arXiv subjects

Wolfhard Janke

Publications and source records attributed to Wolfhard Janke.

At least 163 records · Page 9Linked to original sources

arXiv2007

Freezing and Collapse of Flexible Polymers on Regular Lattices in Three Dimensions

We analyze the crystallization and collapse transition of a simple model for flexible polymer chains on simple cubic and face-centered cubic lattices by means of sophisticated chain-growth methods. In contrast to bond-fluctuation polymer models in certain parameter ranges, where these two conformational transitions were found to merge in the thermodynamic limit, we conclude from our results that the two transitions remain well-separated in the limit of infinite chain lengths. The reason for this qualitatively distinct behavior is presumably due to the ultrashort attractive interaction range in the lattice models considered here.

cond-mat.soft↗

arXiv2007

Specific Adhesion of Peptides on Semiconductor Surfaces in Experiment and Simulation

We report on self-assembly, clustering, and conformational phases of peptides on inorganic semiconductor surfaces. The peptide-covered surface fraction can differ by a factor of 25, depending mainly on surface and peptide polarity. Low adhesion induces large and soft clusters, which also have high contact angles to the surface. Direct surface adhesion of a peptide molecule competes with forming molecular aggregates which offer an overall reduced surface contact. Simulating a simple hybrid model yields a pseudophase diagram with a rich, temperature and solvent-quality dependent variety of subphases which are specific to the hydrophobicity and polarity of the considered substrates.

cond-mat.soft↗

arXiv2007

Structural Properties of Small Semiconductor-Binding Synthetic Peptides

We have performed exhaustive multicanonical Monte Carlo simulations of three 12-residue synthetic peptides in order to investigate the thermodynamic and structural properties as well as the characteristic helix-coil transitions. In these studies, we employ a realistic model where the interactions between all atoms are taken into account. Effects of solvation are also simulated by using an implicit solvent model.

cond-mat.soft↗

arXiv2007

Microcanonical Analyses of Peptide Aggregation Processes

We propose the use of microcanonical analyses for numerical studies of peptide aggregation transitions. Performing multicanonical Monte Carlo simulations of a simple hydrophobic-polar continuum model for interacting heteropolymers of finite length, we find that the microcanonical entropy behaves convex in the transition region, leading to a negative microcanonical specific heat. As this effect is also seen in first-order-like transitions of other finite systems, our results provide clear evidence for recent hints that the characterisation of phase separation in first-order-like transitions of finite systems profits from this microcanonical view.

cond-mat.soft↗

arXiv2007

Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins

Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are permutations of each other. Despite the simplicity of the model, the knowledge of the free-energy landscape in dependence of a suitable system order parameter enables us to reveal complex folding characteristics known from real bioproteins and synthetic peptides, such as two-state folding, folding through weakly stable intermediates, and glassy metastability.

cond-mat.soft↗

arXiv2007

Minimalistic Hybrid Models for the Adsorption of Polymers and Peptides to Solid Substrates

We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the adsorption process. Primarily focusing on the dependence of the conformational behavior on temperature and solubility we obtained pseudophase diagrams with a detailed structure of conformational subphases. In the study of hydrophobic-polar peptides in the vicinity of different types of substrates, we found a noticeable substrate specificity of the assembly of hydrophobic domains in the conformations dominating the adsorption subphases.

cond-mat.soft↗

arXiv2007

Chain-Growth Simulations of Lattice-Peptide Adsorption to Attractive Substrates

Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the conformational transitions the peptide experiences in the binding/unbinding processes. In a single simulation run, we obtained the contact density, i.e., the distribution of intrinsic monomer-monomer contacts and monomer-substrate nearest-neighbor contacts. This allows a systematic reweighting to all values of external control parameters such as temperature and solvent quality after the simulation. The main result is the complete solubility-temperature pseudo-phase diagram which is based on the corresponding specific-heat profile. We find a surprisingly rich structure of pseudo-phases that can roughly be classified into compact and expanded conformations in both regimes, adsorption and desorption. Furthermore, underlying subphases were identified, which, in particular, appear noticeably in the compact pseudo-phases.

cond-mat.soft↗

arXiv2007

Reduction to the Simplest - The Complexity of Minimalistic Heteropolymer Models

Simple coarse-grained hydrophobic-polar models for heteropolymers as the lattice HP and the off-lattice AB model allow a general classification of characteristic behaviors for hydrophobic-core based tertiary folding. The strongly reduced computational efforts enable one to reveal systematically the thermodynamic properties of comparatively long sequences in a wide temperature range of conformational activity. Based on a suitable cooperativity parameter, characteristic folding channels and free-energy landscapes, which have strong similarities with realistic folding paths, can be analysed.

cond-mat.soft↗

arXiv2007

Adsorption Phenomena at Organic-Inorganic Interfaces

The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase diagrams exhibit a complex structure, which can be understood by analysing the minima of the free-energy landscape in dependence of appropriate system parameters.

cond-mat.soft↗

arXiv2007

Substrate Adhesion of a Nongrafted Flexible Polymer in a Cavity

In a contact density chain-growth study we investigate the solubility-temperature pseudo-phase diagram of a lattice polymer in a cavity with an attractive surface. In addition to the main phases of adsorbed and desorbed conformations we find numerous subphases of collapsed and expanded structures.

cond-mat.soft↗

arXiv2007

Density of States for HP Lattice Proteins

The density of states contains all informations on energetic quantities of a statistical system, such as the mean energy, free energy, entropy, and specific heat. As a specific application, we consider in this work a simple lattice model for heteropolymers that is widely used for studying statistical properties of proteins. For short chains, we have derived exact results from conformational enumeration, while for longer ones we developed a multicanonical Monte Carlo variant of the nPERM-based chain growth method in order to directly simulate the density of states. For simplification, only two types of monomers with respective hydrophobic (H) and polar (P) residues are regarded and only the next-neighbour interaction between hydrophobic monomers, being nonadjacent along the chain, is taken into account. This is known as the HP model for the folding of lattice proteins.

