arXiv subjects

Simone Severini

Publications and source records attributed to Simone Severini.

At least 73 records · Page 4Linked to original sources

arXiv2013

A mathematical model of kinetoplastid mitochondrial gene scrambling advantage

We model and discuss advantages of pan-editing, the complex way of expressing mitochondrial genes in kinetoplastids. The rapid spread and preservation of pan-editing seems to be due to its concomitant fragment dispersal. Such dispersal prevents losing temporarily non expressed mitochondrial genes upon intense intraspecific competition, by linking non expressed fragments to parts which are still needed. We mathematically modelled protection against gene loss, due to the absence of selection, by this kind of fragment association. This gives ranges of values for parameters like scrambling extent, population size, and number of generations still retaining full genomes despite limited selection. Values obtained seem consistent with those observed. We find a quasi-linear correlation between dispersal and number of generations after which populations lose genes, showing that pan-editing can be selected to effectively limit gene loss under relaxed selective pressure.

q-bio.PE↗

arXiv2013

alpha-Kuramoto partitions: graph partitions from the frustrated Kuramoto model generalise equitable partitions

The Kuramoto model describes the collective dynamics of a system of coupled oscillators. An alpha-Kuramoto partition is a graph partition induced by the Kuramoto model, when the oscillators include a phase frustration parameter. We prove that every equitable partition is an alpha-Kuramoto partition, but that the converse does necessarily not hold. We give an exact characterisation of alpha-Kuramoto bipartitions.

math.CO↗

arXiv2013

Locality for quantum systems on graphs depends on the number field

Adapting a definition of Aaronson and Ambainis [Theory Comput. 1 (2005), 47--79], we call a quantum dynamics on a digraph "saturated Z-local" if the nonzero transition amplitudes specifying the unitary evolution are in exact correspondence with the directed edges (including loops) of the digraph. This idea appears recurrently in a variety of contexts including angular momentum, quantum chaos, and combinatorial matrix theory. Complete characterization of the digraph properties that allow such a process to exist is a long-standing open question that can also be formulated in terms of minimum rank problems. We prove that saturated Z-local dynamics involving complex amplitudes occur on a proper superset of the digraphs that allow restriction to the real numbers or, even further, the rationals. Consequently, among these fields, complex numbers guarantee the largest possible choice of topologies supporting a discrete quantum evolution. A similar construction separates complex numbers from the skew field of quaternions. The result proposes a concrete ground for distinguishing between complex and quaternionic quantum mechanics.

quant-ph↗

arXiv2013

Sabidussi Versus Hedetniemi for Three Variations of the Chromatic Number

We investigate vector chromatic number, Lovasz theta of the complement, and quantum chromatic number from the perspective of graph homomorphisms. We prove an analog of Sabidussi's theorem for each of these parameters, i.e. that for each of the parameters, the value on the Cartesian product of graphs is equal to the maximum of the values on the factors. We also prove an analog of Hedetniemi's conjecture for Lovasz theta of the complement, i.e. that its value on the categorical product of graphs is equal to the minimum of its values on the factors. We conjecture that the analogous results hold for vector and quantum chromatic number, and we prove that this is the case for some special classes of graphs.

math.CO↗

arXiv2013

Interpreting the von Neumann entropy of graph Laplacians, and coentropic graphs

For any graph, we define a rank-1 operator on a bipartite tensor product space, with components associated to the set of vertices and edges respectively. We show that the partial traces of the operator are the Laplacian and the edge-Laplacian. This provides an interpretation of the von Neumann entropy of the (normalized)\ Laplacian as the amount of quantum entanglement between two systems corresponding to vertices and edges. In this framework, cospectral graphs correspond exactly to local unitarily equivalent pure states. Finally, we introduce the notion of coentropic graphs, that is, graphs with equal von Neumann entropy. The smallest coentropic (but not cospectral) graphs that we are able to construct have 8 vertices. The number of equivalence classes of coentropic graphs with n vertices and m edges is a lower bound to the number of (pure) bipartite entanglement classes with subsystems of corresponding dimension.

math.CO↗

arXiv2013

An example of graph limits of growing sequences of random graphs

We consider a class of growing random graphs obtained by creating vertices sequentially one by one: at each step, we choose uniformly the neighbours of the newly created vertex; its degree is a random variable with a fixed but arbitrary distribution, depending on the number of existing vertices. Examples from this class turn out to be the ER random graph, a natural random threshold graph, etc. By working with the notion of graph limits, we define a kernel which, under certain conditions, is the limit of the growing random graph. Moreover, for a subclass of models, the growing graph on any given n vertices has the same distribution as the random graph with n vertices that the kernel defines. The motivation stems from a model of graph growth whose attachment mechanism does not require information about properties of the graph at each iteration.

