We propose a flat-histogram Monte Carlo method to efficiently sample fractal landscapes such as escape time functions of open chaotic systems. This is achieved by using a random-walk step which depends on the height of the landscape via the largest Lyapunov exponent of the associated chaotic system. By generalizing the Wang-Landau algorithm, we obtain a method which simultaneously constructs the density of states (escape time distribution) and the correct step-length distribution. As a result, averages are obtained in polynomial computational time, a dramatic improvement over the exponential scaling of traditional uniform sampling. Our results are not limited by the dimensionality of the phase space and are confirmed numerically for dimensions as large as 30.
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to basins and transitions between them in the energy landscape. We find power-laws between the folding time and number of nodes and bonds. We show that these scalings are determined by the fractal properties of first-passage networks. Reliable folding is possible in systems with rugged energy landscapes because first passage networks have small fractal dimension.
The free-energy landscape of two peptides is evaluated at various temperatures and an estimate for its fractal dimension at these temperatures calculated. We show that monitoring this quantity as a function of temperature allows to determine the glass transition temperature.
Using numerical simulations of a simple sea-coast mechanical erosion model, we investigate the effect of spatial long-range correlations in the lithology of coastal landscapes on the fractal behavior of the corresponding coastlines. In the model, the resistance of a coast section to erosion depends on the local lithology configuration as well as on the number of neighboring sea sides. For weak sea forces, the sea is trapped by the coastline and the eroding process stops after some time. For strong sea forces erosion is perpetual. The transition between these two regimes takes place at a critic…
Epithelial cell tissues have a slow relaxation dynamics resembling that of supercooled liquids. Yet, they also have distinguishing features. These include an extended short-time sub-diffusive transient, as observed in some experiments and recent studies of model systems, and a sub-Arrhenius dependence of the relaxation time on temperature, as reported in numerical studies. Here we demonstrate that the anomalous glassy dynamics of epithelial tissues originates from the emergence of a fractal-like energy landscape, particles becoming virtually free to diffuse in specific phase space directions u…
Glasses are amorphous solids whose constituent particles are caged by their neighbors and thus cannot flow. This sluggishness is often ascribed to the free energy landscape containing multiple minima (basins) separated by high barriers. Here we show, using theory and numerical simulation, that the landscape is much rougher than is classically assumed. Deep in the glass, it undergoes a "roughness transition" to fractal basins. This brings about isostaticity at jamming and marginality of glassy states near jamming. Critical exponents for the basin width, the weak force distribution, and the spat…
We study the problem of adsorption of self-interacting linear polymers situated in fractal containers that belong to the three-dimensional (3d) Sierpinski gasket (SG) family of fractals. Each member of the 3d SG fractal family has a fractal impenetrable 2d adsorbing surface (which is, in fact, 2d SG fractal) and can be labelled by an integer $b$ ($2\le b\le\infty$). By applying the exact and Monte Carlo renormalization group (MCRG) method, we calculate the critical exponents $ν$ (associated with the mean squared end-to-end distance of polymers) and $ϕ$ (associated with the number of adsorbed m…
Fractals of Simple Random Walks in Two Dimensions: A Monte Carlo Study
Department of Physics, Guizhou University（贵州大学物理系）；Department of Information Science and Technology, Donghua University（东华大学信息科学与技术学院）；Hefei National Laboratory（合肥国家实验室）
The Shcramm-Loewner evolution (SLE) is a correlated exploration process, in which for the chordal set up, the tip of the trace evolves in a self-avoiding manner towards the infinity. The resulting curves are named SLE$_κ$, emphasizing that the process is controlled by one parameter $κ$ which classifies the conformal invariant random curves. This process when experiences some environmental imperfections, or equivalently some scattering random points (which can be absorbing or repelling) results to some other effective scale-invariant curves, which are described by the other effective fractal di…
We propose a new strategy for Monte Carlo (MC) optimization on rugged multidimensional landscapes. The strategy is based on querying the statistical properties of the landscape in order to find the temperature at which the mean first passage time across the current region of the landscape is minimized. Thus, in contrast to other algorithms such as simulated annealing (SA), we explicitly match the temperature schedule to the statistics of landscape irregularities. In cases where this statistics is approximately the same over the entire landscape, or where non-local moves couple distant parts of…
A simple modification of the Monte-Carlo algortihm is proposed to explore the topography and the scaling of the energy landscape. We apply this idea to a simple hard-core fluid. The results for different packing fractions show a power law scaling of the landscape boundary, with a characteristic scale that separates the values of the scaling exponents. Finally, it is shown how the topology determines the freezing point of the system due to the increasing importance and complexity of the boundary.