cond-mat.soft↗

arXiv2007

Conformational Transitions of Heteropolymers

We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar models do not require the knowledge of the native topology for a given sequence of residues as input. Therefore these models are eligible to investigate general properties of the tertiary folding behaviour of such protein-like heteropolymers.

cond-mat.soft↗

arXiv2007

Substrate Specificity of Peptide Adsorption: A Model Study

Applying the contact density chain-growth algorithm to lattice heteropolymers, we identify the conformational transitions of a nongrafted hydrophobic-polar heteropolymer with 103 residues in the vicinity of a polar, a hydrophobic, and a uniformly attractive substrate. Introducing only two system parameters, the numbers of surface contacts and intrinsic hydrophobic contacts, respectively, we obtain surprisingly complex temperature and solvent dependent, substrate-specific pseudo-phase diagrams.

cond-mat.soft↗

arXiv2007

Monte Carlo study of the evaporation/condensation transition on different Ising lattices

In 2002 Biskup et al. [Europhys. Lett. 60, 21 (2002)] sketched a rigorous proof for the behavior of the 2D Ising lattice gas, at a finite volume and a fixed excess δM of particles (spins) above the ambient gas density (spontaneous magnetisation). By identifying a dimensionless parameter Δ(δM) and a universal constant Δ_c, they showed in the limit of large system sizes that for Δ< Δ_c the excess is absorbed in the background (``evaporated'' system), while for Δ> Δ_c a droplet of the dense phase occurs (``condensed'' system). To check the applicability of the analytical results to much smaller, practically accessible system sizes, we performed several Monte Carlo simulations for the 2D Ising model with nearest-neighbour couplings on a square lattice at fixed magnetisation M. Thereby, we measured the largest minority droplet, corresponding to the condensed phase, at various system sizes (L=40, >..., 640). With analytic values for for the spontaneous magnetisation m_0, the susceptibility χand the Wulff interfacial free energy density τ_W for the infinite system, we were able to determine λnumerically in very good agreement with the theoretical prediction. Furthermore, we did simulations for the spin-1/2 Ising model on a triangular lattice and with next-nearest-neighbour couplings on a square lattice. Again, finding a very good agreement with the analytic formula, we demonstrate the universal aspects of the theory with respect to the underlying lattice. For the case of the next-nearest-neighbour model, where τ_W is unknown analytically, we present different methods to obtain it numerically by fitting to the distribution of the magnetisation density P(m).

cond-mat.stat-mech↗

arXiv2007

Self-affirmation model for football goal distributions

Analyzing football score data with statistical techniques, we investigate how the highly co-operative nature of the game is reflected in averaged properties such as the distributions of scored goals for the home and away teams. It turns out that in particular the tails of the distributions are not well described by independent Bernoulli trials, but rather well modeled by negative binomial or generalized extreme value distributions. To understand this behavior from first principles, we suggest to modify the Bernoulli random process to include a simple component of self-affirmation which seems to describe the data surprisingly well and allows to interpret the observed deviation from Gaussian statistics. The phenomenological distributions used before can be understood as special cases within this framework. We analyzed historical football score data from many leagues in Europe as well as from international tournaments and found the proposed models to be applicable rather universally. In particular, here we compare men's and women's leagues and the separate German leagues during the cold war times and find some remarkable differences.

physics.soc-ph↗

arXiv2007

Spacetime Approach to Phase Transitions

In these notes, the application of Feynman's sum-over-paths approach to thermal phase transitions is discussed. The paradigm of such a spacetime approach to critical phenomena is provided by the high-temperature expansion of spin models. This expansion, known as the hopping expansion in the context of lattice field theory, yields a geometric description of the phase transition in these models, with the thermal critical exponents being determined by the fractal structure of the high-temperature graphs. The graphs percolate at the thermal critical point and can be studied using purely geometrical observables known from percolation theory. Besides the phase transition in spin models and in the closely related $ϕ^4$ theory, other transitions discussed from this perspective include Bose-Einstein condensation, and the transitions in the Higgs model and the pure U(1) gauge theory.

cond-mat.stat-mech↗

arXiv2006

Two-Dimensional Critical Potts and its Tricritical Shadow

These notes give examples of how suitably defined geometrical objects encode in their fractal structure thermal critical behavior. The emphasis is on the two-dimensional Potts model for which two types of spin clusters can be defined. Whereas the Fortuin-Kasteleyn clusters describe the standard critical behavior, the geometrical clusters describe the tricritical behavior that arises when including vacant sites in the pure Potts model. Other phase transitions that allow for a geometrical description discussed in these notes include the superfluid phase transition and Bose-Einstein condensation.

cond-mat.stat-mech↗

arXiv2006

Wang-Landau/Multibondic Cluster Simulations for Second-Order Phase Transitions

For a second-order phase transition the critical energy range of interest is larger than the energy range covered by a canonical Monte Carlo simulation at the critical temperature. Such an extended energy range can be covered by performing a Wang-Landau recursion for the spectral density followed by a multicanonical simulation with fixed weights. But in the conventional approach one loses the advantage due to cluster algorithms. A cluster version of the Wang-Landau recursion together with a subsequent multibondic simulation improves for 2D and 3D Ising models the efficiency of the conventional Wang-Landau/multicanonical approach by power laws in the lattice size. In our simulations real gains in CPU time reach two orders of magnitude.

cond-mat.stat-mech↗