arXiv subjects

Wolfhard Janke

Publications and source records attributed to Wolfhard Janke.

At least 109 records · Page 6Linked to original sources

arXiv2012

Scaling Properties of a Parallel Implementation of the Multicanonical Algorithm

The multicanonical method has been proven powerful for statistical investigations of lattice and off-lattice systems throughout the last two decades. We discuss an intuitive but very efficient parallel implementation of this algorithm and analyze its scaling properties for discrete energy systems, namely the Ising model and the 8-state Potts model. The parallelization relies on independent equilibrium simulations in each iteration with identical weights, merging their statistics in order to obtain estimates for the successive weights. With good care, this allows faster investigations of large systems, because it distributes the time-consuming weight-iteration procedure and allows parallel production runs. We show that the parallel implementation scales very well for the simple Ising model, while the performance of the 8-state Potts model, which exhibits a first-order phase transition, is limited due to emerging barriers and the resulting large integrated autocorrelation times. The quality of estimates in parallel production runs remains of the same order at same statistical cost.

cond-mat.stat-mech↗

arXiv2012

Application of Simulated Tempering and Magnetizing to a Two-Dimensional Potts Model

We applied the simulated tempering and magnetizing (STM) method to the two-dimensional three-state Potts model in an external magnetic field in order to perform further investigations of the STM's applicability. The temperature as well as the external field are treated as dynamical variables updated during the STM simulations. After we obtained adequate information for several lattice sizes $L$ (up to $160\times 160$), we also performed a number of conventional canonical simulations of large lattices, especially in order to illustrate the crossover behavior of the Potts model in external field with increasing $L$. The temperature and external field for larger lattice size simulations were chosen by extrapolation of the detail information obtained by STM. We carefully analyzed the crossover scaling at the phase transitions with respect to the lattice size as well as the temperature and external field. The crossover behavior is clearly observed in the simulations in agreement with theoretical predictions.

cond-mat.stat-mech↗

arXiv2012

Influence of lattice disorder on the structure of persistent polymer chains

We study the static properties of a semiflexible polymer exposed to a quenched random environment by means of computer simulations. The polymer is modeled as two-dimensional Heisenberg chain. For the random environment we consider hard disks arranged on a square lattice. We apply an off-lattice growth algorithm as well as the multicanonical Monte Carlo method to investigate the influence of both disorder occupation probability and polymer stiffness on the equilibrium properties of the polymer. We show that the additional length scale induced by the stiffness of the polymer extends the well-known phenomenology considerably. The polymer's response to the disorder is either contraction or extension depending on the ratio of polymer stiffness and void space extension. Additionally, the periodic structure of the lattice is reflected in the observables that characterize the polymer.

cond-mat.soft↗

arXiv2012

Advanced multicanonical Monte Carlo methods for efficient simulations of nucleation processes of polymers

The investigation of freezing transitions of single polymers is computationally demanding, since surface effects dominate the nucleation process. In recent studies we have systematically shown that the freezing properties of flexible, elastic polymers depend on the precise chain length. Performing multicanonical Monte Carlo simulations, we faced several computational challenges in connection with liquid-solid and solid-solid transitions. For this reason, we developed novel methods and update strategies to overcome the arising problems. We introduce novel Monte Carlo moves and two extensions to the multicanonical method.

cond-mat.soft↗

arXiv2012

Simulating flexible polymers in a potential of randomly distributed hard disks

We perform equilibrium computer simulations of a two-dimensional pinned flexible polymer exposed to a quenched disorder potential consisting of hard disks. We are especially interested in the high-density regime of the disorder, where subtle structures such as cavities and channels play a central role. We apply an off-lattice growth algorithm proposed by Garel and Orland [J. Phys. A 23, L621 (1990)], where a distribution of polymers is constructed in parallel by growing each of them monomer by monomer. In addition we use a multicanonical Monte Carlo method in order to cross-check the results of the growth algorithm. We measure the end-to-end distribution and the tangent-tangent correlations. We also investigate the scaling behavior of the mean square end-to-end distance in dependence of the monomer number. While the influence of the potential in the low-density case is merely marginal, it dominates the configurational properties of the polymer for high densities.

