Minimising biases in Full Configuration Interaction Quantum Monte Carlo

We show that Full Configuration Interaction Quantum Monte Carlo (FCIQMC) is a Markov Chain in its present form. We construct the Markov matrix of FCIQMC for a two determinant system and hence compute the stationary distribution. These solutions are used to quantify the dependence of the population dynamics on the parameters defining the Markov chain. Despite the simplicity of a system with only two determinants, it still reveals a population control bias inherent to the FCIQMC algorithm. We investigate the effect of simulation parameters on the population control bias for the neon atom and suggest simulation setups to in general minimise the bias. We show a reweighting scheme to remove the bias caused by population control commonly used in Diffusion Monte Carlo [J. Chem. Phys. 99, 2865 (1993)] is effective and recommend its use as a post processing step.Comment: Supplementary material available as 'Ancillary Files

Cattle Trade and the Risk of Importing Animal Diseases into the Netherlands

Projections of live cattle trade in the EU-25 assist to reduce the uncertainty on the risk of importing animal diseases in the Netherlands. The accession of 10 member states to the European Union has a potentially large impact on livestock trade in the EU as it liberalized in one stroke a trade that was administered by the Management Committee for Beef until May 1, 2004. The approach combines AG-Memod partial equilibrium with GTAP general equilibrium modelling in order to estimate the impact of quota liberalization. Quota removal will substantially alter the regional structure of livestock imports, as the share of new EU member states in the east triples to 25%. The risk outlook indicates a need for enhanced animal health services in the new member states.livestock, animal disease, trade, projections, quota, EU-enlargement, Risk and Uncertainty, F17, I18, Q17,

Exploring the parameter space of an endohedral atom in a cylindrical cavity

Endohedral fullerenes, or endofullerenes, are chemical systems of fullerene cages encapsulating single atoms or small molecules. These species provide an interesting challenge of Potential Energy Surface (PES) determination as examples of non-covalently bonded, bound systems. While the majority of studies focus on C$_{60}$ as the encapsulating cage, introducing some anisotropy by using a different fullerene, e.g., C$_{70}$ can unveil a double well potential along the unique axis. By approximating the potential as a pairwise Lennard-Jones (LJ) summation over the fixed C cage atoms, the parameter space of the Hamiltonian includes three tunable variables: $(M,\varepsilon,\sigma)$ representing the mass of the trapped species, the LJ energy, and length scales respectively. Fixing the mass and allowing the others to vary can imitate the potentials of endohedral species trapped in more elongated fullerenes. We choose to explore the LJ parameter space of an endohedral atom in C$_{70}$ with $\varepsilon\in$ [20cm$^{-1}$, 150cm$^{-1}$], and $\sigma\in$ [2.85\r{A} , 3.05\r{A}]. As the barrier height and positions of these wells vary between [1cm$^{-1}$, 264cm$^{-1}$] and [0.35\r{A}, 0.85\r{A}] respectively, using a 3D direct product basis of 1D harmonic oscillator (HO) wavefunctions centred at the origin where there is a local maximum is unphysical. Instead we propose the use of a non-orthogonal basis set, using 1D HO wavefunctions centred in each minimum and compare this to other choices. The ground state energy of the X@C$_{70}$ is tracked across the LJ parameter space, along with its corresponding nuclear translational wavefunctions. A classification of the wavefunction characteristics, namely the prolateness and ``peanut-likeness'' based on its statistical moments is also proposed.Comment: 14 pages, 14 figure

Homology of free quantum groups

We compute the Hochschild homology of the free orthogonal quantum group $A_o(n)$. We show that it satisfies Poincar\'e duality and should be considered to be a 3-dimensional object. We then use recent results of R. Vergnioux to derive results about the $\ell^2$-homology of $A_o(n)$ and estimates on the free entropy dimension of its set of generators. In particular, we show that the $\ell^2$ Betti-numbers of $A_o(n)$ all vanish and that the free entropy dimension is less than 1.Comment: 8 page

