Monte Carlo sampling for stochastic weight functions.

Conventional Monte Carlo simulations are stochastic in the sense that the acceptance of a trial move is decided by comparing a computed acceptance probability with a random number, uniformly distributed between 0 and 1. Here, we consider the case that the weight determining the acceptance probability itself is fluctuating. This situation is common in many numerical studies. We show that it is possible to construct a rigorous Monte Carlo algorithm that visits points in state space with a probability proportional to their average weight. The same approach may have applications for certain classes of high-throughput experiments and the analysis of noisy datasets.

Structural analysis of high-dimensional basins of attraction.

We propose an efficient Monte Carlo method for the computation of the volumes of high-dimensional bodies with arbitrary shape. We start with a region of known volume within the interior of the manifold and then use the multistate Bennett acceptance-ratio method to compute the dimensionless free-energy difference between a series of equilibrium simulations performed within this object. The method produces results that are in excellent agreement with thermodynamic integration, as well as a direct estimate of the associated statistical uncertainties. The histogram method also allows us to directly obtain an estimate of the interior radial probability density profile, thus yielding useful insight into the structural properties of such a high-dimensional body. We illustrate the method by analyzing the effect of structural disorder on the basins of attraction of mechanically stable packings of soft repulsive spheres.

Critical Fragmentation Properties of Random Drilling: How Many Holes Need to Be Drilled to Collapse a Wooden Cube?

A solid wooden cube fragments into pieces as we sequentially drill holes through it randomly. This seemingly straightforward observation encompasses deep and nontrivial geometrical and probabilistic behavior that is discussed here. Combining numerical simulations and rigorous results, we find off-critical scale-free behavior and a continuous transition at a critical density of holes that significantly differs from classical percolation.

Turning intractable counting into sampling: Computing the configurational entropy of three-dimensional jammed packings.

We present a numerical calculation of the total number of disordered jammed configurations Ω of N repulsive, three-dimensional spheres in a fixed volume V. To make these calculations tractable, we increase the computational efficiency of the approach of Xu et al. [Phys. Rev. Lett. 106, 245502 (2011)10.1103/PhysRevLett.106.245502] and Asenjo et al. [Phys. Rev. Lett. 112, 098002 (2014)10.1103/PhysRevLett.112.098002] and we extend the method to allow computation of the configurational entropy as a function of pressure. The approach that we use computes the configurational entropy by sampling the absolute volume of basins of attraction of the stable packings in the potential energy landscape. We find a surprisingly strong correlation between the pressure of a configuration and the volume of its basin of attraction in the potential energy landscape. This relation is well described by a power law. Our methodology to compute the number of minima in the potential energy landscape should be applicable to a wide range of other enumeration problems in statistical physics, string theory, cosmology, and machine learning that aim to find the distribution of the extrema of a scalar cost function that depends on many degrees of freedom.

Communication: Evidence for non-ergodicity in quiescent states of periodically sheared suspensions.

We present simulations of an equilibrium statistical-mechanics model that uniformly samples the space of quiescent states of a periodically sheared suspension. In our simulations, we compute the structural properties of this model as a function of density. We compare the results of our simulations with the structural data obtained in the corresponding non-equilibrium model of Corté et al. [Nat. Phys. 4, 420 (2008)]. We find that the structural properties of the non-equilibrium model are very different from those of the equilibrium model, even though the two models have exactly the same set of accessible states. This observation shows that the dynamical protocol does not sample all quiescent states with equal probability. In particular, we find that, whilst quiescent states prepared in a non-equilibrium protocol can be hyperuniform [see D. Hexner and D. Levine, Phys. Rev. Lett. 114, 110602 (2015); E. Tjhung and L. Berthier, Phys. Rev. Lett. 114, 148301 (2015); and J. H. Weijs et al., Phys. Rev. Lett. 115, 108301 (2015)], ergodic sampling never leads to hyperuniformity. In addition, we observe ordering phase transitions and a percolation transition in the equilibrium model that do not show up in the non-equilibrium model. Conversely, the quiescent-to-diffusive transition in the dynamical model does not correspond to a phase transition, nor a percolation transition, in the equilibrium model.

Polymorphisms of Toll-like receptors (TLR2 and TLR4) are associated with the risk of infectious complications in acute myeloid leukemia.