cond-mat.soft↗

arXiv2012

Polymer adsorption on a fractal substrate: numerical study

We study the adsorption of flexible polymer macromolecules on a percolation cluster, formed by a regular two-dimensional disordered lattice at critical concentration p_c of attractive sites. The percolation cluster is characterized by a fractal dimension d_s^{p_c}=91/49. The conformational properties of polymer chains grafted to such a fractal substrate are studied by means of the pruned-enriched Rosenbluth method (PERM). We find estimates for the surface crossover exponent governing the scaling of the adsorption energy in the vicinity of the transition point, ϕ_s^{p_c}=0.425\pm0.009, and for the adsorption transition temperature, T_A^{p_c}=2.64\pm0.02. As expected, the adsorption is diminished when the fractal dimension of the substrate is smaller than that of a plain Euclidean surface. The universal size and shape characteristics of a typical spatial conformation which attains a polymer chain in the adsorbed state are analyzed as well.

cond-mat.dis-nn↗

arXiv2011

Comparison of the Adsorption Transition for Grafted and Nongrafted Polymers

We compare the thermodynamic behavior of a finite single nongrafted polymer near an attractive substrate with that of a polymer grafted to that substrate. After we recently found first-order-like signatures in the microcanonical entropy at the adsorption transition in the nongrafted case, and given the fact that many studies on polymer adsorption in the past have been performed for grafted polymers, the question arises, to what extent and in what way does grafting change the nature of the adsorption transition? This question is tackled here using a coarse-grained off-lattice polymer model and covers not only the adsorption transition but also all other transitions a single polymer near an attractive substrate of varying strengths undergoes. Because of the impact of grafting especially on the translational but also on the conformational entropy of desorbed chains, the adsorption transition is affected the strongest. Our results are obtained by a combined canonical and microcanonical analysis of parallel tempering Monte Carlo data.

cond-mat.stat-mech↗

arXiv2011

Thermodynamics of polymer adsorption to a flexible membrane

We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering Monte Carlo simulations it is shown that the system exhibits a rich phase behavior ranging from highly ordered, compact to extended random coil structures and from desorbed to completely adsorbed or even partially embedded conformations. These findings are summarized in a pseudophase diagram indicating the predominant class of conformations as a function of the external parameters temperature and polymer-membrane interaction strength. By comparison with adsorption to a stiff membrane surface it is shown that the flexibility of the membrane gives rise to qualitatively new behavior such as stretching of adsorbed conformations.

cond-mat.soft↗

arXiv2011

Replica-Exchange Cluster Algorithm

In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature/energy range around the critical point. By combining the replica-exchange algorithm with cluster updates and an adaptive routine to find the range of interest, we introduce a new flexible and powerful method for systematic investigations of critical phenomena. As a result, we gain two further orders of magnitude in the performance for 2D and 3D Ising models in comparison with the recently proposed Wang-Landau recursion for cluster algorithms based on the multibondic algorithm, which is already a great improvement over the standard multicanonical variant.

cond-mat.stat-mech↗

arXiv2011

Parallel-tempering cluster algorithm for computer simulations of critical phenomena

In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature range around the critical point. By combining the parallel tempering algorithm with cluster updates and an adaptive routine to find the temperature window of interest, we introduce a flexible and powerful method for systematic investigations of critical phenomena. As a result, we gain one to two orders of magnitude in the performance for 2D and 3D Ising models in comparison with the recently proposed Wang-Landau recursion for cluster algorithms based on the multibondic algorithm, which is already a great improvement over the standard multicanonical variant.

cond-mat.stat-mech↗

arXiv2011

Massively parallelized replica-exchange simulations of polymers on GPUs

We discuss the advantages of parallelization by multithreading on graphics processing units (GPUs) for parallel tempering Monte Carlo computer simulations of an exemplified bead-spring model for homopolymers. Since the sampling of a large ensemble of conformations is a prerequisite for the precise estimation of statistical quantities such as typical indicators for conformational transitions like the peak structure of the specific heat, the advantage of a strong increase in performance of Monte Carlo simulations cannot be overestimated. Employing multithreading and utilizing the massive power of the large number of cores on GPUs, being available in modern but standard graphics cards, we find a rapid increase in efficiency when porting parts of the code from the central processing unit (CPU) to the GPU.