Observation and inverse problems in coupled cell networks

A coupled cell network is a model for many situations such as food webs in ecosystems, cellular metabolism, economical networks... It consists in a directed graph $G$, each node (or cell) representing an agent of the network and each directed arrow representing which agent acts on which one. It yields a system of differential equations $\dot x(t)=f(x(t))$, where the component $i$ of $f$ depends only on the cells $x_j(t)$ for which the arrow $j\rightarrow i$ exists in $G$. In this paper, we investigate the observation problems in coupled cell networks: can one deduce the behaviour of the whole network (oscillations, stabilisation etc.) by observing only one of the cells? We show that the natural observation properties holds for almost all the interactions $f$

Open-source development experiences in scientific software: the HANDE quantum Monte Carlo project

The HANDE quantum Monte Carlo project offers accessible stochastic algorithms for general use for scientists in the field of quantum chemistry. HANDE is an ambitious and general high-performance code developed by a geographically-dispersed team with a variety of backgrounds in computational science. In the course of preparing a public, open-source release, we have taken this opportunity to step back and look at what we have done and what we hope to do in the future. We pay particular attention to development processes, the approach taken to train students joining the project, and how a flat hierarchical structure aids communicationComment: 6 pages. Submission to WSSSPE

Catastrophic regime shifts in model ecological communities are true phase transitions

Ecosystems often undergo abrupt regime shifts in response to gradual external changes. These shifts are theoretically understood as a regime switch between alternative stable states of the ecosystem dynamical response to smooth changes in external conditions. Usual models introduce nonlinearities in the macroscopic dynamics of the ecosystem that lead to different stable attractors among which the shift takes place. Here we propose an alternative explanation of catastrophic regime shifts based on a recent model that pictures ecological communities as systems in continuous fluctuation, according to certain transition probabilities, between different micro-states in the phase space of viable communities. We introduce a spontaneous extinction rate that accounts for gradual changes in external conditions, and upon variations on this control parameter the system undergoes a regime shift with similar features to those previously reported. Under our microscopic viewpoint we recover the main results obtained in previous theoretical and empirical work (anomalous variance, hysteresis cycles, trophic cascades). The model predicts a gradual loss of species in trophic levels from bottom to top near the transition. But more importantly, the spectral analysis of the transition probability matrix allows us to rigorously establish that we are observing the fingerprints, in a finite size system, of a true phase transition driven by background extinctions.Comment: 19 pages, 11 figures, revised versio

Superposition as memory: unlocking quantum automatic complexity

Imagine a lock with two states, "locked" and "unlocked", which may be manipulated using two operations, called 0 and 1. Moreover, the only way to (with certainty) unlock using four operations is to do them in the sequence 0011, i.e., $0^n1^n$ where $n=2$. In this scenario one might think that the lock needs to be in certain further states after each operation, so that there is some memory of what has been done so far. Here we show that this memory can be entirely encoded in superpositions of the two basic states "locked" and "unlocked", where, as dictated by quantum mechanics, the operations are given by unitary matrices. Moreover, we show using the Jordan--Schur lemma that a similar lock is not possible for $n=60$. We define the semi-classical quantum automatic complexity $Q_{s}(x)$ of a word $x$ as the infimum in lexicographic order of those pairs of nonnegative integers $(n,q)$ such that there is a subgroup $G$ of the projective unitary group PU$(n)$ with $|G|\le q$ and with $U_0,U_1\in G$ such that, in terms of a standard basis $\{e_k\}$ and with $U_z=\prod_k U_{z(k)}$, we have $U_x e_1=e_2$ and $U_y e_1 \ne e_2$ for all $y\ne x$ with $|y|=|x|$. We show that $Q_s$ is unbounded and not constant for strings of a given length. In particular, $$Q_{s}(0^21^2)\le (2,12) < (3,1) \le Q_{s}(0^{60}1^{60})$$ and $Q_s(0^{120})\le (2,121)$.Comment: Lecture Notes in Computer Science, UCNC (Unconventional Computation and Natural Computation) 201