Jonathan Gross

Effects of the interaction range on structural phases of flexible polymers.

We systematically investigate how the range of interaction between non-bonded monomers influences the formation of structural phases of elastic, flexible polymers. Massively parallel replica-exchange simulations of a generic, coarse-grained model, performed partly on graphics processing units and in multiple-gaussian modified ensembles, pave the way for the construction of the structural phase diagram, parametrized by interaction range and temperature. Conformational transitions between gas-like, liquid, and diverse solid (pseudo) phases are identified by microcanonical statistical inflection-point analysis. We find evidence for finite-size effects that cause the crossover of collapse and freezing transitions for very short interaction ranges.

Polymer adsorption on reconstructed Au(001): A statistical description of P3HT by scanning tunneling microscopy and coarse-grained Monte Carlo simulations

We report on a combined theoretical and experimental characterization of isolated Poly(3-hexylthiophene) (P3HT) chains weakly adsorbed on a reconstructed Au(001) surface. The local chain conformations of in situ deposited P3HT molecules were investigated by means of scanning tunneling microscopy. For comparison, Monte Carlo simulations of the system were performed up to a maximum chain length of 60 monomer units. The dependence of the end-to-end distance and the radius of gyration on the polymer chain length shows a good agreement between experiment and Monte Carlo simulations using simple updates for short chains.

Thermodynamics of the adsorption of flexible polymers on nanowires

Generalized-ensemble simulations enable the study of complex adsorption scenarios of a coarse-grained model polymer near an attractive nanostring, representing an ultrathin nanowire. We perform canonical and microcanonical statistical analyses to investigate structural transitions of the polymer and discuss their dependence on the temperature and on model parameters such as effective wire thickness and attraction strength. The result is a complete hyperphase diagram of the polymer phases, whose locations and stability are influenced by the effective material properties of the nanowire and the strength of the thermal fluctuations. Major structural polymer phases in the adsorbed state include compact droplets attached to or wrapping around the wire, and tubelike conformations with triangular pattern that resemble ideal boron nanotubes. The classification of the transitions is performed by microcanonical inflection-point analysis.

Massively parallel multicanonical simulations

Abstract Generalized-ensemble Monte Carlo simulations such as the multicanonical method and similar techniques are among the most efficient approaches for simulations of systems undergoing discontinuous phase transitions or with rugged free-energy landscapes. As Markov chain methods, they are inherently serial computationally. It was demonstrated recently, however, that a combination of independent simulations that communicate weight updates at variable intervals allows for the efficient utilization of parallel computational resources for multicanonical simulations. Implementing this approach for the many-thread architecture provided by current generations of graphics processing units (GPUs), we show how it can be efficiently employed with of the order of 1 0 4 parallel walkers and beyond, thus constituting a versatile tool for Monte Carlo simulations in the era of massively parallel computing. We provide the fully documented source code for the approach applied to the paradigmatic example of the two-dimensional Ising model as starting point and reference for practitioners in the field. Program summary Program Title: cudamuca Program Files doi: http://dx.doi.org/10.17632/tzhfpdymv9.1 Licensing provisions: Creative Commons Attribution license (CC BY 4.0) Programming language: C, CUDA External routines/libraries: NVIDIA CUDA Toolkit 6.5 or newer Nature of problem: The program determines weights for a multicanonical simulation of the 2D Ising model to result in a flat energy histogram. A final production run with these weights provides an estimate of the density of states of the model. Solution method: The code uses a parallel variant of the multicanonical method employing many parallel walkers that accumulate a common histogram. The resulting histogram is used to determine the weight function for the next iteration. Once the iteration has converged, simulations visit all possible energies with the same probability. Additional comments including restrictions and unusual features: The system size and size of the population of replicas are limited depending on the memory of the GPU device used. Code repository at https://github.com/CQT-Leipzig/cudamuca .

Comparing atomistic and coarse-grained simulations of P3HT

Poly(3-hexylthiophene) (P3HT) is a key material used in organic photovoltaics. In this study we assess the validity of two coarse-grained models of P3HT by comparing coarse-grained Monte Carlo simulations to fully atomistic molecular dynamics simulations. Structural properties of single polymer chains of short to medium lengths are compared between the three representations.

Two-dimensional Monte Carlo simulations of coarse-grained poly(3-hexylthiophene) (P3HT) adsorbed on striped substrates

We investigate the structural phases of single poly(3-hexylthiophene) (P3HT) polymers that are adsorbed on a two-dimensional substrate with a striped pattern. We use a coarse-grained representation of the polymer and sophisticated Monte Carlo techniques such as a parallelized replica exchange scheme and local as well as non-local updates to the polymers configuration. From peaks in the canonically derived observables, it is possible to obtain structural phase diagrams for varying substrate parameters. We find that the shape of the stripe pattern has a substantial effect on the obtained configurations of the polymer and can be tailored to promote either more stretched out or more compact configurations. In the compact phases, we observe different structural motifs, such as hairpins, double-hairpins, and interlocking zipper states.