Generating functional analysis of complex formation and dissociation in large protein interaction networks

We analyze large systems of interacting proteins, using techniques from the non-equilibrium statistical mechanics of disordered many-particle systems. Apart from protein production and removal, the most relevant microscopic processes in the proteome are complex formation and dissociation, and the microscopic degrees of freedom are the evolving concentrations of unbound proteins (in multiple post-translational states) and of protein complexes. Here we only include dimer-complexes, for mathematical simplicity, and we draw the network that describes which proteins are reaction partners from an ensemble of random graphs with an arbitrary degree distribution. We show how generating functional analysis methods can be used successfully to derive closed equations for dynamical order parameters, representing an exact macroscopic description of the complex formation and dissociation dynamics in the infinite system limit. We end this paper with a discussion of the possible routes towards solving the nontrivial order parameter equations, either exactly (in specific limits) or approximately.Comment: 14 pages, to be published in Proc of IW-SMI-2009 in Kyoto (Journal of Phys Conference Series

Entropy and Entanglement in Quantum Ground States

We consider the relationship between correlations and entanglement in gapped quantum systems, with application to matrix product state representations. We prove that there exist gapped one-dimensional local Hamiltonians such that the entropy is exponentially large in the correlation length, and we present strong evidence supporting a conjecture that there exist such systems with arbitrarily large entropy. However, we then show that, under an assumption on the density of states which is believed to be satisfied by many physical systems such as the fractional quantum Hall effect, that an efficient matrix product state representation of the ground state exists in any dimension. Finally, we comment on the implications for numerical simulation.Comment: 7 pages, no figure

On topological phases of spin chains

Symmetry protected topological phases of one-dimensional spin systems have been classified using group cohomology. In this paper, we revisit this problem for general spin chains which are invariant under a continuous on-site symmetry group G. We evaluate the relevant cohomology groups and find that the topological phases are in one-to-one correspondence with the elements of the fundamental group of G if G is compact, simple and connected and if no additional symmetries are imposed. For spin chains with symmetry PSU(N)=SU(N)/Z_N our analysis implies the existence of N distinct topological phases. For symmetry groups of orthogonal, symplectic or exceptional type we find up to four different phases. Our work suggests a natural generalization of Haldane's conjecture beyond SU(2).Comment: 18 pages, 7 figures, 2 tables. Version v2 corresponds to the published version. It includes minor revisions, additional references and an application to cold atom system

Electronic heat current rectification in hybrid superconducting devices

In this work, we review and expand recent theoretical proposals for the realization of electronic thermal diodes based on tunnel-junctions of normal metal and superconducting thin films. Starting from the basic rectifying properties of a single hybrid tunnel junction, we will show how the rectification efficiency can be largely increased by combining multiple junctions in an asymmetric chain of tunnel-coupled islands. We propose three different designs, analyzing their performance and their potential advantages. Besides being relevant from a fundamental physics point of view, this kind of devices might find important technological application as fundamental building blocks in solid-state thermal nanocircuits and in general-purpose cryogenic electronic applications requiring energy management.Comment: 9 pages, 5 color figure

Local Unitary Quantum Cellular Automata

In this paper we present a quantization of Cellular Automata. Our formalism is based on a lattice of qudits, and an update rule consisting of local unitary operators that commute with their own lattice translations. One purpose of this model is to act as a theoretical model of quantum computation, similar to the quantum circuit model. It is also shown to be an appropriate abstraction for space-homogeneous quantum phenomena, such as quantum lattice gases, spin chains and others. Some results that show the benefits of basing the model on local unitary operators are shown: universality, strong connections to the circuit model, simple implementation on quantum hardware, and a wealth of applications.Comment: To appear in Physical Review