We have performed a Monte Carlo study of the classical XY-model on a Sierpi\' nski carpet, which is a planar fractal structure with infinite order of ramification and fractal dimension 1.8928. We employed the Wolff cluster algorithm in our simulations and our results, in particular those for the susceptibility and the helicity modulus, indicate the absence of finite-temperature Berezinskii-Kosterlitz-Thouless (BKT) transition in this system.
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus to gain an ever-increasing understanding on the general principles underlying the mechanism of protein folding. We show that it is possible to couple metadynamics and Monte Carlo algorithms to obtain the free energy of model proteins in a way which is computationally very economical.
Parallel tempering and population annealing are both effective methods for simulating equilibrium systems with rough free energy landscapes. Parallel tempering, also known as replica exchange Monte Carlo, is a Markov chain Monte Carlo method while population annealing is a sequential Monte Carlo method. Both methods overcome the exponential slowing associated with high free energy barriers. The convergence properties and efficiency of the two methods are compared. For large systems, population annealing initially converges to equilibrium more rapidly than parallel tempering for the same amount…
Anomalous short- and long-time self-diffusion of non-overlapping fractal particles on a percolation cluster with spreading dimension $1.67(2)$ is studied by dynamic Monte Carlo simulations. As reported in Phys. Rev. Lett. 115, 097801 (2015), the disordered phase formed by these particles is that of an unconfined, homogeneous and monodisperse fluid in fractal space. During particle diffusion in thermodynamic equilibrium, the mean squared chemical displacement increases as a nonlinear power of time, with an exponent of $0.96(1)$ at short times and $0.63(1)$ at long times. At finite packing fract…
Tethering methods allow us to perform Monte Carlo simulations in ensembles with conserved quantities. Specifically, one couples a reservoir to the physical magnitude of interest, and studies the statistical ensemble where the total magnitude (system+reservoir) is conserved. The reservoir is actually integrated out, which leaves us with a fluctuation-dissipation formalism that allows us to recover the appropriate Helmholtz effective potential with great accuracy. These methods are demonstrating a remarkable flexibility. In fact, we illustrate two very different applications: hard spheres crysta…
The population annealing algorithm introduced by Hukushima and Iba is described. Population annealing combines simulated annealing and Boltzmann weighted differential reproduction within a population of replicas to sample equilibrium states. Population annealing gives direct access to the free energy. It is shown that unbiased measurements of observables can be obtained by weighted averages over many runs with weight factors related to the free energy estimate from the run. Population annealing is well suited to parallelization and may be a useful alternative to parallel tempering for systems …
In this paper we study crumpled surfaces through Monte Carlo Simulations. The crumpled surface is represented by a cluster of spins pointing up and spins pointing down represent the air both inside and around the surface. We follow the time dynamics of this fractal structure and we have shown that it presents a stretched exponential behaviour.
Using Monte-Carlo simulations, we determine the scaling form for the probability distribution of the shortest path, $\ell$, between two lines in a 3-dimensional percolation system at criticality; the two lines can have arbitrary positions, orientations and lengths. We find that the probability distributions can exhibit up to four distinct power law regimes (separated by cross-over regimes) with exponents depending on the relative orientations of the lines. We explain this rich fractal behavior with scaling arguments.
