Kinetic distance and kinetic maps from molecular dynamics simulation

Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine

The Pivotal Role of Causality in Local Quantum Physics

In this article an attempt is made to present very recent conceptual and computational developments in QFT as new manifestations of old and well establihed physical principles. The vehicle for converting the quantum-algebraic aspects of local quantum physics into more classical geometric structures is the modular theory of Tomita. As the above named laureate to whom I have dedicated has shown together with his collaborator for the first time in sufficient generality, its use in physics goes through Einstein causality. This line of research recently gained momentum when it was realized that it is not only of structural and conceptual innovative power (see section 4), but also promises to be a new computational road into nonperturbative QFT (section 5) which, picturesquely speaking, enters the subject on the extreme opposite (noncommutative) side.Comment: This is a updated version which has been submitted to Journal of Physics A, tcilatex 62 pages. Adress: Institut fuer Theoretische Physik FU-Berlin, Arnimallee 14, 14195 Berlin presently CBPF, Rua Dr. Xavier Sigaud 150, 22290-180 Rio de Janeiro, Brazi

On localization and position operators in Moebius-covariant theories

Some years ago it was shown that, in some cases, a notion of locality can arise from the group of symmetry enjoyed by the theory, thus in an intrinsic way. In particular, when Moebius covariance is present, it is possible to associate some particular transformations to the Tomita Takesaki modular operator and conjugation of a specific interval of an abstract circle. In this context we propose a way to define an operator representing the coordinate conjugated with the modular transformations. Remarkably this coordinate turns out to be compatible with the abstract notion of locality. Finally a concrete example concerning a quantum particle on a line is also given.Comment: 19 pages, UTM 705, version to appear in RM

Generalized Particle Statistics in Two-Dimensions: Examples from the Theory of Free Massive Dirac Field

In the framework of algebraic quantum field theory we analyze the anomalous statistics exhibited by a class of automorphisms of the observable algebra of the two-dimensional free massive Dirac field, constructed by fermionic gauge group methods. The violation of Haag duality, the topological peculiarity of a two-dimensional space-time and the fact that unitary implementers do not lie in the global field algebra account for strange behaviour of statistics, which is no longer an intrinsic property of sectors. Since automorphisms are not inner, we exploit asymptotic abelianness of intertwiners in order to construct a braiding for a suitable $C^*$-tensor subcategory of End($\mathscr{A}$). We define two inequivalent classes of path connected bi-asymptopias, selecting only those sets of nets which yield a true generalized statistics operator.Comment: 24 page

Chiral Vertex Operators in Off-Conformal Theory: The Sine-Gordon Example

We study chiral vertex operators in the sine-Gordon [SG] theory, viewed as an off-conformal system. We find that these operators, which would have been primary fields in the conformal limit, have interesting and, in some ways, unexpected properties in the SG model. Some of them continue to have scale- invariant dynamics even in the presence of the non-conformal cosine interaction. For instance, it is shown that the Mandelstam operator for the bosonic representation of the Fermi field does {\it not} develop a mass term in the SG theory, contrary to what the real Fermi field in the massive Thirring model is expected to do. It is also shown that in the presence of the non-conformal interactions, some vertex operators have unique Lorentz spins, while others do not.Comment: 32 pages, Univ. of Illinois Preprint # ILL-(TH)-93-1

Towards the Construction of Wightman Functions of Integrable Quantum Field Theories

The purpose of the ``bootstrap program'' for integrable quantum field theories in 1+1 dimensions is to construct a model in terms of its Wightman functions explicitly. In this article, this program is mainly illustrated in terms of the sine-Gordon and the sinh-Gordon model and (as an exercise) the scaling Ising model. We review some previous results on sine-Gordon breather form factors and quantum operator equations. The problem to sum over intermediate states is attacked in the short distance limit of the two point Wightman function for the sinh-Gordon and the scaling Ising model.Comment: LATEX 18 pages, Talk presented at the '6th International Workshop on Conformal Field Theories and Integrable Models', in Chernologka, September 200

New Concepts in Particle Physics from Solution of an Old Problem

Recent ideas on modular localization in local quantum physics are used to clarify the relation between on- and off-shell quantities in particle physics; in particular the relation between on-shell crossing symmetry and off-shell Einstein causality. Among the collateral results of this new nonperturbative approach are profound relations between crossing symmetry of particle physics and Hawking-Unruh like thermal aspects (KMS property, entropy attached to horizons) of quantum matter behind causal horizons, aspects which hitherto were exclusively related with Killing horizons in curved spacetime rather than with localization aspects in Minkowski space particle physics. The scope of this modular framework is amazingly wide and ranges from providing a conceptual basis for the d=1+1 bootstrap-formfactor program for factorizable d=1+1 models to a decomposition theory of QFT's in terms of a finite collection of unitarily equivalent chiral conformal theories placed a specified relative position within a common Hilbert space (in d=1+1 a holographic relation and in higher dimensions more like a scanning). The new framework gives a spacetime interpretation to the Zamolodchikov-Faddeev algebra and explains its thermal aspects.Comment: In this form it will appear in JPA Math Gen, 47 pages tcilate

Affine Lie Algebras in Massive Field Theory and Form-Factors from Vertex Operators

We present a new application of affine Lie algebras to massive quantum field theory in 2 dimensions, by investigating the $q\to 1$ limit of the q-deformed affine $\hat{sl(2)}$ symmetry of the sine-Gordon theory, this limit occurring at the free fermion point. Working in radial quantization leads to a quasi-chiral factorization of the space of fields. The conserved charges which generate the affine Lie algebra split into two independent affine algebras on this factorized space, each with level 1 in the anti-periodic sector, and level $0$ in the periodic sector. The space of fields in the anti-periodic sector can be organized using level-$1$ highest weight representations, if one supplements the \slh algebra with the usual local integrals of motion. Introducing a particle-field duality leads to a new way of computing form-factors in radial quantization. Using the integrals of motion, a momentum space bosonization involving vertex operators is formulated. Form-factors are computed as vacuum expectation values in momentum space. (Based on talks given at the Berkeley Strings 93 conference, May 1993, and the III International Conference on Mathematical Physics, String Theory, and Quantum Gravity, Alushta, Ukraine, June 1993.)Comment: 13 pages, CLNS 93/125

Anomalous Scale Dimensions from Timelike Braiding

Using the previously gained insight about the particle/field relation in conformal quantum field theories which required interactions to be related to the existence of particle-like states associated with fields of anomalous scaling dimensions, we set out to construct a classification theory for the spectra of anomalous dimensions. Starting from the old observations on conformal superselection sectors related to the anomalous dimensions via the phases which appear in the spectral decomposition of the center of the conformal covering group $Z(\widetilde{SO(d,2)}),$ we explore the possibility of a timelike braiding structure consistent with the timelike ordering which refines and explains the central decomposition. We regard this as a preparatory step in a new construction attempt of interacting conformal quantum field theories in D=4 spacetime dimensions. Other ideas of constructions based on the $AdS_{5}$-$CQFT_{4}$ or the perturbative SYM approach in their relation to the present idea are briefly mentioned.Comment: completely revised, updated and shortened replacement, 24 pages tcilatex, 3 latexcad figure