Infectious complications continue to be one of the major causes of morbidity and mortality in patients with acute myeloid leukemia (AML). Several single-nucleotide polymorphisms (SNPs) of Toll-like receptors (TLRs) can affect the genetic susceptibility to infections or even sepsis. We sought to investigate the impact of different SNPs on the incidence of developing sepsis and pneumonia in patients with newly diagnosed AML following induction chemotherapy. We analyzed three SNPs in the TLR2 (Arg753Gln) and TLR4 (Asp299Gly and Thr399Ile) gene in a cohort of 155 patients with AML who received induction chemotherapy. The risk of developing sepsis and pneumonia was assessed by multiple logistic regression analyses. The presence of the TLR2 Arg753Gln polymorphism was significantly associated with pneumonia in AML patients (odds ratio (OR): 10.78; 95% confidence interval (CI): 2.0-58.23; P=0.006). Furthermore, the cosegregating TLR4 polymorphisms Asp299Gly and Thr399Ile were independent risk factors for the development of both sepsis and pneumonia (OR: 3.55; 95% CI: 1.21-10.4, P=0.021 and OR: 3.57, 95% CI: 1.3-9.86, P=0.014, respectively). To our best knowledge, this study represents the first analysis demonstrating that polymorphisms of TLR2 and TLR4 influence the risk of infectious complications in patients with AML undergoing induction chemotherapy.

Retention capacity of correlated surfaces.

We extend the water retention model [C. L. Knecht et al., Phys. Rev. Lett. 108, 045703 (2012)] to correlated random surfaces. We find that the retention capacity of discrete random landscapes is strongly affected by spatial correlations among the heights. This phenomenon is related to the emergence of power-law scaling in the lake volume distribution. We also solve the uncorrelated case exactly for a small lattice and present bounds on the retention of uncorrelated landscapes.

Shortest path and Schramm-Loewner evolution.

We numerically show that the statistical properties of the shortest path on critical percolation clusters are consistent with the ones predicted for Schramm-Loewner evolution (SLE) curves for κ = 1.04 ± 0.02. The shortest path results from a global optimization process. To identify it, one needs to explore an entire area. Establishing a relation with SLE permits to generate curves statistically equivalent to the shortest path from a Brownian motion. We numerically analyze the winding angle, the left passage probability, and the driving function of the shortest path and compare them to the distributions predicted for SLE curves with the same fractal dimension. The consistency with SLE opens the possibility of using a solid theoretical framework to describe the shortest path and it raises relevant questions regarding conformal invariance and domain Markov properties, which we also discuss.

Percolation with long-range correlated disorder.

Long-range power-law correlated percolation is investigated using Monte Carlo simulations. We obtain several static and dynamic critical exponents as functions of the Hurst exponent H, which characterizes the degree of spatial correlation among the occupation of sites. In particular, we study the fractal dimension of the largest cluster and the scaling behavior of the second moment of the cluster size distribution, as well as the complete and accessible perimeters of the largest cluster. Concerning the inner structure and transport properties of the largest cluster, we analyze its shortest path, backbone, red sites, and conductivity. Finally, bridge site growth is also considered. We propose expressions for the functional dependence of the critical exponents on H.

Watersheds are Schramm-Loewner evolution curves.

We show that in the continuum limit watersheds dividing drainage basins are Schramm-Loewner evolution (SLE) curves, being described by one single parameter κ. Several numerical evaluations are applied to ascertain this. All calculations are consistent with SLE(κ), with κ = 1.734 ± 0.005, being the only known physical example of an SLE with κ<2. This lies outside the well-known duality conjecture, bringing up new questions regarding the existence and reversibility of dual models. Furthermore, it constitutes a strong indication for conformal invariance in random landscapes and suggests that watersheds likely correspond to a logarithmic conformal field theory with a central charge c ≈ -7/2.

How to share underground reservoirs.

Many resources, such as oil, gas, or water, are extracted from porous soils and their exploration is often shared among different companies or nations. We show that the effective shares can be obtained by invading the porous medium simultaneously with various fluids. Partitioning a volume in two parts requires one division surface while the simultaneous boundary between three parts consists of lines. We identify and characterize these lines, showing that they form a fractal set consisting of a single thread spanning the medium and a surrounding cloud of loops. While the spanning thread has fractal dimension 1.55 ± 0.03, the set of all lines has dimension 1.69 ± 0.02. The size distribution of the loops follows a power law and the evolution of the set of lines exhibits a tricritical point described by a crossover with a negative dimension at criticality.

Corrections to scaling for watersheds, optimal path cracks, and bridge lines.

We study the corrections to scaling for the mass of the watershed, the bridge line, and the optimal path crack in two and three dimensions (2D and 3D). We disclose that these models have numerically equivalent fractal dimensions and leading correction-to-scaling exponents. We conjecture all three models to possess the same fractal dimension, namely, d(f) =1.2168 ± 0.0005 in 2D and d(f) = 2.487 ± 0.003 in 3D, and the same exponent of the leading correction, Ω = 0.9 ± 0.1 and Ω=1.0 ± 0.1, respectively. The close relations between watersheds, optimal path cracks in the strong disorder limit, and bridge lines are further supported by either heuristic or exact arguments.

Bohman-Frieze-Wormald model on the lattice, yielding a discontinuous percolation transition.