We study the mean number of encounters up to time t, E_N(t), taking place in a subspace with dimension d* of a d-dimensional lattice, for N independent random walkers starting simultaneously from the same origin. E_N is first evaluated analytically in a continuum approximation and numerically through Monte Carlo simulations in one and two dimensions. Then we introduce the notion of the intersection of strongly anisotropic fractals and use it to calculate the long-time behaviour of E_N.
Energy landscape approaches have become increasingly popular for analysing a wide variety of chemical physics phenomena. Basic to many of these applications has been the inherent structure mapping, which divides up the potential energy landscape into basins of attraction surrounding the minima. Here, we probe the nature of this division by introducing a method to compute the basin area distribution and applying it to some archetypal supercooled liquids. We find that this probability distribution is a power law over a large number of decades with the lower-energy minima having larger basins of …
Analytic approximations for the radial distribution function, the structure factor, and the equation of state of hard-core fluids in fractal dimension $d$ ($1 \leq d \leq 3$) are developed as heuristic interpolations from the knowledge of the exact and Percus-Yevick results for the hard-rod and hard-sphere fluids, respectively. In order to assess their value, such approximate results are compared with those of recent Monte Carlo simulations and numerical solutions of the Percus-Yevick equation for fractal dimension [M. Heinen et al., Phys. Rev. Lett. \textbf{115}, 097801 (2015)], a good agreem…
We present a grand canonical Monte Carlo simulation study of the phase diagram of a Lennard-Jones fluid adsorbed in a fractal and highly porous aerogel. The gel environment is generated from an off-lattice diffusion limited cluster-cluster aggregation process. Simulations have been performed with the multicanonical ensemble sampling technique. The biased sampling function has been obtained by histogram reweighting calculations. Comparing the confined and the bulk system liquid-vapor coexistence curves we observe a decrease of both the critical temperature and density in qualitative agreement w…
We present the results of a large-scale numerical study of the equilibrium three-dimensional Edwards-Anderson Ising spin glass with Gaussian disorder. Using parallel tempering (replica exchange) Monte Carlo we measure various static, as well as dynamical quantities, such as the autocorrelation times and round-trip times for the parallel tempering Monte Carlo method. The correlation between static and dynamic observables for 5000 disorder realizations and up to 1000 spins down to temperatures at 20% of the critical temperature is examined. Our results show that autocorrelation times are directl…
We investigate the time dependent Ginzburg-Landau (TDGL) equation for a non conserved order parameter on an infinitely ramified (deterministic) fractal lattice employing two alternative methods: the auxiliary field approach and a numerical method of integration of the equations of evolution. In the first case the domain size evolves with time as $L(t)\sim t^{1/d_w}$, where $d_w$ is the anomalous random walk exponent associated with the fractal and differs from the normal value 2, which characterizes all Euclidean lattices. Such a power law growth is identical to the one observed in the study o…
We study the fractal geometry of O($n$) loop configurations in two dimensions by means of scaling and a Monte Carlo method, and compare the results with predictions based on the Coulomb gas technique. The Monte Carlo algorithm is applicable to models with noninteger $n$ and uses local updates. Although these updates typically lead to nonlocal modifications of loop connectivities, the number of operations required per update is only of order one. The Monte Carlo algorithm is applied to the O($n$) model for several values of $n$, including noninteger ones. We thus determine scaling exponents tha…
We have performed a Monte Carlo study of the classical XY-model on a Menger sponge with the Wolff cluster algorithm (U. Wolff, 1989). The Menger sponge is a fractal object with infinite order of ramification and fractal dimension D = log(20)/log(3) = 2.7268. From the dependence of the helicity modulus on system size and on boundary conditions, we conclude that there is no phase transition in the system at any finite temperature.
