Single molecule pulling with large time steps

Recently, we presented a generalisation of the Jarzynski non-equilibrium work theorem for phase space mappings. The formalism shows that one can determine free energy differences from approximate trajectories obtained from molecular dynamics simulations in which very large timesteps are used. In this work we test the method by simulating the force induced unfolding of a deca-alanine helix in vacuum. The excellent agreement between results obtained with a small, conservative time step of 0.5 fs and results obtained with a time step of 3.2 fs (i.e., close to the stability limit) indicates that the large time step approach is practical for such complex biomolecules. We further adapt the method of Hummer and Szabo for the simulation of single-molecule force spectroscopy experiments to the large time step method. While trajectories generated with large steps are approximate and may be unphysical - in the simulations presented here we observe a violation of the equipartition theorem - the computed free energies are exact in principle. In terms of efficiency, the optimum time step for the unfolding simulations lies in the range 1-3 fs.Comment: 8 pages, 8 figure

On the Equivalence of Affine sl(2) and N=2 Superconformal Representation Theories

There exist two different languages, the ^sl(2) and N=2 ones, to describe similar structures; a dictionary is given translating the key representation-theoretic terms related to the two algebras. The main tool to describe the structure of ^sl(2) and N=2 modules is provided by diagrams of extremal vectors. The ^sl(2) and N=2 representation theories of certain highest-weight types turn out to be equivalent modulo the respective spectral flows.Comment: 14 pages, LaTeX209, needs bezier.sty. Contribution to the proceedings of the 30th Int. Symposium Ahrenshoop on the theory of elementary particles, Buckow, Germany, August 27--31, 199

Gauge Independence of IR singularities in Non-Commutative QFT - and Interpolating Gauges

IR divergences of a non-commutative U(1) Maxwell theory are discussed at the one-loop level using an interpolating gauge to show that quadratic IR divergences are independent not only from a covariant gauge fixing but also independent from an axial gauge fixing.Comment: 11 pages, 2 figures, v1 minor correction

Superstrings from Hamiltonian Reduction

In any string theory there is a hidden, twisted superconformal symmetry algebra, part of which is made up by the BRST current and the anti-ghost. We investigate how this algebra can be systematically constructed for strings with $N\!-\!2$ supersymmetries, via quantum Hamiltonian reduction of the Lie superalgebras $osp(N|2)$. The motivation is to understand how one could systematically construct generalized string theories from superalgebras. We also briefly discuss the BRST algebra of the topological string, which is a doubly twisted $N\!=\!4$ superconformal algebra.Comment: 32p, LaTeX, CERN-TH.7379/9

A Vector Supersymmetry in Noncommutative U(1) Gauge Theory with the Slavnov Term

We consider noncommutative U(1) gauge theory with the additional term, involving a scalar field lambda, introduced by Slavnov in order to cure the infrared problem. we show that this theory, with an appropriate space-like axial gauge-fixing, wxhibits a linear vector supersymmetry similar to the one present in the 2-dimensional BF model. This vector supersymmetry implies that all loop corrections are independent of the $\lambda AA$-vertex and thereby explains why Slavnov found a finite model for the same gauge-fixing.Comment: 18 pages, 3 figures; v2 Acknowledgments adde

Strings from N=2N=2 Gauged Wess-Zumino-Witten Models

We present an algebraic approach to string theory. An embedding of $sl(2|1)$ in a super Lie algebra together with a grading on the Lie algebra determines a nilpotent subalgebra of the super Lie algebra. Chirally gauging this subalgebra in the corresponding Wess-Zumino-Witten model, breaks the affine symmetry of the Wess-Zumino-Witten model to some extension of the $N=2$ superconformal algebra. The extension is completely determined by the $sl(2|1)$ embedding. The realization of the superconformal algebra is determined by the grading. For a particular choice of grading, one obtains in this way, after twisting, the BRST structure of a string theory. We classify all embeddings of $sl(2|1)$ into Lie super algebras and give a detailed account of the branching of the adjoint representation. This provides an exhaustive classification and characterization of both all extended $N=2$ superconformal algebras and all string theories which can be obtained in this way.Comment: 50 pages, LaTe

A Generalization of Slavnov-Extended Non-Commutative Gauge Theories

We consider a non-commutative U(1) gauge theory in 4 dimensions with a modified Slavnov term which looks similar to the 3-dimensional BF model. In choosing a space-like axial gauge fixing we find a new vector supersymmetry which is used to show that the model is free of UV/IR mixing problems, just as in the previously discussed model in arXiv:hep-th/0604154. Finally, we present generalizations of our proposed model to higher dimensions.Comment: 25 pages, no figures; v2 minor correction

Free Field Realization of WBCnWBC_{n} and WG2WG_{2} algebras

We study the BRST-cohomology in the quantum hamiltonian reduction of affine Lie algebras of non-simply laced type. We obtain the free field realization of the $W{\bf g}$-algebra for \bg=B_{2}, $B_{3}$, $C_{3}$ and $G_{2}$. The $WC_{3}$ algebra is shown to be equal to the $WB_{3}$ algebra at the quantum level by duality transformation.Comment: 14 pages, late

Rotational friction on small globular proteins: Combined dielectric and hydrodynamic effect

Rotational friction on proteins and macromolecules is known to derive contributions from at least two distinct sources -- hydrodynamic (due to viscosity) and dielectric friction (due to polar interactions). In the existing theoretical approaches, the effect of the latter is taken into account in an {\it ad hoc} manner, by increasing the size of the protein with the addition of a hydration layer. Here we calculate the rotational dielectric friction on a protein ($\zeta_{DF}$) by using a generalized arbitrary charge distribution model (where the charges are obtained from quantum chemical calculation) and the hydrodynamic friction with stick boundary condition, ($\zeta_{hyd}^{stick}$) by using the sophisticated theoretical technique known as tri-axial ellipsoidal method, formulated by Harding [S. E. Harding, Comp. Biol. Med. {\bf 12}, 75 (1982)]. The calculation of hydrodynamic friction is done with only the dry volume of the protein (no hydration layer). We find that the total friction obtained by summing up $\zeta_{DF}$ and $\zeta_{hyd}^{stick}$ gives reasonable agreement with the experimental results, i.e., $\zeta_{exp} \approx \zeta_{DF} + \zeta_{hyd}^{stick}$

TOPOLOGICAL MATTER, MIRROR SYMMETRY AND NON-CRITICAL (SUPER)STRINGS

We study the realization of the (super) conformal topological symmetry in two-dimensional field theories. The mirror automorphism of the topological algebra is represented as a reflection in the space of fields. As a consequence, a double BRST structure for topological matter theories is found. It is shown that the implementation of the topological symmetry in non-critical (super)string theories depends on the matter content of the two realizations connected by the mirror transformation.Comment: 45 pages, phyzzx, no figure