Structure Space of Model Proteins --A Principle Component Analysis

We study the space of all compact structures on a two-dimensional square lattice of size $N=6\times6$. Each structure is mapped onto a vector in $N$-dimensions according to a hydrophobic model. Previous work has shown that the designabilities of structures are closely related to the distribution of the structure vectors in the $N$-dimensional space, with highly designable structures predominantly found in low density regions. We use principal component analysis to probe and characterize the distribution of structure vectors, and find a non-uniform density with a single peak. Interestingly, the principal axes of this peak are almost aligned with Fourier eigenvectors, and the corresponding Fourier eigenvalues go to zero continuously at the wave-number for alternating patterns ($q=\pi$). These observations provide a stepping stone for an analytic description of the distribution of structural points, and open the possibility of estimating designabilities of realistic structures by simply Fourier transforming the hydrophobicities of the corresponding sequences.Comment: 14 pages, 12 figures, Conclusion has been modifie

BTZ Black Hole Entropy from Ponzano-Regge Gravity

The entropy of the BTZ black hole is computed in the Ponzano-Regge formulation of three-dimensional lattice gravity. It is seen that the correct semi-classical behaviour of entropy is reproduced by states that correspond to all possible triangulations of the Euclidean black hole.Comment: 11 pages LaTeX, 3 eps figures, some minor clarifications added, result unchange

Current Oscillations, Interacting Hall Discs and Boundary CFTs

In this paper, we discuss the behavior of conformal field theories interacting at a single point. The edge states of the quantum Hall effect (QHE) system give rise to a particular representation of a chiral Kac-Moody current algebra. We show that in the case of QHE systems interacting at one point we obtain a ``twisted'' representation of the current algebra. The condition for stationarity of currents is the same as the classical Kirchoff's law applied to the currents at the interaction point. We find that in the case of two discs touching at one point, since the currents are chiral, they are not stationary and one obtains current oscillations between the two discs. We determine the frequency of these oscillations in terms of an effective parameter characterizing the interaction. The chiral conformal field theories can be represented in terms of bosonic Lagrangians with a boundary interaction. We discuss how these one point interactions can be represented as boundary conditions on fields, and how the requirement of chirality leads to restrictions on the interactions described by these Lagrangians. By gauging these models we find that the theory is naturally coupled to a Chern-Simons gauge theory in 2+1 dimensions, and this coupling is completely determined by the requirement of anomaly cancellation.Comment: 32 pages, LateX. Uses amstex, amssymb. Typos corrected. To appear in Int. J. Mod. Phys.

Electromagnetic Interaction of Massive Spin-3 State from String Theory

In the given work we study an interaction of second massive state of an open boson string with the constant electromagnetic field. This state contains massive fields with spins 3 and 1. Using the method of an open string BRST quantization, we receive gauge-invariant lagrangian, describing the electromagnetic interaction of these fields. From the explicit view of transformations and lagrangian it follows that the presence of external constant e/m field leads to the mixing of the given level states. Most likely that the presence of the external field will lead to the mixing of the states at other mass string levels as well.Comment: 17 pages, LaTeX, no figure

Symplectic potentials and resolved Ricci-flat ACG metrics

We pursue the symplectic description of toric Kahler manifolds. There exists a general local classification of metrics on toric Kahler manifolds equipped with Hamiltonian two-forms due to Apostolov, Calderbank and Gauduchon(ACG). We derive the symplectic potential for these metrics. Using a method due to Abreu, we relate the symplectic potential to the canonical potential written by Guillemin. This enables us to recover the moment polytope associated with metrics and we thus obtain global information about the metric. We illustrate these general considerations by focusing on six-dimensional Ricci flat metrics and obtain Ricci flat metrics associated with real cones over L^{pqr} and Y^{pq} manifolds. The metrics associated with cones over Y^{pq} manifolds turn out to be partially resolved with two blowup parameters taking special (non-zero)values. For a fixed Y^{pq} manifold, we find explicit metrics for several inequivalent blow-ups parametrised by a natural number k in the range 0<k<p. We also show that all known examples of resolved metrics such as the resolved conifold and the resolution of C^3/Z_3 also fit the ACG classification.Comment: LaTeX, 34 pages, 4 figures (v2)presentation improved, typos corrected and references added (v3)matches published versio

