phys. Rev.

Photonic Clusters

We show through rigorous calculations that dielectric microspheres can be organized by an incident electromagnetic plane wave into stable cluster configurations, which we call photonic molecules. The long-range optical binding force arises from multiple scattering between the spheres. A photonic molecule can exhibit a multiplicity of distinct geometries, including quasicrystal-like configurations, with exotic dynamics. Linear stability analysis and dynamical simulations show that the equilibrium configurations can correspond with either stable or a type of quasi-stable states exhibiting periodic particle motion in the presence of frictional dissipation.Comment: 4 pages, 3 figure