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Alexander K. Hartmann

Publications and source records attributed to Alexander K. Hartmann.

At least 109 records · Page 6Linked to original sources
arXiv2004

Dependence of RNA secondary structure on the energy model

We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative behaviour while going from one model to the other; in particular we test, whether a transition occurs, when continuously moving from one model to the other. For this we calculate various thermodynamic quantities, both at zero temperature as well as at finite temperatures. All calculations can be done efficiently in polynomial time by a dynamic programming algorithm. We do not find a sign for transition between the models, but the critical exponent $ν$ of the correlation length, describing the phase transition in all models to an ordered low-temperature phase, seems to depend continuously on the model. Finally, we apply the epsilon-Coupling method, to study low excitations. The exponent $θ$ describing the energy-scaling of the excitations seems to depend not much on the energy model.

q-bio.QM↗
arXiv2004

Clustering analysis of the ground-state structure of the vertex-cover problem

Vertex cover is one of the classical NP-complete problems in theoretical computer science. A vertex cover of a graph is a subset of vertices such that for each edge at least one of the two endpoints is contained in the subset. When studied on Erdos-Renyi random graphs (with connectivity c) one observes a threshold behavior: In the thermodynamic limit the size of the minimal vertex cover is independent of the specific graph. Recent analytical studies show that on the phase boundary, for small connectivities c<e, the system is replica symmetric, while for larger connectivities replica symmetry breaking occurs. This change coincides with a change of the typical running time of algorithms from polynomial to exponential. To understand the reasons for this behavior and to compare with the analytical results, we numerically analyze the structure of the solution landscape. For this purpose, we have also developed an algorithm, which allows the calculation of the backbone, without the need to enumerate all solutions. We study exact solutions found with a Branch-and-Bound algorithm as well as configurations obtained via a Monte Carlo simulation. We analyze the cluster structure of the solution landscape by direct clustering of the states, by analyzing the eigenvalue spectrum of correlation matrices and by using a hierarchical clustering method. All results are compatible with a change at c=e. For small connectivities, the solutions are collected in a finite small number of clusters, while the number of cluster diverges slowly with system size for larger connectivities and replica symmetry breaking, but not 1-RSB, occurs.

cond-mat.dis-nn↗
arXiv2004

Low-temperature behavior of two-dimensional Gaussian Ising spin glasses

We perform Monte Carlo simulations of large two-dimensional Gaussian Ising spin glasses down to very low temperatures $β=1/T=50$. Equilibration is ensured by using a cluster algorithm including Monte Carlo moves consisting of flipping fundamental excitations. We study the thermodynamic behavior using the Binder cumulant, the spin-glass susceptibility, the distribution of overlaps, the overlap with the ground state and the specific heat. We confirm that $T_c=0$. All results are compatible with an algebraic divergence of the correlation length with an exponent $ν$. We find $-1/ν=-0.295(30)$, which is compatible with the value for the domain-wall and droplet exponent $θ\approx-0.29$ found previously in ground-state studies. Hence the thermodynamic behavior of this model seems to be governed by one single exponent.

cond-mat.dis-nn↗
arXiv2004

On large deviation properties of Erdos-Renyi random graphs

We show that large deviation properties of Erdös-Rényi random graphs can be derived from the free energy of the $q$-state Potts model of statistical mechanics. More precisely the Legendre transform of the Potts free energy with respect to $\ln q$ is related to the component generating function of the graph ensemble. This generalizes the well-known mapping between typical properties of random graphs and the $q\to 1$ limit of the Potts free energy. For exponentially rare graphs we explicitly calculate the number of components, the size of the giant component, the degree distributions inside and outside the giant component, and the distribution of small component sizes. We also perform numerical simulations which are in very good agreement with our analytical work. Finally we demonstrate how the same results can be derived by studying the evolution of random graphs under the insertion of new vertices and edges, without recourse to the thermodynamics of the Potts model.

cond-mat.stat-mech↗
arXiv2003

Statistical mechanics of the vertex-cover problem

We review recent progress in the study of the vertex-cover problem (VC). VC belongs to the class of NP-complete graph theoretical problems, which plays a central role in theoretical computer science. On ensembles of random graphs, VC exhibits an coverable-uncoverable phase transition. Very close to this transition, depending on the solution algorithm, easy-hard transitions in the typical running time of the algorithms occur. We explain a statistical mechanics approach, which works by mapping VC to a hard-core lattice gas, and then applying techniques like the replica trick or the cavity approach. Using these methods, the phase diagram of VC could be obtained exactly for connectivities $c e$, the solution of VC exhibits full replica symmetry breaking. The statistical mechanics approach can also be used to study analytically the typical running time of simple complete and incomplete algorithms for VC. Finally, we describe recent results for VC when studied on other ensembles of finite- and infinite-dimensional graphs.