Nonlocal regularisation of noncommutative field theories

We study noncommutative field theories, which are inherently nonlocal, using a Poincar\'e-invariant regularisation scheme which yields an effective, nonlocal theory for energies below a cut-off scale. After discussing the general features and the peculiar advantages of this regularisation scheme for theories defined in noncommutative spaces, we focus our attention onto the particular case when the noncommutativity parameter is inversely proportional to the square of the cut-off, via a dimensionless parameter $\eta$. We work out the perturbative corrections at one-loop order for a scalar theory with quartic interactions, where the signature of noncommutativity appears in $\eta$-dependent terms. The implications of this approach, which avoids the problems related to UV-IR mixing, are discussed from the perspective of the Wilson renormalisation program. Finally, we remark about the generality of the method, arguing that it may lead to phenomenologically relevant predictions, when applied to realistic field theories.Comment: 1+11 pages, 6 figures; v2: references added, typos corrected, conclusions unchange

N=2 Boundary conditions for non-linear sigma models and Landau-Ginzburg models

We study N=2 nonlinear two dimensional sigma models with boundaries and their massive generalizations (the Landau-Ginzburg models). These models are defined over either Kahler or bihermitian target space manifolds. We determine the most general local N=2 superconformal boundary conditions (D-branes) for these sigma models. In the Kahler case we reproduce the known results in a systematic fashion including interesting results concerning the coisotropic A-type branes. We further analyse the N=2 superconformal boundary conditions for sigma models defined over a bihermitian manifold with torsion. We interpret the boundary conditions in terms of different types of submanifolds of the target space. We point out how the open sigma models correspond to new types of target space geometry. For the massive Landau-Ginzburg models (both Kahler and bihermitian) we discuss an important class of supersymmetric boundary conditions which admits a nice geometrical interpretation.Comment: 48 pages, latex, references and minor comments added, the version to appear in JHE

Preventing transition to turbulence: a viscosity stratification does not always help

In channel flows a step on the route to turbulence is the formation of streaks, often due to algebraic growth of disturbances. While a variation of viscosity in the gradient direction often plays a large role in laminar-turbulent transition in shear flows, we show that it has, surprisingly, little effect on the algebraic growth. Non-uniform viscosity therefore may not always work as a flow-control strategy for maintaining the flow as laminar.Comment: 9 pages, 8 figure

A family of thermostable fungal cellulases created by structure-guided recombination

SCHEMA structure-guided recombination of 3 fungal class II cellobiohydrolases (CBH II cellulases) has yielded a collection of highly thermostable CBH II chimeras. Twenty-three of 48 genes sampled from the 6,561 possible chimeric sequences were secreted by the Saccharomyces cerevisiae heterologous host in catalytically active form. Five of these chimeras have half-lives of thermal inactivation at 63°C that are greater than the most stable parent, CBH II enzyme from the thermophilic fungus Humicola insolens, which suggests that this chimera collection contains hundreds of highly stable cellulases. Twenty-five new sequences were designed based on mathematical modeling of the thermostabilities for the first set of chimeras. Ten of these sequences were expressed in active form; all 10 retained more activity than H. insolens CBH II after incubation at 63°C. The total of 15 validated thermostable CBH II enzymes have high sequence diversity, differing from their closest natural homologs at up to 63 amino acid positions. Selected purified thermostable chimeras hydrolyzed phosphoric acid swollen cellulose at temperatures 7 to 15°C higher than the parent enzymes. These chimeras also hydrolyzed as much or more cellulose than the parent CBH II enzymes in long-time cellulose hydrolysis assays and had pH/activity profiles as broad, or broader than, the parent enzymes. Generating this group of diverse, thermostable fungal CBH II chimeras is the first step in building an inventory of stable cellulases from which optimized enzyme mixtures for biomass conversion can be formulated