The BFW model introduced by Bohman, Frieze, and Wormald [Random Struct. Algorithms, 25, 432 (2004)], and recently investigated in the framework of discontinuous percolation by Chen and D'Souza [Phys. Rev. Lett. 106, 115701 (2011)], is studied on the square and simple-cubic lattices. In two and three dimensions, we find numerical evidence for a strongly discontinuous transition. In two dimensions, the clusters at the threshold are compact with a fractal surface of fractal dimension d(f)=1.49±0.02. On the simple-cubic lattice, distinct jumps in the size of the largest cluster are observed. We proceed to analyze the tree-like version of the model, where only merging bonds are sampled, for dimension two to seven. The transition is again discontinuous in any considered dimension. Finally, the dependence of the cluster-size distribution at the threshold on the spatial dimension is also investigated.

Fracturing ranked surfaces.

Discretized landscapes can be mapped onto ranked surfaces, where every element (site or bond) has a unique rank associated with its corresponding relative height. By sequentially allocating these elements according to their ranks and systematically preventing the occupation of bridges, namely elements that, if occupied, would provide global connectivity, we disclose that bridges hide a new tricritical point at an occupation fraction p = p(c), where p(c) is the percolation threshold of random percolation. For any value of p in the interval p(c) < p ≤ 1, our results show that the set of bridges has a fractal dimension d(BB) ≈ 1.22 in two dimensions. In the limit p → 1, a self-similar fracture is revealed as a singly connected line that divides the system in two domains. We then unveil how several seemingly unrelated physical models tumble into the same universality class and also present results for higher dimensions.

Gaussian model of explosive percolation in three and higher dimensions.

The Gaussian model of discontinuous percolation, recently introduced by Araújo and Herrmann [Phys. Rev. Lett. 105, 035701 (2010)], is numerically investigated in three dimensions, disclosing a discontinuous transition. For the simple cubic lattice, in the thermodynamic limit we report a finite jump of the order parameter J=0.415±0.005. The largest cluster at the threshold is compact, but its external perimeter is fractal with fractal dimension d(A)=2.5±0.2. The study is extended to hypercubic lattices up to six dimensions and to the mean-field limit (infinite dimension). We find that, in all considered dimensions, the percolation transition is discontinuous. The value of the jump in the order parameter, the maximum of the second moment, and the percolation threshold are analyzed, revealing interesting features of the transition and corroborating its discontinuous nature in all considered dimensions. We also show that the fractal dimension of the external perimeter, for any dimension, is consistent with the one from bridge percolation and establish a lower bound for the percolation threshold of discontinuous models with a finite number of clusters at the threshold.

Optimal-path cracks in correlated and uncorrelated lattices.

The optimal path crack model on uncorrelated surfaces, recently introduced by Andrade et al. [Phys. Rev. Lett. 103, 225503 (2009).], is studied in detail and its main percolation exponents computed. In addition to ß/ν=0.46±0.03, we report γ/ν=1.3±0.2 and τ=2.3±0.2. The analysis is extended to surfaces with spatial long-range power-law correlations, where nonuniversal fractal dimensions are obtained when the degree of correlation is varied. The model is also considered on a three-dimensional lattice, where the main crack is found to be a surface with a fractal dimension of 2.46±0.05.

Altered dendritic development of cerebellar Purkinje cells in slice cultures from protein kinase Cgamma-deficient mice.

Protein kinase C (PKC) is a key molecule for the expression of long-term depression at the parallel fiber-Purkinje cell synapse in the cerebellum, a well known model for synaptic plasticity. We have recently shown that activity of PKC also profoundly affects the dendritic morphology of Purkinje cells in rat cerebellar slice cultures suggesting that synaptic efficacy and dendritic development may be controlled by similar intracellular signalling pathways. Here we have analyzed the role of the gamma-isoform of protein kinase C (PKCgamma), which is strongly and specifically expressed in Purkinje cells, during dendritic development. After pharmacological treatment with PKC modulators, phosphorylation of PKCgamma at serine 660 was altered in cerebellar slices suggesting that a change of PKCgamma activity by these treatments was taking place within the Purkinje cells. In PKCgamma-deficient mice, Purkinje cell dendritic trees were enlarged and had an increased number of branching points compared to wild-type mice indicating a role for the PKCgamma isoform as a negative regulator of dendritic growth and branching. Furthermore, the branching-stimulating effects of the PKC inhibitors 2-[1-(3-dimethylaminopropyl)indol-3-yl]-3-(indol-3-yl)maleimide and Gö6976 found in wild-type cultures were abolished in the absence of PKCgamma. In contrast, the strong inhibitory effect on dendritic growth by the PKC activator phorbol-12-myristate-13-acetate (PMA) did not require the presence of the PKCgamma isoform since it was still present in the cultures of PKCgamma-deficient mice. Our results clearly demonstrate an involvement of PKCgamma in Purkinje cell dendritic differentiation in cerebellar slice cultures.