Visualization of Protein Folding Funnels in Lattice Models

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Magnetism in spin models for depleted honeycomb-lattice iridates: Spin-glass order towards percolation

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Random lattice models

This thesis deals with three different physical models, where each model involves a random component which is linked to a cubic lattice. First, a model is studied, which is used in numerical calculations of Quantum Chromodynamics.In these calculations random gauge-fields are distributed on the bonds of the lattice. The formulation of the model is fitted into the mathematical framework of ergodic operator families. We prove, that for small coupling constants, the ergodicity of the underlying probability measure is indeed ensured and that the integrated density of states of the Wilson-Dirac operator exists. The physical situations treated in the next two chapters are more similar to one another. In both cases the principle idea is to study a fermion system in a cubic crystal with impurities, that are modeled by a random potential located at the lattice sites. In the second model we apply the Hartree-Fock approximation to such a system. For the case of reduced Hartree-Fock theory at positive temperatures and a fixed chemical potential we consider the limit of an infinite system. In that case we show the existence and uniqueness of minimizers of the Hartree-Fock functional. In the third model we formulate the fermion system algebraically via C*-algebras. The question imposed here is to calculate the heat production of the system under the influence of an outer electromagnetic field. We show that the heat production corresponds exactly to what is empirically predicted by Joule's law in the regime of linear response.

Edge states and zero modes in quadratic fermionic models on a 1-D lattice

In una formulazione rigorosa della teoria quantistica, la definizione della varietà Riemanniana spaziale su cui il sistema è vincolato gioca un ruolo fondamentale. La presenza di un bordo sottolinea l'aspetto quantistico del sistema: l'imposizione di condizioni al contorno determina la discretizzazione degli autovalori del Laplaciano, come accade con condizioni note quali quelle periodiche, di Neumann o di Dirichlet. Tuttavia, non sono le uniche possibili. Qualsiasi condizione al bordo che garantisca l'autoaggiunzione dell' operatore Hamiltoniano è ammissibile. Tutte le possibili boundary conditions possono essere catalogate a partire dalla richiesta di conservazione del flusso al bordo della varietà. Alcune possibili condizioni al contorno, permettono l'esistenza di stati legati al bordo, cioè autostati dell' Hamiltoniana con autovalori negativi, detti edge states. Lo scopo di questa tesi è quello di investigare gli effetti di bordo in sistemi unidimensionali implementati su un reticolo discreto, nella prospettiva di capire come simulare proprietà di edge in un reticolo ottico. Il primo caso considerato è un sistema di elettroni liberi. La presenza di edge states è completamente determinata dai parametri di bordo del Laplaciano discreto. Al massimo due edge states emergono, e possono essere legati all' estremità destra o sinistra della catena a seconda delle condizioni al contorno. Anche il modo in cui decadono dal bordo al bulk e completamente determinato dalla scelta delle condizioni. Ammettendo un' interazione quadratica tra siti primi vicini, un secondo tipo di stati emerge in relazione sia alle condizioni al contorno che ai parametri del bulk. Questi stati sono chiamati zero modes, in quanto esiste la possibilità che siano degeneri con lo stato fondamentale. Per implementare le più generali condizioni al contorno, specialmente nel caso interagente, è necessario utilizzare un metodo generale per la diagonalizzazione, che estende la tecnica di Lieb-Shultz-Mattis per Hamiltoniane quadratiche a matrici complesse.

O(N) Models with Topological Lattice Actions

A variety of lattice discretisations of continuum actions has been considered, usually requiring the correct classical continuum limit. Here we discuss “weird” lattice formulations without that property, namely lattice actions that are invariant under most continuous deformations of the field configuration, in one version even without any coupling constants. It turns out that universality is powerful enough to still provide the correct quantum continuum limit, despite the absence of a classical limit, or a perturbative expansion. We demonstrate this for a set of O(N) models (or non-linear σ-models). Amazingly, such “weird” lattice actions are not only in the right universality class, but some of them even have practical benefits, in particular an excellent scaling behaviour.

All-loop anomalous dimensions in integrable λ-deformed σ-models

We calculate the all-loop anomalous dimensions of current operators in λ-deformed σ-models. For the isotropic integrable deformation and for a semi-simple group G we compute the anomalous dimensions using two different methods. In the first we use the all-loop effective action and in the second we employ perturbation theory along with the Callan–Symanzik equation and in conjunction with a duality-type symmetry shared by these models. Furthermore, using CFT techniques we compute the all-loop anomalous dimension of bilinear currents for the isotropic deformation case and a general G . Finally we work out the anomalous dimension matrix for the cases of anisotropic SU(2) and the two couplings, corresponding to the symmetric coset G/H and a subgroup H, splitting of a group G.

Stretching lattice models of protein folding

A new class of experiments that probe folding of individual protein domains uses mechanical stretching to cause the transition. We show how stretching forces can be incorporated in lattice models of folding. For fast folding proteins, the analysis suggests a complex relation between the force dependence and the reaction coordinate for folding.

Energy level statistics for models of coupled single-mode Bose-Einstein condensates

We study the distribution of energy level spacings in two models describing coupled single-mode Bose-Einstein condensates. Both models have a fixed number of degrees of freedom, which is small compared to the number of interaction parameters, and is independent of the dimensionality of the Hilbert space. We find that the distribution follows a universal Poisson form independent of the choice of coupling parameters, which is indicative of the integrability of both models. These results complement those for integrable lattice models where the number of degrees of freedom increases with increasing dimensionality of the Hilbert space. Finally, we also show that for one model the inclusion of an additional interaction which breaks the integrability leads to a non-Poisson distribution.

Testing predictions of macroscopic binary diffusion coefficients using lattice models with site heterogeneity

Quantitatively predicting mass transport rates for chemical mixtures in porous materials is important in applications of materials such as adsorbents, membranes, and catalysts. Because directly assessing mixture transport experimentally is challenging, theoretical models that can predict mixture diffusion coefficients using Only single-component information would have many uses. One such model was proposed by Skoulidas, Sholl, and Krishna (Langmuir, 2003, 19, 7977), and applications of this model to a variety of chemical mixtures in nanoporous materials have yielded promising results. In this paper, the accuracy of this model for predicting mixture diffusion coefficients in materials that exhibit a heterogeneous distribution of local binding energies is examined. To examine this issue, single-component and binary mixture diffusion coefficients are computed using kinetic Monte Carlo for a two-dimensional lattice model over a wide range of lattice occupancies and compositions. The approach suggested by Skoulidas, Sholl, and Krishna is found to be accurate in situations where the spatial distribution of binding site energies is relatively homogeneous, but is considerably less accurate for strongly heterogeneous energy distributions.

The D(D-3)-anyon chain: integrable boundary conditions and excitation spectra

Chains of interacting non-Abelian anyons with local interactions invariant under the action of the Drinfeld double of the dihedral group D-3 are constructed. Formulated as a spin chain the Hamiltonians are generated from commuting transfer matrices of an integrable vertex model for periodic and braided as well as open boundaries. A different anyonic model with the same local Hamiltonian is obtained within the fusion path formulation. This model is shown to be related to an integrable fusion interaction round the face model. Bulk and surface properties of the anyon chain are computed from the Bethe equations for the spin chain. The low-energy effective theories and operator content of the models (in both the spin chain and fusion path formulation) are identified from analytical and numerical studies of the finite-size spectra. For all boundary conditions considered the continuum theory is found to be a product of two conformal field theories. Depending on the coupling constants the factors can be a Z(4) parafermion or a M-(5,M-6) minimal model.