cond-mat.dis-nn↗
arXiv2003

Ground state of the Bethe-lattice spin glass and running time of an exact optimization algorithm

We study the Ising spin glass on random graphs with fixed connectivity z and with a Gaussian distribution of the couplings, with mean μand unit variance. We compute exact ground states by using a sophisticated branch-and-cut method for z=4,6 and system sizes up to N=1280 for different values of μ. We locate the spin-glass/ferromagnet phase transition at μ= 0.77 +/- 0.02 (z=4) and μ= 0.56 +/- 0.02 (z=6). We also compute the energy and magnetization in the Bethe-Peierls approximation with a stochastic method, and estimate the magnitude of replica symmetry breaking corrections. Near the phase transition, we observe a sharp change of the median running time of our implementation of the algorithm, consistent with a change from a polynomial dependence on the system size, deep in the ferromagnetic phase, to slower than polynomial in the spin-glass phase.

cond-mat.dis-nn↗
arXiv2003

Solving satisfiability problems by fluctuations: The dynamics of stochastic local search algorithms

Stochastic local search algorithms are frequently used to numerically solve hard combinatorial optimization or decision problems. We give numerical and approximate analytical descriptions of the dynamics of such algorithms applied to random satisfiability problems. We find two different dynamical regimes, depending on the number of constraints per variable: For low constraintness, the problems are solved efficiently, i.e. in linear time. For higher constraintness, the solution times become exponential. We observe that the dynamical behavior is characterized by a fast equilibration and fluctuations around this equilibrium. If the algorithm runs long enough, an exponentially rare fluctuation towards a solution appears.

cond-mat.stat-mech↗
arXiv2003

No spin-glass transition in the "mobile-bond" model

The recently introduced ``mobile-bond'' model for two-dimensional spin glasses is studied. The model is characterized by an annealing temperature T_q. On the basis of Monte Carlo simulations of small systems it has been claimed that this model exhibits a non-trivial spin-glass transition at finite temperature for small values of T_q. Here the model is studied by means of exact ground-state calculations of large systems up to N=256^2. The scaling of domain-wall energies is investigated as a function of the system size. For small values T_q<0.95 the system behaves like a (gauge-transformed) ferromagnet having a small fraction of frustrated plaquettes. For T_q>=0.95 the system behaves like the standard two-dimensional +-J spin-glass, i.e. it does NOT exhibit a phase transition at T>0.

cond-mat.dis-nn↗
arXiv2002

Direct sampling of complex landscapes at low temperatures: the three-dimensional +/-J Ising spin glass

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 low-temperature behavior of this model is characterized by evaluating different overlap quantities, exhibiting a complex low-energy landscape for T>0, while the T=0 behavior appears to be less complex.

cond-mat.dis-nn↗
arXiv2002

Finding Low-Temperature States with Parallel Tempering, Simulated Annealing and Simple Monte Carlo

Monte Carlo simulation techniques, like simulated annealing and parallel tempering, are often used to evaluate low-temperature properties and find ground states of disordered systems. Here we compare these methods using direct calculations of ground states for three-dimensional Ising diluted antiferromagnets in a field (DAFF) and three-dimensional Ising spin glasses (ISG). For the DAFF, we find that, with respect to obtaining ground states, parallel tempering is superior to simple Monte-Carlo and to simulated annealing. However, equilibration becomes more difficult with increasing magnitude of the externally applied field. For the ISG with bimodal couplings, which exhibits a high degeneracy, we conclude that finding true ground states is easy for small systems, as is already known. But finding each of the degenerate ground states with the same probability (or frequency), as required by Boltzmann statistics, is considerably harder and becomes almost impossible for larger systems.

cond-mat.dis-nn↗
arXiv2002

The stiffness exponent of two-dimensional Ising spin glasses for non-periodic boundary conditions using aspect-ratio scaling