Many attempts to relate animal foraging patterns to landscape heterogeneity are focused on the analysis of foragers movements. Resource detection patterns in space and time are not commonly studied, yet they are tightly coupled to landscape properties and add relevant information on foraging behavior. By exploring simple foraging models in unpredictable environments we show that the distribution of intervals between detected prey (detection statistics)is mostly determined by the spatial structure of the prey field and essentially distinct from predator displacement statistics. Detections are e…
The nonequilibrium critical dynamics of the Ising magnet on a fractal substrate, namely the Sierpinski carpet with Hausdorff dimension $d_H$ =1.7925, has been studied within the short-time regime by means of Monte Carlo simulations. The evolution of the physical observables was followed at criticality, after both annealing ordered spin configurations (ground state) and quenching disordered initial configurations (high temperature state), for three segmentation steps of the fractal. The topological effects become evident from the emergence of a logarithmic periodic oscillation superimposed to a…
We use a large cell Monte Carlo Renormalization procedure, to compute the critical exponents of a system of growing linear polymers. We simulate the growth of non-intersecting chains in large MC cells. Dense regions where chains get in each others' way, give rise to connected clusters under coarse graining. At each time step, the fraction of occupied bonds is determined in both the original and the coarse grained configurations, and averaged over many realizations. Our results for the fractal dimension on three dimensional lattices are consistent with the percolation value.
We perform a Monte Carlo Renormalization Group analysis of the critical behavior of the ferromagnetic Ising model on a Sierpiński fractal with Hausdorff dimension $d_f\simeq 1.8928$. This method is shown to be relevant to the calculation of the critical temperature $T_c$ and the magnetic eigen-exponent $y_h$ on such structures. On the other hand, scaling corrections hinder the calculation of the temperature eigen-exponent $y_t$. At last, the results are shown to be consistent with a finite size scaling analysis.
We perform Monte-Carlo simulations to study the Bernoulli ($p$) bond percolation on the enhanced binary tree which belongs to the class of nonamenable graphs with one end. Our numerical results show that the system has two different percolation thresholds $p_{c1}$ and $p_{c2}$. All the points in the intermediate phase $(p_{c1} < p < p_{c2})$ are critical and there exist infinitely many infinite clusters in the intermediate phase. In this phase the corresponding fractal exponent continuously increases with $p$ from zero to unity.
We have performed a Monte Carlo study of the classical XY-model on two-dimensional Sierpinski gaskets of several cluster sizes. From the dependence of the helicity modulus on the cluster size we conclude that there is no phase transition in this system at a finite temperature. This is in agreement with previous findings for the harmonic approximation to the XY-model on Sierpinski gasket and is analogous to the absence of finite temperature phase transition for the Ising model on fractals with a finite order of ramification.
We consider the binary fragmentation problem in which, at any breakup event, one of the daughter segments either survives with probability $p$ or disappears with probability $1\!-\!p$. It describes a stochastic dyadic Cantor set that evolves in time, and eventually becomes a fractal. We investigate this phenomenon, through analytical methods and Monte Carlo simulation, for a generic class of models, where segment breakup points follow a symmetric beta distribution with shape parameter $α$, which also determines the fragmentation rate. For a fractal dimension $d_f$, we find that the $d_f$-th mo…
We report the results of Monte Carlo simulations on several spin glass models at low temperatures. By using the parallel tempering (Exchange Monte Carlo) technique we are able to equilibrate down to low temperatures, for moderate sizes, and hence the data should not be affected by critical fluctuations. Our results for short range models are consistent with a picture proposed earlier that there are large scale excitations which cost only a finite energy in the thermodynamic limit, and these excitations have a surface whose fractal dimension is less than the space dimension. For the infinite ra…
A method is presented, which allows to sample directly low-temperature configurations of glassy systems, like spin glasses. The basic idea is to generate ground states and low lying excited configurations using a heuristic algorithm. Then, with the help of microcanonical Monte Carlo simulations, more configurations are found, clusters of configurations are determined and entropies evaluated. Finally equilibrium configuration are randomly sampled with proper Gibbs-Boltzmann weights. The method is applied to three-dimensional Ising spin glasses with +- J interactions and temperatures T<=0.5. The…
