Dynamics of quantum adiabatic evolution algorithm for Number Partitioning

We have developed a general technique to study the dynamics of the quantum adiabatic evolution algorithm applied to random combinatorial optimization problems in the asymptotic limit of large problem size $n$. We use as an example the NP-complete Number Partitioning problem and map the algorithm dynamics to that of an auxilary quantum spin glass system with the slowly varying Hamiltonian. We use a Green function method to obtain the adiabatic eigenstates and the minimum excitation gap, $g_{\rm min}={\cal O}(n 2^{-n/2})$, corresponding to the exponential complexity of the algorithm for Number Partitioning. The key element of the analysis is the conditional energy distribution computed for the set of all spin configurations generated from a given (ancestor) configuration by simulteneous fipping of a fixed number of spins. For the problem in question this distribution is shown to depend on the ancestor spin configuration only via a certain parameter related to the energy of the configuration. As the result, the algorithm dynamics can be described in terms of one-dimenssional quantum diffusion in the energy space. This effect provides a general limitation on the power of a quantum adiabatic computation in random optimization problems. Analytical results are in agreement with the numerical simulation of the algorithm.Comment: 32 pages, 5 figures, 3 Appendices; List of additions compare to v.3: (i) numerical solution of the stationary Schroedinger equation for the adiabatic eigenstates and eigenvalues; (ii) connection between the scaling law of the minimum gap with the problem size and the shape of the coarse-grained distribution of the adiabatic eigenvalues at the avoided-crossing poin

Tree decompositions of real-world networks from simulated annealing

Decompositions of networks are useful not only for structural exploration. They also have implications and use in analysis and computational solution of processes (such as the Ising model, percolation, SIR model) running on a given network. Tree and branch decompositions considered here directly represent network structure as trees for recursive computation of network properties. Unlike coarse-graining approximations in terms of community structure or metapopulations, tree decompositions of sufficiently small width allow for exact results on equilibrium processes. Here we use simulated annealing to find tree decompositions of narrow width for a set of medium-size empirical networks. Rather than optimizing tree decompositions directly, we employ a search space constituted by so-called elimination orders being permutations on the network's node set. For each in a database of empirical networks with up to 1000 edges, we find a tree decomposition of low width.Comment: 11 pages, 2 figures, 1 tabl

Equation-Free Multiscale Computational Analysis of Individual-Based Epidemic Dynamics on Networks

The surveillance, analysis and ultimately the efficient long-term prediction and control of epidemic dynamics appear to be one of the major challenges nowadays. Detailed atomistic mathematical models play an important role towards this aim. In this work it is shown how one can exploit the Equation Free approach and optimization methods such as Simulated Annealing to bridge detailed individual-based epidemic simulation with coarse-grained, systems-level, analysis. The methodology provides a systematic approach for analyzing the parametric behavior of complex/ multi-scale epidemic simulators much more efficiently than simply simulating forward in time. It is shown how steady state and (if required) time-dependent computations, stability computations, as well as continuation and numerical bifurcation analysis can be performed in a straightforward manner. The approach is illustrated through a simple individual-based epidemic model deploying on a random regular connected graph. Using the individual-based microscopic simulator as a black box coarse-grained timestepper and with the aid of Simulated Annealing I compute the coarse-grained equilibrium bifurcation diagram and analyze the stability of the stationary states sidestepping the necessity of obtaining explicit closures at the macroscopic level under a pairwise representation perspective

Dynamics of Co-translational Membrane Protein Integration and Translocation via the Sec Translocon

An important aspect of cellular function is the correct targeting and delivery of newly synthesized proteins. Central to this task is the machinery of the Sec translocon, a transmembrane channel that is involved in both the translocation of nascent proteins across cell membranes and the integration of proteins into the membrane. Considerable experimental and computational effort has focused on the Sec translocon and its role in nascent protein biosynthesis, including the correct folding and expression of integral membrane proteins. However, the use of molecular simulation methods to explore Sec-facilitated protein biosynthesis is hindered by the large system sizes and long (i.e., minute) timescales involved. In this work, we describe the development and application of a coarse-grained simulation approach that addresses these challenges and allows for direct comparison with both in vivo and in vitro experiments. The method reproduces a wide range of experimental observations, providing new insights into the underlying molecular mechanisms, predictions for new experiments, and a strategy for the rational enhancement of membrane protein expression levels

Coarse-grained dynamics of an activity bump in a neural field model

We study a stochastic nonlocal PDE, arising in the context of modelling spatially distributed neural activity, which is capable of sustaining stationary and moving spatially-localized ``activity bumps''. This system is known to undergo a pitchfork bifurcation in bump speed as a parameter (the strength of adaptation) is changed; yet increasing the noise intensity effectively slowed the motion of the bump. Here we revisit the system from the point of view of describing the high-dimensional stochastic dynamics in terms of the effective dynamics of a single scalar "coarse" variable. We show that such a reduced description in the form of an effective Langevin equation characterized by a double-well potential is quantitatively successful. The effective potential can be extracted using short, appropriately-initialized bursts of direct simulation. We demonstrate this approach in terms of (a) an experience-based "intelligent" choice of the coarse observable and (b) an observable obtained through data-mining direct simulation results, using a diffusion map approach.Comment: Corrected aknowledgement

Multiscale Computations on Neural Networks: From the Individual Neuron Interactions to the Macroscopic-Level Analysis

We show how the Equation-Free approach for multi-scale computations can be exploited to systematically study the dynamics of neural interactions on a random regular connected graph under a pairwise representation perspective. Using an individual-based microscopic simulator as a black box coarse-grained timestepper and with the aid of simulated annealing we compute the coarse-grained equilibrium bifurcation diagram and analyze the stability of the stationary states sidestepping the necessity of obtaining explicit closures at the macroscopic level. We also exploit the scheme to perform a rare-events analysis by estimating an effective Fokker-Planck describing the evolving probability density function of the corresponding coarse-grained observables

Quantum Optimization of Fully-Connected Spin Glasses

The Sherrington-Kirkpatrick model with random $\pm1$ couplings is programmed on the D-Wave Two annealer featuring 509 qubits interacting on a Chimera-type graph. The performance of the optimizer compares and correlates to simulated annealing. When considering the effect of the static noise, which degrades the performance of the annealer, one can estimate an improvement on the comparative scaling of the two methods in favor of the D-Wave machine. The optimal choice of parameters of the embedding on the Chimera graph is shown to be associated to the emergence of the spin-glass critical temperature of the embedded problem.Comment: includes supplemental materia