math.CO↗

arXiv2013

A notion of graph likelihood and an infinite monkey theorem

We play with a graph-theoretic analogue of the folklore infinite monkey theorem. We define a notion of graph likelihood as the probability that a given graph is constructed by a monkey in a number of time steps equal to the number of vertices. We present an algorithm to compute this graph invariant and closed formulas for some infinite classes. We have to leave the computational complexity of the likelihood as an open problem.

cs.DM↗

arXiv2013

Quantum channels from association schemes

We propose in this note the study of quantum channels from association schemes. This is done by interpreting the $(0,1)$-matrices of a scheme as the Kraus operators of a channel. Working in the framework of one-shot zero-error information theory, we give bounds and closed formulas for various independence numbers of the relative non-commutative (confusability) graphs, or, equivalently, graphical operator systems. We use pseudocyclic association schemes as an example. In this case, we show that the unitary entanglement-assisted independence number grows at least quadratically faster, with respect to matrix size, than the independence number. The latter parameter was introduced by Beigi and Shor as a generalization of the one-shot Shannon capacity, in analogy with the corresponding graph-theoretic notion.

quant-ph↗

arXiv2012

Estimating entanglement monotones with a generalization of the Wootters formula

Entanglement monotones, such as the concurrence, are useful tools to characterize quantum correlations in various physical systems. The computation of the concurrence involves, however, difficult optimizations and only for the simplest case of two qubits a closed formula was found by Wootters [Phys. Rev. Lett. 80, 2245 (1998)]. We show how this approach can be generalized, resulting in lower bounds on the concurrence for higher dimensional systems as well as for multipartite systems. We demonstrate that for certain families of states our results constitute the strongest bipartite entanglement criterion so far; moreover, they allow to recognize novel families of multiparticle bound entangled states.

quant-ph↗

arXiv2012

Improved lower bounds on genuine-multipartite-entanglement concurrence

Genuine-multipartite-entanglement (GME) concurrence is a measure of genuine multipartite entanglement that generalizes the well-known notion of concurrence. We define an observable for GME concurrence. The observable permits us to avoid full state tomography and leads to different analytic lower bounds. By means of explicit examples we show that entanglement criteria based on the bounds have a better performance with respect to the known methods.

quant-ph↗

arXiv2012

On dynamic network entropy in cancer

The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level insights into disease mechanisms and ultimately for developing improved therapies. By integrating gene expression data with a protein interaction network to induce a stochastic dynamics on the network, we here demonstrate that cancer cells are characterised by an increase in the dynamic network entropy, compared to cells of normal physiology. Using a fundamental relation between the macroscopic resilience of a dynamical system and the uncertainty (entropy) in the underlying microscopic processes, we argue that cancer cells will be more robust to random gene perturbations. In addition, we formally demonstrate that gene expression differences between normal and cancer tissue are anticorrelated with local dynamic entropy changes, thus providing a systemic link between gene expression changes at the nodes and their local network dynamics. In particular, we also find that genes which drive cell-proliferation in cancer cells and which often encode oncogenes are associated with reductions in the dynamic network entropy. In summary, our results support the view that the observed increased robustness of cancer cells to perturbation and therapy may be due to an increase in the dynamic network entropy that allows cells to adapt to the new cellular stresses. Conversely, genes that exhibit local flux entropy decreases in cancer may render cancer cells more susceptible to targeted intervention and may therefore represent promising drug targets.

q-bio.MN↗

arXiv2012

Number-Theoretic Nature of Communication in Quantum Spin Systems

The last decade has witnessed substantial interest in protocols for transferring information on networks of quantum mechanical objects. A variety of control methods and network topologies have been proposed, on the basis that transfer with perfect fidelity --- i.e. deterministic and without information loss --- is impossible through unmodulated spin chains with more than a few particles. Solving the original problem formulated by Bose [Phys. Rev. Lett. 91, 207901 (2003)], we determine the exact number of qubits in unmodulated chains (with XY Hamiltonian) that permit the transfer with fidelity arbitrarily close to 1, a phenomenon called pretty good state transfer. We prove that this happens if and only if the number of nodes is n=p-1, 2p-1, where p is a prime, or n=2^{m}-1. The result highlights the potential of quantum spin system dynamics for reinterpreting questions about the arithmetic structure of integers, and, in this case, primality.