physics.comp-ph↗

arXiv2011

Microscopic Mechanism of Specific Peptide Adhesion to Semiconductor Substrates

The design of hybrid peptide-solid interfaces for nanotechnological applications such as biomolecular nanoarrays requires a deep understanding of the basic mechanisms of peptide binding and assembly at solid substrates. Here we show by means of experimental and computational analyses that the adsorption properties of mutated synthetic peptides at semiconductors exhibit a clear sequence-dependent adhesion specificity. Our simulations of a novel hybrid peptide-substrate model reveal the correspondence between proline mutation and binding affinity to a clean silicon substrate. After synthesizing theoretically suggested amino-acid sequences with different binding behavior, we confirm the relevance of the selective mutations upon adhesion in our subsequent atomic force microscopy experiments.

cond-mat.mes-hall↗

arXiv2011

Hierarchies in Nucleation Transitions

We discuss the hierarchy of subphase transitions in first-order-like nucleation processes for an exemplified aggregation transition of heteropolymers. We perform an analysis of the microcanonical entropy, i.e., the density of states is considered as the central statistical system quantity since it connects system-specific entropic and energetic information in a natural and unique way.

cond-mat.soft↗

arXiv2011

Statistical Mechanics of Aggregation and Crystallization for Semiflexible Polymers

By means of multicanonical computer simulations, we investigate thermodynamic properties of the aggregation of interacting semiflexible polymers. We analyze a mesoscopic bead-stick model, where nonbonded monomers interact via Lennard-Jones forces. Aggregation turns out to be a process, in which the constituents experience strong structural fluctuations, similar to peptides in coupled folding-binding cluster formation processes. In contrast to a recently studied related proteinlike hydrophobic-polar heteropolymer model, aggregation and crystallization are separate processes for a homopolymer with the same small bending rigidity. Rather stiff semiflexible polymers form a liquid-crystal-like phase, as expected. In analogy to the heteropolymer study, we find that the first-order-like aggregation transition of the complexes is accompanied by strong system-size dependent hierarchical surface effects. In consequence, the polymer aggregation is a phase-separation process with entropy reduction.

cond-mat.soft↗

arXiv2011

Adsorption of finite polymers in different thermodynamic ensembles

We investigate the cooperative effects of a single finite chain of monomers near an attractive substrate by first constructing a conformational pseudo-phase diagram based on the thermal fluctuations of energetic and structural quantities. Then, the adsorption transition is analyzed in more detail. This is conveniently done by a microcanonical analysis of densities of states obtained by extensive multicanonical Monte Carlo simulations. For short chains and strong surface attraction, the microcanonical entropy turns out to be a convex function of energy in the transition regime. This is a characteristic physical effect and deserves a careful consideration in analyses of cooperative macrostate transitions in finite systems.

cond-mat.soft↗

arXiv2010

Shape anisotropy of polymers in disordered environment

We study the influence of structural obstacles in a disordered environment on the size and shape characteristics of long flexible polymer macromolecules. We use the model of self-avoiding random walks on diluted regular lattices at the percolation threshold in space dimensions d=2, 3. Applying the Pruned-Enriched Rosenbluth Method (PERM), we numerically estimate rotationally invariant universal quantities such as the averaged asphericity A_d and prolateness S of polymer chain configurations. Our results quantitatively reveal the extent of anisotropy of macromolecules due to the presence of structural defects.

cond-mat.soft↗

arXiv2010

Theta-polymers in crowded media under the stretching force

We study the peculiarities of stretching of globular polymer macromolecules in a disordered (crowded) environment, using the model of self-attracting self-avoiding walks on site-diluted percolative lattices in space dimensions d=3. Applying the pruned-enriched Rosenbluth chain-growth method (PERM), we construct the phase diagram of collapsed-extended state coexistence when varying temperature and stretching force. The change in shape characteristics of globular polymers under stretching is analyzed as well.

cond-mat.soft↗

arXiv2010

Elastic Lennard-Jones Polymers Meet Clusters -- Differences and Similarities

We investigate solid-solid and solid-liquid transitions of elastic flexible off-lattice polymers with Lennard-Jones monomer-monomer interaction and anharmonic springs by means of sophisticated variants of multicanonical Monte Carlo methods. We find that the low-temperature behavior depends strongly and non-monotonically on the system size and exhibits broad similarities to unbound atomic clusters. Particular emphasis is dedicated to the classification of icosahedral and non-icosahedral low-energy polymer morphologies.

cond-mat.soft↗