We study the scaling behavior of domain-wall energies in two-dimensional Ising spin glasses with Gaussian and bimodal distributions of the interactions and different types of boundary conditions. The domain walls are generated by changing the boundary conditions at T=0 in one direction. The ground states of the original and perturbed system are calculated numerically by applying an efficient matching algorithm. Systems of size LxM with different aspect-ratios 1/8 <= L/M <= 64 are considered. For Gaussian interactions, using the aspect-ratio scaling approach, we find a stiffness exponent theta=-0.287(4), which is independent of the boundary conditions in contrast to earlier results. Furthermore, we find a scaling behavior of the domain-wall energy as predicted by the aspect-ratio approach. Finally, we show that this approach does not work for the bimodal distribution of interactions.

cond-mat.dis-nn↗
arXiv2002

Depinning of elastic manifolds

We compute roughness exponents of elastic d-dimensional manifolds in (d+1)-dimensional embedding spaces at the depinning transition for d=1,...,4. Our numerical method is rigorously based on a Hamiltonian formulation; it allows to determine the critical manifold in finite samples for an arbitrary convex elastic energy. For a harmonic elastic energy, we find values of the roughness exponent between the one-loop and the two-loop functional renormalization group result, in good agreement with earlier cellular automata simulations. We find that the harmonic model is unstable with respect both to slight stiffening and to weakening of the elastic potential. Anharmonic corrections to the elastic energy allow us to obtain the critical exponents of the quenched KPZ class.

cond-mat.dis-nn↗
arXiv2002

Long-Time Effects in a Simulation Model of Sputter Erosion

A simple (2+1) dimensional discrete model is introduced to study the evolution of solid surface morphologies during ion-beam sputtering. The model is based on the same assumptions about the erosion process as the existing analytic theories. Due to its simple structure, simulations of the model can be performed on time scales, where effects beyond the linearized theory become important. Whereas for short times we observe the formation of ripple structures in accordance with the linearized theory, we find a rough surface with scaling properties for intermediate times. The long time behavior of the model strongly depends on the surface relaxation mechanism.

cond-mat.mtrl-sci↗
arXiv2002

Critical exponents of four-dimensional random-field Ising systems

The ferromagnet-to-paramagnet transition of the four-dimensional random-field Ising model with Gaussian distribution of the random fields is studied. Exact ground states of systems with sizes up to 32^4 are obtained using graph theoretical algorithms. The magnetization, the disconnected susceptibility, the susceptibility and a specific heat-like quantity are calculated. Using finite-size scaling techniques, the corresponding critical exponents are obtained: β=0.15(6), γ`=3.12(10), γ=1.57(10) and α=0 (logarithmic divergence). Furthermore, values for the critical randomness h_c=4.18(1) and the correlation-length exponent ν=0.78(10) were found. These independently obtained exponents are compatible with all (hyper-) scaling relations and support the two-exponent scenario (γ`=2γ)

cond-mat.dis-nn↗
arXiv2001

A practical guide to computer simulations

Here practical aspects of conducting research via computer simulations are discussed. The following issues are addressed: software engineering, object-oriented software development, programming style, macros, make files, scripts, libraries, random numbers, testing, debugging, data plotting, curve fitting, finite-size scaling, information retrieval, and preparing presentations. Because of the limited space, usually only short introductions to the specific areas are given and references to more extensive literature are cited. All examples of code are in C/C++.

cond-mat↗
arXiv2001

Sampling rare events: statistics of local sequence alignments

A new method to simulate probability distributions in regions where the events are VERY unlikely (e.g. p ~ 10^{-40}) is presented. The basic idea is to represent the underlying probability space by the phase space of a physical system. The system is held at a temperature T, which is chosen such that the system preferably generates configurations which originally have low probabilities. Since the distribution of such a physical system is know from statistical physics, the original unbiased distribution can be obtained. As an application, local alignment of protein sequences based on BLOSUM62 substitution scores with (12,1) affine gap costs are considered The distribution of optimum sequence-alignment scores S is studied numerically over a large range of scores. The deviation of p(S) from the extreme-value (or Gumbel) distribution is quantified. This deviation decreases with growing sequence length.

cond-mat.dis-nn↗
arXiv2001

Ferromagnetic-spin glass transition in four-dimensional random-bond Ising model

The four-dimensional +-J random-bond Ising model is studied using ground-state calculations. System sizes up to N=6^4 spins are considered. Here it is found that the ferromagnetic-spin glass transition occurs at a critical concentration p_c=0.28(1) of the antiferromagnetic bonds, which is comparable to values found previously by high-temperature series expansions. The transition is characterized by a correlation-length exponent ν=1.0(1) and an order-parameter exponent β=0.4(1). Thus, this transition is in a different universality class from four-dimensional bond percolation, where ν=0.678(50) and β=0.639(20).

cond-mat.dis-nn↗