quant-ph↗

arXiv2012

A Generalization of Kochen-Specker Sets Relates Quantum Coloring to Entanglement-Assisted Channel Capacity

We introduce two generalizations of Kochen-Specker (KS) sets: projective KS sets and generalized KS sets. We then use projective KS sets to characterize all graphs for which the chromatic number is strictly larger than the quantum chromatic number. Here, the quantum chromatic number is defined via a nonlocal game based on graph coloring. We further show that from any graph with separation between these two quantities, one can construct a classical channel for which entanglement assistance increases the one-shot zero-error capacity. As an example, we exhibit a new family of classical channels with an exponential increase.

quant-ph↗

arXiv2012

The von Neumann entropy of networks

We normalize the combinatorial Laplacian of a graph by the degree sum, look at its eigenvalues as a probability distribution and then study its Shannon entropy. Equivalently, we represent a graph with a quantum mechanical state and study its von Neumann entropy. At the graph-theoretic level, this quantity may be interpreted as a measure of regularity; it tends to be larger in relation to the number of connected components, long paths and nontrivial symmetries. When the set of vertices is asymptotically large, we prove that regular graphs and the complete graph have equal entropy, and specifically it turns out to be maximum. On the other hand, when the number of edges is fixed, graphs with large cliques appear to minimize the entropy.

cond-mat.dis-nn↗

arXiv2012

Control by quantum dynamics on graphs

We address the study of controllability of a closed quantum system whose dynamical Lie algebra is generated by adjacency matrices of graphs. We characterize a large family of graphs that renders a system controllable. The key property is a novel graph-theoretic feature consisting of a particularly disordered cycle structure. Disregarding efficiency of control functions, but choosing subfamilies of sparse graphs, the results translate into continuous-time quantum walks for universal computation.

quant-ph↗

arXiv2011

Approximate entropy of network parameters

We study the notion of approximate entropy within the framework of network theory. Approximate entropy is an uncertainty measure originally proposed in the context of dynamical systems and time series. We firstly define a purely structural entropy obtained by computing the approximate entropy of the so called slide sequence. This is a surrogate of the degree sequence and it is suggested by the frequency partition of a graph. We examine this quantity for standard scale-free and Erdős-Rényi networks. By using classical results of Pincus, we show that our entropy measure converges with network size to a certain binary Shannon entropy. On a second step, with specific attention to networks generated by dynamical processes, we investigate approximate entropy of horizontal visibility graphs. Visibility graphs permit to naturally associate to a network the notion of temporal correlations, therefore providing the measure a dynamical garment. We show that approximate entropy distinguishes visibility graphs generated by processes with different complexity. The result probes to a greater extent these networks for the study of dynamical systems. Applications to certain biological data arising in cancer genomics are finally considered in the light of both approaches.

cond-mat.dis-nn↗

arXiv2011

Entropy rate of non-equilibrium growing networks

New entropy measures have been recently introduced for the quantification of the complexity of networks. Most of these entropy measures apply to static networks or to dynamical processes defined on static complex networks. In this paper we define the entropy rate of growing network models. This entropy rate quantifies how many labeled networks are typically generated by the growing network models. We analytically evaluate the difference between the entropy rate of growing tree network models and the entropy of tree networks that have the same asymptotic degree distribution. We find that the growing networks with linear preferential attachment generated by dynamical models are exponentially less than the static networks with the same degree distribution for a large variety of relevant growing network models. We study the entropy rate for growing network models showing structural phase transitions including models with non-linear preferential attachment. Finally, we bring numerical evidence that the entropy rate above and below the structural phase transitions follow a different scaling with the network size.

cond-mat.dis-nn↗

arXiv2011

Logic circuits from zero forcing

We design logic circuits based on the notion of zero forcing on graphs; each gate of the circuits is a gadget in which zero forcing is performed. We show that such circuits can evaluate every monotone Boolean function. By using two vertices to encode each logical bit, we obtain universal computation. We also highlight a phenomenon of "back forcing" as a property of each function. Such a phenomenon occurs in a circuit when the input of gates which have been already used at a given time step is further modified by a computation actually performed at a later stage. Finally, we point out that zero forcing can be also used to implement reversible computation. The model introduced here provides a potentially new tool in the analysis of Boolean functions, with particular attention to monotonicity.

cs.DM↗